eprintid: 10112615
rev_number: 18
eprint_status: archive
userid: 608
dir: disk0/10/11/26/15
datestamp: 2020-10-19 13:56:38
lastmod: 2021-10-04 00:00:27
status_changed: 2020-10-19 13:56:38
type: article
metadata_visibility: show
creators_name: Almeida, P
creators_name: Sandkam, BA
creators_name: Morris, J
creators_name: Darolti, I
creators_name: Breden, F
creators_name: Mank, JE
title: Divergence and Remarkable Diversity of the Y Chromosome in Guppies
ispublished: inpress
divisions: UCL
divisions: B02
divisions: C08
divisions: D09
divisions: F99
keywords: Poecilia reticulata, sex chromosomes, Y haplotypes, recombination suppression, linked-reads
note: Copyright © The Author(s) 2020. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
abstract: The guppy sex chromosomes show an extraordinary diversity in divergence across populations and closely related species. 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. Based on our population-specific genome assemblies, we first confirmed and extended earlier reports of two strata on the guppy sex chromosomes. Stratum I shows significant accumulation of male-specific sequence, consistent with Y divergence, and predates the colonization of Trinidad. 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 to their downstream pair. 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. Instead, we observe a remarkable diversity in Y chromosome haplotypes within each population, even in the ancestral Stratum I. This diversity is likely due to gradual mechanisms of recombination suppression, which, unlike an inversion, allow for the maintenance of multiple haplotypes. 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 colour variation. Our results reveal the complex interplay between recombination suppression and Y chromosome divergence at the earliest stages of sex chromosome divergence.
date: 2020-10-06
date_type: published
official_url: https://doi.org/10.1093/molbev/msaa257
oa_status: green
full_text_type: other
language: eng
primo: open
primo_central: open_green
verified: verified_manual
elements_id: 1822099
doi: 10.1093/molbev/msaa257
pii: 5918473
lyricists_name: Mank, Judith
lyricists_name: Morris, Jake
lyricists_id: JEMAN95
lyricists_id: MORRI72
actors_name: Mank, Judith
actors_id: JEMAN95
actors_role: owner
full_text_status: public
publication: Molecular Biology and Evolution
event_location: United States
citation:        Almeida, P;    Sandkam, BA;    Morris, J;    Darolti, I;    Breden, F;    Mank, JE;      (2020)    Divergence and Remarkable Diversity of the Y Chromosome in Guppies.                   Molecular Biology and Evolution        10.1093/molbev/msaa257 <https://doi.org/10.1093/molbev%2Fmsaa257>.    (In press).    Green open access   
 
document_url: https://discovery.ucl.ac.uk/id/eprint/10112615/1/msaa257.pdf