Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico.

We utilize the efficient GBS technique to obtain thousands of nuclear loci and SNPs to reconstruct the evolutionary history of Mexican leaf-toed geckos (Phyllodactylus). Through the incorporation of unprecedented sampling for this group of geckos, in combination with genomic data analysis, we generate mostly consistent phylogenetic hypotheses using two approaches: supermatrix and coalescent-based inference. All topologies depict three, mutually exclusive major clades. Clade I comprises P. bordai and all species closer to P. bordai than to any other Phyllodactylus. Clade II comprises P. nocticolus and all species closer to P. nocticolus than to any other Phyllodactylus. Clade III comprises P. tuberculosus and all species closer to P. tuberculosus than to any other Phyllodactylus. Analyses estimate the age for the most recent common ancestor of Phyllodactylus in the Eocene (~43 mya), and the ancestors of each major clade date to the Eocene-Oligocene transition (32-36 mya). This group includes one late-Eocene lineage (P. bordai), Oligocene lineages (P. paucituberculatus, P. delcampi), but also topological patterns that indicate a recent radiation occurred during the Pleistocene on islands in the Gulf of California. The wide spatial and temporal scale indicates a complex and unique biogeographic history for each major clade. The 33 species delimited by BPP and stepping-stone BFD*coalescent based genomic approaches reflect this history. This diversity delimited for Mexican leaf-toed geckos demonstrates a vast underestimation in the number of species based on morphological data alone.

Colonization and usage of an artificial urban wetland complex by freshwater turtles.

Conservation authorities invest heavily in the restoration and/or creation of wetlands to counteract the destruction of habitat caused by urbanization. Monitoring the colonization of these new wetlands is critical to an adaptive management process. We conducted a turtle mark-recapture survey in a 250 ha artificially created wetland complex in a large North American city (Toronto, Ontario). We found that two of Ontario's eight native turtle species (Snapping turtle (SN), Chelydra serpentina, and Midland Painted (MP) turtle, Chrysemys picta marginata) were abundant and both were confirmed nesting. The Blanding's turtle (Emydoidea blandingii) was present but not well established. Species richness and turtle density were not equally distributed throughout the wetland complex. We noted SN almost exclusively populated one water body, while other areas of the wetland had a varying representation of both species. The sex ratios of both SN and MP turtles were 1:1. We tracked the movement of Snapping and Blanding's turtles and found that most turtles explored at least two water bodies in the park, that females explored more water bodies than males, and that 95% of turtles showed fidelity to individual overwintering wetlands. We performed DNA analysis of two Blanding's turtles found in the created wetlands and could not assign these turtles to any known profiled populations. The genetic data suggest that the turtles probably belong to a remnant local population. We discuss the implications of our results for connectivity of artificial wetlands and the importance of the whole wetland complex to this turtle assemblage.

Anomaloglossus meansi sp. n., a new Pantepui species of the Anomaloglossus beebei group (Anura, Aromobatidae).

Recent extinctions and drastic population declines have been documented in the Guiana Shield endemic frog genus Anomaloglossus, hence the importance to resolve its alpha-taxonomy. Based on molecular phylogenies, the literature has long reported the occurrence of an undescribed species in the Pakaraima Mountains of Guyana in the Pantepui region. We here describe this new taxon and demonstrate that in addition to divergence at the molecular level the new species differs from congeners by a unique combination of morphological characters, notably a small size (maximum SVL in males 18.86 mm, maximum SVL in females 21.26 mm), Finger I = Finger II when fingers adpressed, Finger III swollen in breeding males, fringes on fingers absent, toes basally webbed but lacking fringes, in life presence of a thin dorsolateral stripe from tip of snout to tip of urostyle, and a black throat in preserved males (immaculate cream in females). Virtually nothing is known about the ecology of the new species. We suggest the new species to be considered as Data Deficient according to IUCN standards.

Large-scale phylogenetic analyses provide insights into unrecognized diversity and historical biogeography of Asian leaf-litter frogs, genus Leptolalax (Anura: Megophryidae).

Southeast Asia and southern China (SEA-SC) harbor a highly diverse and endemic flora and fauna that is under increasing threat. An understanding of the biogeographical history and drivers of this diversity is lacking, especially in some of the most diverse and threatened groups. The Asian leaf-litter frog genus Leptolalax Dubois 1980 is a forest-dependent genus distributed throughout SEA-SC, making it an ideal study group to examine specific biogeographic hypotheses. In addition, the diversity of this genus remains poorly understood, and the phylogenetic relationships among species of Leptolalax and closely related Leptobrachella Smith 1928 remain unclear. Herein, we evaluate species-level diversity based on 48 of the 53 described species from throughout the distribution of Leptolalax. Molecular analyses reveal many undescribed species, mostly in southern China and Indochina. Our well-resolved phylogeny based on multiple nuclear DNA markers shows that Leptolalax is not monophyletic with respect to Leptobrachella and, thus, we assign the former to being a junior synonym of the latter. Similarly, analyses reject monophyly of the two subgenera of Leptolalax. The diversification pattern of the group is complex, involving a high degree of sympatry and prevalence of microendemic species. Northern Sundaland (Borneo) and eastern Indochina (Vietnam) appear to have played pivotal roles as geographical centers of diversification, and paleoclimatic changes and tectonic movements seem to have driven the major divergence of clades. Analyses fail to reject an "upstream" colonization hypothesis, and, thus, the genus appears to have originated in Sundaland and then colonized mainland Asia. Our results reveal that both vicariance and dispersal are responsible for current distribution patterns in the genus.

A novel multilocus phylogenetic estimation reveals unrecognized diversity in Asian horned toads, genus Megophrys sensu lato (Anura: Megophryidae).

The horned toad assemblage, genus Megophrys sensu lato, currently includes three groups previously recognized as the genera Atympanophrys, Xenophrys and Megophrys sensu stricto. The taxonomic status and species composition of the three groups remain controversial due to conflicting phenotypic analyses and insufficient phylogenetic reconstruction; likewise, the position of the monotypic Borneophrys remains uncertain with respect to the horned toads. Further, the diversity of the horned toads remains poorly understood, especially for widespread species. Herein, we evaluate species-level diversity based on 45 of the 57 described species from throughout southern China, Southeast Asia and the Himalayas using Bayesian inference trees and the Generalized Mixed Yule Coalescent (GMYC) approach. We estimate the phylogeny using both mitochondrial and nuclear DNA data. Analyses reveal statistically significant mito-nuclear discordance. All analyses resolve paraphyly for horned toads involving multiple strongly supported clades. These clades correspond with geography. We resurrect the genera Atympanophrys and Xenophrys from the synonymy of Megophrys to eliminate paraphyly of Megophrys s.l. and to account for the morphological, molecular and biogeographic differences among these groups, but we also provide an alternative option. Our study suggests that Borneophrys is junior synonym of Megophrys sensu stricto. We provide an estimation of timeframe for the horned toads. The mitochondrial and nuclear trees indicate the presence of many putative undescribed species. Widespread species, such as Xenophrys major and X. minor, likely have dramatically underestimated diversity. The integration of morphological and molecular evidence can validate this discovery. Montane forest dynamics appear to play a significant role in driving diversification of horned toads.

Multilocus species delimitation in the Crotalus triseriatus species group (Serpentes: Viperidae: Crotalinae), with the description of two new species.

Members of the Crotalus triseriatus species group of montane rattlesnakes are widely distributed across the highlands of Mexico and southwestern USA. Although five species are currently recognized within the group, species limits remain to be tested. Genetic studies suggest that species may be paraphyletic and that at least one cryptic species may be present. We generate 3,346 base pairs of DNA sequence data from seven nuclear loci to test competing models of species delimitation in the C. triseriatus group using Bayes factor delimitation. We also examine museum specimens from the Trans-Mexican Volcanic Belt for evidence of cryptic species. We find strong support for a nine-species model and genetic and morphological evidence for recognizing two new species within the group, which we formally describe here. Our results suggest that the current taxonomy of the C. triseriatus species group does not reflect evolutionary history. We suggest several conservative taxonomic changes to the group, but future studies are needed to better clarify relationships among species and examine genetic patterns and structure within wide-ranging lineages.

Phylogeny of the Cyrtodactylus irregularis species complex (Squamata: Gekkonidae) from Vietnam with the description of two new species.

The number of described species of bent-toed geckos of the Cyrtodactylus irregularis species complex in Vietnam has increased from one to eight in the last six years. We combined morphological and molecular analyses to explore phylogenetic relationships among all described species in the group. The phylogeny required the description of two new species, Cyrtodactylus phuocbinhensis sp. nov. and Cyrtodactylus taynguyenensis sp. nov. Further, the tree resolved two additional undescribed clades that may also be new species. The species C. bugiamapensis and C. ziegleri were found to require redefinition. Cyrtodactylus phuocbinhensis sp. nov. is characterized by a series of enlarged femoral scales separated from preanal scales while Cyrtodactylus taynguyenensis sp. nov. does not possess enlarged femoral scales. Both new species are distinguished from other congeners by a combination of the following characters: small subcaudal scales, not transversely enlarged; presence (C. phuocbinhensis sp. nov.) or absence (C. taynguyenensis sp. nov.) of enlarged femoral scales; number of preanal pores; and dorsal pattern. Genetic distances between described species and new species were 16.5% and 2.0% in COI and RPL35, respectively, for C. phuocbinhensis sp. nov., and these distances were 18.8% and 2.2% for C. taynguyenensis sp. nov., respectively.

The dazed and confused identity of Agassiz's land tortoise, Gopherus agassizii (Testudines, Testudinidae) with the description of a new species, and its consequences for conservation.

We investigate a cornucopia of problems associated with the identity of the desert tortoise, Gopherus agassizii (Cooper). The date of publication is found to be 1861, rather than 1863. Only one of the three original cotypes exists, and it is designated as the lectotype of the species. Another cotype is found to have been destroyed in the 1906 San Francisco earthquake and subsequent fire. The third is lost. The lectotype is genetically confirmed to be from California, and not Arizona, USA as sometimes reported. Maternally, the holotype of Gopherus lepidocephalus (Ottley & Velázques Solis. 1989) from the Cape Region of Baja California Sur, Mexico is also from the Mojavian population of the desert tortoise, and not from Tiburon Island, Sonora, Mexico as previously proposed. A suite of characters serve to diagnose tortoises west and north of the Colorado River, the Mojavian population, from those east and south of the river in Arizona, USA, and Sonora and Sinaloa, Mexico, the Sonoran population. Species recognition is warranted and because Gopherus lepidocephalus is from the Mojavian population, no names are available for the Sonoran species. Thus, a new species, Gopherus morafkaisp. n., is named and this action reduces the distribution of Gopherus agassizii to only 30% of its former range. This reduction has important implications for the conservation and protection of Gopherus agassizii, which may deserve a higher level of protection.

A new species of Dipsas (Squamata: Colubridae) from Guyana.

A new species of Dipsas is described from the Pakaraima Mountains of Guyana. The new species is characterised by 15 dorsal scale rows with the middorsal row slightly enlarged. four pairs of chinshields with the first pair elongate, elongate loreal entering orbit, one preocular, six upper labials, and head narrow anteriorly, increasing in width posteriorly. It could not be determined to which of Peters' (1960) species groups the new species belongs. The new species is known only from 1490 m elevation on Mount Ayanganna. a tepui in the Guiana Shield, where it was found in high-tepui low-canopy habitat, in bromeliads or branches. This is the first record of Dipsas as a member of the Guiana Shield high-tepui herpetofauna.