Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum

The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex (“ciscoes”) radiated rapidly prior to the Last Glacial Maximum (80-90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr (ˆ), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deepwater created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental conte..., , , # Data from: Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum Access this dataset on Dryad [https://doi.org/10.5061/dryad.n02v6wx59](https://doi.org/10.5061/dryad.n02v6wx59) ## Description of data generation For population genomic analyses, genome resequencing data for individuals of each species of *Coregonus* were mapped to the unmasked *Coregonus artedi* reference genome assembly, and SNPs were called with VCF tools. An alignment was created for phylogenetic inference. Historical demography analyses (PSMC and SMC++) were created by mapping resequencing data to a repeat masked version of the reference before calling SNPs. There are additional files for testing the various mutation rates explored in the manuscript. The same methodology was applied to the *Salvelinus namaycush* samples with the addition of a PSMC analysis where we tested the sensitivity of different generation times. ## Description of the da...