Search

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., (© 2011 The Author(s). Evolution© 2011 The Society for the Study of Evolution.)

The rapid accumulation of multilocus data sets has led to dramatic advances in methodologies for estimating evolutionary relationships among closely related species, but relatively less advancement has been made in methods for discriminating between competing species delimitation hypotheses. Multilocus data sets provide an advantage in testing species delimitation scenarios because they offer a direct test of species monophyly and aid in the biological interpretation of such phenomena as allele-sharing and deep coalescent events. Most species tree estimation methods that are designed to analyze multilocus data sets require the a priori assignment of individuals to species categories and therefore do not provide a strategy to directly test competing species delimitation scenarios. An approach was recently proposed that utilizes a coalescent-based species tree estimation method to inform species delimitation decisions by comparing likelihood scores that measure the fit of gene trees within a given species tree. We use a multilocus nuclear and mitochondrial DNA sequence data set to both reexamine a recently proposed species delimitation scenario in the Etheostoma simoterum species complex and test the utility of species tree estimation methods in testing species delimitation hypotheses. Descriptions of species in the E. simoterum species complex of snubnose darters, a group of six teleost freshwater fish species, are based largely on male nuptial coloration. Most of the putative species are nonmonophyletic at every examined locus. Using a novel combination of Bayesian-estimated gene tree topologies, Bayesian phylogenetic species tree inferences, coalescent simulations, and examination of phenotypic variation, we assess the occurrence of shared alleles among species, and we propose that results from our analyses support a three-species rather than a six-species delimitation scenario in the E. simoterum complex. We found that comparing likelihood scores from the species tree estimation approach used across many potential delimitation scenarios resulted in a systematic bias toward over-splitting in the E. simoterum complex and failed to support a species delimitation scenario that was consistent with geography, phenotype, or any previous species delimitation hypothesis. Despite common expectations, we demonstrate that application of molecular approaches to species delimitation can result in the recognition of fewer, instead of a larger number of species. In addition, our analyses highlight the importance of phenotypic character information in providing an independent assessment of alternative species delimitation hypotheses in the E. simoterum species complex.

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.

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.

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 demonstrates that allopatric speciation can occur rapidly.

The Pleistocene Epoch has been frequently cited as a period of intense speciation for a significant portion of temperate continental biotas. To critically assess the role of Pleistocene glaciations on the evolution of the freshwater fish clade Micropterus, we use a phylogenetic analysis of complete gene sequences from two mitochondrial genes (cytochrome b and ND2), and a fossil calibration of the molecular clock to estimate ages of speciation events and rates of diversification. The absence of substantial morphological and ecological divergence together with endemism of five of the eight species in North American tributaries of the Gulf of Mexico may be interpreted as the result of a recent Pleistocene origin for these species. Speciation dates in Micropterus range from 1.01 +/- 0.32 to 11.17 +/- 1.02 million years ago. Only one speciation event is dated to the Pleistocene, and rates of diversification are not significantly variable in Micropterus. The premise that the Pleistocene was an exceptional period of speciation in Micropterus is not supported. Instead, a Gulf Coast allopatric speciation model is proposed, and predicts periods of dynamic speciation driven by sea level fluctuations in the Late Miocene and Pliocene. The Pleistocene, however, was a period of significant intraspecific mitochondrial lineage diversification. The application of the Gulf Coast allopatric speciation model to the remaining aquatic fauna of the Gulf of Mexico coast in North America will rely on robust phylogenetic hypotheses and accurate age estimations of speciation events.