skip to main content

Title: Towards rectifying limitations on species delineation in dusky salamanders (Desmognathus: Plethodontidae): An ecoregion-drainage sampling grid reveals additional cryptic clades
Dusky salamanders (Desmognathus) constitute a large, species-rich group within the family Plethodontidae, and though their systematic relationships have been addressed extensively, most studies have centered on particular species complexes and therefore offer only piecemeal phylogenetic perspective on the genus. Recent work has revealed Desmognathus to be far more clade rich—35 reciprocally monophyletic clades versus 22 recognized species—than previously imagined, results that, in turn, provide impetus for additional survey effort within clades and across geographic areas thus far sparsely sampled. We conceived and implemented a sampling regime combining level IV ecoregions and independent river drainages to yield a geographic grid for comprehensive recovery of all genealogically exclusive clades. We sampled over 550 populations throughout the distribution of Desmognathus in the eastern United States of America and generated mitochondrial DNA sequence data (mtDNA; 1,991 bp) for 536 specimens. A Bayesian phylogenetic reconstruction of the resulting haplotypes revealed forty-five reciprocally monophyletic clades, eleven of which have never been included in a comprehensive phylogenetic reconstruction, and an additional three not represented in any molecular systematic survey. Although general limitations associated with mtDNA data preclude new species delineation, we profile each of the 45 clades and assign names to 10 new clades (following a protocol for previous clade nomenclature). We also redefine several species complexes and erect new informal species complexes. Our dataset, which contains topotypic samples for nearly every currently recognized species and most synonymies, will offer a robust framework for future efforts to delimit species within Desmognathus.  more » « less
Award ID(s):
Author(s) / Creator(s):
Date Published:
Journal Name:
Page Range / eLocation ID:
1 to 61
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Chasmataspidids are a group of Early Paleozoic (Middle Ordovician-Middle Devonian)chelicerates defined by an apparently unique opisthosomal tagmosis consisting of a microtergite, a three-segmented fused buckler, and a nine-segmented postabdomen. Although the number of known chasmataspidid species increased by half during the past decade, the group has not been a subject of detailed phylogenetic analysis, and its placement within Chelicerata is uncertain. Though recent analyses that include chasmataspidids support a monophyletic Chasmataspidida as sister to Sclerophorata (Eurypterida and Arachnida), few have sampled more than three of the 14 currently recognized species. Previous workers have suggested chasmataspidids may be a polyphyletic or paraphyletic group, or that chasmataspidids may resolve as the sister taxon to eurypterids, or even as a clade within Eurypterida. Without a broader sampling of chasmataspidids it is not possible to adequately test these various hypotheses, while a robust phylogenetic framework in necessary for understanding macroevolutionary and biogeographic trends within the group. Chasmataspidids also represent the earliest preserved euchelicerate in the fossil record, with Chasmataspis dated to approximately 478 million years ago, and as such its phylogenetic position in relation to other euchelicerates has implications for the divergence times of those clades. We present a new phylogenetic matrix comprising 81 characters coded for every currently described chasmataspidid species, analysis of which under maximum parsimony and Bayesian inference results in concordant phylogenetic topologies. Chasmataspidida resolves as in most recent analyses as a monophyletic clade sister to Sclerophorata, indicating that Xiphosura, Chasmataspidida, and Sclerophorata likely diverged in the Early Ordovician. The analysis also supports a taxonomic revision within Chasmataspidida; we propose dividing the clade into two superfamilies, with four constituent families. As part of this study the Silurian taxon Loganamaraspis was reevaluated and the morphology of appendage VI, previously considered to be retained as a walking limb, could not be ascertained. 
    more » « less
  2. Abstract

    The family Mutillidae (Hymenoptera) is a species‐rich group of aculeate wasps that occur worldwide. The higher‐level classification of the family has historically been controversial due, in part, to the extreme sexual dimorphism exhibited by these insects and their morphological similarity to other wasp taxa that also have apterous females. Modern hypotheses on the internal higher classification of Mutillidae have been exclusively based on morphology and, further, they include Myrmosinae as a mutillid subfamily. In contrast, several molecular‐based family‐level studies of Aculeata recovered Myrmosinae as a nonmutillid taxon. To test the validity of these morphology‐based classifications and the phylogenetic placement of the controversial taxon Myrmosinae, a phylogenomic study of Mutillidae was conducted using ultraconserved elements (UCEs). All currently recognized subfamilies and tribes of Mutillidae were represented in this study using 140 ingroup taxa. The maximum likelihood criterion (ML) and the maximum parsimony criterion (MP) were used to infer the phylogenetic relationships within the family and related taxa using an aligned data set of 238,764 characters; the topologies of these respective analyses were largely congruent. The modern higher classification of Mutillidae, based on morphology, is largely congruent with the phylogenomic results of this study at the subfamily level, whereas the tribal classification is poorly supported. The subfamily Myrmosinae was recovered as sister to Sapygidae in the ML analysis and sister to Sapygidae + Pompilidae in the MP analysis; it is consequently raised to the family level, Myrmosidae,stat.nov.The two constituent tribes of Myrmosidae are raised to the subfamily level, Kudakrumiinae,stat.nov., and Myrmosinae,stat.nov.All four recognized tribes of Mutillinae were found to be non‐monophyletic; three additional mutilline clades were recovered in addition to Ctenotillini, Mutillini, Smicromyrmini, and Trogaspidiini sensu stricto. Three new tribes are erected for members of these clades: Pristomutillini Waldren,trib.nov., Psammothermini Waldren,trib.nov., and Zeugomutillini Waldren,trib.nov.All three recognized tribes of Sphaeropthalminae were found to be non‐monophyletic; six additional sphaeropthalmine clades were recovered in addition to Dasymutillini, Pseudomethocini, and Sphaeropthalmini sensu stricto. The subtribe Ephutina of Mutillinae: Mutillini was found to be polyphyletic, with theEphutagenus‐group recovered within Sphaeropthalminae and theOdontomutillagenus‐group recovered as sister to Myrmillinae + Mutillinae. Consequently, the subtribe Ephutina is transferred from Mutillinae: Mutillini and is raised to a tribe within Sphaeropthalminae, Ephutini,stat.nov.Further, the taxon Odontomutillinae,stat.nov., is raised from a synonym of Ephutina to the subfamily level. The sphaeropthalmine tribe Pseudomethocini was found to be polyphyletic, with the subtribe Euspinoliina recovered as a separate clade in Sphaeropthalminae; consequently, Euspinoliina is raised to a tribe, Euspinoliini,stat.nov., in Sphaeropthalminae. The dasylabrine tribe Apteromutillini was recovered within Dasylabrini and is proposed as a new synonym of Dasylabrinae. Finally, dating analyses were conducted to infer the ages of the Pompiloidea families (Mutillidae, Myrmosidae, Pompilidae, and Sapygidae) and the ages of the Mutillidae subfamilies and tribes.

    more » « less
  3. Abstract

    Thoroughly sampled and well-supported phylogenetic trees are essential to taxonomy and to guide studies of evolution and ecology. Despite extensive prior inquiry, a comprehensive tree of heron relationships (Aves: Ardeidae) has not yet been published. As a result, the classification of this family remains unstable, and their evolutionary history remains poorly studied. Here, we sample genome-wide ultraconserved elements (UCEs) and mitochondrial DNA sequences (mtDNA) of >90% of extant species to estimate heron phylogeny using a combination of maximum likelihood, coalescent, and Bayesian inference methods. The UCE and mtDNA trees are mostly concordant with one another, providing a topology that resolves relationships among the 5 heron subfamilies and indicates that the genera Gorsachius, Botaurus, Ardea, and Ixobrychus are not monophyletic. We also present the first genetic data from the Forest Bittern Zonerodius heliosylus, an enigmatic species of New Guinea; our results suggest that it is a member of the genus Ardeola and not the Tigrisomatinae (tiger herons), as previously thought. Finally, we compare molecular rates between heron clades in the UCE tree with those in previously constructed mtDNA and DNA–DNA hybridization trees. We show that rate variation in the UCE tree corroborates rate patterns in the previously constructed trees—that bitterns (Ixobrychus and Botaurus) evolved comparatively faster, and some tiger herons (Tigrisoma) and the Boat-billed Heron (Cochlearius) more slowly, than other heron taxa.

    more » « less
  4. Abstract Aim

    To test the importance of alternative diversification drivers and biogeographical processes for the evolution of Amazonian upland forest birds through a densely sampled analysis of diversification of the endemic Amazonian genusRhegmatorhinaat multiple taxonomic and temporal scales.




    Antbirds (Thamnophilidae).


    We sequenced four mtDNAand nuclear gene regions of 120 individuals from 50 localities representing all recognized species and subspecies of the genus. We performed molecular phylogenetic analyses using both gene tree and species tree methods, molecular dating analysis and estimated population demographic history and gene flow.


    Dense sampling throughout the distribution ofRhegmatorhinarevealed that the main Amazonian rivers delimit the geographic distribution of taxa as inferred from mtDNAlineages. Molecular phylogenetic analyses resulted in a strongly supported phylogenetic hypothesis for the genus, with two main clades currently separated by the Madeira River. Molecular dating analysis indicated diversification during the Quaternary. Reconstruction of recent demographic history of populations revealed a trend for population expansion in eastern Amazonia and stability in the west. Estimates of gene flow corroborate the possibility that migration after divergence had some influence on the current patterns of diversity.

    Main Conclusions

    Based on broad‐scale sampling, a clarification of taxonomic boundaries, and strongly supported phylogenetic relationships, we confirm that, first, mitochondrial lineages within this upland forest Amazonian bird genus agree with spatial patterns known for decades based on phenotypes, and second, that most lineages are geographically delimited by the large Amazonian rivers. The association between past demographic changes related to palaeoclimatic cycles and the historically varying strength and size of rivers as barriers to dispersal may be the path to the answer to the long‐standing question of identifying the main drivers of Amazonian diversification.

    more » « less
  5. The extent and nature of genetic differentiation inSemotilus atromaculatus, one of the most abundant and widespread leuciscids in North America, were evaluated based on mitochondrial (mt) and nuclear DNA sequence variation. Phylogenetic relationships were first inferred based on a fragment of the cytochrome b (cytb) region and the nuclear introns7gene forS. atromaculatusand all other congeners as well as representative species from all other genera in the creek chub–plagopterin clade. The phylogeography of major haplogroups ofS. atromaculatuswas also assessed according to variation in a fragment of the mitochondrialcytbregion from 567 individuals across its range. All analyses identifiedS. thoreauianus,S. lumbeeandS. corporalisas reciprocally monophyletic groups. Analyses of nuclear sequence variation resolvedS. atromaculatusas a single clade, whereS. thoreauianusandS. lumbeewere recovered as the sister group toS. atromaculatus, andS. corporaliswas resolved as sister to all other species in the genus. Analyses of mtDNA sequence variation recoveredS. atromaculatusas three well supported and differentiated monophyletic groups, with a widespread genetically homogeneous lineage extending across most of the current range of the species; a more geographically restricted and geographically structured lineage in the southern Appalachians, sister group toS. lumbee; and a geographically restricted lineage was identified from two Gulf Slope basins. Evidence of complex mito‐nuclear discordance and phylogeographic differentiation withinS. atromaculatusillustrates that further analysis of widespread species is warranted to understand North American freshwater fish diversity and distributions.

    more » « less