How to identify sex chromosomes and their turnover

Abstract

Although sex is a fundamental component of eukaryotic reproduction, the genetic systems that control sex determination are highly variable. In many organisms the presence of sex chromosomes is associated with female or male development. Although certain groups possess stable and conserved sex chromosomes, others exhibit rapid sex chromosome evolution, including transitions between male and female heterogamety, and turnover in the chromosome pair recruited to determine sex. These turnover events have important consequences for multiple facets of evolution, as sex chromosomes are predicted to play a central role in adaptation, sexual dimorphism, and speciation. However, our understanding of the processes driving the formation and turnover of sex chromosome systems is limited, in part because we lack a complete understanding of interspecific variation in the mechanisms by which sex is determined. New bioinformatic methods are making it possible to identify and characterize sex chromosomes in a diverse array of non‐model species, rapidly filling in the numerous gaps in our knowledge of sex chromosome systems across the tree of life. In turn, this growing data set is facilitating and fueling efforts to address many of the unanswered questions in sex chromosome evolution. Here, we synthesize the available bioinformatic approaches to produce a guide for characterizing sex chromosome system and identity simultaneously across clades of organisms. Furthermore, we survey our current understanding of the processes driving sex chromosome turnover, and highlight important avenues for future research.

Divergence and Remarkable Diversity of the Y Chromosome in Guppies

“…Degeneration or significant divergence of the Y chromosome results in reduced male coverage when mapped to a female reference genome, and therefore the ratio of male to female mapped reads can be used to identify regions where the Y chromosome has significantly degraded compared to the X 22,[38][39][40][41] . We have previously used this approach to identify a small region of significant Y divergence in all of the populations we assess here 15 , which was present in the common ancestor with P. wingei 22,24 , designated as Stratum I.…”

“…For regions of the X and Y chromosomes that have diverged, but still show little evidence of Y degeneration, we expect an increase in male compared to female diversity, as Y-linked reads will map to the female genome assembly, but will carry male-specific SNPs 22,38 . We previously observed elevated male SNP density 15…”

Sex differences in spiders: from phenotype to genomics

“…However, various affordable approaches are suitable for Xlinked region discovery and ultimately analysis of X chromosome evolution. The difficulty to obtain sex chromosome sequences is increasingly being overcome by methodological advances (reviewed in Muyle et al 2017;Palmer et al 2019). Promising methods associate reasonable sequencing volume and high sensitivity, such as SEX-DETector (Muyle et al 2016).…”

Characterization of a sex-determining region and its genomic context via statistical estimates of haplotype frequencies in daughters and sons sequenced in pools

“…Such endeavor can be very costly if whole-genome sequencing is undertaken on many individuals, especially considering the sample size required for reliable statistical inference. These considerations motivated the use of techniques permitting partial genome sequencing (PALMER et al 2019), such as Restriction-site Associated DNA markers (RAD sequencing) (BAIRD et al 2008), which reduce sequencing costs at the expense of an increase in DNA library preparation costs. An alternative strategy consists of pooling the DNA from multiple individuals prior to sequencing (FUTSCHIK AND SCHLÖTTERER 2010), a method referred to as "poolseq".…”

“…) was higher than the identity measured with the most similar annotated gene of A. nasatum(BECKING et al 2019), which was inferred to have diverged from the A. vulgare lineage ~25 million years ago(BECKING et al 2017). This result suggests relatively recent duplications of the two genes.Segregation analysis methods aimed at locating sex-associated regions generally rely on individual genotyping by partial genome sequencing, using RAD tags or similar techniques as cost-saving measures(PALMER et al 2019). Pool-seq appears to be less utilized for this task, especially compared to its popularity in population genomics analyses using field samples(KOFLER et al 2011).…”