20 results on '"Kayce C. Bell"'
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2. Sucking Lice (Phthiraptera: Anoplura) Parasitizing Mongolian Rodents with the Description of a New Species of Hoplopleura from Mountain Voles (Alticola spp.)
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Lance A, Durden, Chase, Robinson, Joseph A, Cook, Kayce C, Bell, Batsaikhan, Nyamsuren, and Stephen E, Greiman
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Male ,Mammals ,Microscopy ,Insecta ,Arthropoda ,Arvicolinae ,Biodiversity ,Enderleinellidae ,Polyplacidae ,Hoplopleuridae ,Phthiraptera ,Animals ,Animalia ,Female ,Parasitology ,Gerbillinae ,Anoplura ,Psocodea ,Ecology, Evolution, Behavior and Systematics ,Taxonomy - Abstract
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 cricetulis Chin are newly recorded from Mongolia and 2 new host associations in Mongolia are recorded for Hoplopleura acanthopus (Burmeister). We describe Hoplopleura altaiensis n. sp., from the Gobi Altai mountain vole, Alticola barakshin Bannikov (type host) with an additional specimen from Alticola strelzowi (Kastchenko) (Strelzow's mountain vole). Both sexes of the new species are illustrated with scanning electron micrographs and line drawings. We note small morphological differences in the shape of the female subgenital plate between specimens prepared for scanning electron microscopy versus those prepared for light microscopy following DNA extraction.
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- 2022
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3. Lost in a sagebrush sea: comparative genetic assessment of an isolated montane population of Tamias amoenus
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Jane Van Gunst, Marjorie D. Matocq, Kayce C. Bell, Mike B. Teglas, and Jennifer Hsueh
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0106 biological sciences ,0301 basic medicine ,education.field_of_study ,Ecology ,biology ,Population ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Tamias amoenus ,03 medical and health sciences ,030104 developmental biology ,Geography ,Genetics ,Montane ecology ,Animal Science and Zoology ,education ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
The montane sky islands of the Great Basin are characterized by unique, isolated habitats and communities that likely are vulnerable to extirpation with environmental change. A subspecies of yellow pine chipmunk, the Humboldt yellow pine chipmunk (Tamias amoenus celeris), is associated with the whitebark and limber pine forests of the Pine Forest Range (PFR) in Nevada. We sampled T. amoenus and least chipmunks (T. minimus) from the isolated PFR and compared genetic diversity between these populations and more “mainland” populations, including other subspecies of chipmunks. Given the high frequency of hybridization in Tamias, we tested for hybridization between T. amoenus and T. minimus in the PFR. We examined phylogenetic relationships, population divergence and diversity, and screened populations for a common pathogen, Borrelia hermsii, to gain insight into population health. We found T. amoenus of the PFR are closely related to T. amoenus in the Warner Mountains and Sierra Nevada, but maintain substantively lower genetic variation. Microsatellite analyses show PFR T. amoenus are highly genetically differentiated from other populations. In contrast, PFR T. minimus had higher genetic diversity that was comparable to the other T. minimus population we sampled. Pathogen screening revealed that T. amoenus carried higher pathogen loads than T. minimus in the PFR, although the prevalence of infection was similar to other Tamias populations. Our assessment of habitat associations suggests that the Humboldt yellow pine chipmunk almost entirely is restricted to the conifer systems of the PFR, while least chipmunks are prevalent in the other forests. Our work highlights the need for continued conservation and research efforts to identify how response to environmental change can be facilitated in isolated species and habitats.
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- 2021
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4. Natural history collections are critical resources for contemporary and future studies of urban evolution
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Jann E. Vendetti, Benjamin J. Adams, Allison J. Shultz, William B. Ludt, Gregory B. Pauly, and Kayce C. Bell
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0106 biological sciences ,0301 basic medicine ,trends ,Future studies ,Research methodology ,lcsh:Evolution ,urbanization ,Biology ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Urbanization ,Genetics ,lcsh:QH359-425 ,research methodology ,Environmental planning ,Ecology, Evolution, Behavior and Systematics ,Special Issue Perspectives ,Urban evolution ,Biological evolution ,Special Issue Perspective ,Natural history ,030104 developmental biology ,natural history ,biological evolution ,Research questions ,Professional association ,General Agricultural and Biological Sciences ,museums - Abstract
Urban environments are among the fastest changing habitats on the planet, and this change has evolutionary implications for the organisms inhabiting them. Herein, we demonstrate that natural history collections are critical resources for urban evolution studies. The specimens housed in these collections provide great potential for diverse types of urban evolution research, and strategic deposition of specimens and other materials from contemporary studies will determine the resources and research questions available to future urban evolutionary biologists. As natural history collections are windows into the past, they provide a crucial historical timescale for urban evolution research. While the importance of museum collections for research is generally appreciated, their utility in the study of urban evolution has not been explicitly evaluated. Here, we: (a) demonstrate that museum collections can greatly enhance urban evolution studies, (b) review patterns of specimen use and deposition in the urban evolution literature, (c) analyze how urban versus rural and native versus nonnative vertebrate species are being deposited in museum collections, and (d) make recommendations to researchers, museum professionals, scientific journal editors, funding agencies, permitting agencies, and professional societies to improve archiving policies. Our analyses of recent urban evolution studies reveal that museum specimens can be used for diverse research questions, but they are used infrequently. Further, although nearly all studies we analyzed generated resources that could be deposited in natural history collections (e.g., collected specimens), a minority (12%) of studies actually did so. Depositing such resources in collections is crucial to allow the scientific community to verify, replicate, and/or re‐visit prior research. Therefore, to ensure that adequate museum resources are available for future urban evolutionary biology research, the research community—from practicing biologists to funding agencies and professional societies—must make adjustments that prioritize the collection and deposition of urban specimens.
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- 2021
5. Genomic resolution of cryptic species diversity in chipmunks
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Nathanael D. Herrera, Kayce C. Bell, Colin M. Callahan, Erin Nordquist, Brice A. J. Sarver, Jack Sullivan, John R. Demboski, and Jeffrey M. Good
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Idaho ,Genetics ,Animals ,Hybridization, Genetic ,Sciuridae ,Genomics ,General Agricultural and Biological Sciences ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Microsatellite Repeats - Abstract
Discovery of cryptic species is essential to understanding the process of speciation and assessing the impacts of anthropogenic stressors. Here, we used genomic data to test for cryptic species diversity within an ecologically well-known radiation of North American rodents, western chipmunks (Tamias). We assembled a de novo reference genome for a single species (Tamias minimus) combined with new and published targeted sequence-capture data for 21,551 autosomal and 493 X-linked loci sampled from 121 individuals spanning 22 species. We identified at least two cryptic lineages corresponding with an isolated subspecies of least chipmunk (T. minimus grisescens) and with a restricted subspecies of the yellow-pine chipmunk (T. amoenus cratericus) known only from around the extensive Craters of the Moon lava flow. Additional population-level sequence data revealed that the so-called Crater chipmunk is a distinct species that is abundant throughout the coniferous forests of southern Idaho. This cryptic lineage does not appear to be most closely related to the ecologically and phenotypically similar yellow-pine chipmunk but does show evidence for recurrent hybridization with this and other species.
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- 2022
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6. ASM professional awards
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Kayce C. Bell and Edward J. Heske
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Ecology ,media_common.quotation_subject ,Genetics ,Animal Science and Zoology ,Gender studies ,Sociology ,Gender balance ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation ,Diversity (politics) ,media_common - Published
- 2019
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7. Building an integrated infrastructure for exploring biodiversity: field collections and archives of mammals and parasites
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Kayce C. Bell, Altangerel Tsogtsaikhan Dursahinhan, Stephen E. Greiman, Eric P. Hoberg, Albina Tsvetkova, Kurt E. Galbreath, Andrew G. Hope, F. Agustín Jiménez, Blas Armién, Fernando Torres-Pérez, Vasyl V. Tkach, Mariel L. Campbell, Jonathan L. Dunnum, Joseph A. Cook, Batsaikhan Nyamsuren, Anson V. Koehler, Ralph P. Eckerlin, Heikki Henttonen, and Scott Lyell Gardner
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0106 biological sciences ,Ecology ,necropsy ,parasitology ,010604 marine biology & hydrobiology ,Biodiversity ,emerging infectious disease ,15. Life on land ,010603 evolutionary biology ,01 natural sciences ,Field methods ,Feature Articles ,Geography ,integrated collections ,specimens ,Genetics ,field methods ,Animal Science and Zoology ,Humanities ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
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 opportunities for colonization of different hosts and emergence of new pathogens, with implications for wildlife conservation and management, public health, and other societal concerns. Integrated archives that document and preserve mammal specimens along with their communities of associated parasites and ancillary data provide a powerful resource for investigating, anticipating, and mitigating the epidemiological, ecological, and evolutionary impacts of environmental perturbation. Mammalogists who collect and archive mammal specimens have a unique opportunity to expand the scope and impact of their field work by collecting the parasites that are associated with their study organisms. We encourage mammalogists to embrace an integrated and holistic sampling paradigm and advocate for this to become standard practice for museum-based collecting. To this end, we provide a detailed, field-tested protocol to give mammalogists the tools to collect and preserve host and parasite materials that are of high quality and suitable for a range of potential downstream analyses (e.g., genetic, morphological). Finally, we also encourage increased global cooperation across taxonomic disciplines to build an integrated series of baselines and snapshots of the changing biosphere. Los especímenes de museo desempeñan un papel cada vez más importante tanto en la descripción de los resultados de la alteración antropogénica de la biosfera como en la predicción de sus consecuencias. Dado que las comunidades ecológicas responden al cambio ambiental, también se alteran las interacciones hospedador-parásito. Este panorama cambiante de asociaciones hospedador-parásito crea oportunidades para la colonización de diferentes hospedadores y para la aparición de nuevos patógenos, con implicancias en la conservación y manejo de la vida silvestre, la salud pública y otras preocupaciones de importancia para la sociedad. Archivos integrados que documentan y preservan especímenes de mamíferos junto con sus comunidades de parásitos y datos asociados, proporcionan un fuerte recurso para investigar, anticipar y mitigar los impactos epidemiológicos, ecológicos y evolutivos de las perturbaciones ambientales. Los mastozoólogos que recolectan y archivan muestras de mamíferos, tienen una oportunidad única de ampliar el alcance e impacto de su trabajo de campo mediante la recolección de los parásitos que están asociados con los organismos que estudian. Alentamos a los mastozoólogos a adoptar un paradigma de muestreo integrado y holístico y abogamos para que esto se convierta en una práctica estándarizada de la obtención de muestras para museos. Con este objetivo, proporcionamos un protocolo detallado y probado en el campo para brindar a los mastozoólogos las herramientas para recolectar y preservar materiales de parásitos y hospedadores de alta calidad y adecuados para una gran variedad de análisis subsecuentes (e.g., genéticos, morfológicos, etc.). Finalmente, también abogamos por una mayor cooperación global entre las diversas disciplinas taxonómicas para construir una serie integrada de líneas de base y registros actuales de nuestra cambiante biosfera.
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- 2019
8. Disentangling lousy relationships: Comparative phylogenomics of two sucking louse lineages parasitizing chipmunks
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Kevin P. Johnson, Joseph A. Cook, Kayce C. Bell, John R. Demboski, and Julie M. Allen
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0106 biological sciences ,0301 basic medicine ,Paraphyly ,Lineage (evolution) ,Louse ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Species Specificity ,Phylogenomics ,biology.animal ,Genetics ,Animals ,Parasites ,Clade ,Molecular Biology ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Phylogenetic tree ,biology ,Base Sequence ,Sciuridae ,biology.organism_classification ,Obligate parasite ,030104 developmental biology ,Sucking louse ,Evolutionary biology ,Anoplura - Abstract
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 with gene flow, and host two species of sucking lice (Anoplura), Hoplopleura arboricola and Neohaematopinus pacificus. From total genomic sequencing, we obtained sequences of over 1100 loci sampled across the genomes of these lice to compare their evolutionary histories and examine the roles of host association in structuring louse relationships. Within each louse species, clades are largely associated with closely related chipmunk host species. Exceptions to this pattern appear to have a biogeographic component, but differ between the two louse species. Phylogenetic relationships among these major louse clades, in both species, are not congruent with chipmunk relationships. In the context of host associations, each louse lineage has a different evolutionary history, supporting the hypothesis that host-parasite assemblages vary both across the landscape and with the taxa under investigation. In addition, the louse Hoplopleura erratica (parasitizing the eastern Tamias striatus) is embedded within H. arboricola, rendering it paraphyletic. This phylogenetic result, together with comparable divergences within H. arboricola, indicate a need for taxonomic revision. Both host divergence and biogeographic components shape parasite diversification as demonstrated by the distinctive diversification patterns of these two independently evolving lineages that parasitize the same hosts.
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- 2020
9. SNP-based phylogenomic inference in Holarctic ground squirrels (Urocitellus)
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Bryan S, McLean, Kayce C, Bell, and Joseph A, Cook
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Genetics ,Animals ,Sciuridae ,Biological Evolution ,Polymorphism, Single Nucleotide ,Molecular Biology ,Phylogeny ,Ecology, Evolution, Behavior and Systematics - Abstract
Resolution of rapid evolutionary radiatons 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 methods are an underutilized but potentially valuable tool for estimating phylogeny and divergence times because they do not rely on resolved gene trees, allowing information from many or all variant loci to be leveraged in species tree reconstruction. We evaluated the utility of SNP-based methods in resolving phylogeny of Holarctic ground squirrels (Urocitellus), a radiation that has been difficult to disentangle, even in prior phylogenomic studies. We inferred phylogeny from a dataset of3,000 ultraconserved element loci (UCEs) using two methods (SNAPP, SVDquartets) and compared our results with a new mitogenome phylogeny. We also systematically evaluated how phasing of UCEs improves per-locus information content, inference of topology, and other parameters within each of these SNP-based methods. Phasing improved topological resolution and branch length estimation at shallow levels (within species complexes), but less so at deeper levels, likely reflecting true uncertainty due to ancestral polymorphisms segregating in rapidly diverging lineages. We resolved key clades in Urocitellus and present targeted opportunities for future phylogenomic inquiry. Our results also extend the roadmap for use of SNPs to address vertebrate radiations and inform comparative analyses at multiple temporal scales.
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- 2022
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10. Sympatric Parasites Have Similar Host-Associated, but Asynchronous, Patterns of Diversification
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Kayce C. Bell, Joseph A. Cook, and John R. Demboski
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0106 biological sciences ,0301 basic medicine ,Abiotic component ,Phylogenetic tree ,biology ,Genetic Speciation ,Host (biology) ,Sciuridae ,Parasitism ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,Host-Parasite Interactions ,Sympatry ,03 medical and health sciences ,Phylogeography ,030104 developmental biology ,Evolutionary biology ,Phylogenetics ,Sympatric speciation ,Animals ,Oxyurida ,Phylogeny ,Ecology, Evolution, Behavior and Systematics - Abstract
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 parasite-parasite phylogenetic concordance in western North American chipmunks (Rodentia: Sciuridae) and two distantly related species of pinworms (Nematoda: Oxyurida). Deep structure in molecular phylogenies revealed signals of host-associated divergence in both parasite species, while shallower phylogeographic structure varied between the two parasites. This suggests that although these parasites experienced similar landscapes and cyclic climate processes, temporally distinctive diversification events were associated with differences in the initiation of their association with host lineages. When climate cycles initiate diversification, partially congruent, but asynchronous, host-associated parasite phylogenies may emerge.
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- 2018
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11. Soil fungal composition changes with shrub encroachment in the northern Chihuahuan Desert
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D. Lee Taylor, Laura M. Ladwig, Donald O. Natvig, Scott L. Collins, Lukas Bell-Dereske, and Kayce C. Bell
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geography ,geography.geographical_feature_category ,Ecology ,ved/biology ,Ecological Modeling ,Soil organic matter ,fungi ,ved/biology.organism_classification_rank.species ,Biodiversity ,food and beverages ,Plant community ,Plant Science ,Ecotone ,Biology ,complex mixtures ,Shrub ,Grassland ,Shrubland ,Habitat ,Ecology, Evolution, Behavior and Systematics - Abstract
Woody species encroachment of grasslands globally causes many socioecological impacts, including loss of grazing pastures and decreased biodiversity. Soil microbial communities may partially regulate the pace of shrub encroachment, as plant-microbial interactions can strongly influence plant success. We measured fungal composition and activity under dominant plant species across a grassland to shrubland transition to determine if shrubs cultivate soil microbial communities as they invade. Specifically, soil microbial communities, abiotic soil properties, and extracellular enzyme activities were quantified for soils under four common Chihuahuan Desert plant species (three grasses, one shrub) in central New Mexico, U.S.A. Extracellular enzyme activity levels were fairly consistent under different plant species across the grassland to shrubland transition. Activity levels of two enzymes (alkaline phosphatase and beta-N-acetyl-glucosaminidase) were lower in the ecotone, presumably because soil organic matter content was also lower in ecotone soils. Community composition of soil fungi mirrored patterns in the plant community, with distinct plant and fungal communities in the shrubland and grassland, while grassland-shrubland ecotone soils hosted a mix of taxa from both habitats. We show that shrubs cultivate a distinct microbial community on the leading edge of the invasion, which may be necessary for shrub colonization, establishment, and persistence.
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- 2021
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12. Temporal and spatial mosaics: deep host association and shallow geographic drivers shape genetic structure in a widespread pinworm,Rauschtineria eutamii(Nematoda: Oxyuridae)
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Joseph A. Cook, Kayce C. Bell, John R. Demboski, Kendall L. Calhoun, and Eric P. Hoberg
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0106 biological sciences ,0301 basic medicine ,Sympatry ,Genetic diversity ,biology ,Oxyuridae ,Lineage (evolution) ,Zoology ,biology.organism_classification ,010603 evolutionary biology ,01 natural sciences ,03 medical and health sciences ,Monophyly ,030104 developmental biology ,Genetic structure ,Ecological fitting ,Ecology, Evolution, Behavior and Systematics ,Neotamias - Abstract
Climate and host demographic cycling often shape both parasite genetic diversity and host distributions, processes that transcend a history of strict host–parasite association. We explored host associations and histories based on an evaluation of mitochondrial and nuclear sequences to reveal the underlying history and genetic structure of a pinworm, Rauschtineria eutamii, infecting ten species of western North American chipmunks (Rodentia:Tamias, subgenus Neotamias). Rauschtineria eutamii contains divergent lineages influenced by the diversity of hosts and variation across the complex topography of western North America. We recovered six reciprocally monophyletic R. eutamii mitochondrial clades, largely supported by a multilocus concordance tree, exhibiting divergence levels comparable with intraspecific variation reported for other nematodes. Phylogenetic relationships among pinworm clades suggest that R. eutamii colonized an ancestral lineage of western chipmunks and lineages persisted during historical isolation in diverging Neotamias species or species groups. Pinworm diversification, however, is incongruent and asynchronous relative to host diversification. Secondarily, patterns of shallow divergence were shaped by geography through events of episodic colonization reflecting an interaction of taxon pulses and ecological fitting among assemblages in recurrent sympatry. Pinworms occasionally infect geographically proximal host species; however, host switching may be unstable or ephemeral, as there is no signal of host switching in the deeper history of R. eutamii.
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- 2016
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13. A global parasite conservation plan
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Colin J. Carlson, Skylar R. Hopkins, Mackenzie L. Kwak, Kayce C. Bell, Giovanni Strona, Mark E. Torchin, Chelsea L. Wood, Stephanie S. Godfrey, Kevin D. Lafferty, Jorge Doña, Melinda L. Moir, Kelly A. Speer, and Biological Sciences
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0106 biological sciences ,Natural history collections ,Extinction ,010604 marine biology & hydrobiology ,Red listing ,Wildlife ,Biodiversity ,Conservation Plan ,Tree of life ,Biodiversity inventory ,Conservation prioritization ,Symbionts ,010603 evolutionary biology ,01 natural sciences ,Geography ,Work (electrical) ,Obstacle ,Ecosystem ,Coextinction ,Environmental planning ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
Found throughout the tree of life and in every ecosystem, parasites are some of the most diverse, ecologically important animals on Earth-but in almost all cases, the least protected by wildlife or ecosystem conservation efforts. For decades, ecologists have been calling for research to understand parasites' important ecological role, and increasingly, to protect as many species from extinction as possible. However, most conservationists still work within priority systems for funding and effort that exclude or ignore parasites, or treat parasites as an obstacle to be overcome. Our working group identified 12 goals for the next decade that could advance parasite biodiversity conservation through an ambitious mix of research, advocacy, and management. Ecological Society of America; Georgetown Environment Initiative; Smithsonian National Museum of Natural HistorySmithsonian InstitutionSmithsonian National Museum of Natural History; Peter Buck Postdoctoral Fellowship from the Smithsonian National Museum of Natural History; National Science FoundationNational Science Foundation (NSF) [OCE-1829509]; Alfred P. Sloan Foundation Sloan Research FellowshipAlfred P. Sloan Foundation; University of Washington Innovation Award; University of Washington Royalty Research Fund awardUniversity of Washington The authors kindly thank the Ecological Society of America for supporting our workshop, as well as additional participants Kevin Burgio, Tad Dallas, and Roger Jovani; Laura Whitehouse, for her graphic design work on Fig. 1; Jonathan Wojcik for allowing the inclusion of his copyright Diplozoon illustration in Fig. 3; and dozens of collaborators and friends who have been part of the foundational work on parasite conservation, including Anna Phillips, Veronica Bueno, Carrie Cizauskas, Christopher Clements, Graeme Cumming, Eric Dougherty, Kevin Johnson, Wayne Getz, Nyeema Harris, Elizabeth Nichols, Sergey Mironov, Robert Poulin, and Heather Proctor. CJC gratefully acknowledges funding support from the Georgetown Environment Initiative, and research support from Anna Phillips and the Smithsonian National Museum of Natural History. KCB was supported by a Peter Buck Postdoctoral Fellowship from the Smithsonian National Museum of Natural History. CLW was supported by a grant from the National Science Foundation (OCE-1829509), an Alfred P. Sloan Foundation Sloan Research Fellowship, a University of Washington Innovation Award, and a University of Washington Royalty Research Fund award. Any use of trade, product, or firm names in this publication is for descriptive purposes only and does not imply endorsement by the U.S. Government. Public domain – authored by a U.S. government employee
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- 2020
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14. Expanded Host Range of Sucking Lice and Pinworms of Western North American Chipmunks
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Kayce C. Bell, Diego Matek, John R. Demboski, and Joseph A. Cook
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Taxon ,Host (biology) ,Ecology ,Hoplopleura arboricola ,Neohaematopinus pacificus ,Biodiversity ,Zoology ,Parasite hosting ,Parasitology ,Rauschtineria eutamii ,Biology ,Ecology, Evolution, Behavior and Systematics ,Global biodiversity - Abstract
Biological inventories often miss parasites, a critical component of biodiversity, and even well-studied host species generally have a paucity of parasite records. Efforts to document the host diversity and distribution of parasites can use newly collected specimens as well as museum specimens. We focus on a group of widespread, well-documented hosts, western North American chipmunks (Rodentia: genus Tamias). Field-collected and museum specimens of chipmunks from across western North America were examined externally for sucking lice (Anoplura), and gastrointestinal tracts were examined for pinworms (Oxyuriodea). We documented new hosts and expanded the geographic distribution for four parasite taxa under investigation: Hoplopleura arboricola, Neohaematopinus pacificus, Heteroxynema cucullatum, and Rauschtineria eutamii. This effort demonstrates the utility of museum collections as well as the pressing need for continued field collection to characterize global biodiversity.
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- 2015
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15. Climate change, collections and the classroom: using big data to tackle big problems
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Rachel E. Walsh, Joseph A. Cook, Robert P. Guralnick, Pamela S. Soltis, Kayce C. Bell, Eileen A. Lacey, Douglas E. Soltis, Anna Monfils, Scott V. Edwards, Talisin T. Hammond, Elizabeth R. Ellwood, Austin Mast, Stefanie M. Ickert-Bond, and John E. McCormack
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0106 biological sciences ,Specimens ,Big data ,Natural history ,lcsh:Evolution ,Climate change ,010603 evolutionary biology ,01 natural sciences ,Science education ,Education ,Task (project management) ,Undergraduate education ,Digital resources ,lcsh:QH359-425 ,ComputingMilieux_COMPUTERSANDEDUCATION ,Sociology ,Social science ,Ecology, Evolution, Behavior and Systematics ,lcsh:LC8-6691 ,lcsh:Special aspects of education ,business.industry ,05 social sciences ,Global warming ,050301 education ,Life Sciences ,Data science ,Instructional modules ,Lacey [BRII recipient] ,Sociology of Education ,business ,0503 education - Abstract
Preparing students to explore, understand, and resolve societal challenges such as global climate change is an important task for evolutionary and ecological biologists that will require novel and innovative pedagogical approaches. Recent calls to reform undergraduate science education emphasize the importance of engaging students in inquiry-driven, active, and authentic learning experiences. We believe that the vast digital resources (i.e., “big data”) associated with natural history collections provide invaluable but underutilized opportunities to create such experiences for undergraduates in biology. Here, we describe an online, open-access educational module that we have developed that harnesses the power of collections-based information to introduce students to multiple conceptual and analytical elements of climate change, evolutionary, and ecological biology research. The module builds upon natural history specimens and data collected over the span of nearly a century in Yosemite National Park, California, to guide students through a series of exercises aimed at testing hypotheses regarding observed differences in response to climate change by two closely related and partially co-occurring species of chipmunks. The content of the module can readily be modified to meet the pedagogical goals and instructional levels of different courses while the analytical strategies outlined can be adapted to address a wide array of questions in evolutionary and ecological biology. In sum, we believe that specimen-based natural history data represent a powerful platform for reforming undergraduate instruction in biology. Because these efforts will result in citizens who are better prepared to understand complex biological relationships, the benefits of this approach to undergraduate education will have widespread benefits to society.
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- 2017
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16. Impacts of Inference Method and Data set Filtering on Phylogenomic Resolution in a Rapid Radiation of Ground Squirrels (Xerinae: Marmotini)
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Julie M. Allen, Bryan S. McLean, Kristofer M. Helgen, Kayce C. Bell, and Joseph A. Cook
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0106 biological sciences ,0301 basic medicine ,Genetic Speciation ,Inference ,Locus (genetics) ,computer.software_genre ,010603 evolutionary biology ,01 natural sciences ,Coalescent theory ,03 medical and health sciences ,Phylogenetics ,Genetics ,Animals ,Xerinae ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,Genome ,biology ,Phylogenetic tree ,Models, Genetic ,Sciuridae ,biology.organism_classification ,Classification ,Data set ,030104 developmental biology ,Taxon ,Data mining ,computer - Abstract
Phylogenomic data sets are illuminating many areas of the Tree of Life. However, the large size of these data sets 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 the information content of loci employed. We used a data set of $>$3950 ultraconserved element (UCE) loci from a classic mammalian radiation, ground-dwelling squirrels of the tribe Marmotini (Sciuridae: Xerinae), to assess sensitivity of phylogenetic estimates to varying per-locus information content across four different inference methods (RAxML, ASTRAL, NJst, and SVDquartets). Persistent discordance was found in topology and bootstrap support between concatenation- and coalescent-based inferences; among methods within the coalescent framework; and within all methods in response to different filtering scenarios. Contrary to some recent empirical UCE-based studies, filtering by information content did not promote complete among-method concordance. Nevertheless, filtering did improve concordance relative to randomly selected locus sets, largely via improved consistency of two-step summary methods (particularly NJst) under conditions of higher average per-locus variation (and thus increasing gene tree precision). The benefits of phylogenomic data set filtering are variable among classes of inference methods and across different evolutionary scenarios, reiterating the complexities of resolving rapid radiations, even with robust taxon and character sampling.
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- 2017
17. Phylogeography of the ground squirrel subgenusXerospermophilusand assembly of the Mojave Desert biota
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Philip Leitner, Marjorie D. Matocq, David J. Hafner, and Kayce C. Bell
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education.field_of_study ,Ecology ,biology ,Biogeography ,Population ,biology.organism_classification ,Coalescent theory ,Mohave ground squirrel ,Phylogeography ,Refugium (population biology) ,Vicariance ,Xerospermophilus ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
Aim The Mohave ground squirrel (Xerospermophilus mohavensis) is one of a few endemic species of the Mojave Desert of south-western North America. We describe phylogeographic patterns within this species and its sister taxon (Xerospermophilus tereticaudus) and test hypotheses concerning their biogeographical history using genetic signatures of stable versus expanding populations. We compare these patterns with those of other Mojave species to evaluate the role of vicariance in producing phylogeographic structure during the assembly of the Mojave Desert biota. Location The Mojave Desert and adjacent desert regions of south-western North America. Methods Complete cytochrome b gene sequences of X. mohavensis (46 individuals representing 11 localities) and X. tereticaudus (38 individuals representing 14 localities) were analysed using Bayesian methods to infer phylogenetic relationships. Genetic signals of stable or expanding populations were examined based on the distribution of recent mutations and pairwise differences, as well as with a coalescent-based approach. Results The two species are reciprocally monophyletic and may have diverged in response to the late Pliocene–early Pleistocene uplift of the Transverse Ranges and Mojave block. Little phylogeographic structure is evident within X. mohavensis, but there is a signature of northern expansion from a presumably full-pluvial refugium in the Mojave River basin. Four geographic subgroups are evident within X. tereticaudus, and there is a signature of northern expansion from a presumably full-pluvial refugium in the Sonoran coastal plains. Roughly congruent phylogeographic patterns are found within five arid-adapted taxa, indicating a strong element of vicariance during the assembly of the generally transitional Mojave Desert biota. Main conclusions We present a preliminary model for the historical assembly of the Mojave Desert biota that indicates a strong vicariant element producing autochthonous lineages (including X. mohavensis) that diverged during the major geological and climatic events of the last 5 Myr. Phylogeographic partitioning within the Mojave Desert underscores the necessity of immediate conservation measures for this unique and fragile arid ecosystem that is locked between two large metropolitan population centres and is the target of continued adverse environmental impact.
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- 2010
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18. Natural history collections-based research: progress, promise, and best practices
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Kayce C. Bell, Eleanor R. Deardorff, Bethany L. Abrahamson, Jocelyn P. Colella, Joseph A. Cook, Amanda K. Jones, Jessica A. Weber, Fernando Salazar-Miralles, Jonathan L. Dunnum, and Bryan S. McLean
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0106 biological sciences ,0301 basic medicine ,Ecology ,Scope (project management) ,Scientific progress ,Best practice ,Ecology (disciplines) ,Feature Article ,Environmental ethics ,Biology ,Vitality ,010603 evolutionary biology ,01 natural sciences ,Natural history ,03 medical and health sciences ,030104 developmental biology ,Genetics ,Mammalogy ,Animal Science and Zoology ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Abstract
Specimens and associated data in natural history collections (NHCs) foster substantial scientific progress. In this paper, we explore recent contributions of NHCs to the study of systematics and biogeography, genomics, morphology, stable isotope ecology, and parasites and pathogens of mammals. To begin to assess the magnitude and scope of these contributions, we analyzed publications in the Journal of Mammalogy over the last decade, as well as recent research supported by a single university mammal collection (Museum of Southwestern Biology, Division of Mammals). Using these datasets, we also identify weak links that may be hindering the development of crucial NHC infrastructure. Maintaining the vitality and growth of this foundation of mammalogy depends on broader engagement and support from across the scientific community and is both an ethical and scientific imperative given the rapidly changing environmental conditions on our planet.
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- 2015
19. Development and characterization of polymorphic microsatellite loci in the Mohave ground squirrel (Xerospermophilus mohavensis)
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Kayce C. Bell and Marjorie D. Matocq
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education.field_of_study ,biology ,Population ,Locus (genetics) ,biology.organism_classification ,Mohave ground squirrel ,Evolutionary biology ,Genetic structure ,Genetics ,Microsatellite ,Polymorphic Microsatellite Marker ,Xerospermophilus ,Ground squirrel ,education ,Ecology, Evolution, Behavior and Systematics - Abstract
We characterized 12 polymorphic microsatellite markers for Xerospermophilus mohavensis, the Mohave ground squirrel, in order to contribute to the conservation management of this species. We tested polymorphism in the Cactus Peak population (N = 84) and found that allele number ranged from 4 to 9 with observed and expected heterozygosity ranging from 0.25 to 0.84, respectively. One locus deviated from Hardy–Weinberg expectations. Eleven of the 12 loci are polymorphic in the Mohave ground squirrel’s parapatric sister species, Xerospermophilus tereticaudus, the round-tailed ground squirrel. These loci will be useful in studies of parentage, population genetic structure and interspecific hybridization.
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- 2010
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20. Phylogenomics from Whole Genome Sequences Using aTRAM
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Kevin P. Johnson, Barry R. Pittendrigh, Tandy Warnow, Bret M. Boyd, Daisie I. Huang, David L. Reed, M. Soledad Leonardi, Quentin C. B. Cronk, Julie M. Allen, Kayce C. Bell, Patrick G.S. Grady, Lawrence Mugisha, Nam Nguyen, and Pranjal Vachaspati
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0301 basic medicine ,Sequence analysis ,Otras Ciencias Biológicas ,Genomics ,GENE ASSEMBLY ,Computational biology ,PHYLOGENOMICS ,Biology ,Genome ,DNA sequencing ,Ciencias Biológicas ,03 medical and health sciences ,Phylogenomics ,Genetics ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,Whole genome sequencing ,Contig ,Phylogenetic tree ,ATRAM ,Classification ,030104 developmental biology ,GENOME SEQUENCING ,Sequence Analysis ,CIENCIAS NATURALES Y EXACTAS - Abstract
Novel sequencing technologies are rapidly expanding the size of data sets that can be applied to phylogenetic studies. Currently the most commonly used phylogenomic approaches involve some form of genome reduction. While these approaches make assembling phylogenomic data sets more economical for organisms with large genomes, they reduce the genomic coverage and thereby the long-term utility of the data. Currently, for organisms with moderate to small genomes (< 1000 Mbp) it is feasible to sequence the entire genome at modest coverage (10−30×). Computational challenges for handling these large data sets can be alleviated by assembling targeted reads, rather than assembling the entire genome, to produce a phylogenomic data matrix. Here we demonstrate the use of automated Target Restricted Assembly Method (aTRAM) to assemble 1107 single-copy ortholog genes from whole genome sequencing of sucking lice (Anoplura) and out-groups. We developed a pipeline to extract exon sequences from the aTRAM assemblies by annotating them with respect to the original target protein. We aligned these protein sequences with the inferred amino acids and then performed phylogenetic analyses on both the concatenated matrix of genes and on each gene separately in a coalescent analysis. Finally, we tested the limits of successful assembly in aTRAM by assembling 100 genes from close- to distantly related taxa at high to low levels of coverage. Both the concatenated analysis and the coalescent-based analysis produced the same tree topology, which was consistent with previously published results and resolved weakly supported nodes. These results demonstrate that this approach is successful at developing phylogenomic data sets from raw genome sequencing reads. Further, we found that with coverages above 5−10× , aTRAM was successful at assembling 80–90% of the contigs for both close and distantly related taxa. As sequencing costs continue to decline, we expect full genome sequencing will become more feasible for a wider array of organisms, and aTRAM will enable mining of these genomic data sets for an extensive variety of applications, including phylogenomics. [aTRAM; gene assembly; genome sequencing; phylogenomics.] Fil: Allen, Julie M.. University of Illinois at Urbana-Champaign; Estados Unidos Fil: Boyd, Christopher. University of Illinois at Urbana-Champaign; Estados Unidos Fil: Nguyen, Nam Phuong. University of Illinois at Urbana-Champaign; Estados Unidos Fil: Vachaspati, Pranjal. University of Illinois at Urbana-Champaign; Estados Unidos Fil: Warnow, Tandy. University of Illinois at Urbana-Champaign; Estados Unidos Fil: Huang, Daisie I.. University of British Columbia; Canadá Fil: Grady, Patrick G. S.. University of Illinois at Urbana-Champaign; Estados Unidos Fil: Bell, Kayce C.. University Of New Mexico; Estados Unidos Fil: Cronk, Quentin C. B.. University of British Columbia; Canadá Fil: Mugisha, Lawrence. Makerere University; Uganda Fil: Pittendrigh, Barry R.. Michigan State University; Estados Unidos Fil: Leonardi, María Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Centro Nacional Patagónico. Instituto de Biología de Organismos Marinos; Argentina Fil: Reed, David L.. University of Florida; Estados Unidos Fil: Johnson, Kevin P.. University of Illinois at Urbana-Champaign; Estados Unidos
- Published
- 2017
- Full Text
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