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

Milan Malinsky,Richard Durbin,Martin J Genner,Hannes Svardal,Eric A Miska,Alexandra M Tyers,George F Turner

doi:10.1038/s41559-018-0717-x

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.

Highlights

The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation
To reconcile the nested phylogenetic position of A. calliptera with its generalist ‘prototype’ phenotype, we propose a model where the Lake Malawi species flock consists of three separate radiations splitting off from the lineage leading to A. calliptera
Possibilities include parallel selection on variation segregating in both groups owing to common ancestry, selection on the gene flow that we described in a previous section, or independent selection on new mutations

Summary

Introduction

The hundreds of cichlid fish species in Lake Malawi constitute the most extensive recent vertebrate adaptive radiation. 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. Cichlids are one of the most species-rich and diverse families of vertebrates, and nowhere are their radiations more spectacular than in the Great Lakes of East Africa: lakes Malawi, Tanganyika and Victoria[2], each of which contains several hundred endemic species, with the largest number in Lake Malawi[9].

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