Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

Milan Malinsky, Hannes Svardel, Alexandra Tyers, Eric Miska, Martin J Genner, George Turner, Richard Durbin

Research output: Contribution to journalArticle (Academic Journal)peer-review

70 Citations (Scopus)
471 Downloads (Pure)

Abstract

The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. Here we characterize its genomic diversity by sequencing 134 individuals covering 73 species across all major lineages. The average sequence divergence between species pairs is only 0.1-0.25%. These divergence values overlap diversity within species, with 82% of heterozygosity shared between species. Phylogenetic analyses suggest that diversification initially proceeded by serial branching from a generalist Astatotilapia-like ancestor. However, no single species tree adequately represents all species relationships, with evidence for substantial gene flow at multiple times. Common signatures of selection on visual and oxygen transport genes shared by distantly related deep-water species point to both adaptive introgression and independent selection. These findings enhance our understanding of genomic processes underlying rapid species diversification, and provide a platform for future genetic analysis of the Malawi radiation.
Original languageEnglish
Pages (from-to)1940-1955
Number of pages16
JournalNature Ecology and Evolution
Volume2
Issue number12
Early online date19 Nov 2018
DOIs
Publication statusPublished - Dec 2018

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