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( d– f) Networks of Y haplotypes in Aripo ( d), Quare ( e), and Yarra ( f) rivers. The dashed line indicates the estimated diversity for 1,000 randomly sampled autosomal locations.
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Y haplotypes were included only if found in both populations (Y shared) and were consistent with an XY topology in at least one of them.
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( c) Genetic diversity (Watterson’s theta estimator) of X and Y haplotypes within Stratum I in the Aripo, Quare, and Yarra rivers. Shared Y haplotypes were present in both populations and in >66% of males in at least one population. ( b) Barplots showing the proportion of trees compatible with an XY sex chromosome system in Stratum I. The blue markers at the top indicate shared Y haplotypes between populations.
#An extraordinary abundance of tinge windows
Trees were inferred from phased alignments in nonoverlapping windows of 100 SNPs with the neighbor-joining method, see Materials and Methods for more details. ( a) Distribution of tree topologies with separate clustering of X and Y SNPs (X–Y topology) on Chromosome 12 for downstream (black) and upstream (orange) populations in Aripo, Quare, and Yarra watersheds. The guppy Y-chromosome shows exceptional genetic diversity. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. Poecilia reticulata Y haplotypes linked-reads recombination suppression sex chromosomes. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence. In addition, we show that this Y diversity is dominated by low-frequency haplotypes segregating in the population, suggesting a link between haplotype diversity and female preference for rare Y-linked color variation. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I.
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Despite longstanding assumptions that sex chromosome recombination suppression is achieved through inversions, we find no evidence of inversions associated with either Stratum I or Stratum II. In contrast, Stratum II shows divergence from the X, but no Y-specific sequence, and this divergence is greater in three replicate upstream populations compared with their downstream pair. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. In order to understand the dynamics of the guppy Y chromosome, we used linked-read sequencing to assess Y chromosome evolution and diversity across upstream and downstream population pairs that vary in predator and food abundance in three replicate watersheds. The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species.