Duke Herbarium Lichens: Publications since January 2023
%% Lutzoni, Francois M.
@article{fds376708,
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 = {fds376708}
}
@article{fds375868,
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 = {fds375868}
}
@article{fds373327,
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 = {fds373327}
}
@article{fds371575,
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 = {fds371575}
}
%% Miadlikowska, Jolanta M.
@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}
}