Perry L Wood Jr

University of Michigan | U-M

The exploration of unsurveyed areas in southern Thailand discovered two new karst-adapted species, Cyrtodactylus sungaiupe sp. nov. and Cyrtodactylus wangkhramensis sp. nov. , from Thung Wa and La-ngu Districts, Satun Province, respectively. These new species are members of the C. pulchellus group that occur along the Thai-Malay Peninsula. The new...

Two new insular rock geckos in the genus Cnemaspis are described from Ko Samui in Surat Thani Province and Ko Similan in Phang-nga Province, southern Thailand, based on a combination of morphological and mitochondrial NADH dehydrogenase subunit 2 (ND2) data. Both new species represent divergent lineages within the Cnemaspis siamensis species group....

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficu...

An integrative taxonomic analysis of species in the colubrid genus Lycodon Fitzinger, 1826 recovered two new syntopic species of the L. rufozonatus complex from the imperiled Song Giang River valley in Khan Hoa Province, of Southern Vietnam. Although L. truongi sp. nov. and L. anakradaya sp. nov. are syntopic, they are not particularly closely rela...

Convergent morphological specializations for an arboreal lifestyle in most species of the Cyrtodactylus brevipalmatus group have been a confounding factor for establishing a stable taxonomy among its species. Recent references to C. interdigitalis from throughout Thailand and Laos were made without comparisons to the type material from Tham Yai Nam...

We report on the first molecular estimates of phylogenetic relationships of Brachymeles dalawangdaliri (Scincidae) and Pseudogekko isapa (Gekkonidae), and present new data on phenotypic variation in these two poorly known taxa, endemic to the Romblon Island Group of the central Philippines. Because both species were recently described on the basis...

The gekkonid genus Cyrtodactylus is the third largest vertebrate genus on the planet with well over 300 species that range across at least eight biogeographic regions from South Asia to Melanesia. The ecological and morphological plasticity within the genus, has contributed to its ability to disperse across ephemeral seaways, river systems, basins,...

Phylogenetic and multivariate analyses of Gekko smithii Gray, 1842 recover a new species Gekko hulk from Peninsular Malay­sia and support the resurrection of G. albomaculatus (Giebel, 1861)

The COVID-19 pandemic and political turmoil in Myanmar has dealt a severe blow to the country’s progress in herpetological research and the protection of limestone habitats. Both afflictions have reversed much of the scientific and conservation gains made in the past decade, and continue to hinder exploratory surveys and continued monitoring of thr...

In cryptic amphibian complexes, there is a growing trend to equate high levels of genetic structure with hidden cryptic species diversity. Typically, phylogenetic structure and distance-based approaches are used to demonstrate the distinctness of clades and justify the recognition of new cryptic species. However, this approach does not account for...

The bent-toed geckos of the Cyrtodactylus pulchellus group are widely distributed along the Thai-Malay Peninsula. Although taxonomic and phylogenetic studies of this species group have been continuously conducted, only some populations from Thailand have been included, resulting in hidden diversity within this group. In this study, we used morpholo...

Despite the prevalence of high‐throughput sequencing in phylogenetics, many relationships remain difficult to resolve because of conflicting signal among genomic regions. Selection of different types of molecular markers from different genomic regions is required to overcome these challenges. For evolutionary studies in frogs, we introduce the publ...

Many processes of biological diversification can simultaneously affect multiple evolutionary lineages. Examples include multiple members of a gene family diverging when a region of a chromosome is duplicated, multiple viral strains diverging at a “super-spreading” event, and a geological event fragmenting whole communities of species. It is difficu...

The taxonomy and phylogeny of the Cyrtodactylus pulchellus complex along the Thai-Malay Peninsular region has been the focus of many recent studies and has resulted in the recognition of 17 species. However, the majority of these studies were focused on Peninsular and insular Malaysia where there were specimens and genetic vouchers. The taxonomic s...

Karstic landscapes are immense reservoirs of biodiversity and range-restricted endemism. Nowhere is this more evident than in the world’s third-largest vertebrate genus Cyrtodactylus (Gekkonidae) which contains well over 300 species. A stochastic character mapping analysis of 10 different habitat preferences across a phylogeny containing 345 descri...

The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on...

The gekkonid genus Cyrtodactylus is the third most speciose vertebrate genus in the world, containing well over 300 species that collectively range from South Asia to Melanesia across some of the most diverse landscapes and imperiled habitats on the planet. A genus-wide phylogeny of the group has never been presented because researchers working on...

The taxonomic status of the ranid frog Abavorana luctuosa (Peters, 1871) was investigated using a combination of molecular and morphological data. The analyses revealed that A. luctuosa sensu lato is composed of two species in Borneo. One of these species agrees with the description of Rana decorata Mocquard, 1890 which is resurrected in the combin...

Lizards and snakes (squamates) are known for their varied sex determining systems, and gecko lizards are especially diverse, having evolved sex chromosomes independently multiple times. While sex chromosomes frequently turnover among gecko genera, intrageneric turnovers are known only from Gekko and Hemidactylus. Here, we used RADseq to identify se...

Genome-scale data have greatly facilitated the resolution of recalcitrant nodes that Sanger-based datasets have been unable to resolve. However, phylogenomic studies continue to use traditional methods such as boot-strapping to estimate branch support; and high bootstrap values are still interpreted as providing strong support for the correct topol...

Understanding the processes that underpin adaptive evolutionary shifts within major taxonomic groups has long been a research directive among many evolutionary biologists. Such phenomena are best studied in large monophyletic groups that occupy a broad range of habitats where repeated exposure to novel ecological opportunities has happened independ...

An extensive molecular phylogeny of the endemic New Caledonian scincid lizard Marmorosphax based on the mitochondrial ND2 gene retrieves four major lineages. The basal divergences within the phylogeny progressively split off lineages concor-dant with the boundaries of the island's major ultramafic regions, and are believed to be the product of vica...

Philippine False Geckos (genus Pseudogekko) are secretive, delicate, slender-bodied, arboreal members of an obligate forest specialist clade that is substantially more species diverse than previously assumed. Over the last century, few species were added to this Philippine endemic genus. During the last decade, however, revisionary studies have res...

A new gekkonid lizard, Cyrtodactylus maelanoi sp. nov., from Mae Hong Son Province of the Thai Highlands is described using an integrative taxonomic analysis based on morphology, color pattern, and the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNAs. Phylogenetic analyses place the new species within clade 1 of the C. s...

Philippine False Geckos (genus Pseudogekko) are secretive, delicate, slender-bodied, arboreal members of an obligate forest specialist clade that is substantially more species diverse than previously assumed. Over the last century, few species were added to this Philippine endemic genus. During the last decade, however, revisionary studies have res...

Most new cryptic species are described using conventional tree‐ and distance‐based species delimitation methods (SDMs), which rely on phylogenetic arrangements and measures of genetic divergence. However, although numerous factors such as population structure and gene flow are known to confound phylogenetic and species delimitation inferences, the...

Southeast Asia hosts a rich concentration of biodiversity within multiple biodiversity hotspots. Indochina, a region with remarkably high levels of in situ diversification, possesses five major rivers (Chiang Mai, Ayeyarwady, Mekong, Salween, and Red), several of which coincide with phylogenetic breaks of terrestrial taxa. Draco maculatus possesses...

Using FrogCap, a recently-developed sequence-capture protocol, we obtained more than 12,000 highly informative exons, introns, and Ultraconserved elements (UCEs), which we used to illustrate variation in evolutionary histories of these classes of markers, and to resolve long-standing systematic problems in Southeast Asian Golden-backed frogs of the...

The rock-dwelling gecko genus Cnemaspis is one of the most species-diverse genera of gekkonid in Thailand. Earlier studies relied on morphological data to identify species, but cryptic morphology often obscured species diversity in Cnemaspis. In this study, an integrative taxonomic approach based on morphological characters and sequences of the mit...

A new, diminutive species of Rock Gecko Cnemaspis tubaensis sp. nov. of the C. kumpoli group, is described from Tuba Island, Langkawi Archipelago, Kedah, Peninsular Malaysia and is differentiated from all other species in the kumpoli group by having a unique combination of morphological and color pattern characteristics, including a maximum SVL of...

Liopeltis is a genus of poorly known, infrequently sampled species of colubrid snakes in tropical Asia. We collected a specimen of Liopeltis from Pulau Tioman, Peninsular Malaysia, that superficially resembled L. philippina, a rare species that is endemic to the Palawan Pleistocene Aggregate Island Complex, western Philippines. We analyzed morpholo...

A new species of insular Bent-toed Gecko, Cyrtodactylus culaochamensis sp. nov. of the C. irregularis group is described from Cu Lao Cham Mountain, from Hon Lao Island, Hoi An City, Quang Nam Province, Cham Islands, central Vietnam. Cyrtodactylus culaochamensis sp. nov. is the sister species of C. pseudoquadrivirgatus from Ba Na Nui Chua from Danan...

An integrative taxonomic analysis based on morphology, color pattern, and the mitochondrial gene ND2 recovered four new species of Hemiphyllodactylus Bleeker that are endemic to the Shan Plateau or Salween Basin in eastern Myanmar. Hemiphyllodactylus ngwelwini sp. nov. from the Shan Plateau is part of the earlier described “eastern Myanmar clade” r...

The first molecular phylogeny for mountain reed snakes (genus Macrocalamus) based on the mitochondrial gene cytochrome b is not entirely consistent with the previous taxonomy based on morphology and colour pattern. Macrocalamus chanardi is shown to be a species complex composed of three different allopatric lineages distributed across different upl...

A survey of a limestone forest at Gunung Baling, Kedah, West Malaysia lead to the discovery of an undescribed species of Bent-toed Gecko from the Cyrtodactylus pulchellus complex. Cyrtodactylus evanquahi sp. nov. can be distinguished from all other species in the C. pulchellus complex by a suite of morphological and color pattern characteristics: p...

Fifty-eight percent of the 43 known species of the Bent-toed Geckos ( Cyrtodactylus ) from Myanmar are found only in karstic habitats in the Shan Plateau and Salween and Ayeyarwady basins. A stochastic character mapping analysis indicated that the occupation of karstic habitats evolved at least four times independently in Burmese lineages with both...

The historical accuracy of building taxonomies is improved when they are based on phylogenetic inference (i.e., the resultant classifications are less apt to misrepresent evolutionary history). In fact, taxonomies inferred from statistically significant diagnostic morphological characters in the absence of phylogenetic considerations, can contain n...

An integrative taxonomic analysis of the 10 species of the Cyrtodactylus sinyineensis group based on squamation, color pattern, and the mitochondrial gene NADH dehydrogenase subunit 2 (ND2) and its flanking tRNA regions, recovered the newly discovered populations from Datt Kyaik and Taung Wine Hills in Kayin State as the new species Cyrtodactylus d...

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread "generalist" clades. This is especially true in Australasia, where monophyl...

The fi rst herpetological survey of Dalai Mountain in Phnom Samkos Wildlife Sanctuary revealed 24 species (nine amphibians and 15 reptiles), 18 of which are presently known only from the Cardamom Mountains. Of these, four represent fi rst records for Phnom Samkos Wildlife Sanctuary (Megophrys auralensis, Theloderma asperum, Philautus parvulus and D...

As molecular methods continue to elucidate genetic structure at increasingly finer resolutions, delimiting species in the grey zone of the speciation continuum is becoming more relevant in biodiversity research, especially in under-studied biodiversity hotspots such as Southeast Asia where new species are being described at an unprecedented rate. O...

Despite the increasing use of high-throughput sequencing in phylogenetics, many phylogenetic relationships remain difficult to resolve because of conflict between gene trees and species trees. Selection of different types of markers (i.e. protein-coding exons, non-coding introns, ultra-conserved elements) is becoming important to alleviate these ph...

Molecular phylogenetic analyses of the sister species Sphenomorphus stellatus and S. praesignis based on the mitochondrial genes 12S and 16S rRNA recover the former as paraphyletic with respect to the latter in that a specimen of S. stellatus from the type locality in Peninsular Malaysia is more closely related to S. praesignis than to Indochinese...

The manuscript titled “Exons, Introns, and UCEs Reveal Conflicting Phylogenomic Signals in a Rapid Radiation of Frogs (Ranidae: Hylarana )” has been withdrawn from BioRxiv temporarily. The manuscript has been withdrawn because it utilizes a new protocol for data collection, which has yet not been published. Once the paper describing the new method...

A new species of limestone karst-adapted gecko of the Cyrtodactylus pulchellus complex, C. dayangbuntingensis sp. nov., is described from Dayang Bunting Island of the Langkawi Archipelago off the northwest coast of Peninsular Malaysia. It is the third species of the group to be described from the archipelago after C. langkawiensis and C. macrotuber...

A new species of Ansonia is described from the Shan Plateau of Myanmar based on an integrative taxonomic analysis that differentiates it from all other congeners. Molecular phylogenetic analyses based on the mitochondrial genes 12S and 16S rRNA and tRNA-val recover A. kyaiktiyoensis sp. nov. as the sister species to A. inthanon from Thailand but di...

Recent phylogenetic studies of gekkonid lizards have revealed unexpected, widespread paraphyly and polyphyly among genera, unclear generic boundaries, and a tendency towards the nesting of taxa exhibiting specialized, apomorphic morphologies within geographically widespread ''generalist'' clades. This is especially true in the Australasia, where th...

An integrative taxonomic analysis of the Ptychozoon lionotum group across its range in Indochina and Sundaland recovers P. lionotum sensu lato Annandale, 1905 as paraphyletic with respect to P. popaense Grismer, Wood, Thura, Grismer, Brown, & Stuart, 2018a and composed of four allopatric, genetically divergent, ND2 mitochondrial lineages. Multivari...

We describe two new insular gecko species of the genus Cnemaspis from Tarutao, Adang, and Rawi islands in Satun Province, southern Thailand. The new species are distinguished from their congeners in having a unique combination of morphological, scalation, and color pattern characters, and by genetic divergence in the mitochondrial NADH dehydrogenas...

An integrative taxonomic analysis of the Cyrtodactylus linnwayensis group of the Shan Plateau recovered two new populations from isolated karst habitats near Pinlaung Town, Shan State as a new species, C. pinlaungensis sp. nov. Cyrtodactylus pinlaungensis sp. nov. is most closely related to a clade comprising C. linnwayensis and C. ywanganensis fro...

A herpetological survey of the Indawgyi Wildlife Sanctuary in Kachin State, Myanmar resulted in the discovery of a new species of Cyrtodactylus Gray along the eastern watershed of the Mokso Mountains. An integrative taxonomic analysis based on the mitochondrial ND2 gene, morphology, and color pattern recovered this new species, Cyrtodactylus momber...

Two new species of Bent-toed Geckos of the Cyrtodactylus peguensis group are described from foothill areas occurring on opposite sides of the Ayeyarwady Basin. Cyrtodactylus nyinyikyawi sp. nov. from the Shwe Settaw Wildlife Sanctuary, Magway Region in the east and C. pyadalinensis sp. nov. from the Panluang-Pyadalin Wildlife Sanctuary, Shan State...

Accurate species delimitation and description are necessary to guide effective conservation of imperiled species, and this synergy is maximized when multiple data sources are used to delimit species. We illustrate this point by examining Drymarchon couperi (Eastern Indigo Snake), a large, federally-protected species in North America that was recent...

GenBank accession numbers for gene sequence data (CytB, ND4, NT3) for Drymarchon couperi and outgroups from [26]. (DOCX)

Estimated values of K for the four metrics proposed by Puechmaille [55]: Median of medians (MedMedK), median of means (MedMeanK), maximum of medians (MaxMedK), and maximum of means (MaxMeanK). Each metric is estimated at four different thresholds of cluster membership. (DOCX)

Numbers used to group samples by geographic states and counties for use in the Bayesian clustering algorithm Structure; see Fig 1. (DOCX)

Bar plots of population genetic clustering of Drymarchon couperi estimated through the Bayesian clustering algorithm Structure with (A) K = 6, (B) K = 7, (C) K = 9, and (D) K = 10. The y-axis is the proportion of individual ancestry for each cluster; in the x-axis, number represents county where sample was collected. County names for each number ar...

Distributions of clusters along the entire MCMC chain and after burn-in from the Geneland independent run with the highest mean posterior, K = 6. (TIFF)

Results of spatial principle components analysis for population genetic data of Drymarchon couperi using a Delaunay triangulation connection network. The eigenvalues (left) for each axis where positive values indicate global structure and negative values indicate local structure, and the Moran’s I (right) plotted against the variance for each axis....

Additional results of spatial principle components analysis for population genetic data of Drymarchon couperi using a Delaunay triangulation connection network demonstrating the spatially lagged scores from the first (A) and second (B) axes. Atlantic lineage samples are displayed using circles while Gulf lineage samples are displayed using squares....

Results of spatial principle components analysis using a distance-based connection network where samples are considered connected if they are within 22.2 km which is the maximum recorded dispersal distance for Drymarchon couperi. The left figure shows the eigenvalues for each axis where positive values indicate global structure and negative values...

Intersexual variance in home range size (hectares) for 22 species of snakes. See [103] for an earlier review of the topic. (DOCX)

Multiplex PCR panels for Drymarchon couperi microsatellite loci. The names of loci are as in [52]. (DOCX)

A new species of crocodile newt from populations on opposite sides of the Ayeyarwady Basin, Myanmar, previously referred to as Tylototriton cf. verrucosus, is described on the basis of colour pattern, morphology and phylogenetic data from the mitochondrial gene ND2. Tylototriton panwaensis sp. nov. is most closely related to T. verrucosus + T. shan...

An integrative taxonomic analysis using color pattern, morphology, and 1449 base pairs of the ND2 mitochondrial gene and its five flanking tRNAs demonstrated that eight species-level lineages occur within the Cyrtodactylus intermedius complex (Cyrtodactylus intermedius sensu stricto, C. phuquocensis and related populations) of the Cardamom mountain...