I am pleased to announce a new paper I have co-authored with a number of colleagues from Africa, Australia, Europe, and the United States investigating the ecological and genomic basis of adaptive radiation in cichlids. Adaptive radiations are the rapid speciation and ecological divergence from a common ancestor. Well known examples include things such as Darwin’s finches, Hawaiian silverswords, and Caribbean anoles. Cichlids are famous for undergoing adaptive radiations in a number of lakes (such as Lake Tanganyika, Lake Nicaragua, Lake Malawi, and Lake Victoria) as well as at the continental scale. Because of this, cichlids are often used as a model to study various biological aspects of adaptive radiation. In this paper, we investigate what parts of the cichlid tree of life have the fastest rates of speciation and also tested a number of previously proposed biotic (male ornamentation, polygamy, etc.) and abiotic (rainfall, temperature) factors that have been proposed for the staggering diversity.
We built an evolutionary tree of all cichlids and calculated speication rates. We found the fastest rates of speciation in cichlids occur in Lake Victoria, an extremely young lake (some estimates as young as 15,000 years) in East Africa that contains several hundred species. The speciation rate is one of the fastest observed in contemporary animals! Lake Malawi and Lake Nicaragua also possess fast rates. While regression and non-parametric analyses found male ornamentation and water depth to be positively linked to speciation while arid climates and non-cichlid predatory fish lineages were found to negatively effect speciation, but these had weak explanatory power . However when fitting more complex hidden-state models that allow for accounting for rates to be influenced by unobserved states (think of this as a more complex null model), we find that none of these factors actually explains the observed diversification patterns.
Because we found no traits responsible for the explosive radiation of cichlids, we examined the genomic substrate of adaptive radiation by comparing species pairs from a number of cichlid adaptive radiations. We found that speciation rates in these radiations was highly correlated with the number of divergently fixed indels (insertions or deletions of DNA bases in a genome )relative to the age of the radiation. For example, Lake Victoria, which has fast speciation rates and is young had the greatest number of divergently fixed indels. We then did a more in depth genomic analysis of 100 Lake Victorian cichlid species genomes. We find that the cichlids of Lake Victoria share are a hybrid swarm and that there are many indels that segregate between Lake Victorian cichlid species. While some of these were found only in Lake Victoria cichlids, a large number of the indels that segregate between Lake Victorian cichlids were also found in cichlids found outside the radiation and that Lake Victorian cichlids contain variants that existed up to 10 million years before the Lake Victoria adaptive radiation started (remember the Lake Victoria cichlid radiation is quite young, ~15,000 years old). Interestingly, these indels were often found to be associated with various dimensions of ecological diversity, such as traits associated with diet and habitat use, much more so than indels found in only Lake Victorian cichlids. This highlights that the genomic potential of the radiation was in place long before it formed, providing the genomic architecture of the radiation and that recombination of genomic elements through hybridization provided genomic diversity that allowed for the rapid diversification of the radiation.
Paper Citation and Link: McGee MD, Borstein SR, Meier JI, Marques DA, Mwaiko S, Taabu A, Kishe-Machumu MA, O’Meara BC, Bruggmann R, Excoffier L, and Seehausen O. 2020. The ecological and genomic basis of explosive adaptive radiation. 10.1038/s41586-020-2652-7