The natural and human-mediated expansion of a human-commensal lizard into the fringes of Southeast Asia.

Background: Human-commensal species often display deep ancestral genetic structure within their native range and founder-effects and/or evidence of multiple introductions and admixture in newly established areas. We investigated the phylogeography of Eutropis multifasciata, an abundant human-commensal scincid lizard that occurs across Southeast Asia, to determine the extent of its native range and to assess the sources and signatures of human introduction outside of the native range. We sequenced over 350 samples of E.

Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve.

The Indonesian island of Sulawesi has a unique geology and geography, which have produced an astoundingly diverse and endemic flora and fauna and a fascinating biogeographic history. Much biodiversity research has focused on the regional endemism in the island's Central Core and on its four peninsulas, but the biodiversity of the island's many upland regions is still poorly understood for most taxa, including amphibians and reptiles. Here, we report the first of several planned full-mountain checklists from a series of herpetological surveys of Sulawesi's mountains conducted by our team.

Bewildering biogeography: Waves of dispersal and diversification across southern Wallacea by bent-toed geckos (genus: Cyrtodactylus).

Bent-toed Geckos, genus Cyrtodactylus, are one of the most diverse terrestrial vertebrate groups, and their range extends from South Asia into Australo-Papua and adjacent Pacific islands. Given the generally high faunal endemism on Wallacean islands, it is rather paradoxical that the diversity in these geckos appears to be so low (21 species in Wallacea, 15 in the Philippines) compared with continental shelf assemblages (>300 species on Sunda + Sahul Shelves + adjacent islands). To determine whether this shortfall was real or an artifact of historical undersampling, we analyzed mitochondrial DNA sequences of hundreds of southern Wallacean samples (Lesser Sundas + southern Maluku).

Highly-multiplexed and efficient long-amplicon PacBio and Nanopore sequencing of hundreds of full mitochondrial genomes.

Background: Mitochondrial genome sequences have become critical to the study of biodiversity. Genome skimming and other short-read based methods are the most common approaches, but they are not well-suited to scale up to multiplexing hundreds of samples. Here, we report on a new approach to sequence hundreds to thousands of complete mitochondrial genomes in parallel using long-amplicon sequencing.

Phylogenetic relationships of southern Wallacean ranid frogs (Anura: Ranidae: Hylarana).

Frogs in the family Ranidae are diverse in Asia and are thought to have dispersed to the Sahul Shelf approximately 10 million years ago, where they radiated into more than a dozen species. Ranid species in the intervening oceanic islands of Wallacea, such as Hylarana florensis and H. elberti from the Lesser Sundas and H.

Diverge and Conquer: Phylogenomics of southern Wallacean forest skinks (Genus: Sphenomorphus) and their colonization of the Lesser Sunda Archipelago.

The archipelagos of Wallacea extend between the Sunda and Sahul Shelves, serving as a semipermeable two-way filter influencing faunal exchange between Asia and Australo-Papua. Forest skinks (Genus Sphenomorphus) are widespread throughout southern Wallacea and exhibit complex clinal, ontogenetic, sexual, and seasonal morphological variation, rendering species delimitation difficult. We screened a mitochondrial marker for 245 Sphenomorphus specimens from this area to inform the selection of 104 samples from which we used targeted sequence capture to generate a dataset of 1154 nuclear genes (∼1.

Cryptic extinction risk in a western Pacific lizard radiation.

Unlabelled: Cryptic ecologies, the Wallacean Shortfall of undocumented species' geographical ranges and the Linnaean Shortfall of undescribed diversity, are all major barriers to conservation assessment. When these factors overlap with drivers of extinction risk, such as insular distributions, the number of threatened species in a region or clade may be underestimated, a situation we term 'cryptic extinction risk'. The genus is a diverse radiation of insular and arboreal geckos that occurs across the western Pacific.

Whos your daddy? On the identity and distribution of the paternal hybrid ancestor of the parthenogenetic gecko Lepidodactylus lugubris (Reptilia: Squamata: Gekkonidae).

The widespread parthenogenetic gecko Lepidodactylus lugubris is comprised of several clonal lineages, at least one of which has been known for some time to have originated from hybridization between its maternal ancestor, Lepidodactylus moestus, and a putatively undescribed paternal ancestor previously known only from remote islands in the Central Pacific. By integrating new genetic sequences from multiple studies on Lepidodactylus and incorporating new genetic sequences from previously sampled populations, we recovered a phylogenetic tree that shows a close genetic similarity between the generally hypothesized paternal hybrid ancestor and a recently described species from Maluku (Indonesia), Lepidodactylus pantai. Our results suggest that the paternal hybrid ancestor of at least one parthenogenetic clone of L.

Phylogenomic Analysis Reveals Dispersal-Driven Speciation and Divergence with Gene Flow in Lesser Sunda Flying Lizards (Genus Draco).

The Lesser Sunda Archipelago offers exceptional potential as a model system for studying the dynamics of dispersal-driven diversification. The geographic proximity of the islands suggests the possibility for successful dispersal, but this is countered by the permanence of the marine barriers and extreme intervening currents that are expected to hinder gene flow. Phylogenetic and species delimitation analyses of flying lizards (genus Draco) using single mitochondrial genes, complete mitochondrial genomes, and exome-capture data sets identified 9-11 deeply divergent lineages including single-island endemics, lineages that span multiple islands, and parapatrically distributed nonsister lineages on the larger islands.

Multilocus phylogeny of Bornean Bent-Toed geckos (Gekkonidae: Cyrtodactylus) reveals hidden diversity, taxonomic disarray, and novel biogeographic patterns.

The gekkonid genus Cyrtodactylus is a highly diverse group of lizards (280 + species), which covers an expansive geographic range. Although this genus has been the focus of many taxonomic and molecular systematic studies, species on the Southeast Asian island of Borneo have remained understudied, leading to an unclear evolutionary history with cascading effects on taxonomy and biogeographic inferences. We assembled the most comprehensive multilocus Bornean dataset (one mitochondrial and three nuclear loci) that included 129 novel sequences and representatives from each known Cyrtodactylus species on the island to validate taxonomic status, assess species diversity, and elucidate biogeographic patterns.

A new skink of the genus Subdoluseps (Hardwicke amp; Gray, 1828) from Peninsular Malaysia.

An integrative taxonomic analysis of Subdoluseps herberti from southern Thailand and Peninsular Malaysia and S. samajaya from Sarawak, East Malaysia (Borneo) recovers the former as paraphyletic with respect to the latter. The analyses recover the three southernmost populations of S.

Optimizing Phylogenomics with Rapidly Evolving Long Exons: Comparison with Anchored Hybrid Enrichment and Ultraconserved Elements.

Marker selection has emerged as an important component of phylogenomic study design due to rising concerns of the effects of gene tree estimation error, model misspecification, and data-type differences. Researchers must balance various trade-offs associated with locus length and evolutionary rate among other factors. The most commonly used reduced representation data sets for phylogenomics are ultraconserved elements (UCEs) and Anchored Hybrid Enrichment (AHE).

Habitat preference modulates trans-oceanic dispersal in a terrestrial vertebrate.

The importance of long-distance dispersal (LDD) in shaping geographical distributions has been debated since the nineteenth century. In terrestrial vertebrates, LDD events across large water bodies are considered highly improbable, but organismal traits affecting dispersal capacity are generally not taken into account. Here, we focus on a recent lizard radiation and combine a summary-coalescent species tree based on 1225 exons with a probabilistic model that links dispersal capacity to an evolving trait, to investigate whether ecological specialization has influenced the probability of trans-oceanic dispersal.

Unrealized diversity in an urban rainforest: A new species of Lygosoma (Squamata: Scincidae) from western Sarawak, Malaysia (Borneo).

We collected two specimens of an undescribed species of Lygosoma from pitfall traps in an urban rainforest in Kuching and from the base of a forested hill in western Sarawak, East Malaysia. The new species is diagnosable from all south-east Asian congeners by morphological characters, and most closely resembles Lygosoma herberti from the Thai-Malay Peninsula. The new species shows substantial molecular divergence from its closest relatives in two protein-coding genes, one mitochondrial (ND1) and one nuclear (R35) that we sequenced for several south-east Asian congeners.

A new species of (Reptilia: Squamata: Gekkonidae) from the Kei Islands, Maluku, Indonesia.

Lepidodactylus pantai is a new species of gecko from the Kei Islands, Maluku, Indonesia that is closely associated with intertidal habitats. This species does not fit cleanly into any of the three species groups described for the genus because it possesses the unique combination of both divided terminal scansors on all toes and a nearly completely cylindrical tail without fringes or evidence of dorsoventral compression. A phylogenetic analysis including this species demonstrates that it is the sister taxon of a population from Palau, and that this clade is sister to the clade containing Group III species for which we have molecular data.

Ancient divergence time estimates in support the existence of Pleistocene barriers on the exposed Sunda Shelf.

Episodic sea level changes that repeatedly exposed and inundated the Sunda Shelf characterize the Pleistocene. Available evidence points to a more xeric central Sunda Shelf during periods of low sea levels, and despite the broad land connections that persisted during this time, some organisms are assumed to have faced barriers to dispersal between land-masses on the Sunda Shelf. is a secretive, forest adapted scincid lizard that ranges across the Sunda Shelf.

A new species of Tropidophorus Duméril & Bibron, 1839 (Squamata: Sauria: Scincidae) from Sarawak, East Malaysia (Borneo).

A new species of the genus Tropidophorus is described from Putai, upper Baleh, Kapit districts, Sarawak, East Malaysia (Borneo). Tropidophorus sebi sp. nov.

A single origin of extreme matrotrophy in African mabuyine skinks.

Most mammals and approximately 20% of squamates (lizards and snakes) are viviparous, whereas all crocodilians, birds and turtles are oviparous. Viviparity evolved greater than 100 times in squamates, including multiple times in Mabuyinae (Reptilia: Scincidae), making this group ideal for studying the evolution of nutritional patterns associated with viviparity. Previous studies suggest that extreme matrotrophy, the support of virtually all of embryonic development by maternal nutrients, evolved as many as three times in Mabuyinae: in Neotropical Mabuyinae (63 species), Eumecia (2 species; Africa) and Trachylepis ivensii (Africa).

Two new species of diminutive leaf-litter skinks (Squamata: Scincidae: Tytthoscincus) from Gunung Penrissen, Sarawak, Malaysia (northern Borneo).

We describe two new species of skinks from Gunung Penrissen, Sarawak, Malaysia, in northern Borneo, Tytthoscincus batupanggah sp. nov. and T.