Search

Reconstructing deep-time biogeographic histories is limited by the comparatively recent diversification of most extant lineages. Ray-finned fishes, which include nearly half of all living vertebrates, are no exception. Although most lineages of ray-finned fishes radiated around the Cretaceous-Paleogene boundary, a handful of ancient, species-poor clades still persist. These lineages can illuminate very old biogeographic trends, but their low species richness can also limit the reconstruction of these patterns. The seven extant species of gars distributed in freshwater habitats in North America and Cuba are an old clade with a fossil record spanning over 150 million years of Earth history. Using a genomic data set of DNA sequences of 1105 exons for the seven living species and an updated morphological matrix of all extant and extinct taxa, we infer the phylogenetic relationships of gars and test how divergence times and biogeographic reconstructions are influenced by sequential and joint estimation and the effect on these inferences when using different taxon sets based on fossil completeness. Our analyses consistently show that the two extant gar genera Atractosteus and Lepisosteus diverged approximately 105 million years ago and many of the inferred divergences in the gar time-calibrated phylogeny closely track major Mesozoic tectonic events, including the separation of the Americas, the expansion of the early Atlantic, and the Cretaceous reorganization of North American river systems. The crown clades Atractosteus and Lepisosteus originated in the Cenozoic of eastern North America, implying that this region has served as both the origin of extant gar diversity and the refugium of this iconic ancient lineage. These results exemplify how combining phylogenomics with the fossil record provides congruence around the evolutionary history of ancient clades like gars and can reveal long-lost biogeographic patterns. [Lepisosteidae; fossilized birth death; biogeography; phylogenomics; paleontology.] [ABSTRACT FROM AUTHOR]

Introgressive hybridization and incomplete lineage sorting complicate the inference of phylogeny, and available species-tree methods do not simultaneously account for these processes. Both hybridization and ancestral polymorphism have been invoked to explain divergent phylogenies inferred from different datasets for Stigmacerca, a clade of 11 North American darter species. Species of Stigmacerca are characterized by a mating system involving parental care with males guarding nesting territories and fertilized eggs. Males of four species of Stigmacerca develop egg-mimic nuptial structures on their second dorsal fins during the breeding season. Previous phylogenies suggest contrasting scenarios for the evolution of this nuptial trait. Using a combination of coalescent-based methods, we analyzed a dataset comprising a mitochondrial gene and 15 nuclear loci to estimate relationships and simultaneously test for introgressive hybridization. Our analyses identified several instances of interspecific gene flow involving both cytoplamsmic haplotypes and nuclear alleles. The new phylogeny was used to infer a single origin and recent loss of egg-mimic structures in Stigmacerca and led to the discovery of a phylogenetically distinct species. Our results highlight the limited strategies available to account for introgressive hybridization in the inference of species relationships and the likely effects of this process on reconstructing trait evolution. [ABSTRACT FROM AUTHOR]

A major challenge facing biodiversity conservation and management is that a significant portion of species diversity remains undiscovered or undescribed. This is particularly evident in subterranean animals in which species delimitation based on morphology is difficult because differentiation is often obscured by phenotypic convergence. Multilocus genetic data constitute a valuable source of information for species delimitation in such organisms, but until recently, few methods were available to objectively test species delimitation hypotheses using genetic data. Here, we use recently developed methods for discovering and testing species boundaries and relationships using a multilocus dataset in a widely distributed subterranean teleost fish, Typhlichthys subterraneus, endemic to Eastern North America. We provide evidence that species diversity in T. subterraneus is currently underestimated and that the picture of a single, widely distributed species is not supported. Rather, several morphologically cryptic lineages comprise the diversity in this clade, including support for the recognition of T. eigenmanni. The high number of cryptic species in Typhlichthys highlights the utility of multilocus genetic data in delimiting species, particularly in lineages that exhibit slight morphological disparity, such as subterranean organisms. However, results depend on sampling of individuals and loci; this issue needs further study. [ABSTRACT FROM AUTHOR]

Eastern North America is the location of the world's most species-rich temperate freshwater fish fauna. Hypotheses regarding the geographic and temporal scale of teleost diversification in this region have not been broadly investigated using absolute divergence time estimates among the constituent lineages. This study used time-calibrated molecular phylogenies estimated from mitochondrial and nuclear genes to investigate the temporal and geographic signatures of diversification within barcheek darters, a clade of allopatrically distributed species endemic to the Eastern Highlands. Results from divergence time estimates using an uncorrelated lognormal model suggest that the barcheek darters are an ancient group with a crown node estimate of 16.3 mya, 95% highest posterior density (HPD): [12.4, 20.5], and the clade is characterized by substantial intraspecific divergence times within several species. In particular, the Caney Fork endemic Etheostoma basilare comprises five strongly supported and deeply divergent clades with a most recent common ancestor estimated at 8.0 mya, 95% HPD: [5.6, 10.7]. These results are concordant with the hypothesis that geologically stable areas of eastern North America have facilitated both the generation and preservation of lineages across a substantial breadth of evolutionary time, and that allopatric speciation in darters has occurred at much smaller spatial scales than previously realized. [ABSTRACT FROM AUTHOR]

The species diversity of North American freshwater fishes is unparalleled among temperate regions of the planet. This diversity is concentrated in the Central Highlands of eastern North America and this distribution pattern has inspired different models involving either dispersal or vicariance to explain the high species diversity of North American fishes. The most popular of these models is the Central Highlands vicariance hypothesis (CHVH), which proposes an ancient and diverse widespread fauna that existed across a previously continuous highland landscape that is much different from today. The mechanisms of isolation in the CHVH involve specific instances of vicariance that affected several diverse lineages of Central Highlands fishes. We tested predictions of the CHVH and alternative models using a cytochrome b-inferred phylogeny of the darter clade Nothonotus. A Bayesian mixed-model method was used for phylogenetic analysis. The phylogenetic data set included all 20 recognized Nothonotus species, and most species were represented with multiple sequences. We were able to convert genetic branch lengths to absolute age using external fossil calibrations in the freshwater perciform fish clade Centrarchidae. Using a well-resolved Nothonotus phylogeny and divergence time estimates, we identify equal numbers of instances of both vicariance and dispersal among disjunct regions of the Central Highlands, biogeographic pseudocongruence, rather recent speciation in Nothonotus, and a surprisingly large amount of speciation within highland areas. With regard to Nothonotus, previous Central Highlands biogeographic models offer little in the way of providing possible mechanisms responsible for diversification in the clade. Patterns of speciation in Nothonotus are similar to those discovered in recent efforts that have included speciation as a parameter into classic models of island biogeography. [ABSTRACT FROM AUTHOR]

Theory predicts that clades diversifying via sympatric speciation will exhibit high diversification rates. However, the expected rate of diversification in clades characterized by allopatric speciation is less clear. Previous studies have documented significantly higher speciation rates in freshwater fish clades diversifying via sympatric versus allopatric modes, leading to suggestions that the geographic pattern of speciation can be inferred solely from knowledge of the diversification rate. We tested this prediction using an example from darters, a clade of approximately 200 species of freshwater fishes endemic to eastern North America. A resolved phylogeny was generated using mitochondrial DNA gene sequences for logperches, a monophyletic group of darters composed of 10 recognized species. Divergence times among logperch species were estimated using a fossil calibrated molecular clock in centrarchid fishes, and diversification rates in logperches were estimated using several methods. Speciation events in logperches are recent, extending from 4.20 ± 1.06 million years ago (mya) to 0.42 ± 0.22 mya, with most speciation events occurring in the Pleistocene. Diversification rates are high in logperches, at some nodes exceeding rates reported for well-studied adaptive radiations such as Hawaiian silverswords. The geographic pattern of speciation in logperches was investigated by examining the relationship between degree of sympatry and the absolute age of the contrast, with the result that diversification in logperches appears allopatric. The very high diversification rate observed in the logperch phylogeny is more similar to freshwater fish clades thought to represent examples of sympatric speciation than to clades representing allopatric speciation. These results demonstrate that the geographic mode of speciation for a clade cannot be inferred from the diversification rate. The empirical observation of high diversification rates in logperches... [ABSTRACT FROM AUTHOR]

[Display omitted] • Analysis of ∼40,000 ddRAD loci provides robust phylogenetic resolution of the Etheostoma nigrum species complex. • Analyses identify several new allopatric lineages that merit species designation. • Parallel divergence in Atlantic coastal plain river basins is associated with Pliocene inundation. • Secondary contact and hybridization are limited by the geographic structure of river basins. • Strong signal of gene flow threatens the genetic integrity of an endangered species, Etheostoma susanae. The history of riverine fish diversification is largely a product of geographic isolation. Physical barriers that reduce or eliminate gene flow between populations facilitate divergence via genetic drift and natural selection, eventually leading to speciation. For freshwater organisms, diversification is often the product of drainage basin rearrangements. In young clades where the history of isolation is the most recent, evolutionary relationships can resemble a tangled web. One especially recalcitrant group of freshwater fishes is the Johnny Darter (Etheostoma nigrum) species complex, where traditional taxonomy and molecular phylogenetics indicate a history of gene flow and conflicting inferences of species diversity. Here we assemble a genomic dataset using double digest restriction site associated DNA (ddRAD) sequencing and use phylogenomic and population genetic approaches to investigate the evolutionary history of the complex of species that includes E. nigrum, E. olmstedi, E. perlongum, and E. susanae. We reveal and validate several evolutionary lineages that we delimit as species, highlighting the need for additional work to formally describe the diversity of the Etheostoma nigrum complex. Our analyses also identify gene flow among recently diverged lineages, including one instance involving E. susanae , a localized and endangered species. Phylogeographic structure within the Etheostoma nigrum species complex coincides with major geologic events, such as parallel divergence in river basins during Pliocene inundation of the Atlantic coastal plain and multiple northward post-glacial colonization routes tracking river basin rearrangements. Our study serves as a nuanced example of how low dispersal rates coupled with geographic isolation among disconnected river systems in eastern North America has produced one of the world's freshwater biodiversity hotspots. [ABSTRACT FROM AUTHOR]

The Mexican Neovolcanic Plateau sharply divides the vertebrate fauna of Mesoamerica where the climate of both the neotropics and temperate North America gradually blend. Only a few vertebrate groups such as the Heroine cichlids, distributed from South America to the Rio Grande in North America, are found both north and south of the Neovolcanic Plateau. To better understand the geography and temporal diversification of cichlids at this geologic boundary, we used mitochondrial DNA sequences of the cytochrome b (cyt b) gene to reconstruct the relationships of 52 of the approximately 80 species of Heroine cichlids in Mesoamerica. Our analysis suggests several cichlids in South America should be considered as part of the Mesoamerican Heroine clade because they and the cichlids north of the Isthmus of Panama are clearly supported as monophyletic with respect to all other Neotropical cichlids. We also recovered a group containing species in Paratheraps + Paraneetroplus + Vieja as the sister clade to Herichthys. Herichthys is the only cichlid clade north of the Mexican Plateau and it is monophyletic. Non-parametric rate smoothing of cichlid cyt b sequence resulted in an estimated divergence time of approximately 6 million years for Herichthys. This temporal diversification is concordant with divergence times estimated for anurans in the genus Bufo, a group that exhibits a similar geographic distribution. Our results indicate the 5-million-year-old extension of the Mexican Neovolcanic Plateau to the Gulf Coast of Mexico has strongly influenced the current transition between the vertebrate faunas of the Neotropics and Nearctic. [Copyright &y& Elsevier]

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.

The alteration in palaeodrainage river connections has shaped patterns of speciation, genetic diversity and the geographical distribution of the species-rich freshwater fauna of North America. The integration of ancestral range reconstruction methods and divergence time estimates provides an opportunity to infer palaeodrainage connectivity and test alternative palaeodrainage hypotheses. Members of the Orangethroat Darter clade, Ceasia, are endemic to southeastern North America and occur north and south of the Pleistocene glacial front, a distributional pattern that makes this clade of closely related species an ideal system to investigate the number and location of glacial refugia and compare alternative hypotheses regarding the proposed evolution of the Teays-Mahomet palaeodrainage. This study utilized time-calibrated mitochondrial and nuclear gene phylogenies and present-day geographical distributions to investigate hypothesized Teays-Mahomet River connections through time using a dispersal-extinction-cladogenesis (DEC) framework. Results of DEC ancestral area reconstructions indicate that the Teays-Mahomet River was a key dispersal route between disjunct highland regions connecting the Mississippi River tributaries to the Old-Ohio Drainage minimally at two separate occasions during the Pleistocene. There was a dynamic interplay between palaeodrainage connections through time and postglacial range expansion from three glacial refugia that shaped the current genetic structure and geographical distributions of the species that comprise Ceasia., (© 2013 John Wiley & Sons Ltd.)

Investigations into the phylogenetics of closely related animal species are dominated by the use of mitochondrial DNA (mtDNA) sequence data. However, the near-ubiquitous use of mtDNA to infer phylogeny among closely related animal lineages is tempered by an increasing number of studies that document high rates of transfer of mtDNA genomes among closely related species through hybridization, leading to substantial discordance between phylogenies inferred from mtDNA and nuclear gene sequences. In addition, the recent development of methods that simultaneously infer a species phylogeny and estimate divergence times, while accounting for incongruence among individual gene trees, has ushered in a new era in the investigation of phylogeny among closely related species. In this study we assess if DNA sequence data sampled from a modest number of nuclear genes can resolve relationships of a species-rich clade of North American freshwater teleost fishes, the darters. We articulate and expand on a recently introduced method to infer a time-calibrated multi-species coalescent phylogeny using the computer program (*)BEAST. Our analyses result in well-resolved and strongly supported time-calibrated darter species tree. Contrary to the expectation that mtDNA will provide greater phylogenetic resolution than nuclear gene data; the darter species tree inferred exclusively from nuclear genes exhibits a higher frequency of strongly supported nodes than the mtDNA time-calibrated gene tree., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Phylogenies of closely related animal species are often inferred using mitochondrial DNA (mtDNA) gene sequences. The accuracy of mtDNA gene trees is compromised through hybridization that leads to introgression of mitochondrial genomes. Using DNA sequences from 6 single-copy nuclear genes and 2 regions of the mitochondrial genome, we investigated the temporal and geographic signature of mitochondrial and nuclear introgression in the Etheostoma spectabile darter clade. Phylogenetic analyses of the nuclear genes result in the monophyly of the E. spectabile clade; however, with respect to sampled specimens of 5 species (Etheostoma fragi, Etheostoma uniporum, Etheostoma pulchellum, Etheostoma burri, and E. spectabile), the mitochondrial phylogeny is inconsistent with E. spectabile clade monophyly. Etheostoma uniporum and E. fragi are both fixed for heterospecific mitochondrial genomes. Limited nuclear introgression is restricted to E. uniporum. Our analyses show that the pattern of introgression is consistently asymmetric, with movement of heterospecific mitochondrial haplotypes and nuclear alleles into E. spectabile clade species; introgressive hybridization spans broad temporal scales; and introgression is restricted to species and populations in the Ozarks. The introgressed mitochondrial genome observed in E. fragi has an obscure phylogenetic placement among darters, an ancient age, and is possibly a mitochondrial fossil from an Etheostoma species that has subsequently gone extinct. These results indicate that introgression, both ancient and more contemporaneous, characterizes the history of diversification in the E. spectabile species clade and may be relatively common among clades comprising the species-rich North American freshwater fauna.