The comparative genomic landscape of adaptive radiation in Crater Lake cichlid fishes

Factors ranging from ecological opportunity to genome composition might explain why only some lineages form adaptive radiations. While being rare, particular systems can provide natural experiments within an identical ecological setting where the factors promoting increased species numbers and phenotypic divergence in two closely related lineages is notably different. We investigated one such natural experiment using two de novo assembled and 40 re-sequenced genomes and asked why two closely related Neotropical cichlid fish lineages, the Amphilophus citrinellus species complex (Midas cichlids; radiating) and Archocentrus centrarchus (Flyer cichlid; non-radiating), have resulted in such disparate evolutionary outcomes. Although both lineages inhabit many of the same Nicaraguan lakes, whole-genome inferred demography suggests that priority effects are not likely to be the only cause of the dissimilarities. Also, genome-wide levels of selection, transposable element dynamics, gene family e...