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Genomewide patterns of variation in genetic diversity are shared among populations, species and higher‐order taxa
Author(s) -
Vijay Nagarjun,
Weissensteiner Matthias,
Burri Reto,
Kawakami Takeshi,
Ellegren Hans,
Wolf Jochen B. W.
Publication year - 2017
Publication title -
molecular ecology
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 2.619
H-Index - 225
eISSN - 1365-294X
pISSN - 0962-1083
DOI - 10.1111/mec.14195
Subject(s) - biology , evolutionary biology , genetic diversity , population , nucleotide diversity , genetic variation , clade , phylogenetic tree , coalescent theory , lineage (genetic) , population genomics , effective population size , adaptation (eye) , genetic drift , genetics , genome , genomics , haplotype , allele , gene , demography , neuroscience , sociology
Genomewide screens of genetic variation within and between populations can reveal signatures of selection implicated in adaptation and speciation. Genomic regions with low genetic diversity and elevated differentiation reflective of locally reduced effective population sizes ( N e ) are candidates for barrier loci contributing to population divergence. Yet, such candidate genomic regions need not arise as a result of selection promoting adaptation or advancing reproductive isolation. Linked selection unrelated to lineage‐specific adaptation or population divergence can generate comparable signatures. It is challenging to distinguish between these processes, particularly when diverging populations share ancestral genetic variation. In this study, we took a comparative approach using population assemblages from distant clades assessing genomic parallelism of variation in N e . Utilizing population‐level polymorphism data from 444 resequenced genomes of three avian clades spanning 50 million years of evolution, we tested whether population genetic summary statistics reflecting genomewide variation in N e would covary among populations within clades, and importantly, also among clades where lineage sorting has been completed. All statistics including population‐scaled recombination rate (ρ), nucleotide diversity (π) and measures of genetic differentiation between populations ( F ST , PBS, d xy ) were significantly correlated across all phylogenetic distances. Moreover, genomic regions with elevated levels of genetic differentiation were associated with inferred pericentromeric and subtelomeric regions. The phylogenetic stability of diversity landscapes and stable association with genomic features support a role of linked selection not necessarily associated with adaptation and speciation in shaping patterns of genomewide heterogeneity in genetic diversity.