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Jia Y, Fu Q, Li B, Xu Y, Tariq A. Polymorphism analysis of major histocompatibility complex (MHC) DQB gene in the Asiatic black bear (Ursus thibetanus). MAMMAL RES 2023. [DOI: 10.1007/s13364-023-00685-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
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2
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Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Sci Rep 2022; 12:17933. [PMID: 36289307 PMCID: PMC9606363 DOI: 10.1038/s41598-022-21658-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/29/2022] [Indexed: 01/20/2023] Open
Abstract
The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
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Routti H, Atwood TC, Bechshoft T, Boltunov A, Ciesielski TM, Desforges JP, Dietz R, Gabrielsen GW, Jenssen BM, Letcher RJ, McKinney MA, Morris AD, Rigét FF, Sonne C, Styrishave B, Tartu S. State of knowledge on current exposure, fate and potential health effects of contaminants in polar bears from the circumpolar Arctic. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 664:1063-1083. [PMID: 30901781 DOI: 10.1016/j.scitotenv.2019.02.030] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/01/2019] [Accepted: 02/02/2019] [Indexed: 05/03/2023]
Abstract
The polar bear (Ursus maritimus) is among the Arctic species exposed to the highest concentrations of long-range transported bioaccumulative contaminants, such as halogenated organic compounds and mercury. Contaminant exposure is considered to be one of the largest threats to polar bears after the loss of their Arctic sea ice habitat due to climate change. The aim of this review is to provide a comprehensive summary of current exposure, fate, and potential health effects of contaminants in polar bears from the circumpolar Arctic required by the Circumpolar Action Plan for polar bear conservation. Overall results suggest that legacy persistent organic pollutants (POPs) including polychlorinated biphenyls, chlordanes and perfluorooctane sulfonic acid (PFOS), followed by other perfluoroalkyl compounds (e.g. carboxylic acids, PFCAs) and brominated flame retardants, are still the main compounds in polar bears. Concentrations of several legacy POPs that have been banned for decades in most parts of the world have generally declined in polar bears. Current spatial trends of contaminants vary widely between compounds and recent studies suggest increased concentrations of both POPs and PFCAs in certain subpopulations. Correlative field studies, supported by in vitro studies, suggest that contaminant exposure disrupts circulating levels of thyroid hormones and lipid metabolism, and alters neurochemistry in polar bears. Additionally, field and in vitro studies and risk assessments indicate the potential for adverse impacts to polar bear immune functions from exposure to certain contaminants.
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Affiliation(s)
- Heli Routti
- Norwegian Polar Institute, Fram Centre, NO-9296 Tromsø, Norway.
| | - Todd C Atwood
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK 99508, USA
| | - Thea Bechshoft
- Department of Bioscience, Arctic Research Centre (ARC), Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - Andrei Boltunov
- Marine Mammal Research and Expedition Center, 36 Nahimovskiy pr., Moscow 117997, Russia
| | - Tomasz M Ciesielski
- Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway
| | - Jean-Pierre Desforges
- Department of Bioscience, Arctic Research Centre (ARC), Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - Rune Dietz
- Department of Bioscience, Arctic Research Centre (ARC), Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | | | - Bjørn M Jenssen
- Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway; Department of Bioscience, Arctic Research Centre (ARC), Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark; Department of Arctic Technology, University Centre in Svalbard, PO Box 156, NO-9171 Longyearbyen, Norway
| | - Robert J Letcher
- Ecotoxicology and Wildlife Heath Division, Wildlife and Landscape Science Directorate, Environment and Climate Change Canada, National Wildlife Research Centre, Carleton University, 1125 Colonel By Dr., Ottawa, Ontario K1A 0H3, Canada
| | - Melissa A McKinney
- Department of Natural Resource Sciences, McGill University, Ste.-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Adam D Morris
- Ecotoxicology and Wildlife Heath Division, Wildlife and Landscape Science Directorate, Environment and Climate Change Canada, National Wildlife Research Centre, Carleton University, 1125 Colonel By Dr., Ottawa, Ontario K1A 0H3, Canada
| | - Frank F Rigét
- Department of Bioscience, Arctic Research Centre (ARC), Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - Christian Sonne
- Department of Bioscience, Arctic Research Centre (ARC), Faculty of Science and Technology, Aarhus University, Frederiksborgvej 399, PO Box 358, DK-4000 Roskilde, Denmark
| | - Bjarne Styrishave
- Toxicology and Drug Metabolism Group, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen OE, Denmark
| | - Sabrina Tartu
- Norwegian Polar Institute, Fram Centre, NO-9296 Tromsø, Norway
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Whiteman JP, Harlow HJ, Durner GM, Regehr EV, Amstrup SC, Ben-David M. Heightened Immune System Function in Polar Bears Using Terrestrial Habitats. Physiol Biochem Zool 2019; 92:1-11. [DOI: 10.1086/698996] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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5
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Malenfant RM, Davis CS, Richardson ES, Lunn NJ, Coltman DW. Heritability of body size in the polar bears of Western Hudson Bay. Mol Ecol Resour 2018; 18:854-866. [DOI: 10.1111/1755-0998.12889] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Revised: 03/23/2018] [Accepted: 03/29/2018] [Indexed: 12/16/2022]
Affiliation(s)
- René M. Malenfant
- Department of Biology University of New Brunswick Fredericton NB Canada
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Corey S. Davis
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
| | - Evan S. Richardson
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada Winnipeg MB Canada
| | - Nicholas J. Lunn
- Wildlife Research Division Science and Technology Branch Environment and Climate Change Canada University of Alberta Edmonton AB Canada
| | - David W. Coltman
- Department of Biological Sciences University of Alberta Edmonton Alberta Canada
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Gormezano LJ, Ellis-Felege SN, Iles DT, Barnas A, Rockwell RF. Polar Bear Foraging Behavior During the Ice-Free Period in Western Hudson Bay: Observations, Origins, and Potential Significance. AMERICAN MUSEUM NOVITATES 2017. [DOI: 10.1206/3885.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Linda J. Gormezano
- Division of Vertebrate Zoology, American Museum of Natural History, New York
| | | | - David T. Iles
- Department of Biology, Tufts University, Medford, MA
| | - Andrew Barnas
- Department of Biology, University of North Dakota, Grand Forks, ND
| | - Robert F. Rockwell
- Division of Vertebrate Zoology, American Museum of Natural History, New York
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Grogan KE, Sauther ML, Cuozzo FP, Drea CM. Genetic wealth, population health: Major histocompatibility complex variation in captive and wild ring-tailed lemurs ( Lemur catta). Ecol Evol 2017; 7:7638-7649. [PMID: 29043021 PMCID: PMC5632616 DOI: 10.1002/ece3.3317] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/13/2017] [Accepted: 07/18/2017] [Indexed: 12/24/2022] Open
Abstract
Across species, diversity at the major histocompatibility complex (MHC) is critical to individual disease resistance and, hence, to population health; however, MHC diversity can be reduced in small, fragmented, or isolated populations. Given the need for comparative studies of functional genetic diversity, we investigated whether MHC diversity differs between populations which are open, that is experiencing gene flow, versus populations which are closed, that is isolated from other populations. Using the endangered ring-tailed lemur (Lemur catta) as a model, we compared two populations under long-term study: a relatively "open," wild population (n = 180) derived from Bezà Mahafaly Special Reserve, Madagascar (2003-2013) and a "closed," captive population (n = 121) derived from the Duke Lemur Center (DLC, 1980-2013) and from the Indianapolis and Cincinnati Zoos (2012). For all animals, we assessed MHC-DRB diversity and, across populations, we compared the number of unique MHC-DRB alleles and their distributions. Wild individuals possessed more MHC-DRB alleles than did captive individuals, and overall, the wild population had more unique MHC-DRB alleles that were more evenly distributed than did the captive population. Despite management efforts to maintain or increase genetic diversity in the DLC population, MHC diversity remained static from 1980 to 2010. Since 2010, however, captive-breeding efforts resulted in the MHC diversity of offspring increasing to a level commensurate with that found in wild individuals. Therefore, loss of genetic diversity in lemurs, owing to small founder populations or reduced gene flow, can be mitigated by managed breeding efforts. Quantifying MHC diversity within individuals and between populations is the necessary first step to identifying potential improvements to captive management and conservation plans.
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Affiliation(s)
- Kathleen E. Grogan
- University Program in EcologyDuke UniversityDurhamNCUSA
- Department of Evolutionary AnthropologyDuke UniversityDurhamNCUSA
| | | | - Frank P. Cuozzo
- Lajuma Research CentreLouis Trichardt (Makhado)0920South Africa
| | - Christine M. Drea
- University Program in EcologyDuke UniversityDurhamNCUSA
- Department of Evolutionary AnthropologyDuke UniversityDurhamNCUSA
- Department of BiologyDuke UniversityDurhamNCUSA
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Marmesat E, Schmidt K, Saveljev AP, Seryodkin IV, Godoy JA. Retention of functional variation despite extreme genomic erosion: MHC allelic repertoires in the Lynx genus. BMC Evol Biol 2017; 17:158. [PMID: 28676046 PMCID: PMC5496644 DOI: 10.1186/s12862-017-1006-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/23/2017] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Demographic bottlenecks erode genetic diversity and may increase endangered species' extinction risk via decreased fitness and adaptive potential. The genetic status of species is generally assessed using neutral markers, whose dynamic can differ from that of functional variation due to selection. The MHC is a multigene family described as the most important genetic component of the mammalian immune system, with broad implications in ecology and evolution. The genus Lynx includes four species differing immensely in demographic history and population size, which provides a suitable model to study the genetic consequences of demographic declines: the Iberian lynx being an extremely bottlenecked species and the three remaining ones representing common and widely distributed species. We compared variation in the most variable exon of the MHCI and MHCII-DRB loci among the four species of the Lynx genus. RESULTS The Iberian lynx was characterised by lower number of MHC alleles than its sister species (the Eurasian lynx). However, it maintained most of the functional genetic variation at MHC loci present in the remaining and genetically healthier lynx species at all nucleotide, amino acid, and supertype levels. CONCLUSIONS Species-wide functional genetic diversity can be maintained even in the face of severe population bottlenecks, which caused devastating whole genome genetic erosion. This could be the consequence of divergent alleles being retained across paralogous loci, an outcome that, in the face of frequent gene conversion, may have been favoured by balancing selection.
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Affiliation(s)
- Elena Marmesat
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), C/Américo Vespucio, 26, 41092, Sevilla, Spain
| | - Krzysztof Schmidt
- Mammal Research Institute, Polish Academy of Sciences, 17-230, Białowieża, Poland
| | - Alexander P Saveljev
- Department of Animal Ecology, Russian Research Institute of Game Management and Fur Farming, 79 Preobrazhenskaya Str, Kirov, 610000, Russia
| | - Ivan V Seryodkin
- Laboratory of Ecology and Conservation of Animals, Pacific Institute of Geography of Far East Branch of Russian Academy of Sciences, 7 Radio Street, Vladivostok, 690041, Russia
- Far Eastern Federal University, 8 Sukhanova Street, Vladivostok, 690091, Russia
| | - José A Godoy
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), C/Américo Vespucio, 26, 41092, Sevilla, Spain.
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Atwood TC, Marcot BG, Douglas DC, Amstrup SC, Rode KD, Durner GM, Bromaghin JF. Forecasting the relative influence of environmental and anthropogenic stressors on polar bears. Ecosphere 2016. [DOI: 10.1002/ecs2.1370] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Todd C. Atwood
- Alaska Science CenterU.S. Geological Survey Anchorage Alaska 99508 USA
| | - Bruce G. Marcot
- Pacific Northwest Research StationU.S.D.A. Forest Service Portland Oregon 97208 USA
| | - David C. Douglas
- Alaska Science CenterU.S. Geological Survey Juneau Alaska 99801 USA
| | | | - Karyn D. Rode
- Alaska Science CenterU.S. Geological Survey Anchorage Alaska 99508 USA
| | - George M. Durner
- Alaska Science CenterU.S. Geological Survey Anchorage Alaska 99508 USA
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Pečnerová P, Díez-del-Molino D, Vartanyan S, Dalén L. Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth. Sci Rep 2016; 6:25274. [PMID: 27143688 PMCID: PMC4855147 DOI: 10.1038/srep25274] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 04/13/2016] [Indexed: 12/28/2022] Open
Abstract
According to the nearly-neutral theory of evolution, the relative strengths of selection and drift shift in favour of drift at small population sizes. Numerous studies have analysed the effect of bottlenecks and small population sizes on genetic diversity in the MHC, which plays a central role in pathogen recognition and immune defense and is thus considered a model example for the study of adaptive evolution. However, to understand changes in genetic diversity at loci under selection, it is necessary to compare the genetic diversity of a population before and after the bottleneck. In this study, we analyse three fragments of the MHC DQA gene in woolly mammoth samples radiocarbon dated to before and after a well-documented bottleneck that took place about ten thousand years ago. Our results indicate a decrease in observed heterozygosity and number of alleles, suggesting that genetic drift had an impact on the variation on MHC. Based on coalescent simulations, we found no evidence of balancing selection maintaining MHC diversity during the Holocene. However, strong trans-species polymorphism among mammoths and elephants points to historical effects of balancing selection on the woolly mammoth lineage.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
- Department of Zoology, Stockholm University, SE-10691 Stockholm, Sweden
| | - David Díez-del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo, Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS), Magadan, Russia
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405 Stockholm, Sweden
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Faulks LK, Östman Ö. Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics. JOURNAL OF FISH BIOLOGY 2016; 88:1564-1583. [PMID: 26940068 DOI: 10.1111/jfb.12930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 01/29/2016] [Indexed: 06/05/2023]
Abstract
This study assessed the major histocompatibility complex (MHC) and neutral genetic variation and structure in two percid species, perch Perca fluviatilis and zander Sander lucioperca, in a unique brackish ecosystem, the Baltic Sea. In addition, to assess the importance of MHC diversity to disease susceptibility in these populations, comparisons were made to an introduced, disease susceptible, P. fluviatilis population in Australia. Eighty-three MHC class II B exon 2 variants were amplified: 71 variants from 92 P. fluviatilis samples, and 12 variants from 82 S. lucioperca samples. Microsatellite and MHC data revealed strong spatial genetic structure in S. lucioperca, but not P. fluviatilis, across the Baltic Sea. Both microsatellite and MHC data showed higher levels of genetic diversity in P. fluviatilis from the Baltic Sea compared to Australia, which may have facilitated the spread of an endemic virus, EHNV in the Australian population. The relatively high levels of genetic variation in the Baltic Sea populations, together with spatial genetic structure, however, suggest that there currently seems to be little risk of disease epidemics in this system. To ensure this remains the case in the face of ongoing environmental changes, fisheries and habitat disturbance, the conservation of local-scale genetic variation is recommended.
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Affiliation(s)
- L K Faulks
- Department of Ecology and Genetics - Animal Ecology, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden
| | - Ö Östman
- Department of Aquatic Resources - Institute of Coastal Research, Swedish University of Agricultural Sciences, Skolvägen 6, 74242, Öregrund, Sweden
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Plasil M, Mohandesan E, Fitak RR, Musilova P, Kubickova S, Burger PA, Horin P. The major histocompatibility complex in Old World camelids and low polymorphism of its class II genes. BMC Genomics 2016; 17:167. [PMID: 26931144 PMCID: PMC4774177 DOI: 10.1186/s12864-016-2500-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/18/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is a genomic region containing genes with crucial roles in immune responses. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. To counteract the high variability of pathogens, the MHC evolved into a region of considerable heterogeneity in its organization, number and extent of polymorphism. Studies of MHCs in different model species contribute to our understanding of mechanisms of immunity, diseases and their evolution. Camels are economically important domestic animals and interesting biomodels. Three species of Old World camels have been recognized: the dromedary (Camelus dromedarius), Bactrian camel (Camelus bactrianus) and the wild camel (Camelus ferus). Despite their importance, little is known about the MHC genomic region, its organization and diversity in camels. The objectives of this study were to identify, map and characterize the MHC region of Old World camelids, with special attention to genetic variation at selected class MHC II loci. RESULTS Physical mapping located the MHC region to the chromosome 20 in Camelus dromedarius. Cytogenetic and comparative analyses of whole genome sequences showed that the order of the three major sub-regions is "Centromere - Class II - Class III - Class I". DRA, DRB, DQA and DQB exon 2 sequences encoding the antigen binding site of the corresponding class II antigen presenting molecules showed high degree of sequence similarity and extensive allele sharing across the three species. Unexpectedly low extent of polymorphism with low numbers of alleles and haplotypes was observed in all species, despite different geographic origins of the camels analyzed. The DRA locus was found to be polymorphic, with three alleles shared by all three species. DRA and DQA sequences retrieved from ancient DNA samples of Camelus dromedarius suggested that additional polymorphism might exist. CONCLUSIONS This study provided evidence that camels possess an MHC comparable to other mammalian species in terms of its genomic localization, organization and sequence similarity. We described ancient variation at the DRA locus, monomorphic in most species. The extent of molecular diversity of MHC class II genes seems to be substantially lower in Old World camels than in other mammalian species.
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Affiliation(s)
- Martin Plasil
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
| | - Elmira Mohandesan
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria.
| | - Robert R Fitak
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria.
- Department of Biology, Duke University, Durham, NC, USA.
| | - Petra Musilova
- Department of Genetics and Reproduction, Veterinary Research Institute, Brno, Czech Republic.
| | - Svatava Kubickova
- Department of Genetics and Reproduction, Veterinary Research Institute, Brno, Czech Republic.
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.
| | - Petr Horin
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
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Evidence of adoption, monozygotic twinning, and low inbreeding rates in a large genetic pedigree of polar bears. Polar Biol 2015. [DOI: 10.1007/s00300-015-1871-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Lack of Spatial Immunogenetic Structure among Wolverine (Gulo gulo) Populations Suggestive of Broad Scale Balancing Selection. PLoS One 2015; 10:e0140170. [PMID: 26448462 PMCID: PMC4598017 DOI: 10.1371/journal.pone.0140170] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 09/22/2015] [Indexed: 11/19/2022] Open
Abstract
Elucidating the adaptive genetic potential of wildlife populations to environmental selective pressures is fundamental for species conservation. Genes of the major histocompatibility complex (MHC) are highly polymorphic, and play a key role in the adaptive immune response against pathogens. MHC polymorphism has been linked to balancing selection or heterogeneous selection promoting local adaptation. However, spatial patterns of MHC polymorphism are also influenced by gene flow and drift. Wolverines are highly vagile, inhabiting varied ecoregions that include boreal forest, taiga, tundra, and high alpine ecosystems. Here, we investigated the immunogenetic variation of wolverines in Canada as a surrogate for identifying local adaptation by contrasting the genetic structure at MHC relative to the structure at 11 neutral microsatellites to account for gene flow and drift. Evidence of historical positive selection was detected at MHC using maximum likelihood codon-based methods. Bayesian and multivariate cluster analyses revealed weaker population genetic differentiation at MHC relative to the increasing microsatellite genetic structure towards the eastern wolverine distribution. Mantel correlations of MHC against geographical distances showed no pattern of isolation by distance (IBD: r = -0.03, p = 0.9), whereas for microsatellites we found a relatively strong and significant IBD (r = 0.54, p = 0.01). Moreover, we found a significant correlation between microsatellite allelic richness and the mean number of MHC alleles, but we did not observe low MHC diversity in small populations. Overall these results suggest that MHC polymorphism has been influenced primarily by balancing selection and to a lesser extent by neutral processes such as genetic drift, with no clear evidence for local adaptation. This study contributes to our understanding of how vulnerable populations of wolverines may respond to selective pressures across their range.
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Fagre AC, Patyk KA, Nol P, Atwood T, Hueffer K, Duncan C. A Review of Infectious Agents in Polar Bears (Ursus maritimus) and Their Long-Term Ecological Relevance. ECOHEALTH 2015; 12:528-39. [PMID: 25791679 DOI: 10.1007/s10393-015-1023-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Revised: 11/13/2014] [Accepted: 02/06/2015] [Indexed: 05/27/2023]
Abstract
Disease was a listing criterion for the polar bear (Ursus maritimus) as threatened under the Endangered Species Act in 2008; it is therefore important to evaluate the current state of knowledge and identify any information gaps pertaining to diseases in polar bears. We conducted a systematic literature review focused on infectious agents and associated health impacts identified in polar bears. Overall, the majority of reports in free-ranging bears concerned serosurveys or fecal examinations with little to no information on associated health effects. In contrast, most reports documenting illness or pathology referenced captive animals and diseases caused by etiologic agents not representative of exposure opportunities in wild bears. As such, most of the available infectious disease literature has limited utility as a basis for development of future health assessment and management plans. Given that ecological change is a considerable risk facing polar bear populations, future work should focus on cumulative effects of multiple stressors that could impact polar bear population dynamics.
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Affiliation(s)
- Anna C Fagre
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 300 West Drake Road, Fort Collins, CO, 80524, USA
| | - Kelly A Patyk
- Center for Epidemiology and Animal Health, Science Technology and Analysis Services (STAS), Veterinary Services (VS), Animal and Plant Health Inspection Service (APHIS), United States Department of Agriculture (USDA), 2150 Centre Ave., Fort Collins, CO, 80526, USA
| | - Pauline Nol
- Wildlife-Livestock Disease Investigations Team, STAS, VS, APHIS, USDA, 4101 LaPorte Avenue, Fort Collins, CO, 80521, USA
| | - Todd Atwood
- U.S. Geological Survey, Alaska Science Center, 4210 University Drive, Anchorage, AK, 99508, USA
| | - Karsten Hueffer
- Department of Veterinary Medicine, College of Natural Science and Mathematics, University of Alaska Fairbanks, Fairbanks, AK, 99775, USA
| | - Colleen Duncan
- Veterinary Diagnostic Laboratory, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, 300 West Drake Road, Fort Collins, CO, 80524, USA.
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Lillie M, Grueber CE, Sutton JT, Howitt R, Bishop PJ, Gleeson D, Belov K. Selection on MHC class II supertypes in the New Zealand endemic Hochstetter's frog. BMC Evol Biol 2015; 15:63. [PMID: 25886729 PMCID: PMC4415247 DOI: 10.1186/s12862-015-0342-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 03/27/2015] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND The New Zealand native frogs, family Leiopelmatidae, are among the most archaic in the world. Leiopelma hochstetteri (Hochstetter's frog) is a small, semi-aquatic frog with numerous, fragmented populations scattered across New Zealand's North Island. We characterized a major histocompatibility complex (MHC) class II B gene (DAB) in L. hochstetteri from a spleen transcriptome, and then compared its diversity to neutral microsatellite markers to assess the adaptive genetic diversity of five populations ("evolutionarily significant units", ESUs). RESULTS L. hochstetteri possessed very high MHC diversity, with 74 DAB alleles characterized. Extremely high differentiation was observed at the DAB locus, with only two alleles shared between populations, a pattern that was not reflected in the microsatellites. Clustering analysis on putative peptide binding residues of the DAB alleles indicated four functional supertypes, all of which were represented in 4 of 5 populations, albeit at different frequencies. Otawa was an exception to these observations, with only two DAB alleles present. CONCLUSIONS This study of MHC diversity highlights extreme population differentiation at this functional locus. Supertype differentiation was high among populations, suggesting spatial and/or temporal variation in selection pressures. Low DAB diversity in Otawa may limit this population's adaptive potential to future pathogenic challenges.
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Affiliation(s)
- Mette Lillie
- Faculty of Veterinary Science, University of Sydney, Sydney, Australia.
| | - Catherine E Grueber
- Faculty of Veterinary Science, University of Sydney, Sydney, Australia.
- San Diego Zoo Global, San Diego, USA.
| | - Jolene T Sutton
- Department of Biology, University of Hawai'i at Mānoa, Honolulu, USA.
| | | | - Phillip J Bishop
- Department of Biology, University of Otago, Dunedin, New Zealand.
| | - Dianne Gleeson
- Landcare Research, Auckland, New Zealand.
- Institute for Applied Ecology, University of Canberra, Bruce, Australia.
| | - Katherine Belov
- Faculty of Veterinary Science, University of Sydney, Sydney, Australia.
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Jenssen BM, Villanger GD, Gabrielsen KM, Bytingsvik J, Bechshoft T, Ciesielski TM, Sonne C, Dietz R. Anthropogenic flank attack on polar bears: interacting consequences of climate warming and pollutant exposure. Front Ecol Evol 2015. [DOI: 10.3389/fevo.2015.00016] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Du L, Li W, Fan Z, Shen F, Yang M, Wang Z, Jian Z, Hou R, Yue B, Zhang X. First insights into the giant panda (Ailuropoda melanoleuca) blood transcriptome: a resource for novel gene loci and immunogenetics. Mol Ecol Resour 2015; 15:1001-13. [DOI: 10.1111/1755-0998.12367] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 12/20/2022]
Affiliation(s)
- Lianming Du
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Wujiao Li
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zhenxin Fan
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Fujun Shen
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife; Chengdu Research Base of Giant Panda Breeding; Chengdu Sichuan 610081 China
| | - Mingyu Yang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zili Wang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Zuoyi Jian
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Rong Hou
- The Sichuan Key Laboratory for Conservation Biology of Endangered Wildlife; Chengdu Research Base of Giant Panda Breeding; Chengdu Sichuan 610081 China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment; Ministry of Education; College of Life Science; Sichuan University; Chengdu Sichuan 610064 China
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Weber DS, Mandler T, Dyck M, Van Coeverden De Groot PJ, Lee DS, Clark DA. Unexpected and undesired conservation outcomes of wildlife trade bans—An emerging problem for stakeholders? Glob Ecol Conserv 2015. [DOI: 10.1016/j.gecco.2015.01.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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20
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Gormezano LJ, Rockwell RF. What to eat now? Shifts in polar bear diet during the ice-free season in western Hudson Bay. Ecol Evol 2013; 3:3509-23. [PMID: 24223286 PMCID: PMC3797495 DOI: 10.1002/ece3.740] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/15/2013] [Accepted: 07/24/2013] [Indexed: 11/24/2022] Open
Abstract
Under current climate trends, spring ice breakup in Hudson Bay is advancing rapidly, leaving polar bears (Ursus maritimus) less time to hunt seals during the spring when they accumulate the majority of their annual fat reserves. For this reason, foods that polar bears consume during the ice-free season may become increasingly important in alleviating nutritional stress from lost seal hunting opportunities. Defining how the terrestrial diet might have changed since the onset of rapid climate change is an important step in understanding how polar bears may be reacting to climate change. We characterized the current terrestrial diet of polar bears in western Hudson Bay by evaluating the contents of passively sampled scat and comparing it to a similar study conducted 40 years ago. While the two terrestrial diets broadly overlap, polar bears currently appear to be exploiting increasingly abundant resources such as caribou (Rangifer tarandus) and snow geese (Chen caerulescens caerulescens) and newly available resources such as eggs. This opportunistic shift is similar to the diet mixing strategy common among other Arctic predators and bear species. We discuss whether the observed diet shift is solely a response to a nutritional stress or is an expression of plastic foraging behavior.
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Affiliation(s)
- Linda J Gormezano
- Division of Vertebrate Zoology, American Museum of Natural History 79th Street and Central Park West, New York, NY, 10024-5192
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