Phylogenomic Signatures of Ancient Introgression in a Rogue Lineage of Darters (Teleostei: Percidae)

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 approximately 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 between 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.

Figure 1.

a) Previous darter phylogenetic hypothesis based on one mtDNA and two nuclear DNA loci, modified from Near et al. (2011). Blue dashed lines indicate alternative phylogenetic placements of Allohistium from previously published studies. b) RAxML phylogeny, minimum 30 specimens sampled per RAD locus. All nodes have 100% bootstrap support unless labeled otherwise. Black nodes indicate clades not present in at least one the species trees. Asterisks indicate species sampled for SNAPP, BUCKy, and phylogenetic network analyses. Allohistium photo by Nate Tessler.

Figure 2.

Summary of topological differences involving the major lineages of darters between the concatenated ML tree and the species trees. Dashed lines indicate disagreement between the concatenated tree and the species tree. All nodes are supported with a Bayesian posterior of 1.0 or a bootstrap support value of 100 unless otherwise indicated.

Figure 3.

Time-calibrated maximum clade credibility species tree inferred using SNAPP, with potentially introgressed SNPs discarded. Grey bars on the nodes indicate 95% highest posterior density for the node heights. Bayesian posterior support for all nodes is 1.0 unless otherwise indicated. Arrows indicate the potential window of time for introgression between the stem lineages of Allohistium and Simoperca.

Figure 4.

First set of D-statistic test results. a) Concatenated ML RADseq phylogeny. All nodes are supported with 100% bootstrap support unless otherwise indicated. b) Boxplots show distribution of D-statistic values for each combination of Nothonotus, Allohistium, and the adjacent Etheostoma taxon (40 combinations of Nothonotus and Allohistium per Etheostoma species). D-statistic values less than zero indicate gene flow between Allohistium and the Etheostoma species (more ABBA site patterns compared with BABA site patterns). D-statistic values greater than zero indicate gene flow between Nothonotus and the Etheostoma species (more ABBA site patterns compared with BABA site patterns). c) Guide trees used to generate D-statistic test comparisons (3120 total species combinations).

Figure 5.

Second set of D-statistic test results. Each density plot shows the distribution of D-statistic values for a particular combination of P1, P2, and P3 lineages. Rows are the different P1 lineages, columns are the different P2 lineages. Plots below the diagonal surrounded by the green line had Nothonotus as the P3 lineage, whereas plots above the diagonal surrounded by the blue line had Allohistium as the P3 lineage. Vertical black dashed line indicates the average D-statistic value for tests involving that group of lineages. Number of D-statistic tests for each combination of lineages is noted on the x-axis of each plot. D-statistic values less than zero indicate gene flow between P1 and P3, whereas D-statistic values greater than zero indicate gene flow between P2 and P3. Red numbers indicate the percent of D-statistic tests for a particular combination of lineages that were statistically significant after correcting for multiple comparisons (alpha ).

Figure 6.

BUCKy primary concordance tree. Species sampled for each clade are indicated below the clade names. Nodes are labeled with concordance factors, 95% credible interval (CI) in parentheses. Dotted lines indicate conflicting topologies (a-c) with concordance factor 95% CIs that overlap (a-c) with the concordance factor 95% CI of a bipartition in the primary concordance tree.

Figure 7.

a) Maximum pseudolikelihood network, nodes labeled with bootstrap support values. Gamma is the inheritance probability for the minor hybrid edge, 95% confidence interval in parentheses. b) Maximum parsimony network. Gamma is the inheritance probability for the minor hybrid edge.