Genomes reveal age and demographic consequence of ultrafast adaptive radiation

Marques, D. A.; Meier, J. I.; McGee, M. D.; Haesler, M. P.; Mwaiko, S.; Kishe, M. A.; Taabu-Munyaho, A.; Chapman, L.; Chapman, C. A.; Wandera, S. B.; Wagner, C. E.; Excoffier, L. E.; Seehausen, O.

doi:10.1101/2025.03.07.638630

bioRxiv · 10.1101/2025.03.07.638630

Genomes reveal age and demographic consequence of ultrafast adaptive radiation

Marques, D. A.·Meier, J. I.·McGee, M. D.·Haesler, M. P.·Mwaiko, S.·Kishe, M. A.·Taabu-Munyaho, A.·Chapman, L.·Chapman, C. A.·Wandera, S. B.·Wagner, C. E.·Excoffier, L. E.·Seehausen, O.

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Abstract

New species typically evolve over several million years1. However, rates of speciation and ecological diversification vary by orders of magnitude across the tree of life1-3, with the fastest shown by some adaptive radiations. Eight hundred endemic species of cichlid fishes emerged and formed entire food webs in Lake Victoria and nearby lakes in East Africa. According to Victorias paleolimnological history4, five hundred may have arisen within the past 16,700 years, but molecular phylogenies estimated a much older origin5-8. We reconstruct the age and demography of all Lake Victoria region radiations from whole genomes. We show that indeed, in Lake Victoria all trophic guilds diverged <16,700 years ago, corresponding to between 537 and nearly 30000 speciation events per species per million years, the fastest speciation rate in metazoans1,2. Cichlid radiations in lakes Edward, Albert and Kivu too began <20,000 years ago, an order of magnitude faster than previously thought. Evolutionary transitions between trophic levels led to divergence in effective population sizes as predicted by the trophic pyramid of numbers concept9 and replicated across three parallel food web radiations. Our results demonstrate that classical theory of trophic interactions in ecologically assembled food webs applies equally to food webs that assembled through rapid adaptive radiation.

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Marques, D. A., Meier, J. I., McGee, M. D., Haesler, M. P., Mwaiko, S., Kishe, M. A., Taabu-Munyaho, A., Chapman, L., Chapman, C. A., Wandera, S. B., Wagner, C. E., Excoffier, L. E., Seehausen, O.. 2025-03-10. Genomes reveal age and demographic consequence of ultrafast adaptive radiation. https://doi.org/10.1101/2025.03.07.638630

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