Genomics of explosive adaptive radiation

Our newest paper on the ecological and genomic basis of the explosive adaptive radiation of the Lake Victoria haplochromine cichlids has been published today in Nature! In this work led by Matt McGee and Sam Borstein, we found that in a large phylogeny containing all described cichlids, speciation rates in most of the cichlid family are not unusually high compared to other taxa, but a few lineages living in large, young lakes, show extremely high rates of speciation. These increases in speciation rates are associated with the absence of large predators, even though this cannot explain why some lineages show explosive speciation in the same area others don’t.


We sequenced the genomes of 100 haplochromine cichlid species from the fastest explosive adaptive radiation in Lake Victoria, East Africa, that unfolded in the last 15,000 years. We found that the Lake Victoria haplochromines have an exceptional genomic potential in the form of hundreds of ancient haplotypes with insertion or deletion polymorphisms, many of them associated with ecological niches they exploit and originating from hybridization between distant lineages. Our results suggest that the combination of ecological opportunity in a newly formed lake without large predators, strong sexual selection and exceptional genomic potential together led to the huge adaptive radiation of Lake Victoria cichids within the blink of an eye.

Another digest of the story can be read in the Eawag News and I hope you enjoy the full story in our paper (e-mail me for a copy!).

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Origin of Lake Constance stickleback

Today, my newest paper was published in Nature Communications. In this collaboration with Kay Lucek, Vitor Sousa, Laurent Excoffier and Ole Seehausen, we have reconstructed the evolutionary history of threespine stickleback found in Lake Constance and surrounding rivers.

Threespine stickleback lake (left) and stream (right) ecotypes of Lake Constance, Central Europe. Females are shown on top and males in nuptial coloration on the bottom.

With extensive demographic modelling and the analysis of both genomic and phenotypic data from the European biogeographic context, we found out where stickleback lake and stream ecotypes come from and whether genetic differences between them arose from new mutations, standing genetic variation or the admixture of old lineages.

Spoiler alert! The title gives it away:


The evolution of lake and stream ecotypes in Lake Constance is thus a prime example for how combinatorial processes can facilitate rapid speciation.

Enjoy the read of our paper and of this blog post on the Nature Research Ecology & Evolution Community forum outlining the story behind the paper.

A combinatorial view on speciation

A review by Joana Meier, Ole Seehausen and me was just published in Trends in Ecology & Evolution. In this manuscript, we highlight a genetic mechanism that has often be found to facilitate rapid speciation and adaptive radiations in speciation genomic research from the recent years (see a few examples in the figure below). The mechanism we highlight is the reassembly of old genetic variants into new combinations or ‘combinatorial mechanism’.


Adopting such a combinatorial view makes some counter-intuitive predictions, for example that speciation rates might be inversely related to the rate of complete reproductive isolation between speciating taxa, and might throw new light on old issues such as the likelihood of speciation in sympatry. I hope you enjoy the read and feel free to let me know your thoughts of our ideas!