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Conservation genomics reveals fine-scale population structuring and recent declines in the Critically Endangered Australian Kuranda Treefrog. CONSERV GENET 2023. [DOI: 10.1007/s10592-022-01499-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
AbstractThe Kuranda Treefrog occurs in tropical north-east Australia and is listed as Critically Endangered due to its small distribution and population size, with observed declines due to drought and human-associated impacts to habitat. Field surveys identified marked population declines in the mid-2000s, culminating in very low abundance at most sites in 2005 and 2006, followed by limited recovery. Here, samples from before (2001–2004) and after (2007–2009) this decline were analysed using 7132 neutral genome-wide SNPs to assess genetic connectivity among breeding sites, genetic erosion, and effective population size. We found a high level of genetic connectivity among breeding sites, but also structuring between the population at the eastern end of the distribution (Jumrum Creek) versus all other sites. Despite finding no detectable sign of genetic erosion between the two times periods, we observed a marked decrease in effective population size (Ne), from 1720 individuals pre-decline to 818 post-decline. This mirrors the decline detected in the field census data, but the magnitude of the decline suggested by the genetic data is greater. We conclude that the current effective population size for the Kuranda Treefrog remains around 800 adults, split equally between Jumrum Creek and all other sites combined. The Jumrum Creek habitat requires formal protection. Connectivity among all other sites must be maintained and improved through continued replanting of rainforest, and it is imperative that impacts to stream flow and water quality are carefully managed to maintain or increase population sizes and prevent genetic erosion.
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Iosif R, Pop MI, Chiriac S, Sandu RM, Berde L, Szabó S, Rozylowicz L, Popescu VD. Den structure and selection of denning habitat by brown bears in the Romanian Carpathians. URSUS 2020. [DOI: 10.2192/ursus-d-18-00010.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Ruben Iosif
- Faculty of Natural and Agricultural Sciences, University Ovidius Constanta, 1 Aleea Universitatii, Building B, Constanţa, 900470 Romania
| | - Mihai I. Pop
- Centre for Environmental Research (CCMESI), University of Bucharest, 1 N. Balcescu, Bucharest, 010041 Romania
| | - Silviu Chiriac
- Vrancea Environmental Protection Agency, 2 Dinicu Golescu St., Focsani, 620106 Romania
| | - Radu M. Sandu
- Vrancea Environmental Protection Agency, 2 Dinicu Golescu St., Focsani, 620106 Romania
| | - Lajos Berde
- Covasna Environmental Protection Agency, 10 Grigore Balan St., Sf. Gheorghe, 520082 Romania
| | - Szilárd Szabó
- Harghita Environmental Protection Agency, 43 Márton Áron St., Miercurea Ciuc, 530211 România
| | - Laurenţiu Rozylowicz
- Centre for Environmental Research (CCMESI), University of Bucharest, 1 N. Balcescu, Bucharest, 010041 Romania
| | - Viorel D. Popescu
- Centre for Environmental Research (CCMESI), University of Bucharest, 1 N. Balcescu, Bucharest, 010041 Romania
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Noninvasive population assessment of moose (Alces alces) by SNP genotyping of fecal pellets. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1337-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
AbstractNoninvasive genetic studies of wild animals enable the recovery of information infeasible to obtain using other means. However, the low quantity and quality of noninvasively collected DNA often challenge the retrieval of reliable genotypes, which may cause biases in downstream analyses. In this study, we optimized SNP (single nucleotide polymorphism) genotyping of fecal samples from moose (Alces alces) with the main purpose of exploring the potential of using noninvasively retrieved genotypes for individual- and sex identification. Fecal pellets were collected during the late winter of 2016 on the Swedish island of Öland in the Baltic Sea and DNA was extracted and genotyped using 86 autosomal, six sex-specific and five species diagnostic SNPs. The SNP error rate of the quality filtered dataset was 0.06 and the probability of identity for siblings below 0.001. Following a thorough quality filtering process, 182 reliable genotypes were obtained, corresponding to 100 unique individuals (37 males, 63 females), with an estimated male proportion of 37% (± 9%). The population size, estimated using two different capture-mark-recapture approaches, was found to be in the range of 115–156 individuals (95% CI). Furthermore, moose on Öland showed significantly lower heterozygosity levels (zHexp = −5.51, N = 69, pHexp = 3.56·10−8, zHobs = −3.58, N = 69, pHobs = 3.38·10−4) and appeared genetically differentiated from moose on the Swedish mainland. Thus, we show that quality controlled noninvasively derived SNP genotypes can be highly informative for individual and population monitoring in a large ungulate.
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Santos TL, Fernandes C, Henley MD, Dawson DA, Mumby HS. Conservation Genetic Assessment of Savannah Elephants ( Loxodonta africana) in the Greater Kruger Biosphere, South Africa. Genes (Basel) 2019; 10:E779. [PMID: 31590388 PMCID: PMC6826889 DOI: 10.3390/genes10100779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 09/12/2019] [Accepted: 09/29/2019] [Indexed: 11/24/2022] Open
Abstract
Savannah elephant populations have been severely reduced and fragmented throughout its remaining range. In general, however, there is limited information regarding their genetic status, which is essential knowledge for conservation. We investigated patterns of genetic variation in savannah elephants from the Greater Kruger Biosphere, with a focus on those in previously unstudied nature reserves adjacent to Kruger National Park, using dung samples from 294 individuals and 18 microsatellites. The results of genetic structure analyses using several different methods of ordination and Bayesian clustering strongly suggest that elephants throughout the Greater Kruger National Park (GKNP) constitute a single population. No evidence of a recent genetic bottleneck was detected using three moment-based approaches and two coalescent likelihood methods. The apparent absence of a recent genetic bottleneck associated with the known early 1900s demographic bottleneck may result from a combination of rapid post-bottleneck population growth, immigration and long generation time. Point estimates of contemporary effective population size (Ne) for the GKNP were ~ 500-700, that is, at the low end of the range of Ne values that have been proposed for maintaining evolutionary potential and the current ratio of Ne to census population size (Nc) may be quite low (<0.1). This study illustrates the difficulties in assessing the impacts on Ne in populations that have suffered demographic crashes but have recovered rapidly and received gene flow, particularly in species with long generation times in which genetic time lags are longer. This work provides a starting point and baseline information for genetic monitoring of the GKNP elephants.
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Affiliation(s)
- Teresa L Santos
- Bull Elephant Network Project, Conservation Science Group, David Attenborough Building, Pembroke St, Cambridge CB2 3QY, UK.
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal.
| | - Carlos Fernandes
- cE3c - Centre for Ecology, Evolution and Environmental Changes, Department of Animal Biology, Faculty of Sciences, University of Lisbon, Lisbon 1749-016, Portugal.
| | - Michelle D Henley
- Applied Behavioural Ecology and Ecosystem Research Unit, University of South Africa, Florida Campus, Private Bag X6, Florida 1710, Johannesburg, South Africa.
- Elephants Alive, P.O. Box 960. Hoedspruit 1380, South Africa.
| | - Deborah A Dawson
- NERC Biomolecular Analysis Facility, Department of Animal and Plant Sciences, University of Sheffield, Western Bank, Sheffield, South Yorkshire S10 2TN, UK.
| | - Hannah S Mumby
- Bull Elephant Network Project, Conservation Science Group, David Attenborough Building, Pembroke St, Cambridge CB2 3QY, UK.
- Centre for African Ecology, School of Animal, Plant and Environmental Sciences, University of Witwatersrand, 1 Jan Smuts Avenue, Braamfontein, Johannesburg 2000, South Africa.
- Wissenschaftskolleg zu Berlin, Wallotstraße 19, Berlin 14193, Germany.
- School of Biological Sciences and Department of Politics and Public Administration, University of Hong Kong, Hong Kong, China.
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5
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Jasper M, Schmidt TL, Ahmad NW, Sinkins SP, Hoffmann AA. A genomic approach to inferring kinship reveals limited intergenerational dispersal in the yellow fever mosquito. Mol Ecol Resour 2019; 19:1254-1264. [PMID: 31125998 PMCID: PMC6790672 DOI: 10.1111/1755-0998.13043] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Revised: 05/13/2019] [Accepted: 05/17/2019] [Indexed: 12/21/2022]
Abstract
Understanding past dispersal and breeding events can provide insight into ecology and evolution and can help inform strategies for conservation and the control of pest species. However, parent-offspring dispersal can be difficult to investigate in rare species and in small pest species such as mosquitoes. Here, we develop a methodology for estimating parent-offspring dispersal from the spatial distribution of close kin, using pairwise kinship estimates derived from genome-wide single nucleotide polymorphisms (SNPs). SNPs were scored in 162 Aedes aegypti (yellow fever mosquito) collected from eight close-set, high-rise apartment buildings in an area of Malaysia with high dengue incidence. We used the SNPs to reconstruct kinship groups across three orders of kinship. We transformed the geographical distances between all kin pairs within each kinship category into axial standard deviations of these distances, then decomposed these into components representing past dispersal events. From these components, we isolated the axial standard deviation of parent-offspring dispersal and estimated neighbourhood area (129 m), median parent-offspring dispersal distance (75 m) and oviposition dispersal radius within a gonotrophic cycle (36 m). We also analysed genetic structure using distance-based redundancy analysis and linear regression, finding isolation by distance both within and between buildings and estimating neighbourhood size at 268 individuals. These findings indicate the scale required to suppress local outbreaks of arboviral disease and to target releases of modified mosquitoes for mosquito and disease control. Our methodology is readily implementable for studies of other species, including pests and species of conservation significance.
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Affiliation(s)
- Moshe Jasper
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Thomas L Schmidt
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Nazni W Ahmad
- Institute for Medical Research, Ministry of Health Malaysia, Kuala Lumpur, Malaysia
| | | | - Ary A Hoffmann
- School of BioSciences, Bio21 Institute, University of Melbourne, Parkville, Victoria, Australia
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Skrbinšek T, Luštrik R, Majić-Skrbinšek A, Potočnik H, Kljun F, Jelenčič M, Kos I, Trontelj P. From science to practice: genetic estimate of brown bear population size in Slovenia and how it influenced bear management. EUR J WILDLIFE RES 2019. [DOI: 10.1007/s10344-019-1265-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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7
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Javornik J, Hopkins JB, Zavadlav S, Levanič T, Lojen S, Polak T, Jerina K. Effects of ethanol storage and lipids on stable isotope values in a large mammalian omnivore. J Mammal 2019. [DOI: 10.1093/jmammal/gyy187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jernej Javornik
- Biotechnical Faculty, Department of Forestry, University of Ljubljana, Večna pot, Ljubljana, Slovenia
| | - John B Hopkins
- Biotechnical Faculty, Department of Forestry, University of Ljubljana, Večna pot, Ljubljana, Slovenia
- School of Biodiversity Conservation, Unity College, Unity, ME, USA
| | - Saša Zavadlav
- Biotechnical Faculty, Department of Forestry, University of Ljubljana, Večna pot, Ljubljana, Slovenia
- Department of Yield and Silviculture, Slovenian Forestry Institute, Večna pot, Ljubljana, Slovenia
| | - Tom Levanič
- Biotechnical Faculty, Department of Forestry, University of Ljubljana, Večna pot, Ljubljana, Slovenia
- Department of Yield and Silviculture, Slovenian Forestry Institute, Večna pot, Ljubljana, Slovenia
| | - Sonja Lojen
- Biotechnical Faculty, Department of Forestry, University of Ljubljana, Večna pot, Ljubljana, Slovenia
- Department of Environmental Sciences, Jožef Stefan Institute, Jamova cesta, Ljubljana, Slovenia
- School of Environmental Sciences, University of Nova Gorica, Lanthieri mansion, Glavni,Vipava, Slovenia
| | - Tomaž Polak
- Biotechnical Faculty, Department of Food Science and Technology, University of Ljubljana, Jamnikarjeva, Ljubljana, Slovenia
| | - Klemen Jerina
- Biotechnical Faculty, Department of Forestry, University of Ljubljana, Večna pot, Ljubljana, Slovenia
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Reljic S, Jerina K, Nilsen EB, Huber D, Kusak J, Jonozovic M, Linnell JD. Challenges for transboundary management of a European brown bear population. Glob Ecol Conserv 2018. [DOI: 10.1016/j.gecco.2018.e00488] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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9
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Mathieu-Bégné E, Loot G, Chevalier M, Paz-Vinas I, Blanchet S. Demographic and genetic collapses in spatially structured populations: insights from a long-term survey in wild fish metapopulations. OIKOS 2018. [DOI: 10.1111/oik.05511] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eglantine Mathieu-Bégné
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
| | - Géraldine Loot
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
- Inst. Universitaire de France; Paris France
| | - Mathieu Chevalier
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
| | - Ivan Paz-Vinas
- Univ. de Lyon, Ecole Nationale des Travaux Publics de l'Etat (ENTPE), CNRS; UMR5023, Laboratoire d'Ecologie des Hydrosystèmes Naturels et Anthropisés; Villeurbanne France
- UPS, INP, CNRS, Univ. de Toulouse, UMR 5245 Laboratoire Écologie Fonctionnelle et Environnement; Ecolab Toulouse France
| | - Simon Blanchet
- Centre National de la Recherche Scientifique (CNRS), Univ. Paul Sabatier (UPS), Inst. de Recherche pour le Développement (IRD), Ecole Nationale Supérieure de Formation de l'Enseignement Agricole (ENSFEA); UMR5174, Evolution et Diversité Biologique, 118 route de Narbonne; FR-31062 Toulouse France
- CNRS, UPS; UMR5321, Station d'Ecologie Théorique et Expérimentale; Moulis France
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Karamanlidis AA, Skrbinšek T, de Gabriel Hernando M, Krambokoukis L, Munoz-Fuentes V, Bailey Z, Nowak C, Stronen AV. History-driven population structure and asymmetric gene flow in a recovering large carnivore at the rear-edge of its European range. Heredity (Edinb) 2018; 120:168-182. [PMID: 29225354 PMCID: PMC5837125 DOI: 10.1038/s41437-017-0031-4] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 09/21/2017] [Accepted: 10/25/2017] [Indexed: 11/09/2022] Open
Abstract
Understanding the mechanisms and patterns involved in population recoveries is challenging and important in shaping conservation strategies. We used a recovering rear-edge population of brown bears at their southernmost European range in Greece as a case study (2007-2010) to explore the recovery genetics at a species' distribution edge. We used 17 microsatellite and a mitochondrial markers to evaluate genetic structure, estimate effective population size and genetic diversity, and infer gene flow between the identified subpopulations. To understand the larger picture, we also compared the observed genetic diversity of each subpopulation with other brown bear populations in the region. The results indicate that the levels of genetic diversity for bears in western Greece are the lowest recorded in southeastern Europe, but still higher than those of other genetically depauperate bear populations. Apart from a complete separation of bear populations in eastern and western Greece, our results also indicate a considerable genetic sub-structuring in the West. As bear populations in Greece are now recovering, this structure is dissolving through a "recovery cascade" of asymmetric gene flow from South to North between neighboring subpopulations, mediated mainly by males. Our study outlines the importance of small, persisting populations, which can act as "stepping stones" that enable a rapid population expansion and recovery. This in turn makes their importance much greater than their numeric or genetic contribution to a species as a whole.
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Affiliation(s)
- A A Karamanlidis
- ARCTUROS-Civil Society for the Protection and Management of Wildlife and the Natural Environment, Aetos, 53075, Florina, Greece.
- Department of Ecology and Natural Resource Management, Norwegian University of Life Sciences, NO-1432, Ås, Norway.
| | - T Skrbinšek
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Večna pot 111, 1000, Ljubljana, Slovenia
| | | | - L Krambokoukis
- ARCTUROS-Civil Society for the Protection and Management of Wildlife and the Natural Environment, Aetos, 53075, Florina, Greece
| | - V Munoz-Fuentes
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Z Bailey
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - C Nowak
- Conservation Genetics Section, Senckenberg Research Institute and Natural History Museum Frankfurt, Clamecystrasse 12, 63571, Gelnhausen, Germany
| | - A V Stronen
- Department of Chemistry and Bioscience, Aalborg University, Frederik Bajers Vej 7H, DK-9220, Aalborg Øst, Denmark
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Kopatz A, Eiken HG, Schregel J, Aspi J, Kojola I, Hagen SB. Genetic substructure and admixture as important factors in linkage disequilibrium-based estimation of effective number of breeders in recovering wildlife populations. Ecol Evol 2017; 7:10721-10732. [PMID: 29299252 PMCID: PMC5743533 DOI: 10.1002/ece3.3577] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 10/03/2017] [Accepted: 10/04/2017] [Indexed: 01/18/2023] Open
Abstract
The number of effective breeders (Nb ) and effective population size (Ne ) are population parameters reflective of evolutionary potential, susceptibility to stochasticity, and viability. We have estimated these parameters using the linkage disequilibrium-based approach with LDNE through the latest phase of population recovery of the brown bears (Ursus arctos) in Finland (1993-2010; N = 621). This phase of the recovery was recently documented to be associated with major changes in genetic composition. In particular, differentiation between the northern and the southern genetic cluster declined rapidly within 1.5 generations. Based on this, we have studied effects of the changing genetic structure on Nb and Ne , by comparing estimates for whole Finland with the estimates for the two genetic clusters. We expected a potentially strong relationship between estimate sizes and genetic differentiation, which should disappear as the population recovers and clusters merge. Consistent with this, our estimates for whole Finland were lower than the sum of the estimates of the two genetic clusters and both approaches produced similar estimates in the end. Notably, we also found that admixed genotypes strongly increased the estimates. In all analyses, our estimates for Ne were larger than Nb and likely reflective for brown bears of the larger region of Finland and northwestern Russia. Conclusively, we find that neglecting genetic substructure may lead to a massive underestimation of Nb and Ne . Our results also suggest the need for further empirical analysis focusing on individuals with admixed genotypes and their potential high influence on Nb and Ne .
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Affiliation(s)
| | - Hans Geir Eiken
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Julia Schregel
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
| | - Jouni Aspi
- Department of BiologyUniversity of OuluOuluFinland
| | - Ilpo Kojola
- Natural Resources Institute Finland (Luke)RovaniemiFinland
| | - Snorre B. Hagen
- NIBIO—Norwegian Institute of Bioeconomy ResearchSvanvikNorway
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Popescu VD, Iosif R, Pop MI, Chiriac S, Bouroș G, Furnas BJ. Integrating sign surveys and telemetry data for estimating brown bear ( Ursus arctos) density in the Romanian Carpathians. Ecol Evol 2017; 7:7134-7144. [PMID: 28944005 PMCID: PMC5606905 DOI: 10.1002/ece3.3177] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 05/07/2017] [Accepted: 05/25/2017] [Indexed: 11/06/2022] Open
Abstract
Accurate population size estimates are important information for sustainable wildlife management. The Romanian Carpathians harbor the largest brown bear (Ursus arctos) population in Europe, yet current management relies on estimates of density that lack statistical oversight and ignore uncertainty deriving from track surveys. In this study, we investigate an alternative approach to estimate brown bear density using sign surveys along transects within a novel integration of occupancy models and home range methods. We performed repeated surveys along 2-km segments of forest roads during three distinct seasons: spring 2011, fall-winter 2011, and spring 2012, within three game management units and a Natura 2000 site. We estimated bears abundances along transects using the number of unique tracks observed per survey occasion via N-mixture hierarchical models, which account for imperfect detection. To obtain brown bear densities, we combined these abundances with the effective sampling area of the transects, that is, estimated as a function of the median (± bootstrapped SE) of the core home range (5.58 ± 1.08 km2) based on telemetry data from 17 bears tracked for 1-month periods overlapping our surveys windows. Our analyses yielded average brown bear densities (and 95% confidence intervals) for the three seasons of: 11.5 (7.8-15.3), 11.3 (7.4-15.2), and 12.4 (8.6-16.3) individuals/100 km2. Across game management units, mean densities ranged between 7.5 and 14.8 individuals/100 km2. Our method incorporates multiple sources of uncertainty (e.g., effective sampling area, imperfect detection) to estimate brown bear density, but the inference fundamentally relies on unmarked individuals only. While useful as a temporary approach to monitor brown bears, we urge implementing DNA capture-recapture methods regionally to inform brown bear management and recommend increasing resources for GPS collars to improve estimates of effective sampling area.
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Affiliation(s)
- Viorel D Popescu
- Department of Biological Sciences Ohio University Athens OH USA.,Centre for Environmental Research (CCMESI) University of Bucharest Bucharest Romania
| | - Ruben Iosif
- Centre for Environmental Research (CCMESI) University of Bucharest Bucharest Romania
| | - Mihai I Pop
- Centre for Environmental Research (CCMESI) University of Bucharest Bucharest Romania.,Asociatia pentru Conservarea Diversitatii Biologice (ACDB) Focsani Romania
| | | | - George Bouroș
- Asociatia pentru Conservarea Diversitatii Biologice (ACDB) Focsani Romania
| | - Brett J Furnas
- California Department of Fish and Wildlife Wildlife Investigations Laboratory Rancho Cordova CA USA.,Department of Environmental Science, Policy and Management University of California Berkeley CA USA
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14
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Dussex N, Robertson BC. Contemporary effective population size and predicted maintenance of genetic diversity in the endangered kea (Nestor notabilis). NEW ZEALAND JOURNAL OF ZOOLOGY 2017. [DOI: 10.1080/03014223.2017.1325381] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- N. Dussex
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - B. C. Robertson
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago, Dunedin, New Zealand
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15
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Ackerman MW, Hand BK, Waples RK, Luikart G, Waples RS, Steele CA, Garner BA, McCane J, Campbell MR. Effective number of breeders from sibship reconstruction: empirical evaluations using hatchery steelhead. Evol Appl 2016; 10:146-160. [PMID: 28127391 PMCID: PMC5253425 DOI: 10.1111/eva.12433] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/19/2016] [Indexed: 01/21/2023] Open
Abstract
Effective population size (Ne) is among the most important metrics in evolutionary biology. In natural populations, it is often difficult to collect adequate demographic data to calculate Ne directly. Consequently, genetic methods to estimate Ne have been developed. Two Ne estimators based on sibship reconstruction using multilocus genotype data have been developed in recent years: sibship assignment and parentage analysis without parents. In this study, we evaluated the accuracy of sibship reconstruction using a large empirical dataset from five hatchery steelhead populations with known pedigrees and using 95 single nucleotide polymorphism (SNP) markers. We challenged the software COLONY with 2,599,961 known relationships and demonstrated that reconstruction of full‐sib and unrelated pairs was greater than 95% and 99% accurate, respectively. However, reconstruction of half‐sib pairs was poor (<5% accurate). Despite poor half‐sib reconstruction, both estimators provided accurate estimates of the effective number of breeders (Nb) when sample sizes were near or greater than the true Nb and when assuming a monogamous mating system. We further demonstrated that both methods provide roughly equivalent estimates of Nb. Our results indicate that sibship reconstruction and current SNP panels provide promise for estimating Nb in steelhead populations in the region.
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Affiliation(s)
- Michael W Ackerman
- Idaho Department of Fish and Game/Pacific States Marine Fisheries Commission Eagle Fish Genetics Lab Eagle ID USA; Present address: Michael W. Ackerman, Quantitative Consultants, Inc.705 S 8th St.Boise ID 83702 USA
| | - Brian K Hand
- Flathead Lake Biological Station Division of Biological Sciences University of Montana Polson MT USA
| | - Ryan K Waples
- School of Aquatic and Fishery Sciences University of Washington Seattle WA USA
| | - Gordon Luikart
- Flathead Lake Biological Station Division of Biological Sciences University of Montana Polson MT USA
| | - Robin S Waples
- NOAA Fisheries Northwest Fisheries Science Center Seattle WA USA
| | - Craig A Steele
- Idaho Department of Fish and Game/Pacific States Marine Fisheries Commission Eagle Fish Genetics Lab Eagle ID USA
| | - Brittany A Garner
- Flathead Lake Biological Station Division of Biological Sciences University of Montana Polson MT USA
| | - Jesse McCane
- Idaho Department of Fish and Game/Pacific States Marine Fisheries Commission Eagle Fish Genetics Lab Eagle ID USA
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Long-term effective population size dynamics of an intensively monitored vertebrate population. Heredity (Edinb) 2016; 117:290-9. [PMID: 27553455 DOI: 10.1038/hdy.2016.67] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 06/02/2016] [Accepted: 06/03/2016] [Indexed: 11/08/2022] Open
Abstract
Long-term genetic data from intensively monitored natural populations are important for understanding how effective population sizes (Ne) can vary over time. We therefore genotyped 1622 common buzzard (Buteo buteo) chicks sampled over 12 consecutive years (2002-2013 inclusive) at 15 microsatellite loci. This data set allowed us to both compare single-sample with temporal approaches and explore temporal patterns in the effective number of parents that produced each cohort in relation to the observed population dynamics. We found reasonable consistency between linkage disequilibrium-based single-sample and temporal estimators, particularly during the latter half of the study, but no clear relationship between annual Ne estimates () and census sizes. We also documented a 14-fold increase in between 2008 and 2011, a period during which the census size doubled, probably reflecting a combination of higher adult survival and immigration from further afield. Our study thus reveals appreciable temporal heterogeneity in the effective population size of a natural vertebrate population, confirms the need for long-term studies and cautions against drawing conclusions from a single sample.
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17
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Reduced Genetic Diversity and Increased Structure in American Mink on the Swedish Coast following Invasive Species Control. PLoS One 2016; 11:e0157972. [PMID: 27333328 PMCID: PMC4917106 DOI: 10.1371/journal.pone.0157972] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 06/08/2016] [Indexed: 11/19/2022] Open
Abstract
Eradication and population reductions are often used to mitigate the negative impacts of non-native invasive species on native biodiversity. However, monitoring the effectiveness of non-native species control programmes is necessary to evaluate the efficacy of these measures. Genetic monitoring could provide valuable insights into temporal changes in demographic, ecological, and evolutionary processes in invasive populations being subject to control programmes. Such programmes should cause a decrease in effective population size and/or in genetic diversity of the targeted non-native species and an increase in population genetic structuring over time. We used microsatellite DNA data from American mink (Neovison vison) to determine whether the removal of this predator on the Koster Islands archipelago and the nearby Swedish mainland affected genetic variation over six consecutive years of mink culling by trappers as part of a population control programme. We found that on Koster Islands allelic richness decreased (from on average 4.53 to 3.55), genetic structuring increased, and effective population size did not change. In contrast, the mink population from the Swedish coast showed no changes in genetic diversity or structure, suggesting the stability of this population over 6 years of culling. Effective population size did not change over time but was higher on the coast than on the islands across all years. Migration rates from the islands to the coast were almost two times higher than from the coast to the islands. Most migrants leaving the coast were localised on the southern edge of the archipelago, as expected from the direction of the sea current between the two sites. Genetic monitoring provided valuable information on temporal changes in the population of American mink suggesting that this approach can be used to evaluate and improve control programmes of invasive vertebrates.
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Gonzalez EG, Blanco JC, Ballesteros F, Alcaraz L, Palomero G, Doadrio I. Genetic and demographic recovery of an isolated population of brown bear Ursus arctos L., 1758. PeerJ 2016; 4:e1928. [PMID: 27168963 PMCID: PMC4860320 DOI: 10.7717/peerj.1928] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/22/2016] [Indexed: 12/02/2022] Open
Abstract
The brown bear Ursus arctos L., 1758 population of the Cantabrian Mountains (northwestern Spain) became isolated from other bear populations in Europe about 500 years ago and has declined due to hunting and habitat degradation. At the beginning of the 20th century, the Cantabrian population split into eastern and western subpopulations, and genetic exchange between them ceased. In the early 1990s, total population size was estimated to be < 100 bears. Subsequently, reduction in human-caused mortality has brought about an increase in numbers, mainly in the western subpopulation, likely promoting male-mediated migration and gene flow from the western nucleus to the eastern. To evaluate the possible genetic recovery of the small and genetically depauperate eastern subpopulation, in 2013 and 2014 we genotyped hair and faeces samples (116 from the eastern subpopulation and 36 from the western) for 18 microsatellite markers. Data from the annual count of females with cubs of the year (COY) during the past twenty-six years was used to analyze demographic changes. The number of females with COY fell to a minimum of seven in the western and three in eastern subpopulations in the biennium 1993-1994 and reached a respective maximum of 54 and 10 individuals in 2013-2014. We also observed increased bear dispersal and gene flow, mainly from the western to the eastern subpopulation. Of the 26 unique genotypes detected in the eastern subpopulation, 14 (54%) presented an admixture composition, and seven (27%) were determined to be migrants from the western subpopulation. Hence, the two separated and clearly structured subpopulations identified in the past currently show some degree of genetic admixture. This research shows the partial demographic recovery and a change in genetic composition due to migration process in a population of bears that has been isolated for several centuries.
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Affiliation(s)
- Elena G. Gonzalez
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, Madrid, Spain
| | | | | | - Lourdes Alcaraz
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, Madrid, Spain
| | | | - Ignacio Doadrio
- Departamento de Biodiversidad y Biología Evolutiva, Museo Nacional de Ciencias Naturales, MNCN-CSIC, Madrid, Spain
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19
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Population Genetic Structure of Blanding's Turtles (Emydoidea blandingii) in New York. J HERPETOL 2016. [DOI: 10.1670/14-027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Ancient, but not recent, population declines have had a genetic impact on alpine yellow-bellied toad populations, suggesting potential for complete recovery. CONSERV GENET 2016. [DOI: 10.1007/s10592-016-0818-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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21
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Ruzzante DE, McCracken GR, Parmelee S, Hill K, Corrigan A, MacMillan J, Walde SJ. Effective number of breeders, effective population size and their relationship with census size in an iteroparous species, Salvelinus fontinalis. Proc Biol Sci 2016; 283:20152601. [PMID: 26817773 PMCID: PMC4795031 DOI: 10.1098/rspb.2015.2601] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 01/07/2016] [Indexed: 11/12/2022] Open
Abstract
The relationship between the effective number of breeders (Nb) and the generational effective size (Ne) has rarely been examined empirically in species with overlapping generations and iteroparity. Based on a suite of 11 microsatellite markers, we examine the relationship between Nb, Ne and census population size (Nc) in 14 brook trout (Salvelinus fontinalis) populations inhabiting 12 small streams in Nova Scotia and sampled at least twice between 2009 and 2015. Unbiased estimates of Nb obtained with individuals of a single cohort, adjusted on the basis of age at first maturation (α) and adult lifespan (AL), were from 1.66 to 0.24 times the average estimates of Ne obtained with random samples of individuals of mixed ages (i.e. [Formula: see text]). In turn, these differences led to adjusted Ne estimates that were from nearly five to 0.7 times the estimates derived from mixed-aged individuals. These differences translate into the same range of variation in the ratio of effective to census population size [Formula: see text] within populations. Adopting [Formula: see text] as the more precise and unbiased estimates, we found that these brook trout populations differ markedly in their effective to census population sizes (range approx. 0.3 to approx. 0.01). Using AgeNe, we then showed that the variance in reproductive success or reproductive skew varied among populations by a factor of 40, from Vk/k ≈ 5 to 200. These results suggest wide differences in population dynamics, probably resulting from differences in productivity affecting the intensity of competition for access to mates or redds, and thus reproductive skew. Understanding the relationship between Ne, Nb and Nc, and how these relate to population dynamics and fluctuations in population size, are important for the design of robust conservation strategies in small populations with overlapping generations and iteroparity.
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Affiliation(s)
- Daniel E Ruzzante
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Gregory R McCracken
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Samantha Parmelee
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Kristen Hill
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
| | - Amelia Corrigan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada B3J 2R5
| | - John MacMillan
- Inland Fisheries Division, Nova Scotia Department of Fisheries and Aquaculture, Halifax, Nova Scotia, Canada B3J 2R5
| | - Sandra J Walde
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada B3H4R2
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22
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Collins CJ, Chilvers BL, Taylor M, Robertson BC. Historical population size of the threatened New Zealand sea lion
Phocarctos hookeri. J Mammal 2015. [DOI: 10.1093/jmammal/gyv187] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Marine mammal species were exploited worldwide during periods of commercial sealing in the 18th and 19th centuries. For many of these species, an estimate of the pre-exploitation abundance of the species is lacking, as historical catch records are generally scarce and inaccurate. Genetic estimates of long-term effective population size provide a means to estimate the pre-exploitation abundance. Here, we apply genetic methods to estimate the long-term effective population size of the subantarctic lineage of the New Zealand sea lion (NZ sea lion), Phocarctos hookeri . This species is predominantly restricted to the subantarctic islands, south of mainland New Zealand, following commercial sealing in the 19th century. Today, the population consists of ~9,880 animals and population growth is slow. Auckland Island breeding colonies of NZ sea lion are currently impacted by commercial trawl fisheries via regular sea lion deaths as bycatch. In order to estimate sustainable levels of bycatch, an estimate of the population’s carrying capacity ( K ) is required. We apply the genetically estimated long-term effective population size of NZ sea lions as a proxy for the estimated historical carrying capacity of the subantarctic population. The historical abundance of subantarctic NZ sea lions was significantly higher than the target values of K employed by the contemporary management. The current management strategy may allow unsustainable bycatch levels, thereby limiting the recovery of the NZ sea lion population toward historical carrying capacity.
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Affiliation(s)
- Catherine J. Collins
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - B. Louise Chilvers
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - Matthew Taylor
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
| | - Bruce C. Robertson
- Allan Wilson Centre for Molecular Ecology and Evolution, Department of Zoology, University of Otago , P.O. Box 56, Dunedin 9016 , New Zealand (CJC, MT, BCR)
- Department of Conservation, Marine Species and Threats , Wellington 6011 , New Zealand (BLC)
- Wildbase, IVABS, Massey University , Private Bag 11–222, Palmerston North 4442 , New Zealand (BLC)
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23
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Kamath PL, Haroldson MA, Luikart G, Paetkau D, Whitman C, Manen FT. Multiple estimates of effective population size for monitoring a long‐lived vertebrate: an application to
Y
ellowstone grizzly bears. Mol Ecol 2015; 24:5507-21. [DOI: 10.1111/mec.13398] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 09/17/2015] [Accepted: 09/17/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Pauline L. Kamath
- U.S. Geological Survey Northern Rocky Mountain Science Center 2327 University Way, Suite 2 Bozeman MT 59715 USA
| | - Mark A. Haroldson
- U.S. Geological Survey Northern Rocky Mountain Science Center 2327 University Way, Suite 2 Bozeman MT 59715 USA
| | - Gordon Luikart
- Flathead Lake Biological Station Fish and Wildlife Genomics Group Division of Biological Sciences University of Montana Missoula MT 59812 USA
| | - David Paetkau
- Wildlife Genetics International Box 274 Nelson British Columbia V1L 5P9 Canada
| | - Craig Whitman
- U.S. Geological Survey Northern Rocky Mountain Science Center 2327 University Way, Suite 2 Bozeman MT 59715 USA
| | - Frank T. Manen
- U.S. Geological Survey Northern Rocky Mountain Science Center 2327 University Way, Suite 2 Bozeman MT 59715 USA
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24
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Karamanlidis AA, Hernando MDG, Krambokoukis L, Gimenez O. Evidence of a large carnivore population recovery: Counting bears in Greece. J Nat Conserv 2015. [DOI: 10.1016/j.jnc.2015.06.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Álvarez D, Lourenço A, Oro D, Velo-Antón G. Assessment of census (N) and effective population size (N e ) reveals consistency of N e single-sample estimators and a high N e /N ratio in an urban and isolated population of fire salamanders. CONSERV GENET RESOUR 2015. [DOI: 10.1007/s12686-015-0480-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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26
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Zemanová B, Hájková P, Hájek B, Martínková N, Mikulíček P, Zima J, Bryja J. Extremely low genetic variation in endangered Tatra chamois and evidence for hybridization with an introduced Alpine population. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0696-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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27
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Putman AI, Carbone I. Challenges in analysis and interpretation of microsatellite data for population genetic studies. Ecol Evol 2014; 4:4399-428. [PMID: 25540699 PMCID: PMC4267876 DOI: 10.1002/ece3.1305] [Citation(s) in RCA: 237] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 10/02/2014] [Accepted: 10/03/2014] [Indexed: 12/14/2022] Open
Abstract
Advancing technologies have facilitated the ever-widening application of genetic markers such as microsatellites into new systems and research questions in biology. In light of the data and experience accumulated from several years of using microsatellites, we present here a literature review that synthesizes the limitations of microsatellites in population genetic studies. With a focus on population structure, we review the widely used fixation (F ST) statistics and Bayesian clustering algorithms and find that the former can be confusing and problematic for microsatellites and that the latter may be confounded by complex population models and lack power in certain cases. Clustering, multivariate analyses, and diversity-based statistics are increasingly being applied to infer population structure, but in some instances these methods lack formalization with microsatellites. Migration-specific methods perform well only under narrow constraints. We also examine the use of microsatellites for inferring effective population size, changes in population size, and deeper demographic history, and find that these methods are untested and/or highly context-dependent. Overall, each method possesses important weaknesses for use with microsatellites, and there are significant constraints on inferences commonly made using microsatellite markers in the areas of population structure, admixture, and effective population size. To ameliorate and better understand these constraints, researchers are encouraged to analyze simulated datasets both prior to and following data collection and analysis, the latter of which is formalized within the approximate Bayesian computation framework. We also examine trends in the literature and show that microsatellites continue to be widely used, especially in non-human subject areas. This review assists with study design and molecular marker selection, facilitates sound interpretation of microsatellite data while fostering respect for their practical limitations, and identifies lessons that could be applied toward emerging markers and high-throughput technologies in population genetics.
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Affiliation(s)
- Alexander I Putman
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
| | - Ignazio Carbone
- Department of Plant Pathology, North Carolina State University Raleigh, North Carolina, 27695-7616
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28
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Waples RS, Antao T, Luikart G. Effects of overlapping generations on linkage disequilibrium estimates of effective population size. Genetics 2014; 197:769-80. [PMID: 24717176 PMCID: PMC4063931 DOI: 10.1534/genetics.114.164822] [Citation(s) in RCA: 180] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Accepted: 04/02/2014] [Indexed: 11/18/2022] Open
Abstract
Use of single-sample genetic methods to estimate effective population size has skyrocketed in recent years. Although the underlying models assume discrete generations, they are widely applied to age-structured species. We simulated genetic data for 21 iteroparous animal and plant species to evaluate two untested hypotheses regarding performance of the single-sample method based on linkage disequilibrium (LD): (1) estimates based on single-cohort samples reflect the effective number of breeders in one reproductive cycle (Nb), and (2) mixed-age samples reflect the effective size per generation (Ne). We calculated true Ne and Nb, using the model species' vital rates, and verified these with individual-based simulations. We show that single-cohort samples should be equally influenced by Nb and Ne and confirm this with simulated results: [Formula: see text] was a linear (r(2) = 0.98) function of the harmonic mean of Ne and Nb. We provide a quantitative bias correction for raw [Formula: see text] based on the ratio Nb/Ne, which can be estimated from two or three simple life history traits. Bias-adjusted estimates were within 5% of true Nb for all 21 study species and proved robust when challenged with new data. Mixed-age adult samples produced downwardly biased estimates in all species, which we attribute to a two-locus Wahlund effect (mixture LD) caused by combining parents from different cohorts in a single sample. Results from this study will facilitate interpretation of rapidly accumulating genetic estimates in terms of both Ne (which influences long-term evolutionary processes) and Nb (which is more important for understanding eco-evolutionary dynamics and mating systems).
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Affiliation(s)
- Robin S Waples
- Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, Washington 98112
| | - Tiago Antao
- Vector Biology Department, Liverpool School of Tropical Medicine, Liverpool, L3 5QA United Kingdom
| | - Gordon Luikart
- Flathead Lake Biological Station, Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Polson, Montana 59860
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29
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Karamanlidis AA, Paunović M, Ćirović D, Karapandža B, Skrbinšek T, Zedrosser A. Population genetic parameters of brown bears in western Serbia: implications for research and conservation. URSUS 2014. [DOI: 10.2192/ursus-d-1--00033.1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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30
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Louis M, Viricel A, Lucas T, Peltier H, Alfonsi E, Berrow S, Brownlow A, Covelo P, Dabin W, Deaville R, de Stephanis R, Gally F, Gauffier P, Penrose R, Silva MA, Guinet C, Simon-Bouhet B. Habitat-driven population structure of bottlenose dolphins,Tursiops truncatus, in the North-East Atlantic. Mol Ecol 2014; 23:857-74. [DOI: 10.1111/mec.12653] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Revised: 11/30/2013] [Accepted: 12/18/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Marie Louis
- Centre d'Etudes Biologiques de Chizé; UPR 1934; 79360 Villiers-en-Bois France
- Littoral; Environnement et Sociétés (LIENSs); UMR 7266, CNRS/Université de La Rochelle; 2 rue Olympe de Gouges 17000 La Rochelle France
- GECC (Groupe d'Etude des Cétacés du Cotentin); Place des Justes 50130 Cherbourg-Octeville France
| | - Amélia Viricel
- Littoral; Environnement et Sociétés (LIENSs); UMR 7266, CNRS/Université de La Rochelle; 2 rue Olympe de Gouges 17000 La Rochelle France
| | - Tamara Lucas
- Littoral; Environnement et Sociétés (LIENSs); UMR 7266, CNRS/Université de La Rochelle; 2 rue Olympe de Gouges 17000 La Rochelle France
| | - Hélène Peltier
- Observatoire PELAGIS; UMS 3462 CNRS/Université de La Rochelle; Ple Analytique; 5 allée de l'Océan 17000 La Rochelle France
| | - Eric Alfonsi
- Laboratoire d'Etude des Mammiféres Marins; Océanopolis; port de plaisance; BP 91039 29210 Brest Cedex 1 France
- Laboratoire BioGeMME (Biologie et Génétique des Mammiféres Marins dans leur Environnement); Université Européenne de Bretagne & Université de Bretagne Occidentale; Université de Brest; UFR Sciences et Techniques; 6 Av. Victor Le Gorgeu CS93837 29238 Brest Cedex 3 France
| | - Simon Berrow
- Irish Whale and Dolphin Group; Merchants Quay; Kilrush Co Clare Ireland
- Marine and Freshwater Research Centre; Galway-Mayo Institute of Technology; Dublin Road Galway Ireland
| | - Andrew Brownlow
- Scottish Marine Animal Stranding Scheme; SAC Disease Surveillance Centre; Drummond Hill Inverness IV2 4JZ UK
| | - Pablo Covelo
- CEMMA (Coordinadora para o Estudo dos Mamiferos Mariños); Aptdo. 15 36380 Gondomar (Pontevedra) Spain
| | - Willy Dabin
- Observatoire PELAGIS; UMS 3462 CNRS/Université de La Rochelle; Ple Analytique; 5 allée de l'Océan 17000 La Rochelle France
| | - Rob Deaville
- Institute of Zoology, Zoological Society of London; Regent's Park London NWI 4RY UK
| | - Renaud de Stephanis
- Estación Biológica de Doñana-CSIC; Americo Vespuccio S/N; Isla de la Cartuja Sevilla 41092 Spain
| | - François Gally
- GECC (Groupe d'Etude des Cétacés du Cotentin); Place des Justes 50130 Cherbourg-Octeville France
| | - Pauline Gauffier
- CIRCE (Conservation, Information and Research on Cetaceans); Cabeza de Manzaneda 3; Pelayo Algeciras 11390 Cadix Spain
| | - Rod Penrose
- Marine Environmental Monitoring; Penwalk; Llechryd; Cardigan West Wales SA43 2PS UK
| | - Monica A. Silva
- Center of the Institute of Marine Research & Department of Oceanography and Fisheries; University of the Azores; 9901-862 Horta Portugal
- Laboratory of Robotics and Systems in Engineering and Science; 9901-862 Horta Portugal
- Biology Department; Woods Hole Oceanographic Institution; Woods Hole MA 02543 USA
| | - Christophe Guinet
- Centre d'Etudes Biologiques de Chizé; UPR 1934; 79360 Villiers-en-Bois France
| | - Benoit Simon-Bouhet
- Littoral; Environnement et Sociétés (LIENSs); UMR 7266, CNRS/Université de La Rochelle; 2 rue Olympe de Gouges 17000 La Rochelle France
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Casas-Marce M, Soriano L, López-Bao JV, Godoy JA. Genetics at the verge of extinction: insights from the Iberian lynx. Mol Ecol 2013; 22:5503-15. [PMID: 24128177 DOI: 10.1111/mec.12498] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2012] [Revised: 08/12/2013] [Accepted: 08/12/2013] [Indexed: 11/30/2022]
Abstract
Population viability might become compromised by the loss of genetic diversity and the accumulation of inbreeding resulting from population decline and fragmentation. The Iberian lynx (Lynx pardinus) provides a paradigmatic example of a species at the verge of extinction, and because of the well-documented and different demographic histories of the two remaining populations (Doñana and Andújar), it provides the opportunity to evaluate the performance of analytical methods commonly applied to recently declined populations. We used mitochondrial sequences and 36 microsatellite markers to evaluate the current genetic status of the species and to assess the genetic signatures of its past history. Mitochondrial diversity was extremely low with only two haplotypes, alternatively fixed in each population. Both remnant populations have low levels of genetic diversity at microsatellite markers, particularly the population from Doñana, and genetic differentiation between the two populations is high. Bayesian coalescent-based methods suggest an earlier decline starting hundreds of years ago, while heterozygosity excess and M-ratio tests did not provide conclusive and consistent evidence for recent bottlenecks. Also, a model of gene flow received overwhelming support over a model of pure drift. Results that are in conflict with the known recent demography of the species call for caution in the use of these methods, especially when no information on previous demographic history is available. Overall, our results suggest that current genetic patterns in the Iberian lynx are mainly the result of its recent decline and fragmentation and alerts on possible genetic risks for its persistence. Conservation strategies should explicitly consider this threat and incorporate an integrated genetic management of wild, captive and re-introduced populations, including genetic restoration through translocations.
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Affiliation(s)
- M Casas-Marce
- Department of Integrative Ecology, Estación Biológica de Doñana (CSIC), C/ Américo Vespucio s/n, 41092, Sevilla, Spain
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32
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Testing single-sample estimators of effective population size in genetically structured populations. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0518-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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33
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The potential impacts of changes in bear hunting policy for hunting organisations in Croatia. EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0754-3] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Sindičić M, Polanc P, Gomerčić T, Jelenčič M, Huber Đ, Trontelj P, Skrbinšek T. Genetic data confirm critical status of the reintroduced Dinaric population of Eurasian lynx. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0491-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Gomez-Uchida D, Palstra FP, Knight TW, Ruzzante DE. Contemporary effective population and metapopulation size (N e and meta-N e): comparison among three salmonids inhabiting a fragmented system and differing in gene flow and its asymmetries. Ecol Evol 2013; 3:569-80. [PMID: 23532448 PMCID: PMC3605847 DOI: 10.1002/ece3.485] [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: 04/18/2012] [Revised: 12/14/2012] [Accepted: 12/24/2012] [Indexed: 11/15/2022] Open
Abstract
We estimated local and metapopulation effective sizes ([Formula: see text] and meta-[Formula: see text]) for three coexisting salmonid species (Salmo salar, Salvelinus fontinalis, Salvelinus alpinus) inhabiting a freshwater system comprising seven interconnected lakes. First, we hypothesized that [Formula: see text] might be inversely related to within-species population divergence as reported in an earlier study (i.e., FST: S. salar> S. fontinalis> S. alpinus). Using the approximate Bayesian computation method implemented in ONeSAMP, we found significant differences in [Formula: see text] ([Formula: see text]) between species, consistent with a hierarchy of adult population sizes ([Formula: see text]). Using another method based on a measure of linkage disequilibrium (LDNE: [Formula: see text]), we found more finite [Formula: see text] values for S. salar than for the other two salmonids, in line with the results above that indicate that S. salar exhibits the lowest [Formula: see text] among the three species. Considering subpopulations as open to migration (i.e., removing putative immigrants) led to only marginal and non-significant changes in [Formula: see text], suggesting that migration may be at equilibrium between genetically similar sources. Second, we hypothesized that meta-[Formula: see text] might be significantly smaller than the sum of local [Formula: see text]s (null model) if gene flow is asymmetric, varies among subpopulations, and is driven by common landscape features such as waterfalls. One 'bottom-up' or numerical approach that explicitly incorporates variable and asymmetric migration rates showed this very pattern, while a number of analytical models provided meta-[Formula: see text] estimates that were not significantly different from the null model or from each other. Our study of three species inhabiting a shared environment highlights the importance and utility of differentiating species-specific and landscape effects, not only on dispersal but also in the demography of wild populations as assessed through local [Formula: see text]s and meta-[Formula: see text]s and their relevance in ecology, evolution and conservation.
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Use of GPS location clusters analysis to study predation, feeding, and maternal behavior of the Eurasian lynx. Ecol Res 2012. [DOI: 10.1007/s11284-012-1005-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Hoehn M, Gruber B, Sarre SD, Lange R, Henle K. Can genetic estimators provide robust estimates of the effective number of breeders in small populations? PLoS One 2012; 7:e48464. [PMID: 23139784 PMCID: PMC3491051 DOI: 10.1371/journal.pone.0048464] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2012] [Accepted: 09/26/2012] [Indexed: 11/18/2022] Open
Abstract
The effective population size (N(e)) is proportional to the loss of genetic diversity and the rate of inbreeding, and its accurate estimation is crucial for the monitoring of small populations. Here, we integrate temporal studies of the gecko Oedura reticulata, to compare genetic and demographic estimators of N(e). Because geckos have overlapping generations, our goal was to demographically estimate N(bI), the inbreeding effective number of breeders and to calculate the N(bI)/N(a) ratio (N(a) =number of adults) for four populations. Demographically estimated N(bI) ranged from 1 to 65 individuals. The mean reduction in the effective number of breeders relative to census size (N(bI)/N(a)) was 0.1 to 1.1. We identified the variance in reproductive success as the most important variable contributing to reduction of this ratio. We used four methods to estimate the genetic based inbreeding effective number of breeders N(bI(gen)) and the variance effective populations size N(eV(gen)) estimates from the genotype data. Two of these methods - a temporal moment-based (MBT) and a likelihood-based approach (TM3) require at least two samples in time, while the other two were single-sample estimators - the linkage disequilibrium method with bias correction LDNe and the program ONeSAMP. The genetic based estimates were fairly similar across methods and also similar to the demographic estimates excluding those estimates, in which upper confidence interval boundaries were uninformative. For example, LDNe and ONeSAMP estimates ranged from 14-55 and 24-48 individuals, respectively. However, temporal methods suffered from a large variation in confidence intervals and concerns about the prior information. We conclude that the single-sample estimators are an acceptable short-cut to estimate N(bI) for species such as geckos and will be of great importance for the monitoring of species in fragmented landscapes.
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Affiliation(s)
- Marion Hoehn
- UFZ - Helmholtz Centre for Environmental Research, Department of Conservation Biology, Leipzig, Germany.
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Charlier J, Laikre L, Ryman N. Genetic monitoring reveals temporal stability over 30 years in a small, lake-resident brown trout population. Heredity (Edinb) 2012; 109:246-53. [PMID: 22828900 PMCID: PMC3464028 DOI: 10.1038/hdy.2012.36] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Revised: 03/16/2012] [Accepted: 04/19/2012] [Indexed: 11/08/2022] Open
Abstract
Knowledge of the degree of temporal stability of population genetic structure and composition is important for understanding microevolutionary processes and addressing issues of human impact of natural populations. We know little about how representative single samples in time are to reflect population genetic constitution, and we explore the temporal genetic variability patterns over a 30-year period of annual sampling of a lake-resident brown trout (Salmo trutta) population, covering 37 consecutive cohorts and five generations. Levels of variation remain largely stable over this period, with no indication of substructuring within the lake. We detect genetic drift, however, and the genetically effective population size (N(e)) was assessed from allele-frequency shifts between consecutive cohorts using an unbiased estimator that accounts for the effect of overlapping generation. The overall mean N(e) is estimated as 74. We find indications that N(e) varies over time, but there is no obvious temporal trend. We also estimated N(e) using a one-sample approach based on linkage disequilibrium (LD) that does not account for the effect of overlapping generations. Combining one-sample estimates for all years gives an N(e) estimate of 76. This similarity between estimates may be coincidental or reflecting a general robustness of the LD approach to violations of the discrete generations assumption. In contrast to the observed genetic stability, body size and catch per effort have increased over the study period. Estimates of annual effective number of breeders (N(b)) correlated with catch per effort, suggesting that genetic monitoring can be used for detecting fluctuations in abundance.
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Affiliation(s)
- J Charlier
- Department of Zoology, Division of Population
Genetics, Stockholm University, Stockholm, Sweden
| | - L Laikre
- Department of Zoology, Division of Population
Genetics, Stockholm University, Stockholm, Sweden
| | - N Ryman
- Department of Zoology, Division of Population
Genetics, Stockholm University, Stockholm, Sweden
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Using a reference population yardstick to calibrate and compare genetic diversity reported in different studies: an example from the brown bear. Heredity (Edinb) 2012; 109:299-305. [PMID: 22850697 DOI: 10.1038/hdy.2012.42] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In species with large geographic ranges, genetic diversity of different populations may be well studied, but differences in loci and sample sizes can make the results of different studies difficult to compare. Yet, such comparisons are important for assessing the status of populations of conservation concern. We propose a simple approach of using a single well-studied reference population as a 'yardstick' to calibrate results of different studies to the same scale, enabling comparisons. We use a well-studied large carnivore, the brown bear (Ursus arctos), as a case study to demonstrate the approach. As a reference population, we genotyped 513 brown bears from Slovenia using 20 polymorphic microsatellite loci. We used this data set to calibrate and compare heterozygosity and allelic richness for 30 brown bear populations from 10 different studies across the global distribution of the species. The simplicity of the reference population approach makes it useful for other species, enabling comparisons of genetic diversity estimates between previously incompatible studies and improving our understanding of how genetic diversity is distributed throughout a species range.
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