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D Charlesworth - One of the best experts on this subject based on the ideXlab platform.
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evolution of recombination rates between Sex Chromosomes
Philosophical Transactions of the Royal Society B, 2017Co-Authors: D CharlesworthAbstract:In species with genetic Sex-determination, the Chromosomes carrying the Sex-determining genes have often evolved non-recombining regions and subsequently evolved the full set of characteristics denoted by the term 'Sex Chromosomes'. These include size differences, creating chromosomal heteromorphism, and loss of gene functions from one member of the chromosome pair. Such characteristics and changes have been widely reviewed, and underlie molecular genetic approaches that can detect Sex chromosome regions. This review deals mainly with the evolution of new non-recombining regions, focusing on how certain evolutionary situations select for suppressed recombination (rather than the proximate mechanisms causing suppressed recombination between Sex Chromosomes). Particularly important is the likely involvement of Sexually antagonistic polymorphisms in genome regions closely linked to Sex-determining loci. These may be responsible for the evolutionary strata of Sex Chromosomes that have repeatedly formed by recombination suppression evolving across large genome regions. More studies of recently evolved non-recombining Sex-determining regions should help to test this hypothesis empirically, and may provide evidence about whether other situations can sometimes lead to Sex-linked regions evolving. Similarities with other non-recombining genome regions are discussed briefly, to illustrate common features of the different cases, though no general properties apply to all of them.This article is part of the themed issue 'Evolutionary causes and consequences of recombination rate variation in Sexual organisms'.
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plant Sex Chromosomes
Annual Review of Plant Biology, 2016Co-Authors: D CharlesworthAbstract:Although individuals in most flowering plant species, and in many haploid plants, have both Sex functions, dioecious species-in which individuals have either male or female functions only-are scattered across many taxonomic groups, and many species have genetic Sex determination. Among these, some have visibly heteromorphic Sex Chromosomes, and molecular genetic studies are starting to uncover Sex-linked markers in others, showing that they too have fully Sex-linked regions that are either too small or are located in Chromosomes that are too small to be cytologically detectable from lack of pairing, lack of visible crossovers, or accumulation of heterochromatin. Detailed study is revealing that, like animal Sex Chromosomes, plant Sex-linked regions show evidence for accumulation of repetitive sequences and genetic degeneration. Estimating when recombination stopped confirms the view that many plants have young Sex-linked regions, making plants of great interest for studying the timescale of these changes.
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the evolution of restricted recombination in Sex Chromosomes
Trends in Ecology and Evolution, 2009Co-Authors: Roberta Bergero, D CharlesworthAbstract:In species with separate Sexes, Sex determination often has a genetic basis, and in a wide diversity of taxa a pair of cytologically distinguishable 'Sex Chromosomes' are found such that the chromosome complements of males and females differ (males are often XY and females XX, but sometimes females are ZW whereas males are ZZ). Recent evidence from sequences of Sex-linked genes confirms classical genetic evidence that these Chromosomes are a homologous pair, evolved from a normal chromosome pair, between which recombination stopped. We discuss why Sex Chromosomes evolve reduced recombination and why different parts of the Chromosomes stopped recombining at different times, and outline some of the consequences of suppressed recombination, including the evolution of chromosome heteromorphism.
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steps in the evolution of heteromorphic Sex Chromosomes
Heredity, 2005Co-Authors: D Charlesworth, Brian Charlesworth, Gabriel A B MaraisAbstract:We review some recently published results on Sex Chromosomes in a diversity of species. We focus on several fish and some plants whose Sex Chromosomes appear to be 'young', as only parts of the chromosome are nonrecombining, while the rest is pseudoautosomal. However, the age of these systems is not yet very clear. Even without knowing what proportions of their genes are genetically degenerate, these cases are of great interest, as they may offer opportunities to study in detail how Sex Chromosomes evolve. In particular, we review evidence that recombination suppression occurs progressively in evolutionarily independent cases, suggesting that selection drives loss of recombination over increasingly large regions. We discuss how selection during the period when a chromosome is adapting to its role as a Y chromosome might drive such a process.
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Plant Sex determination and Sex Chromosomes
Heredity, 2002Co-Authors: D CharlesworthAbstract:Sex determination systems in plants have evolved many times from hermaphroditic ancestors (including monoecious plants with separate male and female flowers on the same individual), and Sex chromosome systems have arisen several times in flowering plant evolution. Consistent with theoretical models for the evolutionary transition from hermaphroditism to monoecy, multiple Sex determining genes are involved, including male-sterility and female-sterility factors. The requirement that recombination should be rare between these different loci is probably the chief reason for the genetic degeneration of Y Chromosomes. Theories for Y chromosome degeneration are reviewed in the light of recent results from genes on plant Sex Chromosomes.
Doris Bachtrog - One of the best experts on this subject based on the ideXlab platform.
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Dosage compensation and neo-Sex Chromosomes in Drosophila.
2019Co-Authors: Christopher Ellison, Doris BachtrogAbstract:(A) MSL-mediated dosage compensation in Drosophila. The MSL complex consists of several proteins and noncoding RNAs (roX RNAs) and targets the X chromosome at CESs that contain the MSL-binding motif (as GA-rich sequence motif). (B) Formation of neo-Sex Chromosomes in Drosophila. The ancestral karyotype of Drosophila consists of five large rods (the ancestral X, which is conserved across Drosophila, and the autosomal arms Muller element B, C, D, and E) and the small dot chromosome (Muller element F). Autosomes repeatedly fused to the Sex Chromosomes, forming neo-X and neo-Y Chromosomes. Loss of genes on the neo-Y creates selective pressure to dosage compensate neo-X genes and has repeatedly evolved in Drosophila by co-opting the MSL complex through the acquisition of novel MSL-binding sites. (C) ChIRP can be used to identify MSL-binding sites on Drosophila Sex Chromosomes. The roX RNA is bound in vivo to CESs; chromatin is cross-linked and fragmented, and roX2 is affinity purified and sequenced. CES, chromatin entry site; ChIRP, Chromatin Isolation by RNA Purification; MSL, male-specific lethal.
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Sex determination Sex Chromosomes and karyotype evolution in insects
Journal of Heredity, 2017Co-Authors: Heath Blackmon, Laura Ross, Doris BachtrogAbstract:: Insects harbor a tremendous diversity of Sex determining mechanisms both within and between groups. For example, in some orders such as Hymenoptera, all members are haplodiploid, whereas Diptera contain species with homomorphic as well as male and female heterogametic Sex chromosome systems or paternal genome elimination. We have established a large database on karyotypes and Sex Chromosomes in insects, containing information on over 13000 species covering 29 orders of insects. This database constitutes a unique starting point to report phylogenetic patterns on the distribution of Sex determination mechanisms, Sex Chromosomes, and karyotypes among insects and allows us to test general theories on the evolutionary dynamics of karyotypes, Sex Chromosomes, and Sex determination systems in a comparative framework. Phylogenetic analysis reveals that male heterogamety is the ancestral mode of Sex determination in insects, and transitions to female heterogamety are extremely rare. Many insect orders harbor species with complex Sex Chromosomes, and gains and losses of the Sex-limited chromosome are frequent in some groups. Haplodiploidy originated several times within insects, and parthenogenesis is rare but evolves frequently. Providing a single source to electronically access data previously distributed among more than 500 articles and books will not only accelerate analyses of the assembled data, but also provide a unique resource to guide research on which taxa are likely to be informative to address specific questions, for example, for genome sequencing projects or large-scale comparative studies.
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ancestral chromatin configuration constrains chromatin evolution on differentiating Sex Chromosomes in drosophila
PLOS Genetics, 2015Co-Authors: Qi Zhou, Doris BachtrogAbstract:Sex Chromosomes evolve distinctive types of chromatin from a pair of ancestral autosomes that are usually euchromatic. In Drosophila, the dosage-compensated X becomes enriched for hyperactive chromatin in males (mediated by H4K16ac), while the Y chromosome acquires silencing heterochromatin (enriched for H3K9me2/3). Drosophila autosomes are typically mostly euchromatic but the small dot chromosome has evolved a heterochromatin-like milieu (enriched for H3K9me2/3) that permits the normal expression of dot-linked genes, but which is different from typical pericentric heterochromatin. In Drosophila busckii, the dot Chromosomes have fused to the ancestral Sex Chromosomes, creating a pair of ‘neo-Sex’ Chromosomes. Here we collect genomic, transcriptomic and epigenomic data from D. busckii, to investigate the evolutionary trajectory of Sex Chromosomes from a largely heterochromatic ancestor. We show that the neo-Sex Chromosomes formed <1 million years ago, but nearly 60% of neo-Y linked genes have already become non-functional. Expression levels are generally lower for the neo-Y alleles relative to their neo-X homologs, and the silencing heterochromatin mark H3K9me2, but not H3K9me3, is significantly enriched on silenced neo-Y genes. Despite rampant neo-Y degeneration, we find that the neo-X is deficient for the canonical histone modification mark of dosage compensation (H4K16ac), relative to autosomes or the compensated ancestral X chromosome, possibly reflecting constraints imposed on evolving hyperactive chromatin in an originally heterochromatic environment. Yet, neo-X genes are transcriptionally more active in males, relative to females, suggesting the evolution of incipient dosage compensation on the neo-X. Our data show that Y degeneration proceeds quickly after Sex Chromosomes become established through genomic and epigenetic changes, and are consistent with the idea that the evolution of Sex-linked chromatin is influenced by its ancestral configuration.
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numerous transitions of Sex Chromosomes in diptera
PLOS Biology, 2015Co-Authors: Beatriz Vicoso, Doris BachtrogAbstract:Many species groups, including mammals and many insects, determine Sex using heteromorphic Sex Chromosomes. Diptera flies, which include the model Drosophila melanogaster, generally have XY Sex Chromosomes and a conserved karyotype consisting of six chromosomal arms (five large rods and a small dot), but superficially similar karyotypes may conceal the true extent of Sex chromosome variation. Here, we use whole-genome analysis in 37 fly species belonging to 22 different families of Diptera and uncover tremendous hidden diversity in Sex chromosome karyotypes among flies. We identify over a dozen different Sex chromosome configurations, and the small dot chromosome is repeatedly used as the Sex chromosome, which presumably reflects the ancestral karyotype of higher Diptera. However, we identify species with undifferentiated Sex Chromosomes, others in which a different chromosome replaced the dot as a Sex chromosome or in which up to three chromosomal elements became incorporated into the Sex Chromosomes, and others yet with female heterogamety (ZW Sex Chromosomes). Transcriptome analysis shows that dosage compensation has evolved multiple times in flies, consistently through up-regulation of the single X in males. However, X Chromosomes generally show a deficiency of genes with male-biased expression, possibly reflecting Sex-specific selective pressures. These species thus provide a rich resource to study Sex chromosome biology in a comparative manner and show that similar selective forces have shaped the unique evolution of Sex Chromosomes in diverse fly taxa.
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Sex biased gene expression at homomorphic Sex Chromosomes in emus and its implication for Sex chromosome evolution
Proceedings of the National Academy of Sciences of the United States of America, 2013Co-Authors: Beatriz Vicoso, Vera B Kaiser, Doris BachtrogAbstract:Sex Chromosomes originate from autosomes. The accumulation of Sexually antagonistic mutations on protoSex Chromosomes selects for a loss of recombination and sets in motion the evolutionary processes generating heteromorphic Sex Chromosomes. Recombination suppression and differentiation are generally viewed as the default path of Sex chromosome evolution, and the occurrence of old, homomorphic Sex Chromosomes, such as those of ratite birds, has remained a mystery. Here, we analyze the genome and transcriptome of emu (Dromaius novaehollandiae) and confirm that most genes on the Sex chromosome are shared between the Z and W. Surprisingly, however, levels of gene expression are generally Sex-biased for all Sex-linked genes relative to autosomes, including those in the pseudoautosomal region, and the male-bias increases after gonad formation. This expression bias suggests that the emu Sex Chromosomes have become masculinized, even in the absence of ZW differentiation. Thus, birds may have taken different evolutionary solutions to minimize the deleterious effects imposed by Sexually antagonistic mutations: some lineages eliminate recombination along the protoSex Chromosomes to physically restrict Sexually antagonistic alleles to one Sex, whereas ratites evolved Sex-biased expression to confine the product of a Sexually antagonistic allele to the Sex it benefits. This difference in conflict resolution may explain the preservation of recombining, homomorphic Sex Chromosomes in other lineages and illustrates the importance of Sexually antagonistic mutations driving the evolution of Sex Chromosomes.
Jennifer Marshall A. Graves - One of the best experts on this subject based on the ideXlab platform.
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evolution of vertebrate Sex Chromosomes and dosage compensation
Nature Reviews Genetics, 2016Co-Authors: Jennifer Marshall A. GravesAbstract:The differentiation of Sex Chromosomes in vertebrates created a need for mechanisms that compensate for differences in dosage of gene expression between the Sexes. The author reviews the diversity of these mechanisms, their effects on gene expression, and their origin and evolution across the major vertebrate groups. Differentiated Sex Chromosomes in mammals and other vertebrates evolved independently but in strikingly similar ways. Vertebrates with differentiated Sex Chromosomes share the problems of the unequal expression of the genes borne on Sex Chromosomes, both between the Sexes and with respect to autosomes. Dosage compensation of genes on Sex Chromosomes is surprisingly variable — and can even be absent — in different vertebrate groups. Systems that compensate for different gene dosages include a wide range of global, regional and gene-by-gene processes that differ in their extent and their molecular mechanisms. However, many elements of these control systems are similar across distant phylogenetic divisions and show parallels to other gene silencing systems. These dosage systems cannot be identical by descent but were probably constructed from elements of ancient silencing mechanisms that are ubiquitous among vertebrates and shared throughout eukaryotes.
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monotreme Sex Chromosomes implications for the evolution of amniote Sex Chromosomes
Reproduction Fertility and Development, 2009Co-Authors: Paul D Waters, Jennifer Marshall A. GravesAbstract:In vertebrates, a highly conserved pathway of genetic events controls male and female development, to the extent that many genes involved in human Sex determination are also involved in fish Sex determination. Surprisingly, the master switch to this pathway, which intuitively could be considered the most critical step, is inconsistent between vertebrate taxa. Interspersed in the vertebrate tree there are species that determine Sex by environmental cues such as the temperature at which eggs are incubated, and then there are genetic Sex-determination systems, with male heterogametic species (XY systems) and female heterogametic species (ZW systems), some of which have heteromorphic, and others homomorphic, Sex Chromosomes. This plasticity of Sex-determining switches in vertebrates has made tracking the events of Sex chromosome evolution in amniotes a daunting task, but comparative gene mapping is beginning to reveal some striking similarities across even distant taxa. In particular, the recent completion of the platypus genome sequence has completely changed our understanding of when the therian mammal X and Y Chromosomes first arose (they are up to 150 million years younger than previously thought) and has also revealed the unexpected insight that Sex determination of the amniote ancestor might have been controlled by a bird-like ZW system.
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weird animal genomes and the evolution of vertebrate Sex and Sex Chromosomes
Annual Review of Genetics, 2008Co-Authors: Jennifer Marshall A. GravesAbstract:Humans, mice, and even kangaroos have an XX female:XY male system of Sex determination, in which the Y harbors a male-dominant Sex-determining gene SRY. Birds have the opposite, ZZ males and ZW females, and may use a dosage-sensitive Z-borne gene. Other reptiles have genetic Sex but no visible Sex Chromosomes, or determine Sex by temperature of egg incubation. How can we make sense of so much variation? How do systems change in evolution? Studies of some unlikely animals—platypus and dragon lizards, frogs and fish—confirm that evolutionary transitions have occurred between TSD and GSD systems, between XY and ZW systems, and even between male and female heterogametic systems. Here I explore nonmodel systems that offer some new perspectives on some venerable questions of Sex and Sex Chromosomes.
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the dragon lizard pogona vitticeps has zz zw micro Sex Chromosomes
Chromosome Research, 2005Co-Authors: Tariq Ezaz, Ikuo Miura, Stephen D Sarre, Arthur Georges, Alexander E. Quinn, Jennifer Marshall A. GravesAbstract:The bearded dragon, Pogona vitticeps (Agamidae: Reptilia) is an agamid lizard endemic to Australia. Like crocodilians and many turtles, temperature-dependent Sex determination (TSD) is common in agamid lizards, although many species have genotypic Sex determination (GSD). P. vitticeps is reported to have GSD, but no detectable Sex Chromosomes. Here we used molecular cytogenetic and differential banding techniques to reveal Sex Chromosomes in this species. Comparative genomic hybridization (CGH), GTG- and C-banding identified a highly heterochromatic microchromosome specific to females, demonstrating female heterogamety (ZZ/ZW) in this species. We isolated the P. vitticeps W chromosome by microdissection, re-amplified the DNA and used it to paint the W. No unpaired bivalents were detected in male synaptonemal complexes at meiotic pachytene, confirming male homogamety. We conclude that P. vitticeps has differentiated previously unidentifable W and Z micro-Sex Chromosomes, the first to be demonstrated in an agamid lizard. Our finding implies that heterochromatinization of the heterogametic chromosome occurred during Sex chromosome differentiation in this species, as is the case in some lizards and many snakes, as well as in birds and mammals. Many GSD reptiles with cryptic Sex Chromosomes may also prove to have micro-Sex Chromosomes. Reptile microChromosomes, long dismissed as non-functional minutiae and often omitted from karyotypes, therefore deserve closer scrutiny with new and more sensitive techniques.
Dmitry A Filatov - One of the best experts on this subject based on the ideXlab platform.
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the mutation rate and the age of the Sex Chromosomes in silene latifolia
Current Biology, 2018Co-Authors: Marc Krasovec, Michael Chester, Kate Ridout, Dmitry A FilatovAbstract:Summary Many aspects of Sex chromosome evolution are common to both plants and animals [1], but the process of Y chromosome degeneration, where genes on the Y become non-functional over time, may be much slower in plants due to purifying selection against deleterious mutations in the haploid gametophyte [2, 3]. Testing for differences in Y degeneration between the kingdoms has been hindered by the absence of accurate age estimates for plant Sex Chromosomes. Here, we used genome resequencing to estimate the spontaneous mutation rate and the age of the Sex Chromosomes in white campion ( Silene latifolia ). Screening of single nucleotide polymorphisms (SNPs) in parents and 10 F 1 progeny identified 39 de novo mutations and yielded a rate of 7.31 × 10 −9 (95% confidence interval: 5.20 × 10 −9 − 8.00 × 10 −9 ) mutations per site per haploid genome per generation. Applying this mutation rate to the synonymous divergence between homologous X- and Y-linked genes (gametologs) gave age estimates of 11.00 and 6.32 million years for the old and young strata, respectively. Based on SNP segregation patterns, we inferred which genes were Y-linked and found that at least 47% are already dysfunctional. Applying our new estimates for the age of the Sex Chromosomes indicates that the rate of Y degeneration in S. latifolia is nearly 2-fold slower when compared to animal Sex Chromosomes of a similar age. Our revised estimates support Y degeneration taking place more slowly in plants, a discrepancy that may be explained by differences in the life cycles of animals and plants.
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homomorphic plant Sex Chromosomes are coming of age
Molecular Ecology, 2015Co-Authors: Dmitry A FilatovAbstract:Sex Chromosomes are a very peculiar part of the genome that have evolved independently in many groups of animals and plants (Bull 1983). Major research efforts have so far been focused on large heteromorphic Sex Chromosomes in a few animal and plant species (Chibalina & Filatov 2011; Zhou & Bachtrog 2012; Bellott et al. 2014; Hough et al. 2014; Zhou et al. 2014), while homomorphic (cytologically indistinguishable) Sex Chromosomes have largely been neglected. However, this situation is starting to change. In this issue, Geraldes et al. (2015) describe a small (~100 kb long) Sex-determining region on the homomorphic Sex Chromosomes of poplars (Populus trichocarpa and related species, Fig. 1). All species in Populus and its sister genus Salix are dioecious, suggesting that dioecy and the Sex Chromosomes, if any, should be relatively old. Contrary to this expectation, Geraldes et al. (2015) demonstrate that the Sex-determining region in poplars is of very recent origin and probably evolved within the genus Populus only a few million years ago.
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evolutionary history of silene latifolia Sex Chromosomes revealed by genetic mapping of four genes
Genetics, 2005Co-Authors: Dmitry A FilatovAbstract:The Sex Chromosomes of dioecious white campion, Silene latifolia (Caryophyllaceae), are of relatively recent origin (10-20 million years), providing a unique opportunity to trace the origin and evolution of Sex Chromosomes in this genus by comparing closely related Silene species with and without Sex Chromosomes. Here I demonstrate that four genes that are X-linked in S. latifolia are also linked in nondioecious S. vulgaris, which is consistent with Ohno's (1967) hypothesis that Sex Chromosomes evolve from a single pair of autosomes. I also report a genetic map for four S. latifolia X-linked genes, SlX1, DD44X, SlX4, and a new X-linked gene SlssX, which encodes spermidine synthase. The order of the genes on the S. latifolia X chromosome and divergence between the homologous X- and Y-linked copies of these genes supports the "evolutionary strata" model, with at least three consecutive expansions of the nonrecombining region on the Y chromosome (NRY) in this plant species.
Gabriel A B Marais - One of the best experts on this subject based on the ideXlab platform.
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the evolution of Sex Chromosomes and dosage compensation in plants
Genome Biology and Evolution, 2017Co-Authors: Aline Muyle, Rylan Shearn, Gabriel A B MaraisAbstract:Plant Sex Chromosomes can be vastly different from those of the few historical animal model organisms from which most of our understanding of Sex chromosome evolution is derived. Recently, we have seen several advancements from studies on green algae, brown algae, and land plants that are providing a broader understanding of the variable ways in which Sex Chromosomes can evolve in distant eukaryotic groups. Plant Sex-determining genes are being identified and, as expected, are completely different from those in animals. Species with varying levels of differentiation between the X and Y have been found in plants, and these are hypothesized to be representing different stages of Sex chromosome evolution. However, we are also finding that Sex Chromosomes can remain morphologically unchanged over extended periods of time. Where degeneration of the Y occurs, it appears to proceed similarly in plants and animals. Dosage compensation (a phenomenon that compensates for the consequent loss of expression from the Y) has now been documented in a plant system, its mechanism, however, remains unknown. Research has also begun on the role of Sex Chromosomes in Sexual conflict resolution, and it appears that Sex-biased genes evolve similarly in plants and animals, although the functions of these genes remain poorly studied. Because the difficulty in obtaining Sex chromosome sequences is increasingly being overcome by methodological developments, there is great potential for further discovery within the field of plant Sex chromosome evolution.
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steps in the evolution of heteromorphic Sex Chromosomes
Heredity, 2005Co-Authors: D Charlesworth, Brian Charlesworth, Gabriel A B MaraisAbstract:We review some recently published results on Sex Chromosomes in a diversity of species. We focus on several fish and some plants whose Sex Chromosomes appear to be 'young', as only parts of the chromosome are nonrecombining, while the rest is pseudoautosomal. However, the age of these systems is not yet very clear. Even without knowing what proportions of their genes are genetically degenerate, these cases are of great interest, as they may offer opportunities to study in detail how Sex Chromosomes evolve. In particular, we review evidence that recombination suppression occurs progressively in evolutionarily independent cases, suggesting that selection drives loss of recombination over increasingly large regions. We discuss how selection during the period when a chromosome is adapting to its role as a Y chromosome might drive such a process.
