Biology subjects

Cook, J. A.

Publications and source records attributed to Cook, J. A..

6 recordsLinked to original sources

bioRxiv2024

Species limits and hybridization in Andean leaf-eared mice (Phyllotis)

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.

evolutionary biology↗

bioRxiv2024

Selecting sites for strategic surveillance of zoonotic pathogens: a case study in Panama

Surveillance and monitoring of zoonotic pathogens is key to identifying and mitigating emerging public health threats. Surveillance is often designed to be taxonomically targeted or systematically dispersed across geography, however, those approaches may not represent the breadth of environments inhabited by a host, vector, or pathogen, leaving significant gaps in our understanding of pathogen dynamics in their natural reservoirs and environments. As a case study on the design of pathogen surveillance programs, we assess how well 20 years of small mammal surveys in Panama have sampled available environments and propose a multistep approach to selecting survey localities in the future. We use >8,000 georeferenced mammal specimen records, collected as part of a long-term hantavirus surveillance program, to test the completeness of country-wide environmental sampling. Despite 20 years of surveillance, our analyses identified a few key environmental sampling gaps. To refine surveillance strategies, we selected a series of core historically sampled localities, supplemented with additional environmentally distinct sites to more completely represent Panamas environments. Based on lessons learned through decades of surveillance, we propose a series of recommendations to improve strategic sampling for zoonotic pathogen surveillance.

ecology↗

bioRxiv2023

Arctos: Community-driven innovations for managing biodiversity and cultural collections

Museum collections house millions of objects and associated data records that document biological and cultural diversity. In recent decades, digitization efforts have greatly increased accessibility to these data, thereby revolutionizing interdisciplinary studies in evolutionary biology, biogeography, epidemiology, cultural change, and human-mediated environmental impacts. Curators and collection managers can make museum data as accessible as possible to scientists and learners by using a collection management system. However, selecting a system can be a challenging task. Here, we describe Arctos, a community solution for managing and accessing collections data for research and education. Specific goals are to: (1) Describe the core elements of Arctos for a broad audience with respect to the biodiversity informatics principles that enable high quality research; (2) Highlight the unique aspects of Arctos; (3) Illustrate Arctos as a model for supporting and enhancing the Digital Extended Specimen; and (4) Emphasize the role of the Arctos community for improving data discovery and enabling cross-disciplinary, integrative studies within a sustainable governance model. In addition to detailing Arctos as both a community of museum professionals and a collection database platform, we discuss how Arctos achieves its richly annotated data by creating a web of knowledge with deep connections between catalog records and derived or associated data. We also highlight the value of Arctos as an educational resource. Finally, we present a financial model of fiscal sponsorship by a non-profit organization, implemented in 2022, to ensure the long-term success and sustainability of Arctos. We attribute Arctos longevity of nearly three decades to its core development principles of standardization, flexibility, interdisciplinarity, and connectivity within a nimble development model for addressing novel needs and information types in response to changing technology, workflows, ethical considerations, and regulations.

bioinformatics↗

bioRxiv2023

Extraordinary levels of per- and polyfluoroalkyl substances (PFAS) in vertebrate animals at a New Mexico desert oasis: multiple pathways for wildlife and human exposure

Per- and polyfluoroalkyl substances (PFAS) threaten human and wildlife health, but their movement through food webs remains poorly understood. Contamination of the physical environment is widespread, but particularly concentrated at military installations. Here we measured 17 PFAS in wild, free-living mammals and migratory birds at Holloman Air Force Base (AFB), New Mexico, USA, where wastewater catchment lakes form biodiverse oases. PFAS concentrations were among the highest ever reported in animal tissues, and high levels have persisted for at least three decades. The hazardous long carbon-chain form, perfluorooctanosulfonic acid (PFOS), was most abundant, with liver concentrations averaging tens of thousands of ng/g wet weight (ww), reaching as high 97,000 ng/g (ww) in a 1994 specimen of white-footed mouse (Peromyscus leucopus) and 38,000 ng/g ww in a duck, the American wigeon (Mareca americana). Perfluorohexanesulfonic acid (PFHxS) averaged thousands of ng/g ww in the livers of birds and house mice, but one order of magnitude lower in the livers of upland desert rodent species. PFAS levels were strikingly lower at control sites, even for highly mobile migratory species. Tissue concentrations were correlated within individuals, and consistently higher in liver than in muscle or blood. Twenty of 23 vertebrate species sampled at Holloman AFB were heavily contaminated, representing multiple trophic levels and microhabitats, and implicating a range of pathways for PFAS spread: ingestion of surface water, sediments, and dust; foraging on aquatic invertebrates and plants by secondary consumers; and preying upon small vertebrates by higher level consumers, including consumption of game species by hunters. Unlike in other aquatic systems, piscivory was not an important pathway of PFAS uptake. In sum, legacy PFAS at a desert wetland have permeated the local food web across a period of decades, severely contaminating resident and migrant animals, and likely exposing humans via game meat consumption and outdoor recreation. Five highlightsO_LIA biodiverse, wetland food web at a military base is heavily contaminated with PFAS. C_LIO_LILittoral-zone mice and aquatic birds had high liver PFOS, up to 97,000 ng/g ww. C_LIO_LISpecies and ecological variation were high among 16 PFAS detected in animal tissues. C_LIO_LIGame species had dangerously contaminated meat and can transport it long distances. C_LIO_LIBiorepositories provide key temporal and spatial sampling for contaminant studies. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/561778v1_ufig1.gif" ALT="Figure 1"> View larger version (75K): org.highwire.dtl.DTLVardef@96a640org.highwire.dtl.DTLVardef@7cd7f4org.highwire.dtl.DTLVardef@45fb67org.highwire.dtl.DTLVardef@7c33a4_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2023

Choclo virus (CHOV) recovered from deep metatranscriptomics of archived museum tissues

BackgroundHantaviruses are negative-stranded RNA viruses that can sometimes cause severe disease in humans; however, they are maintained in mammalian populations without causing harm. In Panama, sigmodontine rodents serve as hosts to transmissible hantaviruses. Due to natural and anthropogenic forces, these rodent populations are having increased contact with humans. MethodsWe extracted RNA and performed Illumina deep metatranscriptomic sequencing on Orthohantavirus seropositive museum tissues from rodents. We acquired sequence reads mapping to Choclo virus (CHOV, Orthohantavirus chocloense) from the heart and kidney tissue of a two decade old sample from a Costa Rican pygmy rice rat (Oligoryzomys costaricensis) collected in Panama. Reads mapped to the CHOV reference were assembled and then validated by visualization of the mapped reads against the assembly. ResultsWe recovered a 91% complete consensus sequence from a reference-guided assembly to CHOV with an average of 16X coverage. The S and M segments used in our phylogenetic analyses were nearly complete (98% and 99%, respectively). There were 1,199 ambiguous base calls of which 93% were present in the L segment. Our assembled genome varied 1.3% from the CHOV reference sequence resulting in 11 nonsynonymous mutations. Further analysis of all publicly available partial S segment sequences support a clear relationship between CHOV clinical cases and O. costaricensis acquired strains. ConclusionsViruses occurring at extremely low abundances can be recovered from deep metatranscriptomics of archival tissues housed in museums or biorepositories. Our efforts resulted in the second CHOV genome publicly available. This genomic data is important for future surveillance and diagnostic tools as well as understanding the evolution and pathogenicity of CHOV. Author SummaryHantavirus cardiopulmonary syndrome (HCPS) in Panama, caused by Choclo virus (CHOV, Orthohantavirus chocloense), is intimately linked to the primary mammalian reservoir host, the Costa Rican pygmy rice rat (Oligoryzomys costaricensis). Although the prevalence of hantavirus disease is relatively low in Panama, over a quarter of the country has the agroecological conditions that favor this rodent. In addition, serologic evidence suggests infections are under-reported. Sequence data of the pathogen and host collected across temporal and spatial scales is necessary for diagnostics, surveillance, and forecasting; however, only one complete genome is available in NCBI GenBank. By leveraging deep metatranscriptomics of archived frozen mammal tissues, we generated a low-coverage genome using a reference-guided assembly approach. Sequence data can be used to develop pan-hantavirus diagnostic tools to facilitate acquisition of more detailed genetic data from archival samples to increase our understanding of the evolutionary and population dynamics of rare and neglected hantaviruses. Generating additional genomic sequence data will also be essential for developing a rigorous taxonomic framework to improve the understanding of hantavirus diversity and distribution.

genomics↗

bioRxiv2018

Genomic perspectives on adaptation and conservation in the endangered long-tailed goral (Naemorhedus caudatus).

Native to the mountains of East Asia, the long-tailed goral (Naemorhedus caudatus) is a vulnerable wild ungulate in the tribe Caprini. To understand key conservation issues related to fragmentation and subsequent endangerment of this montane species, we sequenced and analyzed the genome of a long-tailed goral to explore historical demography, contemporary levels of genetic diversity, and potential immune response. When compared to ten additional mammalian reference genomes, we identified 357 positively selected genes (PSGs) in the long-tailed goral and 364 PSGs in the Caprini lineage. Gene Ontology analyses showed statistical enrichment in biological processes related to immune function and in genes and pathways related to blood coagulation. We also identified low levels of heterozygosity (0.00114) in the long-tailed goral along with decreases in population size relative to other species of Caprini. Finally, we provide evidence for positive selection on the muscle development gene myostatin (MSTN) in the Caprini lineage, which may have increased the muscle development and climbing ability in the caprine common ancestor. Low effective population size and decreased heterozygosity of the long-tailed goral raise conservation concern about the effects of habitat fragmentation, over harvest, and inbreeding on this vulnerable species.

bioinformatics↗