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Natural history collections are essential to a wide variety of studies in biology because they maintain large collections of specimens and associated data, including genetic material (e.g., tissues) for DNA sequence data, yet they are currently under-funded and collection staff have high workloads. With the advent of aggregate databases and advances in sequencing technologies, there is an increased demand on collection staff for access to tissue samples and associated data. Scientists are rapidly developing large DNA barcode libraries, DNA sequences of specific genes for species across the tree of life, in order to document and conserve biodiversity. In doing so, mistakes are made. For instance, inconsistent taxonomic information is commonly taken from different lending institutions and deposited in data repositories, such as the Barcode of Life Database (BOLD) and GenBank, despite explicit disclaimers regarding the need for taxonomic verification by the lending institutions. Such errors can have profound effects on subsequent research based on these mis-labelled sequences in data repositories. Here, we present the production of a large DNA barcode library of reptiles from the National Museum of Natural History tissue holdings. The library contains 2,758 sequences (2,205 COI and 553 16S ) from 2260 specimens (four crocodilians, 37 turtles, and 2,219 lizards, including snakes), representing 583 named species, from 52 countries. In generating this library, we noticed several common mistakes made by scientists depositing DNA barcode data in public repositories (e.g., BOLD and GenBank). Our goal is to raise awareness of these concerns and offer advice to avoid such mistakes in the future to maintain accurate DNA barcode libraries to properly document Earth’s biodiversity.

Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.

Glassfrogs (family: Centrolenidae) represent a fantastic radiation (~150 described species) of Neotropical anurans that originated in South America and dispersed into Central America. In this study, we review the systematics of Ecuadorian glassfrogs, providing species accounts of all 60 species, including three new species described herein. For all Ecuadorian species, we provide new information on the evolution, morphology, biology, conservation, and distribution. We present a new molecular phylogeny for Centrolenidae and address cryptic diversity within the family. We employ a candidate species system and designate 24 putative new species that require further study to determine their species status. We find that, in some cases, currently recognized species lack justification; specifically, we place Centrolene gemmata and Centrolene scirtetes under the synonymy of Centrolene lynchi; C. guanacarum and C. bacata under the synonymy of Centrolene sanchezi; Cochranella phryxa under the synonymy of Cochranella resplendens; and Hyalinobatrachium ruedai under the synonymy of Hyalinobatrachium munozorum. We also find that diversification patterns are mostly congruent with allopatric speciation, facilitated by barriers to gene flow (e.g., valleys, mountains, linearity of the Andes), and that niche conservatism is a dominant feature in the family. Conservation threats are diverse, but habitat destruction and climate change are of particular concern. The most imperiled glassfrogs in Ecuador are Centrolene buckleyi, C. charapita, C. geckoidea, C. medemi, C. pipilata, Cochranella mache, Nymphargus balionotus, N. manduriacu, N. megacheirus, and N. sucre, all of which are considered Critically Endangered. Lastly, we identify priority areas for glassfrog conservation in Ecuador.

From tiny, burrowing lizards to rainforest canopy-dwellers and giant crocodiles, reptile populations everywhere are changing. Yet government and conservation groups are often forced to make important decisions about reptile conservation and management based on inadequate or incomplete data. With contributions from nearly seventy specialists, this volume offers a comprehensive guide to the best methods for carrying out standardized quantitative and qualitative surveys of reptiles, while maximizing comparability of data between sites, across habitats and taxa, and over time. The contributors discuss each method, provide detailed protocols for its implementation, and suggest ways to analyze the data, making this volume an essential resource for monitoring and inventorying reptile abundance, population status, and biodiversity. Reptile Biodiversity covers topics including: • terrestrial, marine, and aquatic reptiles • equipment recommendations and limitations • ethics of monitoring and inventory activities • statistical procedures • designing sampling programs • using PDAs in the field

Widespread population declines in terrestrial Plethodon salamanders occurred by the 1980s throughout the Appalachian Mountains, the center of global salamander diversity, with no evident recovery. We tested the hypothesis that the historic introduction and spread of the pathogenic fungus Batrachochytrium dendrobatidis (Bd) into the eastern US was followed by Plethodon population declines. We expected to detect elevated prevalence of Bd prior to population declines as observed for Central American plethodontids. We tested 1,498 Plethodon salamanders of 12 species (892 museum specimens, 606 wild individuals) for the presence of Bd, and tested 94 of those for Batrachochytrium salamandrivorans (Bs) and for ranavirus. Field samples were collected in 2011 from 48 field sites across a 767 km transect. Historic samples from museum specimens were collected at five sites with the greatest number and longest duration of collection (1957-987), four of which were sampled in the field in 2011. None of the museum specimens were positive for Bd, but four P. cinereus from field surveys were positive. The overall Bd prevalence from 1957-2011 for 12 Plethodon species sampled across a 757 km transect was 0.2% (95% CI 0.1-0.7%). All 94 samples were negative for Bs and ranavirus. We conclude that known amphibian pathogens are unlikely causes for declines in these Plethodon populations. Furthermore, these exceptionally low levels of Bd, in a region known to harbor Bd, may indicate that Plethodon specific traits limit Bd infection.

Generously illustrated, this essential handbook for herpetologists, ecologists, and naturalists features comprehensive keys to eggs, embryos, salamander larvae, and tadpoles; species accounts; a glossary of terms; and an extensive bibliography. The taxonomic accounts include a summarization of the morphology and basic natural history, as well as an introduction to published information for each species. Tadpole mouthparts exhibit major characteristics used in identifications, and the book includes illustrations for a number of species. Color photographs of larvae of many species are also presented. Handbook of Larval Amphibians of the United States and Canada, written by the foremost experts on larval amphibians, is the first guide of its kind and will transform the fieldwork of scientists and fish and wildlife professionals.

The first part of this synthesis summarizes the morphology of the jelly layers surrounding an amphibian ovum. We propose a standard terminology and discuss the evolution of jelly layers. The second part reviews the morphological diversity and arrangement of deposited eggs—the ovipositional mode; we recognize 5 morphological classes including 14 modes. We discuss some of the oviductal, ovipositional, and postovipositional events that contribute to these morphologies. We have incorporated data from taxa from throughout the world but recognize that other types will be discovered that may modify understanding of these modes. Finally, we discuss the evolutionary context of the diversity of clutch structure and present a first estimate of its evolution.

Eastern Kingsnakes (Lampropeltis getula) are an important component and predator in herpetofaunal communities, but many Eastern Kingsnake populations have declined precipitously in the last few decades, particularly in the southeastern United States. Here, we describe an intensive capture–mark–recapture study of L. getula conducted during 1974–1978 in a canal bank–Water Hyacinth (Eichhornia crassipes) community at Rainey Slough in southern Florida, where annual capture probabilities of adults ranged from 0.662–0.787. Population size and structure, seasonal activity, movements, microhabitat use, behavior, thermal ecology, and predator–prey relationships are described. At this site kingsnakes were susceptible to capture mostly in winter and spring, were diurnal, used rodent (Sigmodon hispidus) burrows on canal banks as nocturnal retreats, and emerged from burrows on 13–26% of the sampling days. Overlap of burrow use by both sexes was extensive with no evidence of territoriality. Kingsnakes readily entered the Water Hyacinths to bask, pursue mates, and forage. At Rainey Slough only snakes were detected in the diet of kingsnakes. Concurrent sampling of potential snake prey in the hyacinths and on canal banks revealed 10 species that varied in use of the two sampled habitats and in body size. A range-wide analysis confirmed that in descending order snakes, reptile eggs, and lizards dominate the diet of L. getula in Florida (94.8%) and remain important prey types elsewhere (80.2%). At Rainey Slough the density of six species of semiaquatic snakes in Water Hyacinths averaged 3534 individuals/ha with a mean annual biomass of 135.8 kg/ha, and kingsnake biomass was only 2.2–3.9% of prey snake biomass. We estimated that the kingsnake population consumed 36.82–63.58 kg/yr, or about 10.0–17.2% of the standing crop of snakes in the Water Hyacinth community. Adult male L. getula lost on average 39.3% of their body mass associated with the spring reproductive season, whereas females lost only 3.4% in the same period. Body condition indices for both sexes improved substantially thereafter. In follow-up surveys at Rainey Slough during 2006–2010 no kingsnakes were found. Semiaquatic snake densities in the Water Hyacinths were 77.2% lower (807.4/ha) than in the 1970s and consisted of only three species. Compared to the enigmatic declines and extirpation of L. getula populations elsewhere, at Rainey Slough the primary cause likely was unsustainable mortality from road reconstruction and paving in the winter–spring of 1979 and subsequent roadkill. Other potentially causative agents of extirpation of L. getula in this system are discussed.