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Martínez-Gil H, Sánchez-Montes G, Montes-Gavilán P, Ugarte G, Martínez-Solano Í. Fine-scale functional connectivity of two syntopic pond-breeding amphibians with contrasting life-history traits: an integrative assessment of direct and indirect estimates of dispersal. CONSERV GENET 2023. [DOI: 10.1007/s10592-023-01506-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
AbstractAssessing patterns of functional connectivity among amphibian demes is crucial to unravel their population dynamics and prevent their isolation and eventual extinction. Integrative studies based on direct (capture-mark-recapture) and indirect (genetic) estimates of dispersal provide robust, biologically realistic inferences on population structure and connectivity, with applications for conservation efforts. We focused on two pond-breeding amphibians with contrasting life-history traits: the short-lived, semi-arboreal Hyla molleri and the long-lived, fossorial Pelobates cultripes. We PIT-tagged 2150 individuals of both species in two ponds (Laguna and Gravera, separated by 700 m) and monitored them from 2009 to 2021 to document the frequency and spatial extent of dispersal events. In addition, we genotyped individuals from these and two additional breeding populations at a maximum distance of 5 km with 15–16 microsatellites to characterize fine-scale patterns of genetic structure. We detected dispersal events connecting Laguna and Gravera in both species, albeit at low frequencies (4.8% and 7.7% of recaptured individuals of H. molleri and P. cultripes, respectively). However, both species were capable of covering long distances, with individual accumulated displacements up to 3.5 km (Hyla) and 1.8 km (Pelobates). Breeding populations > 2 km apart were genetically differentiated, indicating lower connectivity at this spatial scale. Estimates of pairwise migration rates differed between species and were asymmetrical, with different ponds representing “source” populations contributing more migrants to other populations in each species. We discuss the role of differences in life history traits and ecological preferences in shaping population dynamics in the two species and highlight management implications of our results.
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Osmond DR, King RA, Stockley B, Launey S, Stevens JR. A low-density single nucleotide polymorphism panel for brown trout (Salmo trutta L.) suitable for exploring genetic diversity at a range of spatial scales. JOURNAL OF FISH BIOLOGY 2023; 102:258-270. [PMID: 36281821 DOI: 10.1111/jfb.15258] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
The rivers of southern England and northern France which drain into the English Channel contain several genetically unique groups of trout (Salmo trutta L.) that have suffered dramatic declines in numbers over the past 40 years. Knowledge of levels and patterns of genetic diversity is essential for effective management of these vulnerable populations. Using restriction site-associated DNA sequencing (RADseq) data, we describe the development and characterisation of a panel of 95 single nucleotide polymorphism (SNP) loci for trout from this region and investigate their applicability and variability in both target (i.e., southern English) and non-target trout populations from northern Britain and Ireland. In addition, we present three case studies which demonstrate the utility and resolution of these genetic markers at three levels of spatial separation:(a) between closely related populations in nearby rivers, (b) within a catchment and (c) when determining parentage and familial relationships between fish sampled from a single site, using both empirical and simulated data. The SNP loci will be useful for population genetic and assignment studies on brown trout within the UK and beyond.
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Affiliation(s)
- Daniel R Osmond
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - R Andrew King
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
| | - Bruce Stockley
- Westcountry Rivers Trust, Rain-Charm House, Cornwall, UK
| | - Sophie Launey
- ESE, Ecology and Ecosystem Health, Agrocampus Ouest INRAe, Rennes, France
| | - Jamie R Stevens
- Department of Biosciences, Faculty of Health and Life Sciences, Hatherly Laboratories, University of Exeter, Exeter, UK
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Keeney DB, Cobb SA, Jadin RC, Orlofske SA. Atypical life cycle does not lead to inbreeding or selfing in parasites despite clonemate accumulation in intermediate hosts. Mol Ecol 2022; 32:1777-1790. [PMID: 36579456 DOI: 10.1111/mec.16837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022]
Abstract
Many parasites utilize asexual and sexual reproduction and multiple hosts to complete their life cycles. How these taxa avoid inbreeding is an essential question for understanding parasite evolution and ecology. Aquatic trematodes that require multiple host species may benefit from diverse genetic parasite assemblages accumulating within second intermediate hosts prior to sexual reproduction in definitive hosts. However, Cotylurus species are able to utilize the same snail species as first and second intermediate hosts, potentially resulting in the accumulation of genetically identical clones (clonemates) prior to sexual reproduction. In this study, we developed and analysed novel microsatellite loci to determine if clones are accumulating within snail hosts prior to ingestion by bird hosts and the effects this could have on parasite inbreeding. Contrary to previous studies of aquatic trematodes, significantly large numbers of clonemates were present within snails, but full-sibs were not. Genetic structure was present over a relatively small geographical scale despite the use of vagile definitive hosts. Phylogenetic analysis identified the Cotylurus sp. clones as belonging to a single species. Despite the presence of clones within snails, mating between clones/selfing was not common and heterozygosity is maintained within individuals. Potential issues with clones mating may be mitigated by the presence of snails with numerous clones, the consumption of many snails by bird hosts and parasite clone recognition/avoidance. Use of the same host species for multiple life stages may have advantages when parasites are able to avoid inbreeding and the required hosts are common.
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Affiliation(s)
- Devon B Keeney
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, New York, USA
| | - Sarah A Cobb
- Department of Biological and Environmental Sciences, Le Moyne College, Syracuse, New York, USA.,Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Robert C Jadin
- Department of Biology, Northeastern Illinois University, Chicago, Illinois, USA.,Department of Biology, Museum of Natural History, University of Wisconsin - Stevens Point, Stevens Point, Wisconsin, USA
| | - Sarah A Orlofske
- Department of Biology, Northeastern Illinois University, Chicago, Illinois, USA.,Department of Biology, Museum of Natural History, University of Wisconsin - Stevens Point, Stevens Point, Wisconsin, USA
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Cardenas CR, Mularo AJ, Chavez AS, Adams RMM. Limited genetic differentiation of
Mycetomoellerius mikromelanos
in Parque National Soberanía, Panama: Implications for queen dispersal. Biotropica 2022. [DOI: 10.1111/btp.13171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Cody Raul Cardenas
- Department of Evolution Ecology and Organismal Biology & Museum of Biological Diversity The Ohio State University Columbus Ohio USA
- Muséum d'Histoire Naturelle de la Ville de Genève Geneva Switzerland
- Université de Genève Faculté des Sciences Life Sciences PhD School Ecology and Evolution Geneva Switzerland
| | - Andrew J. Mularo
- Department of Evolution Ecology and Organismal Biology & Museum of Biological Diversity The Ohio State University Columbus Ohio USA
- Department of Biological Sciences Purdue University West Lafayette Indiana USA
| | - Andreas S. Chavez
- Department of Evolution Ecology and Organismal Biology & Museum of Biological Diversity The Ohio State University Columbus Ohio USA
- Translational Data Analytics Institute The Ohio State University Columbus Ohio USA
| | - Rachelle M. M. Adams
- Department of Evolution Ecology and Organismal Biology & Museum of Biological Diversity The Ohio State University Columbus Ohio USA
- Department of Entomology National Museum of Natural History Smithsonian Institution Washington District of Colombia USA
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Sai Satyanarayana D, Ahlawat S, Sharma R, Arora R, Sharma A, Tantia MS, Vijh RK. Mitochondrial DNA diversity divulges high levels of haplotype diversity and lack of genetic structure in the Indian camels. Gene X 2022; 820:146279. [PMID: 35143947 DOI: 10.1016/j.gene.2022.146279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 01/08/2022] [Accepted: 02/03/2022] [Indexed: 11/04/2022] Open
Abstract
Camels represent an important genetic resource of the desert ecosystems of India, with the dromedary and Bactrian camels inhabiting the hot and cold deserts, respectively. This study is the first attempt to investigate mitochondrial DNA based genetic diversity in the Indian camel populations and explores their relationship in the context of global genetic diversity of all the three large camel species (Camelus ferus, Camelus bactrianus and Camelus dromedaries). A mitochondrial DNA fragment encompassing part of cytochrome b gene, tRNAThr, tRNAPro and the beginning of the control region was amplified and analyzed in 72 dromedary and 8 Bactrian camels of India. Sequence analysis revealed that the haplotype and nucleotide diversity (Hd: 0.937 and π: 0.00431) in the Indian dromedaries was higher than the indices reported so far for the dromedary or Bactrian camels across the globe. The corresponding values in the Indian Bactrian camels were 1.000 and 0.00393, respectively. Signals of population expansion were evident in the dromedaries of India on the basis of mismatch analysis and Fu's Fs values. The analysis of molecular variance attributed most of the genetic variance (92.15%) between the dromedary, wild Bactrian and domestic Bactrian camels indicating separate maternal origins. The existence of three mitochondrial lineages in the old world camels (C. bactrianus: Lineage A; C. ferus: Lineage B and C. dromedarius: Lineage C) was also substantiated by the topology of the Median-Joining network.
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Affiliation(s)
- D Sai Satyanarayana
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India; ICAR-National Dairy Research Institute, Karnal, Haryana, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India.
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - Annu Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - M S Tantia
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
| | - R K Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
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Genetic Diversity, Admixture and Analysis of Homozygous-by-Descent (HBD) Segments of Russian Wild Boar. BIOLOGY 2022; 11:biology11020203. [PMID: 35205070 PMCID: PMC8869248 DOI: 10.3390/biology11020203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/25/2022] [Indexed: 02/04/2023]
Abstract
The wild boar is the wild ancestor of the domestic pig and one of the most common species of ungulates. At the beginning of the 20th century, the wild boar was practically exterminated in the European part of Russia. In the period 1935-1988, 7705 boars were caught in various regions of the European part of Russia, the Far East, Ukraine, Belarus, Kyrgyzstan, Kazakhstan, Latvia, Lithuania, Estonia, Tajikistan and resettled in the territory of Russia. Asian and European wild boars dwell the territory of Russia. The aim of our research was to study the genetic diversity and structure of wild boar populations in different regions of Russia using genome-wide genotyping. We have determined the genetic distances, population structure, parameters of genetic diversity and significantly expanded our understanding of the genetic state of the Russian wild boar. For the first time, we calculated autozygosity of the wild boar of the European and Asian subspecies using Homozygous-by-Descent (HBD) Segments analysis, which is important in terms of population recovery. We also found evidence of hybridization between Russian wild boar and domestic pigs. A group of European wild boars showed introgression of the Asian boar into population. The mean level of the inbreeding coefficient in European wild boar was higher than in Asian wild boar, and combined groups of the European boar had higher inbreeding coefficient than Russian wild boars. These results obtained can be used in population management.
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Zhang Y, Li M, Liu J, Peng Y, Zuo B, Xu Z. Effects of KPNA7 gene polymorphisms on reproductive traits in France Large White pigs. JOURNAL OF APPLIED ANIMAL RESEARCH 2021. [DOI: 10.1080/09712119.2021.1965609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Yunxia Zhang
- College of life Science and Agronomy, Zhoukou Normal University, Zhoukou, People’s Republic of China
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Mingyang Li
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Jun Liu
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Yaxin Peng
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Bo Zuo
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
| | - Zaiyan Xu
- Key Laboratory of Swine Genetics and Breeding, Ministry of Agriculture and Key Lab of Agricultural Animal Genetics and Breeding, Ministry of Education, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
- Department of Basic Veterinary, College of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, People’s Republic of China
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Hoffmann L, Hull KL, Bierman A, Badenhorst R, Bester-van der Merwe AE, Rhode C. Patterns of Genetic Diversity and Mating Systems in a Mass-Reared Black Soldier Fly Colony. INSECTS 2021; 12:insects12060480. [PMID: 34064077 PMCID: PMC8224309 DOI: 10.3390/insects12060480] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 12/27/2022]
Abstract
The black soldier fly (BSF), Hermetia illucens, is a promising candidate for the emerging insect farming industry with favourable characteristics for both bioremediation and production of animal delivered nutritive and industrial compounds. The genetic management of commercial colonies will become increasingly important for the sustainability of the industry. However, r-selected life history traits of insects pose challenges to conventional animal husbandry and breeding approaches. In this study, the long-term genetic effects of mass-rearing were evaluated as well as mating systems in the species to establish factors that might influence genetic diversity, and by implication fitness and productivity in commercial colonies. Population genetic parameters, based on microsatellite markers, were estimated and compared amongst two temporal wild sampling populations and four generations (F28, F48, F52, and F62) of a mass-reared colony. Furthermore, genetic relationships amongst mate pairs were evaluated and parentage analysis was performed to determine the oc-currence of preferential mate choice and multiple paternity. The mass-reared colony showed a reduction in genetic diversity and evidence for inbreeding with significant successive generational genetic differentiation from the wild progenitor population. Population-level analysis also gave the first tentative evidence of positive assortative mating and genetic polyandry in BSF. The homoge-neity of the mass-reared colony seems to result from a dual action caused by small effective popu-lation size and increased homozygosity due to positive assortative mating. However, the high ge-netic diversity in the wild and a polyandrous mating system might suggest the possible restoration of diversity in mass-reared colonies through augmentation with the wild population.
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Affiliation(s)
- Lelanie Hoffmann
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (L.H.); (K.L.H.); (A.E.B.-v.d.M.)
| | - Kelvin L. Hull
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (L.H.); (K.L.H.); (A.E.B.-v.d.M.)
| | - Anandi Bierman
- Insect Technology Group Holdings UK Ltd., 1 Farnham Road, Guildford GU2 4RG, UK; (A.B.); (R.B.)
| | - Rozane Badenhorst
- Insect Technology Group Holdings UK Ltd., 1 Farnham Road, Guildford GU2 4RG, UK; (A.B.); (R.B.)
| | - Aletta E. Bester-van der Merwe
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (L.H.); (K.L.H.); (A.E.B.-v.d.M.)
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa; (L.H.); (K.L.H.); (A.E.B.-v.d.M.)
- Correspondence:
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9
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Hanson JO, Veríssimo A, Velo‐Antón G, Marques A, Camacho‐Sanchez M, Martínez‐Solano Í, Gonçalves H, Sequeira F, Possingham HP, Carvalho SB. Evaluating surrogates of genetic diversity for conservation planning. CONSERVATION BIOLOGY : THE JOURNAL OF THE SOCIETY FOR CONSERVATION BIOLOGY 2021; 35:634-642. [PMID: 32761662 PMCID: PMC8048567 DOI: 10.1111/cobi.13602] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 07/16/2020] [Accepted: 07/23/2020] [Indexed: 05/13/2023]
Abstract
Protected-area systems should conserve intraspecific genetic diversity. Because genetic data require resources to obtain, several approaches have been proposed for generating plans for protected-area systems (prioritizations) when genetic data are not available. Yet such surrogate-based approaches remain poorly tested. We evaluated the effectiveness of potential surrogate-based approaches based on microsatellite genetic data collected across the Iberian Peninsula for 7 amphibian and 3 reptilian species. Long-term environmental suitability did not effectively represent sites containing high genetic diversity (allelic richness). Prioritizations based on long-term environmental suitability had similar performance to random prioritizations. Geographic distances and resistance distances based on contemporary environmental suitability were not always effective surrogates for identification of combinations of sites that contain individuals with different genetic compositions. Our results demonstrate that population genetic data based on commonly used neutral markers can inform prioritizations, and we could not find an adequate substitute. Conservation planners need to weigh the potential benefits of genetic data against their acquisition costs.
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Affiliation(s)
- Jeffrey O. Hanson
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Ana Veríssimo
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Guillermo Velo‐Antón
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Adam Marques
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Miguel Camacho‐Sanchez
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Íñigo Martínez‐Solano
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
- Museo Nacional de Ciencias Naturales‐CSICCalle de José Gutiérrez Abascal2Madrid28006Spain
| | - Helena Gonçalves
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
- Museu de História Natural e da CiênciaUniversidade do PortoPraça Gomes TeixeiraPorto4099‐002Portugal
| | - Fernando Sequeira
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
| | - Hugh P. Possingham
- The Nature ConservancyMinneapolisMN55415U.S.A.
- Centre for Biodiversity and Conservation Science, School of Biological SciencesThe University of QueenslandBrisbaneQLD 4072Australia
| | - Silvia B. Carvalho
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos GenéticosUniversidade do PortoCampus de Vairão, Rua Padre Armando Quintas, no. 7Vairão4485‐661Portugal
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Tóth B, Khosravi R, Ashrafzadeh MR, Bagi Z, Fehér M, Bársony P, Kovács G, Kusza S. Genetic Diversity and Structure of Common Carp ( Cyprinus carpio L.) in the Centre of Carpathian Basin: Implications for Conservation. Genes (Basel) 2020; 11:E1268. [PMID: 33126496 PMCID: PMC7693397 DOI: 10.3390/genes11111268] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 11/16/2022] Open
Abstract
Hungary is one of the largest common carp-production countries in Europe and now, there is a large number of local breeds and strains in the country. For proper maintenance of the animal genetic resources, information on their genetic diversity and structure is essential. At present, few data are available on the genetic purity and variability of the Hungarian common carp. In this study, we genetically analyzed 13 strains in Hungary and, in addition, the Amur wild carp, using 12 microsatellite markers. A total of 117 unique alleles were detected in 630 individuals. Low levels of genetic differentiation (Fst and Cavalli-Sforza and Edwards distance) were estimated among strains. The AMOVA showed the low but significant level of genetic differentiation among strains (3.79%). Bayesian clustering analysis using STRUCTURE classified the strains into 14 different clusters. The assignment test showed that 93.64% of the individuals could be assigned correctly into their original strain. Overall, our findings can be contributed to complementing scientific knowledge for conservation and management of threatened strains of common carp.
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Affiliation(s)
- Bianka Tóth
- Institutes for Agricultural Research and Educational Farm, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; (B.T.); (Z.B.)
| | - Rasoul Khosravi
- Department of Natural Resources and Environmental Engineering, School of Agriculture, Shiraz University, Shiraz 71441-65186, Iran;
| | - Mohammad Reza Ashrafzadeh
- Department of Fisheries and Environmental Sciences, Faculty of Natural Resources and Earth Sciences, Shahrekord University, Shahrekord 64165478, Iran;
| | - Zoltán Bagi
- Institutes for Agricultural Research and Educational Farm, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; (B.T.); (Z.B.)
| | - Milán Fehér
- Fish Biology Laboratory, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; (M.F.); (P.B.)
| | - Péter Bársony
- Fish Biology Laboratory, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary; (M.F.); (P.B.)
| | - Gyula Kovács
- Department of Fish Biology, National Agricultural Research and Innovation Centre, Research Institute for Fisheries and Aquaculture, 5540 Szarvas Anna-liget utca 35, Hungary;
| | - Szilvia Kusza
- Animal Genetics Laboratory, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, Böszörményi út 138, 4032 Debrecen, Hungary
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Aguirre-Liguori JA, Luna-Sánchez JA, Gasca-Pineda J, Eguiarte LE. Evaluation of the Minimum Sampling Design for Population Genomic and Microsatellite Studies: An Analysis Based on Wild Maize. Front Genet 2020; 11:870. [PMID: 33193568 PMCID: PMC7531271 DOI: 10.3389/fgene.2020.00870] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 07/16/2020] [Indexed: 12/21/2022] Open
Abstract
Massive parallel sequencing (MPS) is revolutionizing the field of molecular ecology by allowing us to understand better the evolutionary history of populations and species, and to detect genomic regions that could be under selection. However, the economic and computational resources needed generate a tradeoff between the amount of loci that can be obtained and the number of populations or individuals that can be sequenced. In this work, we analyzed and compared two simulated genomic datasets fitting a hierarchical structure, two extensive empirical genomic datasets, and a dataset comprising microsatellite information. For all datasets, we generated different subsampling designs by changing the number of loci, individuals, populations, and individuals per population to test for deviations in classic population genetics parameters (HS, FIS, FST). For the empirical datasets we also analyzed the effect of sampling design on landscape genetic tests (isolation by distance and environment, central abundance hypothesis). We also tested the effect of sampling a different number of populations in the detection of outlier SNPs. We found that the microsatellite dataset is very sensitive to the number of individuals sampled when obtaining summary statistics. FIS was particularly sensitive to a low sampling of individuals in the simulated, genomic, and microsatellite datasets. For the empirical and simulated genomic datasets, we found that as long as many populations are sampled, few individuals and loci are needed. For the empirical datasets, we found that increasing the number of populations sampled was important in obtaining precise landscape genetic estimates. Finally, we corroborated that outlier tests are sensitive to the number of populations sampled. We conclude by proposing different sampling designs depending on the objectives.
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Affiliation(s)
- Jonás A Aguirre-Liguori
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Department of Ecology and Evolutionary Biology, UC Irvine, Irvine, CA, United States
| | - Javier A Luna-Sánchez
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Jaime Gasca-Pineda
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Love Stowell SM, Gagne RB, McWhirter D, Edwards W, Ernest HB. Bighorn Sheep Genetic Structure in Wyoming Reflects Geography and Management. J Wildl Manage 2020. [DOI: 10.1002/jwmg.21882] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Sierra M. Love Stowell
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Roderick B. Gagne
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Doug McWhirter
- Wyoming Game and Fish DepartmentJackson Regional Office 420 N Cache St Jackson WY 830001 USA
| | - William Edwards
- Wyoming Game and Fish DepartmentWildlife Health Laboratory 1174 Snowy Range Rd Laramie WY 82070 USA
| | - Holly B. Ernest
- Wildlife Genomics & Disease Ecology Lab, Department of Veterinary SciencesUniversity of Wyoming 1174 Snowy Range Rd Laramie WY 82070 USA
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Hyeun‐Ji L, Broggi J, Sánchez‐Montes G, Díaz‐Paniagua C, Gomez‐Mestre I. Dwarfism in close continental amphibian populations despite lack of genetic isolation. OIKOS 2020. [DOI: 10.1111/oik.07086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Lee Hyeun‐Ji
- Dept of Wetland Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas ES‐41092 Seville Spain
| | - Juli Broggi
- Dept of Wetland Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas ES‐41092 Seville Spain
- Dept of Biology, Section of Evolutionary Ecology, Univ. of Lund Lund Sweden
| | - Gregorio Sánchez‐Montes
- Dept of Wetland Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas ES‐41092 Seville Spain
- Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Carmen Díaz‐Paniagua
- Dept of Wetland Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas ES‐41092 Seville Spain
| | - Ivan Gomez‐Mestre
- Dept of Wetland Ecology, Doñana Biological Station, Consejo Superior de Investigaciones Científicas ES‐41092 Seville Spain
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CapellÀ-Marzo B, SÁnchez-Montes G, MartÍnez-Solano I. Contrasting demographic trends and asymmetric migration rates in a spatially structured amphibian population. Integr Zool 2020; 15:482-497. [PMID: 32329558 DOI: 10.1111/1749-4877.12449] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Natural populations often persist at the landscape scale as metapopulations, with breeding units (subpopulations) experiencing temporal extinction and recolonization events. Important parameters to forecast population viability in these systems include the ratio of the effective number of breeders (Nb ) to the total number of adults (Na ) and migration rates among subpopulations. Here, we present the results of a 10-year integrative monitoring program of a metapopulation of the Iberian green frog (Pelophylax perezi) in central Spain. We characterized population dynamics at two main breeding ponds (Gravera and Laguna) using capture-mark-recapture data to estimate Na in each breeding season, and multilocus genotypes to estimate the effective population size (Ne ), Nb , individual breeding success, and migration rates. Both ponds experienced population decline after a dry season, with Gravera subsequently recovering and Laguna suffering a bottleneck associated with genetic impoverishment. In this subpopulation, average allelic richness and private alleles decreased from 2010 (10.87 and 1.67, respectively) to 2018 (8.0 and 0.20). The Nb /Na ratio in Laguna in 2018 was twice as high (0.95) than in Gravera (0.41) or in pre-bottleneck Laguna (0.50), suggesting plasticity or genetic compensation through increased individual breeding success. Migration rates were asymmetric between ponds, with a stronger contribution from Gravera to Laguna (29.9% vs. 16.2% in the opposite direction) that may result in a rescue effect. This study emphasizes the importance of integrative demographic approaches for the monitoring of natural populations based on a better understanding of their spatio-temporal dynamics, which provides valuable information for conservation actions.
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Affiliation(s)
- Berta CapellÀ-Marzo
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Gregorio SÁnchez-Montes
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Iñigo MartÍnez-Solano
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
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15
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Arntzen JW, van Belkom J. 'Mainland-island' population structure of a terrestrial salamander in a forest-bocage landscape with little evidence for in situ ecological speciation. Sci Rep 2020; 10:1700. [PMID: 32015401 PMCID: PMC6997349 DOI: 10.1038/s41598-020-58551-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Accepted: 01/09/2020] [Indexed: 12/17/2022] Open
Abstract
Adaptation to different ecological environments can, through divergent selection, generate phenotypic and genetic differences between populations, and eventually give rise to new species. The fire salamander (Salamandra salamandra) has been proposed to represent an early stage of ecological speciation, driven by differential habitat adaptation through the deposition and development of larvae in streams versus ponds in the Kottenforst near Bonn (Germany). We set out to test this hypothesis of ecological speciation in an area different from the one where it was raised and we took the opportunity to explore for drivers of genetic differentiation at a landscape scale. A survey over 640 localities demonstrated the species' presence in ponds and streams across forests, hilly terrain and areas with hedgerows ('bocage'). Genetic variation at 14 microsatellite loci across 41 localities in and around two small deciduous forests showed that salamander effective population sizes were higher in forests than in the bocage, with panmixia in the forests (Fst < 0.010) versus genetic drift or founder effects in several of the small and more or less isolated bocage populations (Fst > 0.025). The system fits the 'mainland-island' metapopulation model rather than indicating adaptive genetic divergence in pond versus stream larval habitats. A reanalysis of the Kottenforst data indicated that microsatellite genetic variation fitted a geographical rather than an environmental axis, with a sharp transition from a western pond-breeding to an eastern, more frequently stream-breeding group of populations. A parallel changeover in mitochondrial DNA exists but remains to be well documented. The data support the existence of a hybrid zone following secondary contact of differentiated lineages, more so than speciation in situ.
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Affiliation(s)
- Jan W Arntzen
- Naturalis Biodiversity Center, Leiden, The Netherlands.
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16
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The Genomic Makeup of Nine Horse Populations Sampled in the Netherlands. Genes (Basel) 2019; 10:genes10060480. [PMID: 31242710 PMCID: PMC6627704 DOI: 10.3390/genes10060480] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 06/11/2019] [Accepted: 06/22/2019] [Indexed: 11/16/2022] Open
Abstract
The spectrum of modern horse populations encompasses populations with a long history of development in isolation and relatively recently formed types. To increase our understanding of the evolutionary history and provide information on how to optimally conserve or improve these populations with varying development and background for the future, we analyzed genotype data of 184 horses from 9 Dutch or common horse populations in the Netherlands: The Belgian draft horse, Friesian horse, Shetland pony, Icelandic horse, Gelder horse, Groninger horse, harness horse, KWPN sport horse and the Lipizzaner horse population. Various parameters were estimated (e.g., runs of homozygosity and FST values) to gain insight into genetic diversity and relationships within and among these populations. The identified genomic makeup and quantified relationships did mostly conform to the development of these populations as well as past and current breeding practices. In general, populations that allow gene-flow showed less inbreeding and homozygosity. Also, recent bottlenecks (e.g., related to high selective pressure) caused a larger contribution of long ROHs to inbreeding. Maintaining genetic diversity through tailor-made breeding practices is crucial for a healthy continuation of the investigated, mostly inbred and (effectively) small sized horse populations, of which several already experience inbreeding related issues.
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17
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O'Connell KA, Mulder KP, Maldonado J, Currie KL, Ferraro DM. Sampling related individuals within ponds biases estimates of population structure in a pond-breeding amphibian. Ecol Evol 2019; 9:3620-3636. [PMID: 30962914 PMCID: PMC6434569 DOI: 10.1002/ece3.4994] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/28/2019] [Accepted: 01/28/2019] [Indexed: 12/20/2022] Open
Abstract
Effective conservation and management of pond-breeding amphibians depends on the accurate estimation of population structure, demographic parameters, and the influence of landscape features on breeding-site connectivity. Population-level studies of pond-breeding amphibians typically sample larval life stages because they are easily captured and can be sampled nondestructively. These studies often identify high levels of relatedness between individuals from the same pond, which can be exacerbated by sampling the larval stage. Yet, the effect of these related individuals on population genetic studies using genomic data is not yet fully understood. Here, we assess the effect of within-pond relatedness on population and landscape genetic analyses by focusing on the barred tiger salamanders (Ambystoma mavortium) from the Nebraska Sandhills. Utilizing genome-wide SNPs generated using a double-digest RADseq approach, we conducted standard population and landscape genetic analyses using datasets with and without siblings. We found that reduced sample sizes influenced parameter estimates more than the inclusion of siblings, but that within-pond relatedness led to the inference of spurious population structure when analyses depended on allele frequencies. Our landscape genetic analyses also supported different models across datasets depending on the spatial resolution analyzed. We recommend that future studies not only test for relatedness among larval samples but also remove siblings before conducting population or landscape genetic analyses. We also recommend alternative sampling strategies to reduce sampling siblings before sequencing takes place. Biases introduced by unknowingly including siblings can have significant implications for population and landscape genetic analyses, and in turn, for species conservation strategies and outcomes.
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Affiliation(s)
- Kyle A. O'Connell
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Global Genome InitiativeNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Department of BiologyThe University of Texas at ArlingtonArlingtonTexas
| | - Kevin P. Mulder
- Department of Vertebrate ZoologyNational Museum of Natural History, Smithsonian InstitutionWashingtonDistrict of Columbia
- Centro de Investigação em Biodiversidade e Recursos Genéticos (CIBIO)PortoPortugal
| | - Jose Maldonado
- Department of BiologyThe University of Texas at ArlingtonArlingtonTexas
| | | | - Dennis M. Ferraro
- School of Natural ResourcesUniversity of Nebraska LincolnLincolnNebraska
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18
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Fine-scale genetic structure in a salamander with two reproductive modes: Does reproductive mode affect dispersal? Evol Ecol 2018. [DOI: 10.1007/s10682-018-9957-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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19
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Combining phylogeography and landscape genetics to infer the evolutionary history of a short-range Mediterranean relict, Salamandra salamandra longirostris. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1110-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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21
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Sánchez‐Montes G, Wang J, Ariño AH, Vizmanos JL, Martínez‐Solano I. Reliable effective number of breeders/adult census size ratios in seasonal-breeding species: Opportunity for integrative demographic inferences based on capture-mark-recapture data and multilocus genotypes. Ecol Evol 2017; 7:10301-10314. [PMID: 29238556 PMCID: PMC5723585 DOI: 10.1002/ece3.3387] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 07/20/2017] [Accepted: 08/03/2017] [Indexed: 01/18/2023] Open
Abstract
The ratio of the effective number of breeders (Nb) to the adult census size (Na), Nb/Na, approximates the departure from the standard capacity of a population to maintain genetic diversity in one reproductive season. This information is relevant for assessing population status, understanding evolutionary processes operating at local scales, and unraveling how life-history traits affect these processes. However, our knowledge on Nb/Na ratios in nature is limited because estimation of both parameters is challenging. The sibship frequency (SF) method is adequate for reliable Nb estimation because it is based on sibship and parentage reconstruction from genetic marker data, thereby providing demographic inferences that can be compared with field-based information. In addition, capture-mark-recapture (CMR) robust design methods are well suited for Na estimation in seasonal-breeding species. We used tadpole genotypes of three pond-breeding amphibian species (Epidalea calamita, Hyla molleri, and Pelophylax perezi, n = 73-96 single-cohort tadpoles/species genotyped at 15-17 microsatellite loci) and candidate parental genotypes (n = 94-300 adults/species) to estimate Nb by the SF method. To assess the reliability of Nb estimates, we compared sibship and parentage inferences with field-based information and checked for the convergence of results in replicated subsampled analyses. Finally, we used CMR data from a 6-year monitoring program to estimate annual Na in the three species and calculate the Nb/Na ratio. Reliable ratios were obtained for E. calamita (Nb/Na = 0.18-0.28) and P. perezi (0.5), but in H. molleri, Na could not be estimated and genetic information proved insufficient for reliable Nb estimation. Integrative demographic studies taking full advantage of SF and CMR methods can provide accurate estimates of the Nb/Na ratio in seasonal-breeding species. Importantly, the SF method provides results that can be readily evaluated for reliability. This represents a good opportunity for obtaining robust demographic inferences with wide applications for evolutionary and conservation research.
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Affiliation(s)
- Gregorio Sánchez‐Montes
- Department of Environmental BiologyUniversidad de NavarraPamplonaSpain
- Museo Nacional de Ciencias Naturales, CSICMadridSpain
- Institute of ZoologyZoological Society of LondonLondonUK
- Ecology, Evolution, and Development GroupDepartment of Wetland EcologyDoñana Biological Station, CSICSevilleSpain
| | - Jinliang Wang
- Institute of ZoologyZoological Society of LondonLondonUK
| | - Arturo H. Ariño
- Department of Environmental BiologyUniversidad de NavarraPamplonaSpain
| | - José Luis Vizmanos
- Department of Biochemistry and GeneticsUniversidad de NavarraPamplonaSpain
| | - Iñigo Martínez‐Solano
- Museo Nacional de Ciencias Naturales, CSICMadridSpain
- Ecology, Evolution, and Development GroupDepartment of Wetland EcologyDoñana Biological Station, CSICSevilleSpain
- Instituto de Investigación en Recursos Cinegéticos (IREC‐CSIC‐UCLM‐JCCM)Ciudad RealSpain
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