scholarly journals Why Do Some Sex Chromosomes Degenerate More Slowly Than Others? The Odd Case of Ratite Sex Chromosomes

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1153 ◽  
Author(s):  
Homa Papoli Yazdi ◽  
Willian T. A. F. Silva ◽  
Alexander Suh
Keyword(s):  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Current Data ◽  
W Chromosome ◽  
Sex Chromosome Evolution ◽  
History Of ◽  
Sexually Antagonistic Selection ◽  
Ratite Birds ◽  
Genome Assemblies

The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive patterns of sex chromosome degeneration. Birds are female heterogametic, in which females have a Z and a W chromosome. In Neognathae, the highly-degenerated W chromosome seems to have followed the expected trajectory of sex chromosome evolution. In contrast, among Palaeognathae, sex chromosomes of ratite birds are largely recombining. The underlying reason for maintenance of recombination between sex chromosomes in ratites is not clear. Degeneration of the W chromosome might have halted or slowed down due to a multitude of reasons ranging from selective processes, such as a less pronounced effect of sexually antagonistic selection, to neutral processes, such as a slower rate of molecular evolution in ratites. The production of genome assemblies and gene expression data for species of Palaeognathae has made it possible, during recent years, to have a closer look at their sex chromosome evolution. Here, we critically evaluate the understanding of the maintenance of recombination in ratites in light of the current data. We conclude by highlighting certain aspects of sex chromosome evolution in ratites that require further research and can potentially increase power for the inference of the unique history of sex chromosome evolution in this lineage of birds.

scholarly journals Dynamic Patterns of Sex Chromosome Evolution in Neognath Birds: Many Independent Barriers to Recombination at the ATP5F1A Locus

2021 ◽  
Author(s):  
Rebecca T. Kimball ◽  
Edward L. Braun
Keyword(s):  
Sex Chromosomes ◽  
Substitution Rate ◽  
Chromosome Evolution ◽  
Common Ancestor ◽  
Sex Chromosome ◽  
Purifying Selection ◽  
W Chromosome ◽  
Sex Chromosome Evolution ◽  
Dynamic Nature ◽  
Genome Assemblies

Avian sex chromosomes evolved after the divergence birds and crocodilians from their common ancestor, so they are much younger than the better-studied chromosomes of mammals. It has long been recognized that there may have been several stages to the evolution of avian sex chromosomes. For example, the CHD1 undergoes recombination in paleognaths but not neognaths. Genome assemblies have suggested there may be variation in the timing of barriers to recombination among Neognathae, but there remains little understanding of the extent of this variability. Here, we look at partial sequences of ATP5F1A, which is on the avian Z and W chromosomes. It is known that recombination of this gene has independently ceased in Galliformes, Anseriformes, and at least five neoavian orders, but whether there are other independent cessations of recombination among Neoaves is not understood. We used a combination of data extracted from published chromosomal-level genomes with data collected using PCR and cloning to identify Z and W copies in 22 orders. Our results suggest there may be at least 19 independent cessations of recombination within Neognathae, and 3 clades that may still be undergoing recombination (or have only recently ceased recombination). Analyses of ATP5F1A protein sequences revealed an increased amino acid substitution rate for W chromosome gametologs, suggesting relaxed purifying selection on the W chromosome. Supporting this hypothesis, we found that the increased substitution rate was particularly pronounced for buried residues, which are expected to be more strongly constrained by purifying selection. This highlights the dynamic nature of avian sex chromosomes, and that this level of variation among clades means they should be a good system to understand sex chromosome evolution.

scholarly journals Sex chromosome evolution among amniotes: is the origin of sex chromosomes non-random?

2021 ◽  
Vol 376 (1833) ◽  
pp. 20200108 ◽  
Author(s):  
Lukáš Kratochvíl ◽  
Tony Gamble ◽  
Michail Rovatsos
Keyword(s):  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Current Knowledge ◽  
Current Data ◽  
Divergent Evolution ◽  
Random Pattern ◽  
Sex Chromosome Evolution ◽  
Great Opportunity

Sex chromosomes are a great example of a convergent evolution at the genomic level, having evolved dozens of times just within amniotes. An intriguing question is whether this repeated evolution was random, or whether some ancestral syntenic blocks have significantly higher chance to be co-opted for the role of sex chromosomes owing to their gene content related to gonad development. Here, we summarize current knowledge on the evolutionary history of sex determination and sex chromosomes in amniotes and evaluate the hypothesis of non-random emergence of sex chromosomes. The current data on the origin of sex chromosomes in amniotes suggest that their evolution is indeed non-random. However, this non-random pattern is not very strong, and many syntenic blocks representing putatively independently evolved sex chromosomes are unique. Still, repeatedly co-opted chromosomes are an excellent model system, as independent co-option of the same genomic region for the role of sex chromosome offers a great opportunity for testing evolutionary scenarios on the sex chromosome evolution under the explicit control for the genomic background and gene identity. Future studies should use these systems more to explore the convergent/divergent evolution of sex chromosomes. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part II)’.

scholarly journals Sex chromosome evolution: historical insights and future perspectives

2017 ◽  
Vol 284 (1854) ◽  
pp. 20162806 ◽  
Author(s):  
Jessica K. Abbott ◽  
Anna K. Nordén ◽  
Bengt Hansson
Keyword(s):  
Sex Determination ◽  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Empirical Studies ◽  
Analytical Models ◽  
Specific Gene ◽  
Sex Chromosome Evolution ◽  
Current Thinking

Many separate-sexed organisms have sex chromosomes controlling sex determination. Sex chromosomes often have reduced recombination, specialized (frequently sex-specific) gene content, dosage compensation and heteromorphic size. Research on sex determination and sex chromosome evolution has increased over the past decade and is today a very active field. However, some areas within the field have not received as much attention as others. We therefore believe that a historic overview of key findings and empirical discoveries will put current thinking into context and help us better understand where to go next. Here, we present a timeline of important conceptual and analytical models, as well as empirical studies that have advanced the field and changed our understanding of the evolution of sex chromosomes. Finally, we highlight gaps in our knowledge so far and propose some specific areas within the field that we recommend a greater focus on in the future, including the role of ecology in sex chromosome evolution and new multilocus models of sex chromosome divergence.

scholarly journals A bird’s white-eye view on avian sex chromosome evolution

2018 ◽  
Author(s):  
Thibault Leroy ◽  
Yoann Anselmetti ◽  
Marie-Ka Tilak ◽  
Sèverine Bérard ◽  
Laura Csukonyi ◽  
...  
Keyword(s):  
Molecular Evolution ◽  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Sex Chromosome Evolution ◽  
Weak Support ◽  
Unusual Event ◽  
Calibration Sets ◽  
Molecular Phylogenetic ◽  
Genomic Regions

ABSTRACTChromosomal organization is relatively stable among avian species, especially with regards to sex chromosomes. Members of the large Sylvioidea clade however have a pair of neo-sex chromosomes which is unique to this clade and originate from a parallel translocation of a region of the ancestral 4A chromosome on both W and Z chromosomes. Here, we took advantage of this unusual event to study the early stages of sex chromosome evolution. To do so, we sequenced a female (ZW) of two Sylvioidea species, a Zosterops borbonicus and a Z. pallidus. Then, we organized the Z. borbonicus scaffolds along chromosomes and annotated genes. Molecular phylogenetic dating under various methods and calibration sets confidently confirmed the recent diversification of the genus Zosterops (1-3.5 million years ago), thus representing one of the most exceptional rates of diversification among vertebrates. We then combined genomic coverage comparisons of five males and seven females, and homology with the zebra finch genome (Taeniopygia guttata) to identify sex chromosome scaffolds, as well as the candidate chromosome breakpoints for the two translocation events. We observed reduced levels of within-species diversity in both translocated regions and, as expected, even more so on the neoW chromosome. In order to compare the rates of molecular evolution in genomic regions of the autosomal-to-sex transitions, we then estimated the ratios of non-synonymous to synonymous polymorphisms (πN/πS) and substitutions (dN/dS). Based on both ratios, no or little contrast between autosomal and Z genes was observed, thus representing a very different outcome than the higher ratios observed at the neoW genes. In addition, we report significant changes in base composition content for translocated regions on the W and Z chromosomes and a large accumulation of transposable elements (TE) on the newly W region. Our results revealed contrasted signals of molecular evolution changes associated to these autosome-to-sex transitions, with congruent signals of a W chromosome degeneration yet a surprisingly weak support for a fast-Z effect.

scholarly journals Ecology and the Evolution of Sex Chromosomes

2021 ◽  
Author(s):  
Richard Meisel
Keyword(s):  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Ecological Factors ◽  
Sex Chromosome Evolution ◽  
Sexual Antagonism ◽  
Extrinsic Factors ◽  
Selection Pressures ◽  
Evolutionary Trajectories ◽  
Animal Genomes

This article reviews and discusses ecological factors that affect sex chromosome evolution. Sex chromosomes are common features of animal genomes, and are often the location where master sex determination genes are found. Many important aspects of sex chromosome evolution are thought to be driven by sex-specific selection pressures, such as sexual antagonism and sexual selection. Sex-specific selection affects both the formation of sex chromosomes from autosomes and differences in the evolutionary trajectories between sex chromosomes and autosomes. Most population genetic models are agnostic as to whether the sex-specific selection pressures arise from intrinsic features of organismal biology or extrinsic factors that depend on environment. Here, I review the evidence that extrinsic, or ecological, factors are important determinants of sex-specific selection pressures that shape sex chromosome evolution.

scholarly journals A neutral model for the loss of recombination on sex chromosomes

2021 ◽  
Vol 376 (1832) ◽  
pp. 20200096 ◽  
Author(s):  
Daniel L. Jeffries ◽  
Jörn F. Gerchen ◽  
Mathias Scharmann ◽  
John R. Pannell
Keyword(s):  
Sex Chromosomes ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Sequence Divergence ◽  
Theme Issue ◽  
Recombination Rates ◽  
Natural Systems ◽  
Adaptive Processes ◽  
Sexually Antagonistic Selection ◽  
Suppressed Recombination

The loss of recombination between sex chromosomes has occurred repeatedly throughout nature, with important implications for their subsequent evolution. Explanations for this remarkable convergence have generally invoked only adaptive processes (e.g. sexually antagonistic selection); however, there is still little evidence for these hypotheses. Here we propose a model in which recombination on sex chromosomes is lost due to the neutral accumulation of sequence divergence adjacent to (and thus, in linkage disequilibrium with) the sex determiner. Importantly, we include in our model the fact that sequence divergence, in any form, reduces the probability of recombination between any two sequences. Using simulations, we show that, under certain conditions, a region of suppressed recombination arises and expands outwards from the sex-determining locus, under purely neutral processes. Further, we show that the rate and pattern of recombination loss are sensitive to the pre-existing recombination landscape of the genome and to sex differences in recombination rates, with patterns consistent with evolutionary strata emerging under some conditions. We discuss the applicability of these results to natural systems. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.

scholarly journals Evolution of master sex determiners: TGF-β signalling pathways at regulatory crossroads

2021 ◽  
Vol 376 (1832) ◽  
pp. 20200091 ◽  
Author(s):  
Qiaowei Pan ◽  
Tomas Kay ◽  
Alexandra Depincé ◽  
Mateus Adolfi ◽  
Manfred Schartl ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Sex Chromosomes ◽  
Regulatory Network ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Signalling Pathway ◽  
Signalling Pathways ◽  
Sex Chromosome Evolution ◽  
Theme Issue ◽  
Gene Regulatory

To date, more than 20 different vertebrate master sex-determining genes have been identified on different sex chromosomes of mammals, birds, frogs and fish. Interestingly, six of these genes are transcription factors ( Dmrt1 - or Sox3 - related) and 13 others belong to the TGF-β signalling pathway ( Amh , Amhr2 , Bmpr1b , Gsdf and Gdf6 ). This pattern suggests that only a limited group of factors/signalling pathways are prone to become top regulators again and again. Although being clearly a subordinate member of the sex-regulatory network in mammals, the TGF-β signalling pathway made it to the top recurrently and independently. Facing this rolling wave of TGF-β signalling pathways, this review will decipher how the TGF-β signalling pathways cope with the canonical sex gene regulatory network and challenge the current evolutionary concepts accounting for the diversity of sex-determining mechanisms. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.

scholarly journals Repetitive Sequence and Sex Chromosome Evolution in Vertebrates

2014 ◽  
Vol 2014 ◽  
pp. 1-9 ◽  
Author(s):  
Tariq Ezaz ◽  
Janine E. Deakin
Keyword(s):  
Repetitive Dna ◽  
Sex Chromosomes ◽  
Repetitive Sequence ◽  
Chromosome Evolution ◽  
Sex Chromosome ◽  
Repetitive Sequences ◽  
Sex Chromosome Evolution ◽  
Genomic Changes ◽  
Heteromorphic Sex Chromosomes ◽  
Simple Repetitive Sequences

Sex chromosomes are the most dynamic entity in any genome having unique morphology, gene content, and evolution. They have evolved multiple times and independently throughout vertebrate evolution. One of the major genomic changes that pertain to sex chromosomes involves the amplification of common repeats. It is hypothesized that such amplification of repeats facilitates the suppression of recombination, leading to the evolution of heteromorphic sex chromosomes through genetic degradation of Y or W chromosomes. Although contrasting evidence is available, it is clear that amplification of simple repetitive sequences played a major role in the evolution of Y and W chromosomes in vertebrates. In this review, we present a brief overview of the repetitive DNA classes that accumulated during sex chromosome evolution, mainly focusing on vertebrates, and discuss their possible role and potential function in this process.

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