DOI: 10.5061/dryad.8gtht7701
title: Data from: Pleistocene speciation and glacial refugia in a temperate freshwater biodiversity hotspot

description: Among temperate regions of the world, freshwater fish species richness is
 highest in the Central Highlands of eastern North America. Historical
 biogeographic and phylogeographic researchers have investigated mechanisms
 driving this exceptional diversity, yet the role of major climatic events,
 like Pleistocene glaciation, is incompletely characterized. In this study,
 we analyze genomic DNA sequence data sampled from populations of the
 widely distributed Gilt Darter, Percina evides Jordan & Copeland
 1877, to reconstruct pre-glacial drainage patterns and assess the impact
 of Pleistocene glaciation on generating the high species diversity of
 eastern North American freshwater fishes. Phylogenomics, population
 genomic analyses, and evaluation of morphology delimit four species
 currently classified as P. evides. These species likely diverged via
 allopatric speciation among the disjunct regions of the Central Highlands
 driven by the onset of Pleistocene glaciation. Divergence times among
 newly delimited species of the Gilt Darter complex are congruent with the
 onset of glaciation, periods of river incision and aggradation, and river
 network rearrangement. The discovery of new species in the Percina evides
 complex and their phylogenetic relationships highlight how Pleistocene
 glaciation and glacial refugia contributed to the remarkable temperate
 freshwater biodiversity hotspot of the Central Highlands.
description: # Data from: Pleistocene speciation and glacial refugia in a temperate
 freshwater biodiversity hotspot
 [https://doi.org/10.5061/dryad.8gtht7701](https://doi.org/10.5061/dryad.8gtht7701) ## Description of the data and file structure ddRAD and meristic data and associated analyses files ### File: dryad_submission_3.zip #### File list BPP * Pevi_5sp.ctl * Pevi_5sp.Imap.txt * pevi_loci_BPP.csv fastsimcoal2 * Pevi_MSFS.obs meristic data * P_evides_complex_meristic_data * meristic data * specimen info SNAPP * SNAPP_4-16-25.xml VCFs * branch_fastsimcoal.vcf * branch_popgen_fst_pca.vcf sNMF * P_evides_popgen_structure.u.geno ### Folder Details #### "BPP" folder contains control file, loci file, and Imap file used for BPP and gdi analysis in standard format #### "Fastsimcoal2" folder contains observed site frequency spectrum file for fastsimcoal2 analysis in .obs file format #### "meristics" folder contains raw meristic count data tables and specimen information **Meristic data sheet:** * Species - denotes the designated species * Catalog - this is the catalog number * Individual - this denotes the exact individual: YFTC (Yale fish tissue collection) tag numbers are included if it had YFTC tag * Drainage - the river drainage the fish was collected from * Sex - the sex of the fish, if it was possible to tell * SL - standard length (measured in millimeters) * LL - lateral line scales * PoreLL - number of pored lateral line scales * AbLL - scale rows above the lateral line * BlwLL - scale rows below the lateral line * Trans - transverse scale rows * CD - scales around the caudal peduncle * D1 - counts of number of dorsal fin spines * D2 - counts of number of dorsal fin rays * P1 - counts of number of pectoral fin rays * A1 - counts of number of anal fin spines * A2 - counts of number of anal fin rays * Nape, cheek, opercle, breast, belly % - estimated percentage of nape, cheek, opercle, breast, and belly, with scales * Modified midventer scales (males) - count of number of modified scutes along the belly midline in males * meristic datasets used for principal component analyses, frequency tables, and linear discriminate analysis na where data was not recorded **Specimen info sheet:** Contains the specimen information from which meristic data was collected. #### "SNAPP" folder contains SNAPP input files - in xml format #### "VCFs" folder contains VCF files used for Fst - in VCF format #### "sNMF" folder contains file used for structure analyses - in u.geno format ## Access information Other publicly accessible locations of the data: * NCBI SRA BioProjectID: PRJNA1214323 Data was derived from the following sources: * n/a