Duke Herbarium
Arts & Sciences
Duke University
| |
Lichens Database Duke Herbarium Arts & Sciences Duke University |
|
| HOME > Arts & Sciences > Duke Herbarium > Lichens | Search Help Login |
|
| Publications of Jolanta M. Miadlikowska :chronological alphabetical combined listing:
%% Papers Published
@article{fds376709,
Author = {U'Ren, JM and Oita, S and Lutzoni, F and Miadlikowska, J and Ball, B and Carbone, I and May, G and Zimmerman, NB and Valle, D and Trouet, V and Arnold, AE},
Title = {Environmental drivers and cryptic biodiversity hotspots
define endophytes in Earth's largest terrestrial
biome.},
Journal = {Current biology : CB},
Volume = {34},
Number = {5},
Pages = {1148-1156.e7},
Year = {2024},
Month = {March},
url = {http://dx.doi.org/10.1016/j.cub.2024.01.063},
Abstract = {Understanding how symbiotic associations differ across
environmental gradients is key to predicting the fate of
symbioses as environments change, and it is vital for
detecting global reservoirs of symbiont biodiversity in a
changing world.<sup>1</sup><sup>,</sup><sup>2</sup><sup>,</sup><sup>3</sup>
However, sampling of symbiotic partners at the full-biome
scale is difficult and rare. As Earth's largest terrestrial
biome, boreal forests influence carbon dynamics and climate
regulation at a planetary scale. Plants and lichens in this
biome host the highest known phylogenetic diversity of
fungal endophytes, which occur within healthy photosynthetic
tissues and can influence hosts' resilience to
stress.<sup>4</sup><sup>,</sup><sup>5</sup> We examined how
communities of endophytes are structured across the climate
gradient of the boreal biome, focusing on the dominant plant
and lichen species occurring across the entire
south-to-north span of the boreal zone in eastern North
America. Although often invoked for understanding the
distribution of biodiversity, neither a latitudinal gradient
nor mid-domain effect<sup>5</sup><sup>,</sup><sup>6</sup><sup>,</sup><sup>7</sup>
can explain variation in endophyte diversity at this
trans-biome scale. Instead, analyses considering shifts in
forest characteristics, Picea biomass and age, and nutrients
in host tissues from 46° to 58° N reveal strong and
distinctive signatures of climate in defining endophyte
assemblages in each host lineage. Host breadth of endophytes
varies with climate factors, and biodiversity hotspots can
be identified at plant-community transitions across the
boreal zone at a global scale. Placed against a backdrop of
global circumboreal sampling,<sup>4</sup> our study reveals
the sensitivity of endophytic fungi, their reservoirs of
biodiversity, and their important symbiotic associations, to
climate.},
Doi = {10.1016/j.cub.2024.01.063},
Key = {fds376709}
}
@article{fds375869,
Author = {Magain, N and Miadlikowska, J and Goffinet, B and Goward, T and Pardo-De
la Hoz, CJ and Jüriado, I and Simon, A and Mercado-Díaz, JA and Barlow, T and Moncada, B and Lücking, R and Spielmann, A and Canez, L and Wang, LS and Nelson, P and Wheeler, T and Lutzoni, F and Sérusiaux,
E},
Title = {High species richness in the lichen genus Peltigera
(Ascomycota, Lecanoromycetes): 34 species in the
dolichorhizoid and scabrosoid clades of section
Polydactylon, including 24 new to science},
Journal = {Persoonia: Molecular Phylogeny and Evolution of
Fungi},
Volume = {51},
Pages = {1-88},
Year = {2023},
Month = {December},
url = {http://dx.doi.org/10.3767/persoonia.2023.51.01},
Abstract = {Applying molecular methods to fungi establishing lichenized
associations with green algae or cyanobacteria has
repeatedly revealed the existence of numerous phylogenetic
taxa overlooked by classical taxonomic approaches. Here, we
report taxonomical conclusions based on multiple species
delimitation and validation analyses performed on an
eight-locus dataset that includes world-wide representatives
of the dolichorhizoid and scabrosoid clades in section
Polydactylon of the genus Peltigera. Following the
recommendations resulting from a consensus species
delimitation approach and additional species validation
analysis (BPP) performed in this study, we present a total
of 25 species in the dolichorhizoid clade and nine in the
scabrosoid clade, including respectively 18 and six species
that are new to science and formally described.
Additionally, one combination and three varieties (including
two new to science) are proposed in the dolichorhizoid
clade. The following 24 new species are described: P.
appalachiensis, P. asiatica, P. borealis, P. borinquensis,
P. chabanenkoae, P. clathrata, P. elixii, P. esslingeri, P.
flabellae, P. gallowayi, P. hawaiiensis, P. holtanhartwigii,
P. itatiaiae, P. hokkaidoensis, P. kukwae, P. massonii, P.
mikado, P. nigriventris, P. orientalis, P. rangiferina, P.
sipmanii, P. stanleyensis, P. vitikainenii and P.
willdenowii; the following new varieties are introduced: P.
kukwae var. phyllidiata and P. truculenta var.
austroscabrosa; and the following new combination is
introduced: P. hymenina var. dissecta. Each species from the
dolichorhizoid and scabrosoid clades is morphologically and
chemically described, illustrated, and characterised with
ITS sequences. Identification keys are provided for the main
biogeographic regions where species from the two clades
occur. Morphological and chemical characters that are
commonly used for species identification in the genus
Peltigera cannot be applied to unambiguously recognise most
molecularly circumscribed species, due to high variation of
thalli formed by individuals within a fungal species,
including the presence of distinct morphs in some cases, or
low interspecific variation in others. The four commonly
recognised morphospecies: P. dolichorhiza, P.
neopolydactyla, P. pulverulenta and P. scabrosa in the
dolichorhizoid and scabrosoid clades represent species
complexes spread across multiple and often phylogenetically
distantly related lineages. Geographic origin of specimens
is often helpful for species recognition; however, ITS
sequences are frequently required for a reliable
identification.},
Doi = {10.3767/persoonia.2023.51.01},
Key = {fds375869}
}
@article{fds373352,
Author = {Miadlikowska, J and Magain, N and Medeiros, ID and Pardo-De La Hoz,
CJ and Carbone, I and Lagreca, S and Barlow, T and Myllys, L and Schmull,
M and Lutzoni, F},
Title = {Towards a nomenclatural clarification of the Peltigera
ponojensis/monticola clade including metagenomic sequencing
of type material and the introduction of P. globulata Miadl.
& Magain sp. nov.},
Journal = {Lichenologist},
Volume = {55},
Number = {5},
Pages = {315-324},
Year = {2023},
Month = {September},
url = {http://dx.doi.org/10.1017/S0024282923000373},
Abstract = {Peltigera globulata Miadl. & Magain, a new species in the P.
ponojensis/monticola species complex of section Peltigera,
is formally described. This clade was previously given the
interim designation Peltigera sp. 17. It is found in
sun-exposed and xeric habitats at high altitudes in Peru and
Ecuador. Peltigera globulata can be easily recognized by its
irregularly globulated margins covered mostly by thick,
white pruina, somewhat resembling the sorediate thallus
margins of P. soredians, another South American species from
section Peltigera. The hypervariable region of ITS1
(ITS1-HR), which is in general highly variable among species
of section Peltigera, does not have diagnostic value for
species identification within the P. ponojensis/monticola
complex. Nevertheless, no significant level of gene flow was
detected among eight lineages representing a clade of
putative species (including P. globulata) within this
complex. ITS sequences from the holotype specimens of P.
monticola Vitik. (collected in 1979) and P. soredians Vitik.
(collected in 1981) and lectotype specimens of P. antarctica
C. W. Dodge (collected in 1941) and P. aubertii C. W. Dodge
(collected in 1952) were successfully obtained through
Sanger and Illumina metagenomic sequencing. BLAST results of
these sequences revealed that the type specimen of P.
monticola falls within the P. monticola/ponojensis 7 clade,
which represents P. monticola s. str., and confirmed that
the type specimen of P. aubertii falls within a clade
identified previously as P. aubertii based on morphology.
The ITS sequence from the type specimen of P. soredians,
which superficially resembles P. globulata, confirms its
placement in the P. rufescens clade. Finally, we discovered
that the name P. antarctica was erroneously applied to a
lineage in the P. ponojensis/monticola clade. The ITS
sequence from the type specimen of P. antarctica represents
a lineage within the P. rufescens clade, which is sister to
the P. ponojensis/monticola clade.},
Doi = {10.1017/S0024282923000373},
Key = {fds373352}
}
@article{fds371578,
Author = {Pardo-De la Hoz and CJ and Magain, N and Piatkowski, B and Cornet, L and Dal Forno and M and Carbone, I and Miadlikowska, J and Lutzoni,
F},
Title = {Ancient Rapid Radiation Explains Most Conflicts Among Gene
Trees and Well-Supported Phylogenomic Trees of Nostocalean
Cyanobacteria.},
Journal = {Systematic biology},
Volume = {72},
Number = {3},
Pages = {694-712},
Year = {2023},
Month = {June},
url = {http://dx.doi.org/10.1093/sysbio/syad008},
Abstract = {Prokaryotic genomes are often considered to be mosaics of
genes that do not necessarily share the same evolutionary
history due to widespread horizontal gene transfers (HGTs).
Consequently, representing evolutionary relationships of
prokaryotes as bifurcating trees has long been
controversial. However, studies reporting conflicts among
gene trees derived from phylogenomic data sets have shown
that these conflicts can be the result of artifacts or
evolutionary processes other than HGT, such as incomplete
lineage sorting, low phylogenetic signal, and systematic
errors due to substitution model misspecification. Here, we
present the results of an extensive exploration of
phylogenetic conflicts in the cyanobacterial order
Nostocales, for which previous studies have inferred
strongly supported conflicting relationships when using
different concatenated phylogenomic data sets. We found that
most of these conflicts are concentrated in deep clusters of
short internodes of the Nostocales phylogeny, where the
great majority of individual genes have low resolving power.
We then inferred phylogenetic networks to detect HGT events
while also accounting for incomplete lineage sorting. Our
results indicate that most conflicts among gene trees are
likely due to incomplete lineage sorting linked to an
ancient rapid radiation, rather than to HGTs. Moreover, the
short internodes of this radiation fit the expectations of
the anomaly zone, i.e., a region of the tree parameter space
where a species tree is discordant with its most likely gene
tree. We demonstrated that concatenation of different sets
of loci can recover up to 17 distinct and well-supported
relationships within the putative anomaly zone of
Nostocales, corresponding to the observed conflicts among
well-supported trees based on concatenated data sets from
previous studies. Our findings highlight the important role
of rapid radiations as a potential cause of strongly
conflicting phylogenetic relationships when using
phylogenomic data sets of bacteria. We propose that
polytomies may be the most appropriate phylogenetic
representation of these rapid radiations that are part of
anomaly zones, especially when all possible genomic markers
have been considered to infer these phylogenies. [Anomaly
zone; bacteria; horizontal gene transfer; incomplete lineage
sorting; Nostocales; phylogenomic conflict; rapid radiation;
Rhizonema.].},
Doi = {10.1093/sysbio/syad008},
Key = {fds371578}
}
@article{fds365220,
Author = {McMullin, RT and Miadlikowska, J},
Title = {Two rare Peltigera species new to the Canadian Arctic, P.
islandica and P. lyngei},
Journal = {Plant and Fungal Systematics},
Volume = {67},
Number = {1},
Pages = {17-23},
Year = {2022},
Month = {July},
url = {http://dx.doi.org/10.35535/pfsyst-2022-0002},
Abstract = {Peltigera islandica and P. lyngei are rarely reported
lichens. Previously, P. islandica was known from British
Columbia, Estonia, and Iceland, and P. lyngei from Amchitka
Island (Alaska), Gough Island (South Atlantic), Iceland,
Siberia and Svalbard. Both species are reported here for the
first time from the Canadian Arctic and from the second
localities in North America. Peltigera lyngei is also
reported for the first time from Canada. The identities of
these species are confirmed morphologically, chemically, and
with molecular data. Phylogenetic relationships are inferred
using the ITS region. The widespread, but scattered,
distribution of both species suggests that they may be
underreported throughout their range.},
Doi = {10.35535/pfsyst-2022-0002},
Key = {fds365220}
}
@article{fds360545,
Author = {Franco, MEE and Wisecaver, JH and Arnold, AE and Ju, Y-M and Slot, JC and Ahrendt, S and Moore, LP and Eastman, KE and Scott, K and Konkel, Z and Mondo, SJ and Kuo, A and Hayes, RD and Haridas, S and Andreopoulos, B and Riley, R and LaButti, K and Pangilinan, J and Lipzen, A and Amirebrahimi, M and Yan, J and Adam, C and Keymanesh, K and Ng, V and Louie, K and Northen, T and Drula, E and Henrissat, B and Hsieh, H-M and Youens-Clark, K and Lutzoni, F and Miadlikowska, J and Eastwood, DC and Hamelin, RC and Grigoriev, IV and U'Ren, JM},
Title = {Ecological generalism drives hyperdiversity of secondary
metabolite gene clusters in xylarialean endophytes.},
Journal = {The New phytologist},
Volume = {233},
Number = {3},
Pages = {1317-1330},
Year = {2022},
Month = {February},
url = {http://dx.doi.org/10.1111/nph.17873},
Abstract = {Although secondary metabolites are typically associated with
competitive or pathogenic interactions, the high bioactivity
of endophytic fungi in the Xylariales, coupled with their
abundance and broad host ranges spanning all lineages of
land plants and lichens, suggests that enhanced secondary
metabolism might facilitate symbioses with phylogenetically
diverse hosts. Here, we examined secondary metabolite gene
clusters (SMGCs) across 96 Xylariales genomes in two clades
(Xylariaceae s.l. and Hypoxylaceae), including 88 newly
sequenced genomes of endophytes and closely related
saprotrophs and pathogens. We paired genomic data with
extensive metadata on endophyte hosts and substrates,
enabling us to examine genomic factors related to the
breadth of symbiotic interactions and ecological roles. All
genomes contain hyperabundant SMGCs; however, Xylariaceae
have increased numbers of gene duplications, horizontal gene
transfers (HGTs) and SMGCs. Enhanced metabolic diversity of
endophytes is associated with a greater diversity of hosts
and increased capacity for lignocellulose decomposition. Our
results suggest that, as host and substrate generalists,
Xylariaceae endophytes experience greater selection to
diversify SMGCs compared with more ecologically specialised
Hypoxylaceae species. Overall, our results provide new
evidence that SMGCs may facilitate symbiosis with
phylogenetically diverse hosts, highlighting the importance
of microbial symbioses to drive fungal metabolic
diversity.},
Doi = {10.1111/nph.17873},
Key = {fds360545}
}
@article{fds362657,
Author = {Pardo-De la Hoz and CJ and Medeiros, ID and Gibert, JP and Chagnon, P-L and Magain, N and Miadlikowska, J and Lutzoni, F},
Title = {Phylogenetic structure of specialization: A new approach
that integrates partner availability and phylogenetic
diversity to quantify biotic specialization in ecological
networks.},
Journal = {Ecology and evolution},
Volume = {12},
Number = {3},
Pages = {e8649},
Year = {2022},
Month = {February},
url = {http://dx.doi.org/10.1002/ece3.8649},
Abstract = {Biotic specialization holds information about the assembly,
evolution, and stability of biological communities. Partner
availabilities can play an important role in enabling
species interactions, where uneven partner availabilities
can bias estimates of biotic specialization when using
phylogenetic diversity indices. It is therefore important to
account for partner availability when characterizing biotic
specialization using phylogenies. We developed an index,
phylogenetic structure of specialization (PSS), that avoids
bias from uneven partner availabilities by uncoupling the
null models for interaction frequency and phylogenetic
distance. We incorporate the deviation between observed and
random interaction frequencies as weights into the
calculation of partner phylogenetic α-diversity. To
calculate the PSS index, we then compare observed partner
phylogenetic α-diversity to a null distribution generated
by randomizing phylogenetic distances among the same number
of partners. PSS quantifies the phylogenetic structure
(i.e., clustered, overdispersed, or random) of the partners
of a focal species. We show with simulations that the PSS
index is not correlated with network properties, which
allows comparisons across multiple systems. We also
implemented PSS on empirical networks of host-parasite,
avian seed-dispersal, lichenized fungi-cyanobacteria, and
hummingbird pollination interactions. Across these systems,
a large proportion of taxa interact with phylogenetically
random partners according to PSS, sometimes to a larger
extent than detected with an existing method that does not
account for partner availability. We also found that many
taxa interact with phylogenetically clustered partners,
while taxa with overdispersed partners were rare. We argue
that species with phylogenetically overdispersed partners
have often been misinterpreted as generalists when they
should be considered specialists. Our results highlight the
important role of randomness in shaping interaction
networks, even in highly intimate symbioses, and provide a
much-needed quantitative framework to assess the role that
evolutionary history and symbiotic specialization play in
shaping patterns of biodiversity. PSS is available as an R
package at https://github.com/cjpardodelahoz/pss.},
Doi = {10.1002/ece3.8649},
Key = {fds362657}
}
@article{fds357292,
Author = {Crous, PW and Hernández-Restrepo, M and Schumacher, RK and Cowan,
DA and Maggs-Kölling, G and Marais, E and Wingfield, MJ and Yilmaz, N and Adan, OCG and Akulov, A and Duarte, EÁ and Berraf-Tebbal, A and Bulgakov, TS and Carnegie, AJ and de Beer, ZW and Decock, C and Dijksterhuis, J and Duong, TA and Eichmeier, A and Hien, LT and Houbraken, JAMP and Khanh, TN and Liem, NV and Lombard, L and Lutzoni,
FM and Miadlikowska, JM and Nel, WJ and Pascoe, IG and Roets, F and Roux,
J and Samson, RA and Shen, M and Spetik, M and Thangavel, R and Thanh, HM and Thao, LD and van Nieuwenhuijzen, EJ and Zhang, JQ and Zhang, Y and Zhao,
LL and Groenewald, JZ},
Title = {New and Interesting Fungi. 4.},
Journal = {Fungal systematics and evolution},
Volume = {7},
Pages = {255-343},
Year = {2021},
Month = {June},
url = {http://dx.doi.org/10.3114/fuse.2021.07.13},
Abstract = {An order, family and genus are validated, seven new genera,
35 new species, two new combinations, two epitypes, two
lectotypes, and 17 interesting new host and / or
geographical records are introduced in this study. Validated
order, family and genus: <i>Superstratomycetales</i> and
<i>Superstratomycetaceae</i> (based on <i>Superstratomyces</i>
<i>)</i>. New genera: <i>Haudseptoria</i> (based on
<i>Haudseptoria typhae</i>); <i>Hogelandia</i> (based on
<i>Hogelandia lambearum</i>); <i>Neoscirrhia</i> (based on
<i>Neoscirrhia osmundae</i>); <i>Nothoanungitopsis</i>
(based on <i>Nothoanungitopsis urophyllae</i>);
<i>Nothomicrosphaeropsis</i> (based on <i>Nothomicrosphaeropsis
welwitschiae</i>); <i>Populomyces</i> (based on
<i>Populomyces zwinianus</i>); <i>Pseudoacrospermum</i>
(based on <i>Pseudoacrospermum goniomae</i>). New species:
<i>Apiospora sasae</i> on dead culms of <i>Sasa veitchii</i>
(Netherlands); <i>Apiospora stipae</i> on dead culms of
<i>Stipa gigantea</i> (Spain); <i>Bagadiella
eucalyptorum</i> on leaves of <i>Eucalyptus</i> sp.
(Australia); <i>Calonectria singaporensis</i> from submerged
leaf litter (Singapore); <i>Castanediella neomalaysiana</i>
on leaves of <i>Eucalyptus</i> sp. (Malaysia);
<i>Colletotrichum pleopeltidis</i> on leaves of
<i>Pleopeltis</i> sp. (South Africa); <i>Coniochaeta
deborreae</i> from soil (Netherlands); <i>Diaporthe
durionigena</i> on branches of <i>Durio zibethinus</i>
(Vietnam); <i>Floricola juncicola</i> on dead culm of
<i>Juncus</i> sp. (France); <i>Haudseptoria typhae</i> on
leaf sheath of <i>Typha</i> sp. (Germany); <i>Hogelandia
lambearum</i> from soil (Netherlands); <i>Lomentospora
valparaisensis</i> from soil (Chile); <i>Neofusicoccum
mystacidii</i> on dead stems of <i>Mystacidium capense</i>
(South Africa); <i>Neomycosphaerella guibourtiae</i> on
leaves of <i>Guibourtia</i> sp. (Angola); <i>Niesslia
neoexosporioides</i> on dead leaves of <i>Carex
paniculata</i> (Germany); <i>Nothoanungitopsis
urophyllae</i> on seed capsules of <i>Eucalyptus
urophylla</i> (South Africa); <i>Nothomicrosphaeropsis
welwitschiae</i> on dead leaves of <i>Welwitschia
mirabilis</i> (Namibia); <i>Paracremonium bendijkiorum</i>
from soil (Netherlands); <i>Paraphoma ledniceana</i> on dead
wood of <i>Buxus sempervirens</i> (Czech Republic);
<i>Paraphoma salicis</i> on leaves of <i>Salix cf. alba</i>
(Ukraine); <i>Parasarocladium wereldwijsianum</i> from soil
(Netherlands); <i>Peziza ligni</i> on masonry and plastering
(France); <i>Phyllosticta phoenicis</i> on leaves of
<i>Phoenix reclinata</i> (South Africa); <i>Plectosphaerella
slobbergiarum</i> from soil (Netherlands); <i>Populomyces
zwinianus</i> from soil (Netherlands); <i>Pseudoacrospermum
goniomae</i> on leaves of <i>Gonioma kamassi</i> (South
Africa); <i>Pseudopyricularia festucae</i> on leaves of
<i>Festuca californica</i> (USA); <i>Sarocladium
sasijaorum</i> from soil (Netherlands); <i>Sporothrix
hypoxyli</i> in sporocarp of <i>Hypoxylon petriniae</i> on
<i>Fraxinus</i> wood (Netherlands); <i>Superstratomyces
albomucosus</i> on <i>Pycnanthus angolensis</i>
(Netherlands); <i>Superstratomyces atroviridis</i> on
<i>Pinus sylvestris</i> (Netherlands); <i>Superstratomyces
flavomucosus</i> on leaf of <i>Hakea multilinearis</i>
(Australia); <i>Superstratomyces tardicrescens</i> from
human eye specimen (USA); <i>Taeniolella platani</i> on twig
of <i>Platanus hispanica</i> (Germany), and <i>Tympanis
pini</i> on twigs of <i>Pinus sylvestris</i> (Spain).
<b>Citation:</b> Crous PW, Hernández-Restrepo M, Schumacher
RK, Cowan DA, Maggs-Kölling G, Marais E, Wingfield MJ,
Yilmaz N, Adan OCG, Akulov A, Álvarez Duarte E,
Berraf-Tebbal A, Bulgakov TS, Carnegie AJ, de Beer ZW,
Decock C, Dijksterhuis J, Duong TA, Eichmeier A, Hien LT,
Houbraken JAMP, Khanh TN, Liem NV, Lombard L, Lutzoni FM,
Miadlikowska JM, Nel WJ, Pascoe IG, Roets F, Roux J, Samson
RA, Shen M, Spetik M, Thangavel R, Thanh HM, Thao LD, van
Nieuwenhuijzen EJ, Zhang JQ, Zhang Y, Zhao LL, Groenewald JZ
(2021). New and Interesting Fungi. 4. <i>Fungal Systematics
and Evolution</i> <b>7:</b> 255-343. doi:
10.3114/fuse.2021.07.13.},
Doi = {10.3114/fuse.2021.07.13},
Key = {fds357292}
}
@article{fds355540,
Author = {Oita, S and Ibáñez, A and Lutzoni, F and Miadlikowska, J and Geml, J and Lewis, LA and Hom, EFY and Carbone, I and U'Ren, JM and Arnold,
AE},
Title = {Climate and seasonality drive the richness and composition
of tropical fungal endophytes at a landscape
scale.},
Journal = {Communications biology},
Volume = {4},
Number = {1},
Pages = {313},
Year = {2021},
Month = {March},
url = {http://dx.doi.org/10.1038/s42003-021-01826-7},
Abstract = {Understanding how species-rich communities persist is a
foundational question in ecology. In tropical forests, tree
diversity is structured by edaphic factors, climate, and
biotic interactions, with seasonality playing an essential
role at landscape scales: wetter and less seasonal forests
typically harbor higher tree diversity than more seasonal
forests. We posited that the abiotic factors shaping tree
diversity extend to hyperdiverse symbionts in leaves-fungal
endophytes-that influence plant health, function, and
resilience to stress. Through surveys in forests across
Panama that considered climate, seasonality, and covarying
biotic factors, we demonstrate that endophyte richness
varies negatively with temperature seasonality. Endophyte
community structure and taxonomic composition reflect both
temperature seasonality and climate (mean annual temperature
and precipitation). Overall our findings highlight the vital
role of climate-related factors in shaping the
hyperdiversity of these important and little-known symbionts
of the trees that, in turn, form the foundations of tropical
forest biodiversity.},
Doi = {10.1038/s42003-021-01826-7},
Key = {fds355540}
}
@article{fds355689,
Author = {Stone, DF and Mccune, B and Pardo-De La Hoz and CJ and Magain, N and Miadlikowska, J},
Title = {Sinuicella denisonii, a new genus and species in the
Peltigeraceae from western North America},
Journal = {Lichenologist},
Volume = {53},
Number = {2},
Pages = {185-192},
Year = {2021},
Month = {March},
url = {http://dx.doi.org/10.1017/S0024282920000584},
Abstract = {The new genus Sinuicella, an early successional lichen, was
found on bare soil in Oregon, USA. The thallus is minute
fruticose, grey to nearly black, branching isotomic
dichotomous, branches round, 20-90 μm wide in water mount.
The cortex is composed of interlocking cells shaped like
jigsaw puzzle pieces. Spores are hyaline, 1-septate,
25-40(-50) × 6.5-9(-11) μm. Maximum likelihood
phylogenetic analyses on multilocus data sets, first
spanning the entire order Peltigerales and then restricted
to Peltigeraceae with extended sampling from Solorina and
Peltigera, revealed the placement of Sinuicella outside of
currently recognized genera, sister to Peltigera, with high
support. Based on the phylogenetic, morphological and
ecological distinctness of Sinuicella, we formally introduce
a new genus represented by the single species S. denisonii.
The cyanobiont of S. denisonii is Nostoc from phylogroup XL,
Clade 2, Subclade 3 based on the rbcLX marker.},
Doi = {10.1017/S0024282920000584},
Key = {fds355689}
}
@article{fds361299,
Author = {Medeiros, ID and Mazur, E and Miadlikowska, J and Flakus, A and Rodriguez-Flakus, P and Pardo-De la Hoz and CJ and Cieślak, E and Śliwa, L and Lutzoni, F},
Title = {Turnover of Lecanoroid Mycobionts and Their Trebouxia
Photobionts Along an Elevation Gradient in Bolivia
Highlights the Role of Environment in Structuring the Lichen
Symbiosis.},
Journal = {Frontiers in microbiology},
Volume = {12},
Pages = {774839},
Year = {2021},
Month = {January},
url = {http://dx.doi.org/10.3389/fmicb.2021.774839},
Abstract = {Shifts in climate along elevation gradients structure
mycobiont-photobiont associations in lichens. We obtained
mycobiont (lecanoroid Lecanoraceae) and photobiont
(<i>Trebouxia</i> alga) DNA sequences from 89 lichen thalli
collected in Bolivia from a ca. 4,700 m elevation gradient
encompassing diverse natural communities and environmental
conditions. The molecular dataset included six mycobiont
loci (ITS, nrLSU, mtSSU, <i>RPB1</i>, <i>RPB2</i>, and
<i>MCM7</i>) and two photobiont loci (ITS, <i>rbc</i>L); we
designed new primers to amplify Lecanoraceae <i>RPB1</i> and
<i>RPB2</i> with a nested PCR approach. Mycobionts belonged
to <i>Lecanora</i> s.lat., <i>Bryonora</i>,
<i>Myriolecis</i>, <i>Protoparmeliopsis</i>, the
"<i>Lecanora</i>" <i>polytropa</i> group, and the
"<i>L</i>." saligna group. All of these clades except for
<i>Lecanora</i> s.lat. occurred only at high elevation. No
single species of Lecanoraceae was present along the entire
elevation gradient, and individual clades were restricted to
a subset of the gradient. Most Lecanoraceae samples
represent species which have not previously been sequenced.
<i>Trebouxia</i> clade C, which has not previously been
recorded in association with species of Lecanoraceae,
predominates at low- to mid-elevation sites. Photobionts
from <i>Trebouxia</i> clade I occur at the upper extent of
mid-elevation forest and at some open, high-elevation sites,
while <i>Trebouxia</i> clades A and S dominate open habitats
at high elevation. We did not find <i>Trebouxia</i> clade D.
Several putative new species were found in <i>Trebouxia</i>
clades A, C, and I. These included one putative species in
clade A associated with <i>Myriolecis</i> species growing on
limestone at high elevation and a novel lineage sister to
the rest of clade C associated with <i>Lecanora</i> on bark
in low-elevation grassland. Three different kinds of
photobiont switching were observed, with certain mycobiont
species associating with <i>Trebouxia</i> from different
major clades, species within a major clade, or haplotypes
within a species. Lecanoraceae mycobionts and
<i>Trebouxia</i> photobionts exhibit species turnover along
the elevation gradient, but with each partner having a
different elevation threshold at which the community shifts
completely. A phylogenetically defined sampling of a single
diverse family of lichen-forming fungi may be sufficient to
document regional patterns of <i>Trebouxia</i> diversity and
distribution.},
Doi = {10.3389/fmicb.2021.774839},
Key = {fds361299}
}
@article{fds357529,
Author = {McCune, B and Arup, U and Breuss, O and Di Meglio and E and Di Meglio and J and Esslinger, TL and Miadlikowska, J and Miller, AE and Rosentreter, R and Schultz, M and Sheard, J and Tønsberg, T and Walton,
J},
Title = {Biodiversity and ecology of lichens of Kenai Fjords National
Park, Alaska},
Journal = {Plant and Fungal Systematics},
Volume = {65},
Number = {2},
Pages = {586-619},
Year = {2020},
Month = {December},
url = {http://dx.doi.org/10.35535/pfsyst-2020-0032},
Abstract = {We inventoried lichens in Kenai Fjords National Park in
Alaska, USA We assembled the known information on occurrence
and ecology of lichens in this park by combining field,
herbarium, and literature studies. Our results provide
baseline data on lichen occurrence that may be used in
resource condition assessments, vulnerability assessments,
long-term ecological monitoring, and resource management. We
report a total of 616 taxa of lichenized fungi from the
Park, plus an additional five subspecies and three
varieties, all of which are new additions to the National
Park Service database for this park unit. An additional five
species of nonlichenized lichenicolous fungi are reported
here. Eight non-lichenized fungi that are traditionally
treated with lichens are also included, most of these
associated with bark of particular host species. Four taxa
new to North America are reported here (Arctomia delicatula
var. acutior, Aspicilia dudinensis, Myriospora myochroa, and
Ochrolechia bahusiensis), along with 44 species new to
Alaska. Numerous species have been confirmed using ITS
barcoding sequences. Also several records assigned to the
genus level are reported, many of those are likely new
species.},
Doi = {10.35535/pfsyst-2020-0032},
Key = {fds357529}
}
@article{fds357530,
Author = {Miadlikowska, J and Magain, N and Buck, WR and Castillo, RV and Barlow,
GT and Pardo-De la Hoz and CJ and LaGreca, S and Lutzoni,
F},
Title = {Peltigera hydrophila (Lecanoromycetes, Ascomycota), a new
semi-aquatic cyanolichen species from Chile},
Journal = {Plant and Fungal Systematics},
Volume = {65},
Number = {1},
Pages = {210-218},
Year = {2020},
Month = {June},
url = {http://dx.doi.org/10.35535/pfsyst-2020-0016},
Abstract = {Peltigera hydrophila, a new species from Chile tentatively
distinguished based on phylogenetic evidence but not yet
named, is formally described here. Morphological differences
(e.g., non-tomentose thallus) and habitat preferences
(semi-aquatic) corroborate molecular and phylogenetic
distinctiveness of this early diverging lineage in section
Peltigera. Due to overlapping ecological ranges, P.
hydrophila shares some morphological traits with aquatic
species from the phylogenetically unrelated section
Hydrothyriae.},
Doi = {10.35535/pfsyst-2020-0016},
Key = {fds357530}
}
@article{fds357531,
Author = {Magain, N and Goffinet, B and Simon, A and Seelan, JSS and Medeiros, ID and Lutzoni, F and Miadlikowska, J},
Title = {Peltigera serusiauxii (Lecanoromycetes, Ascomycota), a new
species from Papua New Guinea and Malaysia},
Journal = {Plant and Fungal Systematics},
Volume = {65},
Number = {1},
Pages = {139-146},
Year = {2020},
Month = {June},
url = {http://dx.doi.org/10.35535/pfsyst-2020-0009},
Abstract = {Peltigera serusiauxii is proposed here as a new species from
Papua New Guinea and Sabah, northern Borneo (Malaysia). The
species belongs to the polydactyloid clade of section
Polydactylon. Because of its large thalli with a glabrous
upper surface, this species was previously identified as P.
dolichorhiza, but it differs by its polydactylon-type lower
surface and the high amount of dolichorrhizin. It appears to
be a strict specialist in its association with Nostoc
phylogroup IX throughout its known distribution. This is one
of many undescribed species remaining to be formally
described within the genus Peltigera, especially in Asia and
Australasia.},
Doi = {10.35535/pfsyst-2020-0009},
Key = {fds357531}
}
@article{fds348830,
Author = {Magain, N and Spribille, T and Dimeglio, J and Nelson, PR and Miadlikowska, J and Sérusiaux, E},
Title = {Phylogenetic evidence for an expanded circumscription of
Gabura (Arctomiaceae)},
Journal = {Lichenologist},
Volume = {52},
Number = {1},
Pages = {3-15},
Year = {2020},
Month = {January},
url = {http://dx.doi.org/10.1017/S0024282919000471},
Abstract = {Since the advent of molecular taxonomy, numerous
lichen-forming fungi with homoiomerous thalli initially
classified in the family Collemataceae Zenker have been
transferred to other families, highlighting the extent of
morphological convergence within Lecanoromycetes O. E.
Erikss. & Winka. While the higher level classification of
these fungi might be clarified by such transfers, numerous
specific and generic classifications remain to be addressed.
We examined the relationships within the broadly
circumscribed genus Arctomia Th. Fr., which has been the
recipient of several transfers from Collemataceae. We
demonstrated that Arctomia insignis (P. M. Jorg. & Tonsberg)
Ertz does not belong to Arctomia s. str. but forms a strong
monophyletic group with Gabura fascicularis (L.) P. M. Jorg.
We also confirmed that Arctomia borbonica Magain & Sérus.
and the closely related Arctomia insignis represent two
species. We formally transferred A. insignis and A.
borbonica to the genus Gabura Adans. and introduced two new
combinations: Gabura insignis and Gabura borbonica. We
reported Gabura insignis from Europe (Scotland and Ireland)
for the first time. While material from Europe and North
America is genetically almost identical, specimens from
Madagascar, South Africa and Reunion Island belong to three
distinct phylogenetic lineages, all of which are present in
the latter area and may represent distinct species. In its
current circumscription, the genus Gabura may contain up to
six species, whereas Arctomia s. str. includes only two
species (A. delicatula Th. Fr. and A. teretiuscula P. M.
Jorg.). The Gabura insignis group is shown to have an
unexpectedly large, subcosmopolitan distribution. With the
extended sampling from Arctomiaceae Th. Fr., the placement
of Steinera sorediata P. James & Henssen in the genus
Steinera Zahlbr. is confirmed and the presence of a new
Steinera species from Chile is highlighted.},
Doi = {10.1017/S0024282919000471},
Key = {fds348830}
}
@article{fds366475,
Author = {Flakus, A and Etayo, J and Miadlikowska, J and Lutzoni, F and Kukwa, M and Matura, N and Rodriguez-Flakus, P},
Title = {Biodiversity assessment of ascomycetes inhabiting Lobariella
lichens in Andean cloud forests led to one new family, three
new genera and 13 new species of lichenicolous
fungi},
Journal = {Plant and Fungal Systematics},
Volume = {64},
Number = {2},
Pages = {283-344},
Year = {2019},
Month = {December},
url = {http://dx.doi.org/10.2478/pfs-2019-0022},
Abstract = {Neotropical mountain forests are characterized by having
hyperdiverse and unusual fungi inhabiting lichens. The great
majority of these lichenicolous fungi (i.e., detectable by
light microscopy) remain undescribed and their phylogenetic
relationships are mostly unknown. This study focuses on
lichenicolous fungi inhabiting the genus Lobariella
(Peltigerales), one of the most important lichen hosts in
the Andean cloud forests. Based on molecular and
morphological data, three new genera are introduced:
Lawreyella gen. nov. (Cordieritidaceae, for Unguiculariopsis
lobariella), Neobaryopsis gen. nov. (Cordycipitaceae), and
Pseudodidymocyrtis gen. nov. (Didymosphaeriaceae). Nine
additional new species are described (Abrothallus subhalei
sp. nov., Atronectria lobariellae sp. nov., Corticifraga
microspora sp. nov., Epithamnolia rugosopycnidiata sp. nov.,
Lichenotubeufia cryptica sp. nov., Neobaryopsis andensis sp.
nov., Pseudodidymocyrtis lobariellae sp. nov.,
Rhagadostomella hypolobariella sp. nov., and Xylaria
lichenicola sp. nov.). Phylogenetic placements of 13
lichenicolous species are reported here for Abrothallus,
Arthonia, Globonectria, Lawreyella, Monodictys,
Neobaryopsis, Pseudodidymocyrtis, Sclerococcum,
Trichonectria and Xylaria. The name Sclerococcum ricasoliae
comb. nov. is reestablished for the neotropical populations
formerly named S. lobariellum (Sclerococcales). A key to
sexual and asexual states of 40 species of lobariellicolous
ascomycetous fungi is provided. Teleomorph-anamorph
connections were established for several species using
molecular methods and/or visual observations in nature.
Additionally, we found that the anamorphic species
Cornutispora ophiurospora inhabiting Lobariella was often
accompanied by ascomata of Spirographa. Results of
phylogenetic analyses, including newly generated sequences
of several Cornutispora and Spirographa species inhabiting
various host lichens, support the conclusion that
Cornutispora is a synonym of Spirographa. Our Maximum
Likelihood inference based on multiple loci show that all
studied Spirographa (including Cornutispora) belong to a new
lineage within Ostropales. Based on these highly supported
phylogenetic placements and the distinct character states of
their conidiomata, in comparison with other Lecanoromycetes,
a new family is proposed - Spirographaceae fam. nov. This
new lineage includes broadly distributed mycoparasites,
inhabiting various lichen and fungal hosts, and representing
an early diversification event preceding the lichen-forming
clade of Fissurinaceae, Gomphillaceae and Graphidaceae. Two
lichenicolous species, Asteroglobulus giselae and
Pleoscutula arsenii, were found to be nested within the
Spirographa clade, and their teleomorph-anamorph connections
were confirmed based on genotypic and phenotypic data. This
phylogenetic result is corroborated by their highly similar
ascomata anatomy. Together these results strongly indicate
that both species are congeneric with Spirographa. As a
result, four new species (S. aggregata sp. nov., S.
galligena sp. nov., S. maroneae sp. nov., and S.
parmotrematis sp. nov.) and 15 new combinations are proposed
(Spirographa ascaridiella comb. nov., S. arsenii comb. nov.,
S. ciliata comb. nov., S. giselae comb. nov., S. herteliana
comb. nov., S. hypotrachynae comb. nov., S. intermedia comb.
nov., S. lichenicola comb. nov., S. limaciformis comb. nov.,
S. ophiurospora comb. nov., S. pittii comb. nov., S.
pyramidalis comb. nov., S. triangularis comb. nov., S.
tricupulata comb. nov., and S. vermiformis comb. nov.).
Species of the genus Spirographa, as outlined here, are
strongly host-specific, mainly at the generic level of their
host. Some host genera can harbour more than one Spirographa
species.},
Doi = {10.2478/pfs-2019-0022},
Key = {fds366475}
}
@article{fds346584,
Author = {U'Ren, JM and Lutzoni, F and Miadlikowska, J and Zimmerman, NB and Carbone, I and May, G and Arnold, AE},
Title = {Host availability drives distributions of fungal endophytes
in the imperilled boreal realm.},
Journal = {Nature ecology & evolution},
Volume = {3},
Number = {10},
Pages = {1430-1437},
Year = {2019},
Month = {October},
url = {http://dx.doi.org/10.1038/s41559-019-0975-2},
Abstract = {Boreal forests represent the world's largest terrestrial
biome and provide ecosystem services of global importance.
Highly imperilled by climate change, these forests host
Earth's greatest phylogenetic diversity of endophytes, a
hyperdiverse group of symbionts that are defined by their
occurrence within living, symptomless plant and lichen
tissues. Endophytes shape the ecological and evolutionary
trajectories of plants and are therefore key to the function
and resilience of terrestrial ecosystems. A critical step in
linking the ecological functions of endophytes with those of
their hosts is to understand the distributions of these
symbionts at the global scale; however, turnover in host
taxa with geography and climate can confound insights into
endophyte biogeography. As a result, global drivers of
endophyte diversity and distributions are not known. Here,
we leverage sampling from phylogenetically diverse boreal
plants and lichens across North America and Eurasia to show
that host filtering in distinctive environments, rather than
turnover with geographical or environmental distance, is the
main determinant of the community composition and diversity
of endophytes. We reveal the distinctiveness of boreal
endophytes relative to soil fungi worldwide and endophytes
from diverse temperate biomes, highlighting a high degree of
global endemism. Overall, the distributions of endophytes
are directly linked to the availability of compatible hosts,
highlighting the role of biotic interactions in shaping
fungal communities across large spatial scales, and the
threat that climate change poses to biological diversity and
function in the imperilled boreal realm.},
Doi = {10.1038/s41559-019-0975-2},
Key = {fds346584}
}
@article{fds344599,
Author = {Chagnon, PL and Magain, N and Miadlikowska, J and Lutzoni,
F},
Title = {Species diversification and phylogenetically constrained
symbiont switching generated high modularity in the lichen
genus Peltigera},
Journal = {Journal of Ecology},
Volume = {107},
Number = {4},
Pages = {1645-1661},
Year = {2019},
Month = {July},
url = {http://dx.doi.org/10.1111/1365-2745.13207},
Abstract = {Ecological interactions range from purely specialized to
extremely generalized in nature. Recent research has showed
very high levels of specialization in the cyanolichens
involving Peltigera (mycobionts) and their Nostoc
photosynthetic partners (cyanobionts). Yet, little is known
about the mechanisms contributing to the establishment and
maintenance of such high specialization levels. Here, we
characterized interactions between Peltigera and Nostoc
partners at a global scale, using more than one thousand
thalli. We used tools from network theory, community
phylogenetics and biogeographical history reconstruction to
evaluate how these symbiotic interactions may have evolved.
After splitting the interaction matrix into modules of
preferentially interacting partners, we evaluated how module
membership might have evolved along the mycobionts’
phylogeny. We also teased apart the contributions of
geographical overlap vs phylogeny in driving interaction
establishment between Peltigera and Nostoc taxa. Module
affiliation rarely evolves through the splitting of large
ancestral modules. Instead, new modules appear to emerge
independently, which is often associated with a fungal
speciation event. We also found strong phylogenetic signal
in these interactions, which suggests that partner switching
is constrained by conserved traits. Therefore, it seems that
a high rate of fungal diversification following a switch to
a new cyanobiont can lead to the formation of large modules,
with cyanobionts associating with multiple closely retated
Peltigera species. Finally, when restricting our analyses to
Peltigera sister species, the latter differed more through
partner acquisition/loss than replacement (i.e., switching).
This pattern vanishes as we look at sister species that have
diverged longer ago. This suggests that fungal speciation
may be accompanied by a stepwise process of (a) novel
partner acquisition and (b) loss of the ancestral partner.
This could explain the maintenance of high specialization
levels in this symbiotic system where the transmission of
the cyanobiont to the next generation is assumed to be
predominantly horizontal. Synthesis. Overall, our study
suggests that oscillation between generalization and
ancestral partner loss may maintain high specialization
within the lichen genus Peltigera, and that partner
selection is not only driven by partners’ geographical
overlap, but also by their phylogenetically conserved
traits.},
Doi = {10.1111/1365-2745.13207},
Key = {fds344599}
}
@article{fds345378,
Author = {Carbone, I and White, JB and Miadlikowska, J and Arnold, AE and Miller,
MA and Magain, N and U'Ren, JM and Lutzoni, F},
Title = {T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for
Evolutionary Placement of DNA Sequences and Viewing
Alignments and Specimen Metadata on Curated and Custom
Trees.},
Journal = {Microbiology resource announcements},
Volume = {8},
Number = {29},
Pages = {e00328-e00319},
Year = {2019},
Month = {July},
url = {http://dx.doi.org/10.1128/mra.00328-19},
Abstract = {The Tree-Based Alignment Selector (T-BAS) toolkit combines
phylogenetic-based placement of DNA sequences with alignment
and specimen metadata visualization tools in an integrative
pipeline for analyzing microbial biodiversity. The release
of T-BAS version 2.1 makes available reference phylogenies,
supports multilocus sequence placements and permits
uploading and downloading trees, alignments, and specimen
metadata.},
Doi = {10.1128/mra.00328-19},
Key = {fds345378}
}
@article{fds340996,
Author = {Miadlikowska, J and Magain, N and Pardo-De La Hoz and CJ and Niu, D and Goward, T and Sérusiaux, E and Lutzoni, F},
Title = {Species in section Peltidea (aphthosa group) of the genus
Peltigera remain cryptic after molecular phylogenetic
revision},
Journal = {Plant and Fungal Systematics},
Volume = {63},
Number = {2},
Pages = {45-64},
Year = {2018},
Month = {December},
url = {http://dx.doi.org/10.2478/pfs-2018-0007},
Abstract = {Closely related lichen-forming fungal species circumscribed
using phenotypic traits (morphospecies) do not always align
well with phylogenetic inferences based on molecular data.
Using multilocus data obtained from a worldwide sampling, we
inferred phylogenetic relationships among five currently
accepted morphospecies of Peltigera section Peltidea (P.
aphthosa group). Monophyletic circumscription of all
currently recognized morphospecies (P. britannica, P.
chionophila, P. frippii and P. malacea) except P. aphthosa,
which contained P. britannica, was confirmed with high
bootstrap support. Following their re-delimitation using
bGMYC and Structurama, BPP validated 14 putative species
including nine previously unrecognized potential species
(five within P. malacea, five within P. aphthosa, and two
within P. britannica). Because none of the undescribed
potential species are corroborated morphologically,
chemically, geographically or ecologically, we concluded
that these monophyletic entities represent intraspecific
phylogenetic structure, and, therefore, should not be
recognized as new species. Cyanobionts associated with
Peltidea mycobionts (51 individuals) represented 22 unique
rbcLX haplotypes from five phylogroups in Clade II subclades
2 and 3. With rare exceptions, Nostoc taxa involved in
trimembered and bimembered associations are phylogenetically
closely related (subclade 2) or identical, suggesting a
mostly shared cyanobiont pool with infrequent switches.
Based on a broad geographical sampling, we confirm a high
specificity of Nostoc subclade 2 with their mycobionts,
including a mutualistically exclusive association between
phylogroup III and specific lineages of P.
malacea.},
Doi = {10.2478/pfs-2018-0007},
Key = {fds340996}
}
@article{fds340628,
Author = {Lutzoni, F and Nowak, MD and Alfaro, ME and Reeb, V and Miadlikowska, J and Krug, M and Arnold, AE and Lewis, LA and Swofford, DL and Hibbett, D and Hilu, K and James, TY and Quandt, D and Magallón,
S},
Title = {Contemporaneous radiations of fungi and plants linked to
symbiosis.},
Journal = {Nature communications},
Volume = {9},
Number = {1},
Pages = {5451},
Year = {2018},
Month = {December},
url = {http://dx.doi.org/10.1038/s41467-018-07849-9},
Abstract = {Interactions between fungi and plants, including parasitism,
mutualism, and saprotrophy, have been invoked as key to
their respective macroevolutionary success. Here we evaluate
the origins of plant-fungal symbioses and saprotrophy using
a time-calibrated phylogenetic framework that reveals linked
and drastic shifts in diversification rates of each kingdom.
Fungal colonization of land was associated with at least two
origins of terrestrial green algae and preceded embryophytes
(as evidenced by losses of fungal flagellum, ca. 720 Ma),
likely facilitating terrestriality through endomycorrhizal
and possibly endophytic symbioses. The largest radiation of
fungi (Leotiomyceta), the origin of arbuscular mycorrhizae,
and the diversification of extant embryophytes occurred ca.
480 Ma. This was followed by the origin of extant lichens.
Saprotrophic mushrooms diversified in the Late Paleozoic as
forests of seed plants started to dominate the landscape.
The subsequent diversification and explosive radiation of
Agaricomycetes, and eventually of ectomycorrhizal mushrooms,
were associated with the evolution of Pinaceae in the
Mesozoic, and establishment of angiosperm-dominated biomes
in the Cretaceous.},
Doi = {10.1038/s41467-018-07849-9},
Key = {fds340628}
}
@article{fds339811,
Author = {Hoz, CJPDL and Magain, N and Lutzoni, F and Goward, T and Restrepo, S and Miadlikowska, J},
Title = {Contrasting Symbiotic Patterns in Two Closely Related
Lineages of Trimembered Lichens of the Genus
Peltigera},
Journal = {Frontiers in Microbiology},
Volume = {9},
Number = {NOV},
Publisher = {FRONTIERS MEDIA SA},
Year = {2018},
Month = {November},
url = {http://dx.doi.org/10.3389/fmicb.2018.02770},
Abstract = {Species circumscription is key to the characterization of
patterns of specificity in symbiotic systems at a
macroevolutionary scale. Here, a worldwide phylogenetic
framework was used to assess the biodiversity and symbiotic
patterns of association among partners in trimembered
lichens from the genus Peltigera, section Chloropeltigera.
We sequenced six loci of the main fungal partner and
performed species discovery and validation analyses to
establish putative species boundaries. Single locus
phylogenies were used to establish the identity of both
photobionts, Nostoc (cyanobacterium) and Coccomyxa (green
alga). Distribution and specificity patterns were compared
to the closely related clade, section Peltidea, which
includes mainly Peltigera species with trimembered thalli.
For section Chloropeltigera, eight fungal species (including
five newly delimited putative species) were found in
association with nine Nostoc phylogroups and two Coccomyxa
species. In contrast, eight fungal species (including three
newly delimited putative species) in section Peltidea were
found in association with only four Nostoc phylogroups and
the same two Coccomyxa species as for section
Chloropeltigera. This difference in cyanobiont biodiversity
between these two sections can potentially be explained by a
significantly higher frequency of sexual reproductive
structures in species from section Chloropeltigera compared
to section Peltidea. Therefore, horizontal transmission of
the cyanobiont might be more prevalent in Chloropeltigera
species, while vertical transmission might be more common in
Peltidea species. All Peltigera species in section
Chloropeltigera are generalists in their association with
Nostoc compared to more specialized Peltigera species in
section Peltidea. Constrained distributions of Peltigera
species that associate strictly with one species of green
algae (Coccomyxa subellipsoidea) indicate that the
availability of the green alga and the specificity of the
interaction might be important factors limiting geographic
ranges of trimembered Peltigera, in addition to constraints
imposed by their interaction with Nostoc partners and by
climatic factors.},
Doi = {10.3389/fmicb.2018.02770},
Key = {fds339811}
}
@article{fds339620,
Author = {Magain, N and Truong, C and Goward, T and Niu, D and Goffinet, B and Sérusiaux, E and Vitikainen, O and Lutzoni, F and Miadlikowska,
J},
Title = {Species delimitation at a global scale reveals high species
richness with complex biogeography and patterns of symbiont
association in peltigera section peltigera (Lichenized
ascomycota: Lecanoromycetes)},
Journal = {Taxon},
Volume = {67},
Number = {5},
Pages = {836-870},
Publisher = {WILEY},
Year = {2018},
Month = {October},
url = {http://dx.doi.org/10.12705/675.3},
Abstract = {This comprehensive phylogenetic revision of sections
Peltigera and Retifoveatae of the cyanolichen genus
Peltigera is based on DNA sequences from more than 500
specimens from five continents. We amplified five loci
(nrITS, β-tubulin and three intergenic spacers part of
colinear orthologous regions [COR]) for the mycobiont, and
the rbcLX locus for the cyanobacterial partner Nostoc.
Phylogenetic inferences (RAxML, BEAST) and species
delimitation methods (bGMYC, bPTP, bPP) suggest the presence
of 88 species in section Peltigera, including 50 species new
to science, hence uncovering a surprisingly high proportion
of previously unnoticed biodiversity. The hypervariable
region in ITS1 (ITS1-HR) is a powerful marker to identify
species within sections Peltigera and Retifoveatae. Most
newly delimited species are restricted to a single
biogeographic region, however, up to ten species have a
nearly cosmopolitan distribution. The specificity of
mycobionts in their association with Nostoc cyanobionts
ranges from strict specialists (associate with only one
Nostoc phylogroup) to broad generalists (up to eight Nostoc
phylogroups uncovered), with widespread species recruiting a
broader selection of Nostoc phylogroups than species with
limited distributions. In contrast, species from the P.
didactyla clade characterized by small thalli and asexual
vegetative propagules (soredia) associate with fewer Nostoc
phylogroups (i.e., are more specialized) despite their broad
distributions, and show significantly higher rates of
nucleotide substitutions.},
Doi = {10.12705/675.3},
Key = {fds339620}
}
@article{fds337995,
Author = {Lu, J and Magain, N and Miadlikowska, J and Coyle, JR and Truong, C and Lutzoni, F},
Title = {Bioclimatic factors at an intrabiome scale are more limiting
than cyanobiont availability for the lichen-forming genus
Peltigera.},
Journal = {American journal of botany},
Volume = {105},
Number = {7},
Pages = {1198-1211},
Year = {2018},
Month = {July},
url = {http://dx.doi.org/10.1002/ajb2.1119},
Abstract = {<h4>Premise of the study</h4>Factors shaping spatiotemporal
patterns of associations in mutualistic systems are poorly
understood. We used the lichen-forming fungi Peltigera and
their cyanobacterial partners Nostoc to investigate the
spatial structure of this symbiosis at an intrabiome scale
and to identify potential factors shaping these
associations.<h4>Methods</h4>Ninety-three thalli were
sampled in Québec, Canada, along a south-north and an
east-west transect of ~1300 km each. We identified the two
main partners (Peltigera species and Nostoc phylogroups)
using molecular markers and modeled the effects of
environmental variables and partner occurrence on
Peltigera-Nostoc distributions.<h4>Key results</h4>Peltigera
species showed a high degree of specialization toward
cyanobionts, whereas two Nostoc phylogroups dominated both
transects by associating with several Peltigera species.
Peltigera species had narrower ranges than these two main
cyanobionts. Distributions of three Peltigera species were
highly associated with precipitation and temperature
variables, which was not detected for Nostoc phylogroups at
this spatial scale.<h4>Conclusions</h4>For these
cyanolichens, factors driving patterns of symbiotic
associations are scale dependent. Contrary to global-scale
findings, generalist Peltigera species were not more
widespread within the boreal biome than specialists. Nostoc
availability was not the only driver of Peltigera species'
geographic ranges; environmental factors also contributed to
their intrabiome distributions. Climatic conditions
(especially precipitation) limited the range of some
Peltigera species more than the range of their
cyanobacterial partners at an intrabiome (boreal)
scale.},
Doi = {10.1002/ajb2.1119},
Key = {fds337995}
}
@article{fds337996,
Author = {Chagnon, PL and Magain, N and Miadlikowska, J and Lutzoni,
F},
Title = {Strong specificity and network modularity at a very fine
phylogenetic scale in the lichen genus Peltigera.},
Journal = {Oecologia},
Volume = {187},
Number = {3},
Pages = {767-782},
Publisher = {Springer Nature},
Year = {2018},
Month = {July},
url = {http://dx.doi.org/10.1007/s00442-018-4159-6},
Abstract = {Identifying the drivers and evolutionary consequences of
species interactions is a major goal of community ecology.
Network-based analyses can provide mathematical tools to
detect non-random patterns of interactions, and potentially
help predicting the consequences of such patterns on
evolutionary dynamics of symbiotic systems. Here, we
characterize the structure of a lichen network at a very
fine phylogenetic scale, by identifying the photosynthetic
partners (i.e., cyanobacteria of the genus Nostoc) of
lichenized fungi belonging to a monophyletic section of a
single genus (i.e., section Polydactylon of the genus
Peltigera), worldwide. Even at such a fine phylogenetic
scale, we found that interactions were highly modular and
anti-nested, indicating strong preferences in interactions.
When considering local Peltigera communities, i.e., datasets
at small spatial scales with only a slightly broader
phylogenetic range, interactions remained modular but were
asymmetric, with generalist Nostoc partners interacting with
specialized Peltigera species. This asymmetry was not
detected with our global spatial scale dataset. We discuss
these results in the light of lichen community assembly, and
explore how such interaction patterns may influence
coevolution in lichens and the evolutionary stability of the
mutualism in general.},
Doi = {10.1007/s00442-018-4159-6},
Key = {fds337996}
}
@article{fds352215,
Author = {McCune, B and Arup, U and Breuss, O and Di Meglio and ED and Di Meglio and JD and Esslinger, TL and Magain, N and Miadlikowska, J and Miller, AE and Muggia, L and Nelson, PR and Rosentreter, R and Schultz, M and Sheard,
JW and Tønsberg, T and Walton, J},
Title = {Biodiversity and ecology of lichens of Katmai and Lake Clark
National Parks and Preserves, Alaska},
Journal = {Mycosphere},
Volume = {9},
Number = {4},
Pages = {859-930},
Year = {2018},
Month = {January},
url = {http://dx.doi.org/10.5943/mycosphere/9/4/10},
Abstract = {We inventoried lichens in Lake Clark (LACL) and Katmai
(KATM) National Parks and Preserves. We assembled the known
information on lichens in these parks by combining field,
herbarium, and literature studies. Our results provide
baseline data on lichen occurrence that may be used in
resource condition assessments, vulnerability assessments,
long-term ecological monitoring, and resource management. We
report a total of 896 taxa of lichenized fungi from the
Parks, adding 889 taxa to the total of seven taxa reported
for the Parks by the National Park Service database and
including ten new species first published elsewhere. An
additional 15 lichenicolous fungi are reported here. Seven
non-lichenized fungi associated with young living twigs of
particular host species are also included. Sixteen species
are new to Alaska, and six species new to North America
(Caloplaca fuscorufa, Lecanora leucococca s.l., Ochrolechia
brodoi, Protoparmelia memnonia, and Rhizocarpon leptolepis).
Four new combinations are made, Cetraria minuscula,
Enchylium millegranum var. bachmanianum, Lathagrium
undulatum var. granulosum, and Protomicarea alpestris.
Additional new species based on collections from the Parks
have been described in separate publications.},
Doi = {10.5943/mycosphere/9/4/10},
Key = {fds352215}
}
@article{fds329418,
Author = {Magain, N and Miadlikowska, J and Mueller, O and Gajdeczka, M and Truong, C and Salamov, AA and Dubchak, I and Grigoriev, IV and Goffinet,
B and Sérusiaux, E and Lutzoni, F},
Title = {Conserved genomic collinearity as a source of broadly
applicable, fast evolving, markers to resolve species
complexes: A case study using the lichen-forming genus
Peltigera section Polydactylon.},
Journal = {Molecular phylogenetics and evolution},
Volume = {117},
Pages = {10-29},
Year = {2017},
Month = {December},
url = {http://dx.doi.org/10.1016/j.ympev.2017.08.013},
Abstract = {Synteny can be maintained for certain genomic regions across
broad phylogenetic groups. In these homologous genomic
regions, sites that are under relaxed purifying selection,
such as intergenic regions, could be used broadly as markers
for population genetic and phylogenetic studies on species
complexes. To explore the potential of this approach, we
found 125 Collinear Orthologous Regions (COR) ranging from 1
to >10kb across nine genomes representing the
Lecanoromycetes and Eurotiomycetes (Pezizomycotina,
Ascomycota). Twenty-six of these COR were found in all 24
eurotiomycete genomes surveyed for this study. Given the
high abundance and availability of fungal genomes we believe
this approach could be adopted for other large groups of
fungi outside the Pezizomycotina. Asa proof of concept, we
selected three Collinear Orthologous Regions (COR1b, COR3,
and COR16), based on synteny analyses of several genomes
representing three classes of Ascomycota: Eurotiomycetes,
Lecanoromycetes, and Lichinomycetes. COR16, for example, was
found across these three classes of fungi. Here we compare
the resolving power of these three new markers with five
loci commonly used in phylogenetic studies of fungi, using
section Polydactylon of the cyanolichen-forming genus
Peltigera (Lecanoromycetes) - a clade with several
challenging species complexes. Sequence data were subjected
to three species discovery and two validating methods. COR
markers substantially increased phylogenetic resolution and
confidence, and highly contributed to species delimitation.
The level of phylogenetic signal provided by each of the COR
markers was higher than the commonly used fungal barcode
ITS. High cryptic diversity was revealed by all methods. As
redefined here, most species represent lineages that have
relatively narrower, and more homogeneous biogeographical
ranges than previously understood. The scabrosoid clade
consists of ten species, seven of which are new. For the
dolichorhizoid clade, twenty-two new species were discovered
for a total of twenty-nine species in this
clade.},
Doi = {10.1016/j.ympev.2017.08.013},
Key = {fds329418}
}
@article{fds328939,
Author = {Heiđmarsson, S and Gueidan, C and Miadlikowska, J and Lutzoni,
F},
Title = {Multi-locus phylogeny supports the placement of endocarpon
pulvinatum within staurothele s. Str. (lichenised
ascomycetes, eurotiomycetes, verrucariaceae)},
Journal = {Phytotaxa},
Volume = {306},
Number = {1},
Pages = {37-48},
Publisher = {MAGNOLIA PRESS},
Year = {2017},
Month = {May},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Within the lichen family Verrucariaceae, the genera
Endocarpon, Willeya and Staurothele are characterised by
muriform ascospores and the presence of algal cells in the
hymenium. Endocarpon thalli are squamulose to subfruticose,
whereas Willeya and Staurothele include only crustose
species. Endocarpon pulvinatum, an arctic-alpine species
newly reported for Iceland, is one of the few Endocarpon
with a subfruticose thallus formed by long and narrow
erected squamules. Molecular phylogenetic analyses of four
loci (ITS, nrLSU, mtSSU, and mcm7) newly obtained from E.
pulvinatum specimens from Iceland, Finland and North America
does not confirm its current classification within the
mostly squamulose genus Endocarpon, but instead supports its
placement within the crustose genus Staurothele. The new
combination Staurothele pulvinata is therefore proposed
here. It includes also E. tortuosum, which was confirmed as
a synonym of E. pulvinatum based on a single
sequence.},
Doi = {10.11646/phytotaxa.306.1.3},
Key = {fds328939}
}
@article{fds328940,
Author = {Carbone, I and White, JB and Miadlikowska, J and Arnold, AE and Miller,
MA and Kauff, F and U'Ren, JM and May, G and Lutzoni,
F},
Title = {T-BAS: Tree-Based Alignment Selector toolkit for
phylogenetic-based placement, alignment downloads and
metadata visualization: an example with the Pezizomycotina
tree of life.},
Journal = {Bioinformatics (Oxford, England)},
Volume = {33},
Number = {8},
Pages = {1160-1168},
Year = {2017},
Month = {April},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {<h4>Motivation</h4>High-quality phylogenetic placement of
sequence data has the potential to greatly accelerate
studies of the diversity, systematics, ecology and
functional biology of diverse groups. We developed the
Tree-Based Alignment Selector (T-BAS) toolkit to allow
evolutionary placement and visualization of diverse DNA
sequences representing unknown taxa within a robust
phylogenetic context, and to permit the downloading of
highly curated, single- and multi-locus alignments for
specific clades.<h4>Results</h4>In its initial form, T-BAS
v1.0 uses a core phylogeny of 979 taxa (including 23
outgroup taxa, as well as 61 orders, 175 families and 496
genera) representing all 13 classes of largest subphylum of
Fungi-Pezizomycotina (Ascomycota)-based on sequence
alignments for six loci (nr5.8S, nrLSU, nrSSU, mtSSU, RPB1,
RPB2 ). T-BAS v1.0 has three main uses: (i) Users may
download alignments and voucher tables for members of the
Pezizomycotina directly from the reference tree,
facilitating systematics studies of focal clades. (ii) Users
may upload sequence files with reads representing unknown
taxa and place these on the phylogeny using either BLAST or
phylogeny-based approaches, and then use the displayed tree
to select reference taxa to include when downloading
alignments. The placement of unknowns can be performed for
large numbers of Sanger sequences obtained from fungal
cultures and for alignable, short reads of environmental
amplicons. (iii) User-customizable metadata can be
visualized on the tree.<h4>Availability and
implementation</h4>T-BAS Version 1.0 is available online at
http://tbas.hpc.ncsu.edu . Registration is required to
access the CIPRES Science Gateway and NSF XSEDE's large
computational resources.<h4>Contact</h4>icarbon@ncsu.edu.<h4>Supplementary
information</h4>Supplementary data are available at
Bioinformatics online.},
Doi = {10.1093/bioinformatics/btw808},
Key = {fds328940}
}
@article{fds332336,
Author = {Magain, N and Miadlikowska, J and Goffinet, B and Sérusiaux, E and Lutzoni, F},
Title = {Macroevolution of Specificity in Cyanolichens of the Genus
Peltigera Section Polydactylon (Lecanoromycetes,
Ascomycota).},
Journal = {Systematic biology},
Volume = {66},
Number = {1},
Pages = {74-99},
Year = {2017},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Patterns of specificity among symbiotic partners are key to
a comprehensive understanding of the evolution of symbiotic
systems. Specificity of mutualistic partners, within a
widespread monophyletic group for which all species are
sampled has rarely been explored. Here, we assess the level
of specificity between the cosmopolitan lichen-forming
fungus (mycobiont) from the genus Peltigera, section
Polydactylon, and its cyanobacterial partner Nostoc
(cyanobiont). The mycobiont and cyanobiont phylogenies are
inferred from five nuclear loci and the rbcLX region,
respectively. These sequences were obtained from 206 lichen
thalli, representing ca. 40 closely related Peltigera
species sampled worldwide, doubling the number of known
species in this group. We found a broad spectrum of
specificity for both partners ranging from strict
specialists to generalists. Overall, mycobionts are more
specialized than cyanobionts by associating mostly with one
or a few Nostoc phylogroups, whereas most cyanobionts
associate frequently with several Peltigera species.
Specialist mycobionts are older than generalists, supporting
the hypothesis that specialization of mycobionts to one or
few cyanobionts, is favored through time in geographic areas
where species have been established for long periods of
time. The relatively recent colonization of a new geographic
area (Central and South America) by members of section
Polydactylon is associated with a switch to a generalist
pattern of association and an increased diversification rate
by the fungal partner, suggesting that switches to
generalism are rare events that are advantageous in new
environments. We detected higher genetic diversity in
generalist mycobionts. We also found that Peltigera species
specialized on a single Nostoc phylogroup have narrower
geographical distributions compared with generalist
species.},
Doi = {10.1093/sysbio/syw065},
Key = {fds332336}
}
@article{fds329419,
Author = {Darnajoux, R and Zhang, X and McRose, DL and Miadlikowska, J and Lutzoni, F and Kraepiel, AML and Bellenger, J-P},
Title = {Biological nitrogen fixation by alternative nitrogenases in
boreal cyanolichens: importance of molybdenum availability
and implications for current biological nitrogen fixation
estimates.},
Journal = {The New phytologist},
Volume = {213},
Number = {2},
Pages = {680-689},
Year = {2017},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Cryptogamic species and their associated cyanobacteria have
attracted the attention of biogeochemists because of their
critical roles in the nitrogen cycle through symbiotic and
asymbiotic biological fixation of nitrogen (BNF). BNF is
mediated by the nitrogenase enzyme, which, in its most
common form, requires molybdenum at its active site.
Molybdenum has been reported as a limiting nutrient for BNF
in many ecosystems, including tropical and temperate
forests. Recent studies have suggested that alternative
nitrogenases, which use vanadium or iron in place of
molybdenum at their active site, might play a more prominent
role in natural ecosystems than previously recognized. Here,
we studied the occurrence of vanadium, the role of
molybdenum availability on vanadium acquisition and the
contribution of alternative nitrogenases to BNF in the
ubiquitous cyanolichen Peltigera aphthosa s.l. We confirmed
the use of the alternative vanadium-based nitrogenase in the
Nostoc cyanobiont of these lichens and its substantial
contribution to BNF in this organism. We also showed that
the acquisition of vanadium is strongly regulated by the
abundance of molybdenum. These findings show that
alternative nitrogenase can no longer be neglected in
natural ecosystems, particularly in molybdenum-limited
habitats.},
Doi = {10.1111/nph.14166},
Key = {fds329419}
}
@article{fds327998,
Author = {Gryganskyi, A. P. and Humber, R. A. and Miadlikowska, J. and Smith, M. and Wu, S. and Rubinstein, N. and Voigt, K. and Walter, G. and Anihchenko, I. M. and Vilgalys, R.},
Title = {Molecular Phylogeny of Entomophthoralean
Fungi.},
Journal = {Molecular Phylogenetics and Evolution},
Volume = {65},
Pages = {682-694},
Year = {2017},
url = {http://lutzonilab.org/publications-datasets/},
Key = {fds327998}
}
@article{fds328021,
Author = {Miadlikowska, J. and Lutzoni, F.},
Title = {Phylogenetic classification of peltigeralean fungi
(Peltigerales, Ascomycota) based on ribosomal RNA small and
large subunits.},
Journal = {American Journal of Botany},
Volume = {91},
Pages = {449–464},
Year = {2017},
url = {http://lutzonilab.org/publications-datasets/},
Key = {fds328021}
}
@article{fds329500,
Author = {Manoharan-Basil, SS and Miadlikowska, J and Goward, T and Andrésson,
ÓS and Miao, VPW},
Title = {Peltigera islandica, a new cyanolichen species in section
Peltigera ('P. canina group')},
Journal = {Lichenologist},
Volume = {48},
Number = {5},
Pages = {451-467},
Publisher = {Cambridge University Press (CUP)},
Year = {2016},
Month = {September},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {A new cyanolichen, Peltigera islandica sp. nov. in the
section Peltigera ('P. canina group') is described from
Iceland. This species is similar in general appearance to P.
rufescens and P. membranacea, but may be recognized by its
downturned lobe tips and narrow lobes, respectively. Most
thalli are bright emerald green in colour when moist,
although a dark khaki green colourmorph is also documented.
Monophyly of P. islandica s. lat. (i.e. including P. sp. A
sensu O'Brien et al., from Canada) is significantly
supported based on ITS sequences and corroborated by
molecular synapomorphy (absence of the ITS1 hypervariable
region). Analysis of the rbcLX locus indicates the
cyanobiont of P. islandica (Nostoc sp.) comprises strains
belonging to a pool of Icelandic genotypes, some of which
are present in other Peltigera species, including P.
neorufescens, another taxon new to Iceland collected during
this study. Association with photobionts that are shared by
other local species suggests P. islandica may be well
established in Iceland, but a review of herbarium
collections as well as broader field surveys are needed to
better characterize its geographical distribution.},
Doi = {10.1017/S0024282916000414},
Key = {fds329500}
}
@article{fds329420,
Author = {Hestmark, G and Lutzoni, F and Miadlikowska, J},
Title = {Photobiont associations in co-occurring umbilicate lichens
with contrasting modes of reproduction in coastal
Norway},
Journal = {Lichenologist},
Volume = {48},
Number = {5},
Pages = {545-557},
Publisher = {Cambridge University Press (CUP)},
Year = {2016},
Month = {September},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The identity and phylogenetic placement of photobionts
associated with two lichen-forming fungi, Umbilicaria
spodochroa and Lasallia pustulata were examined. These
lichens commonly grow together in high abundance on coastal
cliffs in Norway, Sweden and Finland. The mycobiont of U.
spodochroa reproduces sexually through ascospores, and must
find a suitable algal partner in the environment to
re-establish the lichen symbiosis. Lasallia pustulata
reproduces mainly vegetatively using symbiotic propagules
(isidia) containing both symbiotic partners (photobiont and
mycobiont). Based on DNA sequences of the internal
transcribed spacer region (ITS) we detected seven haplotypes
of the green-algal genus Trebouxia in 19 pairs of adjacent
thalli of U. spodochroa and L. pustulata from five coastal
localities in Norway. As expected, U. spodochroa associated
with a higher diversity of photobionts (seven haplotypes)
than the mostly asexually reproducing L. pustulata (four
haplotypes). The latter was associated with the same
haplotype in 15 of the 19 thalli sampled. Nine of the lichen
pairs examined share the same algal haplotype, supporting
the hypothesis that the mycobiont of U. spodochroa might
associate with the photobiont 'pirated' from the abundant
isidia produced by L. pustulata that are often scattered on
the cliff surfaces. Up to six haplotypes of Trebouxia were
found within a single sampling site, indicating a low level
of specificity of both mycobionts for their algal partner.
Most photobiont strains associated with species of
Umbilicaria and Lasallia, including samples from this study,
represent phylogenetically closely related taxa of Trebouxia
grouped within a small number of main clades (Trebouxia sp.,
T. simplex/T. jamesii, and T. incrustata+T. gigantea). Three
of the photobiont haplotypes were found only in U.
spodochroa thalli.},
Doi = {10.1017/S0024282916000232},
Key = {fds329420}
}
@article{fds329421,
Author = {van Nieuwenhuijzen, EJ and Miadlikowska, JM and Houbraken, JAMP and Adan, OCG and Lutzoni, FM and Samson, RA},
Title = {Wood staining fungi revealed taxonomic novelties in
Pezizomycotina: New order Superstratomycetales
and new species Cyanodermella oleoligni.},
Journal = {Studies in mycology},
Volume = {85},
Pages = {107-124},
Year = {2016},
Month = {September},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {A culture-based survey of staining fungi on oil-treated
timber after outdoor exposure in Australia and the
Netherlands uncovered new taxa in <i>Pezizomycotina</i>.
Their taxonomic novelty was confirmed by phylogenetic
analyses of multi-locus sequences (ITS, nrSSU, nrLSU,
mitSSU, <i>RPB1</i>, <i>RPB2</i>, and <i>EF-1α</i>) using
multiple reference data sets. These previously unknown taxa
are recognised as part of a new order (<i>Superstratomycetales</i>)
potentially closely related to <i>Trypetheliales</i>
(<i>Dothideomycetes</i>), and as a new species of
<i>Cyanodermella</i>, <i>C. oleoligni</i> in
<i>Stictidaceae</i> (<i>Ostropales</i>) part of the mostly
lichenised class <i>Lecanoromycetes</i>. Within
<i>Superstratomycetales</i> a single genus named
<i>Superstratomyces</i> with three putative species:
<i>S. flavomucosus</i>, <i>S. atroviridis</i>, and
<i>S. albomucosus</i> are formally described. Monophyly of
each circumscribed <i>Superstratomyces</i> species was
highly supported and the intraspecific genetic variation was
substantially lower than interspecific differences detected
among species based on the ITS, nrLSU, and <i>EF-1α</i>
loci. Ribosomal loci for all members of <i>Superstratomyces</i>
were noticeably different from all fungal sequences
available in GenBank. All strains from this genus grow
slowly in culture, have darkly pigmented mycelia and produce
pycnidia. The strains of <i>C. oleoligni</i> form green
colonies with slimy masses and develop green pycnidia on
oatmeal agar. These new taxa could not be classified
reliably at the class and lower taxonomic ranks by
sequencing from the substrate directly or based solely on
culture-dependent morphological investigations. Coupling
phenotypic observations with multi-locus sequencing of fungi
isolated in culture enabled these taxonomic discoveries.
Outdoor situated timber provides a great potential for
culturable undescribed fungal taxa, including higher rank
lineages as revealed by this study, and therefore, should be
further explored.},
Doi = {10.1016/j.simyco.2016.11.008},
Key = {fds329421}
}
@article{fds329422,
Author = {Chagnon, P-L and U'Ren, JM and Miadlikowska, J and Lutzoni, F and Arnold, AE},
Title = {Erratum to: Interaction type influences ecological network
structure more than local abiotic conditions: evidence from
endophytic and endolichenic fungi at a continental
scale.},
Journal = {Oecologia},
Volume = {181},
Number = {2},
Pages = {633},
Publisher = {Springer Nature},
Year = {2016},
Month = {June},
url = {http://dx.doi.org/10.1007/s00442-016-3589-2},
Doi = {10.1007/s00442-016-3589-2},
Key = {fds329422}
}
@article{fds329423,
Author = {U'Ren, JM and Miadlikowska, J and Zimmerman, NB and Lutzoni, F and Stajich, JE and Arnold, AE},
Title = {Contributions of North American endophytes to the phylogeny,
ecology, and taxonomy of Xylariaceae (Sordariomycetes,
Ascomycota).},
Journal = {Molecular phylogenetics and evolution},
Volume = {98},
Pages = {210-232},
Year = {2016},
Month = {May},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The Xylariaceae (Sordariomycetes) comprise one of the
largest and most diverse families of Ascomycota, with at
least 85 accepted genera and ca. 1343 accepted species. In
addition to their frequent occurrence as saprotrophs,
members of the family often are found as endophytes in
living tissues of phylogenetically diverse plants and
lichens. Many of these endophytes remain sterile in culture,
precluding identification based on morphological characters.
Previous studies indicate that endophytes are highly diverse
and represent many xylariaceous genera; however,
phylogenetic analyses at the family level generally have not
included endophytes, such that their contributions to
understanding phylogenetic relationships of Xylariaceae are
not well known. Here we use a multi-locus, cumulative
supermatrix approach to integrate 92 putative species of
fungi isolated from plants and lichens into a phylogenetic
framework for Xylariaceae. Our collection spans 1933
isolates from living and senescent tissues in five biomes
across the continental United States, and here is analyzed
in the context of previously published sequence data from
described species and additional taxon sampling of type
specimens from culture collections. We found that the
majority of strains obtained in our surveys can be
classified in the hypoxyloid and xylaroid subfamilies,
although many also were found outside of these lineages (as
currently circumscribed). Many endophytes were placed in
lineages previously not known for endophytism. Most
endophytes appear to represent novel species, but inferences
are limited by potential gaps in public databases. By
linking our data, publicly available sequence data, and
records of ascomata, we identify many geographically
widespread, host-generalist clades capable of symbiotic
associations with diverse photosynthetic partners.
Concomitant with such cosmopolitan host use and
distributions, many xylariaceous endophytes appear to
inhabit both living and non-living plant tissues, with
potentially important roles as saprotrophs. Overall, our
study reveals major gaps in the availability of multi-locus
datasets and metadata for this iconic family, and provides
new hypotheses regarding the ecology and evolution of
endophytism and other trophic modes across the family
Xylariaceae.},
Doi = {10.1016/j.ympev.2016.02.010},
Key = {fds329423}
}
@article{fds329424,
Author = {Chagnon, P-L and U'Ren, JM and Miadlikowska, J and Lutzoni, F and Arnold, AE},
Title = {Interaction type influences ecological network structure
more than local abiotic conditions: evidence from endophytic
and endolichenic fungi at a continental scale.},
Journal = {Oecologia},
Volume = {180},
Number = {1},
Pages = {181-191},
Year = {2016},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Understanding the factors that shape community assembly
remains one of the most enduring and important questions in
modern ecology. Network theory can reveal rules of community
assembly within and across study systems and suggest novel
hypotheses regarding the formation and stability of
communities. However, such studies generally face the
challenge of disentangling the relative influence of factors
such as interaction type and environmental conditions on
shaping communities and associated networks. Endophytic and
endolichenic symbioses, characterized by microbial species
that occur within healthy plants and lichen thalli,
represent some of the most ubiquitous interactions in
nature. Fungi that engage in these symbioses are
hyperdiverse, often horizontally transmitted, and
functionally beneficial in many cases, and they represent
the diversification of multiple phylogenetic groups. We
evaluated six measures of ecological network structure for
>4100 isolates of endophytic and endolichenic fungi
collected systematically from five sites across North
America. Our comparison of these co-occurring interactions
in biomes ranging from tundra to subtropical forest showed
that the type of interactions (i.e., endophytic vs.
endolichenic) had a much more pronounced influence on
network structure than did environmental conditions. In
particular, endophytic networks were less nested, less
connected, and more modular than endolichenic networks in
all sites. The consistency of the network structure within
each interaction type, independent of site, is encouraging
for current efforts devoted to gathering metadata on
ecological network structure at a global scale. We discuss
several mechanisms potentially responsible for such patterns
and draw attention to knowledge gaps in our understanding of
networks for diverse interaction types.},
Doi = {10.1007/s00442-015-3457-5},
Key = {fds329424}
}
@article{fds327983,
Author = {Magain, N. and Sérusiaux, E. and Zhurbenko, M. P. and Lutzoni, F. and Miadlikowska, J.},
Title = {Disentangling the Peltigera polydactylon species complex
by recognizing two new taxa, P. polydactylon
subsp. udeghe and P. seneca.},
Journal = {Herzogia},
Volume = {29},
Pages = {514-528},
Year = {2016},
url = {http://lutzonilab.org/publications-datasets/},
Key = {fds327983}
}
@article{fds329501,
Author = {Divakar, PK and Crespo, A and Wedin, M and Leavitt, SD and Hawksworth,
DL and Myllys, L and McCune, B and Randlane, T and Bjerke, JW and Ohmura,
Y and Schmitt, I and Boluda, CG and Alors, D and Roca-Valiente, B and Del-Prado, R and Ruibal, C and Buaruang, K and Núñez-Zapata, J and Amo
de Paz, G and Rico, VJ and Molina, MC and Elix, JA and Esslinger, TL and Tronstad, IKK and Lindgren, H and Ertz, D and Gueidan, C and Saag, L and Mark, K and Singh, G and Dal Grande and F and Parnmen, S and Beck, A and Benatti, MN and Blanchon, D and Candan, M and Clerc, P and Goward, T and Grube, M and Hodkinson, BP and Hur, J-S and Kantvilas, G and Kirika, PM and Lendemer, J and Mattsson, J-E and Messuti, MI and Miadlikowska, J and Nelsen, M and Ohlson, JI and Pérez-Ortega, S and Saag, A and Sipman,
HJM and Sohrabi, M and Thell, A and Thor, G and Truong, C and Yahr, R and Upreti, DK and Cubas, P and Lumbsch, HT},
Title = {Evolution of complex symbiotic relationships in a
morphologically derived family of lichen-forming
fungi.},
Journal = {The New phytologist},
Volume = {208},
Number = {4},
Pages = {1217-1226},
Year = {2015},
Month = {December},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {We studied the evolutionary history of the Parmeliaceae
(Lecanoromycetes, Ascomycota), one of the largest families
of lichen-forming fungi with complex and variable
morphologies, also including several lichenicolous fungi. We
assembled a six-locus data set including nuclear,
mitochondrial and low-copy protein-coding genes from 293
operational taxonomic units (OTUs). The lichenicolous
lifestyle originated independently three times in lichenized
ancestors within Parmeliaceae, and a new generic name is
introduced for one of these fungi. In all cases, the
independent origins occurred c. 24 million yr ago. Further,
we show that the Paleocene, Eocene and Oligocene were key
periods when diversification of major lineages within
Parmeliaceae occurred, with subsequent radiations occurring
primarily during the Oligocene and Miocene. Our phylogenetic
hypothesis supports the independent origin of lichenicolous
fungi associated with climatic shifts at the
Oligocene-Miocene boundary. Moreover, diversification bursts
at different times may be crucial factors driving the
diversification of Parmeliaceae. Additionally, our study
provides novel insight into evolutionary relationships in
this large and diverse family of lichen-forming
ascomycetes.},
Doi = {10.1111/nph.13553},
Key = {fds329501}
}
@article{fds329425,
Author = {Darnajoux, R and Lutzoni, F and Miadlikowska, J and Bellenger,
J-P},
Title = {Determination of elemental baseline using peltigeralean
lichens from Northeastern Canada (Québec): Initial data
collection for long term monitoring of the impact of global
climate change on boreal and subarctic area in
Canada.},
Journal = {The Science of the total environment},
Volume = {533},
Pages = {1-7},
Year = {2015},
Month = {November},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Northeastern Canada is mostly free of anthropogenic
activities. The extent to which this territory has been
impacted by anthropogenic atmospheric depositions remains to
be studied. The main goal of our study was to establish
background levels for metals in boreal muscicolous/terricolous
macrolichens over non-urbanized areas of northeastern Canada
(Québec). Concentrations of 18 elements (Na, Mg, Al, P, K,
Ca, Ti, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, Mo, Cd, and Pb) were
determined for three species of the genus Peltigera
(Peltigera aphthosa (L.) Willd. s.l., Peltigera
neopolydactyla (Gyeln.) Gyeln. s.l., Peltigera scabrosa Th.
Fr. s.l.), and Nephroma arcticum (L.) Torss., along a 1080
km south-north transect and along a of 730 km west-east
transect. We report that elemental contents in the sampled
lichen thalli are very low and similar to background levels
found in other studies performed in pristine places (high
elevation or remote ecosystems) throughout the world.
Overall, our results demonstrate that most of the boreal and
subarctic zone of Québec (northeastern Canada) is still
pristine. The elemental baseline established in these lichen
populations will contribute to monitor metal pollution in
boreal and sub-polar ecosystems due to global climate change
and future industrial expansion.},
Doi = {10.1016/j.scitotenv.2015.06.030},
Key = {fds329425}
}
@article{fds329426,
Author = {Chen, K-H and Miadlikowska, J and Molnár, K and Arnold, AE and U'Ren,
JM and Gaya, E and Gueidan, C and Lutzoni, F},
Title = {Phylogenetic analyses of eurotiomycetous endophytes reveal
their close affinities to Chaetothyriales, Eurotiales, and a
new order - Phaeomoniellales.},
Journal = {Molecular phylogenetics and evolution},
Volume = {85},
Pages = {117-130},
Year = {2015},
Month = {April},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Symbiotic fungi living in plants as endophytes, and in
lichens as endolichenic fungi, cause no apparent symptoms to
their hosts. They are ubiquitous, ecologically important,
hyperdiverse, and represent a rich source of secondary
compounds for new pharmaceutical and biocontrol products.
Due in part to the lack of visible reproductive structures
and other distinctive phenotypic traits for many species,
the diversity and phylogenetic affiliations of these cryptic
fungi are often poorly known. The goal of this study was to
determine the phylogenetic placement of representative
endophytes within the Eurotiomycetes (Pezizomycotina,
Ascomycota), one of the most diverse and evolutionarily
dynamic fungal classes, and to use that information to infer
processes of macroevolution in trophic modes. Sequences of a
single locus marker spanning the nuclear ribosomal internal
transcribed spacer region (nrITS) and 600 base pairs at the
5' end of the nuclear ribosomal large subunit (nrLSU) were
obtained from previous studies of >6000 endophytic and
endolichenic fungi from diverse biogeographic locations and
hosts. We conducted phylum-wide phylogenetic searches using
this marker to determine which fungal strains belonged to
Eurotiomycetes and the results were used as the basis for a
class-wide, seven-locus phylogenetic study focusing on
endophytic and endolichenic Eurotiomycetes. Our cumulative
supermatrix-based analyses revealed that representative
endophytes within Eurotiomycetes are distributed in three
main clades: Eurotiales, Chaetothyriales and
Phaeomoniellales ord. nov., a clade that had not yet been
described formally. This new order, described herein, is
sister to the clade including Verrucariales and
Chaetothyriales. It appears to consist mainly of endophytes
and plant pathogens. Morphological characters of endophytic
Phaeomoniellales resemble those of the pathogenic genus
Phaeomoniella. This study highlights the capacity of
endophytic and endolichenic fungi to expand our
understanding of the ecological modes associated with
particular clades, and provides a first estimation of their
phylogenetic relationships in the Eurotiomycetes.},
Doi = {10.1016/j.ympev.2015.01.008},
Key = {fds329426}
}
@article{fds329427,
Author = {Gueidan, C and Hill, DJ and Miadlikowska, J and Lutzoni,
F},
Title = {Pezizomycotina: Lecanoromycetes},
Pages = {89-120},
Publisher = {Springer Berlin Heidelberg},
Year = {2015},
Month = {January},
url = {http://dx.doi.org/10.1007/978-3-662-46011-5_4},
Abstract = {Lecanoromycetes is the class of Ascomycota with the largest
number of lichen-forming fungi. Members of this class are
important components of most terrestrial ecosystems and
occur in various habitats and on different substrates, from
tropical to polar regions. Morphological, anatomical, and
chemical characters have traditionally been used to classify
orders, families, and genera within Lecanoromycetes. In the
last two decades, molecular phylogenies have shown that
traditional classification systems were not always
consistent with the evolutionary history of this fungal
class, resulting in changes in the delimitation of orders
and families. Here, we revisit the taxonomic value of the
main characters traditionally used for classification in
light of current molecular phylogenies. The current
delimitation of the 14 orders of Lecanoromycetes is also
discussed, and recent changes in classification are
highlighted.},
Doi = {10.1007/978-3-662-46011-5_4},
Key = {fds329427}
}
@article{fds327990,
Author = {Gueidan, C. and Hill, D. J. and Miadlikowska, J. and Lutzoni, F.},
Title = {Chapter 4. Pezizomycotina: Lecanoromycetes.},
Volume = {VIIB},
Pages = {89–120 },
Booktitle = {The Mycota, Systematics and Evolution },
Publisher = {Springer Verlag,},
Address = {Berlin, Germany},
Editor = {D. J. McLaughlin and J. W. Spatafora},
Year = {2015},
Key = {fds327990}
}
@article{fds324524,
Author = {Miadlikowska, J and Kauff, F and Högnabba, F and Oliver, JC and Molnár, K and Fraker, E and Gaya, E and Hafellner, J and Hofstetter, V and Gueidan, C and Otálora, MAG and Hodkinson, B and Kukwa, M and Lücking,
R and Björk, C and Sipman, HJM and Burgaz, AR and Thell, A and Passo, A and Myllys, L and Goward, T and Fernández-Brime, S and Hestmark, G and Lendemer, J and Lumbsch, HT and Schmull, M and Schoch, CL and Sérusiaux, E and Maddison, DR and Arnold, AE and Lutzoni, F and Stenroos, S},
Title = {A multigene phylogenetic synthesis for the class
Lecanoromycetes (Ascomycota): 1307 fungi representing 1139
infrageneric taxa, 317 genera and 66 families.},
Journal = {Molecular phylogenetics and evolution},
Volume = {79},
Pages = {132-168},
Year = {2014},
Month = {October},
url = {http://dx.doi.org/10.1016/j.ympev.2014.04.003},
Abstract = {The Lecanoromycetes is the largest class of lichenized
Fungi, and one of the most species-rich classes in the
kingdom. Here we provide a multigene phylogenetic synthesis
(using three ribosomal RNA-coding and two protein-coding
genes) of the Lecanoromycetes based on 642 newly generated
and 3329 publicly available sequences representing 1139
taxa, 317 genera, 66 families, 17 orders and five subclasses
(four currently recognized: Acarosporomycetidae,
Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae;
and one provisionarily recognized, 'Candelariomycetidae').
Maximum likelihood phylogenetic analyses on four multigene
datasets assembled using a cumulative supermatrix approach
with a progressively higher number of species and missing
data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene
datasets) show that the current classification includes
non-monophyletic taxa at various ranks, which need to be
recircumscribed and require revisionary treatments based on
denser taxon sampling and more loci. Two newly circumscribed
orders (Arctomiales and Hymeneliales in the
Ostropomycetidae) and three families (Ramboldiaceae and
Psilolechiaceae in the Lecanorales, and Strangosporaceae in
the Lecanoromycetes inc. sed.) are introduced. The potential
resurrection of the families Eigleraceae and Lopadiaceae is
considered here to alleviate phylogenetic and classification
disparities. An overview of the photobionts associated with
the main fungal lineages in the Lecanoromycetes based on
available published records is provided. A revised schematic
classification at the family level in the phylogenetic
context of widely accepted and newly revealed relationships
across Lecanoromycetes is included. The cumulative addition
of taxa with an increasing amount of missing data (i.e., a
cumulative supermatrix approach, starting with taxa for
which sequences were available for all five targeted genes
and ending with the addition of taxa for which only two
genes have been sequenced) revealed relatively stable
relationships for many families and orders. However, the
increasing number of taxa without the addition of more loci
also resulted in an expected substantial loss of
phylogenetic resolving power and support (especially for
deep phylogenetic relationships), potentially including the
misplacements of several taxa. Future phylogenetic analyses
should include additional single copy protein-coding markers
in order to improve the tree of the Lecanoromycetes. As part
of this study, a new module ("Hypha") of the freely
available Mesquite software was developed to compare and
display the internodal support values derived from this
cumulative supermatrix approach.},
Doi = {10.1016/j.ympev.2014.04.003},
Key = {fds324524}
}
@article{fds329502,
Author = {U'Ren, JM and Riddle, JM and Monacell, JT and Carbone, I and Miadlikowska, J and Arnold, AE},
Title = {Tissue storage and primer selection influence
pyrosequencing-based inferences of diversity and community
composition of endolichenic and endophytic
fungi.},
Journal = {Molecular ecology resources},
Volume = {14},
Number = {5},
Pages = {1032-1048},
Year = {2014},
Month = {September},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Next-generation sequencing technologies have provided
unprecedented insights into fungal diversity and ecology.
However, intrinsic biases and insufficient quality control
in next-generation methods can lead to difficult-to-detect
errors in estimating fungal community richness,
distributions and composition. The aim of this study was to
examine how tissue storage prior to DNA extraction, primer
design and various quality-control approaches commonly used
in 454 amplicon pyrosequencing might influence ecological
inferences in studies of endophytic and endolichenic fungi.
We first contrast 454 data sets generated contemporaneously
from subsets of the same plant and lichen tissues that were
stored in CTAB buffer, dried in silica gel or freshly frozen
prior to DNA extraction. We show that storage in silica gel
markedly limits the recovery of sequence data and yields a
small fraction of the diversity observed by the other two
methods. Using lichen mycobiont sequences as internal
positive controls, we next show that despite careful
filtering of raw reads and utilization of current
best-practice OTU clustering methods, homopolymer errors in
sequences representing rare taxa artificially increased
estimates of richness c. 15-fold in a model data set. Third,
we show that inferences regarding endolichenic diversity can
be improved using a novel primer that reduces amplification
of the mycobiont. Together, our results provide a rationale
for selecting tissue treatment regimes prior to DNA
extraction, demonstrate the efficacy of reducing mycobiont
amplification in studies of the fungal microbiomes of lichen
thalli and highlight the difficulties in differentiating
true information about fungal biodiversity from
methodological artefacts.},
Doi = {10.1111/1755-0998.12252},
Key = {fds329502}
}
@article{fds329428,
Author = {Miadlikowska, J and Richardson, D and Magain, N and Ball, B and Anderson, F and Cameron, R and Lendemer, J and Truong, C and Lutzoni,
F},
Title = {Phylogenetic placement, species delimitation, and cyanobiont
identity of endangered aquatic Peltigera species
(lichen-forming Ascomycota, Lecanoromycetes).},
Journal = {American journal of botany},
Volume = {101},
Number = {7},
Pages = {1141-1156},
Year = {2014},
Month = {July},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {• Premise of this study: Aquatic cyanolichens from the
genus Peltigera section Hydrothyriae are subject to
anthropogenic threats and, therefore, are considered
endangered. In this study we addressed the phylogenetic
placement of section Hydrothyriae within Peltigera. We
delimited species within the section and identified their
symbiotic cyanobacteria.• Methods: Species delimitation
and population structure were explored using monophyly as a
grouping criterion (RAxML) and Structurama based on three
protein-coding genes in combination with two nuclear
ribosomal loci. The 16S and rbcLX sequences for the
cyanobionts were analyzed in the broad phylogenetic context
of free-living and symbiotic cyanobacteria.• Key results:
We confirm with high confidence the placement of section
Hydrothyriae within the monophyletic genus Peltigera;
however, its phylogenetic position within the genus remains
unsettled. We recovered three distinct monophyletic groups
corresponding to three species: P. hydrothyria, P. gowardii
s.s., and P. aquatica Miadl. & Lendemer, the latter being
formally introduced here. Each species was associated with
an exclusive set of Nostoc haplotypes.• Conclusions: The
ITS region alone provides sufficient genetic information to
distinguish the three morphologically cryptic species within
section Hydrothyriae. Section Hydrothyriae seems to be
associated with a monophyletic lineage of Nostoc, that has
not been found in symbiotic association with other members
of Peltigera. Capsosira lowei should be transferred to the
genus Nostoc. Potential threats to P. aquatica should be
re-examined based on the recognition of two aquatic species
in western North America.},
Doi = {10.3732/ajb.1400267},
Key = {fds329428}
}
@article{fds329429,
Author = {Darnajoux, R and Constantin, J and Miadlikowska, J and Lutzoni, F and Bellenger, J-P},
Title = {Is vanadium a biometal for boreal cyanolichens?},
Journal = {The New phytologist},
Volume = {202},
Number = {3},
Pages = {765-771},
Year = {2014},
Month = {May},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Molybdenum (Mo) nitrogenase has long been considered the
predominant isoenzyme responsible for dinitrogen fixation
worldwide. Recent findings have challenged the paradigm of
Mo hegemony, and highlighted the role of alternative
nitrogenases, such as the vanadium-nitrogenase. Here, we
first characterized homeostasis of vanadium (V) along with
other metals in situ in the dinitrogen fixing cyanolichen
Peltigera aphthosa. These lichens were sampled in natural
sites exposed to various levels of atmospheric metal
deposition. These results were compared with laboratory
experiments where Anabaena variabilis, which is also hosting
the V-nitrogenase, and a relatively close relative of the
lichen cyanobiont Nostoc, was subjected to various levels of
V. We report here that V is preferentially allocated to
cephalodia, specialized structures where dinitrogen fixation
occurs in tri-membered lichens. This specific allocation is
biologically controlled and tightly regulated. Vanadium
homeostasis in lichen cephalodia exposed to various V
concentrations is comparable to the one observed in Anabaena
variabilis and other dinitrogen fixing organisms using
V-nitrogenase. Overall, our findings support current
hypotheses that V could be a more important factor in
mediating nitrogen input in high latitude ecosystems than
previously recognized. They invite the reassessment of
current theoretical models linking metal dynamics and
dinitrogen fixation in boreal and subarctic
ecosystems.},
Doi = {10.1111/nph.12777},
Key = {fds329429}
}
@article{fds329430,
Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F},
Title = {Assessing population structure and host specialization in
lichenized cyanobacteria.},
Journal = {The New phytologist},
Volume = {198},
Number = {2},
Pages = {557-566},
Year = {2013},
Month = {April},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Coevolutionary theory predicts that the distribution of
obligately symbiotic organisms will be determined by the
dispersal ability and ecological range of both partners. We
examined this prediction for lichen-forming fungi that form
obligate symbioses with cyanobacteria. We compared genotypes
of both partners of 250 lichens collected at multiple
spatial scales in British Columbia, Canada. Multilocus
sequence data collected from a subset of 128 of the
specimens were used to determine the degree of recombination
within the cyanobacterial populations. We found that six
distinct clusters of cyanobacterial genotypes are
distributed throughout the known global phylogeny of the
genus Nostoc, and that each appears to be evolving clonally.
Fungal specialization is high, with each species associating
with either one or two of the cyanobacterial clusters, while
cyanobacterial specialization varies, with clusters
associating with between one and 12 different fungal
species. Specialization also varies geographically, with
some combinations restricted to a single site despite the
availability of both partners elsewhere. Photobiont
association patterns are determined by a combination of
genetically based specificity, spatial population structure,
and ecological factors and cannot be easily predicted by
photobiont dispersal syndromes.},
Doi = {10.1111/nph.12165},
Key = {fds329430}
}
@article{fds329432,
Author = {Gazis, R and Miadlikowska, J and Lutzoni, F and Arnold, AE and Chaverri,
P},
Title = {Culture-based study of endophytes associated with rubber
trees in Peru reveals a new class of Pezizomycotina:
Xylonomycetes.},
Journal = {Molecular phylogenetics and evolution},
Volume = {65},
Number = {1},
Pages = {294-304},
Year = {2012},
Month = {October},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Through a culture-based survey of living sapwood and leaves
of rubber trees (Hevea spp.) in remote forests of Peru, we
discovered a new major lineage of Ascomycota, equivalent to
a class rank. Multilocus phylogenetic analyses reveal that
this new lineage originated during the radiation of the
'Leotiomyceta', which resulted not only in the evolution of
the Arthoniomycetes, Dothideomycetes, Eurotiomycetes,
Geoglossomycetes, Lecanoromycetes, Leotiomycetes,
Lichinomycetes, and Sordariomycetes, but also of the
majority of hyperdiverse foliar endophytes. Because its
origin is nested within this major burst of fungal
diversification, we could not recover strong support for its
phylogenetic relationship within the 'Leotiomyceta'.
Congruent with their long phylogenetic history and
distinctive preference for growing in sapwood, this new
lineage displays unique morphological, physiological, and
ecological traits relative to known endophytes and currently
described members of the 'Leotiomyceta'. In marked contrast
to many foliar endophytes, the strains we isolated fail to
degrade cellulose and lignin in vitro. Discovery of the new
class, herein named Xylonomycetes and originally
mis-identified by ITSrDNA sequencing alone, highlights the
importance of inventorying tropical endophytes from
unexplored regions, using multilocus data sets to infer the
phylogenetic placement of unknown strains, and the need to
sample diverse plant tissues using traditional methods to
enhance efforts to discover the evolutionary, taxonomic, and
functional diversity of symbiotrophic fungi.},
Doi = {10.1016/j.ympev.2012.06.019},
Key = {fds329432}
}
@article{fds329431,
Author = {Liwa, L and Miadlikowska, J and Redelings, BD and Molnar, K and Lutzoni,
F},
Title = {Are widespread morphospecies from the Lecanora dispersa
group (lichen-forming Ascomycota) monophyletic?},
Journal = {Bryologist},
Volume = {115},
Number = {2},
Pages = {265-277},
Publisher = {American Bryological and Lichenological Society},
Year = {2012},
Month = {June},
url = {http://dx.doi.org/10.1639/0007-2745-115.2.265},
Abstract = {To evaluate the current delimitation of broadly distributed
morphospecies from the Lecanora dispersa group, the nuclear
ribosomal internal transcribed spacer region (ITS1, 5.8S and
ITS2) was analyzed phylogenetically and compared to
phenotypic data variation within and among species.
Phylogenetic relationships among 34 individuals representing
eight species from the L. dispersa group, collected mainly
from Poland and other European countries, were inferred
using two types of Bayesian analyses (with and without a
priori alignments), maximum likelihood and maximum parsimony
approaches. The highest phylogenetic resolution and the
largest number of significantly supported internodes
resulted from the Bayesian analysis without a priori
alignment. Inferred phylogenies confirmed a broader
delimitation of the L. dispersa group, to include four
additional lobate taxa: L. contractula, L. pruinosa, L.
reuteri, and L. thuleana ( Arctopeltis thuleana). Lecanora
crenulata, L. dispersa, L. reuterii, and the core of L.
albescens and L. semipallida were all found to be
monophyletic with high support (by at least one phylogenetic
analysis) except the first species. Based on the ITS region,
phenotypically similar individuals, thought to belong to one
monophyletic group, were found to belong to multiple
distantly related groups (e.g., members of L. albescens and
L. hagenii), suggesting that morphological, anatomical and
chemical characters may not be consistent in predicting
species boundaries within the L. dispersa group. Potential
undescribed species were found within phenotypically defined
L. albescens and L. semipallida. Phylo-taxonomic studies of
the L. dispersa group with more loci and a more extensive
taxon sampling are urgently needed. © 2012 The American
Bryological and Lichenological Society, Inc.},
Doi = {10.1639/0007-2745-115.2.265},
Key = {fds329431}
}
@article{fds329433,
Author = {U'Ren, JM and Lutzoni, F and Miadlikowska, J and Laetsch, AD and Arnold,
AE},
Title = {Host and geographic structure of endophytic and endolichenic
fungi at a continental scale.},
Journal = {American journal of botany},
Volume = {99},
Number = {5},
Pages = {898-914},
Year = {2012},
Month = {May},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {<h4>Premise of the study</h4>Endophytic and endolichenic
fungi occur in healthy tissues of plants and lichens,
respectively, playing potentially important roles in the
ecology and evolution of their hosts. However, previous
sampling has not comprehensively evaluated the biotic,
biogeographic, and abiotic factors that structure their
communities.<h4>Methods</h4>Using molecular data we examined
the diversity, composition, and distributions of 4154
endophytic and endolichenic Ascomycota cultured from
replicate surveys of ca. 20 plant and lichen species in each
of five North American sites (Madrean coniferous forest,
Arizona; montane semideciduous forest, North Carolina; scrub
forest, Florida; Beringian tundra and forest, western
Alaska; subalpine tundra, eastern central Alaska).<h4>Key
results</h4>Endolichenic fungi were more abundant and
diverse per host species than endophytes, but communities of
endophytes were more diverse overall, reflecting high
diversity in mosses and lycophytes. Endophytes of vascular
plants were largely distinct from fungal communities that
inhabit mosses and lichens. Fungi from closely related hosts
from different regions were similar in higher taxonomy, but
differed at shallow taxonomic levels. These differences
reflected climate factors more strongly than geographic
distance alone.<h4>Conclusions</h4>Our study provides a
first evaluation of endophytic and endolichenic fungal
associations with their hosts at a continental scale. Both
plants and lichens harbor abundant and diverse fungal
communities whose incidence, diversity, and composition
reflect the interplay of climatic patterns, geographic
separation, host type, and host lineage. Although
culture-free methods will inform future work, our study sets
the stage for empirical assessments of ecological
specificity, metabolic capability, and comparative
genomics.},
Doi = {10.3732/ajb.1100459},
Key = {fds329433}
}
@article{fds329503,
Author = {McCune, B and Schoch, C and Root, HT and Kageyama, SA and Miadlikowska,
J},
Title = {Geographic, climatic, and chemical differentiation in the
Hypogymnia imshaugii species complex (Lecanoromycetes,
Parmeliaceae) in North America},
Journal = {Bryologist},
Volume = {114},
Number = {3},
Pages = {526-544},
Publisher = {American Bryological and Lichenological Society},
Year = {2011},
Month = {September},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Hypogymnia imshaugii is one of the most common, conspicuous
and morphologically variable epiphytic lichens of the
Pacific coastal states and provinces. The species varies
greatly in morphology and chemistry, suggesting multiple
closely related species or one or more phenotypically
plastic species. We sought to determine whether additional
ecologically meaningful species might be present within the
H. imshaugii complex. Improving our species concepts could
potentially improve ecological inferences based on community
sampling. Three relatively well-defined genetic groups and
one residual group in the H. imshaugii complex were detected
with haplotype networks based on the ITS locus; however,
phylogenetic reconstructions on combined ITS, mtSSU, GPD1
and TEF1 loci did not reflect this pattern. At present, we
have insufficient evidence to support defining any of these
groups as new taxa. The four major chemotypes in H.
imshaugii differed in frequency among the genetic groups.
None of the genetic groups was, however, qualitatively
uniform in chemotype. Only one chemotype occurred in a
single genetic group, but several chemotypes occurred in
that group. While broadly sympatric, each chemotype had a
distinct geographic distribution, and each chemotype showed
its own relationship to climate, as shown by regression of
occurrences of chemotypes against climatic variables. The
genetic variation detected within H. imshaugii did not
correspond to geographic variation in morphology, chemistry,
or climate. Within the broader H. imshaugii complex, we
recommend treating H. amplexa as a synonym of H. imshaugii
unless it can be more distinctly separated from the clinal
variation in morphology, chemistry, or DNA sequences. In
contrast to H. amplexa, however, H. inactiva and H. gracilis
are both easily separated morphologically from H. imshaugii
and do not intergrade with it. © 2011 The American
Bryological and Lichenological Society, Inc.},
Doi = {10.1639/0007-2745-114.3.526},
Key = {fds329503}
}
@article{fds329436,
Author = {Schmull, M and Miadlikowska, J and Pelzer, M and Stocker-Wörgötter,
E and Hofstetter, V and Fraker, E and Hodkinson, BP and Reeb, V and Kukwa,
M and Lumbsch, HT and Kauff, F and Lutzoni, F},
Title = {Phylogenetic affiliations of members of the heterogeneous
lichen-forming fungi of the genus Lecidea sensu Zahlbruckner
(Lecanoromycetes, Ascomycota).},
Journal = {Mycologia},
Volume = {103},
Number = {5},
Pages = {983-1003},
Year = {2011},
Month = {September},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The genus Lecidea Ach. sensu lato (sensu Zahlbruckner)
includes almost 1200 species, out of which only 100 species
represent Lecidea sensu stricto (sensu Hertel). The
systematic position of the remaining species is mostly
unsettled but anticipated to represent several unrelated
lineages within Lecanoromycetes. This study attempts to
elucidate the phylogenetic placement of members of this
heterogeneous group of lichen-forming fungi and to improve
the classification and phylogeny of Lecanoromycetes.
Twenty-five taxa of Lecidea sensu lato and 22 putatively
allied species were studied in a broad selection of 268
taxa, representing 48 families of Lecanoromycetes. Six loci,
including four ribosomal and two protein-coding genes for
315- and 209-OTU datasets were subjected to maximum
likelihood and Bayesian analyses. The resulting well
supported phylogenetic relationships within Lecanoromycetes
are in agreement with published phylogenies, but the
addition of new taxa revealed putative rearrangements of
several families (e.g. Catillariaceae, Lecanoraceae,
Lecideaceae, Megalariaceae, Pilocarpaceae and Ramalinaceae).
As expected, species of Lecidea sensu lato and putatively
related taxa are scattered within Lecanoromycetidae and
beyond, with several species nested in Lecanoraceae and
Pilocarpaceae and others placed outside currently recognized
families in Lecanorales and orders in Lecanoromycetidae. The
phylogenetic affiliations of Schaereria and Strangospora are
outside Lecanoromycetidae, probably with Ostropomycetidae.
All species referred to as Lecidea sensu stricto based on
morphology (including the type species, Lecidea fuscoatra
[L.] Ach.) form, with Porpidia species, a monophyletic group
with high posterior probability outside Lecanorales,
Peltigerales and Teloschistales, in Lecanoromycetidae,
supporting the recognition of order Lecideales Vain. in this
subclass. The genus name Lecidea must be redefined to apply
only to Lecidea sensu stricto and to include at least some
members of the genus Porpidia. Based on morphological and
chemical similarities, as well as the phylogenetic
relationship of Lecidea pullata sister to Frutidella
caesioatra, the new combination Frutidella pullata is
proposed here.},
Doi = {10.3852/10-234},
Key = {fds329436}
}
@article{fds329434,
Author = {Miadlikowska, J and Schoch, CL and Kageyama, SA and Molnar, K and Lutzoni, F and McCune, B},
Title = {Hypogymnia phylogeny, including Cavernularia, reveals
biogeographic structure},
Journal = {Bryologist},
Volume = {114},
Number = {2},
Pages = {392-400},
Publisher = {American Bryological and Lichenological Society},
Year = {2011},
Month = {June},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {We inferred phylogenetic relationships using Bayesian and
maximum likelihood approaches for two genera of lichenized
fungi, Hypogymnia and Cavernularia (Parmeliaceae). Based on
the combined ITS and GPD1 dataset from 23 species (49
specimens) of Hypogymnia and two species (8 specimens) of
Cavernularia, we conclude that Hypogymnia is paraphyletic,
and that it should include Cavernularia to retain its
monophyly. Hypogymnia hultenii (= Cavernularia hultenii) and
H. lophyrea (= C. lophyrea) are accepted here. Five species
of Hypogymnia represented by more than a single individual
were found to be monophyletic and significantly supported.
The phylogeny reflects a statistically significant
biogeographic pattern where continental-scale endemic taxa
tend to occur within the same phylogenetic group. Sorediate
taxa, which have worldwide or broader geographical ranges
than affiliated species lacking soredia, are spread across
the phylogenetic tree. Hypogymnia contains three species
pairs: H. krogiae and the sorediate counterpart H.
incurvoides, H. minilobata and the sorediate H. mollis, and
H. lophyrea and the sorediate H. hultenii. In the case of H.
minilobata, both members of the pair are restricted to a
small area in southern California. In the other two cases,
the fertile counterpart occurs only in North America, while
the sorediate species occurs in both North America and
Fennoscandia. This suggests but not proves an origin of each
species pair in North America, with migration of the
sorediate member to Fennoscandia following the prevailing
wind direction. © 2011 The American Bryological and
Lichenological Society, Inc.},
Doi = {10.1639/0007-2745-114.2.392},
Key = {fds329434}
}
@article{fds329435,
Author = {Hestmark, G and Miadlikowska, J and Kauff, F and Fraker, E and Molnar,
K and Lutzoni, F},
Title = {Single origin and subsequent diversification of central
Andean endemic Umbilicaria species.},
Journal = {Mycologia},
Volume = {103},
Number = {1},
Pages = {45-56},
Year = {2011},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {We studied an Andean endemic group of species of the
lichen-forming fungal genus Umbilicaria from the subalpine
and low-alpine zone, with their biogeographic center in
Bolivia and Peru. A number of species and varieties have
been described from this element, but apparent instability
in several morphological traits has made it difficult to
precisely delimit taxa. Based on DNA sequences of nuclear
ITS, LSU and mitochondrial SSU from extensive collections
from Argentina, Bolivia, Chile, Colombia, Ecuador and Peru,
we present here a molecular phylogenetic analysis of this
Andean endemic element within genus Umbilicaria. All
analyses (MP, ML and Bayesian) support a single origin for
the element and a division into two major groups
characterized by different apothecium types: the Umbilicaria
dichroa group and U. calvescens group. Taxa U.
krempelhuberi, U. peruviana and U. subcalvescens are nested
withinn U. calvescens and are treated as conspecific with
the latter species. The endemic element shares a most recent
common ancestor with the Umbilicaria vellea group, which has
a worldwide distribution and contains several asexually
reproducing (sorediate) species. Independent reversals to
sexual reproduction might explain the evolution of two types
of apothecia in this monophyletic endemic lineage. A number
of cosmopolitan, mostly high-alpine, species of Umbilicaria
also present in the central Andes are related only remotely
to the endemic element and do not exhibit speciation into
endemics. Because the An-dean element dominates the
Umbilicaria habitats of the low- and subalpine zones we
propose that the founder colonized the Andes at a time when
the mountains had not yet reached their current elevation
while the high-alpine species arrived more
recently.},
Doi = {10.3852/10-012},
Key = {fds329435}
}
@article{fds327999,
Author = {Sliwa, L. and Miadlikowska, J. and Redelings, B. D. and Molnar, K. and Lutzoni, F.},
Title = {Are morphospecies from the Lecanora dispersa group
(lichenized Lecanoromycetes, Pezizomycotina)
monophyletic?},
Journal = {The Bryologist},
Volume = {115},
Pages = {265–277},
Year = {2011},
url = {http://lutzonilab.org/publications-datasets/},
Key = {fds327999}
}
@article{fds329437,
Author = {Crespo, A and Kauff, F and Divakar, PK and del Prado, R and Pérez-Ortega, S and de Paz, GA and Ferencova, Z and Blanco, O and Roca-Valiente, B and Núñez-Zapata, J and Cubas, P and Argüello, A and Elix, JA and Esslinger, TL and Hawksworth, DL and Millanes, A and Molina, MC and Wedin, M and Ahti, T and Aptroot, A and Barreno, E and Bungartz, F and Calvelo, S and Candan, M and Cole, M and Ertz, D and Goffinet, B and Lindblom, L and Lücking, R and Lutzoni, F and Mattsson,
JE and Messuti, MI and Miadlikowska, J and Piercey-Normore, M and Rico,
VJ and Sipman, HJM and Schmitt, I and Spribille, T and Thell, A and Thor,
G and Upreti, DK and Thorsten Lumbsch and H},
Title = {Phylogenetic generic classification of parmelioid lichens
(Parmeliaceae, Ascomycota) based on molecular, morphological
and chemical evidence},
Journal = {Taxon},
Volume = {59},
Number = {6},
Pages = {1735-1753},
Year = {2010},
Month = {December},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Parmelioid lichens are a diverse and ubiquitous group of
foliose lichens. Generic delimitation in parmelioid lichens
has been in a state of flux since the late 1960s with the
segregation of the large, heterogeneous genus Parmelia into
numerous smaller genera. Recent molecular phylogenetic
studies have demonstrated that some of these new genera were
monophyletic, some were not, and others, previously believed
to be unrelated, fell within single monophyletic groups,
indicating the need for a revision of the generic
delimitations. This study aims to give an overview of
current knowledge of the major clades of all parmelioid
lichens. For this, we assembled a dataset of 762 specimens,
including 31 of 33 currently accepted parmelioid genera (and
63 of 84 accepted genera of Parmeliaceae). We performed
maximum likelihood and Bayesian analyses of combined
datasets including two, three and four loci. Based on these
phylogenies and the correlation of morphological and
chemical characters that characterize monophyletic groups,
we accept 27 genera within nine main clades. We
re-circumscribe several genera and reduce Parmelaria to
synonymy with Parmotrema. Emodomelanelia Divakar & A. Crespo
is described as a new genus (type: E. masonii).
Nipponoparmelia (Kurok.) K.H. Moon, Y. Ohmura & Kashiw. ex
A. Crespo & al. is elevated to generic rank and 15 new
combinations are proposed (in the genera Flavoparmelia,
Parmotrema, Myelochroa, Melanelixia and Nipponoparmelia). A
short discussion of the accepted genera is provided and
remaining challenges and areas requiring additional taxon
sampling are identified.},
Doi = {10.1002/tax.596008},
Key = {fds329437}
}
@article{fds329438,
Author = {U'Ren, J and Lutzoni, F and Miadlikowska, J and Arnold,
AE},
Title = {Community analysis reveals close affinities between
endophytic and endolichenic fungi in mosses and
lichens},
Journal = {Microbial Ecology},
Volume = {60},
Number = {2},
Pages = {340-353},
Year = {2010},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Endolichenic fungi live in close association with algal
photobionts inside asymptomatic lichen thalli and resemble
fungal endophytes of plants in terms of taxonomy, diversity,
transmission mode, and evolutionary history. This similarity
has led to uncertainty regarding the distinctiveness of
endolichenic fungi compared with endophytes. Here, we
evaluate whether these fungi represent distinct ecological
guilds or a single guild of flexible symbiotrophs capable of
colonizing plants or lichens indiscriminately. Culturable
fungi were sampled exhaustively from replicate sets of
phylogenetically diverse plants and lichens in three
microsites in a montane forest in southeastern Arizona
(USA). Intensive sampling combined with a small spatial
scale permitted us to decouple spatial heterogeneity from
host association and to sample communities from living
leaves, dead leaves, and lichen thalli to statistical
completion. Characterization using data from the nuclear
ribosomal internal transcribed spacer and partial large
subunit (ITS-LSU rDNA) provided a first estimation of host
and substrate use for 960 isolates representing five classes
and approximately 16 orders, 32 families, and 65 genera of
Pezizomycotina. We found that fungal communities differ at a
broad taxonomic level as a function of the phylogenetic
placement of their plant or lichen hosts. Endolichenic
fungal assemblages differed as a function of lichen
taxonomy, rather than substrate, growth form, or photobiont.
In plants, fungal communities were structured more by plant
lineage than by the living vs. senescent status of the leaf.
We found no evidence that endolichenic fungi are
saprotrophic fungi that have been "entrapped" by lichen
thalli. Instead, our study reveals the distinctiveness of
endolichenic communities relative to those in living and
dead plant tissues, with one notable exception: we identify,
for the first time, an ecologically flexible group of
symbionts that occurs both as endolichenic fungi and as
endophytes of mosses.},
Doi = {10.1007/s00248-010-9698-2},
Key = {fds329438}
}
@article{fds329439,
Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F},
Title = {Assessing reproductive isolation in highly diverse
communities of the lichen-forming fungal genus
peltigera.},
Journal = {Evolution; international journal of organic
evolution},
Volume = {63},
Number = {8},
Pages = {2076-2086},
Year = {2009},
Month = {August},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The lichen-forming fungal genus Peltigera includes a number
of species that are extremely widespread, both
geographically and ecologically. However, morphological
variability has lead to doubts about the distinctness of
some species, and it has been suggested that hybridization
is common in nature. We examined species boundaries by
looking for evidence of hybridization and gene flow among
seven described species collected at five sites in British
Columbia, Canada. We found no evidence of gene flow or
hybridization between described species, with fixed
differences between species for two or more of the three
loci examined. Reproductive isolation did not reflect a
solely clonal mode of reproduction as there was evidence of
ongoing gene flow within species. In addition, we found five
undescribed species that were reproductively isolated,
although there was evidence of ongoing or historical gene
flow between two of the new species. These results indicate
that the genus Peltigera is more diverse in western North
America than originally perceived, and that morphological
variability is due largely to the presence of undescribed
species rather than hybridization or intraspecific
variation.},
Doi = {10.1111/j.1558-5646.2009.00685.x},
Key = {fds329439}
}
@article{fds329440,
Author = {Lutzoni, F and Miadlikowska, J},
Title = {Lichens.},
Journal = {Current biology : CB},
Volume = {19},
Number = {13},
Pages = {R502-R503},
Year = {2009},
Month = {July},
url = {http://lutzonilab.org/publications-datasets/},
Doi = {10.1016/j.cub.2009.04.034},
Key = {fds329440}
}
@article{fds329441,
Author = {Arnold, AE and Miadlikowska, J and Higgins, KL and Sarvate, SD and Gugger, P and Way, A and Hofstetter, V and Kauff, F and Lutzoni,
F},
Title = {A phylogenetic estimation of trophic transition networks for
ascomycetous fungi: are lichens cradles of symbiotrophic
fungal diversification?},
Journal = {Systematic biology},
Volume = {58},
Number = {3},
Pages = {283-297},
Year = {2009},
Month = {June},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Fungi associated with photosynthetic organisms are major
determinants of terrestrial biomass, nutrient cycling, and
ecosystem productivity from the poles to the equator.
Whereas most fungi are known because of their fruit bodies
(e.g., saprotrophs), symptoms (e.g., pathogens), or emergent
properties as symbionts (e.g., lichens), the majority of
fungal diversity is thought to occur among species that
rarely manifest their presence with visual cues on their
substrate (e.g., the apparently hyperdiverse fungal
endophytes associated with foliage of plants). Fungal
endophytes are ubiquitous among all lineages of land plants
and live within overtly healthy tissues without causing
disease, but the evolutionary origins of these highly
diverse symbionts have not been explored. Here, we show that
a key to understanding both the evolution of endophytism and
the diversification of the most species-rich phylum of Fungi
(Ascomycota) lies in endophyte-like fungi that can be
isolated from the interior of apparently healthy lichens.
These "endolichenic" fungi are distinct from lichen
mycobionts or any other previously recognized fungal
associates of lichens, represent the same major lineages of
Ascomycota as do endophytes, largely parallel the high
diversity of endophytes from the arctic to the tropics, and
preferentially associate with green algal photobionts in
lichen thalli. Using phylogenetic analyses that incorporate
these newly recovered fungi and ancestral state
reconstructions that take into account phylogenetic
uncertainty, we show that endolichenism is an incubator for
the evolution of endophytism. In turn, endophytism is
evolutionarily transient, with endophytic lineages
frequently transitioning to and from pathogenicity. Although
symbiotrophic lineages frequently give rise to free-living
saprotrophs, reversions to symbiosis are rare. Together,
these results provide the basis for estimating trophic
transition networks in the Ascomycota and provide a first
set of hypotheses regarding the evolution of symbiotrophy
and saprotrophy in the most species-rich fungal phylum.
[Ancestral state reconstruction; Ascomycota; Bayesian
analysis; endolichenic fungi; fungal endophytes; lichens;
pathogens; phylogeny; saprotrophy; symbiotrophy; trophic
transition network.].},
Doi = {10.1093/sysbio/syp001},
Key = {fds329441}
}
@article{fds329443,
Author = {Schoch, CL and Sung, G-H and López-Giráldez, F and Townsend, JP and Miadlikowska, J and Hofstetter, V and Robbertse, B and Matheny, PB and Kauff, F and Wang, Z and Gueidan, C and Andrie, RM and Trippe, K and Ciufetti, LM and Wynns, A and Fraker, E and Hodkinson, BP and Bonito, G and Groenewald, JZ and Arzanlou, M and de Hoog, GS and Crous, PW and Hewitt,
D and Pfister, DH and Peterson, K and Gryzenhout, M and Wingfield, MJ and Aptroot, A and Suh, S-O and Blackwell, M and Hillis, DM and Griffith,
GW and Castlebury, LA and Rossman, AY and Lumbsch, HT and Lücking, R and Büdel, B and Rauhut, A and Diederich, P and Ertz, D and Geiser, DM and Hosaka, K and Inderbitzin, P and Kohlmeyer, J and Volkmann-Kohlmeyer,
B and Mostert, L and O'Donnell, K and Sipman, H and Rogers, JD and Shoemaker, RA and Sugiyama, J and Summerbell, RC and Untereiner, W and Johnston, PR and Stenroos, S and Zuccaro, A and Dyer, PS and Crittenden,
PD and Cole, MS and Hansen, K and Trappe, JM and Yahr, R and Lutzoni, F and Spatafora, JW},
Title = {The Ascomycota tree of life: a phylum-wide phylogeny
clarifies the origin and evolution of fundamental
reproductive and ecological traits.},
Journal = {Systematic biology},
Volume = {58},
Number = {2},
Pages = {224-239},
Year = {2009},
Month = {April},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {We present a 6-gene, 420-species maximum-likelihood
phylogeny of Ascomycota, the largest phylum of Fungi. This
analysis is the most taxonomically complete to date with
species sampled from all 15 currently circumscribed classes.
A number of superclass-level nodes that have previously
evaded resolution and were unnamed in classifications of the
Fungi are resolved for the first time. Based on the 6-gene
phylogeny we conducted a phylogenetic informativeness
analysis of all 6 genes and a series of ancestral character
state reconstructions that focused on morphology of
sporocarps, ascus dehiscence, and evolution of nutritional
modes and ecologies. A gene-by-gene assessment of
phylogenetic informativeness yielded higher levels of
informativeness for protein genes (RPB1, RPB2, and TEF1) as
compared with the ribosomal genes, which have been the
standard bearer in fungal systematics. Our reconstruction of
sporocarp characters is consistent with 2 origins for
multicellular sexual reproductive structures in Ascomycota,
once in the common ancestor of Pezizomycotina and once in
the common ancestor of Neolectomycetes. This first report of
dual origins of ascomycete sporocarps highlights the
complicated nature of assessing homology of morphological
traits across Fungi. Furthermore, ancestral reconstruction
supports an open sporocarp with an exposed hymenium
(apothecium) as the primitive morphology for Pezizomycotina
with multiple derivations of the partially (perithecia) or
completely enclosed (cleistothecia) sporocarps. Ascus
dehiscence is most informative at the class level within
Pezizomycotina with most superclass nodes reconstructed
equivocally. Character-state reconstructions support a
terrestrial, saprobic ecology as ancestral. In contrast to
previous studies, these analyses support multiple origins of
lichenization events with the loss of lichenization as less
frequent and limited to terminal, closely related
species.},
Doi = {10.1093/sysbio/syp020},
Key = {fds329443}
}
@article{fds329442,
Author = {Ertz, D and Miadlikowska, J and Lutzoni, F and Dessein, S and Raspé, O and Vigneron, N and Hofstetter, V and Diederich, P},
Title = {Towards a new classification of the Arthoniales (Ascomycota)
based on a three-gene phylogeny focussing on the genus
Opegrapha.},
Journal = {Mycological research.},
Volume = {113},
Number = {Pt 1},
Pages = {141-152},
Year = {2009},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {A multi-locus phylogenetic study of the order Arthoniales is
presented here using the nuclear ribosomal large subunit
(nuLSU), the second largest subunit of RNA polymerase II
(RPB2) and the mitochondrial ribosomal small subunit
(mtSSU). These genes were sequenced from 43 specimens or
culture isolates representing 33 species from this order, 16
of which were from the second largest genus, Opegrapha. With
the inclusion of sequences from GenBank, ten genera and 35
species are included in this study, representing about 18%
of the genera and ca 3% of the species of this order. Our
study revealed the homoplastic nature of morphological
characters traditionally used to circumscribe genera within
the Arthoniales, such as exciple carbonization and ascomatal
structure. The genus Opegrapha appears polyphyletic, species
of that genus being nested in all the major clades
identified within Arthoniales. The transfer of O. atra and
O. calcarea to the genus Arthonia will allow this genus and
family Arthoniaceae to be recognized as monophyletic. The
genus Enterographa was also found to be polyphyletic.
Therefore, the following new combinations are needed:
Arthonia calcarea (basionym: O. calcarea), and O. anguinella
(basionym: Stigmatidium anguinellum); and the use of the
names A. atra and Enterographa zonata are proposed here. The
simultaneous use of a mitochondrial gene and two nuclear
genes led to the detection of what seems to be a case of
introgression of a mitochondrion from one species to another
(mitochondrion capture; cytoplasmic gene flow) resulting
from hybridization.},
Doi = {10.1016/j.mycres.2008.09.002},
Key = {fds329442}
}
@article{fds328008,
Author = {Sérusiaux, E. and Goffinet, B. and Miadlikowska, J. and Vitikainen, O.},
Title = {Taxonomy, phylogeny, and biogeography of the lichen genus
Peltigera in Papua New Guinea},
Journal = {Fungal Diversity},
Volume = {38},
Pages = {185-224},
Year = {2009},
url = {http://lutzonilab.org/publications-datasets/},
Key = {fds328008}
}
@article{fds329444,
Author = {Amtoft, A and Lutzoni, F and Miadlikowska, J},
Title = {Dermatocarpon (Verrucariaceae) in the Ozark Highlands, North
America},
Journal = {Bryologist},
Volume = {111},
Number = {1},
Pages = {1-40},
Publisher = {American Bryological and Lichenological Society},
Year = {2008},
Month = {March},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Dermatocarpon, a saxicolous lichen, is common throughout the
Ozarks Highlands of North America where exposed rock is
abundant. Dermatocarpon is an understudied genus. Species
delimitation is difficult because of a paucity of
morphological characters and a large degree of variation
within this genus. The taxonomy of Dermatocarpon in North
America was recently thrown into flux because of a molecular
study which limited the use of a once widely applied name,
D. miniatum. The Melzer's reagent test, currently used for
identifying members of the miniatum-complex in North
America, is not useful for identifying Ozark specimens. A
revision of Dermatocarpon for the Ozark Highlands of North
America is presented based on morphological, molecular and
ecological studies. The results of these studies indicate
that eight taxa are present in the Ozarks. Four taxa are
described new to science: D. arenosaxi, D. dolomiticum, D.
luridum var. xerophilum and D. multifolium. Copyright ©2008
by The American Bryological and Lichenological Society,
Inc.},
Doi = {10.1639/0007-2745(2008)111[1:DVITOH]2.0.CO;2},
Key = {fds329444}
}
@article{fds329445,
Author = {Hofstetter, V and Miadlikowska, J and Kauff, F and Lutzoni,
F},
Title = {Phylogenetic comparison of protein-coding versus ribosomal
RNA-coding sequence data: a case study of the
Lecanoromycetes (Ascomycota).},
Journal = {Molecular phylogenetics and evolution},
Volume = {44},
Number = {1},
Pages = {412-426},
Year = {2007},
Month = {July},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The resolving power and statistical support provided by two
protein-coding (RPB1 and RPB2) and three ribosomal
RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually
and in various combinations were investigated based on
maximum likelihood bootstrap analyses on lichen-forming
fungi from the class Lecanoromycetes (Ascomycota). Our
results indicate that the optimal loci (single and combined)
to use for molecular systematics of lichen-forming
Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1
and RPB2 genes individually were phylogenetically more
efficient than all two- and three-locus combinations of
ribosomal loci. The 3rd codon position of each of these two
loci provided the most characters in support of phylogenetic
relationships within the Lecanoromycetes. Of the three
ribosomal loci we used in this study, mitSSU contributed the
most to phylogenetic analyses when combined with RPB1 and
RPB2. Except for the mitSSU, ribosomal genes were the most
difficult to recover because they often contain many
introns, resulting in PCR bias toward numerous and
intronless co-extracted contaminant fungi (mainly
Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in
the Ascomycota, and members of the Basidiomycota), which
inhabit lichen thalli. Maximum likelihood analysis on the
combined five-locus data set for 82 members of the
Lecanoromycetes provided a well resolved and well supported
tree compared to existing phylogenies. We confirmed the
monophyly of three recognized subclasses in the
Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae,
and Lecanoromycetideae; the latter delimited as monophyletic
for the first time, with the exclusion of the family
Umbilicariaceae and Hypocenomyce scalaris. The genus
Candelariella (formerly in the Candelariaceae, currently a
member of the Lecanoraceae) represents the first
evolutionary split within the Lecanoromycetes, before the
divergence of the Acarosporomycetidae. This study provides a
foundation necessary to guide the selection of loci for
future multilocus phylogenetic studies on lichen-forming and
allied ascomycetes.},
Doi = {10.1016/j.ympev.2006.10.016},
Key = {fds329445}
}
@article{fds329446,
Author = {Higgins, KL and Arnold, AE and Miadlikowska, J and Sarvate, SD and Lutzoni, F},
Title = {Phylogenetic relationships, host affinity, and geographic
structure of boreal and arctic endophytes from three major
plant lineages.},
Journal = {Molecular phylogenetics and evolution},
Volume = {42},
Number = {2},
Pages = {543-555},
Year = {2007},
Month = {February},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Although associated with all plants, fungal endophytes
(microfungi that live within healthy plant tissues)
represent an unknown proportion of fungal diversity. While
there is a growing appreciation of their ecological
importance and human uses, little is known about their host
specificity, geographic structure, or phylogenetic
relationships. We surveyed endophytic Ascomycota from
healthy photosynthetic tissues of three plant species
(Huperzia selago, Picea mariana, and Dryas integrifolia,
representing lycophytes, conifers, and angiosperms,
respectively) in northern and southern boreal forest
(Québec, Canada) and arctic tundra (Nunavut, Canada).
Endophytes were recovered from all plant species surveyed,
and were present in <1-41% of 2 mm2 tissue segments examined
per host species. Sequence data from the nuclear ribosomal
internal transcribed spacer region (ITS) were obtained for
280 of 558 isolates. Species-accumulation curves based on
ITS genotypes remained non-asymptotic, and bootstrap
analyses indicated that a large number of genotypes remain
to be found. The majority of genotypes were recovered from
only a single host species, and only 6% of genotypes were
shared between boreal and arctic communities. Two
independent Bayesian analyses and a neighbor-joining
bootstrapping analysis of combined data from the nuclear
large and small ribosomal subunits (LSUrDNA, SSUrDNA; 2.4
kb) showed that boreal and arctic endophytes represent
Dothideomycetes, Sordariomycetes, Chaetothyriomycetidae,
Leotiomycetes, and Pezizomycetes. Many well-supported
phylotypes contained only endophytes despite exhaustive
sampling of available sequences of Ascomycota. Together,
these data demonstrate greater than expected diversity of
endophytes at high-latitude sites and provide a framework
for assessing the evolution of these poorly known but
ubiquitous symbionts of living plants.},
Doi = {10.1016/j.ympev.2006.07.012},
Key = {fds329446}
}
@article{fds329447,
Author = {Hibbett, DS and Binder, M and Bischoff, JF and Blackwell, M and Cannon,
PF and Eriksson, O and Huhndorf, S and James, T and Kirk, PM and Lücking,
R and Lumbsch, T and Lutzoni, F and Matheny, PB and McLaughlin, DJ and Powell, MJ and Redhead, S and Schoch, CL and Spatafora, JW and Stalpers,
JA and Vilgalys, R and Aime, MC and Aptroot, A and Bauer, R and Begerow, D and Benny, GL and Castlebury, LA and Crous, PW and Dai, YC and Gams, W and Geiser, DM and Griffith, GW and Gueidan, C and Hawksworth, DL and Hestmark, G and Hosaka, K and Humber, RA and Hyde, K and Koljalg, U and Kurtzman, CP and Larsson, KH and Lichtward, R and Longcore, J and Miadlikowska, J and Miller, A and Monclavo, JM and Mozley Standridge,
S and Oberwinkler, F and Parmasto, E and Reeb, V and Rogers, JD and Roux,
C and Ryvarden, L and Sampaio, JP and Schuessler, A and Sugiyama, J and Thorn, RG and Tibell, L and Untereiner, WA and Walker, C and Wang, Z and Weir, A and Weiss, M and White, M and Winka, K and Yao, YJ and Zhang,
N},
Title = {A higher-level phylogenetic classification of the
Fungi},
Journal = {Mycological Research},
Volume = {111},
Number = {Pt 5},
Pages = {509-547},
Year = {2007},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {A comprehensive phylogenetic classification of the kingdom
Fungi is proposed, with reference to recent molecular
phylogenetic analyses, and with input from diverse members
of the fungal taxonomic community. The classification
includes 195 taxa, down to the level of order, of which 16
are described or validated here: Dikarya subkingdom nov.;
Chytridiomycota, Neocallimastigomycota phyla nov.;
Monoblepharidomycetes, Neocallimastigomycetes class. nov.;
Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae
subclass. nov.; Acarosporales, Corticiales, Baeomycetales,
Candelariales, Gloeophyllales, Melanosporales,
Trechisporales, Umbilicariales ords. nov. The clade
containing Ascomycota and Basidiomycota is classified as
subkingdom Dikarya, reflecting the putative synapomorphy of
dikaryotic hyphae. The most dramatic shifts in the
classification relative to previous works concern the groups
that have traditionally been included in the Chytridiomycota
and Zygomycota. The Chytridiomycota is retained in a
restricted sense, with Blastocladiomycota and
Neocallimastigomycota representing segregate phyla of
flagellated Fungi. Taxa traditionally placed in Zygomycota
are distributed among Glomeromycota and several subphyla
incertae sedis, including Mucoromycotina,
Entomophthoromycotina, Kickxellomycotina, and
Zoopagomycotina. Microsporidia are included in the Fungi,
but no further subdivision of the group is proposed. Several
genera of 'basal' Fungi of uncertain position are not placed
in any higher taxa, including Basidiobolus, Caulochytrium,
Olpidium, and Rozella.},
Doi = {10.1016/j.mycres.2007.03.004},
Key = {fds329447}
}
@article{fds329449,
Author = {Geiser, DM and Gueidan, C and Miadlikowska, J and Lutzoni, F and Kauff,
F and Hofstetter, V and Fraker, E and Schoch, CL and Tibell, L and Untereiner, WA and Aptroot, A},
Title = {Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae.},
Journal = {Mycologia},
Volume = {98},
Number = {6},
Pages = {1053-1064},
Year = {2006},
Month = {November},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a
monophyletic group comprising two major clades of very
different ascomycetous fungi: (i) the subclass
Eurotiomycetidae, a clade that contains most of the fungi
previously recognized as Plectomycetes because of their
mostly enclosed ascomata and prototunicate asci; and (ii)
the subclass Chaetothyriomycetidae, a group of fungi that
produce ascomata with an opening reminiscent of those
produced by Dothideomycetes or Sordariomycetes. In this
paper we use phylogenetic analyses based on data available
from the Assembling the Fungal Tree of Life project (AFTOL),
in addition to sequences in GenBank, to outline this
important group of fungi. The Eurotiomycetidae include
producers of toxic and useful secondary metabolites,
fermentation agents used to make food products and enzymes,
xerophiles and psychrophiles, and the important genetics
model Aspergillus nidulans. The Chaetothyriomycetidae
include the common black yeast fungi, some of which are
pathogens of humans and animals, as well as some primarily
lichenized groups newly found to be phylogenetically
associated with this group. The recently proposed order
Mycocaliciales shows a sister relationship with
Eurotiomycetes. The great majority of human pathogenic
Pezizomycotina are Eurotiomycetes, particularly in
Eurotiales, Onygenales and Chaetothyriales. Due to their
broad importance in basic research, industry and public
health, several genome projects have focused on species in
Onygenales and Eurotiales.},
Doi = {10.3852/mycologia.98.6.1053},
Key = {fds329449}
}
@article{fds329450,
Author = {Spatafora, JW and Sung, G-H and Johnson, D and Hesse, C and O'Rourke, B and Serdani, M and Spotts, R and Lutzoni, F and Hofstetter, V and Miadlikowska, J and Reeb, V and Gueidan, C and Fraker, E and Lumbsch, T and Lücking, R and Schmitt, I and Hosaka, K and Aptroot, A and Roux, C and Miller, AN and Geiser, DM and Hafellner, J and Hestmark, G and Arnold,
AE and Büdel, B and Rauhut, A and Hewitt, D and Untereiner, WA and Cole,
MS and Scheidegger, C and Schultz, M and Sipman, H and Schoch,
CL},
Title = {A five-gene phylogeny of Pezizomycotina.},
Journal = {Mycologia},
Volume = {98},
Number = {6},
Pages = {1018-1028},
Year = {2006},
Month = {November},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Pezizomycotina is the largest subphylum of Ascomycota and
includes the vast majority of filamentous, ascoma-producing
species. Here we report the results from weighted parsimony,
maximum likelihood and Bayesian phylogenetic analyses of
five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and
EF-lalpha) from 191 taxa. Nine of the 10 Pezizomycotina
classes currently recognized were represented in the
sampling. These data strongly supported the monophyly of
Pezizomycotina, Arthoniomycetes, Eurotiomycetes,
Orbiliomycetes and Sordariomycetes. Pezizomycetes and
Dothideomycetes also were resolved as monophyletic but not
strongly supported by the data. Lecanoromycetes was resolved
as paraphyletic in parsimony analyses but monophyletic in
maximum likelihood and Bayesian analyses. Leotiomycetes was
polyphyletic due to exclusion of Geoglossaceae. The two most
basal classes of Pezizomycotina were Orbiliomycetes and
Pezizomycetes, both of which comprise species that produce
apothecial ascomata. The seven remaining classes formed a
monophyletic group that corresponds to Leotiomyceta. Within
Leotiomyceta, the supraclass clades of Leotiomycetes s.s.
plus Sordariomycetes and Arthoniomycetes plus
Dothideomycetes were resolved with moderate
support.},
Doi = {10.3852/mycologia.98.6.1018},
Key = {fds329450}
}
@article{fds324069,
Author = {Miadlikowska, J and Kauff, F and Hofstetter, V and Fraker, E and Grube,
M and Hafellner, J and Reeb, V and Hodkinson, BP and Kukwa, M and Lücking,
R and Hestmark, G and Otalora, MG and Rauhut, A and Büdel, B and Scheidegger, C and Timdal, E and Stenroos, S and Brodo, I and Perlmutter, GB and Ertz, D and Diederich, P and Lendemer, JC and May, P and Schoch, CL and Arnold, AE and Gueidan, C and Tripp, E and Yahr, R and Robertson, C and Lutzoni, F},
Title = {New insights into classification and evolution of the
Lecanoromycetes (Pezizomycotina, Ascomycota) from
phylogenetic analyses of three ribosomal RNA- and two
protein-coding genes.},
Journal = {Mycologia},
Volume = {98},
Number = {6},
Pages = {1088-1103},
Year = {2006},
Month = {November},
url = {http://dx.doi.org/10.1080/15572536.2006.11832636},
Abstract = {The Lecanoromycetes includes most of the lichen-forming
fungal species (> 13500) and is therefore one of the most
diverse class of all Fungi in terms of phenotypic
complexity. We report phylogenetic relationships within the
Lecanoromycetes resulting from Bayesian and maximum
likelihood analyses with complementary posterior
probabilities and bootstrap support values based on three
combined multilocus datasets using a supermatrix approach.
Nine of 10 orders and 43 of 64 families currently recognized
in Eriksson's classification of the Lecanoromycetes (Outline
of Ascomycota--2006 Myconet 12:1-82) were represented in
this sampling. Our analyses strongly support the
Acarosporomycetidae and Ostropomycetidae as monophyletic,
whereas the delimitation of the largest subclass, the
Lecanoromycetidae, remains uncertain. Independent of future
delimitation of the Lecanoromycetidae, the Rhizocarpaceae
and Umbilicariaceae should be elevated to the ordinal level.
This study shows that recent classifications include several
nonmonophyletic taxa at different ranks that need to be
recircumscribed. Our phylogenies confirm that ascus
morphology cannot be applied consistently to shape the
classification of lichen-forming fungi. The increasing
amount of missing data associated with the progressive
addition of taxa resulted in some cases in the expected loss
of support, but we also observed an improvement in
statistical support for many internodes. We conclude that a
phylogenetic synthesis for a chosen taxonomic group should
include a comprehensive assessment of phylogenetic
confidence based on multiple estimates using different
methods and on a progressive taxon sampling with an
increasing number of taxa, even if it involves an increasing
amount of missing data.},
Doi = {10.1080/15572536.2006.11832636},
Key = {fds324069}
}
@article{fds329448,
Author = {James, TY and Kauff, F and Schoch, C and Matheny, PB and Hofstetter, V and Cox, CJ and Celio, G and Gueidan, C and Fraker, E and Miadlikowska, J and Lumbsch, T and Rauhut, A and Reeb, V and Arnold, AE and Amtoft, A and Stajich, JE and Hosaka, K and Sung, GH and Johnson, D and O’Rourke, B and Binder, M and Curtis, JM and Slot, JC and Wang, Z and Wilson, AW and Schüßler, A and Longcore, JE and O’Donnell, K and Mozley
Standridge, S and Porter, D and Letcher, PM and Powell, MJ and Taylor,
JW and White, MM and Griffith, GW and Davies, DR and Sugiyama, J and Rossman, AY and Rogers, JD and Pfister, DH and Hewitt, D and Hansen, K and Hambleton, S and Shoemaker, RA and Kohlmeyer, J and Volkmann
Kohlmeyer, B and Spotts, RA and Serdani, M and Crous, PW and Hughes, KW and Matsuura, K and Langer, E and Langer, G and Untereiner, WA and Lücking,
R and Büdel, B and Geiser, DM and Aptroot, A and Buck, WR and Cole, MS and Diederich, P and Printzen, C and Schmitt, I and Schultz, M and Yahr, R and Zavarzin, A and Hibbett, DH and Lutzoni, F and McLaughlin, DJ and Spatafora, JW and Vilgalys, R},
Title = {Reconstructing the early evolution of the Fungi using a
six-gene phylogeny},
Journal = {Nature},
Volume = {443},
Number = {7113},
Pages = {818-822},
Year = {2006},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The ancestors of fungi are believed to be simple aquatic
forms with flagellated spores, similar to members of the
extant phylum Chytridiomycota (chytrids). Current
classifications assume that chytrids form an early-diverging
clade within the kingdom Fungi and imply a single loss of
the spore flagellum, leading to the diversification of
terrestrial fungi. Here we develop phylogenetic hypotheses
for Fungi using data from six gene regions and nearly 200
species. Our results indicate that there may have been at
least four independent losses of the flagellum in the
kingdom Fungi. These losses of swimming spores coincided
with the evolution of new mechanisms of spore dispersal,
such as aerial dispersal in mycelial groups and polar tube
eversion in the microsporidia (unicellular forms that lack
mitochondria). The enigmatic microsporidia seem to be
derived from an endoparasitic chytrid ancestor similar to
Rozella allomycis, on the earliest diverging branch of the
fungal phylogenetic tree.},
Doi = {10.1038/nature05110},
Key = {fds329448}
}
@article{fds329451,
Author = {O'Brien, HE and Miadlikowska, J and Lutzoni, F},
Title = {Assessing host specialization in symbiotic cyanobacteria
associated with four closely related species of the lichen
fungus Peltigera},
Journal = {European Journal of Phycology},
Volume = {40},
Number = {4},
Pages = {363-378},
Publisher = {Informa UK Limited},
Year = {2005},
Month = {November},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Heterocystous cyanobacteria form symbiotic associations with
a wide range of plant and fungal hosts. We used a molecular
phylogenetic approach to investigate the degree of host
specialization of cyanobacteria associated with four closely
related species of the lichenized fungus Peltigera, and to
compare these strains with other symbiotic cyanobacteria. We
conducted phylogenetic analyses on 16S, rbcLX, and trnL
sequences from cyanobacteria associated with multiple
specimens of each lichen species and from symbionts of other
fungi and plants, as well as from free-living strains of
Nostoc and related genera of cyanobacteria. The genus Nostoc
comprises two divergent lineages, but symbiotic strains
occur primarily within a single monophyletic lineage that
also includes free-living representatives. Cyanobacteria
from the same lichen species were often more closely related
to strains from other species or to plant symbionts or
free-living strains than to each other. These results
indicate that host specialization is low for the genus
Nostoc, and suggest that opportunities for coevolution with
its partners may be rare. © 2005 British Phycological
Society.},
Doi = {10.1080/09670260500342647},
Key = {fds329451}
}
@article{fds329452,
Author = {Lutzoni, F and Kauff, F and Cox, CJ and McLaughlin, D and Celio, G and Dentinger, B and Padamsee, M and Hibbett, D and James, TY and Baloch, E and Grube, M and Reeb, V and Hofstetter, V and Schoch, C and Arnold, AE and Miadlikowska, J and Spatafora, J and Johnson, D and Hambleton, S and Crockett, M and Shoemaker, R and Sung, G-H and Lücking, R and Lumbsch,
T and O'Donnell, K and Binder, M and Diederich, P and Ertz, D and Gueidan,
C and Hansen, K and Harris, RC and Hosaka, K and Lim, Y-W and Matheny, B and Nishida, H and Pfister, D and Rogers, J and Rossman, A and Schmitt, I and Sipman, H and Stone, J and Sugiyama, J and Yahr, R and Vilgalys,
R},
Title = {Assembling the fungal tree of life: progress,
classification, and evolution of subcellular
traits.},
Journal = {American journal of botany},
Volume = {91},
Number = {10},
Pages = {1446-1480},
Year = {2004},
Month = {October},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Based on an overview of progress in molecular systematics of
the true fungi (Fungi/Eumycota) since 1990, little overlap
was found among single-locus data matrices, which explains
why no large-scale multilocus phylogenetic analysis had been
undertaken to reveal deep relationships among fungi. As part
of the project "Assembling the Fungal Tree of Life" (AFTOL),
results of four Bayesian analyses are reported with
complementary bootstrap assessment of phylogenetic
confidence based on (1) a combined two-locus data set
(nucSSU and nucLSU rDNA) with 558 species representing all
traditionally recognized fungal phyla (Ascomycota,
Basidiomycota, Chytridiomycota, Zygomycota) and the
Glomeromycota, (2) a combined three-locus data set (nucSSU,
nucLSU, and mitSSU rDNA) with 236 species, (3) a combined
three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with
157 species, and (4) a combined four-locus data set (nucSSU,
nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of
the lack of complementarity among single-locus data sets,
the last three analyses included only members of the
Ascomycota and Basidiomycota. The four-locus analysis
resolved multiple deep relationships within the Ascomycota
and Basidiomycota that were not revealed previously or that
received only weak support in previous studies. The impact
of this newly discovered phylogenetic structure on
supraordinal classifications is discussed. Based on these
results and reanalysis of subcellular data, current
knowledge of the evolution of septal features of fungal
hyphae is synthesized, and a preliminary reassessment of
ascomal evolution is presented. Based on previously
unpublished data and sequences from GenBank, this study
provides a phylogenetic synthesis for the Fungi and a
framework for future phylogenetic studies on
fungi.},
Doi = {10.3732/ajb.91.10.1446},
Key = {fds329452}
}
@article{fds329453,
Author = {Miadlikowska, J and Lutzoni, F},
Title = {Phylogenetic classification of peltigeralean fungi
(Peltigerales, Ascomycota) based on ribosomal RNA small and
large subunits.},
Journal = {American journal of botany},
Volume = {91},
Number = {3},
Pages = {449-464},
Year = {2004},
Month = {March},
url = {http://dx.doi.org/10.3732/ajb.91.3.449},
Abstract = {To provide a comprehensive molecular phylogeny for
peltigeralean fungi and to establish a classification based
on monophyly, phylogenetic analyses were carried out on
sequences from the nuclear ribosomal large (LSU) and small
(SSU) subunits obtained from 113 individuals that represent
virtually all main lineages of ascomycetes. Analyses were
also conducted on a subset of 77 individuals in which the
ingroup consisted of 59 individuals representing six
families, 12 genera, and 54 species potentially part of the
Peltigerineae/Peltigerales. Our study revealed that all six
families together formed a strongly supported monophyletic
group within the Lecanoromycetidae. We propose here a new
classification for these lichens consisting of the order
Peltigerales and two suborders-Collematineae subordo nov.
(Collemataceae, Placynthiaceae, and Pannariaceae) and
Peltigerineae (Lobariaceae, Nephromataceae, and
Peltigeraceae). To accommodate these new monophyletic
groups, we redefined the Lecanorineae, Pertusariales, and
Lecanorales sensu Eriksson et al. (Outline of
Ascomycota-2003, Myconet 9: 1-103, 2003). Our study confirms
the monophyly of the Collemataceae, Lobariaceae,
Nephromataceae, and Peltigeraceae, and the genera Nephroma,
Sticta, and Peltigera. However, Leptogium, Lobaria,
Pseudocyphellaria, and Solorina were found to be
nonmonophyletic genera. Reconstruction of ancestral
symbiotic states within the Peltigerales, using maximum
likelihood (ML) and a Bayesian approach to account for
phylogenetic uncertainty, revealed an evolutionary scenario
in which bimembered associations with cyanobacteria were
ancestral, followed by multiple independent acquisitions of
green algae to form tripartite symbioses and rare subsequent
losses of the cyanobiont to form bimembered symbioses with
green algae.},
Doi = {10.3732/ajb.91.3.449},
Key = {fds329453}
}
@article{fds329504,
Author = {Ertz, D and Diederich, P and Miadlikowska, J},
Title = {The lichenicolous Opegrapha species (Roccellaceae,
Ascomycota) with 3-septate ascospores on Pertusaria and
Ochrolechia},
Journal = {Botanical Journal of the Linnean Society},
Volume = {144},
Number = {2},
Pages = {235-241},
Publisher = {Oxford University Press (OUP)},
Year = {2004},
Month = {February},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The Opegrapha species with 3-septate ascospores growing on
Pertusaria and Ochrolechia are revised. Two species are
recognized: Opegrapha anomea (of which O. pertusariae, O.
quaternella, O. wetmorei and possibly Leciographa weissii
are considered to be synonyms), and O. blakii Ertz &
Diederich sp. nov. described from a sterile lichen with an
Ochrolechia-like thallus, known from Ecuador and Venezuela.
Opegrapha anomea and several related lichenicolous species
with roundish or irregular, often multilocular ascomata are
morphologically intermediate between Opegrapha and
Plectocarpon, and might represent a distinct genus. © 2004
The Linnean Society of London.},
Doi = {10.1111/j.1095-8339.2003.00239.x},
Key = {fds329504}
}
@article{fds329454,
Author = {Miadlikowska, J and Lutzoni, F and Goward, T and Zoller, S and Posada,
D},
Title = {New approach to an old problem: Incorporating signal from
gap-rich regions of ITS and rDNA large subunit into
phylogenetic analyses to resolve the Peltigera canina
species complex.},
Journal = {Mycologia},
Volume = {95},
Number = {6},
Pages = {1181-1203},
Year = {2003},
Month = {November},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The Peltigera canina species complex consists of foliose
lichenized bitunicate ascohymenial discomycetes forming
section Peltigera within the genus Peltigera
(Lecanoromycetes, lichen-forming Ascomycetes). To test the
circumscription of highly polymorphic species and to resolve
relationships among putative members of the P. canina
complex, part of the nuclear ribosomal DNA large subunit
(LSU rDNA) and the entire internal-transcribed spacer (ITS
rDNA) were sequenced for 84 individuals representing 33
putative Peltigera taxa. Seventeen of the 25 taxa from the
P. canina complex are well established and widely accepted.
The remaining eight taxa have been proposed recently but are
undescribed. A hypervariable region in ITS1 (ITS1-HR, sites
111-237 in our alignment) showed remarkable variation in
length, especially in the P. canina complex, ranging from 8
to 126 bp, and contained several microsatellites. We
describe here an alignment-free method to code such large
gap-rich hypervariable regions for phylogenetic analyses.
Variation among ITS1-HR sequences greatly contributed to
species delimitation and species identification and can be a
major asset to future population studies for specific
species within section Peltigera. Sequences of ITS1-HR alone
were sufficient to identify all existing species of
Peltigera from the P. canina species complex and related
sections Retifoveatae and Horizontales included in this
study. However, only when INAASE (for short ambiguously
aligned regions) and ITS1-HR coded characters were added to
the combined analysis of nonambiguous LSU and ITS sites was
it possible to reach the level of phylogenetic resolution
and support necessary to disentangle the P. canina complex.
We report here complete concordance between phylogenetically
based and morphologically based species delimitation for 15
of the 17 species from the P. canina complex (P. canina, P.
cinnamomea, P. degenii, P. evansiana, P. frigida, P.
kristinssonii, P. laciniata, P. lambinonii, P. lepidophora,
P. membranacea, P. monticola, P. ponojensis, P. praetextata,
P. rufescens and P. ulcerata). Four of the eight newly
proposed but undescribed taxa most likely represent new
species (P. "fuscopraetextata", P. "neocanina", P.
"neorufescens" and P. "scotteri") within the P. canina
complex. We found that morphologically and chemically
distinct P. didactyla s. str. and P. didactyla var.
extenuata form two non-sister monophyletic entities,
therefore the latter taxon should be recognized at the
species level (P. extenuata). The North American and
European populations of the morphologically uniform P.
degenii might represent two sibling species because they
were found to be genetically distinct and monophyletic. Two
major monophyletic groups within the P. canina complex
(CICADE = CInnamomea + CAnina + DEgenii group and PORUDI =
POnojensis + RUfescens + DIdactyla group) seem to be
correlated with different humidity preferences. Although
some authors previously have suggested interspecies
recombination within the P. canina complex, we did not find
statistically significant evidence for this phenomenon based
on LSU and ITS sequences.},
Doi = {10.1080/15572536.2004.11833027},
Key = {fds329454}
}
@article{fds329505,
Author = {Goffinet, B and Miadlikowska, J and Goward, T},
Title = {Phylogenetic inferences based on nrDNA sequences support
five morphospecies within the Peltigera didactyla complex
(Lichenized Ascomycota)},
Journal = {Bryologist},
Volume = {106},
Number = {3},
Pages = {349-364},
Publisher = {American Bryological and Lichenological Society},
Year = {2003},
Month = {January},
url = {http://dx.doi.org/10.1639/01},
Abstract = {The Peltigera didactyla complex comprises species of section
Peltigera with laminal and submarginal soredia. Three
species (P. didactyla, P. lambinonii, and P. ulcerata) and
one atypical variety (P. didactyla var. extenuata) are
currently recognized within this complex. Phylogenetic
inferences of the entire Internal Transcribed Spacer region
(ITS) and the 5′ half of the gene encoding the large
subunit of the rRNA reveal a robust structure within the
complex. Under both the maximum parsimony and the maximum
likelihood criterion, P. didactyla is resolved as a
polyphyletic entity, whereas P. ulcerata, P. lambinonii, and
P. didactyla var. extenuata are delimited as monophyletic
entities. Peltigera didactyla var. extenuata appears basal
within the group, whereas var. didactyla is nested within a
clade that also comprises P. lambinonii and P. ulcerata. The
polyphyly of P. didactyla is further characterized by the
existence of populations that resemble var. extenuata, but
differ by their brownish upper cortex. These populations,
all from the boreal zone of Canada, compose a monophyletic
group sister to the P. didactyla-P. lambinonii clade. For P.
didactyla to satisfy a phylogenetic species concept, the
var. extenuata is reinstated at the species level, and a new
species, P. castanea, is described. Three populations
sampled are characterized by unique sequences that may
indicate the presence of additional cryptic taxa within the
complex. A key to the accepted species is provided. The
presence of P. lambinonii in Australia is confirmed and P.
ulcerata is reported as new for Chile.},
Doi = {10.1639/01},
Key = {fds329505}
}
@article{fds329506,
Author = {Ertz, D and Zhurbenko, M and Diederich, P and Miadlikowska,
J},
Title = {A new species of Plectocarpon (Lichenicolous Roccellaceae,
Ascomycota) on Peltigera},
Journal = {Bryologist},
Volume = {106},
Number = {3},
Pages = {465-467},
Publisher = {American Bryological and Lichenological Society},
Year = {2003},
Month = {January},
url = {http://dx.doi.org/10.1639/15},
Abstract = {A new lichenicolous species, Plectocarpon peltigerae,
growing on Peltigera leucophlebia thalli, is described from
Canada and Russia.},
Doi = {10.1639/15},
Key = {fds329506}
}
@article{fds329455,
Author = {McDonald, T and Miadlikowska, J and Lutzoni, F},
Title = {The lichen genus Sticta in the Great Smoky Mountains: A
phylogenetic study of morphological, chemical, and molecular
data},
Journal = {Bryologist},
Volume = {106},
Number = {1},
Pages = {61-79},
Publisher = {American Bryological and Lichenological Society},
Year = {2003},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {In this paper we segregate specimens from the genus Sticta
in the Great Smoky Mountains National Park into phenotypic
groups corresponding to putative species using traditional
taxonomic methods, paying particular attention to specimens
from the S. weigelii s. 1. group, then employ phylogenetic
analyses and rigorous statistics to test the robustness of
these species groups. In order to circumscribe putative
species and to resolve the S. weigelii complex,
morphological, chemical, and molecular characters from the
nuclear ribosomal DNA sequences of the entire Internal
Transcribed Spacer region are analyzed separately and
simultaneously using maximum parsimony or maximum
likelihood. In addition to the bootstrap method, Bayesian
statistics with the Markov Chain Monte Carlo algorithm are
used to estimate branch robustness on the resulting
reconstructed trees. Five out of six analyses recover the
same five monophyletic putative species from the genus
Sticta, indicating the concordance of DNA-based and
morphology-based species delimitation. The phylogenies show
that lichens identified as S. weigelii represented S.
beauvoisii and the two new species described here - S.
carolinensis and S. fragilinata. Sticta weigelii s. s. does
not occur in the park. Specimens from Oregon identified as
S. weigelii belong to another unnamed Sticta taxon. The
remaining two monophyletic groups represent two species well
known from the park-S. fuliginosa and S. limbata.
Characteristics of secondary compounds detected by Thin
Layer Chromatography (TLC) and High Performance Liquid
Chromatography (HPLC) in S. fragilinata thalli are provided.
Detailed descriptions, including morphology and chemistry,
are provided for four Sticta species found in the Smoky
Mountains: S. beauvoisii, S. carolinensis, S. fragilinata
and S. fuliginosa.},
Doi = {10.1639/0007-2745(2003)106[0061:TLGSIT]2.0.CO;2},
Key = {fds329455}
}
@article{fds328024,
Author = {Goffinet, B. and Miadlikowska, J. and Goward, T.},
Title = {Phylogenetic inferences support five morphospecies within
the morphologically, chemically, and ecologically diverse
Peltigera didactyla species complex (lichenized
Ascomycota).},
Journal = {The Bryologist},
Volume = {106},
Pages = {349-364},
Year = {2003},
url = {http://lutzonilab.org/publications-datasets/},
Key = {fds328024}
}
@article{fds328026,
Author = {Ertz, D. and Zhurbenko, M. and Diederich, P. and Miadlikowska, J.},
Title = {A new species of Plectocarpon on Peltigera (lichenicolous
Roccellaceae, Ascomycota).},
Journal = {The Lichenologist},
Volume = {106},
Pages = {465-467},
Year = {2003},
url = {http://lutzonilab.org/publications-datasets/},
Key = {fds328026}
}
@article{fds329456,
Author = {Miadlikowska, J and McCune, B and Lutzoni, F},
Title = {Pseudocyphellaria perpetua, a new lichen from western North
America},
Journal = {Bryologist},
Volume = {105},
Number = {1},
Pages = {1-10},
Publisher = {American Bryological and Lichenological Society},
Year = {2002},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Pseudocyphellaria perpetua McCune & Miadlikowska is
described as a new species of lichenized fungus from Oregon,
U.S.A. Morphologically similar to some forms of P. crocata,
P. perpetua is separated from that species by a yellow
medulla and predominantly marginal soralia. Comparison of
ITS and LSU nrDNA sequences support taxonomic distinctness
of these two species. Phylogenetic analyses were conducted
on LSU and ITS nrDNA data sets separately and simultaneously
using maximum parsimony and maximum likelihood as
optimization criteria. All analyses except one (maximum
parsimony on LSU nrDNA data alone) confirmed the monophyly
of P. perpetua. There are two distinct groups within the P.
perpetua clade represented by specimens sampled from near
the type locality in Oregon, and specimens outside of Oregon
(eastern Canada, eastern Russia and eastern U.S.A.). The
genus Pseudocyphellaria is very likely polyphyletic,
consisting of at least two highly divergent
groups.},
Doi = {10.1639/0007-2745(2002)105[0001:PPANLF]2.0.CO;2},
Key = {fds329456}
}
@article{fds329457,
Author = {Miadlikowska, J and Lutzoni, F},
Title = {Phylogenetic revision of the genus Peltigera (lichen-forming
Ascomycota) based on morphological, chemical, and large
subunit nuclear ribosomal DNA data},
Journal = {International Journal of Plant Sciences},
Volume = {161},
Number = {6},
Pages = {925-958},
Publisher = {University of Chicago Press},
Year = {2000},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {Peltigera (Peltigerineae, lichenized Ascomycota) is one of
the most widespread lichen genera incorporating bi- and
trimembered associations involving fungi, green algae (cf.
Coccomyxa), and cyanobacteria (cf. Nostoc). A wide range of
morphological and chemical (secondary compounds) variation
at both the intra- and inter-specific levels is present in
this genus. Compared to many other genera of macrolichens:
its taxonomy, including chemotaxonomy, still remains poorly
understood. Existing infrageneric classifications of
Peltigera are almost exclusively based on photobiont
composition of the thallus. These classifications assumed
that bi- and trimembered taxa were distinct monophyletic
entities. The genus Peltigera has never been the focus of a
comprehensive phylogenetic study. The most recent and widely
accepted subdivision of the genus into seven groups is based
mainly on morphological and chemical characters.
Relationships among species of Peltigera are investigated
here using chemical, morphological, and large subunit
nuclear ribosomal DNA (LSU nrDNA) data. We test the
monophyly of these seven morpho-chemical Peltigera groups
and propose a classification based on a phylogenetic
approach. Data sets of 42 chemical characters (terpenoids),
31 morphological characters, and 1135 LSU nrDNA characters
for 96 samples representing 38 Peltigera species, eight
undescribed putative Peltigera species, and nine species
from seven potentially closely related genera from
Peltigerineae were subjected to maximum parsimony analyses.
Morphological, chemical, and molecular analyses were carried
out independently and on a combined data set. Monophyly of
Peltigera, including Hydrothyria, was confirmed. The genus
Hydrothyria is transferred to Peltigera and a new
combination Peltigera hydrothyria Miadlikowska and Lutzoni
is proposed. Eight monophyletic sections within the genus
Peltigera, with high bootstrap support, are circumscribed:
sections Peltigera, Polydactylon Miadlikowska and Lutzoni,
Chloropeltigera Gyeln., Peltidea (Ach.) Vain., Horizontales
Miadlikowska and Lutzoni, Retifoveatae Miadlikowska and
Lutzoni, Phlebia Wallr., and Hydrothyriae Miadlikowska and
Lutzoni. Unequivocal morphological and chemical
synapomorphies for all sections except section Peltidea are
recognized and presented. A key for identification of the
sections is provided. In addition, a key based on four main
terpenoids for determination of the chemotypes and species
within section Polydactylon is included. Five terpenoids
(50-54) identified on thin-layer chromatography plates for
P. elisabethae and P. horizontalis chemotype I are added to
the list of substances found in Peltigera. Five chemotypes,
mainly from Poland and Norway, are reported from Peltigera
thalli for the first time: P. malacea chemotype V, P.
leucophlebia chemotype II, P. hymenina chemotypes II and
III, and P. collina chemotype IV. Three main types of vein
structure in Peltigera were recognized based on SEM
studies.},
Doi = {10.1086/317568},
Key = {fds329457}
}
@article{fds329507,
Author = {Goffinet, B and Miadlikowska, J},
Title = {Peltigera phyllidiosa (Peltigeraceae, ascomycotina), a new
species from the Southern Appalachians corroborated by its
sequences},
Journal = {Lichenologist},
Volume = {31},
Number = {3},
Pages = {247-256},
Publisher = {Cambridge University Press (CUP)},
Year = {1999},
Month = {January},
url = {http://lutzonilab.org/publications-datasets/},
Abstract = {The new species Peltigera phyllidiosa Goffinet and
Miadlikowska from the Southern Appalachians, eastern U.S.A.,
is closely related to P. collina and P. neckeri. Like these
species it has a glabrous upper cortex and black fingernail-
or saddle-shaped apothecial discs, but differs in its
laminal phyllidia. Variation in nucleotide sequences of the
Internal Transcribed Spacer (ITS) of the nrDNA repeat region
correlates with the presence or absence of phyllidia,
supporting the distinction of P. phyllidiosa from P. collina
and P. neckeri.},
Doi = {10.1006/lich.1998.0201},
Key = {fds329507}
}
@article{fds329508,
Author = {Hawksworth, DL and Miadlikowska, J},
Title = {New species of lichenicolous fungi occurring on Peltigera in
Ecuador and Europe},
Journal = {Mycological Research},
Volume = {101},
Number = {9},
Pages = {1127-1134},
Publisher = {Elsevier BV},
Year = {1997},
Month = {January},
url = {http://dx.doi.org/10.1017/S0953756297003778},
Abstract = {A study of the lichenicolous fungi occurring on species of
the lichenized genus Peltigera has resulted in six new
species: Libertiella curvispora, L. didymospora, L. fennica
Alstrup, Polycoccum superficiale, Roselliniella
peltigericola, and Zwackhiomyces Kiszkianus. A key to the
five known species of Libertiella is included. This paper
brings the number of fungi known on this host to 87, of
which 61 are not known from any other host genus, providing
additional evidence for the richness of Peltigera thalli as
a host for novel fungi. The possible hypotheses to explain
the richness of this host genus for lichenicolous fungi are
enumerated; these are not mutually exclusive.},
Doi = {10.1017/S0953756297003778},
Key = {fds329508}
}
@article{fds329509,
Author = {Hawksworth, DL and Mia̧dlikowska, J},
Title = {Vagnia, a remarkable coelomycete producing a black columnar
cirrus on Peltigera in Poland},
Journal = {Lichenologist},
Volume = {29},
Number = {1},
Pages = {45-49},
Publisher = {Cambridge University Press (CUP)},
Year = {1997},
Month = {January},
url = {http://dx.doi.org/10.1006/lich.1996.0059},
Abstract = {The new genus Vagnia is introduced for the single species V.
cirriformia discovered on thalli of Peltigera in Poland; it
appears to be a pathogen as the cortex is destroyed in a
rounded patch within which the conidiomata occur. The fungus
is characterized by cupulate to doliiform conidiomata
clothed in white hairs and from which a black columnar
cirrus of conidia arises. The simple ellipsoid conidia are
hyaline when viewed individually and are formed
enteroblastically from elongate conidiogenous cells
supported by branched conidiophores.},
Doi = {10.1006/lich.1996.0059},
Key = {fds329509}
}
@article{fds328030,
Author = {Hawksworth, D. L. and Miadlikowska, J.},
Title = {Vagnia, a remarkable celeomycete producing black columnar
cirrus on Peltigera in Poland.},
Journal = {The Lichenologist},
Volume = {29},
Pages = {45-49},
Year = {1997},
Key = {fds328030}
}
| |
Duke University * Arts & Sciences * Algae * Brophytes * Fungi * Lichens * Vasculars * Reload * Login | ||
