TY - JOUR

T1 - Whole genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow

AU - Malinsky, Milan

AU - Svardal, Hannes

AU - Tyers, Alexandra

AU - Miska, Eric.A.

AU - Genner, Martin J.

AU - Turner, George

AU - Durbin, Richard

PY - 2018/12

Y1 - 2018/12

N2 - 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.

AB - 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.

UR - https://static-content.springer.com/esm/art%3A10.1038%2Fs41559-018-0717-x/MediaObjects/41559_2018_717_MOESM1_ESM.pdf

U2 - 10.1038/s41559-018-0717-x

DO - 10.1038/s41559-018-0717-x

M3 - Article

VL - 2

SP - 1940

EP - 1955

JO - Nature Ecology and Evolution

JF - Nature Ecology and Evolution

SN - 2397-334X

ER -