Data from: Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)
Data files
Oct 31, 2018 version files 5.15 GB
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c88d6m10p3_RAxML.loci
299.81 MB
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c88d6m10p3_RAxML.nex
636.61 MB
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c88d6m10p3_RAxML.phy
509.26 MB
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c88d6m20p3_RAxML.loci
264.48 MB
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c88d6m20p3_RAxML.nex
480.91 MB
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c88d6m20p3_RAxML.phy
384.70 MB
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c88d6m30p3_RAxML.loci
244.46 MB
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c88d6m30p3_RAxML.phy
313.27 MB
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c88d6m30p3.nex
522.22 MB
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c88d6m4p3_RAxML.loci
354.80 MB
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c88d6m4p3_RAxML.nex
629.84 MB
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c88d6m4p3_RAxML.phy
503.84 MB
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FigA1_SVDQuartetsTree.pdf
1.21 MB
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FigA2_ASTRALTree.pdf
32.55 KB
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FigA3_allDarterClades_noAllo_primaryConcordance.tree_alt.pdf
128.94 KB
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FigA4_allDarterClades_noSimo_primaryConcordance.tree_alt.pdf
109.42 KB
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FigA5_SNAPP.combined.mcc.pdf
31.59 KB
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MacGuigan&Near_appendix_v2_clean.docx
50.37 KB
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params_Darter_m10_RAxML.txt
3.90 KB
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params_Darter_m20_RAxML.txt
3.90 KB
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params_Darter_m30_RAxML.txt
3.90 KB
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params_Darter_m4_RAxML.txt
3.90 KB
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TableA4_allDstat_final_pAdjust.xlsx
295.67 KB
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TableA5_P2-P3Clade_propSig.xlsx
10.99 KB
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TableA6_P3_propSig.xlsx
12.01 KB
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TableA7_P1-P3_propSig copy.xlsx
16.60 KB
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TableA8_DstatSummary_pAdjust.xlsx
2.65 MB
Oct 31, 2018 version files 6.16 GB
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c88d6m20p3_RAxML.nex
480.91 MB
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c88d6m30p3.nex
522.22 MB
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FigA1_SVDQuartetsTree.pdf
1.21 MB
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FigA2_ASTRALTree.pdf
32.55 KB
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FigA3_allDarterClades_noAllo_primaryConcordance.tree_alt.pdf
128.94 KB
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FigA4_allDarterClades_noSimo_primaryConcordance.tree_alt.pdf
109.42 KB
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FigA5_SNAPP.combined.mcc.pdf
31.59 KB
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Figure_A1.pdf
1.21 MB
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Figure_A2.pdf
32.55 KB
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Figure_A3.pdf
128.94 KB
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Figure_A4.pdf
109.42 KB
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Figure_A5.pdf
31.59 KB
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MacGuigan&Near_appendix_v2_clean.docx
50.37 KB
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MacGuigan&Near_appendix.docx
50.37 KB
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min10.loci
299.81 MB
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min10.nex
636.61 MB
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min10.phy
509.26 MB
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min20.loci
264.48 MB
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min20.nex
480.91 MB
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min20.phy
384.70 MB
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min30.loci
244.46 MB
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min30.nex
522.22 MB
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min30.phy
313.27 MB
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min4.loci
354.80 MB
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min4.nex
629.84 MB
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min4.phy
503.84 MB
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params_Darter_m10_RAxML.txt
3.90 KB
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params_Darter_m20_RAxML.txt
3.90 KB
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params_Darter_m30_RAxML.txt
3.90 KB
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params_Darter_m4_RAxML.txt
3.90 KB
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Table_A4.xlsx
295.67 KB
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Table_A5.xlsx
10.99 KB
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Table_A6.xlsx
12.01 KB
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Table_A7.xlsx
16.60 KB
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Table_A8.xlsx
2.65 MB
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TableA4_allDstat_final_pAdjust.xlsx
295.67 KB
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TableA5_P2-P3Clade_propSig.xlsx
10.99 KB
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TableA6_P3_propSig.xlsx
12.01 KB
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TableA7_P1-P3_propSig copy.xlsx
16.60 KB
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TableA8_DstatSummary_pAdjust.xlsx
2.65 MB
Abstract
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.