DOI: 10.5061/dryad.51s8p
title: Data from: Explicit tests of paleodrainage connections of southeastern North America and the historical biogeography of Orangethroat Darters (Percidae: Etheostoma: Ceasia)

description: The alteration of paleodrainage river connections has shaped patterns of
 speciation, genetic diversity, and the geographic distribution of the
 species-rich freshwater fauna of North America. The integration of
 ancestral range reconstruction methods and divergence time estimates
 provides an opportunity to infer paleodrainage connectivity and test
 alternative paleodrainage hypotheses. Members of the Orangethroat Darter
 clade, Ceasia, are endemic to southeastern North America and occur north
 and south of the Pleistocene glacial front, a distributional pattern that
 makes this clade of closely related species an ideal system to investigate
 the number and location of glacial refugia and compare alternative
 hypotheses regarding the proposed evolution of the Teays-Mahomet
 paleodrainage. This study utilized time-calibrated mitochondrial and
 nuclear gene phylogenies and present-day geographic distributions to
 investigate hypothesized Teays-Mahomet River connections through time
 using a dispersal-extinction cladogenesis framework (DEC). Results of DEC
 ancestral area reconstructions indicate that the Teays-Mahomet River was a
 key dispersal route between disjunct highland regions connecting the
 Mississippi River tributaries to the Old-Ohio Drainage minimally at two
 separate occasions during the Pleistocene. There was a dynamic interplay
 between paleodrainage connections through time and postglacial range
 expansion from three glacial refugia that shaped the current genetic
 structure and geographic distributions of the species that comprise
 Ceasia.
description: lagrange_analysis_filesWe applied the DEC model implemented in lagrange (Ree & Smith 2008) to obtain reconstructed ancestral areas at all internal nodes and infer probable dispersal scenarios over a distribution of dated mitonuclear phylogenies and dated nuclear species trees. The files implemented in lagrange include the geographic data for the mitonuclear data set and the nuclear species tree data set (.data files), the rate matrices for each time period within each paleodrainage hypothesis (.rm files), the distribution of mitonuclear phylogenies and species trees (.trees files) and the scripts to call each (.lg files).BEAST and *BEAST analysesWe utilized a Bayesian strategy that relied on external fossil calibrations in the perciform fish clade Centrarchidae to time-calibrate the mtDNA phylogeny, individual gene trees inferred from each of the ten nuclear genes and a phylogeny inferred from the concatenation of ten nuclear genes, and a phylogeny inferred from the concatenation of ten nuclear and two mitochondrial genes in BEAST. We also calibrated divergence times on a nuclear species tree using *BEAST, excluding the mitochondrial genes to avoid incongruence among gene trees resulting from mitochondrial replacement via introgressive hybridization that is common among species of Ceasia. The xml files were generated in BEAUti, however the species tree divergence time xml file were also changed by hand. All samples were collected in the field and accession numbers for each gene accompany this dryad submissiondating_analyses_files.zipSpecimen_GenbankA tab-delimited spread sheet of the specimens and genbank accession numbers generated in this study. The first column is the species identity, second column is the clode code identifier, and the remaining column are the gene names. The ten nuclear genes are placed above the two mitochondrial genes.spectabmtDNA_phyloParsed71911Partitioned Bayesian analyses were used to infer sets of posterior phylogenetic trees from the densely sampled mtDNA dataset, these analyses were applied in BEAST and MrBayes. We sampled the Ceasia clade much more extensively, however centrarchid fossil calibration priors were not used to conduct divergence time analyses on the larger data set. The xml file was created in BEAUti. All samples were collected in the field and accession numbers for each gene accompany this dryad submission.spectabmtDNA_2phyloParsed71911.xmlspectabDNA_phyloParsed1.bay.unsafe