Search

Addressing climate change and biodiversity loss will be the defining ecological, political, and humanitarian challenge of our time. Alarmingly, policymakers face a narrowing window of opportunity to prevent the worst impacts, necessitating complex decisions about which land to set aside for biodiversity preservation. Yet, our ability to make these decisions is hindered by our limited capacity to predict how species will respond to synergistic drivers of extinction risk. We argue that a rapid integration of biogeography and behavioral ecology can meet these challenges because of the distinct, yet complementary levels of biological organization they address, scaling from individuals to populations, and from species and communities to continental biotas. This union of disciplines will advance efforts to predict biodiversity’s responses to climate change and habitat loss through a deeper understanding of how biotic interactions and other behaviors modulate extinction risk, and how responses of individuals and populations impact the communities in which they are embedded. Fostering a rapid mobilization of expertise across behavioral ecology and biogeography is a critical step toward slowing biodiversity loss.

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 microbial communities between captive and wild Fijian crested iguanas (Brachylophus vitiensis) and (ii) resampled gut microbiota in captive iguanas released onto a native island to monitor microbiome restructuring in the wild. We used both cloacal swabs and fecal samples to further increase our understanding of gut microbial ecology in this IUCN Critically Endangered species. We found significant differentiation in gut microbial community composition and structure between captive and wild iguanas in both sampling schemes. Approximately two months postrelease, microbial communities in cloacal samples from formerly captive iguanas closely resembled wild counterparts. Interestingly, microbial communities in fecal samples from these individuals remained significantly distinct from wild conspecifics. Our results indicate that captive upbringings can lead to differences in microbial assemblages in headstart iguanas as compared to wild individuals even after host reintroduction into native conditions. This investigation highlights the necessity of continuous monitoring of reintroduced animals in the wild to ensure successful acclimatization and release., We show that captivity impacts gut microbial assemblages in headstart animals compared with wild individuals long after host reintroduction into native conditions. This advances our understanding of microbiome diversity and evolution in a Critically Endangered reptile and shows how captivity influences the microbiome of reptiles in general.

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, includes species with a range of limb morphologies, from pentadactyl to functionally and structurally limbless species. Adults of the small, snake-like species Brachymeles lukbani show no sign of external limbs in the adult except for small depressions where they might be expected to occur. Here, we show that embryos of B. lukbani in early stages of development, on the other hand, show a truncated but well-developed limb with a stylopod and a zeugopod, but no signs of an autopod. As development proceeds, the limb's small size persists even while the embryo elongates. These observations are made based on external morphology. We used florescent whole-mount immunofluorescence to visualize the morphology of skeletal elements and muscles within the embryonic limb of B. lukabni. Early stages have a humerus and separated ulna and radius cartilages; associated with these structures are dorsal and ventral muscle masses as those found in the embryos of other limbed species. While the limb remains small, the pectoral girdle grows in proportion to the rest of the body, with well-developed skeletal elements and their associated muscles. In later stages of development, we find the small limb is still present under the skin, but there are few indications of its presence, save for the morphology of the scale covering it. By use of CT scanning, we find that the adult morphology consists of a well-developed pectoral girdle, small humerus, extremely reduced ulna and radius, and well-developed limb musculature connected to the pectoral girdle. These muscles form in association with a developing limb during embryonic stages, a hint that "limbless" lizards that possess these muscles may have or have had at least transient developing limbs, as we find in B. lukbani. Overall, this newly observed pattern of ontogenetic reduction leads to an externally limbless adult in which a limb rudiment is hidden and covered under the trunk skin, a situation called cryptomelia. The results of this work add to our growing understanding of clade-specific patterns of limb reduction and the convergent evolution of limbless phenotypes through different developmental processes.

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 different groups were using different genetic markers to construct phylogenies that could not be integrated. We present here Maximum likelihood and Bayesian inference mitochondrial and mito-nuclear phylogenies incorporating of 310 species that include dozens of species that had never been included in a genus-wide analysis. Based on the mitochondrial phylogeny, we partition Cyrtodactylus into 31 well-supported monophyletic species groups which, if used as recommended herein, will increase the information content of future integrative taxonomic analyses that continue to add new species to this genus at an ever-increasing annual rate. Data presented here reiterate the outcome of several previous studies indicating that Cyrtodactylus comprises an unprecedented number of narrow-range endemics restricted to single mountain tops, small islands, or karst formations that still remain unprotected. This phylogeny can provide a platform for various comparative ecological studies that can be integrated with conservation management programs across the broad diversity of landscapes and habitats occupied by this genus. Additionally, these data indicate that the true number of Cyrtodactylus remains substantially underrepresented.

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), and Chicken Turtle (Deirochelys reticularia). A set of primers and probes amplifying a 64–72 bp target regions were designed for each species from DNA sequence data for either the mitochondrial Cytochrome Oxidase I or Cytochrome B gene. All assays were assessed for target specificity, with no evidence of amplification in closely related or sympatrically-distributed non-target species. In vitro tests indicate that all assays consistently detect focal species down to concentrations of 2 × 10− 9 pg/µL. We evaluated the utility of qPCR assays on the eDNA samples collected during field surveys across Eastern Oklahoma, focusing on counties with vouchered historical records for the target species. Although detection rates were low for field applications of the assays, positive detection of Ambystoma annulatum, Rana areolata, and Deirochelys reticularia, but not Amphiuma tridactylum, were recorded. These assays can provide a practical tool for a non-invasive, genetic monitoring program that allows for both rapid detection and tracking of native aquatic and semi-aquatic amphibian and reptile species of conservation concern.

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 South-East Asia. Despite including the iconic mangrove snakes (Boiga dendrophila complex) and the brown tree snake (Boiga irregularis; infamous for avian extinctions on small islands of the Pacific), species-level phylogenetic relationships and the biogeographic history of this ecologically and morphologically distinct clade are poorly understood. In this study, we sequenced mitochondrial and nuclear DNA for 24 Boiga species and used these data to estimate a robust phylogenetic inference, in order to (1) test the hypothesis that Boiga is monophyletic, (2) evaluate the validity of current species-level taxonomy and (3) examine whether geographic range evolution in Boiga is consistent with expectations concerning dispersal and colonization of vertebrates between continents and islands. Our results support the prevailing view that most dispersal events are downstream – from continents to oceanic islands – but we also identify a role for upstream dispersal from oceanic islands to continents. Additionally, the novel phylogeny of Boiga presented here is informative for updating species-level taxonomy within the genus.

Synopsis 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 coincides with convergence at other biological levels. Here, we present the first craniate-wide analysis of how many times elongate body forms have evolved, as well as rates of its evolution and reversion to a non-elongate form. We then focus on five convergently elongate squamate species and test if they converged in vertebral number and shape, as well as their locomotor performance and kinematics. We compared each elongate species to closely related quadrupedal species and determined whether the direction of vertebral or locomotor change matched in each case. The five lineages examined are obscure species from remote locations, providing a valuable glimpse into their biology. They are the skink lizards Brachymeles lukbani, Lerista praepedita, and Isopachys anguinoides, the basal squamate Dibamus novaeguineae, and the basal snake Malayotyphlops cf. ruficaudus. Our results support convergence among these species in the number of trunk and caudal vertebrae, but not vertebral shape. We also find that the elongate species are relatively slower than their limbed counterparts and move with lower frequency and higher amplitude body undulations, with the exception of Isopachys. This is among the first evidence of locomotor convergence across distantly related, elongate species.

Activity density (AD), the rate that an individual taxon or its biomass moves through the environment, is used both to monitor communities and quantify the potential for ecosystem work. The Abundance Velocity Hypothesis posited that AD increases with aboveground net primary productivity (ANPP) and is a unimodal function of temperature. Here we show that, at continental extents, increasing ANPP may have nonlinear effects on AD: increasing abundance, but decreasing velocity as accumulating vegetation interferes with movement. We use 5 yr of data from the NEON invertebrate pitfall trap arrays including 43 locations and four habitat types for a total of 77 habitat–site combinations to evaluate continental drivers of invertebrate AD. ANPP and temperature accounted for one-third to 92% of variation in AD. As predicted, AD was a unimodal function of temperature in forests and grasslands but increased linearly in open scrublands. ANPP yielded further nonlinear effects, generating unimodal AD curves in wetlands, and bimodal curves in forests. While all four habitats showed no AD trends over 5 yr of sampling, these nonlinearities suggest that trends in AD, often used to infer changes in insect abundance, will vary qualitatively across ecoregions.

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 methods were used in the publications: Blair, J.,M.D. Weiser, M. Kaspari, M.J. Miller, C. Siler and K. Marshall. 2020. Robust and simplified machine learning identification of pitfall trap-collected ground beetles at the continental scale. Ecology and Evolution 10(23): 13143-13153. DOI:10.1002/ece3.6905. Weiser, M.D., K.E. Marshall, M.J. Miller, C.D. Siler, S.N. Smith & M. Kaspari. in review at Oikos (October 2021). Robust metagenomic evidence that local assemblage richness increases with latitude in ground-active invertebrates of North America.

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 datasets to train their models.In this study, we describe a practical methodology for including machine learning in ecological data acquisition pipelines. Here we train and test machine learning algorithms to classify over 56,000 bulk terrestrial invertebrate specimens from morphometric data and contextual metadata. All vouchered specimens were collected in pitfall traps by the National Ecological Observatory Network (NEON) at 27 locations across the United States in 2016. Specimens were photographed, and morphometric data was extracted as feature vectors using ImageJ. Issues stemming from inconsistent taxonomic label specificity were resolved by making classifications at the lowest identified taxonomic level (LITL). Taxa with too few specimens to be included in the training dataset were classified by the model using zero-shot classification.When classifying specimens that were known and seen by our models, we reached an accuracy of 72.7% using extreme gradient boosting (XGBoost) at the LITL. Models that were trained without contextual metadata underperformed models with contextual metadata by an average of 7.2%. We also classified invertebrate taxa that were unknown to the model using zero-shot classification, with an accuracy of 39.4%, resulting in an overall accuracy of 71.5% across the entire NEON dataset.The general methodology outlined here represents a realistic application of machine learning as a tool for ecological studies. Hierarchical and LITL classifications allow for flexible taxonomic specificity at the input and output layers. These methods also help address the ‘long tail’ problem of underrepresented taxa missed by machine learning models. Finally, we encourage researchers to consider more than just morphometric data when training their models, as we have shown that the inclusion of contextual metadata can provide significant improvements to accuracy.

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 just the northern portions of the archipelago. Here, we evaluate Lepidodactylus species diversity in the Lepidodactylus yami–balioburius clade and describe four new forest species from Luzon Island and surrounding minor island groups. Interestingly, these species are the first endemic Lepidodactylus taxa described from Luzon proper and peripheral islands. In this first review of Philippine Scaly-toed Gecko diversity in nearly half a century, we use a suite of morphological characters along with molecular data to delimit evolutionary lineages. All species described in this paper can be distinguished from congeners by an array of discrete external traits; all are also monophyletic groups, separated in our phylogenetic analyses of the mitochondrial ND2 gene. This study increases significantly the number of known Scaly-toed Geckos in the Philippines from 7 to 11, which is likely still an underestimate of the species diversity in this understudied clade.

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 analysis of diet and body condition of wild Philippine crocodiles and headstarted (i.e. captive-reared) individuals released into the wild over the last decade, and uses these results to show how diet and body condition can be pertinent intermediate metrics of translocation success. Analyses of stomach contents revealed 17 different aquatic and terrestrial invertebrate and vertebrate prey species. Interestingly, 70% of Philippine crocodiles showed snails to be the predominent prey type, followed by fish (36.7%), birds (33.3%) and reptiles (33.3%). More than 50% of crocodiles consumed the invasive golden apple snail, a leading agricultural pest. Regardless of crocodile history (wild vs. headstarted) or size class (juvenile vs. adult), no evidence was found for dietary differences in percentage occurrence, percentage composition or prey diversity. Body condition was significantly higher in wild compared with headstarted individuals when analysed together in a pooled group, although neither group differed significantly from the standardized expectation, and headstarted individuals were not significantly different when body condition was derived independently for the two groups. This study provides a working example of how assessing the convergence of diet and body condition between translocated and wild individuals can provide complementary monitoring parameters to demonstrate post-release establishment of translocated crocodylians. The congruent dietary composition and comparable body condition observed in this study suggest that headstarted crocodiles adapt well following release. Crocodylus mindorensis survives in an agricultural landscape and is likely to play an ecologically important role by exploiting invasive species, reinforcing the importance of this species to local communities.

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 sequence data set and comprehensive sampling of 161 individuals from throughout the Mindanao Pleistocene aggregate island complex landmasses (a distinct faunal region of the southern Philippines) we characterize geographically structured genetic diversity, focusing on the phylogenetic placement of individuals from each species' type locality. We also present new morphometric data from large samples of freshly collected material from the type localities of each included species; together with examination of the name-bearing original type specimens, we conclude that an overestimation of species diversity has occurred and has been exacerbated by the indiscriminate acceptance of the hypothesis of the existence of widespread cryptic species in this group. We place L. ferneri in synonymy with L. diuatus, clarify the identification of the latter taxon with respect to L. magnus, and apply this name to the widespread, generalist, highly variable giant Fanged Frog distributed throughout the Mindanao faunal region of the southern Philippines.

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 Lepidodactylus is a diverse radiation of insular and arboreal geckos that occurs across the western Pacific. Previous work on Lepidodactylus showed evidence of evolutionary displacement around continental fringes, suggesting an inherent vulnerability to extinction from factors such as competition and predation. We sought to (1) comprehensively review status and threats, (2) estimate the number of undescribed species, and (3) estimate extinction risk in data deficient and candidate species, in Lepidodactylus. From our updated IUCN Red List assessment, 60% of the 58 recognized species are threatened (n = 15) or Data Deficient (n = 21), which is higher than reported for most other lizard groups. Species from the smaller and isolated Pacific islands are of greatest conservation concern, with most either threatened or Data Deficient, and all particularly vulnerable to invasive species. We estimated 32 undescribed candidate species and linear modelling predicted that an additional 18 species, among these and the data deficient species, are threatened with extinction. Focusing efforts to resolve the taxonomy and conservation status of key taxa, especially on small islands in the Pacific, is a high priority for conserving this remarkably diverse, yet poorly understood, lizard fauna. Our data highlight how cryptic ecologies and cryptic diversity combine and lead to significant underestimation of extinction risk.

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 thelower Yalong River Basin in southern Sichuan Province. Thenew species is morphologically most similar to D. dymondiand D. varcoae, but it can be differentiated by a considerablegenetic divergence and a suite of morphological characters,including having taller nuchal crest scales, smaller tympana,and a distinct oral coloration. Additionally, we discuss otherputative species complexes within the genus Diploderma inChina.

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 of the group have provided some clarification of species-level relationships, but a number of issues regarding higher level relationships among genera still remain. Here we present a phylogenetic estimate of relationships among species in Lygosoma, Mochlus and Lepidothyris generated by concatenated and species tree analyses of multilocus data using the most extensive taxonomic sampling of the group to date. We also use multivariate statistics to examine species and clade distributions in morpho space. Our results reject the monophyly of Lygosoma s.l., Lygosoma s.s. and Mochlus, which highlights the instability of the current taxonomic classification of the group. We, therefore, revise the taxonomy of the writhing skinks to better reflect the evolutionary history of Lygosoma s.l. by restricting Lygosoma for Southeast Asia, resurrecting the genus Riopa for a clade of Indian and Southeast Asian species, expanding the genus Mochlus to include all African species of writhing skinks and describing a new genus in Southeast Asia.

Mountain Dragons of the genus Diploderma Hallowell, 1861 were recently resurrected from the paraphyletic genus Japalura sensu lato (Wang et al., 2019a). Despite the recent split, Diploderma still represents one of the most diverse groups of agamid lizard from Asia, including 25 species recognized currently, with most species found in China ((Wang et al., 2019a, 2019b). Although increasing attention has been paid to cryptic diversity within the genus in Southwest China during the past decade, most studies have focused on a single species complex, D. flaviceps, only (Manthey et al., 2012; Wang et al., 2015, 2016, 2017, 2019a), with few studies on other congeners that also have widespread distributions. One such example is D. dymondi (Boulenger, 1906).

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 captures the majority of the microbial diversity found in the GIT of snakes—yet little is known about the oral microbiota of snakes. Most research on the snake mouth and gut microbiota are limited to studies of a single species or captive-bred individuals. It therefore remains unclear how a host’s life history, diet, or evolutionary history correlate with differences in the microbial composition within the mouths and guts of wild snakes. We sampled the mouth and gut microbial communities from three species of Asian venomous snakes and utilized 16S rRNA microbial inventories to test if host phylogenetic and ecological differences correlate with distinct microbial compositions within the two body sites. These species occupy three disparate habitat types: marine, semi-arboreal, and arboreal, our results suggest that the diversity of snake mouth and gut microbial communities correlate with differences in both host ecology and phylogeny.

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 evaluations of morphological, genetic, and distribution data. The two new species are morphologically most similar to D. angustelinea and D. vela, but they can be diagnosed from both recognized taxa and all remaining congeners by a suite of morphological features, particularly the distinct coloration of gular spots. Additionally, both new species either render other recognized species paraphyletic or are allopatric with respect to their morphologically similar congeners. Furthermore, we rediscover D. brevicaudum in the wild for the first time, which was known from historical museum specimens only. We estimate the phylogenetic position of D. brevicaudum within the genus Diploderma based on mitochondrial genealogy, and we provide an expanded diagnosis and comparisons against closely related congeners and provide a detailed description of coloration in life based on newly collected specimens. Our discoveries of the new Diploderma species further highlight the urgent conservation needs of the currently neglected hot-dry valley ecosystems in the Hengduan Mountain Region of China.

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 describe an additional cyclocorid genus and species, Levitonius mirus, new genus and species, from Samar and Leyte Islands, Philippines. Molecular data support Levitonius, new genus, to be most closely related to Myersophis and Oxyrhabdium, and it shares multiple skeletal characteristics with these genera; Levitonius, new genus, differs from all of these taxa in body size, scalation, and other characters. Skeletal and other phenotypic data suggest that Levitonius, new genus, is fossorial and likely has a diet that is specialized on earthworms. Levitonius mirus, new genus and species, has a maximum total length of 172 mm and is at present the smallest known species in Elapoidea. Our results highlight the need for future work on Samar and Leyte Islands, which have received relatively little attention from systematists, in part because of a prevailing biogeographic paradigm that predicted (not necessarily correctly) that these islands would simply have a nested faunal subset of the Mindanao faunal region land vertebrates. The discovery of a strikingly distinct and phylogenetically divergent snake lineage on these landmasses joins numerous related studies calling for a wholesale reconsideration of the Pleistocene Aggregate Island Complex model (the PAIC paradigm of diversification) biogeographic framework.

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 inChalcidesand limb reduction inScelotes). The genusBrachymeles, a Southeast Asian clade of skinks, includes species with a range of limb morphologies, from pentadactyl to functionally as well as structurally limbless species. Adults of the small, snake-like speciesBrachymeles lukbanishow no sign of external limbs in the adult except for small depressions where they might be expected to occur. Embryos ofB. lukbaniin early stages of development, on the other hand, show a truncated but well-developed limb with a stylopod and a zeugopod, but no signs of an autopod. As development proceeds, the limb’s small size persists even while the embryo elongates. These observations are made based on external morphology. We used florescent whole-mount immunofluorescence to visualize the morphology of skeletal elements and muscles within the embryonic limb ofB. lukabni. Early stages have a humerus and separated ulna and radius cartilages; associated with these structures are dorsal and ventral muscle masses as those found in the embryos of other limbed species. While the limb remains small, the pectoral girdle grows in proportion to the rest of the body, with well-developed skeletal elements and their associated muscles. In later stages of development, the small limb is still present under the skin but there are few indications of its presence, save for the morphology of the scale covering it. The adult morphology consists of a well-developed pectoral girdle, small humerus, extremely reduced ulna and radius, and well-developed limb musculature connected to the pectoral girdle. These muscles form in association with a developing limb during embryonic stages, a hint that “limbless” lizards that possesses these muscles may have or have had at least transient developing limbs, as we find inB. lukbani.Overall, the observed pattern of ontogenetic reduction, leading to an externally limbless adult in which a limb rudiment is hidden and covered under the trunk skin, is a situation called cryptomelia. The results of this work add to our growing understanding of clade-specific patterns of limb reduction and the convergent evolution of limbless phenotypes through different developmental processes.

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 Aggregate Island Complexes (PAICs). One group in particular for which widespread cryptic diversity has been common is the clade of Philippine skinks of the genus Brachymeles. Recent phylogenetic studies of the formerly recognized widespread species Brachymeles bonitae have indicated that this species is actually a complex distributed across several major PAICs and smaller island groups in the central and northern Philippines, with numerous species that exhibit an array of digit loss and limb reduction patterns. Despite the recent revisions to the B. bonitae species complex, studies suggest that unique cryptic lineages still exist within this group. In this paper, we resurrect the species Brachymeles burksi Taylor 1917, for a lineage of non-pentadactyl, semi-fossorial skink from Mindoro and Marinduque islands. First described in 1917, B. burksi was synonymized with B. bonitae in 1956, and has rarely been reconsidered since. Evaluation of genetic and morphological data (qualitative traits, meristic counts, and mensural measurements), and comparison of recently-obtained specimens to Taylor’s original description support this species’ recognition, as does its insular distribution on isolated islands in the central portions of the archipelago. Morphologically, B. burksi is differentiated from other members of the genus based on a suite of unique phenotypic characteristics, including a small body size, digitless limbs, a high number of presacral vertebrae, the absence of auricular openings, and discrete (non-overlapping) meristic scale counts. The recognition of this central Philippine species further increases the diversity of non-pentadactyl members of the B. bonitae complex, and reinforces the biogeographic uniqueness of the Mindoro faunal region. KEYWORDS: biodiversity, endemism, faunal region, fossoriality, limb reduction

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 body form and locomotion data for species ranging from snake-like to quadrupedal to address how a quadrupedal form could re-evolve. We show that large, quadrupedal species are faster at burying and surface locomotion than snake-like species, indicating a lack of expected performance trade-off between these modes of locomotion. Species with limbs use them while burying, suggesting that limbs are useful for burying in wet, packed substrates. Palaeoclimatological data suggest that Brachymeles originally evolved a snake-like form under a drier climate probably with looser soil in which it was easier to dig. The quadrupedal clade evolved as the climate became humid, where limbs and large size facilitated fossorial locomotion in packed soils.

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. marmoratus and all recognized species, supporting its valid species status. We provide a detailed redescription of the holotype based on a robust morphometric dataset and expanded comparisons with recognized congeners from the Pan-Himalayas and Southeast Asia. In addition, we discuss the remaining suspicious records of A. cf. afghanus in Nepal and China based on available specimens, and comment on the validity of two remaining junior synonyms of A. marmoratus, namely Ixalus argus Annandale, 1912 and Rana latopalmata Boulenger, 1882, suggesting that they may represent subjective synonyms of A. gerbillus (Annandale, 1912) and A. panhai Matsui and Nabhitabhata, 2006, respectively.

Insect populations are changing rapidly, and monitoring these changes is essential for understanding the causes and consequences of such shifts. However, large‐scale insect identification projects are time‐consuming and expensive when done solely by human identifiers. Machine learning offers a possible solution to help collect insect data quickly and efficiently.Here, we outline a methodology for training classification models to identify pitfall trap‐collected insects from image data and then apply the method to identify ground beetles (Carabidae). All beetles were collected by the National Ecological Observatory Network (NEON), a continental scale ecological monitoring project with sites across the United States. We describe the procedures for image collection, image data extraction, data preparation, and model training, and compare the performance of five machine learning algorithms and two classification methods (hierarchical vs. single‐level) identifying ground beetles from the species to subfamily level. All models were trained using pre‐extracted feature vectors, not raw image data. Our methodology allows for data to be extracted from multiple individuals within the same image thus enhancing time efficiency, utilizes relatively simple models that allow for direct assessment of model performance, and can be performed on relatively small datasets.The best performing algorithm, linear discriminant analysis (LDA), reached an accuracy of 84.6% at the species level when naively identifying species, which was further increased to >95% when classifications were limited by known local species pools. Model performance was negatively correlated with taxonomic specificity, with the LDA model reaching an accuracy of ~99% at the subfamily level. When classifying carabid species not included in the training dataset at higher taxonomic levels species, the models performed significantly better than if classifications were made randomly. We also observed greater performance when classifications were made using the hierarchical classification method compared to the single‐level classification method at higher taxonomic levels.The general methodology outlined here serves as a proof‐of‐concept for classifying pitfall trap‐collected organisms using machine learning algorithms, and the image data extraction methodology may be used for nonmachine learning uses. We propose that integration of machine learning in large‐scale identification pipelines will increase efficiency and lead to a greater flow of insect macroecological data, with the potential to be expanded for use with other noninsect taxa., We outline a methodology for training classification models to identify pitfall trap‐collected insects from image data and then apply the method to identify ground beetles (Carabidae). The best performing model reached an accuracy of 84.6% at the species level, which was further increased to >95% when classifications were limited by known local species pools.

Global amphibian decline continues to be a great concern despite our increased understanding of the causes behind the observed patterns of the decline, such as habitat modification and infectious diseases. Although there is a large body of literature on the topic of amphibian infectious diseases, pathogen prevalence and distribution among entire communities of species in many regions remain poorly understood. In addition to these geographic gaps in our understanding, past work has focused largely on individual pathogens, either Batrachochytrium dendrobatidis (Bd) or ranavirus (RV), rather than dual infection rates among host species. We sampled for prevalence and infection load of both pathogens in 514 amphibians across 16 total sites in northeastern Oklahoma. Amphibians were caught by hand, net, or seine; they were swabbed to screen for Bd; and liver tissue samples were collected to screen for RV. Overall results of quantitative PCR assays showed that 7% of screened individuals were infected with RV only, 37% were infected with Bd only, and 9% were infected with both pathogens simultaneously. We also documented disease presence in several rare amphibian species that are currently being monitored as species of concern due to their small population sizes in Oklahoma. This study synthesizes a growing body of research regarding infectious diseases among amphibian communities in the central United States.

The aridification of Africa resulted in the fragmentation of forests and the expansion of an arid corridor stretching from the northeast to southwest portion of sub-Saharan Africa, but the role this corridor has had in species-level diversification of southern African vertebrates is poorly understood. The skink species Mochlus afer and M. sundevallii inhabit wide areas of the arid corridor and are therefore an ideal species pair for studying patterns of genetic and phenotypic diversity associated with this landscape. However, species boundaries between these taxa have been controversial. Using multi-locus molecular and morphological datasets, we investigate diversification patterns of the M. afer-sundevallii Species Complex across the arid corridor. Although analyses of genetic data reveals some genetic structure among geographic populations, results of phylogenetic and morphological analyses provide little support for two distinct evolutionary lineages, suggesting that populations previously referred to as M. afer and M. sundevallii represent a single species, Mochlus sundevallii. Genetic diversity is unequally distributed across the arid corridor, with observed patterns consistent with aridification-facilitated diversification southward across southern Africa. Additional geographic and population-level sampling is necessary before more conclusive inferences can be drawn about the role historical climate transitions have played in skink diversification patterns across southern Africa.

Aplectana samarensis sp. nov. (Ascaridida, Cosmocercidae) from the intestines of Limnonectes magnus (Anura, Dicroglossidae) is described and illustrated. Aplectana samarensis sp. nov. represents the 53rd species assigned to the genus and the 6th species reported from the Oriental region. It is easily separated from the 5 species previously reported from the region by the presence of a gubernaculum and the distribution pattern of male caudal papillae: A. macintoshii has an irregular pattern, no precloacal papillae in rows; both A. akhrami and A. dubrajpuri lack a gubernaculum; A. duttaphryni has 3 pairs of precloacal papillae forming 2 rows; A. ranae has 7 pairs of precloacal papillae forming 2 rows; A. samarensis sp. nov. has 4 pairs of precloacal papillae in 2 rows. In addition to the new species, individuals of Falcaustra dubia and Pseudoacanthocephalus bufonis as well as cestode plerocercoids were also found.

Based on molecular and morphological data sets, we describe a new species of scincid lizard of the genus Lygosoma from Indochina, and redescribe true Lygosoma quadrupes (Linnaeus, 1766). The new species is small and slender, and represents the third member of the L. quadrupes complex, increasing the diversity of Lygosoma species recognized in Southeast Asia to 24. Based on the reevaluation of vouchered specimens from the type locality of L. quadrupes sensu Linnaeus (1766), the recognized geographic distribution of true L. quadrupes is restricted to the island of Java in Indonesia. With 10 species of Lygosoma recognized in Thailand, the country possesses considerable species-level diversity of these enigmatic, semifossorial skinks. In addition to being one of the smallest species in the genus, the new species can be distinguished from all congeners by features of its external morphology, including having small relative limb lengths, longer trunk length, and greater numbers of axilla–groin and para...

Evolutionary simplification of autopodial structures is a major theme in studies of body-form evolution. Previous studies on amniotes have supported Morse's law, that is, that the first digit reduced is Digit I, followed by Digit V. Furthermore, the question of reversibility for evolutionary digit loss and its implications for "Dollo's law" remains controversial. Here, we provide an analysis of limb and digit evolution for the skink genus Brachymeles. Employing phylogenetic, morphological, osteological, and myological data, we (a) test the hypothesis that digits have re-evolved, (b) describe patterns of morphological evolution, and (c) investigate whether patterns of digit loss are generalizable across taxa. We found strong statistical support for digit, but not limb re-evolution. The feet of pentadactyl species of Brachymeles are very similar to those of outgroup species, while the hands of these lineages are modified (2-3-3-3-2) and a have a reduced set of intrinsic hand muscles. Digit number variation suggests a more labile Digit V than Digit I, contrary to Morse's law. The observed pattern of digit variation is different from that of other scincid lizards (Lerista, Hemiergis, Carlia). Our results present the first evidence of clade-specific modes of digit reduction.

Although the recognized distribution of Japalura kumaonensis is restricted largely to western Himalaya, a single, isolated outlier population was reported in eastern Himalaya at the China-Nepal border in southeastern Tibet, China in Zhangmu, Nyalam County. Interestingly, subsequent studies have recognized another morphologically similar species, J. tricarinata, from the same locality in Tibet based on photographic evidence only. Despite these reports, no studies have examined the referred specimens for either record to confirm their taxonomic identifications with robust comparisons to congener species. Here, we examine the referred specimen of the record of J. kumaonensis from southeastern Tibet, China; recently collected specimens from the same locality in southeastern Tibet; type specimens; and topotypic specimens of both J. kumaonensis and J. tricarinata, to clarify the taxonomic identity of the focal population from southeastern Tibet, China. Our results indicate that individuals of the refer...