DOI: 10.5061/dryad.1c9g5mm
title: Data from: Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)

description: Evolutionary history is typically portrayed as a branching phylogenetic
 tree, yet not all evolution proceeds in a purely bifurcating manner.
 Introgressive hybridization is one process that results in reticulate
 evolution. Most known examples of genome-wide introgression occur among
 closely related species with relatively recent common ancestry; however,
 we present evidence for ancient hybridization and genome-wide
 introgression between major stem lineages of darters, a species-rich clade
 of North American freshwater fishes. Previous attempts to resolve the
 relationships of darters have been confounded by the uncertain
 phylogenetic resolution of the lineage Allohistium. In this study we
 investigate the phylogenomics of darters, specifically the relationships
 of Allohistium, through analyses of ~30,000 RADseq loci sampled from 112
 species. Our phylogenetic inferences are based on traditional approaches
 in combination with strategies that accommodate reticulate evolution.
 These analyses result in a novel phylogenetic hypothesis for darters that
 includes ancient introgression involving Allohistium and other two major
 darter lineages, minimally occurring 20 million years ago. Darters offer a
 compelling case for the necessity of incorporating phylogenetic networks
 in reconstructing the evolutionary history of diversification in
 species-rich lineages. We anticipate that the growing wealth of genomic
 data for clades of non-model organisms will reveal more examples of
 ancient hybridization, eventually requiring a re-evaluation of how
 evolutionary history is visualized and utilized in macroevolutonary
 investigations.
description: min4.lociPyrad .loci file for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.min10.lociPyrad .loci file for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.min20.lociPyrad .loci file for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML.txt" for more information on assembly parameters.min30.lociPyrad .loci file for the dataset containing minimum 30 samples per locus. See "params_Darter_m30_RAxML.txt" for more information on assembly parameters.min4.phyConcatenated phylip alignment for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.min10.phyConcatenated phylip alignment for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.min20.phyConcatenated phylip alignment for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML.txt" for more information on assembly parameters.min30.phyConcatenated phylip alignment for the dataset containing minimum 30 samples per locus. See "params_Darter_m30_RAxML.txt" for more information on assembly parameters.min4.nexConcatenated nexus alignment for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.min10.nexConcatenated nexus alignment for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.min20.nexConcatenated nexus alignment for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML" for more information on assembly parameters.min30.nexConcatenated nexus alignment for the dataset containing minimum 30 samples per locus. See "params_Darter_m30_RAxML.txt" for more information on assembly parameters.params_Darter_m4_RAxMLPyrad parameter file for minimum 4 samples per locus assembly.params_Darter_m10_RAxMLPyrad parameter file for minimum 10 samples per locus assembly.params_Darter_m20_RAxMLPyrad parameter file for minimum 20 samples per locus assembly.params_Darter_m30_RAxMLPyrad parameter file for minimum 30 samples per locus assembly.Figure A1Figure A1. Species trees inferred by tetrad, with bootstrap support values = 100% unless indicated. Nodes with less than 50% boostrap support have been collapsed. White nodes represent topological conflicts between the tetrad min4 tree and min30 tree. Gray nodes represent topological conflicts between either of the tetrad trees and the RAxML tree (Fig. 1). Black nodes represent topological conflicts between the tetrad min4 tree and m30 tree plus conflict between either of the tetrad trees and the concatenated RAxML tree.Figure_A1.pdfFigure A2Figure A2. ASTRAL species tree. Nodes have local posterior probability = 1.0 unless otherwise noted. Branch lengths are in coalescent units. ASTRAL cannot estimate terminal branch lenghs, so all terminal branches arbitrarily = 1.0 coalescent units. Black nodes represent topological conflicts between the ASTRAL species tree and the concatenated RAxML tree.Figure_A2.pdfFigure A3Figure A3. Primary concordance tree. Species sampled for each clade are indicated below the clade names. Nodes are labeled with concordance factors, 95% CI in parentheses. Dotted lines indicate conflicting topologies with concordance factor 95% CIs that overlap with the concordance factor 95% CI of a bipartition in the primary concordance tree.Figure_A3.pdfFigure A4Figure A4. Primary concordance tree. Species sampled for each clade are indicated below the clade names. Nodes are labeled with concordance factors, 95% CI in parentheses.Figure_A4.pdfFigure A5Fig. A5. Time-calibrated maximum clade credibility species tree inferred using SNAPP with all unlinked SNPs shared by the eleven sampled taxa. Grey bars on the nodes indicate 95% highest posterior density for the node heights. Bayesian posterior support is 1.0 unless otherwise labeled. Arrows indicate the potential window for introgression between the stem lineage of Allohistium and the stem lineage of Simoperca.Figure_A5.pdfTable A4Table A4. Results of the first set of D-statistic tests (Fig. 4).Table_A4.xlsxTable A5Table A5. Results of the first set of D-statistic tests, grouped by P2 taxa + P3 clade. Proportion of D-statistic tests significantly different from 0 after adjusting for multiple comparisons (alpha = 0.05).Table_A5.xlsxTable A6Table A6. Results of the first set of D-statistic tests, grouped by P3 taxa. Proportion of D-statistic tests significantly different from 0 after adjusting for multiple comparisons (alpha = 0.05).Table_A6.xlsxTable A7Table A7. Results of the first set of D-statistic tests (Fig. 4), grouped by P1 taxa + P3 taxa. Proportion of D-statistic tests significantly different from 0 after adjusting for multiple comparisons (alpha = 0.05).Table_A7.xlsxTable A8Table A8. Results of the second set of D-statistic tests (Fig. 5).Table_A8.xlsxMacGuigan&Near_appendixOnline appendix for "Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)" by Daniel J. MacGuigan and Thomas J. Near. Table A1, A2, and A3 are included in this file.