Joseph A Cook

Joseph A Cook
University of New Mexico | UNM · Department of Biology

PhD

About

480
Publications
124,456
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8,622
Citations

Publications

Publications (480)
Article
The sucking louse fauna associated with Mongolian mammals is inadequately known. We provide a list of 25 species of sucking lice recorded from Mongolian rodents including previously published records, and new records of specimens collected during an expedition to northwestern Mongolia in 2015. Hoplopleura inagakii Ono and Hasegawa and Polyplax cric...
Article
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Zoos and natural history museums are both collections-based institutions with important missions in biodiversity research and education. Animals in zoos are a repository and living record of the world's biodiversity, whereas natural history museums are a permanent historical record of snapshots of biodiversity in time. Surprisingly, despite signifi...
Article
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Orthohantaviruses are negative-stranded RNA viruses with trisegmented genomes that can cause severe disease in humans and are carried by several host reservoirs throughout the world. Old World orthohantaviruses are primarily located throughout Europe and Asia, causing hemorrhagic fever with renal syndrome, and New World orthohantaviruses are found...
Article
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Aim: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroeco...
Article
Resolution of rapid evolutionary radiations requires harvesting maximal signal from phylogenomic datasets. However, studies of non-model clades often target conserved loci that are characterized by reduced information content, which can negatively affect gene tree precision and species tree accuracy. Single nucleotide polymorphism (SNP)-based metho...
Article
Sin Nombre orthohantavirus (SNV), a negative-sense, single-stranded RNA virus that is carried and transmitted by the North American deer mouse Peromyscus maniculatus , can cause infection in humans through inhalation of aerosolized excreta from infected rodents. This infection can lead to hantavirus cardiopulmonary syndrome (HCPS), which has a ∼36%...
Article
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The discovery of genetically distinct hantaviruses (family Hantaviridae) in multiple species of shrews, moles and bats has revealed a complex evolutionary history involving cross-species transmission. Seewis virus (SWSV) is widely distributed throughout the geographic ranges of its soricid hosts, including the Eurasian common shrew (Sorex araneus),...
Article
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The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic reveals a major gap in global biosecurity infrastructure: a lack of publicly available biological samples representative across space, time, and taxonomic diversity. The shortfall, in this case for vertebrates, prevents accurate and rapid identification and monitoring of emer...
Article
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Cyclic climatic and glacial fluctuations of the Late Quaternary produced a dynamic biogeographic history for high latitudes. To refine our understanding of this history in northwestern North America, we explored geographic structure in a wide-ranging carnivore, the wolverine (Gulo gulo). We examined genetic variation in populations across mainland...
Article
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Aim Refugial isolation during glaciation is an established driver of speciation; however, the opposing role of interglacial population expansion, secondary contact, and gene flow on the diversification process remains less understood. The consequences of glacial cycling on diversity are complex and especially so for archipelago species, which exper...
Article
Aim Numerous glacial refugia have been hypothesized along North America's North Pacific Coast that may have increased divergence of refugial taxa, leading to elevated endemism and subsequently clustered hybrid zones following deglaciation. The locations and community composition of these ice‐free areas remains controversial, but whole‐genome sequen...
Article
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Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host spec...
Article
The evolution of obligate parasites is often interpreted in light of their hosts' evolutionary history. An expanded approach is to examine the histories of multiple lineages of parasites that inhabit similar environments on a particular host lineage. Western North American chipmunks (genus Tamias) have a broad distribution, a history of divergence...
Article
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Sydney Anderson and the "Mammalian Diversity in Bolivia" (MDB) project (1984-1993) established a highly productive model for integrated specimen-based field expeditions. We assess the extended impact of that decade-long series of holistic surveys of mammalian diversity as a productive model for building enduring and highly integrated infrastructure...
Article
Aim We test the predictions of the Stockholm Paradigm, a synthesis of eco‐evolutionary theory explaining the nature of faunal assembly, host range and parasite diversification. Faunal diversification and assembly, manifested in patterns of host colonization, co‐adaptation and parasite speciation, are predicted to emerge as a consequence of alternat...
Article
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https://www.researchgate.net/deref/https%3A%2F%2Facademic.oup.com%2Fbioscience%2Farticle%2Fdoi%2F10.1093%2Fbiosci%2Fbiaa064%2F5857068
Article
The Stockholm Paradigm suggests that the capacity for pathogens to be associated with a given host is related to the occurrence of specific traits possessed by the host that represent required resources for the pathogen. The capacity for a pathogen to be associated with more than one host is related to how phylogenetically widespread those same res...
Article
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Introduction On 30 January 2020, the World Health Organization (WHO) declared a Global Health Emergency of international concern attendant to the emergence and spread of SARS-CoV-2, nearly two months after the first reported emergence of human cases in Wuhan, China. In the subsequent two months, global, national and local health personnel and infra...
Preprint
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Molecular studies of Neotropical Myotis (Chiroptera, Vespertilionidae) in the last decade have uncovered substantial cryptic diversity. One example is M. keaysi pilosatibialis, which is characterized by a complex taxonomy derived from low morphological variation. Herein, we studied cryptic diversity of a high elevation clade from premontane and mon...
Article
Conservation efforts rely on robust taxonomic assessments that should be based on critical assessment of interspecific boundaries, infraspecific variation, and potentially distinctive peripheral populations. The meadow vole (Microtus pennsylvanicus) is widely distributed across North America, including 28 morphologically defined subspecies and nume...
Article
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Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization—the conversion of specimen data into accessible digital content—has greatly expanded the use of NHC collections across a diversity of disciplines....
Article
Full-text available
Natural history museums are unique spaces for interdisciplinary research and educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they can provide a place-based window to focus on integration of science and discovery, as well...
Article
Although logistically challenging to study, the Arctic is a bellwether for global change and is becoming a model for questions pertinent to the persistence of biodiversity. Disruption of Arctic ecosystems is accelerating, with impacts ranging from mixing of biotic communities to individual behavioral responses. Understanding these changes is crucia...
Article
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The Systematic Collections Committee of the American Society of Mammalogists advises curators and other personnel affiliated with natural history collections in matters relating to administration, curation, and accreditation of mammal specimens and their associated data. The Systematic Collections Committee also maintains a list of curatorial stand...
Article
Full-text available
With the recent discovery of genetically distinct hantaviruses (family Hantaviridae) in shrews (order Eulipotyphla, family Soricidae), the once-conventional view that rodents (order Rodentia) served as the primordial reservoir hosts now appears improbable. The newly identified soricid-borne hantaviruses generally demonstrate well-resolved lineages...
Preprint
Full-text available
Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines....
Preprint
Full-text available
Natural history collections (NHCs) are the foundation of historical baselines for assessing anthropogenic impacts on biodiversity. Along these lines, the online mobilization of specimens via digitization–the conversion of specimen data into accessible digital content–has greatly expanded the use of NHC collections across a diversity of disciplines....
Article
Full-text available
Orthohantaviruses are tightly linked to the ecology and evolutionary history of their mammalian hosts. We hypothesized that in regions with dramatic climate shifts throughout the Quaternary, orthohantavirus diversity and evolution are shaped by dynamic host responses to environmental change through processes such as host isolation, host switching,...
Article
Members of the genus Linognathoides are ectoparasites of ground squirrels and marmots (Rodentia: Sciuridae) in the Nearctic, Palearctic, and Afrotropical regions. Linognathoides urocitelli n. sp. is described based on adult male and female and third-instar nymphal specimens collected from the long-tailed ground squirrel (Urocitellus undulatus) in M...
Article
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Museum specimens play an increasingly important role in predicting the outcomes and revealing the consequences of anthropogenically driven disruption of the biosphere. As ecological communities respond to ongoing environmental change, host-parasite interactions are also altered. This shifting landscape of host-parasite associations creates opportun...
Preprint
Full-text available
Natural history museums are unique spaces for interdisciplinary research and for educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they provide a place-based window to focus on integration of science and discovery, as well...
Preprint
Full-text available
Natural history museums are unique spaces for interdisciplinary research and for educational innovation. Through extensive exhibits and public programming and by hosting rich communities of amateurs, students, and researchers at all stages of their careers, they provide a place-based window to focus on integration of science and discovery, as well...
Article
Full-text available
The evolutionary consequences of natural introgression provide a rare opportunity to retrospectively evaluate how the introduction of exotics or genetic rescue efforts may impact endemic faunas. Phylogeographic structure among mainland, endemic insular, and introduced North American marten (Martes americana and M. caurina) populations have been sha...
Article
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Although islands are of long‐standing interest to biologists, only a handful of studies have investigated the role of climatic history in shaping evolutionary diversification in high‐latitude archipelagos. In this study of the Alexander Archipelago (AA) of Southeast Alaska, we address the impact of glacial cycles on geographic genetic structure for...
Article
Full-text available
Natural history museums and the specimen collections they curate are vital scientific infrastructure, a fact as true today as it was when biologists began collecting and preserving specimens over 200 years ago. The importance of museum specimens in studies of taxonomy, systematics, ecology and evolutionary biology is evidenced by a rich and abundan...
Preprint
Full-text available
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, conte...
Article
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Proechimys pattoni da Silva, 1998 is one of the 3 small-bodied species of Proechimys and its geographic range is only known in western Brazil and eastern and southern Peru. However, based on morphological and molecular analyses, we report P. pattoni from the lowland forest of Bolivia (Pando: Rio Madre de Dios, near San Rosa). This is the first repo...
Article
Molecular investigations recently resurrected the Pacific marten (Martes caurina) as a species distinct from the American pine marten (M. americana). Previously, 2 hybrid zones for these species were identified, 1 in the northern Rocky Mountains and another on Kuiu Island off the coast of Southeast Alaska. We test the molecular perspectives on spec...
Article
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Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds...
Article
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Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host a...
Article
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Phylogenomic datasets are illuminating many areas of the Tree of Life. However, the large size of these datasets alone may be insufficient to resolve problematic nodes in the most rapid evolutionary radiations, because inferences in zones of extraordinarily low phylogenetic signal can be sensitive to the model and method of inference, as well as th...
Article
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Natural history collections have stimulated insights into systematics and evolution, but the extensive biodiversity sampling held in museums is increasingly employed to address other critical societal concerns, especially those related to changing environmental conditions on our planet. Due to large-scale digitization efforts in the last decade, sp...
Article
Full-text available
The last 50 years have witnessed rapid changes in the ways that natural history specimens are collected, preserved, analyzed, and documented. Those changes have produced unprecedented access to specimens, images, and data as well as impressive research results in organismal biology. The stage is now set for a new generation of collecting, preservin...
Article
Parasitism is a common symbiotic interaction across diverse natural systems. Using a comparative evolutionary approach, we investigated the contributions of both host phylogeny and abiotic factors toward diversification of phylogenetically independent endoparasites that inhabit essentially the same physical space. We tested for host-parasite and pa...
Article
Full-text available
At high latitudes, climatic shifts hypothetically initiate recurrent episodes of divergence by isolating populations in glacial refugia—ice-free regions that enable terrestrial species persistence. Upon glacial recession, populations subsequently expand and often come into contact with other independently diverging populations, resulting in gene fl...
Conference Paper
Full-text available
Arctos (https://arctosdb.org), an online collection management information system, was developed in 1999 to manage museum specimen data and to make those data publicly available. The portal (arctos.database.museum) now serves data on over 3.5 million cataloged specimens from more than 130 collections throughout North America in an instance at the T...
Article
Full-text available
Impacts of Quaternary environmental changes on mammal faunas of central Asia remain poorly understood due to a lack of geographically comprehensive phylogeographic sampling for most species. To help address this knowledge gap, we conducted the most extensive molecular analysis to date of the long-tailed ground squirrel (Urocitellus undulatus Pallas...
Article
We compared isotopic niche widths of small mammals that co-occur across the Alexander Archipelago and adjacent mainland in southeastern Alaska to test the prediction that dietary niche widths will be greater for individuals living in communities with fewer potential competitors and predators. We quantified the carbon (δ¹³ C) and nitrogen (δ15 N) is...
Article
Our understanding of mechanisms operating over deep timescales to shape phenotypic diversity often hinges on linking variation in one or few trait(s) to specific evolutionary processes. When distinct processes are capable of similar phenotypic signatures, however, identifying these drivers is difficult. We explored ecomorphological evolution across...
Article
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Hantaviruses are zoonotic viruses with a complex evolutionary history of virus-host coevolution and cross-species transmission. While hantaviruses have a broad reservoir host range, virus-host relationships were previously thought to be strict, with a single virus species infecting a single host species. Here, we describe Bruges virus, a novel hant...
Article
Full-text available
Several studies have claimed that reduction in body size comprises a nearly universal response to global warming; however, doubts about the validity of this pattern for endothermic species have been raised recently. Accordingly, we assessed temporal changes in body mass for 27 bird and 17 mammal species, to evaluate if a reduction in body size duri...
Data
Appendix with supplementary Tables A and B, and supplementary Figures A, B, C and D. (DOCX)
Data
Compilation of data on body size change from 46 published studies, comprising a total of 369 populations of birds and mammals. Studies reporting the changes due to experimental manipulations, colonization of islands, or spanning over < 10 years were excluded. (XLSX)
Data
Body mass, year of collection, latitude, longitude and sex for each individual analyzed in the present study (20,496 records). (XLSX)