Drivers of genomic landscapes of differentiation across a Populus divergence gradient

Huiying Shang, David L Field, Ovidiu Paun, Martha Rendón-Anaya, Jaqueline Hess, Claus Vogl, Jianquan Liu, Pär K Ingvarsson, Christian Lexer, Thibault Leroy

Publications: Contribution to journalArticlePeer Reviewed

Abstract

Speciation, the continuous process by which new species form, is often investigated by looking at the variation of nucleotide diversity and differentiation across the genome (hereafter genomic landscapes). A key challenge lies in how to determine the main evolutionary forces at play shaping these patterns. One promising strategy, albeit little used to date, is to comparatively investigate these genomic landscapes as progression through time by using a series of species pairs along a divergence gradient. Here, we resequenced 201 whole-genomes from eight closely related Populus species, with pairs of species at different stages along the divergence gradient to learn more about speciation processes. Using population structure and ancestry analyses, we document extensive introgression between some species pairs, especially those with parapatric distributions. We further investigate genomic landscapes, focusing on within-species (i.e. nucleotide diversity and recombination rate) and among-species (i.e. relative and absolute divergence) summary statistics of diversity and divergence. We observe relatively conserved patterns of genomic divergence across species pairs. Independent of the stage across the divergence gradient, we find support for signatures of linked selection (i.e. the interaction between natural selection and genetic linkage) in shaping these genomic landscapes, along with gene flow and standing genetic variation. We highlight the importance of investigating genomic patterns on multiple species across a divergence gradient and discuss prospects to better understand the evolutionary forces shaping the genomic landscapes of diversity and differentiation.

Original languageEnglish
Pages (from-to)4348-4361
Number of pages14
JournalMolecular Ecology
Volume32
Issue number15
Early online date4 Jun 2023
DOIs
Publication statusPublished - Aug 2023

Austrian Fields of Science 2012

  • 106012 Evolutionary research
  • 106014 Genomics

Keywords

  • differentiation islands
  • divergence
  • identity-by-descent
  • introgression
  • linked selection
  • recombination

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