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Guy Sella - One of the best experts on this subject based on the ideXlab platform.
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life history effects on neutral diversity levels of Autosomes and sex chromosomes
Genetics, 2020Co-Authors: Guy Amster, Guy SellaAbstract:Understanding the determinants of neutral diversity patterns on Autosomes and sex chromosomes provides a bedrock for the interpretation of population genetic data; in particular, differences between the two informs our understanding of sex-specific demographic and mutation processes. While sex-specific age-structure and variation in reproductive success have long been known to affect neutral diversity, theoretical descriptions of these effects were complicated and lacking in generality, stymying attempts to relate diversity patterns of species with their life history. Here, we derive general yet simple expressions for these effects. In particular, we show that life history effects on X-to-Autosome ratios of pairwise diversity levels (X:A diversity ratios) depend only on the male-to-female ratios of mutation rates, generation times, and reproductive variances. Our results reveal that changing the male-to-female ratio of generation times has opposite effects on X:A ratios of diversity and divergence. They also explain how sex-specific life histories modulate the response of X:A diversity ratios to changes in population size. More generally, they clarify that sex-specific life history—generation times in particular—should have marked effects on X:A diversity ratios in many taxa and enable further investigation of these effects.
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life history effects on neutral diversity levels of Autosomes and sex chromosomes
Genetics, 2020Co-Authors: Guy Amster, Guy SellaAbstract:Understanding the determinants of neutral diversity patterns on Autosomes and sex chromosomes provides a bedrock for the interpretation of population genetic data; in particular, differences between the two informs our understanding of sex-specific demographic and mutation processes. While sex-specific age-structure and variation in reproductive success have long been known to affect neutral diversity, theoretical descriptions of these effects were complicated and lacking in generality, stymying attempts to relate diversity patterns of species with their life history. Here we derive general yet simple expressions for these effects. In particular, we show that life history effects on X-to-Autosome ratios of pairwise diversity levels (the X:A diversity ratio) depend only on the male-to-female ratios of mutation rates, generation times, and reproductive variances. Our results reveal that changing the male-to-female ratio of generation times has opposite effects on X:A ratios of diversity and divergence. They also explain how sex-specific life histories modulate the response of X:A diversity ratios to changes in population size. More generally, they clarify that sex-specific life history-generation times in particular-should have marked effects on X:A diversity ratios in many taxa and enable further investigation of these effects.
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life history effects on neutral polymorphism levels of Autosomes and sex chromosomes
bioRxiv, 2017Co-Authors: Guy Amster, Guy SellaAbstract:In human and other hominid (great apes) populations, estimates of the relative levels of neutral polymorphism on the X and Autosomes differ from each other and from the naive theoretical expectation of 3/4. These differences have garnered considerable attention over the past decade, with studies highlighting the potential importance of several factors, including historical changes in population size and linked selection near genes. Here, we examine a more realistic neutral model than has been considered to date, which incorporates sex- and age-dependent mortalities, fecundities, reproductive variances and mutation rates, and ask whether such a model can account for diversity levels observed far from genes. To this end, we derive analytical expressions for the X to Autosome ratio of polymorphism levels, which incorporate all of these factors and clarify their effects. In particular, our model shows that the genealogical effects of life history can be reduced to ratios of sex-specific generation times and reproductive variances. Applying our results to hominids by relying on estimated life-history parameters and approximate relationships of mutation rates to age and sex, we find that life history effects, and the effects of male and female generation times in particular, may account for much of the observed variation in X to Autosome ratios of polymorphism levels across populations and species.
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Life history effects on neutral diversity levels of Autosomes and sex chromosomes
2017Co-Authors: Guy Amster, Guy SellaAbstract:Abstract All else being equal, the ratio of genetic diversity levels on X and Autosomes at selectively neutral sites should mirror the ratio of their numbers in the population and thus equal ¾. Because X chromosomes spend twice as many generations in females as in males, however, the ratio of diversity levels is also affected by sex differences in life history. The effects of life history on diversity levels, notably those of sex-specific age structures and reproductive variances, have been studied for decades, yet existing theory relies on many parameters that are difficult to measure and lacks generality in ways that limit their applicability. We derive general yet simple expressions for these effects and show that life history effects on X-to-Autosome (X:A) ratios of diversity levels depend only on sex-ratios of mutation rates, generation times, and reproductive variances. These results reveal that changing the sex-ratio of generation times has opposite effects on X:A ratios of polymorphism and divergence. They also explain how sex-specific life histories modulate the response of X:A polymorphism ratios to changes in population size. More generally, they clarify that sex-specific life history—generation times in particular—should have a marked effect on X:A polymorphism ratios in many taxa and enable the investigation of these effects. Significance Statement Understanding the determinants of neutral diversity patterns on Autosomes and sex chromosomes provides a bedrock for our interpretation of population genetic data. Sex-specific age-structure and variation in reproductive success have long been thought to affect neutral diversity, but theoretical descriptions of these effects were complicated and/or lacked in generality, stymying attempts to relate diversity patterns of species with their life history. We derive general yet simple expressions for these effects, which clarify how they impact neutral diversity and should enable studies of relative diversity levels on the Autosomes and sex chromosomes in many taxa.
Guy Amster - One of the best experts on this subject based on the ideXlab platform.
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life history effects on neutral diversity levels of Autosomes and sex chromosomes
Genetics, 2020Co-Authors: Guy Amster, Guy SellaAbstract:Understanding the determinants of neutral diversity patterns on Autosomes and sex chromosomes provides a bedrock for the interpretation of population genetic data; in particular, differences between the two informs our understanding of sex-specific demographic and mutation processes. While sex-specific age-structure and variation in reproductive success have long been known to affect neutral diversity, theoretical descriptions of these effects were complicated and lacking in generality, stymying attempts to relate diversity patterns of species with their life history. Here, we derive general yet simple expressions for these effects. In particular, we show that life history effects on X-to-Autosome ratios of pairwise diversity levels (X:A diversity ratios) depend only on the male-to-female ratios of mutation rates, generation times, and reproductive variances. Our results reveal that changing the male-to-female ratio of generation times has opposite effects on X:A ratios of diversity and divergence. They also explain how sex-specific life histories modulate the response of X:A diversity ratios to changes in population size. More generally, they clarify that sex-specific life history—generation times in particular—should have marked effects on X:A diversity ratios in many taxa and enable further investigation of these effects.
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life history effects on neutral diversity levels of Autosomes and sex chromosomes
Genetics, 2020Co-Authors: Guy Amster, Guy SellaAbstract:Understanding the determinants of neutral diversity patterns on Autosomes and sex chromosomes provides a bedrock for the interpretation of population genetic data; in particular, differences between the two informs our understanding of sex-specific demographic and mutation processes. While sex-specific age-structure and variation in reproductive success have long been known to affect neutral diversity, theoretical descriptions of these effects were complicated and lacking in generality, stymying attempts to relate diversity patterns of species with their life history. Here we derive general yet simple expressions for these effects. In particular, we show that life history effects on X-to-Autosome ratios of pairwise diversity levels (the X:A diversity ratio) depend only on the male-to-female ratios of mutation rates, generation times, and reproductive variances. Our results reveal that changing the male-to-female ratio of generation times has opposite effects on X:A ratios of diversity and divergence. They also explain how sex-specific life histories modulate the response of X:A diversity ratios to changes in population size. More generally, they clarify that sex-specific life history-generation times in particular-should have marked effects on X:A diversity ratios in many taxa and enable further investigation of these effects.
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life history effects on neutral polymorphism levels of Autosomes and sex chromosomes
bioRxiv, 2017Co-Authors: Guy Amster, Guy SellaAbstract:In human and other hominid (great apes) populations, estimates of the relative levels of neutral polymorphism on the X and Autosomes differ from each other and from the naive theoretical expectation of 3/4. These differences have garnered considerable attention over the past decade, with studies highlighting the potential importance of several factors, including historical changes in population size and linked selection near genes. Here, we examine a more realistic neutral model than has been considered to date, which incorporates sex- and age-dependent mortalities, fecundities, reproductive variances and mutation rates, and ask whether such a model can account for diversity levels observed far from genes. To this end, we derive analytical expressions for the X to Autosome ratio of polymorphism levels, which incorporate all of these factors and clarify their effects. In particular, our model shows that the genealogical effects of life history can be reduced to ratios of sex-specific generation times and reproductive variances. Applying our results to hominids by relying on estimated life-history parameters and approximate relationships of mutation rates to age and sex, we find that life history effects, and the effects of male and female generation times in particular, may account for much of the observed variation in X to Autosome ratios of polymorphism levels across populations and species.
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Life history effects on neutral diversity levels of Autosomes and sex chromosomes
2017Co-Authors: Guy Amster, Guy SellaAbstract:Abstract All else being equal, the ratio of genetic diversity levels on X and Autosomes at selectively neutral sites should mirror the ratio of their numbers in the population and thus equal ¾. Because X chromosomes spend twice as many generations in females as in males, however, the ratio of diversity levels is also affected by sex differences in life history. The effects of life history on diversity levels, notably those of sex-specific age structures and reproductive variances, have been studied for decades, yet existing theory relies on many parameters that are difficult to measure and lacks generality in ways that limit their applicability. We derive general yet simple expressions for these effects and show that life history effects on X-to-Autosome (X:A) ratios of diversity levels depend only on sex-ratios of mutation rates, generation times, and reproductive variances. These results reveal that changing the sex-ratio of generation times has opposite effects on X:A ratios of polymorphism and divergence. They also explain how sex-specific life histories modulate the response of X:A polymorphism ratios to changes in population size. More generally, they clarify that sex-specific life history—generation times in particular—should have a marked effect on X:A polymorphism ratios in many taxa and enable the investigation of these effects. Significance Statement Understanding the determinants of neutral diversity patterns on Autosomes and sex chromosomes provides a bedrock for our interpretation of population genetic data. Sex-specific age-structure and variation in reproductive success have long been thought to affect neutral diversity, but theoretical descriptions of these effects were complicated and/or lacked in generality, stymying attempts to relate diversity patterns of species with their life history. We derive general yet simple expressions for these effects, which clarify how they impact neutral diversity and should enable studies of relative diversity levels on the Autosomes and sex chromosomes in many taxa.
Laurence D Hurst - One of the best experts on this subject based on the ideXlab platform.
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the constrained maximal expression level owing to haploidy shapes gene content on the mammalian x chromosome
PLOS Biology, 2015Co-Authors: Laurence D Hurst, Avazeh T Ghanbarian, Alistair R R Forrest, Lukasz HuminieckiAbstract:X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on Autosomes: on average, maximal expression is three times lower on the X chromosome than on Autosomes. Similarly, Autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-Autosome retrogenes on Autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution.
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timing of replication is a determinant of neutral substitution rates but does not explain slow y chromosome evolution in rodents
Molecular Biology and Evolution, 2010Co-Authors: Catherine Pink, Laurence D HurstAbstract:Mutation rates, assayed as substitution rates of putatively neutral sites, are highly variable around mammalian genomes: There is heterogeneity between genes, between Autosomes, and between X, Y, and Autosomes. The differences between X, Y, and Autosomes are typically assumed to reflect the greater number of cell divisions in the male germ-line. Such an effect can neither account for within-Autosome differences nor does it predict the differences between X, Y, and Autosome observed in rodents. It has recently been proposed that in primates, the time during S-phase when a gene is replicated is an important determinant of neutral rates of evolution. Here we ask 1) whether we can replicate this result in rodents, 2) whether different Autosomes replicate on average at different times, and 3) whether this might explain differences in their substitution rates. Finally we ask 4) whether X, Y, and Autosome replicate at different times and 5) whether any difference might explain why the number of replication events alone cannot explain their substitution rates. We find that, as in primates, autosomal intronic rates of evolution increase significantly during S-phase. Different Autosomes do have different average replication times, and together with rearrangement, this is a significant predictor of between-Autosome differences in substitution rate. Although we find that autosomal, X-, and Y-linked genes replicate at different times, it is paradoxical that the Y-linked genes replicate latest, and replicate more often, but are not especially fast evolving. These results support the hypothesis that replication timing is an important source of substitution rate heterogeneity.
Lukasz Huminiecki - One of the best experts on this subject based on the ideXlab platform.
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the constrained maximal expression level owing to haploidy shapes gene content on the mammalian x chromosome
PLOS Biology, 2015Co-Authors: Laurence D Hurst, Avazeh T Ghanbarian, Alistair R R Forrest, Lukasz HuminieckiAbstract:X chromosomes are unusual in many regards, not least of which is their nonrandom gene content. The causes of this bias are commonly discussed in the context of sexual antagonism and the avoidance of activity in the male germline. Here, we examine the notion that, at least in some taxa, functionally biased gene content may more profoundly be shaped by limits imposed on gene expression owing to haploid expression of the X chromosome. Notably, if the X, as in primates, is transcribed at rates comparable to the ancestral rate (per promoter) prior to the X chromosome formation, then the X is not a tolerable environment for genes with very high maximal net levels of expression, owing to transcriptional traffic jams. We test this hypothesis using The Encyclopedia of DNA Elements (ENCODE) and data from the Functional Annotation of the Mammalian Genome (FANTOM5) project. As predicted, the maximal expression of human X-linked genes is much lower than that of genes on Autosomes: on average, maximal expression is three times lower on the X chromosome than on Autosomes. Similarly, Autosome-to-X retroposition events are associated with lower maximal expression of retrogenes on the X than seen for X-to-Autosome retrogenes on Autosomes. Also as expected, X-linked genes have a lesser degree of increase in gene expression than autosomal ones (compared to the human/Chimpanzee common ancestor) if highly expressed, but not if lowly expressed. The traffic jam model also explains the known lower breadth of expression for genes on the X (and the Z of birds), as genes with broad expression are, on average, those with high maximal expression. As then further predicted, highly expressed tissue-specific genes are also rare on the X and broadly expressed genes on the X tend to be lowly expressed, both indicating that the trend is shaped by the maximal expression level not the breadth of expression per se. Importantly, a limit to the maximal expression level explains biased tissue of expression profiles of X-linked genes. Tissues whose tissue-specific genes are very highly expressed (e.g., secretory tissues, tissues abundant in structural proteins) are also tissues in which gene expression is relatively rare on the X chromosome. These trends cannot be fully accounted for in terms of alternative models of biased expression. In conclusion, the notion that it is hard for genes on the Therian X to be highly expressed, owing to transcriptional traffic jams, provides a simple yet robustly supported rationale of many peculiar features of X's gene content, gene expression, and evolution.
Genevieve Leducrobert - One of the best experts on this subject based on the ideXlab platform.
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multiple origins of sex chromosome fusions correlated with chiasma localization in habronattus jumping spiders araneae salticidae
Evolution, 2013Co-Authors: Wayne P Maddison, Genevieve LeducrobertAbstract:Entelegyne spiders rarely show fusions yielding neo-Y chromosomes, which M. J. D. White attributed to a constraint in spiders, namely their proximal chiasma localization acting to upset meiotic segregation in males with fusions. Of the 75 taxa of Habronattus and outgroups studied, 47 have X1 X2 0 sex chromosomes in males, 10 have X1 X2 Y, 15 have X1 X2 X3 Y, 2 have X0, and one has both X1 X2 0 and X1 X2 X3 Y. Chromosome numbers and behavior suggest neo-Ys formed by an Autosome-X fusion to make X1 X2 Y, with a second fusion to an Autosome to make X1 X2 X3 Y. Phylogeny shows at least 8-15 gains (or possibly some losses) of neo-Y (i.e., X-Autosome fusions), a remarkable number for such a small clade. In contrast to the many X-Autosome fusions, at most one Autosome-Autosome fusion is indicated. Origins of neo-Y are correlated significantly with distal localization of chiasmata, supporting White's hypothesis that evolution of neo-Y systems is facilitated by looser pairing (distal chiasmata) at meiosis. However, an alternative (or contributing) explanation for the correlation is that X-Autosome fusions were selected to permit isolation of male-favored alleles to the neo-Y chromosome, aided by distal chiasmata limiting recombination. This intralocus sexual conflict hypothesis could explain both the many X-Autosome fusions, and the stunning complexity of male Habronattus courtship displays.