Sex-Chromosome Homomorphy in Palearctic Tree Frogs Results from Both Turnovers and X-Y Recombination

An Inversion Polymorphism Under Balancing Selection, Involving Giant Mobile Elements, in an Invasive Fungal Pathogen

Recombination suppression can evolve in sex or mating-type chromosomes, or in autosomal supergenes, with different haplotypes being maintained by balancing selection. In the invasive chestnut blight fungus Cryphonectria parasitica, a genomic region was suggested to lack recombination and to be partially physically linked to the mating-type (MAT) locus based on segregation analyses. Using hundreds of available C. parasitica genomes and generating new high-quality genome assemblies, we show that a ca. 1.2 Mb genomic region proximal to the mating-type locus lacks recombination, with the segregation of two highly differentiated haplotypes in balanced proportions in invasive populations. High-quality genome assemblies further revealed an inversion in one of the haplotypes in the invaded range. The two haplotypes were estimated to have diverged 1.5 million years ago, and each harboured specific genes, some of which likely belonging to Starships. These are large transposable elements, mobilized by tyrosine recombinases, able to move accessory genes, and involved in adaptation in multiple fungi. The MAT-proximal region carried genes upregulated under virus infection or vegetative incompatibility reaction. In the native range, the MAT-proximal region also appeared to have a different evolutionary history than the rest of the genome. In all continents, the MAT-Proximal region was enriched in nonsynonymous substitutions, in gene presence/absence polymorphism, in tyrosine recombinases and in transposable elements. This study thus sheds light on a case of a large nonrecombining region partially linked to a mating compatibility locus, likely maintained by balancing selection on differentiated haplotypes, possibly involved in adaptation in a devastating tree pathogen.

Rapid Sex Chromosome Turnover in African Clawed Frogs (Xenopus) and the Origins of New Sex Chromosomes

Sex chromosomes of some closely related species are not homologous, and sex chromosome turnover is often attributed to mechanisms that involve linkage to or recombination arrest around sex-determining loci. We examined sex chromosome turnover and recombination landscapes in African clawed frogs (genus Xenopus) with reduced representation genome sequences from 929 individuals from 19 species. We recovered extensive variation in sex chromosomes, including at least eight nonhomologous sex-associated regions-five newly reported here, with most maintaining female heterogamety, but two independent origins of Y chromosomes. Seven of these regions are found in allopolyploid species in the subgenus Xenopus, and all of these reside in one of their two subgenomes, which highlights functional asymmetry between subgenomes. In three species with chromosome-scale genome assemblies (Xenopus borealis, Xenopus laevis, and Xenopus tropicalis), sex-specific recombination landscapes have similar patterns of sex differences in rates and locations of recombination. Across these Xenopus species, sex-associated regions are significantly nearer chromosome ends than expected by chance, even though this is where the ancestral recombination rate is highest in both sexes before the regions became sex associated. As well, expansions of sex-associated recombination arrest occurred multiple times. New information on sex linkage along with among-species variation in female specificity of the sex-determining gene dm-w argues against a "jumping gene" model, where dm-w moves around the genome. The diversity of sex chromosomes in Xenopus raises questions about the roles of natural and sexual selection, polyploidy, the recombination landscape, and neutral processes in driving sex chromosome turnover in animal groups with mostly heterogametic females.

Sex chromosome turnover in hybridizing stickleback lineages

Recent discoveries of sex chromosome diversity across the tree of life have challenged the canonical model of conserved sex chromosome evolution and evoked new theories on labile sex chromosomes that maintain less differentiation and undergo frequent turnover. However, theories of labile sex chromosome evolution lack direct empirical support due to the paucity of case studies demonstrating ongoing sex chromosome turnover in nature. Two divergent lineages (viz. WL & EL) of nine-spined sticklebacks (Pungitius pungitius) with different sex chromosomes (linkage group [LG] 12 in the EL, unknown in the WL) hybridize in a natural secondary contact zone in the Baltic Sea, providing an opportunity to study ongoing turnover between coexisting sex chromosomes. In this study, we first identify an 80 kbp genomic region on LG3 as the sex-determining region (SDR) using whole-genome resequencing data of family crosses of a WL population. We then verify this region as the SDR in most other WL populations and demonstrate a potentially ongoing sex chromosome turnover in admixed marine populations where the evolutionarily younger and homomorphic LG3 sex chromosome replaces the older and heteromorphic LG12 sex chromosome. The results provide a rare glimpse of sex chromosome turnover in the wild and indicate the possible existence of additional yet undiscovered sex chromosome diversity in Pungitius sticklebacks.

SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering

Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.

Homology in Sex Determination in Two Distant Spiny Frogs, Nanorana quadranus and Quasipaa yei

Sex determination is remarkably diverse, with frequent transitions between sex chromosomes, in amphibians. Under these transitions, some chromosomes are more likely to be recurrently co-opted as sex chromosomes, as they are often observed across deeply divergent taxa. However, little is known about the pattern of sex chromosome evolution among closely related groups. Here, we examined sex chromosome and sex determination in two spiny frogs, Nanorana quadranus and Quasipaa yei. We conducted an analysis of genotyping-by-sequencing (GBS) data from a total of 34 individuals to identify sex-specific makers, with the results verified by PCR. The results suggest that chromosome 1 is a homologous sex chromosome with an XY pattern in both species. This chromosome has been evolutionarily conserved across these closely related groups within a period of time. The DMRT1 gene is proposed to be implicated in homology across two distantly related spiny frog species as a putative candidate sex-determining gene. Harboring the DMRT1 gene, chromosome 1 would have been independently co-opted for sex determination in deeply divergent groups of anurans.

Multiple Transitions between Y Chromosome and Autosome in Tago's Brown Frog Species Complex

Sex chromosome turnover is the transition between sex chromosomes and autosomes. Although many cases have been reported in poikilothermic vertebrates, their evolutionary causes and genetic mechanisms remain unclear. In this study, we report multiple transitions between the Y chromosome and autosome in the Japanese Tago's brown frog complex. Using chromosome banding and molecular analyses (sex-linked and autosomal single nucleotide polymorphisms, SNPs, from the nuclear genome), we investigated the frogs of geographic populations ranging from northern to southern Japan of two species, Rana tagoi and Rana sakuraii (2n = 26). Particularly, the Chiba populations of East Japan and Akita populations of North Japan in R. tagoi have been, for the first time, investigated here. As a result, we identified three different sex chromosomes, namely chromosomes 3, 7, and 13, in the populations of the two species. Furthermore, we found that the transition between the Y chromosome (chromosome 7) and autosome was repeated through hybridization between two or three different populations belonging to the two species, followed by restricted chromosome introgression. These dynamic sex chromosome turnovers represent the first such findings in vertebrates and imply that speciation associated with inter- or intraspecific hybridization plays an important role in sex chromosome turnover in frogs.

The first linkage map for Australo-Papuan Treefrogs (family: Pelodryadidae) reveals the sex-determination system of the Green-eyed Treefrog (Litoria serrata)

Amphibians represent a useful taxon to study the evolution of sex determination because of their highly variable sex-determination systems. However, the sex-determination system for many amphibian families remains unknown, in part because of a lack of genomic resources. Here, using an F1 family of Green-eyed Treefrogs (Litoria serrata), we produce the first genetic linkage map for any Australo-Papuan Treefrogs (family: Pelodryadidae). The resulting linkage map contains 8662 SNPs across 13 linkage groups. Using an independent set of sexed adults, we identify a small region in linkage group 6 matching an XY sex-determination system. These results suggest Litoria serrata possesses a male heterogametic system, with a candidate sex-determination locus on linkage group 6. Furthermore, this linkage map represents the first genomic resource for Australo-Papuan Treefrogs, an ecologically diverse family of over 220 species.

Heterogeneous Evolution of Sex Chromosomes in the Torrent Frog Genus Amolops

In sharp contrast to birds and mammals, in numerous cold-blooded vertebrates, sex chromosomes have been described as homomorphic. This sex chromosome homomorphy has been suggested to result from the high turnovers often observed across deeply diverged clades. However, little is known about the tempo and mode of sex chromosome evolution among the most closely related species. Here, we examined the evolution of sex chromosome among nine species of the torrent frog genus Amolops. We analyzed male and female GBS and RAD-seq from 182 individuals and performed PCR verification for 176 individuals. We identified signatures of sex chromosomes involving two pairs of chromosomes. We found that sex-chromosome homomorphy results from both turnover and X–Y recombination in the Amolops species, which simultaneously exhibits heterogeneous evolution on homologous and non-homologous sex chromosomes. A low turnover rate of non-homologous sex chromosomes exists in these torrent frogs. The ongoing X–Y recombination in homologous sex chromosomes will act as an indispensable force in preventing sex chromosomes from differentiating.

Highly rapid and diverse sex chromosome evolution in the Odorrana frog species complex

Sex chromosomes in poikilothermal vertebrates are characterized by rapid and diverse evolution at the species or population level. Our previous study revealed that the Taiwanese frog Odorrana swinhoana (2n = 26) has a unique system of multiple sex chromosomes created by three sequential translocations among chromosomes 1, 3, and 7. To reveal the evolutionary history of sex chromosomes in the Odorrana species complex, we first identified the original, homomorphic sex chromosomes, prior to the occurrence of translocations, in the ancestral-type population of O. swinhoana. Then, we extended the investigation to a closely related Japanese species, Odorrana utsunomiyaorum, which is distributed on two small islands. We used a high-throughput nuclear genomic approach to analyze single-nucleotide polymorphisms and identify the sex-linked markers. Those isolated from the O. swinhoana ancestral-type population were found to be aligned to chromosome 1 and showed male heterogamety. In contrast, almost all the sex-linked markers isolated from O. utsunomiyaorum were heterozygous in females and homozygous in males and were aligned to chromosome 9. Morphologically, we confirmed chromosome 9 to be heteromorphic in females, showing a ZZ-ZW sex determination system, in which the W chromosomes were heterochromatinized in a stripe pattern along the chromosome axis. These results indicated that after divergence of the two species, the ancestral homomorphic sex chromosome 1 underwent highly rapid and diverse evolution, i.e., sequential translocations with two autosomes in O. swinhoana, and turnover to chromosome 9 in O. utsunomiyaorum, with a transition from XY to ZW heterogamety and change to heteromorphy.

Sex chromosomes as supergenes of speciation: why amphibians defy the rules?

As reflected by the two rules of speciation (Haldane's rule and the large X-/Z-effect), sex chromosomes are expected to behave like supergenes of speciation: they recombine only in one sex (XX females or ZZ males), supposedly recruit sexually antagonistic genes and evolve faster than autosomes, which can all contribute to pre-zygotic and post-zygotic isolation. While this has been mainly studied in organisms with conserved sex-determining systems and highly differentiated (heteromorphic) sex chromosomes like mammals, birds and some insects, these expectations are less clear in organismal groups where sex chromosomes repeatedly change and remain mostly homomorphic, like amphibians. In this article, we review the proposed roles of sex-linked genes in isolating nascent lineages throughout the speciation continuum and discuss their support in amphibians given current knowledge of sex chromosome evolution and speciation modes. Given their frequent recombination and lack of differentiation, we argue that amphibian sex chromosomes are not expected to become supergenes of speciation, which is reflected by the rarity of empirical studies consistent with a 'large sex chromosome effect' in frogs and toads. The diversity of sex chromosome systems in amphibians has a high potential to disentangle the evolutionary mechanisms responsible for the emergence of sex-linked speciation genes in other organisms. This article is part of the theme issue 'Genomic architecture of supergenes: causes and evolutionary consequences'.

Identification of ancestral sex chromosomes in the frog Glandirana rugosa bearing XX-XY and ZZ-ZW sex-determining systems

Sex chromosomes constantly exist in a dynamic state of evolution: rapid turnover and change of heterogametic sex during homomorphic state, and often stepping out to a heteromorphic state followed by chromosomal decaying. However, the forces driving these different trajectories of sex chromosome evolution are still unclear. The Japanese frog Glandirana rugosa is one taxon well suited to the study on these driving forces. The species has two different heteromorphic sex chromosome systems, XX-XY and ZZ-ZW, which are separated in different geographic populations. Both XX-XY and ZZ-ZW sex chromosomes are represented by chromosome 7 (2n = 26). Phylogenetically, these two systems arose via hybridization between two ancestral lineages of West Japan and East Japan populations, of which sex chromosomes are homomorphic in both sexes and to date have not yet been identified. Identification of the sex chromosomes will give us important insight into the mechanisms of sex chromosome evolution in this species. Here, we used a high-throughput genomic approach to identify the homomorphic XX-XY sex chromosomes in both ancestral populations. Sex-linked DNA markers of West Japan were aligned to chromosome 1, whereas those of East Japan were aligned to chromosome 3. These results reveal that at least two turnovers across three different sex chromosomes 1, 3 and 7 occurred during evolution of this species. This finding raises the possibility that cohabitation of the two different sex chromosomes from ancestral lineages induced turnover to another new one in their hybrids, involving transition of heterogametic sex and evolution from homomorphy to heteromorphy.

Sequencing of laser captured Z and W chromosomes of the tocantins paradoxical frog (Pseudis tocantins) provides insights on repeatome and chromosomal homology

Pseudis tocantins is the only frog species of the hylid genus Pseudis that possesses highly heteromorphic sex chromosomes. Z and W chromosomes of Ps. tocantins differ in size, morphology, position of the nucleolar organizer region (NOR) and the amount and distribution of heterochromatin. A chromosomal inversion and heterochromatin amplification on the W chromosome were previously inferred to be involved in the evolution of this sex chromosome pair. Despite these findings, knowledge related to the molecular composition of the large heterochromatic band of this W chromosome is restricted to the PcP190 satellite DNA, and no data are available regarding the gene content of either the W or the Z chromosome of Ps. tocantins. Here, we sequenced microdissected Z and W chromosomes of this species to further resolve their molecular composition. Comparative genomic analysis suggests that Ps. tocantins sex chromosomes are likely homologous to chromosomes 4 and 10 of Xenopus tropicalis. Analyses of the repetitive DNA landscape in the Z and W assemblies allowed for the identification of several transposable elements and putative satellite DNA sequences. Finally, some transposable elements from the W assembly were found to be highly diverse and divergent from elements found elsewhere in the genome, suggesting a rapid amplification of these elements on the W chromosome.

Sex-related differences in aging rate are associated with sex chromosome system in amphibians

Sex‐related differences in mortality are widespread in the animal kingdom. Although studies have shown that sex determination systems might drive lifespan evolution, sex chromosome influence on aging rates have not been investigated so far, likely due to an apparent lack of demographic data from clades including both XY (with heterogametic males) and ZW (heterogametic females) systems. Taking advantage of a unique collection of capture–recapture datasets in amphibians, a vertebrate group where XY and ZW systems have repeatedly evolved over the past 200 million years, we examined whether sex heterogamy can predict sex differences in aging rates and lifespans. We showed that the strength and direction of sex differences in aging rates (and not lifespan) differ between XY and ZW systems. Sex‐specific variation in aging rates was moderate within each system, but aging rates tended to be consistently higher in the heterogametic sex. This led to small but detectable effects of sex chromosome system on sex differences in aging rates in our models. Although preliminary, our results suggest that exposed recessive deleterious mutations on the X/Z chromosome (the “unguarded X/Z effect”) or repeat‐rich Y/W chromosome (the “toxic Y/W effect”) could accelerate aging in the heterogametic sex in some vertebrate clades.

Sex-chromosome evolution in frogs: what role for sex-antagonistic genes?

Sex-antagonistic (SA) genes are widely considered to be crucial players in the evolution of sex chromosomes, being instrumental in the arrest of recombination and degeneration of Y chromosomes, as well as important drivers of sex-chromosome turnovers. To test such claims, one needs to focus on systems at the early stages of differentiation, ideally with a high turnover rate. Here, I review recent work on two families of amphibians, Ranidae (true frogs) and Hylidae (tree frogs), to show that results gathered so far from these groups provide no support for a significant role of SA genes in the evolutionary dynamics of their sex chromosomes. The findings support instead a central role for neutral processes and deleterious mutations. 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)'.

Sex Differentiation in Amphibians: Effect of Temperature and Its Influence on Sex Reversal

The role of environmental factors in sexual differentiation in amphibians is not new. The effect of hormones or hormone-like compounds is widely demonstrated. However, the effect of temperature has traditionally been regarded as something anecdotal that occurs in extreme situations and not as a factor to be considered. The data currently available reveal a different situation. Sexual differentiation in some amphibian species can be altered even by small changes in temperature. On the other hand, although not proven, it is possible that temperature is related to the appearance of sex-reversed individuals in natural populations under conditions unrelated to environmental contaminants. According to this, temperature, through sex reversal (phenotypic sex opposed to genetic sex), could play an important role in the turnover of sex-determining genes and in the maintenance of homomorphic sex chromosomes in this group. Accordingly, and given the expected increase in global temperatures, growth and sexual differentiation in amphibians could easily be affected, altering the sex ratio in natural populations and posing major conservation challenges for a group in worldwide decline. It is therefore particularly urgent to understand the mechanism by which temperature affects sexual differentiation in amphibians.

The Diversity and Evolution of Sex Chromosomes in Frogs

Frogs are ideal organisms for studying sex chromosome evolution because of their diversity in sex chromosome differentiation and sex-determination systems. We review 222 anuran frogs, spanning ~220 Myr of divergence, with characterized sex chromosomes, and discuss their evolution, phylogenetic distribution and transitions between homomorphic and heteromorphic states, as well as between sex-determination systems. Most (~75%) anurans have homomorphic sex chromosomes, with XY systems being three times more common than ZW systems. Most remaining anurans (~25%) have heteromorphic sex chromosomes, with XY and ZW systems almost equally represented. There are Y-autosome fusions in 11 species, and no W-/Z-/X-autosome fusions are known. The phylogeny represents at least 19 transitions between sex-determination systems and at least 16 cases of independent evolution of heteromorphic sex chromosomes from homomorphy, the likely ancestral state. Five lineages mostly have heteromorphic sex chromosomes, which might have evolved due to demographic and sexual selection attributes of those lineages. Males do not recombine over most of their genome, regardless of which is the heterogametic sex. Nevertheless, telomere-restricted recombination between ZW chromosomes has evolved at least once. More comparative genomic studies are needed to understand the evolutionary trajectories of sex chromosomes among frog lineages, especially in the ZW systems.

When Sex Chromosomes Recombine Only in the Heterogametic Sex: Heterochiasmy and Heterogamety in Hyla Tree Frogs

Sex chromosomes are classically predicted to stop recombining in the heterogametic sex, thereby enforcing linkage between sex-determining (SD) and sex-antagonistic (SA) genes. With the same rationale, a pre-existing sex asymmetry in recombination is expected to affect the evolution of heterogamety, for example, a low rate of male recombination might favor transitions to XY systems, by generating immediate linkage between SD and SA genes. Furthermore, the accumulation of deleterious mutations on nonrecombining Y chromosomes should favor XY-to-XY transitions (which discard the decayed Y), but disfavor XY-to-ZW transitions (which fix the decayed Y as an autosome). Like many anuran amphibians, Hyla tree frogs have been shown to display drastic heterochiasmy (males only recombine at chromosome tips) and are typically XY, which seems to fit the above expectations. Instead, here we demonstrate that two species, H. sarda and H. savignyi, share a common ZW system since at least 11 Ma. Surprisingly, the typical pattern of restricted male recombination has been maintained since then, despite female heterogamety. Hence, sex chromosomes recombine freely in ZW females, not in ZZ males. This suggests that heterochiasmy does not constrain heterogamety (and vice versa), and that the role of SA genes in the evolution of sex chromosomes might have been overemphasized.

Snake W Sex Chromosome: The Shadow of Ancestral Amniote Super-Sex Chromosome

: Heteromorphic sex chromosomes, particularly the ZZ/ZW sex chromosome system of birds and some reptiles, undergo evolutionary dynamics distinct from those of autosomes. The W sex chromosome is a unique karyological member of this heteromorphic pair, which has been extensively studied in snakes to explore the origin, evolution, and genetic diversity of amniote sex chromosomes. The snake W sex chromosome offers a fascinating model system to elucidate ancestral trajectories that have resulted in genetic divergence of amniote sex chromosomes. Although the principal mechanism driving evolution of the amniote sex chromosome remains obscure, an emerging hypothesis, supported by studies of W sex chromosomes of squamate reptiles and snakes, suggests that sex chromosomes share varied genomic blocks across several amniote lineages. This implies the possible split of an ancestral super-sex chromosome via chromosomal rearrangements. We review the major findings pertaining to sex chromosomal profiles in amniotes and discuss the evolution of an ancestral super-sex chromosome by collating recent evidence sourced mainly from the snake W sex chromosome analysis. We highlight the role of repeat-mediated sex chromosome conformation and present a genomic landscape of snake Z and W chromosomes, which reveals the relative abundance of major repeats, and identifies the expansion of certain transposable elements. The latest revolution in chromosomics, i.e., complete telomere-to-telomere assembly, offers mechanistic insights into the evolutionary origin of sex chromosomes.

Hybridization and introgression between toads with different sex chromosome systems

The growing interest in the lability of sex determination in non‐model vertebrates such as amphibians and fishes has revealed high rates of sex chromosome turnovers among closely related species of the same clade. Can such lineages hybridize and admix with different sex‐determining systems, or could the changes have precipitated their speciation? We addressed these questions in incipient species of toads (Bufonidae), where we identified a heterogametic transition and characterized their hybrid zone with genome‐wide markers (RADseq). Adult and sibship data confirmed that the common toad B. bufo is female heterogametic (ZW), while its sister species the spined toad B. spinosus is male heterogametic (XY). Analysis of a fine scale transect across their parapatric ranges in southeastern France unveiled a narrow tension zone (∼10 km), with asymmetric mitochondrial and nuclear admixture over hundreds of kilometers southward and northward, respectively. The geographic extent of introgression is consistent with an expansion of B. spinosus across B. bufo’s former ranges in Mediterranean France, as also suggested by species distribution models. However, widespread cyto‐nuclear discordances (B. spinosus backrosses carrying B. bufo mtDNA) run against predictions from the dominance effects of Haldane's rule, perhaps because Y and W heterogametologs are not degenerated. Common and spined toads can thus successfully cross‐breed despite fundamental differences in their sex determination mechanisms, but remain partially separated by reproductive barriers. Whether and how the interactions of their XY and ZW genes contribute to these barriers shall provide novel insights on the debated role of labile sex chromosomes in speciation.

Genomic architecture and evolutionary antagonism drive allelic expression bias in the social supergene of red fire ants

Supergene regions maintain alleles of multiple genes in tight linkage through suppressed recombination. Despite their importance in determining complex phenotypes, our empirical understanding of early supergene evolution is limited. Here we focus on the young ‘social’ supergene of fire ants, a powerful system for disentangling the effects of evolutionary antagonism and suppressed recombination. We hypothesize that gene degeneration and social antagonism shaped the evolution of the fire ant supergene, resulting in distinct patterns of gene expression. We test these ideas by identifying allelic differences between supergene variants, characterizing allelic expression across populations, castes and body parts, and contrasting allelic expression biases with differences in expression between social forms. We find strong signatures of gene degeneration and gene-specific dosage compensation. On this background, a small portion of the genes has the signature of adaptive responses to evolutionary antagonism between social forms.

Red fire ants (Solenopsis invicta) are native to South America, but the species has spread to North America, Australia and New Zealand where it can be an invasive pest. A reason for this species’ invasiveness types of colonies : one with a single egg-laying queen and another with several queens. However, it is not possible to simply add more queens to a colony with one queen. Instead, the number of queens in a colony is controlled genetically, by a chromosome known as the ‘social chromosome’.

Like many other animals, red fire ants are diploid: their cells have two copies of each chromosome, which can carry two different versions of each gene. The social chromosome is no different, and it comes in two variants, SB and Sb. Each ant can therefore have either two SB chromosomes, leading to a colony with a single queen; or one SB chromosome and one Sb chromosome, leading to a colony with multiple queens. Ants with two copies of the Sb variant die when they are young, so the Sb version is inherited in a similar way to how the Y chromosome is passed on in humans. However, the social chromosome in red fire ants appeared less than one million years ago, making it much younger than the human Y chromosome, which is 180 million years old. This makes the social chromosome a good candidate for examining the early evolution of special chromosome variants that are only inherited.

How differences between the SB and the Sb chromosomes are evolving is an open question, however. Perhaps each version of the social chromosome has been optimised through natural selection to one colony type. Another suggestion is that the Sb chromosome has degenerated over time because its genes cannot be ‘reshuffled’ as they would be on normal chromosomes.

Martinez-Ruiz et al. compared genetic variants on the SB and Sb chromosomes, along with their expression in different types of ant colonies. The analysis showed that the Sb variant is in fact breaking down because of the lack of gene shuffling. This loss is compensated by intact copies of the same genes found on the SB variant, which explains why ants with the Sb variant can only survive if they also carry the SB version. Only a handful of genes on the social chromosomes appear to have been optimised by natural selection. Therefore Martinez-Ruiz et al. concluded the differences between the two chromosomes that lead to different colony types are collateral effects of Sb’s inability to reshuffle its genes.

This work reveals how a special chromosome similar to the Y chromosome in humans evolved. It also shows how multiple complex evolutionary forces can shape a species’ genetic makeup and social forms.

Large-Scale Hybridisation as an Extinction Threat to the Suweon Treefrog (Hylidae: Dryophytes suweonensis)

Simple Summary

A large number of amphibian species are now endangered, mostly because of human activities. An example is land modification, which may bring species that were previously isolated in contact, and allows them to hybridise. Here, we assessed the presence of hybrid individuals between the endangered Suweon treefrog (Dryophytes suweonensis) and the widespread Japanese treefrog (Dryophytes japonicus). We found hybrids to be relatively widespread and present at all populations where the Suweon treefrog occurred. This is important, as it results in an additional threat to the Suweon treefrog.

Abstract

Amphibians are in the midst of a sixth mass extinction, and human activities play a major role in pushing species towards extinction. Landscape anthropisation has impacts that indirectly threaten species, in addition to the obvious destruction of natural habitats. For instance, land modification may bring human-commensal species in contact with sister-clades from which they were previously isolated. The species in these new contact zones are then able to hybridise to the point of reaching lineage fusion, through which the gene pool of the two species merges and one of the parental lineages becomes extirpated. Here, we documented the patterns of hybridisation between the spatially restricted D. suweonensis and the widespread D. japonicus. On the basis of the analysis of Cytochrome c oxidase subunit I mitochondrial DNA sequences (404 individuals from 35 sites) and six polymorphic microsatellites (381 individuals from 34 sites), we revealed a generalised, bi-directional, and geographically widespread hybridisation between the two species. Evidence of fertile back-crosses is provided by relatively high numbers of individuals in cyto-nuclear disequilibrium, as well as the presence of hybrid individuals further south than the species distribution limit, determined on the basis of call properties. Hybridisation is an additional threat to the endangered D. suweonensis.

Sex Chromosome Evolution in Muscid Flies

Sex chromosomes and sex determining genes can evolve fast, with the sex-linked chromosomes often differing between closely related species. Population genetics theory has been developed and tested to explain the rapid evolution of sex chromosomes and sex determination. However, we do not know why the sex chromosomes are divergent in some taxa and conserved in others. Addressing this question requires comparing closely related taxa with conserved and divergent sex chromosomes to identify biological features that could explain these differences. Cytological karyotypes suggest that muscid flies (e.g., house fly) and blow flies are such a taxonomic pair. The sex chromosomes appear to differ across muscid species, whereas they are conserved across blow flies. Despite the cytological evidence, we do not know the extent to which muscid sex chromosomes are independently derived along different evolutionary lineages. To address that question, we used genomic and transcriptomic sequence data to identify young sex chromosomes in two closely related muscid species, horn fly (Haematobia irritans) and stable fly (Stomoxys calcitrans). We provide evidence that the nascent sex chromosomes of horn fly and stable fly were derived independently from each other and from the young sex chromosomes of the closely related house fly (Musca domestica). We present three different scenarios that could have given rise to the sex chromosomes of horn fly and stable fly, and we describe how the scenarios could be distinguished. Distinguishing between these scenarios in future work could identify features of muscid genomes that promote sex chromosome divergence.

The effect of phylogeographic history on species boundaries: a comparative framework in Hyla tree frogs

Because it is indicative of reproductive isolation, the amount of genetic introgression across secondary contact zones is increasingly considered in species delimitation. However, patterns of admixture at range margins can be skewed by the regional dynamics of hybrid zones. In this context, we posit an important role for phylogeographic history: hybrid zones located within glacial refugia (putatively formed during the Late-Pleistocene) should be better defined than those located in post-glacial or introduced ranges (putatively formed during the Holocene and the Anthropocene). We test this hypothesis in a speciation continuum of tree frogs from the Western Palearctic (Hyla), featuring ten identified contacts between species spanning Plio-Pleistocene to Miocene divergences. We review the rich phylogeographic literature of this group and examine the overlooked transition between H. arborea and H. molleri in Western France using a multilocus dataset. Our comparative analysis supports a trend that contacts zones resulting from post-glacial expansions and human translocations feature more extensive introgression than those established within refugial areas. Integrating the biogeographic history of incipient species, i.e. their age since first contact together with their genetic divergence, thus appears timely to draw sound evolutionary and taxonomic inferences from patterns of introgression across hybrid zones.

Evolutionary Dynamics of Sex Chromosomes of Paleognathous Birds

Standard models of sex chromosome evolution propose that recombination suppression leads to the degeneration of the heterogametic chromosome, as is seen for the Y chromosome in mammals and the W chromosome in most birds. Unlike other birds, paleognaths (ratites and tinamous) possess large nondegenerate regions on their sex chromosomes (PARs or pseudoautosomal regions). It remains unclear why these large PARs are retained over >100 Myr, and how this retention impacts the evolution of sex chromosomes within this system. To address this puzzle, we analyzed Z chromosome evolution and gene expression across 12 paleognaths, several of whose genomes have recently been sequenced. We confirm at the genomic level that most paleognaths retain large PARs. As in other birds, we find that all paleognaths have incomplete dosage compensation on the regions of the Z chromosome homologous to degenerated portions of the W (differentiated regions), but we find no evidence for enrichments of male-biased genes in PARs. We find limited evidence for increased evolutionary rates (faster-Z) either across the chromosome or in differentiated regions for most paleognaths with large PARs, but do recover signals of faster-Z evolution in tinamou species with mostly degenerated W chromosomes, similar to the pattern seen in neognaths. Unexpectedly, in some species, PAR-linked genes evolve faster on average than genes on autosomes, suggested by diverse genomic features to be due to reduced efficacy of selection in paleognath PARs. Our analysis shows that paleognath Z chromosomes are atypical at the genomic level, but the evolutionary forces maintaining largely homomorphic sex chromosomes in these species remain elusive.

Identifying sex-linked markers in Litoria aurea: a novel approach to understanding sex chromosome evolution in an amphibian

Few taxa exhibit the variability of sex-determining modes as amphibians. However, due to the presence of homomorphic sex chromosomes in many species, this phenomenon has been difficult to study. The Australian frog, Litoria aurea, has been relatively well studied over the past 20 years due to widespread declines largely attributable to chytrid fungus. However, it has been subject to few molecular studies and its mode of sex determination remained unknown. We applied DArTseq™ to develop sex-linked single nucleotide polymorphisms (SNPs) and restriction fragment presence/absence (PA) markers in 44 phenotypically sexed L. aurea individuals from the Molonglo River in NSW, Australia. We conclusively identified a male heterogametic (XX-XY) sex determination mode in this species, identifying 11 perfectly sex-linked SNP and six strongly sex-linked PA markers. We identified a further 47 moderately sex-linked SNP loci, likely serving as evidence indicative of XY recombination. Furthermore, within these 47 loci, a group of nine males were found to have a feminised Y chromosome that significantly differed to all other males. We postulate ancestral sex-reversal as a means for the evolution of this now pseudoautosomal region on the Y chromosome. Our findings present new evidence for the ‘fountain of youth’ hypothesis for the retention of homomorphic sex chromosomes in amphibians and describe a novel approach for the study of sex chromosome evolution in amphibia.

Extreme heterogeneity in sex chromosome differentiation and dosage compensation in livebearers

Once recombination is halted between the X and Y chromosomes, sex chromosomes begin to differentiate and transition to heteromorphism. While there is a remarkable variation across clades in the degree of sex chromosome divergence, far less is known about the variation in sex chromosome differentiation within clades. Here, we combined whole-genome and transcriptome sequencing data to characterize the structure and conservation of sex chromosome systems across Poeciliidae, the livebearing clade that includes guppies. We found that the Poecilia reticulata XY system is much older than previously thought, being shared not only with its sister species, Poecilia wingei, but also with Poecilia picta, which diverged roughly 20 million years ago. Despite the shared ancestry, we uncovered an extreme heterogeneity across these species in the proportion of the sex chromosome with suppressed recombination, and the degree of Y chromosome decay. The sex chromosomes in P. reticulata and P. wingei are largely homomorphic, with recombination in the former persisting over a substantial fraction. However, the sex chromosomes in P. picta are completely nonrecombining and strikingly heteromorphic. Remarkably, the profound degradation of the ancestral Y chromosome in P. picta is counterbalanced by the evolution of functional chromosome-wide dosage compensation in this species, which has not been previously observed in teleost fish. Our results offer important insight into the initial stages of sex chromosome evolution and dosage compensation.

Satellite DNA Mapping in Pseudis fusca (Hylidae, Pseudinae) Provides New Insights into Sex Chromosome Evolution in Paradoxical Frogs

In the frog genus Pseudis, previous works found a sex-linked heteromorphism of the PcP190 satellite DNA in the nucleolus organizer region (NOR)-bearing chromosome pairs of Pseudis bolbodactyla and Pseudis tocantins, which possess a ZZ/ZW sex determination system. A pericentromeric inversion was inferred to have occurred during W chromosome evolution, moving a chromosomal cluster enriched by the PcP190 from the short arm (as observed in P. bolbodactyla) to the NOR-bearing long arm (as observed in P. tocantins). However, whether such an inversion happened in P. tocantins or in the common ancestor of Pseudis fusca and P. tocantins remained unclear. To assess this question, we mapped PcP190 in the karyotype of P. fusca from three distinct localities. Southern blotting was used to compare males and females. The mitochondrial H1 fragment (which contains the 12S ribosomal RNA (rRNA), tRNAval, and 16S rRNA genes) and cytochrome b gene were partially sequenced, and a species tree was inferred to guide our analysis. Pseudis fusca specimens were placed together as the sister group of P. tocantins, but based on genetic distance, one of the analyzed populations is probably an undescribed species. A cluster of PcP190, located in the long arm of chromosome 7, is sex linked in this putative new species but not in the remaining P. fusca. We could infer that the pericentromeric inversion that moved the PcP190 site to the NOR-bearing chromosome arm (long arm) occurred in the common ancestor of P. fusca, the putative undescribed species, and P. tocantins.

Evolution of Young Sex Chromosomes in Two Dioecious Sister Plant Species with Distinct Sex Determination Systems

In the last decade, progress has been made in methods to identify the sex determination system in plants. This gives the opportunity to study sex chromosomes that arose independently at different phylogenetic scales, and thus allows the discovery and the understanding of early stages of sex chromosome evolution. In the genus Silene, sex chromosomes have evolved independently in at least two clades from a nondioecious ancestor, the Melandrium and Otites sections. In the latter, sex chromosomes could be younger than in the section Melandrium, based on phylogenetic studies and as no heteromorphic sex chromosomes have been detected. This section might also exhibit lability in sex determination, because male heterogamy and female heterogamy have been suggested to occur.

In this study, we investigated the sex determination system of two dioecious species in the section Otites (Silene otites and its close relative Silene pseudotites). Applying the new probabilistic method SEX-DETector on RNA-seq data from cross-controlled progenies, we inferred their most likely sex determination system and a list of putative autosomal and sex-linked contigs. We showed that the two phylogenetically close species differed in their sex determination system (XY versus ZW) with sex chromosomes that derived from two different pairs of autosomes. We built a genetic map of the sex chromosomes and showed that both pairs exhibited a large region with lack of recombination. However, the sex-limited chromosomes exhibited no strong degeneration. Finally, using the “ancestral” autosomal expression of sex-linked orthologs of nondioecious S. nutans, we found a slight signature of dosage compensation in the heterogametic females of S. otites.

An investigation of Y chromosome incorporations in 400 species of Drosophila and related genera

Y chromosomes are widely believed to evolve from a normal autosome through a process of massive gene loss (with preservation of some male genes), shaped by sex-antagonistic selection and complemented by occasional gains of male-related genes. The net result of these processes is a male-specialized chromosome. This might be expected to be an irreversible process, but it was found in 2005 that the Drosophila pseudoobscura Y chromosome was incorporated into an autosome. Y chromosome incorporations have important consequences: a formerly male-restricted chromosome reverts to autosomal inheritance, and the species may shift from an XY/XX to X0/XX sex-chromosome system. In order to assess the frequency and causes of this phenomenon we searched for Y chromosome incorporations in 400 species from Drosophila and related genera. We found one additional large scale event of Y chromosome incorporation, affecting the whole montium subgroup (40 species in our sample); overall 13% of the sampled species (52/400) have Y incorporations. While previous data indicated that after the Y incorporation the ancestral Y disappeared as a free chromosome, the much larger data set analyzed here indicates that a copy of the Y survived as a free chromosome both in montium and pseudoobscura species, and that the current Y of the pseudoobscura lineage results from a fusion between this free Y and the neoY. The 400 species sample also showed that the previously suggested causal connection between X-autosome fusions and Y incorporations is, at best, weak: the new case of Y incorporation (montium) does not have X-autosome fusion, whereas nine independent cases of X-autosome fusions were not followed by Y incorporations. Y incorporation is an underappreciated mechanism affecting Y chromosome evolution; our results show that at least in Drosophila it plays a relevant role and highlight the need of similar studies in other groups.

In contrast to other chromosomes (X and autosomes), which are present in males and females, Y chromosomes spend all time in males. Hence it is not surprising that along evolution they became male specialized, e.g., containing a disproportionate amount of male-fertility genes. Interestingly it was found in 2005 that in Drosophila pseudoobscura the Y chromosome reverted to "male-female existence", being incorporated into an autosome. These "Y chromosome incorporations" have important consequences on sex-chromosome evolution, and allow the study of the evolutionary forces that shaped Y chromosomes as they act backwards. As D. pseudoobscura was the second Drosophila species investigated in this respect, it is likely that other cases exist, and that perhaps it is a common phenomenon. In order to answer this question we studied 400 Drosophila species. We found one additional case of Y incorporation, which occurred in the ancestor of Drosophila montium, and currently affects a large number of species; overall 13% of the species we sampled (52/400) have Y incorporations. We also found that a previously suggested cause of Y incorporations (X-autosome fusions) is not a general explanation. Our results show that in Drosophila Y incorporations play a relevant role and highlight the need of similar studies in other groups.

A rapid rate of sex-chromosome turnover and non-random transitions in true frogs

The canonical model of sex-chromosome evolution predicts that, as recombination is suppressed along sex chromosomes, gametologs will progressively differentiate, eventually becoming heteromorphic. However, there are numerous examples of homomorphic sex chromosomes across the tree of life. This homomorphy has been suggested to result from frequent sex-chromosome turnovers, yet we know little about which forces drive them. Here, we describe an extremely fast rate of turnover among 28 species of Ranidae. Transitions are not random, but converge on several chromosomes, potentially due to genes they harbour. Transitions also preserve the ancestral pattern of male heterogamety, in line with the ‘hot-potato’ model of sex-chromosome transitions, suggesting a key role for mutation-load accumulation in non-recombining genomic regions. The importance of mutation-load selection in frogs might result from the extreme heterochiasmy they exhibit, making frog sex chromosomes differentiate immediately from emergence and across their entire length.

The evolutionary forces that favour transitions in sex chromosomes are not well understood. Here, Jeffries and colleagues show a very high rate of sex chromosome turnover in true frogs, which may be driven by rapid mutation-load accumulation due to the low recombination rate in males.

Repeated translocation of a gene cassette drives sex-chromosome turnover in strawberries

Turnovers of sex-determining systems represent important diversifying forces across eukaryotes. Shifts in sex chromosomes—but conservation of the master sex-determining genes—characterize distantly related animal lineages. Yet in plants, in which separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive sex-chromosome turnovers within closely related taxonomic groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heterogametic (ZW) inheritance, yet sex maps to three different chromosomes in different taxa. To characterize these turnovers, we identified sequences unique to females and assembled their reads into contigs. For most octoploid Fragaria taxa, a short (13 kb) sequence was observed in all females and never in males, implicating it as the sex-determining region (SDR). This female-specific “SDR cassette” contains both a gene with a known role in fruit and pollen production and a novel retrogene absent on Z and autosomal chromosomes. Phylogenetic comparison of SDR cassettes revealed three clades and a history of repeated translocation. Remarkably, the translocations can be ordered temporally due to the capture of adjacent sequence with each successive move. The accumulation of the “souvenir” sequence—and the resultant expansion of the hemizygous SDR over time—could have been adaptive by locking genes into linkage with sex. Terminal inverted repeats at the insertion borders suggest a means of movement. To our knowledge, this is the first plant SDR shown to be translocated, and it suggests a new mechanism (“move-lock-grow”) for expansion and diversification of incipient sex chromosomes.

Sex chromosomes frequently restructure themselves during organismal evolution, often becoming highly differentiated. This dynamic process is poorly understood for most taxa, especially during the early stages typical of many dioecious flowering plants. We show that in wild strawberries, a female-specific region of DNA is associated with sex and has repeatedly changed its genomic location, each time increasing the size of the hemizygous female-specific sequence on the W sex chromosome. This observation shows, for the first time to our knowledge, that plant sex regions can “jump” and suggests that this phenomenon may be adaptive by gathering and locking new genes into linkage with sex. This conserved and presumed causal sex-determining sequence, which varies in both genomic location and degree of differentiation, will facilitate future studies to understand how sex chromosomes first begin to differentiate.

Chromosome evolution in Cophomantini (Amphibia, Anura, Hylinae)

The hylid tribe Cophomantini is a diverse clade of Neotropical treefrogs composed of the genera Aplastodiscus, Boana, Bokermannohyla, Hyloscirtus, and Myersiohyla. The phylogenetic relationships of Cophomantini have been comprehensively reviewed in the literature, providing a suitable framework for the study of chromosome evolution. Employing different banding techniques, we studied the chromosomes of 25 species of Boana and 3 of Hyloscirtus; thus providing, for the first time, data for Hyloscirtus and for 15 species of Boana. Most species showed karyotypes with 2n = 2x = 24 chromosomes; some species of the B. albopunctata group have 2n = 2x = 22, and H. alytolylax has 2n = 2x = 20. Karyotypes are all bi-armed in most species presented, with the exception of H. larinopygion (FN = 46) and H. alytolylax (FN = 38), with karyotypes that have a single pair of small telocentric chromosomes. In most species of Boana, NORs are observed in a single pair of chromosomes, mostly in the small chromosomes, although in some species of the B. albopunctata, B. pulchella, and B. semilineata groups, this marker occurs on the larger pairs 8, 1, and 7, respectively. In Hyloscirtus, NOR position differs in the three studied species: H. alytolylax (4p), H. palmeri (4q), and H. larinopygion (1p). Heterochromatin is a variable marker that could provide valuable evidence, but it would be necesserary to understand the molecular composition of the C-bands that are observed in different species in order to test its putative homology. In H. alytolylax, a centromeric DAPI+ band was observed on one homologue of chromosome pair 2. The band was present in males but absent in females, providing evidence for an XX/XY sex determining system in this species. We review and discuss the importance of the different chromosome markers (NOR position, C-bands, and DAPI/CMA3 patterns) for their impact on the taxonomy and karyotype evolution in Cophomantini.

Impact of land reclamation and agricultural water regime on the distribution and conservation status of the endangered Dryophytes suweonensis

Knowledge about the distribution and habitat preferences of a species is critical for its conservation. The Suweon Treefrog (Dryophytes suweonensis) is an endangered species endemic to the Republic of Korea. We conducted surveys from 2014 to 2016 at 890 potentially suitable sites across the entire range of the species in South Korea. We then assessed whether D. suweonensis was found in the current and ancestral predicted ranges, reclaimed and protected areas, and how the presence of agricultural floodwater affected its occurrence. Our results describe a 120 km increase in the southernmost known distribution of the species, and the absence of the species at lower latitudes. We then demonstrate a putative constriction on the species ancestral range due to urban encroachment, and provide evidence for a significant increase in its coastal range due to the colonisation of reclaimed land by the species. In addition, we demonstrate that D. suweonensis is present in rice fields that are flooded with water originating from rivers as opposed to being present in rice fields that are irrigated from underground water. Finally, the non-overlap of protected areas and the occurrence of the species shows that only the edge of a single site where D. suweonensis occurs is legally protected. Based on our results and the literature, we suggest the design of a site fitting all the ecological requirements of the species, and suggest the use of such sites to prevent further erosion in the range of D. suweonensis.

Using conventional F-statistics to study unconventional sex-chromosome differentiation

Species with undifferentiated sex chromosomes emerge as key organisms to understand the astonishing diversity of sex-determination systems. Whereas new genomic methods are widening opportunities to study these systems, the difficulty to separately characterize their X and Y homologous chromosomes poses limitations. Here we demonstrate that two simple F-statistics calculated from sex-linked genotypes, namely the genetic distance (F_st) between sexes and the inbreeding coefficient (F_is) in the heterogametic sex, can be used as reliable proxies to compare sex-chromosome differentiation between populations. We correlated these metrics using published microsatellite data from two frog species (Hyla arboreaand Rana temporaria), and show that they intimately relate to the overall amount of X–Y differentiation in populations. However, the fits for individual loci appear highly variable, suggesting that a dense genetic coverage will be needed for inferring fine-scale patterns of differentiation along sex-chromosomes. The applications of these F-statistics, which implies little sampling requirement, significantly facilitate population analyses of sex-chromosomes.

Stable Cretaceous sex chromosomes enable molecular sexing in softshell turtles (Testudines: Trionychidae)

Turtles demonstrate variability in sex determination ranging from environmental sex determination (ESD) to highly differentiated sex chromosomes. However, the evolutionary dynamics of sex determining systems in this group is not well known. Differentiated ZZ/ZW sex chromosomes were identified in two species of the softshell turtles (Trionychidae) from the subfamily Trionychinae and Z-specific genes were identified in a single species. We tested Z-specificity of a subset of these genes by quantitative PCR comparing copy gene numbers in male and female genomes in 10 species covering the phylogenetic diversity of trionychids. We demonstrated that differentiated ZZ/ZW sex chromosomes are conserved across the whole family and that they were already present in the common ancestor of the extant trionychids. As the sister lineage, Carettochelys insculpta, possess ESD, we can date the origin of the sex chromosomes in trionychids between 200 Mya (split of Trionychidae and Carettochelyidae) and 120 Mya (basal splitting of the recent trionychids). The results support the evolutionary stability of differentiated sex chromosomes in some lineages of ectothermic vertebrates. Moreover, our approach determining sex-linkage of protein coding genes can be used as a reliable technique of molecular sexing across trionychids useful for effective breeding strategy in conservation projects of endangered species.

Phylogeography reveals an ancient cryptic radiation in East-Asian tree frogs (Hyla japonica group) and complex relationships between continental and island lineages

Background

In contrast to the Western Palearctic and Nearctic biogeographic regions, the phylogeography of Eastern-Palearctic terrestrial vertebrates has received relatively little attention. In East Asia, tectonic events, along with Pleistocene climatic conditions, likely affected species distribution and diversity, especially through their impact on sea levels and the consequent opening and closing of land-bridges between Eurasia and the Japanese Archipelago. To better understand these effects, we sequenced mitochondrial and nuclear markers to determine phylogeographic patterns in East-Asian tree frogs, with a particular focus on the widespread H. japonica.

Results

We document several cryptic lineages within the currently recognized H. japonica populations, including two main clades of Late Miocene divergence (~5 Mya). One occurs on the northeastern Japanese Archipelago (Honshu and Hokkaido) and the Russian Far-East islands (Kunashir and Sakhalin), and the second one inhabits the remaining range, comprising southwestern Japan, the Korean Peninsula, Transiberian China, Russia and Mongolia. Each clade further features strong allopatric Plio-Pleistocene subdivisions (~2-3 Mya), especially among continental and southwestern Japanese tree frog populations. Combined with paleo-climate-based distribution models, the molecular data allowed the identification of Pleistocene glacial refugia and continental routes of postglacial recolonization. Phylogenetic reconstructions further supported genetic homogeneity between the Korean H. suweonensis and Chinese H. immaculata, suggesting the former to be a relic population of the latter that arose when the Yellow Sea formed, at the end of the last glaciation.

Conclusions

Patterns of divergence and diversity were likely triggered by Miocene tectonic activities and Quaternary climatic fluctuations (including glaciations), causing the formation and disappearance of land-bridges between the Japanese islands and the continent. Overall, this resulted in a ring-like diversification of H. japonica around the Sea of Japan. Our findings urge for important taxonomic revisions in East-Asian tree frogs. First, they support the synonymy of H. suweonensis (Kuramoto, 1980) and H. immaculata (Boettger, 1888). Second, the nominal H. japonica (Günther, 1859) represents at least two species: an eastern (new taxon A) on the northern Japanese and Russian Far East islands, and a southwestern species (n. t. B) on southern Japanese islands and possibly also forming continental populations. Third, these continental tree frogs may also represent an additional entity, previously described as H. stepheni Boulenger, 1888 (senior synonym of H. ussuriensis Nikolskii, 1918). A complete revision of this group requires further taxonomic and nomenclatural analyses, especially since it remains unclear to which taxon the species-epitheton japonica corresponds to.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-016-0814-x) contains supplementary material, which is available to authorized users.

Identifying homomorphic sex chromosomes from wild-caught adults with limited genomic resources

We demonstrate a genotyping-by-sequencing approach to identify homomorphic sex chromosomes and their homolog in a distantly related reference genome, based on noninvasive sampling of wild-caught individuals, in the moor frog Rana arvalis. Double-digest RADseq libraries were generated using buccal swabs from 30 males and 21 females from the same population. Search for sex-limited markers from the unfiltered data set (411 446 RAD tags) was more successful than searches from a filtered data set (33 073 RAD tags) for markers showing sex differences in heterozygosity or in allele frequencies. Altogether, we obtained 292 putatively sex-linked RAD loci, 98% of which point to male heterogamety. We could map 15 of them to the Xenopus tropicalis genome, all but one on chromosome pair 1, which seems regularly co-opted for sex determination among amphibians. The most efficient mapping strategy was a three-step hierarchical approach, where R. arvalis reads were first mapped to a low-coverage genome of Rana temporaria (17 My divergence), then the R. temporaria scaffolds to the Nanorana parkeri genome (90 My divergence), and finally the N. parkeri scaffolds to the X. tropicalis genome (210 My). We validated our conclusions with PCR primers amplifying part of Dmrt1, a candidate sex determination gene mapping to chromosome 1: a sex-diagnostic allele was present in all 30 males but in none of the 21 females. Our approach is likely to be productive in many situations where biological samples and/or genomic resources are limited.

Homomorphic ZW chromosomes in a wild strawberry show distinctive recombination heterogeneity but a small sex-determining region

Recombination in ancient, heteromorphic sex chromosomes is typically suppressed at the sex-determining region (SDR) and proportionally elevated in the pseudoautosomal region (PAR). However, little is known about recombination dynamics of young, homomorphic plant sex chromosomes. We examine male and female function in crosses and unrelated samples of the dioecious octoploid strawberry Fragaria chiloensis in order to map the small and recently evolved SDR controlling both traits and to examine recombination patterns on the incipient ZW chromosome. The SDR of this ZW system is located within a 280 kb window, in which the maternal recombination rate is lower than the paternal one. In contrast to the SDR, the maternal PAR recombination rate is much higher than the rates of the paternal PAR or autosomes, culminating in an elevated chromosome-wide rate. W-specific divergence is elevated within the SDR and a single polymorphism is observed in high species-wide linkage disequilibrium with sex. Selection for recombination suppression within the small SDR may be weak, but fluctuating sex ratios could favor elevated recombination in the PAR to remove deleterious mutations on the W. The recombination dynamics of this nascent sex chromosome with a modestly diverged SDR may be typical of other dioecious plants.

How to make a sex chromosome

Sex chromosomes can evolve once recombination is halted between a homologous pair of chromosomes. Owing to detailed studies using key model systems, we have a nuanced understanding and a rich review literature of what happens to sex chromosomes once recombination is arrested. However, three broad questions remain unanswered. First, why do sex chromosomes stop recombining in the first place? Second, how is recombination halted? Finally, why does the spread of recombination suppression, and therefore the rate of sex chromosome divergence, vary so substantially across clades? In this review, we consider each of these three questions in turn to address fundamental questions in the field, summarize our current understanding, and highlight important areas for future work.

Sex chromosome evolution begins when recombination between a homologous pair of chromosomes is halted. Here, Wright et al. review our current understanding of the causes and mechanisms of recombination suppression between incipient sex chromosomes and suggest future directions for the field.

Evidence for Sex Chromosome Turnover in Proteid Salamanders

A major goal of genomic and reproductive biology is to understand the evolution of sex determination and sex chromosomes. Species of the 2 genera of the Salamander family Proteidae - Necturus of eastern North America, and Proteus of Southern Europe - have similar-looking karyotypes with the same chromosome number (2n = 38), which differentiates them from all other salamanders. However, Necturus possesses strongly heteromorphic X and Y sex chromosomes that Proteus lacks. Since the heteromorphic sex chromosomes of Necturus were detectable only with C-banding, we hypothesized that we could use C-banding to find sex chromosomes in Proteus. We examined mitotic material from colchicine-treated intestinal epithelium, and meiotic material from testes in specimens of Proteus, representing 3 genetically distinct populations in Slovenia. We compared these results with those from Necturus. We performed FISH to visualize telomeric sequences in meiotic bivalents. Our results provide evidence that Proteus represents an example of sex chromosome turnover in which a Necturus-like Y-chromosome has become permanently translocated to another chromosome converting heteromorphic sex chromosomes to homomorphic sex chromosomes. These results may be key to understanding some unusual aspects of demographics and reproductive biology of Proteus, and are discussed in the context of models of the evolution of sex chromosomes in amphibians.

Dmrt1 polymorphism covaries with sex-determination patterns in Rana temporaria

Patterns of sex-chromosome differentiation and gonadal development have been shown to vary among populations of Rana temporaria along a latitudinal transect in Sweden. Frogs from the northern-boreal population of Ammarnäs displayed well-differentiated X and Y haplotypes, early gonadal differentiation, and a perfect match between phenotypic and genotypic sex. In contrast, no differentiated Y haplotypes could be detected in the southern population of Tvedöra, where juveniles furthermore showed delayed gonadal differentiation. Here, we show that Dmrt1, a gene that plays a key role in sex determination and sexual development across all metazoans, displays significant sex differentiation in Tvedöra, with a Y-specific haplotype distinct from Ammarnäs. The differential segment is not only much shorter in Tvedöra than in Ammarnäs, it is also less differentiated and associates with both delayed gonadal differentiation and imperfect match between phenotypic and genotypic sex. Whereas Tvedöra juveniles with a local Y haplotype tend to ultimately develop as males, those without it may nevertheless become functional XX males, but with strongly female-biased progeny. Our findings suggest that the variance in patterns of sex determination documented in common frogs might result from a genetic polymorphism within a small genomic region that contains Dmrt1. They also substantiate the view that recurrent convergences of sex determination toward a limited set of chromosome pairs may result from the co-option of small genomic regions that harbor key genes from the sex-determination pathway.

The genetic contribution to sex determination and number of sex chromosomes vary among populations of common frogs (Rana temporaria)

The patterns of sex determination and sex differentiation have been shown to differ among geographic populations of common frogs. Notably, the association between phenotypic sex and linkage group 2 (LG2) has been found to be perfect in a northern Swedish population, but weak and variable among families in a southern one. By analyzing these populations with markers from other linkage groups, we bring two new insights: (1) the variance in phenotypic sex not accounted for by LG2 in the southern population could not be assigned to genetic factors on other linkage groups, suggesting an epigenetic component to sex determination; (2) a second linkage group (LG7) was found to co-segregate with sex and LG2 in the northern population. Given the very short timeframe since post-glacial colonization (in the order of 1000 generations) and its seemingly localized distribution, this neo-sex chromosome system might be the youngest one described so far. It does not result from a fusion, but more likely from a reciprocal translocation between the original Y chromosome (LG2) and an autosome (LG7), causing their co-segregation during male meiosis. By generating a strict linkage between several important genes from the sex-determination cascade (Dmrt1, Amh and Amhr2), this neo-sex chromosome possibly contributes to the 'differentiated sex race' syndrome (strictly genetic sex determination and early gonadal development) that characterizes this northern population.

Trans-species variation in Dmrt1 is associated with sex determination in four European tree-frog species

Empirical studies on the relative roles of occasional XY recombination versus sex-chromosome turnover in preventing sex-chromosome differentiation may shed light on the evolutionary forces acting on sex-determination systems. Signatures of XY recombination are difficult to distinguish from those of homologous transitions (i.e., transitions in sex-determination systems that keep sex-chromosome identity): both models predict X and Y alleles at sex-linked genes to cluster by species. However, the XY-recombination model specifically predicts the reverse pattern (clustering by gametologs) for those genes that are directly involved in sex determination. Hence, the latter model can only be validated by identification of an ancestral sex-determining region (SDR) with trans-species polymorphism associated to sex. Here we combine a candidate-gene approach with a genome scan to identify a small SDR shared by four species of a monophyletic clade of European tree frogs. This SDR encompasses at least the N-terminal part of Dmrt1 and immediate upstream sequences. Our findings provide definitive evidence that sex-chromosome homomorphy in this clade results only from XY recombination, and take an important step toward the identification of the sex-determining locus. Moreover, the sex-diagnostic markers we identify will enable research on environmental sex reversal in a wider range of frog species.

Empirical evidence for large X-effects in animals with undifferentiated sex chromosomes

Reproductive isolation is crucial for the process of speciation to progress. Sex chromosomes have been assigned a key role in driving reproductive isolation but empirical evidence from natural population processes has been restricted to organisms with degenerated sex chromosomes such as mammals and birds. Here we report restricted introgression at sex-linked compared to autosomal markers in a hybrid zone between two incipient species of European tree frog, Hyla arborea and H. orientalis, whose homologous X and Y sex chromosomes are undifferentiated. This large X-effect cannot result from the dominance or faster-X aspects of Haldane's rule, which are specific to degenerated sex chromosomes, but rather supports a role for faster-heterogametic-sex or faster-male evolutionary processes. Our data suggest a prominent contribution of undifferentiated sex chromosomes to speciation.

High-density linkage maps fail to detect any genetic component to sex determination in a Rana temporaria family

Sex chromosome differentiation in Rana temporaria varies strikingly among populations or families: whereas some males display well-differentiated Y haplotypes at microsatellite markers on linkage group 2 (LG2), others are genetically undistinguishable from females. We analysed with RADseq markers one family from a Swiss lowland population with no differentiated sex chromosomes, and where sibship analyses had failed to detect any association between the phenotypic sex of progeny and parental haplotypes. Offspring were reared in a common tank in outdoor conditions and sexed at the froglet stage. We could map a total of 2177 SNPs (1123 in the mother, 1054 in the father), recovering in both adults 13 linkage groups (= chromosome pairs) that were strongly syntenic to Xenopus tropicalis despite > 200 My divergence. Sexes differed strikingly in the localization of crossovers, which were uniformly distributed in the female but limited to chromosome ends in the male. None of the 2177 markers showed significant association with offspring sex. Considering the very high power of our analysis, we conclude that sex determination was not genetic in this family; which factors determined sex remain to be investigated.