Cameron D. Siler

EVIDENCE FOR CLIMATE‐DRIVEN DIVERSIFICATION? A CAUTION FOR INTERPRETING ABC INFERENCES OF SIMULTANEOUS HISTORICAL EVENTS

Approximate Bayesian computation (ABC) is rapidly gaining popularity in population genetics. One example, msBayes, infers the distribution of divergence times among pairs of taxa, allowing phylogeographers to test hypotheses about historical causes of diversification in co‐distributed groups of organisms. Using msBayes, we infer the distribution of divergence times among 22 pairs of populations of vertebrates distributed across the Philippine Archipelago. Our objective was to test whether sea‐level oscillations during the Pleistocene caused diversification across the islands. To guide interpretation of our results, we perform a suite of simulation‐based power analyses. Our empirical results strongly support a recent simultaneous divergence event for all 22 taxon pairs, consistent with the prediction of the Pleistocene‐driven diversification hypothesis. However, our empirical estimates are sensitive to changes in prior distributions, and our simulations reveal low power of the method to detect random variation in divergence times and bias toward supporting clustered divergences. Our results demonstrate that analyses exploring power and prior sensitivity should accompany ABC model selection inferences. The problems we identify are potentially mitigable with uniform priors over divergence models (rather than classes of models) and more flexible prior distributions on demographic and divergence‐time parameters.

Multilocus phylogeny and Bayesian estimates of species boundaries reveal hidden evolutionary relationships and cryptic diversity in Southeast Asian monitor lizards

Recent conceptual, technological and methodological advances in phylogenetics have enabled increasingly robust statistical species delimitation in studies of biodiversity. As the variety of evidence purporting species diversity has increased, so too have the kinds of tools and inferential power of methods for delimiting species. Here, we showcase an organismal system for a data‐rich, comparative molecular approach to evaluating strategies of species delimitation among monitor lizards of the genus Varanus. The water monitors (Varanus salvator Complex), a widespread group distributed throughout Southeast Asia and southern India, have been the subject of numerous taxonomic treatments, which have drawn recent attention due to the possibility of undocumented species diversity. To date, studies of this group have relied on purportedly diagnostic morphological characters, with no attention given to the genetic underpinnings of species diversity. Using a 5‐gene data set, we estimated phylogeny and used multilocus genetic networks, analysis of population structure and a Bayesian coalescent approach to infer species boundaries. Our results contradict previous systematic hypotheses, reveal surprising relationships between island and mainland lineages and uncover novel, cryptic evolutionary lineages (i.e. new putative species). Our study contributes to a growing body of literature suggesting that, used in concert with other sources of data (e.g. morphology, ecology, biogeography), multilocus genetic data can be highly informative to systematists and biodiversity specialists when attempting to estimate species diversity and identify conservation priorities. We recommend holding in abeyance taxonomic decisions until multiple, converging lines of evidence are available to best inform taxonomists, evolutionary biologists and conservationists.

Multilocus phylogeny reveals unexpected diversification patterns in Asian wolf snakes (genus Lycodon)

The diverse group of Asian wolf snakes of the genus Lycodon represents one of many poorly understood radiations of advanced snakes in the superfamily Colubroidea. Outside of three species having previously been represented in higher‐level phylogenetic analyses, nothing is known of the relationships among species in this unique, moderately diverse, group. The genus occurs widely from central to Southeast Asia, and contains both widespread species to forms that are endemic to small islands. One‐third of the diversity is found in the Philippine archipelago. Both morphological similarity and highly variable diagnostic characters have contributed to confusion over species‐level diversity. Additionally, the placement of the genus among genera in the subfamily Colubrinae remains uncertain, although previous studies have supported a close relationship with the genus Dinodon. In this study, we provide the first estimate of phylogenetic relationships within the genus Lycodon using a new multi‐locus data set. We provide statistical tests of monophyly based on biogeographic, morphological and taxonomic hypotheses. With few exceptions, we are able to reject many of these hypotheses, indicating a need for taxonomic revisions and a reconsideration of the groups biogeography. Mapping of color patterns on our preferred phylogenetic tree suggests that banded and blotched types have evolved on multiple occasions in the history of the genus, whereas the solid‐color (and possibly speckled) morphotype color patterns evolved only once. Our results reveal that the colubrid genus Dinodon is nested within Lycodon—a clear finding that necessitates the placing of the former genus in synonymy with the latter.

A NEW LIMB-REDUCED, LOAM-SWIMMING SKINK (SQUAMATA: SCINCIDAE: BRACHYMELES) FROM CENTRAL LUZON ISLAND, PHILIPPINES

Abstract We describe a new species of scincid lizard of the genus Brachymeles from montane forests (1400–1450 m) of Mt. Palali, Caraballo Mountain Range, in central Luzon Island, Philippines. The new species is the second known species of Brachymeles that has only three digits on both the forelimb and hindlimbs. Additional morphological characters include unique scale pigmentation and absence of a pineal eyespot and an auricular opening. The new species is the eighth known Brachymeles from Luzon Island and the twelfth non-pentadactyl species. With this new discovery, the Luzon Faunal Region holds the greatest diversity of species of the genus Brachymeles in the world.

Review of morphometric measurements used in anuran species descriptions and recommendations for a standardized approach

Standardization and repeatability is at the heart of all scientific research, yet very little literature exists to standardize morphometric measurements within vertebrate groups. This is particularly true for amphibians. Our study attempts to rectify this lack of methodological standardization for the measurement of morphological characters in anurans through an extensive literature survey of 136 species descriptions representing 45 currently recognized families of frogs. The survey revealed 42 morphological measurements represented in five percent or more of the literature reviewed. All measurements are listed by most commonly used name, acronym, and most precise definition, and we provide statistics summarizing the variation in measurement use and description from the surveyed literature. Of these 42 measurements, a subset of 16 were found in the top 75% of all surveyed descriptions and identified as a focal set of recommended measurements in an effort to standardize the morphometric measurements that describe anuran species diversity. Illustrations of these 16 measurements are provided as a visual reference for standardizing their measurement.

Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) III: a new species from Tablas Island

Studies of the diversity of Philippine amphibians and reptiles have resulted in the continued description of cryptic species. Species formerly thought to range across multiple recognized faunal regions are now considered to be assemblages of multiple unique species, each restricted to a single faunal region. This pattern continues to hold true when considering Philippine skinks of the genus Brachymeles. Recent studies have resulted in the description of numerous unique species with many exhibiting various degrees of digit loss or limb reduction, as well as suggesting that unique lineages are still present in the B. bonitae Complex. In this paper, we describe a new species of fossorial skink within this species complex from Tablas Island based on collections made nearly 50 years ago. Although no genetic data are available for the new species, examinations of morphological data (qualitative traits, meristic counts, and mensural measurements) support its distinction from all other members of the genus. Brachymeles dalawangdaliri sp. nov. is differentiated from other members of the genus based on a suite of unique phenotypic characteristics, including a small body size (SVL 66.0-80.9 mm), bidactyl fore-limbs, digitless, unidactyl, or bidactyl hind limbs, a high number of presacral vertebrae (49), the absence of auricular openings, and distinct dorsal head scale patterns. The description of the new species increases the diversity of endemic vertebrates recognized to occur in the Romblon Island Group in the central Philippines.

Additions to Philippine Slender Skinks of the Brachymeles bonitae Complex (Reptilia: Squamata: Scincidae) II: a new species from the northern Philippines.

We describe a new digitless scincid lizard of the genus Brachymeles from northern Luzon and Camiguin Norte islands in the Philippines. This species belongs to the Brachymeles bonitae Complex, and both molecular and morphological data confirm that this species is distinct from all other congeners. Formerly considered to be a single widespread species, this group of species has been the focus of recent systematic reviews. Here we describe a new species in the B. bonitae Complex, recognized currently to constitute five species. Brachymeles ilocandia sp. nov. is the second digitless and the seventeenth non-pentadactyl species in genus. The description of this species brings the total number of species in the genus to 40, and provides new insight into unique distribution patterns of species of the northern Philippines.

Lizards of the lost arcs: Mid-Cenozoic diversification, persistence and ecological marginalization in the west pacific

Regions with complex geological histories often have diverse and highly endemic biotas, yet inferring the ecological and historical processes shaping this relationship remains challenging. Here, in the context of the taxon cycle model of insular community assembly, we investigate patterns of lineage diversity and habitat usage in a newly characterized vertebrate radiation centred upon the worlds most geologically complex insular region: island arcs spanning from the Philippines to Fiji. On island arcs taxa are ecologically widespread, and provide evidence to support one key prediction of the taxon cycle, specifically that interior habitats (lowland rainforests, montane habitats) are home to a greater number of older or relictual lineages than are peripheral habitats (coastal and open forests). On continental fringes, however, the clade shows a disjunct distribution away from lowland rainforest, occurring in coastal, open or montane habitats. These results are consistent with a role for biotic interactions in shaping disjunct distributions (a central tenant of the taxon cycle), but we find this pattern most strongly on continental fringes not islands. Our results also suggest that peripheral habitats on islands, and especially island arcs, may be important for persistence and diversification, not just dispersal and colonization. Finally, new phylogenetic evidence for subaerial island archipelagos (with an associated biota) east of present-day Wallaces Line since the Oligocene has important implications for understanding long-term biotic interchange and assembly across Asia and Australia.

A new species of Cosmocerca (Nematoda: Cosmocercidae) and other helminths in Cyrtodactylus gubaot (Squamata: Gekkonidae) from the Philippines.

Cosmocerca leytensis sp. nov. (Ascaridida, Cosmocercidae) from the large intestine of Cyrtodactylus gubaot (Squamata: Gekkonidae) collected on Leyte Island, Philippines is described and illustrated. Cosmocerca leytensis sp. nov. is the 30th species assigned to the genus, the 4th from the Oriental region, and the first from the Philippine Islands. The new species is most similar to those species possessing 4 pairs of plectanes, i.e., C. archeyi, C. australis, C. oroensis, and C sardiniae. Cosmocerca sardiniae lacks lateral alae; C. archeyi, C. australis, C. leytensis sp. nov. and C. oroensis possess lateral alae. Spicule length of C. oroensis is less than 75 µm, while C. archeyi, C. australis, and C. leytensis sp. nov. have spicule lengths greater than 75 µm. Males of C. australis possess 2 pairs of rosette caudal papillae, which are lacking in C. archeyi and C. leytensis sp. nov. Females of C. archeyi posses a conical tail, females of C. leytensis sp. nov. have a rounded posterior end supporting a flexible filament.