Shared and Species-Specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species

Morris, Jeffrey J.; Darolti, Iulia; Bloch, Natasha I.; Wright, Alison E.; Mank, Judith E.

doi:10.3390/genes9050238

Cited by 30 publications

(69 citation statements)

References 68 publications

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“…Identifying the equidistant point between the maximum of these two peaks can help minimize the error in identifying sex‐linked regions, and has been employed successfully across a number of species (Huylmans, Toups, Macon, Gammerdinger, & Vicoso, ; Vicoso & Bachtrog, ). Lastly, the k ‐mer counting approach (Akagi, Henry, Tao, & Comai, ; Carvalho & Clark, ; Li et al, ; Morris, Darolti, Bloch, Wright, & Mank, ; Pucholt, Wright, Conze, Mank, & Berlin, ) is based on similar underlying principles. Male and female genomes are broken up into k ‐mers, counted computationally, and autosomal, Y‐, and X‐linked k ‐mers are identified on the basis of read coverage.…”

Section: Guide For Identifying Sex Chromosomesmentioning

confidence: 99%

“…Male and female genomes are broken up into k ‐mers, counted computationally, and autosomal, Y‐, and X‐linked k ‐mers are identified on the basis of read coverage. This method is unaffected by differences in filtering and read length and can be useful for identifying sex chromosomes across species where next‐generation sequencing data sets are of varying quality (Morris et al, ). Additionally, k‐mer analyses have been used to provide insight into the amount of repetitive elements accumulating on recently evolved Y chromosomes (Carvalho & Clark, ; Morris et al, ; Pucholt et al, ).…”

Section: Guide For Identifying Sex Chromosomesmentioning

confidence: 99%

“…In contrast, very short k‐mers are likely to be overrepresented in the data set, leading to low resolution to identify sex‐limited regions (Kelley, Schatz, & Salzberg, ). The choice of optimal k ‐mer size can range from 15–31 bp depending on genome size of the organism (Carvalho & Clark, ; Morris et al, ). Coverage‐based approaches have been used to identify sex chromosomes from DNA‐seq data obtained from only one individual from each sex (Vicoso & Bachtrog, ) but read depth must be reasonably high to avoid confounding effects of sequencing errors (see Box 1) (>20‐fold; Carvalho & Clark, ; Hall et al, ; Smeds et al, ; Vicoso & Bachtrog, ).…”

Section: Guide For Identifying Sex Chromosomesmentioning

confidence: 99%

“…Lastly, the k-mer counting approach (Akagi, Henry, Tao, & Comai, 2014;Carvalho & Clark, 2013;Li et al, 2018;Morris, Darolti, Bloch, Wright, & Mank, 2018;Pucholt, Wright, Conze, Mank, & Berlin, 2017) is based on similar underlying principles. Male and female genomes are broken up into k-mers, counted computationally, and autosomal, Y-, and X-linked k-mers are identified on the basis of read coverage.…”

Section: Genomic Coverage Approachmentioning

confidence: 99%

“…This method is unaffected by differences in filtering and read length and can be useful for identifying sex chromosomes across species where next-generation sequencing data sets are of varying quality (Morris et al, 2018). Additionally, k-mer analyses have been used to provide insight into the amount of repetitive elements accumulating on recently evolved Y chromosomes (Carvalho & Clark, 2013;Morris et al, 2018;Pucholt et al, 2017). Finally, in combination with next-generation sequencing data obtained from flow-sorted Y chromosomes, k-mer approaches can filter contaminant autosomal and X-linked sequences, thus improving the quality of the downstream Y chromosome assembly (Rangavittal et al, 2018).…”

Section: Genomic Coverage Approachmentioning

confidence: 99%

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How to identify sex chromosomes and their turnover

et al. 2019

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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.

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Section: Guide For Identifying Sex Chromosomesmentioning

confidence: 99%

Section: Guide For Identifying Sex Chromosomesmentioning

confidence: 99%

Section: Guide For Identifying Sex Chromosomesmentioning

confidence: 99%

Section: Genomic Coverage Approachmentioning

confidence: 99%

Section: Genomic Coverage Approachmentioning

confidence: 99%

See 3 more Smart Citations

How to identify sex chromosomes and their turnover

et al. 2019

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A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy

et al. 2022

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Male colour patterns of the Trinidadian guppy (Poecilia reticulata) are typified by extreme variation governed by both natural and sexual selection. Since guppy colour patterns are often inherited faithfully from fathers to sons, it has been hypothesised that many of the colour trait genes must be physically linked to sex determining loci as a ‘supergene’ on the sex chromosome. Here, we phenotype and genotype four guppy ‘Iso-Y lines’, where colour was inherited along the patriline for 40 generations. Using an unbiased phenotyping method, we confirm the breeding design was successful in creating four distinct colour patterns. We find that genetic differentiation among the Iso-Y lines is repeatedly associated with a diverse haplotype on an autosome (LG1), not the sex chromosome (LG12). Moreover, the LG1 haplotype exhibits elevated linkage disequilibrium and evidence of sex-specific diversity in the natural source population. We hypothesise that colour pattern polymorphism is driven by Y-autosome epistasis.

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Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish

et al. 2021

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Loss of recombination between sex chromosomes often depletes Y chromosomes of functional content and genetic variation, which might limit their potential to generate adaptive diversity. Males of the freshwater fish Poecilia parae occur as one of five discrete morphs, all of which shoal together in natural populations where morph frequency has been stable for over 50 years. Each morph utilizes a different complex reproductive strategy, and morphs differ dramatically in color, body size, and mating behavior.Morph phenotype is passed perfectly from father to son, indicating there are five Y haplotypes segregating in the species, which encode the complex male morph characteristics. Here, we examine Y diversity in natural populations of P. parae. Using linked-read sequencing on multiple P. parae females and males of all five morphs, we find that the genetic architecture of the male morphs evolved on the Y chromosome after recombination suppression had occurred with the X. Comparing Y chromosomes between each of the morphs, we show that although the Ys of the three minor morphs that differ in color are highly similar, there are substantial amounts of unique genetic material and divergence between the Ys of the three major morphs that differ in reproductive strategy, body size and mating behavior.Altogether, our results suggest that the Y chromosome is able to overcome the constraints of recombination loss to generate extreme diversity, resulting in five discrete Y chromosomes that control complex reproductive strategies. morphs. Most importantly, multigeneration pedigrees show that morph phenotype is always passed perfectly from father to son 13 , indicating the five P. parae morphs are controlled by five different Y chromosomes. This system therefore offers the potential for a unique insight into the adaptive potential of Y chromosomes, and the role of these regions of the genome in male phenotypes. Y chromosomes are formed once recombination with the X is halted 1 , and the loss of recombination on the Y leads to a complex cascade of non-adaptive processes that lead to the rapid buildup of heterochromatin and loss of gene activity [21][22][23] . However, the process of Y degeneration is not linear 24 , and although poecilid species closely related to P. parae share the same homologous sex chromosome as Poecilia reticulata 25 (guppies), the extent of Y chromosome degeneration differs markedly across the clade. Although the Y chromosome in P. reticulata and Poecilia wingei contains only a small area of limited degeneration [25][26][27][28] , the entirety of the Y chromosome of Poecilia picta is highly degenerate 25 . P. parae is a sister species of P. picta (diverging ~14.8 mya 29 ), however P. picta males are markedly different from P. parae and do not resemble any of the five P. parae morphs 18,20,[30][31][32] , suggesting remarkable diversity was generated on the P. parae Y chromosome after recombination was halted with the X chromosome. Work on model systems has indeed shown Y chromosomes can accumulate new genetic...

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Shared and Species-Specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species

Cited by 30 publications

References 68 publications

How to identify sex chromosomes and their turnover

How to identify sex chromosomes and their turnover

A large and diverse autosomal haplotype is associated with sex-linked colour polymorphism in the guppy

Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish

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