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. 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.

The genomic causes and effects of divergent ecological selection during speciation are still poorly understood. Here, we report the discovery and detailed characterization of early-stage adaptive divergence of two cichlid fish ecomorphs in a small (700m diameter) isolated crater lake in Tanzania. The ecomorphs differ in depth preference, male breeding color, body shape, diet and trophic morphology. With whole genome sequences of 146 fish, we identify 98 clearly demarcated genomic 'islands' of high differentiation and demonstrate association of genotypes across these islands to divergent mate preferences. The islands contain candidate adaptive genes enriched for functions in sensory perception (including rhodopsin and other twilight vision associated genes), hormone signaling and morphogenesis. Our study suggests mechanisms and genomic regions that may play a role in the closely related mega-radiation of Lake Malawi. * Publisher's Disclaimer: This manuscript has been accepted for publication in Science. This version has not undergone final editing.Please refer to the complete version of record at http://www.sciencemag.org/. The manuscript may not be reproduced or used in any manner that does not fall within the fair use provisions of the

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. 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.One Sentence Summary: The genomes of 73 cichlid fish species from Lake Malawi uncover evolutionary processes underlying a large adaptive evolutionary radiation.. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/143859 doi: bioRxiv preprint first posted online May. 31, 2017; Main Text: The formation of every lake or island represents a fresh opportunity for colonization, proliferation and diversification of living forms. In some cases, the ecological opportunities presented by underutilized habitats facilitate adaptive radiation -rapid and extensive diversification of the descendants of the colonizing lineages (1-3). Adaptive radiations are thus exquisite examples of the power of natural selection, as recognized by Darwin in the case of Galapagos finches (4, 5), and seen for example in Anoles lizards of the Caribbean (6) and in East African cichlid fishes (7,8).Cichlids are the most species rich and diverse family of vertebrates, and nowhere are their radiations more spectacular than in the Great Lakes of East Africa: Malawi, Tanganyika, and Victoria (2), each of which contains several hundred endemic species, with the largest number in Lake Malawi. Molecular genetic studies have made major contributions to reconstructing the evolutionary histories of these adaptive radiations, especially in terms of the relationships between the lakes (9), between some major lineages in Lake Tanganyika (10), and in describing the role of hybridization in the origins of the Lake Victoria radiation (11). However, the task of reconstructing within-lake relationships and of identifying sister species in lakes Malawi and Victoria remains challenging due both to retention of large amounts of ancestral genetic polymorphism (i.e. incomplete lineage sorting) and to evidence suggesting gene flow between taxa (12, 13).Initial genome assemblies of cichlids from ...