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.
min4.loci
Pyrad .loci file for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.
min10.loci
Pyrad .loci file for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.
min20.loci
Pyrad .loci file for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML.txt" for more information on assembly parameters.
min30.loci
Pyrad .loci file for the dataset containing minimum 30 samples per locus. See "params_Darter_m30_RAxML.txt" for more information on assembly parameters.
min4.phy
Concatenated phylip alignment for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.
min10.phy
Concatenated phylip alignment for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.
min20.phy
Concatenated phylip alignment for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML.txt" for more information on assembly parameters.
min30.phy
Concatenated phylip alignment for the dataset containing minimum 30 samples per locus. See "params_Darter_m30_RAxML.txt" for more information on assembly parameters.
min4.nex
Concatenated nexus alignment for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.
min10.nex
Concatenated nexus alignment for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.
min20.nex
Concatenated nexus alignment for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML" for more information on assembly parameters.
min30.nex
Concatenated 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_RAxML
Pyrad parameter file for minimum 4 samples per locus assembly.
params_Darter_m10_RAxML
Pyrad parameter file for minimum 10 samples per locus assembly.
params_Darter_m20_RAxML
Pyrad parameter file for minimum 20 samples per locus assembly.
params_Darter_m30_RAxML
Pyrad parameter file for minimum 30 samples per locus assembly.
Figure A1
Figure 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.pdf
Figure A2
Figure 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.pdf
Figure A3
Figure 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.pdf
Figure A4
Figure 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.pdf
Figure A5
Fig. 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.pdf
Table A4
Table A4. Results of the first set of D-statistic tests (Fig. 4).
Table_A4.xlsx
Table A5
Table 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.xlsx
Table A6
Table 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.xlsx
Table A7
Table 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.xlsx
Table A8
Table A8. Results of the second set of D-statistic tests (Fig. 5).
Table_A8.xlsx
MacGuigan&Near_appendix
Online 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.