The ecological and genomic basis of explosive adaptive radiation

Mc Gee, Matthew D.; Borstein, Samuel R.; Meier, Joana I.; Marques, David A.; Mwaiko, Salome; Taabu, Anthony; Kishe, Mary A.; O’Meara, Brian; Bruggmann, Rémy; Excoffier, Laurent; Seehausen, Ole (2020). The ecological and genomic basis of explosive adaptive radiation. Nature, 586(7827), pp. 75-79. Springer Nature 10.1038/s41586-020-2652-7

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Speciation rates vary considerably among lineages, and our understanding of what
drives the rapid succession of speciation events within young adaptive radiations
remains incomplete1–11. The cichlid fish family provides a notable example of such
variation, with many slowly speciating lineages as well as several exceptionally large
and rapid radiations12. Here, by reconstructing a large phylogeny of all currently
described cichlid species, we show that explosive speciation is solely concentrated in
species flocks of several large young lakes. Increases in the speciation rate are
associated with the absence of top predators; however, this does not sufficiently
explain explosive speciation. Across lake radiations, we observe a positive relationship
between the speciation rate and enrichment of large insertion or deletion polymorphisms.
Assembly of 100 cichlid genomes within the most rapidly speciating cichlid radiation,
which is found in Lake Victoria, reveals exceptional ‘genomic potential’—hundreds of
ancient haplotypes bear insertion or deletion polymorphisms, many of which are
associated with specific ecologies and shared with ecologically similar species from
other older radiations elsewhere in Africa. Network analysis reveals fundamentally
non-treelike evolution through recombining old haplotypes, and the origins of
ecological guilds are concentrated early in the radiation. Our results suggest that the
combination of ecological opportunity, sexual selection and exceptional genomic
potential is the key to understanding explosive adaptive radiation.

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