DOI: 10.5061/dryad.n02v6wx59
title: Data from: Origin of the Laurentian Great Lakes fish fauna through upward adaptive radiation cascade prior to the Last Glacial Maximum

description: 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
 context for the origin of the Laurentian Great Lakes fish fauna and firmly
 establishes this system as a driver of ecological diversification and
 rapid speciation through cyclical glaciation.
description: # 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 data and file structure **Coregonus_PCA_biallelic_no_missing.maf0.05.noSingletons.min4.phy** * phylip formatted alignment containing Coregonus genome-wide SNPs for IQTree2 phylogenetic inference * used by the "run_IQTree2.sh" script **Coregonus_PCA_biallelic_no_missing.maf0.05.vcf** * VCF format file containing Coregonus genome-wide SNPs for PCA * used by the "PCA_maf0.05.R" **CA_combined_biallelic.vcf.gz, CH_combined_biallelic.vcf.gz, CK_combined_biallelic.vcf.gz, CN_combined_biallelic.vcf.gz, SN-lean_combined_biallelic.vcf.gz, SN-siscowet_combined_biallelic.vcf.gz** * variant call files used for SMC++, which are grouped by species **CA01.masked.vcf.gz, CA02.masked.vcf.gz, CA03.masked.vcf.gz, CA04.masked.vcf.gz, CH01.masked.vcf.gz, CH02.masked.vcf.gz, CH03.masked.vcf.gz, CH04.masked.vcf.gz, CK01.masked.vcf.gz, CK02.masked.vcf.gz, CK03.masked.vcf.gz, CK04.masked.vcf.gz, CN01.masked.vcf.gz, CN02.masked.vcf.gz, LS01.masked.vcf.gz, LS02.masked.vcf.gz, LS05.masked.vcf.gz, LS07.masked.vcf.gz, LS08.masked.vcf.gz, LS09.masked.vcf.gz** * variant call files used for PSMC * each file represents an individual sample **psmc_masked_bs_all.xlsx** * PSMC results for *Coregonus* spp. and *Salvelinus namaycush* samples in an excel spreadsheet. Each tab represents a result of a PSMC run. * The tabs marked "main" are the results of the whole genome. The tabs marked "bs" are the concatenated bootstrap replicates.  **psmc_Coregonus_masked_mut_rate_bs_all.xlsx** * PSMC results for *Coregonus* spp. at different mutation rates. Each tab represents a result of a PSMC run. * The tabs marked "[sample]_main" are the results of the whole genome. The tabs marked "[sample]_bs" are the concatenated bootstrap replicates.  * The "low" mutation rate is 2.5e-09 and the "high" rate is 8.23e-09 mutations per site per generation. **psmc_Salvelinus_masked_generation_time_bs_all.xlsx** * PSMC results for *Salvelinus namaycush* sample LS01 for generation times 6-20 at increments of every two years. * The tabs marked "main" are the results of the whole genome. The tabs marked "bs" are the concatenated bootstrap replicates.  **smc++_masked_bs_all.xlsx** * SMC++ results for *Coregonus* spp. and *Salvelinus namaycush* samples in an excel spreadsheet. Each tab represents a result of a SMC++ run. * Tabs marked "[sample]7 26 e-9t10-10000 gen" are the results of the whole genome. Tabs marked "*[sample]_bs_all_gen" are the concatenated bootstrap replicates. **smc++_masked_mut_rate_all.xlsx** * SMC++ results for *Coregonus* species at 2.5e-09 and 8.23e-09 mutations per site per generation (6). ## Sharing/Access information Sequence and assembly data can be found at the following sources: *Coregonus* genome assembly and resequencing data. * NCBI BioProject: PRJNA1062807 *Salvelinus namaycush* resequencing data. * NCBI BioProject: PRJNA1077361 ## Code/Software Code available at [https://github.com/KrabbenhoftLab/Coregonus_demography.git](https://github.com/KrabbenhoftLab/Coregonus_demography.git)