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345 results for “Sex chromosome”
Data from: A sex chromosome polymorphism maintains divergent plumage phenotypes between extensively hybridizing yellowhammers (Emberiza citrinella) and pine buntings (E. leucocephalos)
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Data from: Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark
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Data from: Phylogenomics resolves key relationships in Rumex and uncovers a dynamic history of independently evolving sex chromosomes
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Range-wide study in a sexually polymorphic wild strawberry reveals climatic and soil associations of sex ratio, sexual dimorphism, and sex chromosomes
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Data from: Conserved ZZ/ZW sex chromosomes in Caribbean croaking geckos (Aristelliger : Sphaerodactylidae)
<p>Current understanding of sex chromosome evolution is largely dependent on species with highly degenerated, heteromorphic sex chromosomes, but by studying species with recently evolved or morphologically indistinct sex chromosomes we can greatly increase our understanding of sex chromosome origins, degeneration, and turnover. Here, we examine sex chromosome evolution and stability in the gecko genus Aristelliger. We used RADseq to identify sex-specific markers and show that four Aristelliger species, spanning the phylogenetic breadth of the genus, share a conserved ZZ/ZW system syntenic with avian chromosome two. These conserved sex chromosomes contrast with many other gecko sex chromosome systems by showing a degree of stability among a group known for its dynamic sex determining mechanisms. Cytogenetic data from A. expectatus revealed homomorphic sex chromosomes with an accumulation of repetitive elements on the W chromosome. Taken together, the large number of female-specific A. praesignis RAD markers and the accumulation of repetitive DNA on the A. expectatus W karyotype suggests that the Z and W chromosomes are highly differentiated despite their overall morphological similarity. We discuss this paradoxical situation and suggest that it may, in fact, be common in many animal species.</p>
Sex-linked markers by genome-wide RAD sequencing to identify XX/XY Sex Chromosomes in the spiny frog (Quasipaa boulengeri)
<p><span>We use genotyping by sequencing as an approach to identify sex-linked markers in the spiny frog <i>Quasipaa boulengeri</i> with 43 wild-collected adults from a single site. The GBS methodology identified 2 loci on sex differences in allele frequencies, 50 loci on sex differences in heterozygosity, and 523 loci on male-limited occurrence, altogether associated with males heterogamety, indicating an XX-XY system. The sex specificity of five markers was further validated by PCR amplification with a large number of additional individuals from 26 various populations in this species. A total of 27 sex linkage markers were matched to Dmrt1 gene, a ubiquitous role in sex determination and differentiation from flies and nematodes to mammals. Chromosome 1, that harboring Dmrt1, has further been assigned to a highly potential candidate sex chromosome in anurans. Five sex-linked SNP makers explored 3 sex reversals out of 133 individuals here, sparsely showing sex reversal detected in wild amphibian populations. </span></p>
High elevation increases the risk of Y chromosome loss in Alpine skink populations with sex reversal
<p>The view genotypic sex determination (GSD) and environmental sex determination (ESD) are mutually exclusive states has been contradicted by the discovery that chromosomal sex and environmental influences can co-exist within the same species, hinting at a continuum of intermediate states. Systems where genes and the environment interact to determine sex present the opportunity for sex reversal to occur, where the phenotypic sex is the opposite of that predicted by their sex chromosome complement. The skink Bassiana duperreyi has XX:XY sex chromosomes with sex reversal of the XX genotype to a male phenotype in response to exposure to cold incubation temperatures. Here we studied the frequency of sex reversal in B. duperreyi in response to climatic variation, using elevation as a surrogate for environmental temperatures. We demonstrate sex reversal for the first time in free-ranging adults of a reptile species with XX/XY sex determination. The highest frequency of sex reversal occurred at the highest elevation location, Mount Ginini (18.64%) and decreases in frequency with elevation. We model the impact of this under Fisher's frequency dependent selection to show that, only at the highest elevations, populations risk the loss of the Y chromosome and a transition to TSD. This study contributes to our understanding of the risks of extinction from climate change in species subject to sex reversal by temperature, and will provide focus for future research to test on-the-ground management strategies to mitigate the effects of climate in local populations.</p> <div> <div> <div class="msocomtxt"> <p class="MsoCommentText"> </p> </div> </div> </div>
Widespread recombination suppression facilitates plant sex chromosome evolution
<p>Classical models suggest that recombination rates on sex chromosomes evolve in a stepwise manner to localize sexually antagonistic variants in the sex in which they are beneficial, thereby lowering rates of recombination between X and Y chromosomes. However, it is also possible that sex chromosome formation occurs in regions with pre-existing recombination suppression. To evaluate these possibilities, we constructed linkage maps and a chromosome-scale genome assembly for the dioecious plant <i>Rumex hastatulus</i>. This species has a polymorphic karyotype with a young neo-sex chromosome, resulting from a Robertsonian fusion between the X chromosome and an autosome, in part of its geographical range. We identified the shared and neo-sex chromosome using comparative genetic maps of the two cytotypes. We found that sex-linked regions of both the ancestral and the neo-sex chromosome are embedded in large regions of low recombination. Furthermore, our comparison of the recombination landscape of the neo-sex chromosome to its autosomal homologue indicates that low recombination rates preceded sex linkage. These patterns are not unique to the sex chromosomes; all chromosomes were characterized by massive regions of suppressed recombination spanning most of each chromosome. This represents an extreme case of the periphery-biased recombination seen in other systems with large chromosomes. Across all chromosomes, gene and repetitive sequence density correlated with recombination rate, with patterns of variation differing between repetitive element type. Our findings suggest that ancestrally low rates of recombination may facilitate the formation and subsequent evolution of heteromorphic sex chromosomes.</p>
Data from: Sex is determined by XY chromosomes across the radiation of dioecious Nepenthes pitcher plants
Species with separate sexes (dioecy) are a minority among flowering plants, but dioecy has evolved multiple times independently in their history. The sex determination system and sex-linked genomic regions are currently identified in a limited number of dioecious plants only. Here, we study the sex-determination system in a genus of dioecious plants that lack heteromorphic sex chromosomes and are not amenable to controlled breeding: <i>Nepenthes</i> pitcher plants. We genotyped wild populations of flowering males and females of three <i>Nepenthes</i> taxa using ddRAD-seq, and sequenced a male inflorescence transcriptome. We developed a statistical tool (privacy rarefaction) to distinguish true sex-specificity from stochastic noise in read coverage of sequencing data from wild populations and identified male-specific loci and XY-patterned SNPs in all three <i>Nepenthes</i> taxa, suggesting the presence of homomorphic XY sex chromosomes. The male-specific region of the Y chromosome showed little conservation among the three taxa, except for the essential pollen development gene DYT1 which was confirmed as male-specific by PCR in additional <i>Nepenthes</i> taxa. Hence, dioecy and part of the male-specific region of the <i>Nepenthes</i> Y-chromosomes likely have a single evolutionary origin.
Data from: Genetic responsiveness of African buffalo to environmental stressors: a role for epigenetics in balancing autosomal and sex chromosome interactions?
In the African buffalo (Syncerus caffer) population of the Kruger National Park (South Africa) a primary sex-ratio distorter and a primary sex-ratio suppressor have been shown to occur on the Y chromosome. A subsequent autosomal microsatellite study indicated that two types of deleterious alleles with a negative effect on male body condition, but a positive effect on relative fitness when averaged across sexes and generations, occur genome-wide and at high frequencies in the same population. One type negatively affects body condition of both sexes, while the other acts antagonistically: it negatively affects male but positively affects female body condition. Here we show that high frequencies of male-deleterious alleles are attributable to Y-chromosomal distorter-suppressor pair activity and that these alleles are suppressed in individuals born after three dry pre-birth years, likely through epigenetic modification. Epigenetic suppression was indicated by statistical interactions between pre-birth rainfall, a proxy for parental body condition, and the phenotypic effect of homozygosity/heterozygosity status of microsatellites linked to male-deleterious alleles, while a role for the Y-chromosomal distorter-suppressor pair was indicated by between-sex genetic differences among pre-dispersal calves. We argue that suppression of male-deleterious alleles results in negative frequency-dependent selection of the Y distorter and suppressor; a prerequisite for a stable polymorphism of the Y distorter-suppressor pair. The Y distorter seems to be responsible for positive selection of male-deleterious alleles during resource-rich periods and the Y suppressor for positive selection of these alleles during resource-poor periods. Male-deleterious alleles were also associated with susceptibility to bovine tuberculosis, indicating that Kruger buffalo are sensitive to stressors such as diseases and droughts. We anticipate that future genetic studies on African buffalo will provide important new insights into gene fitness and epigenetic modification in the context of sex-ratio distortion and infectious disease dynamics.
Sex-biased gene content associates with sex chromosome turnover in Danaini butterflies
<p>Sex chromosomes play an outsized role in adaptation and speciation, and thus deserve particular attention in evolutionary genomics. In particular, fusions between sex chromosomes and autosomes can produce neo-sex chromosomes, which offer important insights into the evolutionary dynamics of sex chromosomes. Here we investigate the evolutionary origin of the previously reported <em>Danaus</em> neo-sex chromosome within the tribe Danaini. We assembled and annotated genomes of <em>Tirumala septentrionis</em> (subtribe Danaina), <em>Ideopsis similis</em> (Amaurina), <em>Idea leuconoe</em> (Euploeina), and <em>Lycorea halia</em> (Itunina) and identified their Z-linked scaffolds. We found that the <em>Danaus </em>neo-sex chromosome resulting from the fusion between a Z chromosome and an autosome corresponding to the <em>Melitaea cinxia</em> chromosome (McChr) 21 arose in a common ancestor of Danaina, Amaurina, and Euploina. We also identified two additional fusions as the W chromosome further fused with the synteny block McChr31 in <em>I. similis</em> and independent fusion occurred between the ancestral Z chromosome and McChr12 in <em>L. halia</em>. We further tested a possible role of sexually antagonistic selection in sex chromosome turnover by analyzing the genomic distribution of sex-biased genes in <em>I. leuconoe</em> and <em>L. halia</em>. The autosomes corresponding to McChr21 and McChr31 involved in the fusions are significantly enriched in female- and male-biased genes, respectively, which could have hypothetically facilitated fixation of the neo-sex chromosomes. This suggests a role of sexual antagonism in sex chromosome turnover in Lepidoptera. The neo-Z chromosomes of both <em>I. leuconoe</em> and <em>L. halia</em> appear fully compensated in somatic tissues, but the extent of dosage compensation for the ancestral Z is variable across tissues and species.</p>
Heterogeneous histories of recombination suppression on stickleback sex chromosomes
<p>How consistent are the evolutionary trajectories of sex chromosomes shortly after they form? Insights into the evolution of recombination, differentiation, and degeneration can be provided by comparing closely related species with homologous sex chromosomes. The sex chromosomes of the threespine stickleback (<em>Gasterosteus aculeatus</em>) and its sister species, the Japan Sea stickleback (<em>G. nipponicus)</em>, have been well characterized. Little is known, however, about the sex chromosomes of their congener, the blackspotted stickleback (<em>G. wheatlandi</em>). We used pedigrees to obtain experimentally phased whole genome sequences from blackspotted stickleback X and Y chromosomes. Using multispecies gene trees and analysis of shared duplications, we demonstrate that Chromosome 19 is the ancestral sex chromosome and that its oldest stratum evolved in the common ancestor of the genus. After the blackspotted lineage diverged, its sex chromosomes experienced independent and more extensive recombination suppression, greater X-Y differentiation, and a much higher rate of Y degeneration than the other two species. These patterns may result from a smaller effective population size in the blackspotted stickleback. A recent fusion between the ancestral blackspotted stickleback Y chromosome and Chromosome 12, which produced a neo-X and neo-Y, may have been favored by the very small size of the recombining region on the ancestral sex chromosome. We identify six strata on the ancestral and neo-sex chromosomes where recombination between the X and Y ceased at different times. These results confirm that sex chromosomes can evolve large differences within and between species over short evolutionary timescales.</p>
Data and code from: Multiple sex chromosome drivers in a mammal with three sex chromosomes
<p><span>Eukaryotes with separate males and females display a great diversity in the way they determine sex, but it is still unclear what evolutionary forces cause transitions between sex-determining systems. Rather that the lack of hypotheses, the problem is the scarcity of adequate biological systems to test them. Here, we take advantage of the recent evolution of a feminizing X chromosome (called X*) in the African pygmy mouse <em>Mus minutoides</em>, to investigate one of the evolutionary forces hypothesized to cause such transitions, namely sex chromosome drive (i.e., biased transmission of sex chromosomes to the next generation). Through extensive molecular sexing of pups at weaning, we reveal the existence of a remarkable male sex chromosome drive system in this species, whereby direction and strength of drive is conditional upon the genotype of males' partners: males transmit their Y at a rate close to 80% when mating with XX or XX* females, and only 36% when mating with X*Y females. Using mathematical modelling, we explore the joint evolution of these unusual sex-determining and drive systems, revealing that different sequences of events could have led to the evolution of this bizarre system, and that the "conditional" nature of sex chromosome drive plays a crucial role in the short- and long-term maintenance of the three sex chromosomes.</span></p>
Data for: New insights into Xenopus sex chromosome genomics from the Marsabit clawed frog, X. borealis
<p><span>In many groups, sex chromosomes change frequently but the drivers of their rapid evolution are varied and often poorly characterized. With an aim of further understanding sex chromosome turnover, we investigated the polymorphic sex chromosomes of the Marsabit clawed frog, <em>Xenopus borealis,</em> using genomic data and a new chromosome-scale genome assembly. We confirmed previous findings that 54.1 Mb of chromosome 8L is sex-linked in animals from east Kenya and a lab strain, but most (or all) of this region is not sex-linked in natural populations from west Kenya. Previous work suggests possible degeneration of the Z chromosomes in the east population because many sex-linked transcripts of this female heterogametic population have female-biased expression, and we therefore expected this chromosome to not be present in the west population. In contrast, our simulations support a model where the sex-linked portion of the Z chromosome from the east acquired autosomal segregation in the west, and where the W chromosome from the east was lost in the west. These recent changes are consistent with the hot potato model, wherein sex chromosome turnover is favoured by natural selection if it purges a (minimally) degenerate sex-specific sex chromosome, but counterintuitively suggest natural selection failed to purge a Z chromosome that has signs of more advanced and possibly more ancient regulatory degeneration. These findings highlight complex evolutionary dynamics of young, rapidly evolving <em>Xenopus</em> sex chromosomes, and set the stage for mechanistic work aimed at pinpointing additional sex-determining genes in this group.</span></p>
A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds
<p><span>We report the discovery of a novel neo-sex chromosome in an African warbler, <em>Sylvietta brachyura</em> (northern crombec; Macrosphenidae). This species is part of the Sylvioidea superfamily, where four separate autosome–sex chromosome translocation events have previously been discovered via comparative genomics of 11 of the 22 families in this clade. Our discovery here resulted from analyses of genomic data of single-species representatives from three additional Sylvioidea families (Macrosphenidae, Pycnonotidae, and Leiothrichidae). In all three species, we confirmed the translocation of a part of chromosome 4A to the sex chromosomes, which originated basally in Sylvioidea. In <em>S. brachyura</em>, we found that a part of chromosome 8 has been translocated to the sex chromosomes, forming a unique neo-sex chromosome in this lineage. Furthermore, the non-recombining part of 4A in <em>S. brachyura</em> is smaller than in other Sylvioidea species which suggests that recombination continued along this region after the fusion event in the Sylvioidea ancestor. These findings reveal additional sex chromosome diversity among the Sylvioidea, where five separate translocation events are now confirmed.</span></p>
Heterogeneous evolution of sex chromosomes in the torrent frog genus Amolops
<p>In sharp contrast with birds and mammals, sex chromosomes have been described as homomorphic in cold-blooded vertebrates. This sex-chromosome homomorphy has been suggested to result from high turnovers when they are often observed across deeply diverged clades. However, little is known about the tempo and mode of sex chromosome evolution among most closely related species. Here, we examine patterns of sex chromosome evolution among nine species of the torrent frog genus <em>Amolops</em>. Through the analysis of male and female GBS and RAD-seq from 182 individuals and of PCR verification for 176 individuals, we identify signatures of sex chromosomes involving two pairs of chromosomes. We find that the sex-chromosome homomorphy results from both turnover and X–Y recombination in the <em>Amolops</em> species, simultaneously exhibiting heterogeneous evolution on homologous and non-homologous sex chromosomes. The lower turnover rate of non-homologous sex chromosomes exists in these torrent frogs, whereas the ongoing X–Y recombination in homologous sex chromosomes would act as an indispensable force to prevent the sex chromosomes from differentiations. </p>
Supplementary material 1 from: Steinberg E, Nieves M, Mudry M (2014) Multiple sex chromosome systems in howler monkeys (Platyrrhini, Alouatta). Comparative Cytogenetics 8(1): 43-69. https://doi.org/10.3897/compcytogen.v8i1.6716
Data matrix. (doi: 10.3897/CompCytogen.v8i1.6716.app1) File format: Microsoft Word file (doc).:
Data from: The role of conflict in the formation and maintenance of variant sex chromosome systems in mammals
<p>The XX/XY sex chromosome system is deeply conserved in therian mammals, as is the role of <em>Sry</em> in testis determination, giving the impression of stasis relative to other taxa. However, the long tradition of cytogenetic studies in mammals documents sex chromosome karyotypes that break this norm in myriad ways, ranging from fusions between sex chromosomes and autosomes to Y chromosome loss. Evolutionary conflict, in the form of sexual antagonism or meiotic drive, is the primary predicted driver of sex chromosome transformation and turnover. Yet conflict-based hypotheses are less considered in mammals, perhaps because of the perceived stability of the sex chromosome system. To address this gap, we catalogue and characterize all described sex chromosome variants in mammals, test for family-specific rates of accumulation, and consider the role of conflict between the sexes or within the genome in the evolution of these systems. We identify 152 species with sex chromosomes that differ from the ancestral state and find evidence for different rates of ancestral to derived transitions among families. Sex chromosome-autosome fusions account for 80% of all variants whereas documented sex chromosome fissions are limited to three species. We propose that meiotic drive and drive suppression provide viable explanations for the evolution of many of these variant systems, particularly those involving autosomal fusions. We highlight taxa particularly worthy of further study and provide experimental predictions for testing the role of conflict and its alternatives in generating observed sex chromosome diversity.</p>
Data from: Rewinding the ratchet: Rare recombination locally rescues neo-W degeneration and generates plateaus of sex-chromosome divergence
<p>Natural selection is less efficient in the absence of recombination. As a result, non-recombining sequences, such as sex chromosomes, tend to degenerate over time. Although the outcomes of recombination arrest are typically observed after many millions of generations, recent neo-sex chromosomes can give insight into the early stages of this process. Here we investigate the evolution of neo-sex chromosomes in the Spanish marbled white butterfly, <em>Melanargia ines</em>, where a Z-autosome fusion has turned the homologous autosome into a non-recombining neo-W chromosome. We show that these neo-sex chromosomes are likely limited to the Iberian population of <em>M. ines</em>, and that they arose around the time when this population split from North-African populations, around 1.5 million years ago. Recombination arrest of the neo-W chromosome has led to an excess of premature stop codons and frameshift mutations, and reduced gene expression compared to the neo-Z chromosome. Surprisingly, we identified two regions of 1 Mb at one end of the neo-W that are both less diverged from the neo-Z and less degraded than the rest of the chromosome, suggesting a history of rare but repeated genetic exchange between the two neo-sex chromosomes. These plateaus of neo-sex chromosome divergence suggest that neo-W degradation can be locally reversed by rare recombination between neo-W and neo-Z chromosomes.</p>
R codes prepared for the manuscript, entitled "The roles of Y chromosomal genes in mouse sex spectrum phenotypes"
<p>R codes for the manuscript, entitled "The roles of Y chromosomal genes in mouse sex spectrum phenotypes" </p>
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