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Publications (414)
Automated invertebrate classification using computer vision has shown significant potential to improve specimen processing efficiency. However, challenges such as invertebrate diversity and morphological similarity among taxa can make it difficult to infer fine-scale taxonomic classifications using computer vision. As a result, many invertebrate co...
Introduction
Given the role of microbiomes in promoting host health and homeostasis, understanding the factors shaping skin microbial communities in wild vertebrates has become increasingly important in conservation. This goal is even more pressing for amphibians, for which the skin has multiple critical functions, and pathogens currently decimatin...
Nonnative species are a key agent of global change. However, nonnative invertebrates remain understudied at the community scales where they are most likely to drive local extirpations. We use the North American NEON pitfall trapping network to document the number of nonnative species from 51 invertebrate communities, testing four classes of drivers...
Background
Mosquitoes are the deadliest organisms in the world, killing an estimated 750,000 people per year due to the pathogens they can transmit. Mosquitoes also pose a major threat to other vertebrate animals. Culex territans is a mosquito species found in temperate zones worldwide that feeds almost exclusively on amphibians and can transmit pa...
Anurans (frogs and toads) are an ecologically diverse group of vertebrate organisms that display a myriad of reproductive modes and life history traits. To persist in such an expansive array of habitats, these organisms have evolved specialized skin that is used for respiration while also protecting against moisture loss, pathogens, and environment...
Activity density (AD), the rate at which animals collectively move through their environment, emerges as the product of a taxon's local abundance and its velocity. We analyze drivers of seasonal AD using 47 localities from the National Ecological Observatory Network (NEON) both to better understand variation in ecosystem rates like pollination and...
Despite growing concerns over the health of global invertebrate diversity, terrestrial invertebrate monitoring efforts remain poorly geographically distributed. Machine-assisted classification has been proposed as a potential solution to quickly gather large amounts of data; however, previous studies have often used unrealistic or idealized dataset...
Given the rapidly changing landscapes of habitats across the globe, a sound understanding of host-associated microbial communities and the ecoevolutionary forces that shape them is needed to assess general organismal adaptability. Knowledge of the symbiotic endogenous microbiomes of most reptilian species worldwide remains limited. We sampled gut m...
Despite multiple recent field studies, herpetological species diversity of the Romblon Island Group in the central Philippines—particularly Sibuyan Island—has remained underestimated. Recently, we investigated the diversity of the herpetofauna of Mount Guiting-Guiting Natural Park, based on an elevational transect (10–1557 m a.s.l.). Our surveys re...
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...
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 undere...
The study of animal personality is a growing field that has applications for welfare of animals living in captive settings. We measured personality traits (activity, exploration, and neophobia) in Texas horned lizards (Phrynosoma cornutum) living in human care before they were released to their natal habitat as part of a headstart program. We found...
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 Philippine coral snakes of the genus Hemibungarus consist of three poorly known endemic species, constituting some of the most enigmatic elapid snakes in the world. Because of their secretive, subterranean, and heretofore undocumented microhabitat preferences, very little is known of these lineages. We present a synthetic description of aposema...
Biodiversity monitoring is imperative for understanding how changing climate may impact the distributions of taxa from single species to the spatial distribution of biological diversity. Large‐scale and cross‐taxa biodiversity monitoring also allows an empirical understanding of biogeographic patterns across taxa. One such pattern, where in taxonom...
The University of Oklahoma Biological Station (UOBS) was established in 1950 in Marshall Co., Oklahoma along the newly created reservoir, Lake Texoma. Generations of biology students and independent researchers have documented the flora and fauna on the station grounds and surrounding areas. Herein we compare herpetological records for the area pub...
Batrachochytrium dendrobatidis (Bd) and ranavirus (RV) are pathogens contributing to the global decline of amphibian populations. Both pathogens can be spread through direct contact between amphibians, through water carrying the infection, the accidental movement of disease particles between waterbodies by cattle, boats, or aquatic recreational equ...
Recent higher level phylogenetic analyses of gekkonid lizards of the genus Lepidodactylus uncovered an array of unrecognized species diversity, particularly within the Philippine archipelago. Novel phylogenetic analyses of multilocus data sets suggest that as many as five, previously undescribed, species-level lineages of Scaly-toed Geckos occur in...
We revisit the question of species diversity among Mindanao Fanged Frogs of the Limnonectes magnus complex consisting of L. magnus, L. diuatus, L. ferneri, and a previously hypothesized putative new species, inferred in the first molecular phylogenetic studies of the genus almost 2 decades ago. Using a multilocus molecular deoxyribonucleic acid seq...
• Intermediate metrics of translocation success are useful for long-lived, slow to mature species where survival and reproduction happen over decades.
• With fewer than 150 individuals in the wild, the Critically Endangered Philippine crocodile (Crocodylus mindorensis) is one of the most threatened species on Earth. This study presents the first an...
We describe the development and validation of a qPCR assay to detect Poecilia reticulata, a highly invasive species of freshwater fish invasive to the Caribbean islands, through environmental DNA (eDNA) sampling. Originating from Trinidad, this species is invasive and detrimental to countless native tropical fish communities. A qPCR assay, consisti...
Habitat fragmentation has negative consequences on threatened and endangered species by creating isolated populations. The Texas horned lizard (Phrynosoma cornutum) is experiencing population declines and localized extirpations throughout its range and has been classified as a species of greatest conservation need in Oklahoma, USA. Younger age clas...
This protocol is the complete methods used to extract abundance, morphology and color data from samples of invertebrates. We developed this protocol specifically to measure invertebrate by-catch from pitfall traps collected by the National Ecological Observatory Network (NEON), but these methods could be extended to any invertebrate samples. These...
We describe a new species of fanged frog (genus Limnonectes) from Mindoro and Semirara Islands, of the Mindoro Pleistocene Aggregate Island Complex, of the central Philippines. Although morphologically indistinguishable from its closest relative, Limnonectes acanthi, of the Palawan faunal region, the two species can be readily diagnosed on the basi...
Reduced limbs and limblessness have evolved independently in many lizard clades. Scincidae exhibit a wide range of limb‐reduced morphologies, but only some species have been used to study the embryology of limb reduction (e.g., digit reduction in Chalcides and limb reduction in Scelotes). The genus Brachymeles, a Southeast Asian clade of skinks, in...
The gastrointestinal tract (GIT) of vertebrates contains a series of organs beginning with the mouth and ending with the anus or cloacal opening. Each organ represents a unique environment for resident microorganisms. Due to their simple digestive anatomy, snakes are good models for studying microbiome variation along the GIT. Cloacal sampling capt...
Animals often exhibit distinct microbial communities when maintained in captivity as compared to when in the wild. Such differentiation may be significant in headstart and reintroduction programs where individuals spend some time in captivity before release into native habitats. Using 16S rRNA gene sequencing, we (i) assessed differences in gut mic...
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...
Recent studies have highlighted the underestimated diversity of the genus Diploderma Hallowell, 1861 in the Hengduan Mountain Region in Southwest China, but much of the region remains poorly surveyed for reptile diversity. In this study we describe two new species of Diploderma from the upper Jinsha and middle Yalong River Valley, based on evaluati...
We describe the development and testing of qPCR assays to detect four species of amphibians and reptiles of conservation concern in the South Central United States through environmental DNA (eDNA) samples. The target species include the Ringed Salamander (Ambystoma annulatum), Three-toed Amphiuma (Amphiuma tridactylum), Crawfish Frog (Rana areolata...
Cryptic diversity not only introduces confusion to taxonomic studies, but it also poses major challenges to conservation and environmental legislation. One such troubling group are the Mountain Dragons in the genus Diploderma in Southwest China. Previous studies have suggested that the genus contains considerable cryptic diversity, particularly in...
The Philippine archipelago is an exceptionally biodiverse region that includes at least 112 species of land snakes from 41 genera and 12 families. Recently, Cyclocoridae (formerly Lamprophiidae: Cyclocorinae) was proposed as a distinct, Philippine-endemic family, containing four genera: Cyclocorus, Hologerrhum, Myersophis, and Oxyrhabdium. Here, we...
Because of the importance of specimen identification, and for establishing protocols for new species boundaries, novel methods and tools for identifying and sharing specimen data for vertebrate organisms, particularly amphibians and reptiles, is an important aim for taxonomists (Dayrat 2005; McDiarmid et al. 2011). In general, the gold standard for...
Reduced limbs and limblessness have evolved independently in many lizard clades. Skinks exhibit a wide range of limb-reduced morphologies, but only some species have been used to study the embryology of limb reduction (i.g., digit reduction in Chalcides and limb reduction in Scelotes ). The genus Brachymeles , a Southeast Asian clade of skinks, inc...
Evolutionary reversals, including re-evolution of lost structures, are commonly found in phylogenetic studies. However, we lack an understanding of how these reversals happen mechanistically. A snake-like body form has evolved many times in vertebrates, and occasionally a quadrupedal form has re-evolved, including in Brachymeles lizards. We use bod...
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...
The diversity of Philippine amphibians and reptiles has increased over the last few decades, in part due to re-evaluation of species formerly believed to be widespread. Many of these investigations of widespread species have uncovered multiple closely related cryptic lineages comprising species complexes, each restricted to individual Pleistocene A...
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...
We describe a new species of frog of the genus Platymantis Günther (subgenus Tirahanulap), from the east-central regions of the Philippines. It belongs to the the previously-defined P. hazelae Group) based on morphological and bioacoustic datasets. The new species is phenotypically and ecologically most similar to members of Tirahanulap, an assembl...
The genus Boiga includes 35, primarily arboreal snake species distributed from the Middle East to Australia and many islands in the western Pacific, with particularly high species diversity in SouthEast Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian exti...
The taxonomic validity of the controversial taxon, Amolops nepalicus Yang, 1991, is evaluated based on the examination of its holotype, along with topotypic A. marmoratus (Blyth, 1855) and A. afghanus (Günther, 1858), and other related congeners. Morphological comparison shows the holotype of A. nepalicus differs from its senior synonym A. marmorat...
Species descriptions of reptiles historically have relied exclusively on the use of morphological data; however, these external, phenotypic data do not always co-vary with lineage divergence. Consequently, it has become increasingly clear that species diversity has been underestimated in many evolutionary radiations. With the use of an integrative...
Elongate, snake- or eel-like, body forms have evolved convergently many times in most major lineages of vertebrates. Despite studies of various clades with elongate species, we still lack an understanding of their evolutionary dynamics and distribution on the vertebrate tree of life. We also do not know whether this convergence in body form coincid...
Recognizing species-level diversity is important for studying evolutionary patterns across biological disciplines and is critical for conservation efforts. However, challenges remain in delimiting species-level diversity, especially in cryptic radiations where species are genetically divergent but show little morphological differentiation. Using mu...
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...
Falcaustra samarensis n. sp. (Ascaridida, Kathlaniidae) from the intestines of Megophrys stejnegeri Taylor 1920 (Anura, Megophryidae) is described and illustrated. Falcaustra samarensis n. sp. represents the one hundred fourth species assigned to the genus and the thirty-seventh Oriental species. It is distinguished from other Oriental species by t...
The Plateau Pit Viper, Gloydius strauchi, from southwest and central China has long been considered a single, widespread species despite suspicion that it represents a potential complex of distinct evolutionary lineages. Although series of works were published on the G. strauchi species complex over the last 10 yr, species boundaries and diagnostic...
Despite continuous studies on the cryptic diversity of the Diploderma flaviceps complex in Southwest China for the pastdecade, little attention has been given to other widespreadcongeners in China. Combining both morphological and phylogenetic data, we describe a new species of Diplodermafrom populations identified previously as D. dymondi in thelo...
Although recent studies have made considerable progresses on the taxonomy of the genus Diploderma, there are still many questionable records of Diploderma species in China. Among these are suspicious sympatric distributions of congeners, locality records that fall well outside of the recognized range of a given species, and records that are in zoog...
Several infectious diseases are threatening amphibian species worldwide and have resulted in mass-mortality events across the globe. An emerging group of viral pathogens (ranaviruses) are documented to cause die-offs in amphibian populations worldwide, including in several regions of the U.S. Unfortunately, large gaps remain in our understanding of...
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...
The genera Lepidothyris, Lygosoma and Mochlus comprise the writhing or supple skinks, a group of semi-fossorial, elongate-bodied skinks distributed across the Old World Tropics. Due to their generalized morphology and lack of diagnostic characters, species- and clade-level relationships have long been debated. Recent molecular phylogenetic studies...
Chytridiomycosis, an infectious disease caused by the fungus Batrachochytrium dendrobatidis (chytrid or Bd), has not been well studied in Oklahoma. This is of particular concern regarding the connection between seasonality and chytrid infection. To further investigate this connection, chytrid prevalence and infection load were quantified within amp...
Despite its recognition since the early 1900s, the agamid lizard Pseudocalotes austeniana remains known based on 3 vouchered specimens only from the East Himalaya, and little is known about its general biology. During herpetological surveys of Tibet, China, we collected 3 specimens of P. austeniana from Medog County, southeastern Tibet, including t...
A primary goal of biogeography is to understand how large‐scale environmental processes, like climate change, affect diversification. One often‐invoked but seldom tested process is the “species‐pump” model, in which repeated bouts of co‐speciation are driven by oscillating climate‐induced habitat connectivity cycles. For example, over the past thre...
Despite being recognized as ecologically and biogeographically important, the biodiversity of the Hengduan Mountain Region, particularly along the upper Mekong River, remains poorly understood. Here we describe a new species of Mountain Dragon of the genus Japalura sensu lato Gray, 1853 from the headwater region of the Mekong River in Chamdo, Tibet...
Although the genus Japalura s.l. has long been recognized as paraphyletic based on limited genetic sampling, its problematic taxonomy has not been revised, and phylogenetic relationships among the majority of congeners remain unknown. Here we utilize a densely sampled dataset of both multilocus genetic and morphological data to provide the first ph...
In an attempt to add to our knowledge of the biodiversity of helminths infecting Philippine amphibians, three species of dicroglossid frogs (Dicroglossidae) were examined for helminths: Limnonectes macrocephalus (n = 5), L. visayanus (n=5), and L. woodworthi (n=5). Wefound four species of Nematoda (Abbreviata bufonis, Aplectana samarensis, Falcaust...