Joseph A. Cook
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View article: Field+Genomics Workshop: an initiative to build Nanopore sequencing capacity in field-based host-pathogen research
Field+Genomics Workshop: an initiative to build Nanopore sequencing capacity in field-based host-pathogen research Open
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 mad…
View article: dciWebMapper2: Enhancing the dciWebMapper framework toward integrated, interactive visualization of linked multi-type maps, charts, and spatial statistics and analysis
dciWebMapper2: Enhancing the dciWebMapper framework toward integrated, interactive visualization of linked multi-type maps, charts, and spatial statistics and analysis Open
As interactive web-based geovisualization becomes increasingly vital across disciplines, there is a growing need for open-source frameworks that support dynamic, multi-attribute spatial analysis and accessible design. This paper introduces…
View article: Extending mammal specimens with their essential phenotypic traits
Extending mammal specimens with their essential phenotypic traits Open
Natural history collections are repositories of biodiversity specimens that provide critical infrastructure for studies of mammals. Over the past 3 decades, digitization of collections has opened up the temporal and spatial properties of s…
View article: Species Limits and Hybridization in Andean Leaf‐Eared Mice ( <i>Phyllotis</i> )
Species Limits and Hybridization in Andean Leaf‐Eared Mice ( <i>Phyllotis</i> ) Open
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 mountai…
View article: Harnessing natural history collections for collaborative pandemic preparedness
Harnessing natural history collections for collaborative pandemic preparedness Open
View article: Genetically distinct hantaviruses in two bat species in Panamá
Genetically distinct hantaviruses in two bat species in Panamá Open
Recent discoveries of hantaviruses in bats in Europe, Asia, and Africa have prompted expanded explorations of their host diversity and geographic distribution. In screening lung tissue of 218 bats from Panamá, representing 19 genera and fi…
View article: Global natural history infrastructure requires international solidarity, support, and investment in local capacity
Global natural history infrastructure requires international solidarity, support, and investment in local capacity Open
Amid global challenges like climate change, extinctions, and disease epidemics, science and society require nuanced, international solutions that are grounded in robust, interdisciplinary perspectives and datasets that span deep time. Natu…
View article: A human pathogenic hantavirus circulates and is shed in taxonomically diverse rodent reservoirs
A human pathogenic hantavirus circulates and is shed in taxonomically diverse rodent reservoirs Open
Background Orthohantaviruses are negative-sense RNA viruses that can cause hantavirus cardiopulmonary syndrome (HCPS) in humans. In the United States, Sin Nombre orthohantavirus (SNV) is the primary cause of HCPS, with a fatality rate of 3…
View article: Integrative species delimitation reveals an Idaho-endemic ground squirrel, <i>Urocitellus idahoensis</i> (Merriam 1913)
Integrative species delimitation reveals an Idaho-endemic ground squirrel, <i>Urocitellus idahoensis</i> (Merriam 1913) Open
The “small-eared” species group of Urocitellus ground squirrels (Sciuridae: Xerinae: Marmotini) is endemic to the Great Basin, United States, and surrounding cold desert ecosystems. Most specific and subspecific lineages in this group occu…
View article: Design, development, and implementation of IsoBank: A centralized repository for isotopic data
Design, development, and implementation of IsoBank: A centralized repository for isotopic data Open
Stable isotope data have made pivotal contributions to nearly every discipline of the physical and natural sciences. As the generation and application of stable isotope data continues to grow exponentially, so does the need for a unifying …
View article: Species limits and hybridization in Andean leaf-eared mice (<i>Phyllotis</i>)
Species limits and hybridization in Andean leaf-eared mice (<i>Phyllotis</i>) Open
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 mountai…
View article: Selecting sites for strategic surveillance of zoonotic pathogens: a case study in Panamá
Selecting sites for strategic surveillance of zoonotic pathogens: a case study in Panamá Open
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…
View article: Phylogeography of mammals in Southeast Alaska and implications for management of the Tongass National Forest
Phylogeography of mammals in Southeast Alaska and implications for management of the Tongass National Forest Open
Insular evolution on archipelagos generates a significant proportion of global biodiversity, yet islands are among the ecosystems most sensitive to accelerating anthropogenic disturbance, introductions of non‐native species, and emerging p…
View article: Ecological displacement in a Rocky Mountain hybrid zone informs management of North American martens (Martes)
Ecological displacement in a Rocky Mountain hybrid zone informs management of North American martens (Martes) Open
Context Parapatric sister species are ideal for tests of ecological interactions. Pacific ( Martes caurina ) and American pine ( M. americana ) martens are economically and culturally valuable furbearers that hybridize in the north-central…
View article: Author Correction: Climate warming restructures food webs and carbon flow in high-latitude ecosystems
Author Correction: Climate warming restructures food webs and carbon flow in high-latitude ecosystems Open
View article: Epigenetic predictors of species maximum life span and other life-history traits in mammals
Epigenetic predictors of species maximum life span and other life-history traits in mammals Open
By analyzing 15,000 samples from 348 mammalian species, we derive DNA methylation (DNAm) predictors of maximum life span ( R = 0.89), gestation time ( R = 0.96), and age at sexual maturity ( R = 0.85). Our maximum life-span predictor indic…
View article: Arctos: Community-driven innovations for managing natural and cultural history collections
Arctos: Community-driven innovations for managing natural and cultural history collections Open
More than tools for managing physical and digital objects, museum collection management systems (CMS) serve as platforms for structuring, integrating, and making accessible the rich data embodied by natural history collections. Here we des…
View article: Uncovering further diversity of Ochoterenatrema Caballero, 1943 (Digenea: Lecithodendriidae) in South American bats
Uncovering further diversity of Ochoterenatrema Caballero, 1943 (Digenea: Lecithodendriidae) in South American bats Open
Ochoterenatrema Caballero, 1943 is a genus of lecithodendriid digeneans that prior to this study included 8 species parasitic in bats in the Western Hemisphere. Species of Ochoterenatrema possess a unique morphological feature in form of t…
View article: Genome sequencing identifies “Limestone Canyon virus” as Montaño virus (Hantaviridae: Orthohantavirus montanoense) circulating in brush deermice in New Mexico
Genome sequencing identifies “Limestone Canyon virus” as Montaño virus (Hantaviridae: Orthohantavirus montanoense) circulating in brush deermice in New Mexico Open
Orthohantaviruses infect distinct eulipotyphlan and rodent reservoirs throughout the world; some rodent orthohantaviruses can cause disease in humans. In the United States, a primary rodent reservoir for the human-pathogenic Sin Nombre vir…
View article: Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories
Choclo virus (CHOV) recovered from deep metatranscriptomics of archived frozen tissues in natural history biorepositories Open
Background Hantaviruses are negative-stranded RNA viruses that can sometimes cause severe disease in humans; however, they are maintained in mammalian host populations without causing harm. In Panama, sigmodontine rodents serve as hosts to…
View article: Publisher Correction: Climate warming restructures food webs and carbon flow in high-latitude ecosystems
Publisher Correction: Climate warming restructures food webs and carbon flow in high-latitude ecosystems Open
View article: Arctos: Community-driven innovations for managing biodiversity and cultural collections
Arctos: Community-driven innovations for managing biodiversity and cultural collections Open
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 i…
View article: Specimen collection is essential for modern science
Specimen collection is essential for modern science Open
Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying w…
View article: Extraordinary levels of per- and polyfluoroalkyl substances (PFAS) in vertebrate animals at a New Mexico desert oasis: multiple pathways for wildlife and human exposure
Extraordinary levels of per- and polyfluoroalkyl substances (PFAS) in vertebrate animals at a New Mexico desert oasis: multiple pathways for wildlife and human exposure Open
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 milita…
View article: Choclo virus (CHOV) recovered from deep metatranscriptomics of archived museum tissues
Choclo virus (CHOV) recovered from deep metatranscriptomics of archived museum tissues Open
Background Hantaviruses 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 tran…
View article: DNA methylation networks underlying mammalian traits
DNA methylation networks underlying mammalian traits Open
Using DNA methylation profiles ( n = 15,456) from 348 mammalian species, we constructed phyloepigenetic trees that bear marked similarities to traditional phylogenetic ones. Using unsupervised clustering across all samples, we identified 5…
View article: Reply letter to “Cost-effectiveness of influenza vaccination with a high dose quadrivalent vaccine of the elderly population in Belgium, Finland, and Portugal”
Reply letter to “Cost-effectiveness of influenza vaccination with a high dose quadrivalent vaccine of the elderly population in Belgium, Finland, and Portugal” Open
Keywords: standard-dose quadrivalent influenza vaccinehigh-dose quadrivalent influenza vaccinecost effectivenessinfluenza vaccinationolder adultsJEL codes: C52C5CD61D6D
View article: Hantavirus in Panama: Twenty Years of Epidemiological Surveillance Experience
Hantavirus in Panama: Twenty Years of Epidemiological Surveillance Experience Open
Twenty years have passed since the emergence of hantavirus zoonosis in Panama at the beginning of this millennium. We provide an overview of epidemiological surveillance of hantavirus disease (hantavirus pulmonary syndrome and hantavirus f…
View article: Two Decades of Wildlife Pathogen Surveillance: Case Study of Choclo orthohantavirus and Its Wild Reservoir Oligoryzomys costaricensis
Two Decades of Wildlife Pathogen Surveillance: Case Study of Choclo orthohantavirus and Its Wild Reservoir Oligoryzomys costaricensis Open
The Costa Rican pygmy rice rat (Oligoryzomys costaricensis) is the primary reservoir of Choclo orthohantavirus (CHOV), the causal agent of hantavirus disease, pulmonary syndrome, and fever in humans in Panama. Since the emergence of CHOV i…
View article: Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens
Advancing the central role of non-model biorepositories in predictive modeling of emerging pathogens Open
The COVID-19 pandemic demonstrated the insufficiency of a reactive approach to emerging zoonotic pathogens. With spillover increasing in frequency as environments change and the human footprint continues to grow, pandemic prevention will r…