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Joseph A. Cook

Publications and source records attributed to Joseph A. Cook.

At least 19 recordsLinked to original sources
USGS2024

Design, development, and implementation of IsoBank: A centralized repository for isotopic data

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 data repository to improve accessibility and promote collaborative engagement. This paper provides an overview of the design, development, and implementation of IsoBank , a community-driven initiative to create an open-access repository for stable isotope data implemented online in 2021. A central goal of IsoBank is to provide a web-accessible database supporting interdisciplinary stable isotope research and educational opportunities. To achieve this goal, we convened a multi-disciplinary group of over 40 analytical experts, stable isotope researchers, database managers, and web developers to collaboratively design the database. This paper outlines the main features of IsoBank and provides a focused description of the core metadata structure. We present plans for future database and tool development and engagement across the scientific community. These efforts will help facilitate interdisciplinary collaboration among the many users of stable isotopic data while also offering useful data resources and standardization of metadata reporting across eco-geoinformatics landscapes.

PLoS ONE↗
USGS2023

Ancient bears provide insights into Pleistocene ice age refugia in Southeast Alaska

During the Late Pleistocene, major parts of North America were periodically covered by ice sheets. However, there are still questions about whether ice-free refugia were present in the Alexander Archipelago along the Southeast (SE) Alaska coast during the last glacial maximum (LGM). Numerous subfossils have been recovered from caves in SE Alaska, including American black ( Ursus americanus ) and brown ( U. arctos ) bears, which today are found in the Alexander Archipelago but are genetically distinct from mainland bear populations. Hence, these bear species offer an ideal system to investigate long-term occupation, potential refugial survival and lineage turnover. Here, we present genetic analyses based on 99 new complete mitochondrial genomes from ancient and modern brown and black bears spanning the last ~45,000 years. Black bears form two SE Alaskan subclades, one preglacial and another postglacial, that diverged >100,000 years ago. All postglacial ancient brown bears are closely related to modern brown bears in the archipelago, while a single preglacial brown bear is found in a distantly related clade. A hiatus in the bear subfossil record around the LGM and the deep split of their pre- and postglacial subclades fail to support a hypothesis of continuous occupancy in SE Alaska throughout the LGM for either species. Our results are consistent with an absence of refugia along the SE Alaska coast, but indicate that vegetation quickly expanded after deglaciation, allowing bears to recolonize the area after a short-lived LGM peak.

Alaska↗
USGS2021

Dynamic landscapes in northwestern North America structured populations of wolverines (Gulo gulo)

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 Alaska, coastal Southeast Alaska, and mainland western Canada using nuclear microsatellite genotypes and sequence data from the mitochondrial DNA (mtDNA) control region and Cytochrome b ( Cytb ) gene. Data from maternally inherited mtDNA reflect stable populations in Northwest Alaska, suggesting the region harbored wolverine populations since at least the Last Glacial Maximum (LGM; 21 Kya), consistent with their persistence in the fossil record of Beringia. Populations in Southeast Alaska are characterized by minimal divergence, with no genetic signature of long-term refugial persistence (consistent with the lack of pre-Holocene fossil records there). The Kenai Peninsula population exhibits mixed signatures depending on marker type: mtDNA data indicate stability (i.e., historical persistence) and include a private haplotype, whereas biparentally inherited microsatellites exhibit relatively low variation and a lack of private alleles consistent with a more recent Holocene colonization of the peninsula. Our genetic work is largely consistent with the early 20 th century taxonomic hypothesis that wolverines on the Kenai Peninsula belong to a distinct subspecies. Our finding of significant genetic differentiation of wolverines inhabiting the Kenai Peninsula, coupled with the peninsula’s burgeoning human population and the wolverine’s known sensitivity to anthropogenic impacts, provides valuable foundational data that can be used to inform conservation and management prescriptions for wolverines inhabiting these landscapes.

Alaska, British Columbia, Northwest Territories, N↗
USGS2021

Whole‐genome resequencing reveals persistence of forest‐associated mammals in Late Pleistocene refugia along North America’s North Pacific Coast

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 sequences now enable detailed analysis of the demographic and evolutionary histories of refugial taxa. Here, we use genomic data to test spatial and temporal processes of diversification among martens with respect to the Coastal Refugium Hypothesis, to understand the role of climate cycling in shaping diversity across complex landscapes. Location North America and North Pacific Coast archipelagos. Taxon North American martens ( Martes ). Methods Short‐read whole‐genome resequencing data were generated for 11 martens: four M. americana , four M. caurina , two hybrids, and one outgroup ( Martes zibellina ). Sampling was representative of known genetic clades within New World martens, including sampling within insular and continental hybrid zones and along the North Pacific Coast (five island populations). ADMIXTURE , F‐statistics, and D ‐statistics (ABBA‐BABA) were used to identify introgression and infer directionality. Heterozygosity densities, estimated via PSMC, were used to characterize historical demography at and below the species level to infer refugial and colonization processes. Results Forest‐associated Pacific martens ( M. caurina ) are divided into distinct insular and continental clades consistent with the Coastal Refugium Hypothesis. There was no evidence of introgression on islands that received historical translocations of American pine martens ( M. americana ), but introgression was detected in two active zones of secondary contact: one insular and one continental. Only early‐generational hybrids were identified across multiple hybrid zones, a pattern consistent with potential genetic swamping of M. caurina by M. americana . Main conclusions Despite an incomplete fossil record, genomic evidence supports the persistence of forest‐associated martens, likely the insular Pacific marten lineage, along the western edges of the Alexander Archipelago during the Last Glacial Maximum. This discovery informs our understanding of refugial paleoenvironments, critical to interpreting refugial timing, duration, and community composition. Genomic reevaluations of other taxa along North America's North Pacific Coast may yield new and deeper perspectives on the history of refugial forest communities and the role of dynamic climate shifts in shaping high‐latitude diversity across complex insular landscapes.

Alaska, British Columbia, California, Oregon, Wash↗
USGS2020

Microbiomes from biorepositories? 16S rRNA bacterial amplicon sequencing of archived and contemporary intestinal samples of wild mammals (Eulipotyphla: Soricidae)

Interest in gut microbial community composition has exploded recently as a result of the increasing ability to characterize these organisms and a growing understanding of their role in host fitness. New technologies, such as next generation amplicon (16S rRNA) sequencing, have enabled identification of bacterial communities from samples of diverse origin (e.g., fecal, skin, genital, environmental, etc.). Relatively little work, however, has explored the feasibility of utilizing historical samples (e.g., museum archived samples) of varying age, quality, and preservation type. Because natural history collections span multiple decades, these biorepositories have the potential to provide fundamental historical baselines to measure and better understand biodiversity on a changing planet. Utilizing even a small proportion of museum specimens could provide a means of sampling past microbial communities, allowing for direct comparison to contemporary communities and more complete understanding of dynamic shifts through time. We examined the feasibility of obtaining 16S rRNA amplicon microbiome data from whole gastrointestinal tracts (GIs) of shrews of varying age and preservation method, including 5 freshly collected shrew GIs immediately fixed in liquid nitrogen (LN2), 10 ten-year old shrew GIs frozen at −20°C (whole animal), and 10 shrews of varying ages (4 from 1968, 1 from 1980, 1 from 2001, 1 from 2004, 1 from 2007, 1 from 2011 and 2 from 2013) fixed and stored whole in 70% ethanol. Not surprisingly, results of 16S rDNA amplicon sequencing reveal significantly different bacterial communities between different preservation techniques and age of samples. Ten-year old frozen samples had bacterial communities most similar to freshly collected (LN2) samples, while the bacterial communities of both were significantly different from the 70% ethanol preserved samples of various ages. Amongst those preserved in 70% ethanol, age of samples also influenced bacterial community composition. Additionally, we compare results of OTU based and ASV based analyses. Looking ahead, field collectors and museums should develop and adopt best practices related to frozen preservation to ensure adequate material for future microbiome investigations.

Frontiers in Ecology and Evolution↗
USGS2020

Conservation genomics in a changing arctic

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 crucial for conservation and sustainable economic development. Genomic approaches are providing transformative insights into biotic responses to environmental change, but have seen limited application in the Arctic due to a series of limitations. To meet the promise of genome analyses, we urge rigorous development of biorepositories from high latitudes to provide essential libraries to improve the conservation, monitoring, and management of Arctic ecosystems through genomic approaches.

Trends in Ecology and Evolution↗
USGS2018

Implications of introgression for wildlife translocations: the case of North American martens

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 shaped by a complex history of natural, post-glacial population expansion followed by a series of anthropogenic introductions. In some cases, both natural colonization and translocations facilitated secondary contact, offering a series of replicated experiments that demonstrate how introgression, in these cases following isolation (insular and refugial), shapes genetic diversity. We test whether genetic exchange is occurring between North American marten species using mitochondrial genomes and ten nuclear loci. We present evidence of biased nuclear introgression from M. caurina into M. americana across two natural hybrid zones (insular and mainland) and found no remnant evidence of M. caurina on islands that received M. americana translocations, suggesting prior absence, potential extirpation, or genetic swamping of M. caurina from these islands. Our results highlight the importance of understanding phylogeographic variation prior to identifying source populations for wildlife translocations and caution the use of genetic rescue for North American marten populations. Although previously managed as a single species, these two species show substantial genetic divergence. When the two are placed into contact, they exhibit unidirectional, asymmetric introgression with potentially negative consequences for M. caurina , underscoring the value of mindful consideration of introgression in wildlife management.

Conservation Genetics↗
USGS2018

Whole-genome analysis of Mustela erminea finds that pulsed hybridization impacts evolution at high latitudes

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 flow. To understand how recurrent periods of isolation and contact may have impacted evolution at high latitudes, we investigated introgression dynamics in the stoat ( Mustela erminea ), a Holarctic mammalian carnivore, using whole-genome sequences. We identify two spatio-temporally distinct episodes of introgression coincident with large-scale climatic shifts: contemporary introgression in a mainland contact zone and ancient contact ~200 km south of the contemporary zone, in the archipelagos along North America’s North Pacific Coast. Repeated episodes of gene flow highlight the central role of cyclic climates in structuring high-latitude diversity, through refugial divergence and introgressive hybridization. When introgression is followed by allopatric isolation (e.g., insularization) it may ultimately expedite divergence.

Communications Biology↗
USGS2018

Museum metabarcoding: a novel method revealing gut helminth communities of small mammals across space and time

Natural history collections spanning multiple decades provide fundamental historical baselines to measure and understand changing biodiversity. New technologies such as next generation DNA sequencing (NGS) have considerably increased the potential of museum specimens to address significant questions regarding the impact of environmental changes on host and parasite/pathogen dynamics. We developed a new technique to identify intestinal helminth parasites and applied it to shrews (Eulipotyphla: Soricidae) because they are ubiquitous, occupy diverse habitats, and host a diverse and abundant parasite fauna. Notably, we included museum specimens preserved in various ways to explore the efficacy of using metabarcoding analyses that may enable identification of helminth symbiont communities from historical archives. We successfully sequenced the parasite communities (using 12S mtDNA, 16S mtDNA, 28S rDNA) of 23 whole gastrointestinal (GI) tracts. All GI tracts were obtained from the Museum of Southwestern Biology (MSB), USA, and from recent field collections, varying both in time since fixation (ranging from 4 months to 16 years) and preservation method (70% or 95% ethanol stored at room temperature, or flash frozen in liquid nitrogen and stored at -80°C). Our proof of concept demonstrates the feasibility of applying NGS techniques to authoritatively identify the parasite/pathogen communities within whole GI tracts from museum specimens of varying age and fixation, and the value of future preservation of host-associated whole GI tracts in public research archives. This powerful approach facilitates future comparative examinations of the distributions and interactions among multiple associated groups of organisms through time and space.

International Journal for Parasitology↗
USGS2017

Historical biogeography sets the foundation for contemporary conservation of martens (genus Martes) in northwestern North America

Effective conservation of insular populations requires careful consideration of biogeography, including colonization histories and patterns of endemism. Across the Pacific Northwest of North America, Pacific martens ( Martes caurina ) and American pine martens ( Martes americana ) are parapatric sister species with distinctive postglacial histories. Using mitochondrial DNA and 12 nuclear microsatellite loci, we examine processes of island colonization and anthropogenic introductions across 25 populations of martens. Along the North Pacific Coast (NPC), M. caurina is now found on only 2 islands, whereas M. americana occurs on mainland Alaska and British Columbia and multiple associated islands. Island populations of M. caurina have a longer history of isolation reflected in divergent haplotypes, private microsatellite alleles, and relatively low within-population diversity. In contrast, insular M. americana have lower among-population divergence and higher metrics of within-population diversity. On some NPC islands, introductions of M. americana may be related to decline of M. caurina . Long-term persistence of these species likely has been influenced by anthropogenic manipulations, including wildlife translocations and industrial-scale deforestation, yet, the distinctive histories of these martens have not been incorporated into natural resource policies.

Journal of Mammalogy↗
USGS2017

Opinion: Why we need a centralized repository for isotopic data

Stable isotopes encode and integrate the origin of matter; thus, their analysis offers tremendous potential to address questions across diverse scientific disciplines ( 1 , 2 ). Indeed, the broad applicability of stable isotopes, coupled with advancements in high-throughput analysis, have created a scientific field that is growing exponentially, and generating data at a rate paralleling the explosive rise of DNA sequencing and genomics ( 3 ). Centralized data repositories, such as GenBank, have become increasingly important as a means for archiving information, and “Big Data” analytics of these resources are revolutionizing science and everyday life.

Proceedings of the National Academy of Sciences of↗
USGS2017

The Beringian coevolution project: Holistic collections of mammals and associated parasites reveal novel perspectives on evolutionary and environmental change in the North

The Beringian Coevolution Project (BCP), a field program underway in the high northern latitudes since 1999, has focused on building key scientific infrastructure for integrated specimen-based studies on mammals and their associated parasites. BCP has contributed new insights across temporal and spatial scales into how ancient climate and environmental change have shaped faunas, emphasizing processes of assembly, persistence, and diversification across the vast Beringian region. BCP collections also represent baseline records of biotic diversity from across the northern high latitudes at a time of accelerated environmental change. These specimens and associated data form an unmatched resource for identifying hidden diversity, interpreting past responses to climate oscillations, documenting contemporary conditions, and anticipating outcomes for complex biological systems in a regime of ecological perturbation. Because of its dual focus on hosts and parasites, the BCP record also provides a foundation for comparative analyses that can document the effects of dynamic change on the geographic distribution, transmission dynamics, and emergence of pathogens. By using specific examples from carnivores, shrews, lagomorphs, rodents and their associated parasites, we demonstrate how broad, integrated field collections provide permanent infrastructure that informs policy decisions regarding human impact and the effect of climate change on natural populations.

Arctic Science↗
USGS2017

Small mammals as indicators of climate, biodiversity, and ecosystem change

Climate is a driving evolutionary force for biodiversity in high-latitude Alaska. This region is complex and dynamic with high annual variation in temperature and light. Through deeper time, Alaska has experienced major climate extremes over much longer periodicity. For example, the Quaternary Period (the last ~2.5 million years), commonly known as the Ice Age, was punctuated by more than 20 major glacial-interglacial cycles. During glacial phases, water was locked up in ice sheets that covered much of North America, and the resulting lower sea levels exposed a land connection between Alaska and Siberia, a combined region known as Beringia (Figure 1). This isthmus provided vast expanses of land for species to inhabit, provided they could withstand potentially harsh polar conditions. Each extended glacial phase periodically transitioned into a shorter interglacial warm phase. These climate reversals melted continental ice sheets to expose corridors for reinvasion of terrestrial species, particularly those associated with forested habitats further south. Those species that survived at northern latitudes through repeated glacial-interglacial cycles formed the Arctic tundra communities that persist today. At present, Alaska supports diverse communities associated with both tundra and forests (Figure 2). These communities often interact with one another across latitudinal and elevational gradients, with tundra species generally found further north or higher in elevation. Alaska’s climate is continuing to change today, strongly influencing local environments and the distribution and dynamics of wildlife species.

Alaska, Siberia↗
USGS2014

Multilocus phylogeography and systematic revision of North American water shrews (genus: Sorex )

North American water shrews, which have traditionally included Sorex alaskanus , S. bendirii , and S. palustris , are widely distributed through Nearctic boreal forests and adapted for life in semiaquatic environments. Molecular mitochondrial signatures for these species have recorded an evolutionary history with variable levels of regional divergence, suggesting a strong role of Quaternary environmental change in speciation processes. We expanded molecular analyses, including more-comprehensive rangewide sampling of specimens representing North American water shrew taxa, except S. alaskanus , and sequencing of 4 independent loci from the nuclear and mitochondrial genomes. We investigated relative divergence of insular populations along the North Pacific Coast, and newly recognized diversity from southwestern montane locations, potentially representing refugial isolates. Congruent independent genealogies, lack of definitive evidence for contemporary gene flow, and high support from coalescent species trees indicated differentiation of 4 major geographic lineages over multiple glacial cycles of the late Quaternary, similar to a growing number of boreal taxa. Limited divergence of insular populations suggested colonization following the last glacial. Characterization of southwestern montane diversity will require further sampling but divergence over multiple loci is indicative of a relictual sky-island fauna. We have reviewed and revised North American water shrew taxonomy including the recognition of 3 species within what was previously known as S. palustris . The possibility of gene flow between most distantly related North American water shrew lineages coupled with unresolved early diversification of this group and other sibling species reflects a complex but potentially productive system for investigating speciation processes.

Journal of Mammalogy↗
USGS2014

Accounting for rate variation among lineages in comparative demographic analyses

Genetic analyses of contemporary populations can be used to estimate the demographic histories of species within an ecological community. Comparison of these demographic histories can shed light on community responses to past climatic events. However, species experience different rates of molecular evolution, and this presents a major obstacle to comparative demographic analyses. We address this problem by using a Bayesian relaxed-clock method to estimate the relative evolutionary rates of 22 small mammal taxa distributed across northwestern North America. We found that estimates of the relative molecular substitution rate for each taxon were consistent across the range of sampling schemes that we compared. Using three different reference rates, we rescaled the relative rates so that they could be used to estimate absolute evolutionary timescales. Accounting for rate variation among taxa led to temporal shifts in our skyline-plot estimates of demographic history, highlighting both uniform and idiosyncratic evolutionary responses to directional climate trends for distinct ecological subsets of the small mammal community. Our approach can be used in evolutionary analyses of populations from multiple species, including comparative demographic studies.

Evolution↗
USGS2013

A multilocus evaluation of ermine ( Mustela erminea ) across the Holarctic, testing hypotheses of Pleistocene diversification in response to climate change

Aim: We examined data for ermine (Mustela erminea) to test two sets of diversification hypotheses concerning the number and location of late Pleistocene refugia, the timing and mode of diversification, and the evolutionary influence of insularization. Location: Temperate and sub-Arctic Northern Hemisphere. Methods: We used up to two mitochondrial and four nuclear loci from 237 specimens for statistical phylogeographical and demographic analyses. Coalescent species-tree estimation used a Bayesian approach for clade divergence based on external mutation rate calibrations. Approximate Bayesian methods were used to assess population size, timing of divergence and gene flow. Results: Limited structure coupled with evidence of population growth across broad regions, including previously ice-covered areas, indicated expansion from multiple centres of differentiation, but high endemism along the North Pacific coast (NPC). A bifurcating model of diversification with recent growth spanning three glacial cycles best explained the empirical data. Main conclusions: A newly identified clade in North America indicated a fourth refugial area for ermine. The shallow coalescence of all extant ermine reflects a recent history of diversification overlying a deeper fossil record. Post-glacial colonization has led to potential contact zones for multiple lineages in north-western North America. A model of diversification of ermine accompanied by recent gene flow was marginally less well supported than a model of divergence of major clades in response to the most recent glacial cycles.

Journal of Biogeography↗