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Wehrenberg G, Tokarska M, Cocchiararo B, Nowak C. A reduced SNP panel optimised for non-invasive genetic assessment of a genetically impoverished conservation icon, the European bison. Sci Rep 2024; 14:1875. [PMID: 38253649 PMCID: PMC10803807 DOI: 10.1038/s41598-024-51495-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The European bison was saved from the brink of extinction due to considerable conservation efforts since the early twentieth century. The current global population of > 9500 individuals is the result of successful ex situ breeding based on a stock of only 12 founders, resulting in an extremely low level of genetic variability. Due to the low allelic diversity, traditional molecular tools, such as microsatellites, fail to provide sufficient resolution for accurate genetic assessments in European bison, let alone from non-invasive samples. Here, we present a SNP panel for accurate high-resolution genotyping of European bison, which is suitable for a wide variety of sample types. The panel accommodates 96 markers allowing for individual and parental assignment, sex determination, breeding line discrimination, and cross-species detection. Two applications were shown to be utilisable in further Bos species with potential conservation significance. The new SNP panel will allow to tackle crucial tasks in European bison conservation, including the genetic monitoring of reintroduced populations, and a molecular assessment of pedigree data documented in the world's first studbook of a threatened species.
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Affiliation(s)
- Gerrit Wehrenberg
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany.
- Department of Ecology and Evolution, Biologicum, Johann Wolfgang Goethe-University, Max-von-Laue-Straße 13, 60438, Frankfurt am Main, Germany.
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany.
- Ecology and Genetics Research Unit, University of Oulu, P.O. Box 8000, 90014, Oulu, Finland.
| | | | - Berardino Cocchiararo
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
| | - Carsten Nowak
- Centre for Wildlife Genetics, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystraße 12, 63571, Gelnhausen, Germany
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325, Frankfurt am Main, Germany
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2
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Pilowsky JA, Brown SC, Llamas B, van Loenen AL, Kowalczyk R, Hofman-Kamińska E, Manaseryan NH, Rusu V, Križnar M, Rahbek C, Fordham DA. Millennial processes of population decline, range contraction and near extinction of the European bison. Proc Biol Sci 2023; 290:20231095. [PMID: 38087919 PMCID: PMC10716654 DOI: 10.1098/rspb.2023.1095] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 11/19/2023] [Indexed: 12/18/2023] Open
Abstract
European bison (Bison bonasus) were widespread throughout Europe during the late Pleistocene. However, the contributions of environmental change and humans to their near extinction have never been resolved. Using process-explicit models, fossils and ancient DNA, we disentangle the combinations of threatening processes that drove population declines and regional extinctions of European bison through space and across time. We show that the population size of European bison declined abruptly at the termination of the Pleistocene in response to rapid environmental change, hunting by humans and their interaction. Human activities prevented populations of European bison from rebounding in the Holocene, despite improved environmental conditions. Hunting caused range loss in the north and east of its distribution, while land use change was responsible for losses in the west and south. Advances in hunting technologies from 1500 CE were needed to simulate low abundances observed in 1870 CE. While our findings show that humans were an important driver of the extinction of the European bison in the wild, vast areas of its range vanished during the Pleistocene-Holocene transition because of post-glacial environmental change. These areas of its former range have been climatically unsuitable for millennia and should not be considered in reintroduction efforts.
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Affiliation(s)
- July A. Pilowsky
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
| | - Stuart C. Brown
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen K 1350, Denmark
| | - Bastien Llamas
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, South Australia 5005, Australia
- Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, South Australia 5001, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Ayla L. van Loenen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, 17-230 Białowieża, Poland
| | | | - Ninna H. Manaseryan
- The Scientific Centre of Zoology and Hydroecology of National Academy of Sciences of Armenia, Institute of Zoology, 0014 Yerevan, Republic of Armenia
| | - Viorelia Rusu
- Institute of Zoology, Academy of Sciences of Moldova, Chisinau MD-2028, Republic of Moldova
| | - Matija Križnar
- Slovenian Museum of Natural History, Department of Geology, SI-1001 Ljubljana, Slovenia
| | - Carsten Rahbek
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Center for Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Danish Institute for Advanced Study, University of Southern Denmark, Odense M 5230, Denmark
- Institute of Ecology, Peking University, Beijing, People's Republic of China
| | - Damien A. Fordham
- The Environment Institute and School of Biological Sciences, University of Adelaide, South Australia 5005, Australia
- Center for Macroecology, Evolution and Climate, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
- Center for Mountain Biodiversity, Globe Institute, University of Copenhagen, Copenhagen Ø 2100, Denmark
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3
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Bluhm H, Diserens TA, Engleder T, Heising K, Heurich M, Janík T, Jirků M, Klich D, König HJ, Kowalczyk R, Kuijper D, Maślanko W, Michler F, Neumann W, Oeser J, Olech W, Perzanowski K, Ratkiewicz M, Romportl D, Šálek M, Kuemmerle T. Widespread habitat for Europe's largest herbivores, but poor connectivity limits recolonization. DIVERS DISTRIB 2023. [DOI: 10.1111/ddi.13671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Hendrik Bluhm
- Geography Department Humboldt‐Universität zu Berlin Berlin Germany
| | - Tom A. Diserens
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
- Faculty of Biology University of Warsaw Warsaw Poland
| | | | - Kaja Heising
- Wisent‐Welt Wittgenstein e.V Bad Berleburg Germany
| | - Marco Heurich
- Chair of Wildlife Ecology and Wildlife Management University of Freiburg Freiburg Germany
- Department of Visitor Management and National Park Monitoring Bavarian Forest National Park Grafenau Germany
- Institute for Forest and Wildlife Management Inland Norway University of Applied Sciences Koppang Norway
| | - Tomáš Janík
- Department of Physical Geography and Geoecology, Faculty of Science Charles University Praha Czechia
- Department of Spatial Ecology The Silva Tarouca Research Institute for Landscape and Ornamental Gardening (VÚKOZ) Průhonice Czechia
| | - Miloslav Jirků
- Institute of Parasitology, Biology Centre Czech Academy of Sciences České Budějovice Czech Republic
| | - Daniel Klich
- Department of Animal Genetics and Conservation Warsaw University of Life Sciences Warsaw Poland
| | - Hannes J. König
- Junior Research Group Human‐Wildlife Conflict and Coexistence Leibniz Centre for Agricultural Landscape Research (ZALF) Müncheberg Germany
| | - Rafał Kowalczyk
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - Dries Kuijper
- Mammal Research Institute Polish Academy of Sciences Białowieża Poland
| | - Weronika Maślanko
- Department of Animal Ethology and Wildlife Management University of Life Sciences in Lublin Lublin Poland
| | - Frank‐Uwe Michler
- Faculty of Forest and Environment Eberswalde University for Sustainable Development Eberswalde Germany
| | - Wiebke Neumann
- Department of Wildlife, Fish and Environmental Studies Swedish University of Agricultural Sciences
| | - Julian Oeser
- Geography Department Humboldt‐Universität zu Berlin Berlin Germany
| | - Wanda Olech
- Department of Animal Genetics and Conservation Warsaw University of Life Sciences Warsaw Poland
| | - Kajetan Perzanowski
- Institute of Biological Sciences Catholic University of Lublin Lublin Poland
| | | | - Dušan Romportl
- Department of Physical Geography and Geoecology, Faculty of Science Charles University Praha Czechia
- Department of Spatial Ecology The Silva Tarouca Research Institute for Landscape and Ornamental Gardening (VÚKOZ) Průhonice Czechia
| | - Martin Šálek
- Czech Academy of Sciences Institute of Vertebrate Biology Brno Czech Republic
- Faculty of Environmental Sciences Czech University of Life Sciences Prague Suchdol Czech Republic
| | - Tobias Kuemmerle
- Geography Department Humboldt‐Universität zu Berlin Berlin Germany
- Integrative Research Institute on Transformation in Human‐Environment Systems (IRI THESys) Humboldt‐Universität zu Berlin Berlin Germany
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4
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Ferreiro AM, Soibelzon E, Pinotti JD, Poljak S, Chiappero MB. Reconstructing the distribution of Chacoan biota from current and past evidence: the case of the southern three-banded armadillo Tolypeutes matacus (Desmarest, 1804). J MAMM EVOL 2022. [DOI: 10.1007/s10914-022-09627-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Demographic Expansions and the Emergence of Host Specialization in Genetically Distinct Ecotypes of the Tick-Transmitted Bacterium Anaplasma phagocytophilum. Appl Environ Microbiol 2022; 88:e0061722. [PMID: 35867580 PMCID: PMC9317897 DOI: 10.1128/aem.00617-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
In Europe, genetically distinct ecotypes of the tick-vectored bacterium Anaplasma phagocytophilum circulate among mammals in three discrete enzootic cycles. To date, potential ecological factors that contributed to the emergence of these divergent ecotypes have been poorly studied. Here, we show that the ecotype that predominantly infects roe deer (Capreolus capreolus) is evolutionarily derived. Its divergence from a host generalist ancestor occurred after the last glacial maximum as mammal populations, including roe deer, recolonized the European mainland from southern refugia. We also provide evidence that this host specialist ecotype's effective population size (Ne) has tracked changes in the population of its roe deer host. Specifically, both host and bacterium have undergone substantial increases in Ne over the past 1,500 years. In contrast, we show that while it appears to have undergone a major population expansion starting ~3,500 years ago, in the past 500 years, the contemporary host generalist ecotype has experienced a substantial reduction in genetic diversity levels, possibly as a result of reduced opportunities for transmission between competent hosts. IMPORTANCE The findings of this study reveal specific events important for the evolution of host specialization in a naturally occurring, obligately intracellular bacterial pathogen. Specifically, they show that host range shifts and the emergence of host specialization may occur during periods of population growth in a generalist ancestor. Our results also demonstrate the close correlation between demographic patterns in host and pathogen for a specialist system. These findings have important relevance for understanding the evolution of host range diversity. They may inform future work on host range dynamics, and they provide insights for understanding the emergence of pathogens that have human and veterinary health implications.
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6
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Handler SD, Ledee OE, Hoving CL, Zuckerberg B, Swanston CW. A menu of climate change adaptation actions for terrestrial wildlife management. WILDLIFE SOC B 2022. [DOI: 10.1002/wsb.1331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Stephen D. Handler
- USDA Forest Service and Northern Institute of Applied Climate Science 410 MacInnes Drive Houghton MI 49931 USA
| | - Olivia E. Ledee
- U.S. Geological Survey, Midwest Climate Adaptation Science Center 1992 Folwell Ave St. Paul MN 55116 USA
| | | | - Benjamin Zuckerberg
- Department of Forest and Wildlife Ecology University of Wisconsin‐Madison 1620 Linden Drive Madison WI 53705 USA
| | - Christopher W. Swanston
- USDA Forest Service and Northern Institute of Applied Climate Science 410 MacInnes Drive Houghton MI 49931 USA
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7
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The Reintroduction Analysis of European Bison (Bison bonasus L., 1758) in the North of Romania and the Identification of the Most Favourable Locations. FORESTS 2022. [DOI: 10.3390/f13060920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We analysed the possibility of reintroducing the European bison (Bison bonasus L.) in the north of Romania—in Suceava, Neamț, and Maramureș counties—as well as increasing the wild European bison population in Neamț county to improve the genetic quality of the existing population. Currently, there is a population of over 50 individuals in the wild in Vânători Neamț Natural Park, Romania. At the same time, an attempt was made to identify the connecting corridors between the free European bison in Neamț county and other populations through new nuclei of European bison released in Suceava and Maramureș counties. In this regard, the hunting grounds with the highest ecological potential for the analysed species were identified using GIS spatial analysis techniques. The aim was also to trace possible ecological corridors linking different reintroduction locations, taking into account the ecological claims of the species. The analysis also followed the size of the European bison groups to be released, the sex ratio of each group, and the periodicity of their releasing. In order to reach viable populations, scenarios and simulations were carried out depending on the age, number, and sex of the relocated specimens. In this regard, the dynamics and the minimum viable population that could survive without risk of extinction were highlighted. The analysis showed that the analysed area has a high potential for the reintroduction of European bison in the wild. The release and creation of new European bison nuclei in the wild creates the premises for natural contacts with the existing free populations in the wild, genetic improvement, and increasing fauna diversity with ecological, social, and economic implications.
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8
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Williams S, Perkins SE, Dennis R, Byrne JP, Thomas RJ. An evidence‐based assessment of the past distribution of Golden and White‐tailed Eagles across Wales. CONSERVATION SCIENCE AND PRACTICE 2020. [DOI: 10.1111/csp2.240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Affiliation(s)
- Sophie‐lee Williams
- School of Biosciences, Sir Martin Evans Building, Cardiff University Cardiff UK
- The Eagle Reintroduction Wales (ERW) Project Cardiff UK
| | - Sarah E. Perkins
- School of Biosciences, Sir Martin Evans Building, Cardiff University Cardiff UK
- The Eagle Reintroduction Wales (ERW) Project Cardiff UK
| | - Roy Dennis
- The Eagle Reintroduction Wales (ERW) Project Cardiff UK
- Roy Dennis Wildlife Foundation Moray UK
| | - James P. Byrne
- The Eagle Reintroduction Wales (ERW) Project Cardiff UK
- Wildlife Trusts Wales Cardiff UK
| | - Robert J. Thomas
- School of Biosciences, Sir Martin Evans Building, Cardiff University Cardiff UK
- The Eagle Reintroduction Wales (ERW) Project Cardiff UK
- Eco‐explore Community Interest Company Nelson UK
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9
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Kuemmerle T, Perzanowski K, Bleyhl B. European bison conservation must move beyond entrenched debates – response to Kerley
et al.
(2020). Anim Conserv 2020. [DOI: 10.1111/acv.12606] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- T. Kuemmerle
- Geography Department Humboldt‐University Berlin Berlin Germany
- Integrative Research Institute on Transformations of Human‐Environment Systems (IRI THESys) Humboldt‐University Berlin Berlin Germany
| | - K. Perzanowski
- Faculty of Science and Health Catholic University of Lublin Lublin Poland
| | - B. Bleyhl
- Geography Department Humboldt‐University Berlin Berlin Germany
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10
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Pedersen PBM, Olsen JB, Sandel B, Svenning JC. Wild Steps in a semi-wild setting? Habitat selection and behavior of European bison reintroduced to an enclosure in an anthropogenic landscape. PLoS One 2019; 14:e0198308. [PMID: 31697680 PMCID: PMC6837835 DOI: 10.1371/journal.pone.0198308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 10/10/2019] [Indexed: 01/05/2023] Open
Abstract
Recently, several wild or semi-wild herds of European bison have been reintroduced across Europe. It is essential for future successful bison reintroductions to know how the European bison use different habitats, which environmental parameters drive their habitat selection, and whether their habitat use and behavioural patterns in new reintroduction sites differ from habitats where European bison have been roaming freely for a long time. Here, we address these questions for a 40-ha enclosed site that has been inhabited by semi-free ranging European bison since 2012. The site, Vorup Meadows, is adjacent to the Gudenå river in Denmark and consists of human-modified riparian meadows. During 2013 we monitored the behavioural pattern and spatial use of the 11 bison present and in parallel carried out floristic analyses to assess habitat structure and food quality in the enclosure. We tested habitat use and selection against environmental parameters such as habitat characteristics, plant community traits, topography, and management area (release area vs. meadow area) using linear regression and spatial models. The bison herd had comparable diurnal activity patterns as observed in previous studies on free-roaming bison herds. Topography emerged as the main predictor of the frequency of occurrence in our spatial models, with high-lying drier areas being used more. Bison did not prefer open areas over areas with tree cover when accounting for habitat availability. However, they spent significantly more time in the release area, a former agricultural field with supplementary fodder, than expected from availability compared to the rest of the enclosure, a meadow with tree patches. We wish to increase awareness of possible long-term ethological effects of the release site and the management protocols accomplished here that might reduce the ecological impact by the bison in the target habitat, and thereby compromise or even oppose the conservation goals of the conservation efforts.
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Affiliation(s)
- Pil Birkefeldt Møller Pedersen
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
- Department of Bioscience, Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Aarhus University, Aarhus, Denmark
- * E-mail:
| | - Joanna B. Olsen
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
| | - Brody Sandel
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
| | - Jens-Christian Svenning
- Department of Bioscience, Section for Ecoinformatics & Biodiversity, Aarhus University, Aarhus, Denmark
- Department of Bioscience, Center for Biodiversity Dynamics in a Changing World (BIOCHANGE), Aarhus University, Aarhus, Denmark
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11
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Perzanowski K, Bleyhl B, Olech W, Kuemmerle T. Connectivity or isolation? Identifying reintroduction sites for multiple conservation objectives for wisents in Poland. Anim Conserv 2019. [DOI: 10.1111/acv.12530] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- K. Perzanowski
- Institute of Landscape Architecture Catholic University of Lublin Lublin Poland
| | - B. Bleyhl
- Geography Department Humboldt‐University Berlin Berlin Germany
| | - W. Olech
- Department of Animal Genetics and Breeding Warsaw University of Life Sciences Warsaw Poland
| | - T. Kuemmerle
- Geography Department Humboldt‐University Berlin Berlin Germany
- Integrative Research Institute on Transformations of Human‐Environment Systems (IRI THESys) Humboldt‐University Berlin Berlin Germany
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12
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Romero-Muñoz A, Torres R, Noss AJ, Giordano AJ, Quiroga V, Thompson JJ, Baumann M, Altrichter M, McBride R, Velilla M, Arispe R, Kuemmerle T. Habitat loss and overhunting synergistically drive the extirpation of jaguars from the Gran Chaco. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12843] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
| | - Ricardo Torres
- Museo de Zoología; Facultad de Ciencias Exactas; Físicas y Naturales; Universidad Nacional de Córdoba; Córdoba Argentina
- Instituto de Diversidad y Ecología Animal (IDEA-CONICET); Universidad Nacional de Córdoba; Córdoba Argentina
| | - Andrew J. Noss
- Department of Geography; University of Florida; Gainesville Florida
| | - Anthony J. Giordano
- S.P.E.C.I.E.S. (Society for the Preservation of Endangered Carnivores and their International Ecological Study); Ventura California
- Center for Tropical Research; Institute of the Environment and Sustainability; University of California - Los Angeles; Los Angeles California
| | - Verónica Quiroga
- Instituto de Diversidad y Ecología Animal (IDEA-CONICET); Universidad Nacional de Córdoba; Córdoba Argentina
- Centro de Investigaciones del Bosque Atlántico (CeIBA); Puerto Iguazú Misiones Argentina
| | - Jeffrey J. Thompson
- Guyra Paraguay; Asunción Paraguay
- Consejo Nacional de Ciencia y Tecnología (CONACYT); Asunción Paraguay
- Instituto Saite; Asunción Paraguay
| | - Matthias Baumann
- Geography Department; Humboldt University Berlin; Berlin Germany
| | | | - Roy McBride
- Faro Moro Eco Research; Departamento de Boquerón; Paraguay
| | - Marianela Velilla
- Guyra Paraguay; Asunción Paraguay
- Consejo Nacional de Ciencia y Tecnología (CONACYT); Asunción Paraguay
- Instituto Saite; Asunción Paraguay
| | - Rosario Arispe
- Museo de Historia Natural Noel Kempff Mercado; Santa Cruz de la Sierra Bolivia
| | - Tobias Kuemmerle
- Geography Department; Humboldt University Berlin; Berlin Germany
- Integrative Research Institute on Transformations of Human-Environment Systems (IRI THESys); Berlin Germany
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13
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Wecek K, Hartmann S, Paijmans JLA, Taron U, Xenikoudakis G, Cahill JA, Heintzman PD, Shapiro B, Baryshnikov G, Bunevich AN, Crees JJ, Dobosz R, Manaserian N, Okarma H, Tokarska M, Turvey ST, Wójcik JM, Zyla W, Szymura JM, Hofreiter M, Barlow A. Complex Admixture Preceded and Followed the Extinction of Wisent in the Wild. Mol Biol Evol 2017; 34:598-612. [PMID: 28007976 PMCID: PMC5356474 DOI: 10.1093/molbev/msw254] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Retracing complex population processes that precede extreme bottlenecks may be impossible using data from living individuals. The wisent (Bison bonasus), Europe’s largest terrestrial mammal, exemplifies such a population history, having gone extinct in the wild but subsequently restored by captive breeding efforts. Using low coverage genomic data from modern and historical individuals, we investigate population processes occurring before and after this extinction. Analysis of aligned genomes supports the division of wisent into two previously recognized subspecies, but almost half of the genomic alignment contradicts this population history as a result of incomplete lineage sorting and admixture. Admixture between subspecies populations occurred prior to extinction and subsequently during the captive breeding program. Admixture with the Bos cattle lineage is also widespread but results from ancient events rather than recent hybridization with domestics. Our study demonstrates the huge potential of historical genomes for both studying evolutionary histories and for guiding conservation strategies.
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Affiliation(s)
- Karolina Wecek
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Stefanie Hartmann
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Ulrike Taron
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - James A Cahill
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | - Peter D Heintzman
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA.,University of California Santa Cruz Genomics Institute, University of California, Santa Cruz, CA
| | - Gennady Baryshnikov
- Laboratory of Theriology, Zoological Institute of the Russian Academy of Sciences, Petersberg, Russia
| | | | - Jennifer J Crees
- Zoological Society of London, Institute of Zoology, Regent's Park, London, United Kingdom
| | - Roland Dobosz
- Upper Silesian Museum, Bytom, Poland.,Department of Zoology, Faculty of Biology and Environmental Protection, University of Silesia, Katowice, Poland
| | - Ninna Manaserian
- Institute of Zoology Armenian National Academy of Sciences, Yerevan, Armenia
| | - Henryk Okarma
- Institute of Nature Conservation Polish Academy of Sciences, Kraków, Poland
| | | | - Samuel T Turvey
- Zoological Society of London, Institute of Zoology, Regent's Park, London, United Kingdom
| | - Jan M Wójcik
- Mammal Research Institute Polish Academy of Sciences, Bialowieza, Poland
| | | | - Jacek M Szymura
- Department of Comparative Anatomy, Institute of Zoology, Jagiellonian University, Kraków, Poland
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Axel Barlow
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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14
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Crees JJ, Carbone C, Sommer RS, Benecke N, Turvey ST. Millennial-scale faunal record reveals differential resilience of European large mammals to human impacts across the Holocene. Proc Biol Sci 2016; 283:20152152. [PMID: 27009229 PMCID: PMC4822451 DOI: 10.1098/rspb.2015.2152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 02/26/2016] [Indexed: 11/26/2022] Open
Abstract
The use of short-term indicators for understanding patterns and processes of biodiversity loss can mask longer-term faunal responses to human pressures. We use an extensive database of approximately 18 700 mammalian zooarchaeological records for the last 11 700 years across Europe to reconstruct spatio-temporal dynamics of Holocene range change for 15 large-bodied mammal species. European mammals experienced protracted, non-congruent range losses, with significant declines starting in some species approximately 3000 years ago and continuing to the present, and with the timing, duration and magnitude of declines varying individually between species. Some European mammals became globally extinct during the Holocene, whereas others experienced limited or no significant range change. These findings demonstrate the relatively early onset of prehistoric human impacts on postglacial biodiversity, and mirror species-specific patterns of mammalian extinction during the Late Pleistocene. Herbivores experienced significantly greater declines than carnivores, revealing an important historical extinction filter that informs our understanding of relative resilience and vulnerability to human pressures for different taxa. We highlight the importance of large-scale, long-term datasets for understanding complex protracted extinction processes, although the dynamic pattern of progressive faunal depletion of European mammal assemblages across the Holocene challenges easy identification of ‘static’ past baselines to inform current-day environmental management and restoration.
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Affiliation(s)
- Jennifer J Crees
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Chris Carbone
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
| | - Robert S Sommer
- Department of Landscape Ecology, Institute for Natural Resource Conservation, University of Kiel, Olshausenstrasse 75, 24118 Kiel, Germany
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, Im Dol 2-6, Berlin 14195, Germany
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, Regent's Park, London NW1 4RY, UK
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15
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Niche overlap of mountain hare subspecies and the vulnerability of their ranges to invasion by the European hare; the (bad) luck of the Irish. Biol Invasions 2016. [DOI: 10.1007/s10530-016-1330-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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16
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Gautier M, Moazami-Goudarzi K, Levéziel H, Parinello H, Grohs C, Rialle S, Kowalczyk R, Flori L. Deciphering the Wisent Demographic and Adaptive Histories from Individual Whole-Genome Sequences. Mol Biol Evol 2016; 33:2801-2814. [PMID: 27436010 PMCID: PMC5062319 DOI: 10.1093/molbev/msw144] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
As the largest European herbivore, the wisent (Bison bonasus) is emblematic of the continent wildlife but has unclear origins. Here, we infer its demographic and adaptive histories from two individual whole-genome sequences via a detailed comparative analysis with bovine genomes. We estimate that the wisent and bovine species diverged from 1.7 × 106 to 850,000 years before present (YBP) through a speciation process involving an extended period of limited gene flow. Our data further support the occurrence of more recent secondary contacts, posterior to the Bos taurus and Bos indicus divergence (∼150,000 YBP), between the wisent and (European) taurine cattle lineages. Although the wisent and bovine population sizes experienced a similar sharp decline since the Last Glacial Maximum, we find that the wisent demography remained more fluctuating during the Pleistocene. This is in agreement with a scenario in which wisents responded to successive glaciations by habitat fragmentation rather than southward and eastward migration as for the bovine ancestors. We finally detect 423 genes under positive selection between the wisent and bovine lineages, which shed a new light on the genome response to different living conditions (temperature, available food resource, and pathogen exposure) and on the key gene functions altered by the domestication process.
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Affiliation(s)
- Mathieu Gautier
- CBGP, INRA, CIRAD, IRD, Supagro, Montferrier-sur-Lez, France IBC, Institut de Biologie Computationnelle, Montpellier, France
| | | | | | - Hugues Parinello
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Cécile Grohs
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Stéphanie Rialle
- MGX-Montpellier GenomiX, c/o Institut de Génomique Fonctionnelle, Montpellier, France
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Białowieża, Poland
| | - Laurence Flori
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France INTERTRYP, CIRAD, IRD, Montpellier, France
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17
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Ohashi H, Kominami Y, Higa M, Koide D, Nakao K, Tsuyama I, Matsui T, Tanaka N. Land abandonment and changes in snow cover period accelerate range expansions of sika deer. Ecol Evol 2016; 6:7763-7775. [PMID: 30128126 PMCID: PMC6093158 DOI: 10.1002/ece3.2514] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 08/29/2016] [Accepted: 08/31/2016] [Indexed: 11/09/2022] Open
Abstract
Ongoing climate change and land‐use change have the potential to substantially alter the distribution of large herbivores. This may result in drastic changes in ecosystems by changing plant–herbivore interactions. Here, we developed a model explaining sika deer persistence and colonization between 25 years in terms of neighborhood occupancy and habitat suitability. We used climatic, land‐use, and topographic variables to calculate the habitat suitability and evaluated the contributions of the variables to past range changes of sika deer. We used this model to predict the changes in the range of sika deer over the next 100 years under four scenario groups with the combination of land‐use change and climate change. Our results showed that both climate change and land‐use change had affected the range of sika deer in the past 25 years. Habitat suitability increased in northern or mountainous regions, which account for 71.6% of Japan, in line with a decrease in the snow cover period. Habitat suitability decreased in suburban areas, which account for 28.4% of Japan, corresponding to land‐use changes related to urbanization. In the next 100 years, the decrease in snow cover period and the increase in land abandonment were predicted to accelerate the range expansion of sika deer. Comparison of these two driving factors revealed that climate change will contribute more to range expansion, particularly from the 2070s onward. In scenarios that assumed the influence of both climate change and land‐use change, the total sika deer range increased by between +4.6% and +11.9% from the baseline scenario. Climate change and land‐use change will require additional efforts for future management of sika deer, particularly in the long term.
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Affiliation(s)
- Haruka Ohashi
- Department of Plant Ecology Forestry and Forest Products Research Institute 1 Matsunosato Tsukuba Ibaraki 305-8687 Japan.,Center for International Partnerships and Research on Climate Change Forestry and Forest Products Research Institute 1 Matsunosato Tsukuba Ibaraki 305-8687 Japan
| | - Yuji Kominami
- Kansai Research Center Forestry and Forest Products Research Institute 68 Nagaikyutaro, Momoyama-cho Fushimi Kyoto Kyoto 612-0855 Japan
| | - Motoki Higa
- Faculty of Science Kochi University 2-5-1 Akebono-cho Kochi Kochi 780-8520 Japan
| | - Dai Koide
- Department of Plant Ecology Forestry and Forest Products Research Institute 1 Matsunosato Tsukuba Ibaraki 305-8687 Japan.,Center for Global Environmental Research National Institute for Environmental Studies 16-2 Onogawa Tsukuba Ibaraki 305-8687 Japan
| | - Katsuhiro Nakao
- Kansai Research Center Forestry and Forest Products Research Institute 68 Nagaikyutaro, Momoyama-cho Fushimi Kyoto Kyoto 612-0855 Japan
| | - Ikutaro Tsuyama
- Hokkaido Research Center Forestry and Forest Products Research Institute 7 Hitsujigaoka, Toyohira Sapporo Hokkaido 062-8516 Japan
| | - Tetsuya Matsui
- Department of Plant Ecology Forestry and Forest Products Research Institute 1 Matsunosato Tsukuba Ibaraki 305-8687 Japan.,Center for International Partnerships and Research on Climate Change Forestry and Forest Products Research Institute 1 Matsunosato Tsukuba Ibaraki 305-8687 Japan
| | - Nobuyuki Tanaka
- Department of Plant Ecology Forestry and Forest Products Research Institute 1 Matsunosato Tsukuba Ibaraki 305-8687 Japan.,Department of International Agricultural Development Tokyo University of Agriculture 1-1-1 Sakuragaoka Setagaya Tokyo 156-8502 Japan
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18
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Wang WJ, He HS, III FRT, Fraser JS, Hanberry BB, Dijak WD. Importance of succession, harvest, and climate change in determining future composition in U.S. Central Hardwood Forests. Ecosphere 2015. [DOI: 10.1890/es15-00238.1] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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19
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Labay BJ, Hendrickson DA, Cohen AE, Bonner TH, King RS, Kleinsasser LJ, Linam GW, Winemiller KO. Can Species Distribution Models Aid Bioassessment when Reference Sites are Lacking? Tests Based on Freshwater Fishes. ENVIRONMENTAL MANAGEMENT 2015; 56:835-846. [PMID: 26092052 DOI: 10.1007/s00267-015-0567-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 06/15/2015] [Indexed: 06/04/2023]
Abstract
Recent literature reviews of bioassessment methods raise questions about use of least-impacted reference sites to characterize natural conditions that no longer exist within contemporary landscapes. We explore an alternate approach for bioassessment that uses species site occupancy data from museum archives as input for species distribution models (SDMs) stacked to predict species assemblages of freshwater fishes in Texas. When data for estimating reference conditions are lacking, deviation between richness of contemporary versus modeled species assemblages could provide a means to infer relative biological integrity at appropriate spatial scales. We constructed SDMs for 100 freshwater fish species to compare predicted species assemblages to data on contemporary assemblages acquired by four independent surveys that sampled 269 sites. We then compared site-specific observed/predicted ratios of the number of species at sites to scores from a multimetric index of biotic integrity (IBI). Predicted numbers of species were moderately to strongly correlated with the numbers observed by the four surveys. We found significant, though weak, relationships between observed/predicted ratios and IBI scores. SDM-based assessments identified patterns of local assemblage change that were congruent with IBI inferences; however, modeling artifacts that likely contributed to over-prediction of species presence may restrict the stand-alone use of SDM-derived patterns for bioassessment and therefore warrant examination. Our results suggest that when extensive standardized survey data that include reference sites are lacking, as is commonly the case, SDMs derived from generally much more readily available species site occupancy data could be used to provide a complementary tool for bioassessment.
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Affiliation(s)
- Ben J Labay
- Department of Integrative Biology, Biodiversity Collections, University of Texas, Austin, TX, USA,
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20
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Kolanowska M, Konowalik K. Niche Conservatism and Future Changes in the Potential Area Coverage ofArundina graminifolia, an Invasive Orchid Species from Southeast Asia. Biotropica 2014. [DOI: 10.1111/btp.12089] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marta Kolanowska
- Department of Plant Taxonomy and Nature Conservation; University of Gdańsk; ul. Wita Stwosza 59 80-308 Gdańsk Poland
| | - Kamil Konowalik
- Institute of Botany; University of Regensburg; Universitätsstr. 31 D-93053 Regensburg Bavaria
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21
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Scheiter S, Langan L, Higgins SI. Next-generation dynamic global vegetation models: learning from community ecology. THE NEW PHYTOLOGIST 2013; 198:957-969. [PMID: 23496172 DOI: 10.1111/nph.12210] [Citation(s) in RCA: 179] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2012] [Accepted: 01/28/2013] [Indexed: 05/18/2023]
Abstract
Dynamic global vegetation models (DGVMs) are powerful tools to project past, current and future vegetation patterns and associated biogeochemical cycles. However, most models are limited by how they define vegetation and by their simplistic representation of competition. We discuss how concepts from community assembly theory and coexistence theory can help to improve vegetation models. We further present a trait- and individual-based vegetation model (aDGVM2) that allows individual plants to adopt a unique combination of trait values. These traits define how individual plants grow and compete. A genetic optimization algorithm is used to simulate trait inheritance and reproductive isolation between individuals. These model properties allow the assembly of plant communities that are adapted to a site's biotic and abiotic conditions. The aDGVM2 simulates how environmental conditions influence the trait spectra of plant communities; that fire selects for traits that enhance fire protection and reduces trait diversity; and the emergence of life-history strategies that are suggestive of colonization-competition trade-offs. The aDGVM2 deals with functional diversity and competition fundamentally differently from current DGVMs. This approach may yield novel insights as to how vegetation may respond to climate change and we believe it could foster collaborations between functional plant biologists and vegetation modellers.
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Affiliation(s)
- Simon Scheiter
- Biodiversität und Klima Forschungszentrum (LOEWE BiK-F), Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325, Frankfurt am Main, Germany
| | - Liam Langan
- Institut für Physische Geographie, Goethe-Universität Frankfurt am Main, Altenhöferallee 1, D-60438, Frankfurt am Main, Germany
| | - Steven I Higgins
- Institut für Physische Geographie, Goethe-Universität Frankfurt am Main, Altenhöferallee 1, D-60438, Frankfurt am Main, Germany
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22
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Kuemmerle T, Hickler T, Olofsson J, Schurgers G, Radeloff VC. Refugee species: which historic baseline should inform conservation planning? DIVERS DISTRIB 2012. [DOI: 10.1111/ddi.12013] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Tobias Kuemmerle
- Geography Department; Humboldt-Universität zu Berlin; Unter den Linden 6 10099 Berlin Germany
- Earth System Analysis; Potsdam Institute for Climate Impact Research (PIK); PO Box 60 12 03 Telegraphenberg A62 D-14412 Potsdam Germany
| | - Thomas Hickler
- LOEWE Biodiversity and Climate Research Centre (BiK-F); Senckenberganlage 25 D-60325 Frankfurt Germany
| | - Jörgen Olofsson
- Department of Physical Geography and Ecosystem Science; Lund University; Sölvegatan 12 SE-223 62 Lund Sweden
| | - Guy Schurgers
- Department of Physical Geography and Ecosystem Science; Lund University; Sölvegatan 12 SE-223 62 Lund Sweden
| | - Volker C. Radeloff
- Department of Forest and Wildlife Ecology; University of Wisconsin-Madison; 1630 Linden Drive Madison WI 53706, USA
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23
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Cromsigt JPGM, Kerley GIH, Kowalczyk R. The difficulty of using species distribution modelling for the conservation of refugee species - the example of European bison. DIVERS DISTRIB 2012. [DOI: 10.1111/j.1472-4642.2012.00927.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Joris P. G. M. Cromsigt
- Department of Wildlife, Fish, and Environmental Studies; Swedish University of Agricultural Sciences; 901 83 Umeå Sweden
- Department of Zoology; Centre for African Conservation Ecology; Nelson Mandela Metropolitan University; PO Box 77000 Port Elizabeth South Africa
| | - Graham I. H. Kerley
- Department of Zoology; Centre for African Conservation Ecology; Nelson Mandela Metropolitan University; PO Box 77000 Port Elizabeth South Africa
- Mammal Research Institute; Polish Academy of Sciences; ul. Waszkiewicza 1c 17-230 Białowieża Poland
| | - Rafał Kowalczyk
- Mammal Research Institute; Polish Academy of Sciences; ul. Waszkiewicza 1c 17-230 Białowieża Poland
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