New Mexico Museum of Natural History and Science

ABSTRACT Freshwater crayfishes of the South American family Parastacidae include the Chilean‐endemic genus Virilastacus , currently comprising four described species. Despite their ecological importance and restricted distributions, the genetic diversity, phylogenetic relationships, and species boundaries within Virilastacus remain poorly understood. Here, we analyze mitochondrial DNA (COI) sequences from populations across the genus's known range in southern Chile to assess species limits, divergence times, and geographic structure. Phylogenetic analyses and multiple single‐locus species delimitation methods support the identification of five candidate species, comprising the four currently recognised species and a newly identified lineage, Virilastacus sp. ‘Calfuco’. Divergence time estimates place the origin of Virilastacus in the Middle Oligocene, indicating an ancient evolutionary history. We also report an expanded range for V. jarai , a narrower distribution for V. araucanius , and strong geographic structuring across the genus. These findings highlight previously overlooked diversity in Virilastacus and emphasise the need for further integrative taxonomic and conservation assessments.

Wildlife disease surveillance has received considerable attention following recent emergence of high-consequence zoonotic pathogens in humans. Increased portability and affordability of sequencing technologies over the last decade have made real-time sequencing of wild animals and their pathogens a reality. Wildlife samples screened for pathogens, however, are rarely permanently archived in museum biorepositories, which limits potential for scientific validation and prevents extension by related disciplines (e.g., ecology, evolution, conservation). To better connect biodiversity and biomedical sciences, the Museums and Emerging Pathogens in the Americas (MEPA) network developed the Field+Genomics Workshop to build capacity for surveillance of wildlife and their pathogens in biodiverse countries. Here, we share workshop resources, in English and Spanish, to facilitate reproducibility and expansion of the workshop into the future. The workshop lasted 10 days, 6 days of fieldwork and 4 days of molecular lab and bioinformatic techniques. The field component emphasized the importance of holistic collecting—that is, permanently preserving many parts and symbionts from each sampled organism—as a critical step in wildlife and pathogen surveillance and to build foundational scientific infrastructure. The molecular component of the workshop used samples collected during the field portion to identify hosts and pathogens in real-time. For this component, we trained participants in methods of DNA extraction, library preparation, and Nanopore Adaptive Sampling (a software feature for real-time selective enrichment or depletion of target sequences). Bioinformatic training consisted of a basic introduction to computational genomics, a worked example to analyze a small sequence dataset, and an exercise using data generated from samples collected during the workshop. In total, the workshop cost ~$37K (~$3K per participant), however, ~25% of those funds are invested in basic equipment and infrastructure that is reusable in future workshops (e.g., sequencer, computer, etc.). This workshop highlights the effort and expertise required to conduct voucher-backed surveillance of wildlife and their pathogens and the many benefits of uniting biodiversity and biomedical sciences to build local capacity.

ABSTRACT Radiocarbon dating of bones is essential for reconstructing timelines of species' occurrences, domestication, extinction, migrations, and interactions with Quaternary environments. Many studies compile these chronologies at continental to global scales by aggregating radiocarbon dates from various sources, often balancing data quantity and quality. A major challenge, however, is the frequent lack of reported bone‐collagen pretreatment protocols, which directly affect dating accuracy. Without this information, radiocarbon dates cannot be reliably quality‐ranked, and retrieving unpublished pretreatment details is often difficult due to lost data, outdated contacts, or restricted access to records. Researchers should ensure that pretreatments are replicable in their publications; and dated materials, taxonomic identities, geolocation details and genetic sequences are linked to individual radiocarbon dates. Journals should mandate the inclusion of reproducible radiocarbon chemistry and liaise with reviewers or advisory board members with expertise in chronological methods for studies presenting new dates or compilations of published dates. Radiocarbon facilities can enhance accessibility and transparency by publishing pretreatment protocols, documenting their history and digitizing older data. We advocate for the creation of a global radiocarbon database, emphasizing the need for close collaboration among the scientific community, dating facilities, research institutions and universities, as well as the adequate allocation of resources to generate and curate reliable radiocarbon data. The scientific community should recognize that current limitations in collagen purification compromise dating accuracy and might significantly affect critical research on Quaternary chronologies, megafaunal extinctions and human evolutionary history.

Abstract Bats of the widely distributed genus Myotis have been examined in order to address processes of diversification, speciation, and historical biogeography on a global scale. The taxonomy of the genus, however, is notoriously intractable due to limited morphological variation that does not adequately capture the extent of species diversity, and recent molecular studies over the past decade on Neotropical Myotis have unveiled substantial cryptic diversity. In Peru, 9 species of Myotis have been documented, with the majority inhabiting the Amazonian region. This study employs an integrative methodology incorporating qualitative morphological assessment, linear morphometrics, and molecular phylogenetics to describe a novel Myotis species from the coastal desert of southern Peru. Although it bears morphological similarities to M. oxyotus sensu stricto, this new species exhibits a 12% genetic divergence at the mitochondrial cytochrome b locus from M. oxyotus. Additionally, it differs from South and Central American counterparts by having a long forearm (longest documented among Neotropical myotine bats) and a notably large skull with a broad, elevated, and globular braincase. Recognition of this new species elevates the diversity of Myotis in Peru to 10 species, thereby increasing the total number of known bat species in the country to 190.

ABSTRACTLeaf‐eared mice (genus Phyllotis) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high‐elevation deserts. Here, we report a combined analysis of mitochondrial DNA variation and whole‐genome sequence (WGS) variation in Phyllotis mice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence based on cytb data suggest that most diversification of Phyllotis occurred during the past 3 million years. Consistent with the Pleistocene Aridification hypothesis, our results suggest that diversification of Phyllotis largely coincided with climatically induced environmental changes in the mid‐ to late‐Pleistocene. Contrary to the Montane Uplift hypothesis, most diversification in the group occurred well after the major phase of uplift of the Central Andean Plateau. Species delimitation analyses revealed surprising patterns of cryptic diversity within several nominal forms, suggesting the presence of much undescribed alpha diversity in the genus. Results of genomic analyses revealed evidence of hybridization between the sister species P. limatus and P. vaccarum, suggesting that the contemporary zone of range overlap between the two species represents a hybrid zone.

The Placerias quarry is a dicynodont-dominated bonebed in Upper Triassic Chinle Group strata near St. Johns in east-central Arizona, USA. Though long identified as being in strata of the lower Chinle Group, recently published numerical ages apparently indicate a stratigraphically much higher (younger) position in the Chinle section for the Placerias quarry. Nevertheless, recent analysis of outcrop and subsurface (hydrologic) data in the vicinity of the Placerias quarry confirms its stratigraphic position very low in the Chinle Group section, close to the base of the Bluewater Creek Formation. A regional Upper Triassic lithostratigraphy has been established across east-central Arizona and west-central New Mexico by nearly a century of stratigraphic studies and geologic mapping by diverse workers, and is supported by biostratigraphy; in this lithostratigraphy the Placerias quarry is near the Chinle Group base. However, U/Pb ages on zircons from Upper Triassic strata in eastern Arizona/western New Mexico have been used to reorganize this lithostratigraphy to indicate intertonguing and dramatic lithofacies changes over relatively short lateral distances. But, if the well-established lithostratigraphy is followed, the U/Pb ages are problematic, particularly where younger ages (such as at the Placerias quarry) are stratigraphically below older ages. A handful of numerical ages should not be used to over-rule well-established understanding of lithostratigraphy and biostratigraphy, unless the lithostratigraphy and biostratigraphy need to be modified based on stratigraphic data. Numerical ages need to be used judiciously and evaluated critically with regard to established lithostratigraphy, biostratigraphy and other age constraints.

Biodiversity science depends on rigorous characterization of species diversity and ecological roles, yet the ecology of many invertebrate species remains virtually unknown. One pragmatic way to change this is to make use of deceased animals and their companions, such as by salvaging and examining carcasses reported by citizen scientists. Here, we demonstrate how bird carcasses reported by citizen scientists can help generate functional biodiversity data on parasites. We reveal 44 hippoboscid flies (Diptera: Hippoboscidae) found on 36 of 148 salvaged bird carcasses (~24% success rate). Using the principles of large‐scale integrative taxonomy (LIT), we first delimited 10 hippoboscid species. One of these, Pseudolynchia maai Lee & Oboňa, sp. nov., was new to science and is here formally described. We also provide a pictorial key, image‐based diagnostics, and molecular diagnostics for all 10 species. We report 25 species interactions between flies and birds. This study illustrates how combining the efforts of citizen scientists and biologists can support species discovery and generate functional parasite–host data.

Leaf-eared mice (genus Phyllotis) are among the most widespread and abundant small mammals in the Andean Altiplano, but species boundaries and distributional limits are often poorly delineated due to sparse survey data from remote mountains and high-elevation deserts. Here we report a combined analysis of mitochondrial DNA variation and whole-genome sequence (WGS) variation in Phyllotis mice to delimit species boundaries, to assess the timescale of diversification of the group, and to examine evidence for interspecific hybridization. Estimates of divergence dates suggest that most diversification of Phyllotis occurred during the past 3 million years. Consistent with the Pleistocene Aridification hypothesis, our results suggest that diversification of Phyllotis largely coincided with climatically induced environmental changes in the mid- to late Pleistocene. Contrary to the Montane Uplift hypothesis, most diversification in the group occurred well after the major phase of uplift of the Central Andean Plateau. Species delimitation analyses revealed surprising patterns of cryptic diversity within several nominal forms, suggesting the presence of much undescribed alpha diversity in the genus. Results of genomic analyses revealed evidence of ongoing hybridization between the sister species Phyllotis limatus and P. vaccarum and suggest that the contemporary zone of range overlap between the two species represents an active hybrid zone.

Abstract In nature, small populations are often of concern because of limited genetic diversity, which underlies adaptive potential in the face of environmental change. Assessing patterns of genetic variation within co-distributed species sampled across varied landscapes can therefore illuminate their capacity to persist over time. We sequenced new genome-wide sequence data (double-digest restriction site-associated DNA sequencing) for four frog species (Anaxyrus terrestris, Hyla cinerea, Hyla squirella, and Rana sphenocephala) sampled from two barrier islands and the adjacent mainland of northern Florida. We calculated genomic diversity metrics and analysed spatial patterns of genomic variation for each species. We found higher genomic diversity within mainland individuals compared to island individuals for all species, suggesting a consistent effect of small island area on diversity across species. Three species (all but A. terrestris) showed significant signatures of isolation by distance, and some clustering analyses indicated separation of island and mainland individuals within species. We identified subtle differences in the strength of these patterns among species, with the strongest genetic differentiation observed in R. sphenocephala. Finally, we found evidence of recent migration between island and mainland populations for all species, which likely explains the limited genetic structure observed and contributes to the persistence of these small populations.