Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data

Using a Handful of Transcriptomes to Detect Sex-Linked Markers and Develop Molecular Sexing Assays in a Species with Homomorphic Sex Chromosomes

To understand the biology of a species, it is often crucial to be able to differentiate males and females. However, many species lack easily identifiable sexually dimorphic traits. In those that possess sex chromosomes, molecular sexing offers a good alternative, and molecular sexing assays can be developed through the comparison of male and female genomic sequences. However, in many nonmodel species, sex chromosomes are poorly differentiated, and identifying sex-linked sequences and developing sexing assays can be challenging. In this study, we highlight a simple transcriptome-based procedure for the detection of sex-linked markers suitable for the development of sexing assays that circumvents limitations of more commonly used approaches. We apply it to the spotted snow skink Carinascincus ocellatus, a viviparous lizard with homomorphic XY chromosomes that has environmentally induced sex reversal. With transcriptomes from three males and three females alone, we identify thousands of putative Y-linked sequences. We confirm linkage through alignment of assembled transcripts to a distantly related lizard genome and readily design multiple single locus polymerase chain reaction primers to sex C. ocellatus and related species. Our approach also facilitates valuable comparisons of sex determining systems on a broad taxonomic scale.

Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data

The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non-model organisms.

Sex chromosome heteromorphism and the Fast-X effect in poeciliids

Fast-X evolution has been observed in a range of heteromorphic sex chromosomes. However, it remains unclear how early in the process of sex chromosome differentiation the Fast-X effect becomes detectible. Recently, we uncovered an extreme variation in sex chromosome heteromorphism across poeciliid fish species. The common guppy, Poecilia reticulata, Endler's guppy, P. wingei, swamp guppy, P. picta and para guppy, P. parae, appear to share the same XY system and exhibit a remarkable range of heteromorphism. Species outside this group lack this sex chromosome system. We combined analyses of sequence divergence and polymorphism data across poeciliids to investigate X chromosome evolution as a function of hemizygosity and reveal the causes for Fast-X effects. Consistent with the extent of Y degeneration in each species, we detect higher rates of divergence on the X relative to autosomes, a signal of Fast-X evolution, in P. picta and P. parae, species with high levels of X hemizygosity in males. In P. reticulata, which exhibits largely homomorphic sex chromosomes and little evidence of hemizygosity, we observe no change in the rate of evolution of X-linked relative to autosomal genes. In P. wingei, the species with intermediate sex chromosome differentiation, we see an increase in the rate of nonsynonymous substitutions on the older stratum of divergence only. We also use our comparative approach to test for the time of origin of the sex chromosomes in this clade. Taken together, our study reveals an important role of hemizygosity in Fast-X evolution.

Evolutionary History of the Poecilia picta Sex Chromosomes

The degree of divergence between the sex chromosomes is not always proportional to their age. In poeciliids, four closely related species all exhibit a male heterogametic sex chromosome system on the same linkage group, yet show a remarkable diversity in X and Y divergence. In Poecilia reticulata and P. wingei, the sex chromosomes remain homomorphic, yet P. picta and P. parae have a highly degraded Y chromosome. To test alternative theories about the origin of their sex chromosomes, we used a combination of pedigrees and RNA-seq data from P. picta families in conjunction with DNA-seq data collected from P. reticulata, P. wingei, P. parae, and P. picta. Phylogenetic clustering analysis of X and Y orthologs, identified through segregation patterns, and their orthologous sequences in closely related species demonstrates a similar time of origin for both the P. picta and P. reticulata sex chromosomes. We next used k-mer analysis to identify shared ancestral Y sequence across all four species, suggesting a single origin to the sex chromosome system in this group. Together, our results provide key insights into the origin and evolution of the poeciliid Y chromosome and illustrate that the rate of sex chromosome divergence is often highly heterogenous, even over relatively short evolutionary time frames.

Genomic trajectories of a near-extinction event in the Chatham Island black robin

Background

Understanding the micro-­evolutionary response of populations to demographic declines is a major goal in evolutionary and conservation biology. In small populations, genetic drift can lead to an accumulation of deleterious mutations, which will increase the risk of extinction. However, demographic recovery can still occur after extreme declines, suggesting that natural selection may purge deleterious mutations, even in extremely small populations. The Chatham Island black robin (Petroica traversi) is arguably the most inbred bird species in the world. It avoided imminent extinction in the early 1980s and after a remarkable recovery from a single pair, a second population was established and the two extant populations have evolved in complete isolation since then. Here, we analysed 52 modern and historical genomes to examine the genomic consequences of this extreme bottleneck and the subsequent translocation.

Results

We found evidence for two-fold decline in heterozygosity and three- to four-fold increase in inbreeding in modern genomes. Moreover, there was partial support for temporal reduction in total load for detrimental variation. In contrast, compared to historical genomes, modern genomes showed a significantly higher realised load, reflecting the temporal increase in inbreeding. Furthermore, the translocation induced only small changes in the frequency of deleterious alleles, with the majority of detrimental variation being shared between the two populations.

Conclusion

Our results highlight the dynamics of mutational load in a species that recovered from the brink of extinction, and show rather limited temporal changes in mutational load. We hypothesise that ancestral purging may have been facilitated by population fragmentation and isolation on several islands for thousands of generations and may have already reduced much of the highly deleterious load well before human arrival and introduction of pests to the archipelago. The majority of fixed deleterious variation was shared between the modern populations, but translocation of individuals with low mutational load could possibly mitigate further fixation of high-frequency deleterious variation.