Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

Nagarjun Vijay; Matthias Weissensteiner; Reto Burri; Takeshi Kawakami; Hans Ellegren; Jochen B W Wolf

doi:10.1111/mec.14195

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

Mol Ecol. 2017 Aug;26(16):4284-4295. doi: 10.1111/mec.14195. Epub 2017 Jun 27.

Authors

Nagarjun Vijay^{1

2}, Matthias Weissensteiner^{1

3}, Reto Burri^{1

4}, Takeshi Kawakami^{1

5}, Hans Ellegren¹, Jochen B W Wolf^{1

3}

Affiliations

¹ Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.
² Lab of Molecular and Genomic Evolution, Department of Ecology and Evolutionary Biology, College of Literature, Science, and the Arts, University of Michigan, Ann Arbor, MI, USA.
³ Division of Evolutionary Biology, Faculty of Biology, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany.
⁴ Department of Population Ecology, Friedrich Schiller University Jena, Jena, Germany.
⁵ Department of Animal and Plant Sciences, University of Sheffield, Sheffield, UK.

PMID: 28570015
DOI: 10.1111/mec.14195

Abstract

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.

Keywords: background selection; genetic diversity; genetic draft; genetic hitchhiking; linked selection; recombination rate; speciation genetics.

MeSH terms

Animals
Biological Evolution*
Birds / classification*
Genetic Variation*
Genetics, Population*
Phylogeny
Reproductive Isolation
Selection, Genetic*

Associated data

GENBANK/GCA_000247815
GENBANK/GCA_000738735
GENBANK/GCA_000277835