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.
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.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
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.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Species that went extinct prior to the genomic era are often considered out-of-reach for modern phylogenetic studies. This is particularly limiting for conservation studies, as genetic data from such ...taxa may be key to understanding extinction risks and causes of decline that can inform the management of related, extant populations. Fortunately, continual advances in biochemistry and DNA sequencing offer increasing ability to recover DNA from historical fluid-preserved museum specimens. Here, we report on success in recovering nuclear and mitochondrial data from the putative subspecies
Desmognathus fuscus carri
Neill 1951, a plethodontid salamander from spring runs in central Florida that is apparently extinct. The two ethanol-preserved topotypic specimens we studied are 50 years old and were likely fixed in unbuffered formalin, but application of a recently derived extraction procedure yielded usable DNA and partially successful Anchored Hybrid Enrichment sequencing. These data suggest that
D. f. carri
from peninsular Florida is conspecific with the
D. auriculatus
A lineage as suggested by previous authors, but may have represented an ecogeographically distinct population segment that has now been lost. Genetic data from this enigmatic disappearance thus confirm the geographic extent of population declines and extirpations as well as their ecological context, suggesting a possibly disproportionate loss from sandy-bottom clearwater streams compared to blackwater swamps. Success of these laboratory methods bodes well for large-scale application to fluid-preserved natural history specimens from relevant historical populations, but the possibility of significant DNA damage and related sequencing errors remains a hurdle to overcome.
Aim: The river drainages of the Appalachian Mountains have experienced a dynamic history as glacial cycles, stream capture and other geological processes have led to the fragmentation and fusion of ...formerly isolated palaeodrainages. Some ancient rivers have gone extinct, including portions of the great Teays River. Here we investigate the contribution of contemporary and historical drainages to patterns of phylogeographical structure in the spring salamander complex, Gyrinophilus porphyriticus. Location: Eastern North America, USA. Methods: Sampling spanned the range of the G. porphyriticus complex, and included representative samples of the cave species of Gyrinophilus as well. Molecular sequence data included the mitochondrial DNA locus cytochrome b and the nuclear locus recombination-activating gene 1 (RAG-1). Time-calibrated phylogenies were inferred, and Bayes-LAGRANGE was used to reconstruct ancestral distributions. Contemporary and historical river influences on patterns of genetic diversity were tested using distance-based redundancy analysis (db-RDA). Results: The G. porphyriticus complex originated prior to the Pleistocene glacial cycles, and historical river systems explained more genetic variation than did contemporary drainages or geographical distance. Patterns of genetic variation suggest that extinct or remodelled palaeodrainages, including the Teays River, played an important role in structuring contemporary patterns of genetic variation. Main conclusions: The hydrogeological history of eastern North American drainage basins has been instrumental in structuring patterns of regional biodiversity in freshwater species. Here we show that hydrological remodelling has also left its genetic signature in the semi-aquatic spring salamander complex, G. porphyriticus. Historical drainages accounted for the largest fraction of phylogeographical structure, more so than did contemporary drainages or geographical distance, with spatial and temporal patterns of variation associated with the extinct Teays River.
Due to their limited geographic distributions and specialized ecologies, cave species are often highly endemic and can be especially vulnerable to habitat degradation within and surrounding the cave ...systems they inhabit. We investigated the evolutionary history of the West Virginia Spring Salamander (
Gyrinophilus subterraneus)
, estimated the population trend from historic and current survey data, and assessed the current potential for water quality threats to the cave habitat. Our genomic data (mtDNA sequence and ddRADseq-derived SNPs) reveal two, distinct evolutionary lineages within General Davis Cave corresponding to
G. subterraneus
and its widely distributed sister species,
Gyrinophilus porphyriticus
, that are also differentiable based on morphological traits. Genomic models of evolutionary history strongly support asymmetric and continuous gene flow between the two lineages, and hybrid classification analyses identify only parental and first generation cross (F1) progeny. Collectively, these results point to a rare case of sympatric speciation occurring within the cave, leading to strong support for continuing to recognize
G. subterraneus
as a distinct and unique species. Due to its specialized habitat requirements, the complete distribution of
G. subterraneus
is unresolved, but using survey data in its type locality (and currently the only known occupied site), we find that the population within General Davis Cave has possibly declined over the last 45 years. Finally, our measures of cave and surface stream water quality did not reveal evidence of water quality impairment and provide important baselines for future monitoring. In addition, our unexpected finding of a hybrid zone and partial reproductive isolation between
G. subterraneus
and
G. porphyriticus
warrants further attention to better understand the evolutionary and conservation implications of occasional hybridization between the species.
As a first step toward making sense of an infamously enigmatic and taxonomically problematic group of Philippine blind snakes, we redescribe Malayotyphlops luzonensis (Taylor, 1919) and ...Malayotyphlops ruber (Boettger, 1897) and clarify their taxonomic status with respect to each other and to additional phenotypically similar taxa. We also describe two other new species of Malayotyphlops from the Sierra Madre Mountain Range of northern Luzon Island, each on the basis of a single specimen. We suspect that species diversity of the typhlopid fauna of the Philippines is severely underestimated, with progress towards a comprehensive understanding of this group most hampered by a lack of sufficient comparative material available in biodiversity repositories.
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.
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