Publications of Mohamed A. Noor :chronological combined listing:
%% Papers Published
@article{fds152666,
Author = {MAF Noor},
Title = {Mutagenesis from meiotic recombination is not a primary
driver of sequence divergence between Saccharomyces
species.},
Journal = {Molecular Biology and Evolution},
Volume = {25},
Number = {11},
Pages = {2439-2444},
Year = {2008},
Month = {November},
ISSN = {1537-1719},
Abstract = {Local rates of recombination positively correlate with DNA
sequence diversity in many species. To test whether this
relationship stems from mutagenicity of meiotic
recombination, studies often look for a similar association
between local rates of recombination and sequence
"divergence" between species. Because recombination is
mutagenic in yeast, I evaluate this assay by testing whether
noncoding DNA sequence divergence between Saccharomyces
species is related to measures of meiotic double-strand DNA
breaks or crossover rates derived from Saccharomyces
cerevisiae. Contrary to expectation, I find that sequence
divergence is either uncorrelated or negatively correlated
with rates of both double-strand break and crossover.
Several caveats are mentioned, but these results suggest
that mutagenesis from meiotic recombination is not the
primary driver of sequence divergence between Saccharomyces
species. This study demonstrates that the association
between interspecies nucleotide divergence and local
recombination rates is not always a reliable indicator of
recombination's mutagenicity.},
Key = {fds152666}
}
@article{fds152667,
Author = {MAF Noor and RS Parnell and BS Grant},
Title = {A reversible color polyphenism in American peppered moth
(Biston betularia cognataria) caterpillars.},
Journal = {PLoS ONE},
Volume = {3},
Number = {9},
Pages = {e3142},
Year = {2008},
Month = {September},
ISSN = {1932-6203},
Abstract = {Insect body color polyphenisms enhance survival by producing
crypsis in diverse backgrounds. While color polyphenisms are
often indirectly induced by temperature, rearing density, or
diet, insects can benefit from immediate crypsis if they
evolve polyphenisms directly induced by exposure to the
background color, hence immediately deriving protection from
predation. Here, we examine such a directly induced color
polyphenism in caterpillars of the geometrid peppered moth
(Biston betularia). This larval color polyphenism is
unrelated to the genetic polymorphism for melanic phenotypes
in adult moths. B. betularia caterpillars are generalist
feeders and develop body colors that closely match the brown
or green twigs of their host plant. We expand on previous
studies examining the proximal cues that stimulate color
development. Under controlled rearing conditions, we
manipulated diets and background reflectance, using both
natural and artificial twigs, and show that visual
experience has a much stronger effect than does diet in
promoting precise color matching. Their induced body color
was not a simple response to reflectance or light intensity
but instead specifically matched the wavelength of light to
which they were exposed. We also show that the potential to
change color is retained until the final (sixth) larval
instar. Given their broad host range, this directly induced
color polyphenism likely provides the caterpillars with
strong protection from bird predation.},
Key = {fds152667}
}
@article{fds152670,
Author = {MAF Noor},
Title = {Connecting recombination, nucleotide diversity and species
divergence in Drosophila.},
Journal = {Fly},
Volume = {2},
Number = {5},
Year = {2008},
Month = {September},
ISSN = {1933-6942},
Abstract = {The association between recombination rate and nucleotide
diversity provides compelling evidence for the action of
natural selection across much of the Drosophila melanogaster
genome. This conclusion is further supported by the lack of
association between recombination rate and nucleotide
divergence between species. However, studies of other
species, including other Drosophila, have not always yielded
the same results. Our recent study measured these parameters
within the D. pseudoobscura species group using
next-generation sequencing and high-throughput genotyping
technologies. We documented fine-scale variation in
crossover rate within D. pseudoobscura, and we observed that
crossover variation was strongly associated with nucleotide
diversity only when measured at a fine-scale. We also
observed associations between crossover rate and sequence
differences between D. pseudoobscura and its close
relatives. These latter associations could have been driven
in part by mutagenic effects associated with double-strand
break repair, but we cannot exclude the possibility that it
results primarily from shared ancestral polymorphisms.
Overall, this work strongly underscores the importance of
scale in testing for associations of recombination rate with
other parameters, and it brings us one small step closer to
understanding the role of natural selection and other
evolutionary forces in shaping divergence among
genomes.},
Key = {fds152670}
}
@article{fds152663,
Author = {DJ Catron and MAF Noor},
Title = {Gene expression disruptions of organism versus organ in
Drosophila species hybrids.},
Journal = {PLoS ONE},
Volume = {3},
Number = {8},
Pages = {e3009},
Year = {2008},
Month = {August},
ISSN = {1932-6203},
Abstract = {Hybrid dysfunctions, such as sterility, may result in part
from disruptions in the regulation of gene expression.
Studies of hybrids within the Drosophila simulans clade have
reported genes expressed above or below the expression
observed in their parent species, and such misexpression is
associated with male sterility in multigenerational
backcross hybrids. However, these studies often examined
whole bodies rather than testes or had limited replication
using less-sensitive but global techniques. Here, we use a
new RNA isolation technique to re-examine hybrid gene
expression disruptions in both testes and whole bodies from
single Drosophila males by real-time quantitative RT-PCR. We
find two early-spermatogenesis transcripts are
underexpressed in hybrid whole-bodies but not in assays of
testes alone, while two late-spermatogenesis transcripts
seem to be underexpressed in both whole-bodies and testes
alone. Although the number of transcripts surveyed is
limited, these results provide some support for a previous
hypothesis that the spermatogenesis pathway in these sterile
hybrids may be disrupted sometime after the expression of
the early meiotic arrest genes.},
Key = {fds152663}
}
@article{fds152664,
Author = {RJ Kulathinal and SM Bennett and CL Fitzpatrick and MAF
Noor},
Title = {Fine-scale mapping of recombination rate in Drosophila
refines its correlation to diversity and
divergence.},
Journal = {Proceedings of the National Academy of Sciences
USA},
Volume = {105},
Number = {29},
Pages = {10051-6},
Year = {2008},
Month = {July},
ISSN = {1091-6490},
Keywords = {Animals • Base Sequence • Chromosome Mapping
• Crosses, Genetic • Crossing Over, Genetic •
DNA • DNA Breaks • DNA Repair • Drosophila
• Drosophila melanogaster • Evolution, Molecular
• Gene Conversion • Genome, Insect • Models,
Genetic • Mutation • Polymorphism, Genetic •
Recombination, Genetic* • Species Specificity •
Variation (Genetics) • genetics • genetics* •
metabolism},
Abstract = {Regional rates of recombination often correlate with levels
of nucleotide diversity, and either selective or neutral
hypotheses can explain this relationship. Regional
recombination rates also correlate with nucleotide
differences between human and chimpanzee, consistent with
models where recombination is mutagenic; however, a lack of
correlation is observed in the Drosophila melanogaster
group, consistent with models invoking natural selection.
Here, we revisit the relationship among recombination,
diversity, and interspecies difference by generating
empirical estimates of these parameters in Drosophila
pseudoobscura. To measure recombination rate, we genotyped
1,294 backcross hybrids at 50 markers across the largest
assembled linkage group in this species. Genome-wide
diversity was estimated by sequencing a second isolate of D.
pseudoobscura at shallow coverage. Alignment to the
sequenced genome of the closely related species, Drosophila
persimilis, provided nucleotide site orthology. Our findings
demonstrate that scale is critical in determining correlates
to recombination rate: fine-scale cross-over rate estimates
are far stronger predictors of both diversity and
interspecies difference than broad-scale estimates. The
correlation of fine-scale recombination rate to diversity
and interspecies difference appears to be genome-wide,
evidenced by examination of an X-linked region in greater
detail. Because we observe a strong correlation of
cross-over rate with interspecies difference, even after
correcting for segregating ancestral variation, we suggest
that both mutagenic and selective forces generate these
correlations, the latter in regions of low crossing over. We
propose that it is not cross-overs per se that are
mutagenic, but rather repair of DNA double-strand break
precursors via crossing over and gene conversion.},
Key = {fds152664}
}
@article{fds152669,
Author = {SW Schaeffer and et al (Noor is 20th of 39 authors)},
Title = {Polytene chromosomal maps of 11 Drosophila species: the
order of genomic scaffolds inferred from genetic and
physical maps.},
Journal = {Genetics},
Volume = {179},
Number = {3},
Pages = {1601-55},
Year = {2008},
Month = {July},
ISSN = {0016-6731},
Keywords = {Animals • Chromosomes • Drosophila • Genetic
Markers • Genome, Insect • Karyotyping •
Physical Chromosome Mapping* • Sequence Alignment
• Synteny • genetics*},
Abstract = {The sequencing of the 12 genomes of members of the genus
Drosophila was taken as an opportunity to reevaluate the
genetic and physical maps for 11 of the species, in part to
aid in the mapping of assembled scaffolds. Here, we present
an overview of the importance of cytogenetic maps to
Drosophila biology and to the concepts of chromosomal
evolution. Physical and genetic markers were used to anchor
the genome assembly scaffolds to the polytene chromosomal
maps for each species. In addition, a computational approach
was used to anchor smaller scaffolds on the basis of the
analysis of syntenic blocks. We present the chromosomal map
data from each of the 11 sequenced non-Drosophila
melanogaster species as a series of sections. Each section
reviews the history of the polytene chromosome maps for each
species, presents the new polytene chromosome maps, and
anchors the genomic scaffolds to the cytological maps using
genetic and physical markers. The mapping data agree with
Muller's idea that the majority of Drosophila genes are
syntenic. Despite the conservation of genes within
homologous chromosome arms across species, the karyotypes of
these species have changed through the fusion of chromosomal
arms followed by subsequent rearrangement
events.},
Key = {fds152669}
}
@article{fds152662,
Author = {CV Barnwell and MAF Noor},
Title = {Failure to replicate two mate preference QTLs across
multiple strains of Drosophila pseudoobscura.},
Journal = {Journal of Heredity},
Volume = {99},
Number = {6},
Pages = {653-656},
Year = {2008},
ISSN = {1465-7333},
Keywords = {Alleles • Animals • Crosses, Genetic •
Drosophila • Genotype • Quantitative Trait Loci*
• Sexual Behavior, Animal • Variation (Genetics)
• classification • genetics*},
Abstract = {Behavioral genetic mapping studies in model organisms
predominantly use crosses originating from a single pair of
inbred lines to determine the location of alleles that
confer genetic variation in the trait of interest, and they
often make sweeping generalizations about the genetic
architecture of the trait based on these results. A previous
study fine mapped mate preference variation between one pair
of Drosophila pseudoobscura lines and identified 2
strong-effect behavioral quantitative trait loci (QTLs).
Here, we replicated the previous study's mapping design to
examine the extent of variation at these behavioral QTLs
across 6 pairs of lines, but we were unable to detect
effects of either QTL region in the pairs of lines studied.
We suggest that the low-discrimination alleles at these 2
QTLs may occur at low frequency within D. pseudoobscura,
although other explanations for the inconsistency are
possible. These results underscore the need to examine
multiple strains across a species when describing the
genetic variation underlying behavioral traits.},
Key = {fds152662}
}
@article{fds139204,
Author = {Drosophila 12 Genomes Consortium (Noor is 151st author of
417)},
Title = {Evolution of genes and genomes on the Drosophila
phylogeny.},
Journal = {Nature},
Volume = {450},
Number = {7167},
Pages = {203-218},
Year = {2007},
Month = {November},
ISSN = {1476-4687},
Abstract = {Comparative analysis of multiple genomes in a phylogenetic
framework dramatically improves the precision and
sensitivity of evolutionary inference, producing more robust
results than single-genome analyses can provide. The genomes
of 12 Drosophila species, ten of which are presented here
for the first time (sechellia, simulans, yakuba, erecta,
ananassae, persimilis, willistoni, mojavensis, virilis and
grimshawi), illustrate how rates and patterns of sequence
divergence across taxa can illuminate evolutionary processes
on a genomic scale. These genome sequences augment the
formidable genetic tools that have made Drosophila
melanogaster a pre-eminent model for animal genetics, and
will further catalyse fundamental research on mechanisms of
development, cell biology, genetics, disease, neurobiology,
behaviour, physiology and evolution. Despite remarkable
similarities among these Drosophila species, we identified
many putatively non-neutral changes in protein-coding genes,
non-coding RNA genes, and cis-regulatory regions. These may
prove to underlie differences in the ecology and behaviour
of these diverse species.},
Key = {fds139204}
}
@article{fds139209,
Author = {MAF Noor and DA Garfield and SW Schaeffer and CA Machado},
Title = {Divergence Between the Drosophila pseudoobscura and D.
persimilis Genome Sequences in Relation to Chromosomal
Inversions.},
Journal = {Genetics},
Volume = {177},
Number = {3},
Pages = {1417-1428},
Year = {2007},
Month = {November},
ISSN = {0016-6731},
Abstract = {As whole-genome sequence assemblies accumulate, a challenge
is to determine how these can be used to address fundamental
evolutionary questions, such as inferring the process of
speciation. Here, we use the sequence assemblies of
Drosophila pseudoobscura and D. persimilis to test
hypotheses regarding divergence with gene flow. We observe
low differentiation between the two genome sequences in
pericentromeric and peritelomeric regions. We interpret this
result as primarily a remnant of the correlation between
levels of variation and local recombination rate observed
within populations. However, we also observe lower
differentiation far from the fixed chromosomal inversions
distinguishing these species and greater differentiation
within and near these inversions. This finding is consistent
with models suggesting that chromosomal inversions
facilitate species divergence despite interspecies gene
flow. We also document heterogeneity among the inverted
regions in their degree of differentiation, suggesting
temporal differences in the origin of each inverted region
consistent with the inversions arising during a process of
divergence with gene flow. While this study provides
insights into the speciation process using two single-genome
sequences, it was informed by lower throughput but more
rigorous examinations of polymorphism and divergence. This
reliance highlights the need for complementary genomic and
population genetic approaches for tackling fundamental
evolutionary questions such as speciation.},
Key = {fds139209}
}
@article{fds139202,
Author = {AS Chang and MAF Noor},
Title = {The genetics of hybrid male sterility between the allopatric
species pair Drosophila persimilis and D. pseudoobscura
bogotana: dominant sterility alleles in collinear autosomal
regions.},
Journal = {Genetics},
Volume = {176},
Number = {1},
Pages = {343-349},
Year = {2007},
Month = {May},
ISSN = {0016-6731},
Keywords = {Alleles* • Animals • Chromosomes • Drosophila
• Genes, Dominant* • Infertility, Male • Male
• Molecular Sequence Data • Software •
classification* • genetics*},
Abstract = {F(1) hybrid male sterility is thought to result from
interactions between loci on the X chromosome and
dominant-acting loci on the autosomes. While X-linked loci
that contribute to hybrid male sterility have been precisely
localized in many animal taxa, their dominant autosomal
interactors have been more difficult to localize precisely
and/or have been shown to be of relatively smaller effect.
Here, we identified and mapped at least four dominant
autosomal factors contributing to hybrid male sterility in
the allopatric species pair Drosophila persimilis and D.
pseudoobscura bogotana. Using these results, we tested
predictions of reduced recombination models of speciation.
Consistent with these models, three of the four QTL
associated with hybrid male sterility occur in collinear
(uninverted) regions of these genomes. Furthermore, these
QTL do not contribute significantly to hybrid male sterility
in crosses between the sympatric species D. persimilis and
D. pseudoobscura pseudoobscura. The autosomal loci
identified in this study provide the basis for introgression
mapping and, ultimately, for molecular cloning of
interacting genes that contribute to F(1) hybrid
sterility.},
Key = {fds139202}
}
@article{fds139205,
Author = {WJ Etges and CC de Oliveira and E Gragg and D Ortiz-Barrientos and MAF
Noor, MG Ritchie},
Title = {Genetics of incipient speciation in Drosophila mojavensis.
I. Male courtship song, mating success, and genotype x
environment interactions.},
Journal = {Evolution},
Volume = {61},
Number = {5},
Pages = {1106-1119},
Year = {2007},
Month = {May},
ISSN = {0014-3820},
Keywords = {Animals • Cactaceae • Drosophila • Ecosystem*
• Environment • Female • Genetic Speciation*
• Genotype • Host-Parasite Interactions •
Likelihood Functions • Male • Quantitative Trait
Loci • Reproduction • Selection (Genetics) •
Sexual Behavior, Animal* • Variation (Genetics) •
genetics • genetics* • parasitology*},
Abstract = {Few studies have examined genotype by environment (GxE)
effects on premating reproductive isolation and associated
behaviors, even though such effects may be common when
speciation is driven by adaptation to different
environments. In this study, mating success and courtship
song differences among diverging populations of Drosophila
mojavensis were investigated in a two-environment
quantitative trait locus (QTL) analysis. Baja California and
mainland Mexico populations of D. mojavensis feed and breed
on different host cacti, so these host plants were used to
culture F2 males to examine host-specific QTL effects and
GxE interactions influencing mating success and courtship
songs. Linear selection gradient analysis showed that
mainland females mated with males that produced songs with
significantly shorter L(long)-IPIs, burst durations, and
interburst intervals. Twenty-one microsatellite loci
distributed across all five major chromosomes were used to
localize effects of mating success, time to copulation, and
courtship song components. Male courtship success was
influenced by a single detected QTL, the main effect of
cactus, and four GxE interactions, whereas time to
copulation was influenced by three different QTLs on the
fourth chromosome. Multiple-locus restricted maximum
likelihood (REML) analysis of courtship song revealed
consistent effects linked with the same fourth chromosome
markers that influenced time to copulation, a number of GxE
interactions, and few possible cases of epistasis. GxE
interactions for mate choice and song can maintain genetic
variation in populations, but alter outcomes of sexual
selection and isolation, so signal evolution and
reproductive isolation may be slowed in diverging
populations. Understanding the genetics of incipient
speciation in D. mojavensis clearly depends on
cactus-specific expression of traits associated with
courtship behavior and sexual isolation.},
Key = {fds139205}
}
@article{fds139210,
Author = {C Situma and AJ Moehring and MAF Noor and SA Soper},
Title = {Immobilized molecular beacons: a new strategy using
UV-activated poly(methyl methacrylate) surfaces to provide
large fluorescence sensitivities for reporting on molecular
association events.},
Journal = {Analytical Biochemistry},
Volume = {363},
Number = {1},
Pages = {35-45},
Year = {2007},
Month = {April},
ISSN = {0003-2697},
Keywords = {Animals • Antimutagenic Agents • Base Sequence
• Biosensing Techniques • DNA Probes • DNA,
Complementary • Drosophila Proteins • Drosophila
melanogaster • Fluorescence* • Homeodomain
Proteins • Microfluidics • Molecular Sequence Data
• Nerve Tissue Proteins • Polymethyl Methacrylate
• Transcription Factors • Ultraviolet Rays* •
chemistry • chemistry* • genetics •
instrumentation* • metabolism • metabolism* •
methods • radiation effects},
Abstract = {We have designed appropriately prepared solid supports
consisting of poly(methyl methacrylate) (PMMA) that provide
enhanced performance levels for molecular beacons (MBs) that
are used for recognizing and reporting on signature DNA
sequences in solution. The attachment of primary
amine-containing MBs to the PMMA surface was carried out by
UV activating the PMMA to produce surface-confined
carboxylate groups, which could then be readily coupled to
the MBs using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide
hydrochloride (EDC) chemistry. The fluorescence properties
of the MBs covalently attached onto this UV-activated PMMA
surface were evaluated and compared with the same MBs
immobilized onto glass supports. We observed improved limits
of detection for the solution complement to the MBs when
immobilized onto PMMA, and this was attributed to both the
lower autofluorescence levels exhibited by PMMA at the
detection wavelengths used and the improved quenching
efficiency of the MBs when in their closed hairpin
configuration when strapped to a PMMA surface as opposed to
glass. As an example of the utility of the PMMA-based
immobilization strategies developed for MBs, we report on
the analysis of complementary DNAs specific for fruitless
(fru) and Ods-site homeobox (OdsH) genes extracted from
Drosophila melanogaster fruit flies. The fru gene functions
in the central nervous system, where it is necessary for sex
determination and male courtship behavior, whereas the OdsH
gene is involved in the regulation of transcription.},
Key = {fds139210}
}
@article{fds139208,
Author = {CA Machado and TS Haselkorn and MAF Noor},
Title = {Evaluation of the genomic extent of effects of fixed
inversion differences on intraspecific variation and
interspecific gene flow in Drosophila pseudoobscura and D.
persimilis.},
Journal = {Genetics},
Volume = {175},
Number = {3},
Pages = {1289-1306},
Year = {2007},
Month = {March},
ISSN = {0016-6731},
Keywords = {Animals • Base Sequence • Chromosome Breakage
• Cluster Analysis • Crossing Over, Genetic •
Drosophila • Gene Flow • Genetics, Population*
• Genome • Inversion, Chromosome • Linkage
Disequilibrium • Models, Genetic* • Molecular
Sequence Data • Polymorphism, Genetic* • Sequence
Analysis, DNA • Species Specificity • genetics
• genetics*},
Abstract = {There is increasing evidence that chromosomal inversions may
facilitate the formation or persistence of new species by
allowing genetic factors conferring species-specific
adaptations or reproductive isolation to be inherited
together and by reducing or eliminating introgression.
However, the genomic domain of influence of the inverted
regions on introgression has not been carefully studied.
Here, we present a detailed study on the consequences that
distance from inversion breakpoints has had on the inferred
level of gene flow and divergence between Drosophila
pseudoobscura and D. persimilis. We identified the locations
of the inversion breakpoints distinguishing D. pseudoobscura
and D. persimilis in chromosomes 2, XR, and XL. Population
genetic data were collected at specific distances from the
inversion breakpoints of the second chromosome and at two
loci inside the XR and XL inverted regions. For loci outside
the inverted regions, we found that distance from the
nearest inversion breakpoint had a significant effect on
several measures of divergence and gene flow between D.
pseudoobscura and D. persimilis. The data fitted a
logarithmic relationship, showing that the suppression of
crossovers in inversion heterozygotes also extends to loci
located outside the inversion but close to it (within 1-2
Mb). Further, we detected a significant reduction in
nucleotide variation inside the inverted second chromosome
region of D. persimilis and near one breakpoint, consistent
with a scenario in which this inversion arose and was fixed
in this species by natural selection.},
Key = {fds139208}
}
@article{fds52114,
Author = {D Ortíz-Barrientos and BA Counterman and MAF Noor},
Title = {Gene expression divergence and the origin of hybrid
dysfunctions.},
Journal = {Genetica},
Volume = {129},
Number = {1},
Pages = {71-81},
Year = {2007},
Month = {January},
Abstract = {Hybrids between closely related species are often sterile or
inviable as a consequence of failed interactions between
alleles from the different species. Most genetic studies
have focused on localizing the alleles associated with these
failed interactions, but the mechanistic/biochemical nature
of the failed interactions is poorly understood. This review
discusses recent studies that may contribute to our
understanding of these failed interactions. We focus on the
possible contribution of failures in gene expression as an
important contributor to hybrid dysfunctions. Although
regulatory pathways that share elements in highly divergent
taxa may contribute to hybrid dysfunction, various studies
suggest that misexpression may be disproportionately great
in regulatory pathways containing rapidly evolving,
particularly male-biased, genes. We describe three systems
that have been analyzed recently with respect to global
patterns of gene expression in hybrids versus pure species,
each in Drosophila. These studies reveal that quantitative
misexpression of genes is associated with hybrid
dysfunction. Misexpression of genes has been documented in
sterile hybrids relative to pure species, and variation in
upstream factors may sometimes cause the over- or
under-expression of genes resulting in hybrid sterility or
inviability. Studying patterns of evolution between species
in regulatory pathways, such as spermatogenesis, should help
in identifying which genes are more likely to be
contributors to hybrid dysfunction. Ultimately, we hope more
functional genetic studies will complement our understanding
of the genetic disruptions leading to hybrid dysfunctions
and their role in the origin of species.},
Key = {fds52114}
}
@article{fds52115,
Author = {ET Cirulli and RM Kliman and MAF Noor},
Title = {Fine-Scale Crossover Rate Heterogeneity in Drosophila
pseudoobscura.},
Journal = {J Mol Evol},
Volume = {64},
Pages = {129-135},
Year = {2007},
Month = {January},
Abstract = {Broad-scale differences in crossover rate across the genome
have been characterized in most genomes studied. Fine-scale
differences, however, have only been examined in a few taxa,
such as Arabidopsis, yeast, humans, and mice. No prior
studies have directly looked for fine-scale recombination
rate heterogeneity in Drosophila. We produced 370 Drosophila
pseudoobscura containing a crossover event within the
2-megabase (MB) region between the genes yellow and white.
We then examined 19 intervals within this region and
determined where the crossovers occurred. We found that
recombination events occur nonrandomly on a small scale and
that mild "hotspots" of a few kilobases exist in Drosophila.
Among the regions studied, recombination rates varied from
1.4 to 52 cM/MB. We also observed a trend toward high codon
bias in regions of high recombination. Finally, we
identified a significantly positive correlation between
recombination rate and simple repeats, as well as the motif
CACAC. These sequence features may contribute to broad-scale
variation in crossover rate and, thus, shed light on
features associated with crossover rate heterogeneity at a
genome-wide scale.},
Key = {fds52115}
}
@article{fds52118,
Author = {AJ Moehring and KC Teeter and MAF Noor},
Title = {Genome-Wide Patterns of Expression in Drosophila Pure
Species and Hybrid Males. II. Examination of
Multiple-Species Hybridizations, Platforms, and Life Cycle
Stages.},
Journal = {Mol Biol Evol},
Volume = {24},
Number = {1},
Pages = {137-145},
Year = {2007},
Month = {January},
Abstract = {Species often produce sterile hybrids early in their
evolutionary divergence, and some evidence suggests that
hybrid sterility may be associated with deviations or
disruptions in gene expression. In support of this idea,
many studies have shown that a high proportion of
male-biased genes are underexpressed, compared with
non-sex-biased genes, in sterile F(1) male hybrids of
Drosophila species. In this study, we examined and compared
patterns of misexpression in sterile F(1) male hybrids of
Drosophila simulans and 2 of its sibling species, Drosophila
mauritiana and Drosophila sechellia, at both the larval and
adult life stages. We analyzed hybrids using both commercial
Drosophila melanogaster microarrays and arrays we developed
from reverse transcriptase-polymerase chain reactions of
spermatogenesis and reproduction-related transcripts from
these species (sperm array). Although the majority of
misexpressed transcripts were underexpressed, a
disproportionate number of the overexpressed transcripts
were located on the X chromosome. We detected a high overlap
in the genes misexpressed between the 2 species pairs, and
our sperm array was better at detecting such misexpression
than the D. melanogaster array, suggesting possible
weaknesses in the use of an array designed from another
species. We found only minimal misexpression in the larval
samples with the sperm array, suggesting that disruptions in
spermatogenesis occur after this life stage. Further study
of these misexpressed loci may allow us to identify
precisely where disruptions in the spermatogenesis pathway
occur.},
Key = {fds52118}
}
@article{fds52109,
Author = {MAF Noor and JL Feder},
Title = {Speciation genetics: evolving approaches.},
Journal = {Nat Rev Genet},
Volume = {7},
Number = {11},
Pages = {851-861},
Year = {2006},
Month = {November},
Abstract = {Much progress has been made in the past two decades in
understanding Darwin's mystery of the origins of species.
Applying genomic techniques to the analysis of laboratory
crosses and natural populations has helped to determine the
genetic basis of barriers to gene flow which create new
species. Although new methodologies have not changed the
prevailing hypotheses about how species form, they have
accelerated the pace of data collection. By facilitating the
compilation of case studies, advances in genetic techniques
will help to provide answers to the next generation of
questions concerning the relative frequency and importance
of different processes that cause speciation.},
Key = {fds52109}
}
@article{fds52105,
Author = {BA Counterman and MAF Noor},
Title = {Multilocus Test for Introgression between the Cactophilic
Species Drosophila mojavensis and Drosophila
arizonae.},
Journal = {Am Nat},
Volume = {168},
Number = {5},
Pages = {682-696},
Year = {2006},
Month = {November},
Abstract = {Information obtained from laboratory studies regarding the
efficacy of barriers to gene flow (reproductive isolation)
between species is often incomplete or misleading, so
detailed genetic analyses are needed to determine whether
hybridization and introgression occur in nature. Previous
laboratory studies of the cactophilic species Drosophila
mojavensis and Drosophila arizonae suggest that reproductive
isolation is incomplete and that gene flow may occur in
sympatry. We sampled 18 nuclear and one mitochondrial loci
from multiple populations of D. arizonae and D. mojavensis
to test for the signature of recent or historic gene flow
between these two species. We located chromosomal regions
that were inverted between these species and analyzed those
regions independently of others. Statistical tests for
introgression using all loci or only collinear loci failed
to reject expectations of an isolation model. Further tests
using average nucleotide differences between species and
phylogenetic analyses also failed to find support for
introgression between D. mojavensis and D. arizonae.
Additional ecological and behavioral studies of these
species in their natural habitats are required to explain
why the signature of gene flow was not detected at the DNA
sequence level in populations when laboratory studies
suggest such gene flow should be possible.},
Key = {fds52105}
}
@article{fds52113,
Author = {MAF Noor and AS Chang},
Title = {Evolutionary genetics: jumping into a new
species.},
Journal = {Curr Biol},
Volume = {16},
Number = {20},
Pages = {R890-R892},
Year = {2006},
Month = {October},
Abstract = {A new study finds a dramatic increase in transposable
element numbers in three new sunflower hybrid species, and
may suggest a novel role for transposable elements in
speciation.},
Key = {fds52113}
}
@article{fds52108,
Author = {JP Masly and CD Jones and MAF Noor and J Locke and HA
Orr},
Title = {Gene transposition as a cause of hybrid sterility in
Drosophila.},
Journal = {Science},
Volume = {313},
Number = {5792},
Pages = {1448-1450},
Year = {2006},
Month = {September},
Abstract = {We describe reproductive isolation caused by a gene
transposition. In certain Drosophila melanogaster-D.
simulans hybrids, hybrid male sterility is caused by the
lack of a single-copy gene essential for male fertility,
JYAlpha. This gene is located on the fourth chromosome of D.
melanogaster but on the third chromosome of D. simulans.
Genomic and molecular analyses show that JYAlpha transposed
to the third chromosome during the evolutionary history of
the D. simulans lineage. Because of this transposition, a
fraction of hybrids completely lack JYAlpha and are sterile,
representing reproductive isolation without sequence
evolution.},
Key = {fds52108}
}
@article{fds52112,
Author = {MAF Noor and KJ Zimmerman and KC Teeter},
Title = {Data sharing: how much doesn't get submitted to
GenBank?},
Journal = {PLoS Biol},
Volume = {4},
Number = {7},
Pages = {e228},
Year = {2006},
Month = {July},
Key = {fds52112}
}
@article{fds52110,
Author = {MAF Noor and D Ortíz-Barrientos},
Title = {Simulating natural conditions in the laboratory: a
re-examination of sexual isolation between sympatric and
allopatric populations of Drosophila pseudoobscura and D.
persimilis.},
Journal = {Behav Genet},
Volume = {36},
Number = {2},
Pages = {322-327},
Year = {2006},
Month = {March},
Abstract = {Simulating natural conditions in the laboratory poses one of
the most significant challenges to behavioral studies. Some
authors have argued that laboratory "choice" experiments
reflect mate choice in nature more accurately than
"no-choice" experiments. A recent choice experiment study
questioned the conclusions of several earlier studies by
failing to detect a published difference in sexual isolation
between populations of Drosophila pseudoobscura, and
suggested their result was more robust because of the more
realistic design. Here, we re-examine the methods and
analyses of this recent study, and we find there was indeed
a difference in sexual isolation between populations of D.
pseudoobscura. We also conduct a more rigorously controlled
choice experiment and, in agreement with previous studies,
note that D. pseudoobscura females from populations
sympatric to their sibling species, D. persimilis, exhibit
greater sexual isolation than those from allopatric
populations. Our results confirm the existence of a
geographic pattern in sexual isolation in D. pseudoobscura,
and we discuss differences in experimental designs in light
of the biology of this species.},
Key = {fds52110}
}
@article{fds52111,
Author = {D Ortiz-Barrientos and AS Chang and MAF Noor},
Title = {A recombinational portrait of the Drosophila pseudoobscura
genome.},
Journal = {Genet Res},
Volume = {87},
Number = {1},
Pages = {23-31},
Year = {2006},
Month = {February},
Abstract = {Drosophila pseudoobscura has been intensively studied by
evolutionary biologists for over 70 years. The recent
publication of the genome sequence not only permits studies
of comparative genomics with other dipterans but also opens
the door to identifying genes associated with adaptive
traits or speciation or testing for the signature of natural
selection across the genome. Information on regional rates
of recombination, localization of inversion breakpoints
distinguishing it from its sibling species D. persimilis,
and known polymorphic markers may be useful in such studies.
Here, we present a molecular linkage map of four of the five
major chromosome arms of D. pseudoobscura. In doing so, we
order and orient several sequence contig groups, localize
the inversion breakpoints on chromosome 2 to intervals of
200 kilobases, and identify one error in the published
sequence assembly. Our results show that regional
recombination rates in D. pseudoobscura are much higher than
in D. melanogaster and significantly higher even than in D.
persimilis. Furthermore, we detect a non-significant
positive correlation between recombination rate and
published DNA sequence variation. Finally, the online
Appendix presents 200 primer sequence pairs for molecular
markers that can be used for mapping of quantitative trait
loci, of which 125 are known to be polymorphic within or
between species.},
Key = {fds52111}
}
@article{fds52102,
Author = {S. Velez and M. S. Taylor and M. A. F. Noor and N. F. Lobo and J. L.
Feder},
Title = {Isolation and characterization of microsatellite loci from
the apple maggot fly Rhagoletis pomonella (Diptera:
Tephritidae)},
Journal = {Molecular Ecology Notes},
Volume = {6},
Pages = {90-92},
Year = {2006},
Key = {fds52102}
}
@article{fds52103,
Author = {R.M. Hamill and M. A. F. Noor and E. T. Watson and M. G.
Ritchie},
Title = {New microsatellite loci for the European bushcricket,
Ephippiger ephippiger (Orthoptera: Tettigoniidae)},
Journal = {Molecular Ecology Notes},
Volume = {6},
Pages = {340-342},
Year = {2006},
Key = {fds52103}
}
@article{fds139207,
Author = {M.A.F. Noor and J. A. Coyne},
Title = {Speciation in the new millennium: What's left to
know?},
Journal = {Israel Journal of Ecology and Evolution},
Volume = {52},
Pages = {431-441},
Year = {2006},
Key = {fds139207}
}
@article{fds52107,
Author = {NP Kandul and KM Wright and EV Kandul and MAF Noor},
Title = {No evidence for learned mating discrimination in male
Drosophila pseudoobscura.},
Journal = {BMC Evol Biol},
Volume = {6},
Pages = {54},
Year = {2006},
Abstract = {BACKGROUND: Since females often pay a higher cost for
heterospecific matings, mate discrimination and species
recognition are driven primarily by female choice. In
contrast, frequent indiscriminate matings are hypothesized
to maximize male fitness. However, recent studies show that
previously indiscriminate males (e.g., Drosophila
melanogaster and Poecilia reticulata) can learn to avoid
heterospecific courtship. This ability of males to
discriminate against heterospecific courtship may be
advantageous in populations where two species co-occur if
courtship or mating is costly. RESULTS: Here, we tested
whether Drosophila pseudoobscura males learn to discriminate
against heterospecific females after being exposed to and
rejected by D. persimilis females. In most of our assays, we
failed to observe differences in D. pseudoobscura courtship
intensity of heterospecific females by males that had
previously courted heterospecific females vs. males that had
been maintained in isolation. CONCLUSION: We conclude that
learning to avoid heterospecific courtship may not be
universal, even within the genus Drosophila, and may
possibly be dependent on the natural history of the
species.},
Key = {fds52107}
}
@article{fds43245,
Author = {D Ortiz-Barrientos and MAF Noor},
Title = {Evidence for a one-allele assortative mating
locus},
Journal = {Science},
Volume = {310},
Number = {3753},
Pages = {1467},
Year = {2005},
Month = {December},
Abstract = {Theoretical models have shown that speciation with gene flow
can occur readily via a "one-allele mechanism," wherein the
spread of the same allele within both of two diverging
species reduces their subsequent hybridization. Here, we
present the first direct genetic evidence for such an allele
in Drosophila pseudoobscura. Alleles conferring high or low
assortative mating in D. pseudoobscura produce the same
effects when inserted into D. persimilis. This observation
suggests that the type of genetic variation most conducive
to controversial modes of speciation with gene flow, such as
reinforcement or sympatric speciation, is present in
nature.},
Key = {fds43245}
}
@article{fds43219,
Author = {SC Leman and Y Chen and JE Stajich and MAF Noor and MK
Uyenoyama},
Title = {Likelihoods from summary statistics: recent divergence
between species.},
Journal = {Genetics, United States},
Volume = {171},
Number = {3},
Pages = {1419-36},
Year = {2005},
Month = {November},
Abstract = {We describe an importance-sampling method for approximating
likelihoods of population parameters based on multiple
summary statistics. In this first application, we address
the demographic history of closely related members of the
Drosophila pseudoobscura group. We base the maximum-
likelihood estimation of the time since speciation and the
effective population sizes of the extant and ancestral
populations on the pattern of nucleotide variation at
DPS2002, a noncoding region tightly linked to a paracentric
inversion that strongly contributes to reproductive
isolation. Consideration of summary statistics rather than
entire nucleotide sequences permits a compact description of
the genealogy of the sample. We use importance sampling
first to propose a genealogical and mutational history
consistent with the observed array of summary statistics and
then to correct the likelihood with the exact probability of
the history determined from a system of recursions. Analysis
of a subset of the data, for which recursive computation of
the exact likelihood was feasible, indicated close agreement
between the approximate and exact likelihoods. Our results
for the complete data set also compare well with those
obtained through Metropolis-Hastings sampling of fully
resolved genealogies of entire nucleotide
sequences.},
Key = {fds43219}
}
@article{fds43218,
Author = {MAF Noor},
Title = {Patterns of evolution of genes disrupted in expression in
Drosophila species hybrids.},
Journal = {Genet Res, England},
Volume = {85},
Number = {2},
Pages = {119-25},
Year = {2005},
Month = {April},
Abstract = {Divergence between species in regulatory pathways may
contribute to hybrid incompatibilities such as sterility.
Consistent with this idea, genes involved in male fertility
often evolve faster than most other genes both in amino acid
sequence and in expression. Previously, we identified a
panel of male-specific genes under-expressed in sterile male
hybrids of Drosophila simulans and D. mauritiana relative to
pure species, and we showed that this under- expression is
associated with infertility. In a preliminary effort to
assess the generalities in the patterns of evolution of
these genes, I examined patterns of mRNA expression in three
of these genes in sterile F 1 hybrid males of D.
pseudoobscura and D. persimilis . F 1 hybrid males bearing
D. persimilis X chromosomes under-expressed all these genes
relative to the parental species, while hybrids bearing D.
pseudoobscura X chromosomes under-expressed two of these
three genes. Interestingly, the third gene, CG5762 , has
undergone extensive amino acid evolution within the D.
pseudoobscura species group, possibly driven by positive
natural selection. We conclude that some of the same genes
exhibit disruptions in expression within each of the two
species groups, which could suggest commonalities in the
regulatory architecture of sterility in these groups.
Alternative explanations are also considered.},
Key = {fds43218}
}
@article{fds43220,
Author = {S Richards and et al. (M. A. F. Noor is 45th of 52
authors)},
Title = {Comparative genome sequencing of Drosophila pseudoobscura:
chromosomal, gene, and cis-element evolution.},
Journal = {Genome Res, United States},
Volume = {15},
Number = {1},
Pages = {1-18},
Year = {2005},
Month = {January},
Abstract = {We have sequenced the genome of a second Drosophila species,
Drosophila pseudoobscura, and compared this to the genome
sequence of Drosophila melanogaster, a primary model
organism. Throughout evolution the vast majority of
Drosophila genes have remained on the same chromosome arm,
but within each arm gene order has been extensively
reshuffled, leading to a minimum of 921 syntenic blocks
shared between the species. A repetitive sequence is found
in the D. pseudoobscura genome at many junctions between
adjacent syntenic blocks. Analysis of this novel repetitive
element family suggests that recombination between offset
elements may have given rise to many paracentric inversions,
thereby contributing to the shuffling of gene order in the
D. pseudoobscura lineage. Based on sequence similarity and
synteny, 10,516 putative orthologs have been identified as a
core gene set conserved over 25-55 million years (Myr) since
the pseudoobscura/melanogaster divergence. Genes expressed
in the testes had higher amino acid sequence divergence than
the genome-wide average, consistent with the rapid evolution
of sex-specific proteins. Cis-regulatory sequences are more
conserved than random and nearby sequences between the
species--but the difference is slight, suggesting that the
evolution of cis- regulatory elements is flexible. Overall,
a pattern of repeat-mediated chromosomal rearrangement, and
high coadaptation of both male genes and cis-regulatory
sequences emerges as important themes of genome divergence
between these species of Drosophila.},
Key = {fds43220}
}
@article{fds28657,
Author = {D Ortiz-Barrientos and BA Counterman and MAF Noor},
Title = {The genetics of speciation by reinforcement.},
Journal = {PLoS Biol},
Volume = {2},
Number = {12},
Pages = {e416},
Year = {2004},
Month = {December},
Abstract = {Reinforcement occurs when natural selection strengthens
behavioral discrimination to prevent costly interspecies
matings, such as when matings produce sterile hybrids. This
evolutionary process can complete speciation, thereby
providing a direct link between Darwin's theory of natural
selection and the origin of new species. Here, by examining
a case of speciation by reinforcement in Drosophila,we
present the first high-resolution genetic study of variation
within species for female mating discrimination that is
enhanced by natural selection. We show that reinforced
mating discrimination is inherited as a dominant trait,
exhibits variability within species, and may be influenced
by a known set of candidate genes involved in olfaction. Our
results show that the genetics of reinforced mating
discrimination is different from the genetics of mating
discrimination between species, suggesting that overall
mating discrimination might be a composite phenomenon, which
in Drosophila could involve both auditory and olfactory
cues. Examining the genetics of reinforcement provides a
unique opportunity for both understanding the origin of new
species in the face of gene flow and identifying the genetic
basis of adaptive female species preferences, two major gaps
in our understanding of speciation.},
Key = {fds28657}
}
@article{fds43221,
Author = {AS Boyle and MAF Noor},
Title = {Variation in recombination rate may bias human genetic
disease mapping studies.},
Journal = {Genetica, Netherlands},
Volume = {122},
Number = {3},
Pages = {245-52},
Year = {2004},
Month = {November},
Abstract = {The availability of the human genome sequence and
variability information (as from the International HapMap
project) will enhance our ability to map genetic disorders
and choose targets for therapeutic intervention. However,
several factors, such as regional variation in recombination
rate, can bias conclusions from genetic mapping studies.
Here, we examine the impact of regional variation in
recombination rate across the human genome. Through computer
simulations and literature surveys, we conclude that genetic
disorders have been mapped to regions of low recombination
more often than expected if such diseases were randomly
distributed across the genome. This concentration in low
recombination regions may be an artifact, and disorders
appearing to be caused by a few genes of large effect may be
polygenic. Future genetic mapping studies should be
conscious of this potential complication by noting the
regional recombination rate of regions implicated in
diseases.},
Key = {fds43221}
}
@article{fds28655,
Author = {KM Brown and LM Burk and LM Henagan and MAF Noor},
Title = {A test of the chromosomal rearrangement model of speciation
in Drosophila pseudoobscura.},
Journal = {Evolution},
Volume = {58},
Number = {8},
Pages = {1856-1860},
Year = {2004},
Month = {August},
Abstract = {Recent studies suggest that chromosomal rearrangements play
a significant role in speciation by preventing recombination
and maintaining species persistence despite interspecies
gene flow. Factors conferring adaptation or reproductive
isolation are maintained in rearranged regions in the face
of hybridization, while such factors are eliminated from
collinear regions. As a direct test of this rearrangement
model, we evaluated the genetic basis of hybrid male
sterility in a sympatric species pair, Drosophila
pseudoobscura pseudoobscura and D. persimilis, and an
allopatric species pair, D. pseudoobscura bogotana and D.
persimilis. Our results are consistent with the proposed
model: virtually all of the sterility factors in the former
pair are associated with three inverted regions, whereas
sterility factors are present in the collinear regions in
the latter pair. These findings indicate recombination and
selection may have eliminated sterility factors outside the
inverted regions between D. p. pseudoobscura and D.
persimilis, suggesting chromosomal rearrangements may
facilitate species persistence despite hybridization.},
Key = {fds28655}
}
@article{fds28656,
Author = {P Michalak and MAF Noor},
Title = {Association of misexpression with sterility in hybrids of
Drosophila simulansand D. mauritiana.},
Journal = {J Mol Evol, United States},
Volume = {59},
Number = {2},
Pages = {277-82},
Year = {2004},
Month = {August},
Abstract = {Recent studies have identified genes associated with hybrid
sterility and other hybrid dysfunctions, but the
consequences of introgressions of these "speciation genes"
are often poorly understood. Previously, we identified a
panel of genes that are underexpressed in sterile male
hybrids of Drosophila simulans and D. mauritiana relative to
pure species. Here, we build on this reverse-genetics
approach to demonstrate that the underexpression of at least
five of these genes in hybrids is associated with hybrid
sterility and that these five genes are coordinately
regulated. We map one upstream regulator of these genes to a
region previously shown to harbor one or more factors
causing hybrid sterility. Finally, we show that the genes
underexpressed in hybrids are often highly conserved, as
might be predicted for downstream targets of the genetic
changes that cause hybrid sterility. This approach
integrates forward genetics with reverse genetics to show a
proximate consequence of the introgression of particular
hybrid sterility-conferring regions between species:
underexpression of genes necessary for normal
spermatogenesis.},
Key = {fds28656}
}
@article{fds43223,
Author = {R Staten and SD Schully and MAF Noor},
Title = {A microsatellite linkage map of Drosophila
mojavensis.},
Journal = {BMC Genet, England},
Volume = {5},
Pages = {12},
Year = {2004},
Month = {May},
Abstract = {BACKGROUND: Drosophila mojavensis has been a model system
for genetic studies of ecological adaptation and speciation.
However, despite its use for over half a century, no linkage
map has been produced for this species or its close
relatives. RESULTS: We have developed and mapped 90
microsatellites in D. mojavensis, and we present a detailed
recombinational linkage map of 34 of these microsatellites.
A slight excess of repetitive sequence was observed on the
X-chromosome relative to the autosomes, and the linkage
groups have a greater recombinational length than the
homologous D. melanogaster chromosome arms. We also
confirmed the conservation of Muller's elements in 23
sequences between D. melanogaster and D. mojavensis.
CONCLUSIONS: The microsatellite primer sequences and
localizations are presented here and made available to the
public. This map will facilitate future quantitative trait
locus mapping studies of phenotypes involved in adaptation
or reproductive isolation using this species.},
Key = {fds43223}
}
@article{fds43222,
Author = {BA Counterman and D Ortiz-Barrientos and MAF
Noor},
Title = {Using comparative genomic data to test for fast-X
evolution.},
Journal = {Evolution Int J Org Evolution, United States},
Volume = {58},
Number = {3},
Pages = {656-60},
Year = {2004},
Month = {March},
Abstract = {Genes may acquire nonsynonymous substitutions more rapidly
when X-linked than when autosomal, but evidence for "fast- X
evolution" has been elusive. Fast-X evolution could explain
the disproportionate contribution of X-linked genes to
hybrid sterility and other traits. Here, we use a
comparative genomic approach, with sequences of 30-110 genes
in four Drosophila species, to test for fast-X evolution.
Specifically, the 3L autosome arm in D. melanogaster and D.
simulans is homologous to the right arm of the X chromosome
in D. pseudoobscura and D. miranda. We executed two paired
comparisons to determine how often genes on this chromosome
arm exhibit higher rates of nonsynonymous substitution in
the D. pseudoobscura species group, as predicted by fast-X
evolution. We found a statistically significant pattern
consistent with fast-X evolution in one comparison and a
similar trend in the other comparison. Variation in
functional constraints across genes may have masked the
signature of fast-X evolution in some previous studies, and
we conclude paired comparisons are more powerful for
examining rates of evolution of genes when X- linked over
autosomal.},
Key = {fds43222}
}
@article{fds43224,
Author = {LS Stevison and BA Counterman and MA Noor},
Title = {Molecular evolution of X-linked accessory gland proteins in
Drosophila pseudoobscura.},
Journal = {J Hered, United States},
Volume = {95},
Number = {2},
Pages = {114-8},
Year = {2004},
Abstract = {In Drosophila melanogaster and Drosophila simulans, positive
Darwinian selection drives high rates of evolution of male
reproductive genes, and accessory gland proteins (Acps) in
particular. Here, we tested whether 13 X-linked
male-specific genes, 4 Acps and 9 non-Acps, are under
selective forces in the Drosophila pseudoobscura species
group, much as those in the D. melanogaster group. We
observed a statistically significant correlation in relative
rates of nonsynonymous evolution between the two species
groups tested. One Acp examined had a higher rate of
nonsynonymous substitution than predicted by a neutral model
in both species groups, suggesting its divergence was driven
by positive Darwinian selection. To further test for the
signature of selection, we examined polymorphism of three
Acps within D. pseudoobscura. From this test, no Acp
individually bore the signature of positive selection, but
the 3 Acps together possessed an excess of nonsynonymous
differences between species, relative to polymorphism within
species. We conclude that faster evolution of Acps in the D.
pseudoobscura group appears to be driven by positive
selection, as previously suggested in the D. melanogaster
group.},
Key = {fds43224}
}
@article{fds28659,
Author = {MAF Noor and P Michalak and D Donze},
Title = {Characterization of a male-predominant antisense transcript
underexpressed in hybrids of Drosophila pseudoobscura and D.
persimilis.},
Journal = {Genetics, United States},
Volume = {165},
Number = {4},
Pages = {1823-30},
Year = {2003},
Month = {December},
Abstract = {Characterizing genes that are misregulated in hybrids may
elucidate the genetic basis of hybrid sterility or other
hybrid dysfunctions that contribute to speciation.
Previously, a small segment of a male- predominant
transcript that is underexpressed in adult male hybrids of
Drosophila pseudoobscura and D. persimilis relative to pure
species was identified in a differential display screen.
Here, we obtained the full sequence of this 1330-bp
transcript and determined that it is an antisense message
with high sequence similarity to the D. melanogaster TRAP100
gene, part of the Mediator protein complex that regulates
transcriptional initiation during development. Both the
sense and the antisense messages are transcribed in D.
pseudoobscura, but only the sense message (TRAP100) is
transcribed in D. melanogaster complex species. Unlike the
antisense message, the sense message is transcribed
similarly in D. pseudoobscura males and females and in
hybrids of D. pseudoobscura and D. persimilis. The high
sequence similarity between distantly related species
suggests that the sense message is functionally constrained
within the genus. We speculate that the antisense transcript
may have evolved a role in male-specific
post-transcriptional regulation of TRAP100 in the D.
pseudoobscura lineage and that its underexpression in
sterile hybrid males may cause an overproduction of TRAP100
protein, possibly yielding deleterious effects.},
Key = {fds28659}
}
@article{fds28658,
Author = {P Michalak and MAF Noor},
Title = {Genome-wide patterns of expression in Drosophila pure
species and hybrid males.},
Journal = {Mol Biol Evol},
Volume = {20},
Number = {7},
Pages = {1070-1076},
Year = {2003},
Month = {July},
Abstract = {One of the most fundamental questions for understanding the
origin of species is why genes that function to cause
fertility in a pure-species genetic background fail to
produce fertility in a hybrid genetic background. A related
question is why the sex that is most often sterile or
inviable in hybrids is the heterogametic (usually male) sex.
In this survey, we have examined the extent and nature of
differences in gene expression between fertile adult males
of two Drosophila species and sterile hybrid males produced
from crosses between these species. Using oligonucleotide
microarrays and real-time quantitative polymerase chain
reaction, we have identified and confirmed that differences
in gene expression exist between pure species and hybrid
males, and many of these differences are quantitative rather
than qualitative. Furthermore, genes that are expressed
primarily or exclusively in males, including several
involved in spermatogenesis, are disproportionately
misexpressed in hybrids, suggesting a possible genetic cause
for their sterility.},
Key = {fds28658}
}
@article{fds28667,
Author = {MAF Noor and KL Grams and LA Bertucci and J Reiland},
Title = {Chromosomal inversions and the reproductive isolation of
species.},
Journal = {Proc Natl Acad Sci U S A, United States},
Volume = {98},
Number = {21},
Pages = {12084-8},
Year = {2001},
Month = {October},
Abstract = {Recent genetic studies have suggested that many genes
contribute to differences between closely related species
that prevent gene exchange, particularly hybrid male
sterility and female species preferences. We have examined
the genetic basis of hybrid sterility and female species
preferences in Drosophila pseudoobscura and Drosophila
persimilis, two occasionally hybridizing North American
species. Contrary to findings in other species groups, very
few regions of the genome were associated with these
characters, and these regions are associated also with fixed
arrangement differences (inversions) between these species.
From our results, we propose a preliminary genic model
whereby inversions may contribute to the speciation process,
thereby explaining the abundance of arrangement differences
between closely related species that co- occur
geographically. We suggest that inversions create linkage
groups that cause sterility to persist between hybridizing
taxa. The maintenance of this sterility allows the species
to persist in the face of gene flow longer than without such
inversions, and natural selection will have a greater
opportunity to decrease the frequency of interspecies
matings.},
Key = {fds28667}
}
@article{fds43217,
Author = {MA Noor},
Title = {Speciation driven by natural selection in
Drosophila.},
Journal = {Nature, ENGLAND},
Volume = {375},
Number = {6533},
Pages = {674-5},
Year = {1995},
Month = {June},
Abstract = {Reinforcement is the process by which natural selection
strengthens sexual isolation between incipient species,
reducing the frequency of maladaptive hybridization and
hence completing reproductive isolation. Although this model
of speciation was once widely accepted, its plausibility and
experimental support have been recently attacked. Here we
provide an example of speciation by reinforcement, in the
North American fruitfly Drosophila pseudoobscura. The
results suggest that females of D. pseudoobscura evolved
increased sexual isolation from their sibling species, D.
persimilis, by natural selection against maladaptive
hybridization.},
Key = {fds43217}
}
@article{fds139203,
Author = {ET Cirulli and MAF Noor},
Title = {Localization and characterization of X chromosome inversion
breakpoints separating Drosophila mojavensis and Drosophila
arizonae.},
Journal = {Journal of Heredity},
Volume = {98},
Number = {2},
Pages = {111-114},
ISSN = {0022-1503},
Keywords = {Animals • Drosophila • Female • Inversion,
Chromosome* • Male • X Chromosome* •
genetics*},
Abstract = {Ectopic exchange between transposable elements or other
repetitive sequences along a chromosome can produce
chromosomal inversions. As a result, genome sequence studies
typically find sequence similarity between corresponding
inversion breakpoint regions. Here, we identify and
investigate the breakpoint regions of the X chromosome
inversion distinguishing Drosophila mojavensis and
Drosophila arizonae. We localize one inversion breakpoint to
13.7 kb and localize the other to a 1-Mb interval. Using
this localization and assuming microsynteny between
Drosophila melanogaster and D. arizonae, we pinpoint likely
positions of the inversion breakpoints to windows of less
than 3000 bp. These breakpoints define the size of the
inversion to approximately 11 Mb. However, in contrast to
many other studies, we fail to find significant sequence
similarity between the 2 breakpoint regions. The
localization of these inversion breakpoints will facilitate
future genetic and molecular evolutionary studies in this
species group, an emerging model system for ecological
genetics.},
Key = {fds139203}
}
%% Papers Accepted
@article{fds152668,
Author = {DE Runcie and MAF Noor},
Title = {Sequence signatures of a recent chromosomal rearrangement in
Drosophila mojavensis.},
Journal = {Genetica},
Year = {2008},
Month = {July},
ISSN = {0016-6707},
Abstract = {The X-chromosome inversion, Xe, distinguishes Drosophila
mojavensis and D. arizonae. Earlier work mapped the
breakpoints of this inversion to large intervals and
provided hypotheses for the locations of the breakpoints
within 3000-bp intergenic regions on the D. mojavensis
genome sequence assembly. Here, we sequenced these regions
directly in the putatively ancestral D. arizonae
X-chromosome. We find that the two inversion breakpoints are
near an inverted gene duplication and a common repetitive
element, respectively, and these features were likely
present in the non-inverted ancestral chromosome on the D.
mojavensis lineage. Contrary to an earlier hypothesis, the
inverted gene duplication appears to predate the inversion.
We find no sequence similarity between the breakpoint
regions in the D. mojavensis ancestor, excluding an
ectopic-exchange model of chromosome rearrangements. We also
found no evidence that staggered single-strand breaks caused
the inversion. We suggest these features may have
contributed to the chromosomal breakages resulting in this
inversion.},
Key = {fds152668}
}
%% Book Chapters
@article{fds52104,
Author = {P. Michalak, and M. A. F. Noor},
Title = {Genetics of reproductive isolation and species differences
in model organisms},
Pages = {387-398},
Booktitle = {Evolutionary Genetics: Concepts and Case
Studies},
Publisher = {Oxford University Press},
Editor = {C. Fox and J. Wolf},
Year = {2006},
Key = {fds52104}
}
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