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.

An annotated checklist of the amphibians and reptiles of North Padre Island, Texas, USA, with comparisons to adjacent barrier island and mainland herpetofauna

Padre Island is the world's longest barrier island and includes the longest stretch of undeveloped barrier island in the world. Largely due to harsh environmental conditions and difficult access, only cursory and incomplete checklists and subjective estimates of abundance have been produced. The results of an inventory of amphibians and reptiles of North Padre Island conducted 2002-2020, including the results of extensive field surveys conducted 2002-2003, are reported herein. Natural history museum and iNaturalist records are summarized and compared among North and South Padre and Mustang islands and the mainland portion of the seven counties in which the islands occur. The conservation status of rare species and extirpation of others is noted. The morphology and taxonomic status of some unique occurrences are discussed. Eleven species of amphibians and 39 species of reptiles presently occur or have occurred naturally or as introduced or accidental species on North Padre Island. Twelve species of amphibians and 50 species of reptiles occur or have occurred on North Padre, South Padre, and Mustang islands. Thirty-one species of amphibians and 93 species of reptiles have been reported from the seven counties in which the islands occur.

Historical biogeography of the genus Rhadinaea (Squamata: Dipsadinae)

Multiple geological and climatic events have created geographical or ecological barriers associated with speciation events, playing a role in biological diversification in North and Central America. Here, we evaluate the influence of the Neogene and Quaternary geological events, as well as the climatic changes in the diversification of the colubrid snake genus Rhadinaea using molecular dating and ancestral area reconstruction. A multilocus sequence dataset was generated for 37 individuals of Rhadinaea from most of the biogeographical provinces where the genus is distributed, representing 19 of the 21 currently recognized species, and two undescribed species. Our analyses show that the majority of the Rhadinaea species nest in two main clades, herein identified as "Eastern" and "Southern". These clades probably diverged from each other in the early Miocene, and their divergence was followed by 11 divergences during the middle to late Miocene, three divergences during the Pliocene, and six divergences in the Pleistocene. The ancestral distribution of Rhadinaea was reconstructed across the Sierra Madre del Sur. Our phylogenetic analyses do not support the monophyly of Rhadinaea. The Miocene and Pliocene geomorphology, perhaps in conjunction with climate change, appears to have triggered the diversification of the genus, while the climatic changes during the Miocene probably induced the diversification of Rhadinaea in the Sierra Madre del Sur. Our analysis suggests that the uplifting of the Trans-Mexican Volcanic Belt and Chiapan-Guatemalan highlands in this same period resulted in northward and southward colonization events. This was followed by more recent, independent colonization events in the Pliocene and Pleistocene involving the Balsas Basin, Chihuahuan Desert, Pacific Coast, Sierra Madre Occidental, Sierra Madre Oriental, Sierra Madre del Sur, Trans-Mexican Volcanic Belt, and Veracruz provinces, probably driven by the climatic fluctuations of the time.

Biogeographic barriers, Pleistocene refugia, and climatic gradients in the southeastern Nearctic drive diversification in cornsnakes (Pantherophis guttatus complex)

The southeastern Nearctic is a biodiversity hotspot that is also rich in cryptic species. Numerous hypotheses (e.g., vicariance, local adaptation, and Pleistocene speciation in glacial refugia) have been tested in an attempt to explain diversification and the observed pattern of extant biodiversity. However, previous phylogeographic studies have both supported and refuted these hypotheses. Therefore, while data support one or more of these diversification hypotheses, it is likely that taxa are forming within this region in species-specific ways. Here, we generate a genomic data set for the cornsnakes (Pantherophis guttatus complex), which are widespread across this region, spanning both biogeographic barriers and climatic gradients. We use phylogeographic model selection combined with hindcast ecological niche models to determine regions of habitat stability through time. This combined approach suggests that numerous drivers of population differentiation explain the current diversity of this group of snakes. The Mississippi River caused initial speciation in this species complex, with more recent divergence events linked to adaptations to ecological heterogeneity and allopatric Pleistocene refugia. Lastly, we discuss the taxonomy of this group and suggest there may be additional cryptic species in need of formal recognition.

Amphibians and reptiles of C. E. Miller Ranch and the Sierra Vieja, Chihuahuan Desert, Texas, USA

We report the occurrence of 50 species of amphibians and reptiles recently collected on C. E. Miller Ranch and the Sierra Vieja in the Chihuahuan Desert of Texas, USA and describe their perceived distribution and abundance across various habitat associations of the region. Our recent surveys follow intense, historic sampling of amphibians and reptiles from this region in 1948. Of the 50 species detected in recent surveys, six were not collected in 1948 and an additional three species documented in 1948 have yet to be detected in a 14-year period of recent surveys. Combining data from both historic and recent surveys, a total of 53 species of amphibians and reptiles are known from the ranch (11 amphibians, 42 reptiles). Land stewardship and conservation practices have likely contributed to the persistence of the majority of these species through time. Additionally, we discuss the status of amphibians and reptiles not collected during recent surveys and comment on potential species that have not yet been detected.

Geographical features are the predominant driver of molecular diversification in widely distributed North American whipsnakes

Allopatric divergence following the formation of geographical features has been implicated as a major driver of evolutionary diversification. Widespread species complexes provide opportunities to examine allopatric divergence across varying degrees of isolation in both time and space. In North America, several geographical features may play such a role in diversification, including the Mississippi River, Pecos River, Rocky Mountains, Cochise Filter Barrier, Gulf of California and Isthmus of Tehuantepec. We used thousands of nuclear single nucleotide polymorphisms (SNPs) and mitochondrial DNA from several species of whipsnakes (genera Masticophis and Coluber) distributed across North and Central America to investigate the role that these geographical features have played on lineage divergence. We hypothesize that these features restrict gene flow and separate whipsnakes into diagnosable genomic clusters. We performed genomic clustering and phylogenetic reconstructions at the species and population levels using Bayesian and likelihood analyses and quantified migration levels across geographical features to assess the degree of genetic isolation due to allopatry. Our analyses suggest that (i) major genetic divisions are often consistent with isolation by geographical features, (ii) migration rates between clusters are asymmetrical across major geographical features, and (iii) areas that receive proportionally more migrants possess higher levels of genetic diversity. Collectively, our findings suggest that multiple features of the North American landscape contributed to allopatric divergence in this widely distributed snake group.