Galápagos tortoise stable isotope ecology and the 1850s Floreana Island Chelonoidis niger niger extinction.

A consequence of over 400 years of human exploitation of Galápagos tortoises (Chelonoidis niger ssp.) is the extinction of several subspecies and the decimation of others. As humans captured, killed, and/or removed tortoises for food, oil, museums, and zoos, they also colonized the archipelago resulting in the introduction of invasive plants, animals, and manipulated landscapes for farming, ranching, and infrastructure. Given current conservation and revitalization efforts for tortoises and their habitats, here we investigate nineteenth and twentieth century Galápagos tortoise dietary ecology using museum and archaeological specimens coupled with analysis of carbon (δ13Ccollagen and δ13Capatite), nitrogen (δ15N), hydrogen (δD) and oxygen (δ18Oapatite) stable isotopes and radiocarbon dating. We identify that Galápagos tortoise diets vary between and within islands over time, and that long-term anthropogenic impacts influenced change in tortoise stable isotope ecology by using 57 individual tortoises from 10 different subspecies collected between 1833 and 1967-a 134-year period. On lower elevation islands, which are often hotter and drier, tortoises tend to consume more C4 vegetation (cacti and grasses). Our research suggests human exploitation of tortoises and anthropogenic impacts on vegetation contributed to the extinction of the Floreana Island tortoise (C. n. niger) in the 1850s.

DNA barcoding of the National Museum of Natural History reptile tissue holdings raises concerns about the use of natural history collections and the responsibilities of scientists in the molecular age.

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.

Genomic library preparation and hybridization capture of formalin-fixed tissues and allozyme supernatant for population genomics and considerations for combining capture- and RADseq-based single nucleotide polymorphism data sets.

Until recently many historical museum specimens were largely inaccessible to genomic inquiry, but high-throughput sequencing (HTS) approaches have allowed researchers to successfully sequence genomic DNA from dried and fluid-preserved museum specimens. In addition to preserved specimens, many museums contain large series of allozyme supernatant samples, but the amenability of these samples to HTS has not yet been assessed. Here, we compared the performance of a target-capture approach using alternative sources of genomic DNA from 10 specimens of spring salamanders (Plethodontidae: Gyrinophilus porphyriticus) collected between 1985 and 1990: allozyme supernatants, allozyme homogenate pellets and formalin-fixed tissues. We designed capture probes based on double-digest restriction-site associated sequencing (RADseq) derived loci from frozen blood samples available for seven of the specimens and assessed the success and consistency of capture and RADseq approaches. This study design enabled direct comparisons of data quality and potential biases among the different data sets for phylogenomic and population genomic analyses. We found that in phylogenetic analyses, all enrichment types for a given specimen clustered together. In principal component space all capture-based samples clustered together, but RADseq samples did not cluster with corresponding capture-based samples. Single nucleotide polymorphism calls were on average 18.3% different between enrichment types for a given individual, but these discrepancies were primarily due to differences in heterozygous/homozygous single nucleotide polymorphism calls. We demonstrate that both allozyme supernatant and formalin-fixed samples can be successfully used for population genomic analyses and we discuss ways to identify and reduce biases associated with combining capture and RADseq data.

A new species of Gerrhopilus (family: Gerrhopilidae), with comments on the taxonomic status of Gerrhopilus ater suturalis (Brongersma).

The genus Gerrhopilus is briefly reviewed with a reevaluation of Gerrhopilus ater suturalis and its elevation to full species. In addition, a new species from Sumatra is described based on a single specimen, one of the three species of Gerrhopilus having both an inferior preocular and inferior ocular, and further distinguishable by the supralabial overlap pattern.

A global catalog of primary reptile type specimens.

We present information on primary type specimens for 13,282 species and subspecies of reptiles compiled in the Reptile Database, that is, holotypes, neotypes, lectotypes, and syntypes. These represent 99.4% of all 13,361 currently recognized taxa (11,050 species and 2311 subspecies). Type specimens of 653 taxa (4.9%) are either lost or not located, were never designated, or we did not find any information about them. 51 species are based on iconotypes. To map all types to physical collections we have consolidated all synonymous and ambiguous collection acronyms into an unambiguous list of 364 collections holding these primary types. The 10 largest collections possess more than 50% of all (primary) reptile types, the 36 largest collections possess more than 10,000 types and the largest 73 collections possess over 90% of all types. Of the 364 collections, 107 hold type specimens of only 1 species or subspecies. Dozens of types are still in private collections. In order to increase their utility, we recommend that the description of type specimens be supplemented with data from high-resolution images and CT-scans, and clear links to tissue samples and DNA sequence data (when available). We request members of the herpetological community provide us with any missing type information to complete the list.

How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation.

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.

Blindsnake evolutionary tree reveals long history on Gondwana.

Worm-like snakes (scolecophidians) are small, burrowing species with reduced vision. Although largely neglected in vertebrate research, knowledge of their biogeographical history is crucial for evaluating hypotheses of snake origins. We constructed a molecular dataset for scolecophidians with detailed sampling within the largest family, Typhlopidae (blindsnakes). Our results demonstrate that scolecophidians have had a long Gondwanan history, and that their initial diversification followed a vicariant event: the separation of East and West Gondwana approximately 150 Ma. We find that the earliest blindsnake lineages, representing two new families described here, were distributed on the palaeolandmass of India+Madagascar named here as Indigascar. Their later evolution out of Indigascar involved vicariance and several oceanic dispersal events, including a westward transatlantic one, unexpected for burrowing animals. The exceptional diversification of scolecophidians in the Cenozoic was probably linked to a parallel radiation of prey (ants and termites) as well as increased isolation of populations facilitated by their fossorial habits.

LINKAGE DISEQUILIBRIUM AND A CONTACT ZONE IN PLETHODON CINEREUS ON THE DEL-MAR-VA PENINSULA.

A contact zone between two electrophoretically differentiated forms of Plethodon cinereus extends across the Del-Mar-Va Peninsula. Based on the presumed nature of regional climates during the late Pleistocene, it is suggested that the climate was inhospitable for P. cinereus on the Del-Mar-Va Peninsula at the Wisconsin maximum. It is postulated that, after the Laurentide ice sheet receded about 14,000 years BP, the peninsula was invaded by populations of P. cinereus from the north and south. When the two forms of P. cinereus met, a secondary zone of contact was produced. This contact zone is now apparent in an area in which six electrophoretic loci have concordant clinal changes in allele frequency. The lack of evidence for heterozygote deficiencies, the broad width of the contact zone, and the overall symmetry of introgression suggest that fusion of the populations is occurring freely. Two esterase loci are in linkage disequilibrium in four of eight populations to the north of the contact zone. As all populations of P. cinereus studied to date have disequilibrium coefficients of similar sign, selection is likely important in the maintenance of this linkage disequilibrium. Within the contact zone, the incidence of the linkage disequilibrium increases, but exchange of genes between the two introgressing populations may account for the higher incidence of linkage disequilibrium.