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Nat Ecol Evol. 2018 Dec;2(12):1940-1955. doi: 10.1038/s41559-018-0717-x. Epub 2018 Nov 19.

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

Author information

1
Wellcome Sanger Institute, Cambridge, UK. millanek@gmail.com.
2
Zoological Institute, University of Basel, Basel, Switzerland. millanek@gmail.com.
3
Wellcome Sanger Institute, Cambridge, UK.
4
Department of Genetics, University of Cambridge, Cambridge, UK.
5
Department of Biology, University of Antwerp, Antwerp, Belgium.
6
Naturalis Biodiversity Center, Leiden, The Netherlands.
7
School of Natural Sciences, Bangor University, Bangor, UK.
8
Max Planck Institute for Biology of Ageing, Cologne, Germany.
9
Gurdon Institute, University of Cambridge, Cambridge, UK.
10
School of Biological Sciences, University of Bristol, Bristol, UK.
11
Wellcome Sanger Institute, Cambridge, UK. rd109@cam.ac.uk.
12
Department of Genetics, University of Cambridge, Cambridge, UK. rd109@cam.ac.uk.

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.

PMID:
30455444
DOI:
10.1038/s41559-018-0717-x

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