Molecular phylogenetic and biogeography of Sphenomorphini (Squamata: Scincidae)

Sphenomorphini consists of 549 species in 34 genera, making it the most diverse skink tribes. Species diversity is highest in Southeast Asia with species found from the middle east, Asia, Australia, North and Central America. Taxonomic relationships among many of the genera and species within the genera are contentious due to poor morphological diagnoses. This dissertation resolves many of these issues through the examination of multiple independent molecular markers. Using traditional and new phylogenetic approaches an estimate of the relationships in Sphenomorphini is obtained. Additionally, the biogeographic history of Sphenomorphini and certain subgroups are examined under a variety of different approaches. A new taxonomy is defined for portions of Sphenomorphini and new species are described in the Philippines. These taxonomic changes and the new estimate of phylogenetic relationships of Sphenomorphini contribute a substantial step forward in the understanding of skink relationships

Implications of uniformly distributed, empirically informed priors for phylogeographical model selection: A reply to Hickerson et al

Establishing that a set of population-splitting events occurred at the same time can be a potentially persuasive argument that a common process affected the populations. Oaks et al. (2013) assessed the ability of an approximate-Bayesian method (msBayes) to estimate such a pattern of simultaneous divergence across taxa, to which Hickerson et al. (2014) responded. Both papers agree the method is sensitive to prior assumptions and often erroneously supports shared divergences; the papers differ about the explanation and solution. Oaks et al. (2013) suggested the method's behavior is caused by the strong weight of uniform priors on divergence times leading to smaller marginal likelihoods of models with more divergence-time parameters (Hypothesis 1); they proposed alternative priors to avoid strongly weighted posteriors. Hickerson et al. (2014) suggested numerical approximation error causes msBayes analyses to be biased toward models of clustered divergences (Hypothesis 2); they proposed using narrow, empirical uniform priors. Here, we demonstrate that the approach of Hickerson et al. (2014) does not mitigate the method's tendency to erroneously support models of clustered divergences, and often excludes the true parameter values. Our results also show that the tendency of msBayes analyses to support models of shared divergences is primarily due to Hypothesis 1. This series of papers demonstrate that if our prior assumptions place too much weight in unlikely regions of parameter space such that the exact posterior supports the wrong model of evolutionary history, no amount of computation can rescue our inference. Fortunately, more flexible distributions that accommodate prior uncertainty about parameters without placing excessive weight in vast regions of parameter space with low likelihood increase the method's robustness and power to detect temporal variation in divergences.Comment: 24 pages, 4 figures, 1 table, 14 pages of supporting information with 10 supporting figure

Biodiversity in a forest island: reptiles and amphibians of the West African Togo Hills

Our recent surveys of the herpetological diversity of the West African Togo Hills documented a total of 65 reptile and amphibian species, making Kyabobo National Park one of the most diverse sites surveyed in Ghana. We provide accounts for all species recorded along with photographs to aid in identification. We recorded 26 amphibians, including six new records for Kyabobo N. P., one of which is a record for the Togo Hills. Our collection of reptile species (22 lizards, 16 snakes, and one crocodile) also provides new records and range extensions for Kyabobo N. P., such as the first observation of the dwarf crocodile, Osteolaemus tetraspis. Amphibian species still lacking from our surveys in the Togo Hills include several species that are adapted to fast running water or large closed forests, like the Togo toad, Bufo togoensis and the slippery frog, Conraua derooi. Appropriate habitat for such species still remains in Kyabobo, highlighting the need for additional survey work. We draw attention to the importance of conserving forest stream habitats, which will in turn help ensure the persistence of forest-restricted species. We also highlight those species that may prove most useful for evolutionary studies of West African rain forest biogeography

Species boundaries in Philippine montane forest skinks (Genus Sphenomorphus): three new species from the mountains of Luzon and clarification of the status of the poorly known S. beyeri, S. knollmanae, and S. laterimaculatus

Recent collections of Sphenomorphus beyeri Taylor 1915 from the type locality (Mt. Banahao, Luzon Isl., Philippines) serve as the basis for a thorough analysis of topotypic variation in external morphology within the species, and allow for detailed comparisons to other taxa. We clarify the taxonomic status of S. beyeri with respect to other, phenotypically similar species and evaluate species boundaries between allopatric populations referred to this taxon. The high elevation (1400–1700 m) population of Sphenomorphus (Brown et al., 1995a) from the Zambales Mountains and Bataan Peninsula of Luzon Island (previously referred by us to S. beyeri) is a new species that we describe here. We also describe two additional new species from the isolated, high elevation (1650–1750 m) forests of the Northern Cordillera and the Sierra Madre of Luzon, specimens of both of which had been previously identified as S. beyeri. All three new species differ from each other and all other Sphenomorphus species by scalation, body size, and coloration and all have non-overlapping distributions, associated with separate, isolated, geological components of Luzon Island. In this paper we also formally redescribe S. beyeri on the basis of a large series of specimens from the type locality (Mt. Banahao, southern Luzon Island) that we have accumulated over the last 15 years. We place S. knollmanae Brown, Ruedas, and Ferner 1995 in synonymy with S. laterimaculatus (Brown and Alcala, 1980) and redescribe the latter species on the basis of the holotype and 20 additional newly collected specimens from six localities on the Bicol Peninsula of Luzon Island and Marinduque Island. These and other data suggest that species boundaries in Philippine Sphenomorphus are poorly understood and that taxonomic diversity is substantially underestimated and in need of comprehensive taxonomic review

Cryptic diversity in the Mexican highlands: Thousands of UCE loci help illuminate phylogenetic relationships, species limits and divergence times of montane rattlesnakes (Viperidae: Crotalus )

With the continued adoption of genome‐scale data in evolutionary biology comes the challenge of adequately harnessing the information to make accurate phylogenetic inferences. Coalescent‐based methods of species tree inference have become common, and concatenation has been shown in simulation to perform well, particularly when levels of incomplete lineage sorting are low. However, simulation conditions are often overly simplistic, leaving empiricists with uncertainty regarding analytical tools. We use a large ultraconserved element data set (\u3e3,000 loci) from rattlesnakes of the Crotalus triseriatus group to delimit lineages and estimate species trees using concatenation and several coalescent‐based methods. Unpartitioned and partitioned maximum likelihood and Bayesian analysis of the concatenated matrix yield a topology identical to coalescent analysis of a subset of the data in bpp . ASTRAL analysis on a subset of the more variable loci also results in a tree consistent with concatenation and bpp , whereas the SVDquartets phylogeny differs at additional nodes. The size of the concatenated matrix has a strong effect on species tree inference using SVDquartets , warranting additional investigation on optimal data characteristics for this method. Species delimitation analyses suggest up to 16 unique lineages may be present within the C. triseriatus group, with divergences occurring during the Neogene and Quaternary. Network analyses suggest hybridization within the group is relatively rare. Altogether, our results reaffirm the Mexican highlands as a biodiversity hotspot and suggest that coalescent‐based species tree inference on data subsets can provide a strongly supported species tree consistent with concatenation of all loci with a large amount of missing data

Systematic revision of the Parvoscincus decipiens (Boulenger, 1894) complex of Philippine forest skinks (Squamata: Scincidae: Lygosominae) with descriptions of seven new species

Linkem, Charles W., Brown, Rafe M. (2013): Systematic revision of the Parvoscincus decipiens (Boulenger, 1894) complex of Philippine forest skinks (Squamata: Scincidae: Lygosominae) with descriptions of seven new species. Zootaxa 3700 (4): 501-533, DOI: 10.11646/zootaxa.3700.4.

Data from: Phylogenomics of horned lizards (genus: Phrynosoma) using targeted sequence capture data

New genome sequencing techniques are enabling phylogenetic studies to scale-up from using a handful of loci to hundreds or thousands of loci from throughout the genome. In this study, we use targeted sequence capture (TSC) data from 540 ultraconserved elements and 44 protein-coding genes to estimate the phylogenetic relationships among all 17 species of horned lizards in the genus Phrynosoma. Previous molecular phylogenetic analyses of Phrynosoma based on a few nuclear genes, restriction site associated DNA (RAD) sequencing, or mitochondrial DNA (mtDNA) have produced conflicting relationships. Some of these conflicts are likely the result of rapid speciation at the start of Phrynosoma diversification, whereas other examples of gene tree discordance appear to be caused by active and residual traces of hybridization. Concatenation and coalescent-based species tree phylogenetic analyses of these new TSC data support the same topology, and a divergence dating analysis suggests that the Phrynosoma crown group is up to 30 million years old. The new phylogenomic tree supports the recognition of four main clades within Phrynosoma, including Anota (P. mcallii, P. solare, and the P. coronatum complex), Doliosaurus (P. modestum, P. goodei, and P. platyrhinos), Tapaja (P. ditmarsi, P. douglasii, P. hernandesi, and P. orbiculare), and Brevicauda (P. braconnieri, P. sherbrookei, and P. taurus). The phylogeny provides strong support for the relationships among all species of Phrynosoma and provides a robust new framework for conducting comparative analyses

Loci

Targeted sequence capture data for horned lizards (Phrynosoma). The file contains nexus data files for 584 loci, as well as a concatenated data file containing partition information

Detecting the Anomaly Zone in Species Trees and Evidence for a Misleading Signal in Higher-Level Skink Phylogeny (Squamata: Scincidae).

The anomaly zone, defined by the presence of gene tree topologies that are more probable than the true species tree, presents a major challenge to the accurate resolution of many parts of the Tree of Life. This discrepancy can result from consecutive rapid speciation events in the species tree. Similar to the problem of long-branch attraction, including more data via loci concatenation will only reinforce the support for the incorrect species tree. Empirical phylogenetic studies often employ coalescent-based species tree methods to avoid the anomaly zone, but to this point these studies have not had a method for providing any direct evidence that the species tree is actually in the anomaly zone. In this study, we use 16 species of lizards in the family Scincidae to investigate whether nodes that are difficult to resolve place the species tree within the anomaly zone. We analyze new phylogenomic data (429 loci), using both concatenation and coalescent-based species tree estimation, to locate conflicting topological signal. We then use the unifying principle of the anomaly zone, together with estimates of ancestral population sizes and species persistence times, to determine whether the observed phylogenetic conflict is a result of the anomaly zone. We identify at least three regions of the Scincidae phylogeny that provide demographic signatures consistent with the anomaly zone, and this new information helps reconcile the phylogenetic conflict in previously published studies on these lizards. The anomaly zone presents a real problem in phylogenetics, and our new framework for identifying anomalous relationships will help empiricists leverage their resources appropriately for investigating and overcoming this challenge