title: Phylogeny and temporal diversification of darters (Percidae: Etheostomatinae).
abstract: Discussions aimed at resolution of the Tree of Life are most often focused on the interrelationships of major organismal lineages. In this study, we focus on the resolution of some of the most apical branches in the Tree of Life through exploration of the phylogenetic relationships of darters, a species-rich clade of North American freshwater fishes. With a near-complete taxon sampling of close to 250 species, we aim to investigate strategies for efficient multilocus data sampling and the estimation of divergence times using relaxed-clock methods when a clade lacks a fossil record. Our phylogenetic data set comprises a single mitochondrial DNA (mtDNA) gene and two nuclear genes sampled from 245 of the 248 darter species. This dense sampling allows us to determine if a modest amount of nuclear DNA sequence data can resolve relationships among closely related animal species. Darters lack a fossil record to provide age calibration priors in relaxed-clock analyses. Therefore, we use a near-complete species-sampled phylogeny of the perciform clade Centrarchidae, which has a rich fossil record, to assess two distinct strategies of external calibration in relaxed-clock divergence time estimates of darters: using ages inferred from the fossil record and molecular evolutionary rate estimates. Comparison of Bayesian phylogenies inferred from mtDNA and nuclear genes reveals that heterospecific mtDNA is present in approximately 12.5% of all darter species. We identify three patterns of mtDNA introgression in darters: proximal mtDNA transfer, which involves the transfer of mtDNA among extant and sympatric darter species, indeterminate introgression, which involves the transfer of mtDNA from a lineage that cannot be confidently identified because the introgressed haplotypes are not clearly referable to mtDNA haplotypes in any recognized species, and deep introgression, which is characterized by species diversification within a recipient clade subsequent to the transfer of heterospecific mtDNA. The results of our analyses indicate that DNA sequences sampled from single-copy nuclear genes can provide appreciable phylogenetic resolution for closely related animal species. A well-resolved near-complete species-sampled phylogeny of darters was estimated with Bayesian methods using a concatenated mtDNA and nuclear gene data set with all identified heterospecific mtDNA haplotypes treated as missing data. The relaxed-clock analyses resulted in very similar posterior age estimates across the three sampled genes and methods of calibration and therefore offer a viable strategy for estimating divergence times for clades that lack a fossil record. In addition, an informative rank-free clade-based classification of darters that preserves the rich history of nomenclature in the group and provides formal taxonomic communication of darter clades was constructed using the mtDNA and nuclear gene phylogeny. On the whole, the appeal of mtDNA for phylogeny inference among closely related animal species is diminished by the observations of extensive mtDNA introgression and by finding appreciable phylogenetic signal in a modest sampling of nuclear genes in our phylogenetic analyses of darters.
authors.affiliation: Department of Ecology and Evolutionary Biology and Peabody Museum of Natural History, Yale University, New Haven, CT 06520, USA. thomas.near@yale.edu
authors.forename: Thomas J
authors.initials: TJ
authors.lastname: Near
authors.forename: Christen M
authors.initials: CM
authors.lastname: Bossu
authors.forename: Gideon S
authors.initials: GS
authors.lastname: Bradburd
authors.forename: Rose L
authors.initials: RL
authors.lastname: Carlson
authors.forename: Richard C
authors.initials: RC
authors.lastname: Harrington
authors.forename: Phillip R
authors.initials: PR
authors.lastname: Hollingsworth
authors.forename: Benjamin P
authors.initials: BP
authors.lastname: Keck
authors.forename: David A
authors.initials: DA
authors.lastname: Etnier
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D002467:Cell Nucleus / Q000235:genetics; D003573:Cytochrome b Group / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D005091:Exons / Q000235:genetics; D016654:Genes, RAG-1 / Q000235:genetics; D006239:Haplotypes; D006824:Hybridization, Genetic; D007438:Introns / Q000235:genetics; D008969:Molecular Sequence Data; D010471:Perches / Q000145:classification* / Q000235:genetics*; D010473:Perciformes / Q000145:classification / Q000235:genetics; D010802:Phylogeny; D012269:Ribosomal Proteins / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D003573:Cytochrome b Group; D004272:DNA, Mitochondrial; D012269:Ribosomal Proteins; C037442:ribosomal protein S7