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

Articles https://doi.org/10.1038/s41559-018-0717-x Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow Milan Malinsky 1,2,10*, Hannes Svardal 1,3,4,5,10, Alexandra M. Tyers6,9, Eric A. Miska Martin J. Genner8, George F. Turner6 and Richard Durbin 1,3* , 1,3,7 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. T he 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 lineages1–3. Adaptive radiations are thus exquisite examples of the power of natural selection, as seen for example in Darwin’s finches in the Galapagos4,5, the Anolis lizards of the Caribbean6 and in East African cichlid fishes7,8. 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 Victoria2, each of which contains several hundred endemic species, with the largest number in Lake Malawi9. Molecular genetic studies have made major contributions to reconstructing the evolutionary histories of these adaptive radiations, especially in terms of the relationships between the lakes10,11, between some major lineages in Lake Tanganyika12, and in describing the role of hybridization in the origins of the Lake Victoria radiation13. However, the task of reconstructing within-lake relationships remains challenging owing both to the retention of large amounts of ancestral genetic polymorphism (that is, incomplete lineage sorting) and the gene flow between taxa12,14–18. Initial genome assemblies of cichlids from East Africa suggest that an increased rate of gene duplication, together with accelerated evolution of some regulatory elements and protein coding genes, may have contributed to the radiations11. However, our understanding of the genomic mechanisms contributing to adaptive radiations is still in its infancy3. Here we provide an overview of and insights into the genomic signatures of the haplochromine cichlid radiation of Lake Malawi. The species that comprise the radiation can be divided into seven groups with differing ecology and morphology (see Supplementary Note): (1) the rock-dwelling ‘mbuna’; (2) Rhamphochromis—typically midwater pelagic piscivores; (3) Diplotaxodon—typically deepwater pelagic zooplanktivores and piscivores; (4) deep-water and twilight-feeding benthic species; (5) ‘utaka’ feeding on zooplankton in the water column but breeding on or near the lake bottom (here utaka corresponds to the genus Copadichromis); (6) a diverse group of benthic species, mainly found in shallow non-rocky habitats; and (7) Astatotilapia calliptera, a closely related generalist that inhabits shallow weedy margins of Lake Malawi, and other lakes and rivers in the catchment, as well as river systems to the east and south of the Lake Malawi catchment. This division into seven groups has been partially supported by previous molecular phylogenies based on mitochondrial DNA (mtDNA) and amplified fragment length polymorphism data18–20. However, published phylogenies show numerous inconsistencies and, in particular, the question of whether the groups are genetically separate remained unanswered. To characterize the genetic diversity, species relationships, and signatures of selection across the whole radiation, we obtained Illumina whole-genome sequence data from 134 individuals of 73 species distributed broadly across the seven groups (Fig. 1a; Supplementary Note). This includes 102 individuals at ~15×coverage and 32 additional individuals at ~6×coverage (Supplementary Table 1). Results Low genetic diversity and species divergence. Sequence data were aligned to and variants called against a Metriaclima zebra reference genome11. Average divergence from the reference was 0.19% to 0.27% (Supplementary Fig. 1). After filtering and variant refine- Wellcome Sanger Institute, Cambridge, UK. 2Zoological Institute, University of Basel, Basel, Switzerland. 3Department of Genetics, University of Cambridge, Cambridge, UK. 4Department of Biology, University of Antwerp, Antwerp, Belgium. 5Naturalis Biodiversity Center, Leiden, The Netherlands. 6 School of Natural Sciences, Bangor University, Bangor, UK. 7Gurdon Institute, University of Cambridge, Cambridge, UK. 8School of Biological Sciences, University of Bristol, Bristol, UK. 9Present address: Max Planck Institute for Biology of Ageing, Cologne, Germany. 10These authors contributed equally: Milan Malinsky, Hannes Svardal. *e-mail: ; 1 1940 Nature Ecology & Evolution | VOL 2 | DECEMBER 2018 | 1940–1955 | www.nature.com/natecolevol Articles NaTure ECoLogy & EvoLuTion Lake malawi Shallow benthic 100% Overall 100% Proportion sampled a Diplotaxodon 5 cm 5 cm 200 km 0% 0% Total: 34/54 73/854* 134 specimens Genera Species (*high-end estimates) 100% Deep benthic 100% 100% 5 cm 0% 19/32 41/287 76 specimens Mbuna 100% 3/5 9/150 100% Utaka 0% 11 specimens 2/2 7/19 7 specimens Rhamphochromis A. calliptera 5 cm 5 cm 21 specimens sampled across its geographic distribution b 5 cm 0% 0% 0% 7/12 8/328 8 specimens 1/1 4/55 5 cm 1/1 8 specimens 3/14 3 specimens c 25 Mbuna Divergence within individuals (heterozygosity) Divergence between species (d dXY) A. calliptera 0.2 PC2 4.2% of genetic variation 20 Density 15 10 5 Shallow benthic 0.1 C. cf. trewavasae C. trimaculatus 0 Utaka Rhamphochromis −0.1 Deep benthic Diplotaxodon −0.2 0 0.5 1.0 1.5 2.0 −0.20 2.5 A. stuartgranti A.steveni −0.15 −0.10 −0.05 0.00 0.05 0.10 PC1 7.9% of genetic variation –3 Average sequence divergence (× 10 ) Fig. 1 | The Lake Malawi haplochromine cichlid radiation. a, The sampling coverage of this study (...truncated)