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Affiliation(s)
- Hugo D Yacobaccio
- CONICET-Instituto de Arqueología, Universidad de Buenos Aires, Buenos Aires, Argentina
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Mesas A, Baldi R, González BA, Burgi V, Chávez A, Johnson WE, Marín JC. Past and Recent Effects of Livestock Activity on the Genetic Diversity and Population Structure of Native Guanaco Populations of Arid Patagonia. Animals (Basel) 2021; 11:ani11051218. [PMID: 33922526 PMCID: PMC8146674 DOI: 10.3390/ani11051218] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Simple Summary Determining the impacts of human activities on natural populations is important for biodiversity conservation. In this paper, we study the past and more recent effects of urbanization and livestock activity on the genetic diversity and population structure of endemic guanaco populations of the arid Monte and Patagonian Steppe of central Argentina. Our results reveal that urbanization, the installation of fences, and the competition from sheep grazing coincided with the isolation of several guanaco populations, especially in areas with the highest intensity of livestock activity. However, our genetic analyses suggest that a more recent increase in connectivity among groups is occurring. Our results highlight the importance of implementing conservation management plans for natural populations in arid and human-intervened environments. Abstract Extensive livestock production and urbanization entail modifications of natural landscapes, including installation of fences, development of agriculture, urbanization of natural areas, and construction of roads and infrastructure that, together, impact native fauna. Here, we evaluate the diversity and genetic structure of endemic guanacos (Lama guanicoe) of the Monte and Patagonian Steppe of central Argentina, which have been reduced and displaced by sheep ranching and other impacts of human activities. Analyses of genetic variation of microsatellite loci and d-loop revealed high levels of genetic variation and latitudinal segregation of mitochondrial haplotypes. There were indications of at least two historical populations in the Monte and the Patagonian Steppe based on shared haplotypes and shared demographic history among localities. Currently, guanacos are structured into three groups that were probably reconnected relatively recently, possibly facilitated by a reduction of sheep and livestock in recent decades and a recovery of the guanaco populations. These results provide evidence of the genetic effects of livestock activity and urbanization on wild herbivore populations, which were possibly exacerbated by an arid environment with limited productive areas. The results highlight the importance of enacting conservation management plans to ensure the persistence of ancestral and ecologically functional populations of guanacos.
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Affiliation(s)
- Andrés Mesas
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bio-Bío, Chillán 3780000, Chile; (A.M.); (A.C.)
| | - Ricardo Baldi
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Centro Nacional Patagónico, CONICET, Puerto Madryn U9120 ACD, Argentina; (R.B.); (V.B.)
- Wildlife Conservation Society, Buenos Aires C1426 AKC, Argentina
- South American Camelids Specialist Group, SSC, IUCN, Santiago 8330015, Chile;
| | - Benito A. González
- South American Camelids Specialist Group, SSC, IUCN, Santiago 8330015, Chile;
- Laboratorio de Ecología de Vida Silvestre, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago 8330015, Chile
| | - Virginia Burgi
- Instituto Patagónico para el Estudio de los Ecosistemas Continentales, Centro Nacional Patagónico, CONICET, Puerto Madryn U9120 ACD, Argentina; (R.B.); (V.B.)
- Wildlife Conservation Society, Buenos Aires C1426 AKC, Argentina
- South American Camelids Specialist Group, SSC, IUCN, Santiago 8330015, Chile;
| | - Alexandra Chávez
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bio-Bío, Chillán 3780000, Chile; (A.M.); (A.C.)
| | - Warren E. Johnson
- Center for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA 22630, USA;
| | - Juan C. Marín
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bio-Bío, Chillán 3780000, Chile; (A.M.); (A.C.)
- Correspondence:
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Diaz-Maroto P, Rey-Iglesia A, Cartajena I, Núñez L, Westbury MV, Varas V, Moraga M, Campos PF, Orozco-terWengel P, Marin JC, Hansen AJ. Ancient DNA reveals the lost domestication history of South American camelids in Northern Chile and across the Andes. eLife 2021; 10:63390. [PMID: 33724183 PMCID: PMC8032396 DOI: 10.7554/elife.63390] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 03/15/2021] [Indexed: 01/14/2023] Open
Abstract
The study of South American camelids and their domestication is a highly debated topic in zooarchaeology. Identifying the domestic species (alpaca and llama) in archaeological sites based solely on morphological data is challenging due to their similarity with respect to their wild ancestors. Using genetic methods also presents challenges due to the hybridization history of the domestic species, which are thought to have extensively hybridized following the Spanish conquest of South America that resulted in camelids slaughtered en masse. In this study, we generated mitochondrial genomes for 61 ancient South American camelids dated between 3,500 and 2,400 years before the present (Early Formative period) from two archaeological sites in Northern Chile (Tulán-54 and Tulán-85), as well as 66 modern camelid mitogenomes and 815 modern mitochondrial control region sequences from across South America. In addition, we performed osteometric analyses to differentiate big and small body size camelids. A comparative analysis of these data suggests that a substantial proportion of the ancient vicuña genetic variation has been lost since the Early Formative period, as it is not present in modern specimens. Moreover, we propose a domestication hypothesis that includes an ancient guanaco population that no longer exists. Finally, we find evidence that interbreeding practices were widespread during the domestication process by the early camelid herders in the Atacama during the Early Formative period and predating the Spanish conquest.
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Affiliation(s)
| | - Alba Rey-Iglesia
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Isabel Cartajena
- Faculty of Social Sciences, University of Chile, Santiago de Chile, Chile
| | - Lautaro Núñez
- Institute of Archaeological Research and Museum, Católica del Norte University, San Pedro de Atacama, Chile
| | - Michael V Westbury
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Valeria Varas
- School of Science Ecology and Evolution, Faculty of Sciences, Austral of Chile University, Valdivia, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Paula F Campos
- CIIMAR Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Porto, Portugal
| | - Pablo Orozco-terWengel
- School of Biosciences, Cardiff University, Cardiff, United Kingdom.,ICCMISAC - International Consortium for the Conservation Management and Improvement of South American Camelids, Cardiff, United Kingdom
| | - Juan Carlos Marin
- ICCMISAC - International Consortium for the Conservation Management and Improvement of South American Camelids, Cardiff, United Kingdom.,Genomic and Biodiversity Laboratory, Basic Sciences Department, Faculty of Sciences, Bio-Bio University, Chillán, Chile
| | - Anders J Hansen
- The GLOBE Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Genetic and demographic history define a conservation strategy for earth's most endangered pinniped, the Mediterranean monk seal Monachus monachus. Sci Rep 2021; 11:373. [PMID: 33431977 PMCID: PMC7801404 DOI: 10.1038/s41598-020-79712-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 12/07/2020] [Indexed: 01/29/2023] Open
Abstract
The Mediterranean monk seal (Monachus monachus) is a flagship species for marine conservation, but important aspects of its life history remain unknown. Concerns over imminent extinction motivated a nuclear DNA study of the species in its largest continuous subpopulation in the eastern Mediterranean Sea. Despite recent evidence of partial subpopulation recovery, we demonstrate that there is no reason for complacency, as the species still shares several traits that are characteristic of a critically endangered species: Mediterranean monk seals in the eastern Mediterranean survive in three isolated and genetically depauperate population clusters, with small effective population sizes and high levels of inbreeding. Our results indicated male philopatry over short distances, which is unexpected for a polygynous mammal. Such a pattern may be explained by the species' unique breeding behavior, in which males defend aquatic territories near breeding sites, while females are often forced to search for new pupping areas. Immediate action is necessary to reverse the downward spiral of population decline, inbreeding accumulation and loss of genetic diversity. We propose concrete conservation measures for the Mediterranean monk seal focusing on reducing anthropogenic threats, increasing the population size and genetic diversity, and thus improving the long-term prospects of survival.
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Price E, Larrabure D, Gonzales B, McClure P, Espinoza E. Forensic identification of the keratin fibers of South American camelids by ambient ionization mass spectrometry: Vicuña, alpaca and guanaco. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8916. [PMID: 32770752 DOI: 10.1002/rcm.8916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/14/2020] [Accepted: 08/02/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE The keratin fleece of the endangered vicuña (Vicugna vicugna) commands a high value in international markets, and this trade has caused illegal poaching and a substantial decrease in vicuña populations. Morphological analysis of hairs does not have the resolution to determine the species of origin of camelid natural fibers. In addition, commerce in camelid fleece also includes the legal trade of alpaca (Vicugna pacos) and guanaco (Lama guanicoe) wool. METHODS The keratin fiber spectra of vicuña (n = 19), guanaco (n = 20) and alpaca (n = 20) were collected using X-ray fluorescence (XRF) spectrometry, Horizontal attenuated total reflectance Fourier transform infrared (HATR-FTIR) spectroscopy and direct analysis in real time time-of-flight mass spectrometry (DART-TOFMS). Analysis with each technique evaluated the data to determine if the three taxa could be separated using either descriptive or multivariate statistics. RESULTS XRF analysis showed that the elements detected and their relative concentrations were similar in all three species, whereas HATR-FTIR analysis could identify alpaca fleece but could not differentiate vicuña from guanaco. Ions detected by ambient ionization using DART-TOFMS, in either positive- or negative-ion mode, gave the best results and showed that each taxonomic group is distinctive. Multivariate analysis of the mass spectra created robust models which resolved each species (LOOCV = 99.9%). The analyses of eight validation samples were correctly assigned to the appropriate species and demonstrated the reliability of DART-TOFMS to infer taxonomic source. CONCLUSIONS The DART-TOFMS spectra of unmodified keratin fibers infer that the chemotype of each species is heavily influenced by fatty acids, cholesterol and its analogs, and that these ions are useful in separating the fleece of vicuña, alpaca and guanaco. We posit that the etiological source of these chemotype differences is consistent with genetic modulations and is less influenced by diet. Accurate taxonomic identification of fleece is important to identify violations and assists in the protection of rare species.
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Affiliation(s)
- Erin Price
- National Fish and Wildlife Forensic Laboratory, 1490 E. Main St., Ashland, OR 97520, USA
| | | | - Benito Gonzales
- Faculty of Forest Sciences and Nature Conservation, Universidad de Chile, Chile
| | - Pamela McClure
- National Fish and Wildlife Forensic Laboratory, 1490 E. Main St., Ashland, OR 97520, USA
| | - Edgard Espinoza
- National Fish and Wildlife Forensic Laboratory, 1490 E. Main St., Ashland, OR 97520, USA
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Azémard C, Dufour E, Zazzo A, Wheeler JC, Goepfert N, Marie A, Zirah S. Untangling the fibre ball: Proteomic characterization of South American camelid hair fibres by untargeted multivariate analysis and molecular networking. J Proteomics 2020; 231:104040. [PMID: 33152504 DOI: 10.1016/j.jprot.2020.104040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2020] [Revised: 08/27/2020] [Accepted: 10/29/2020] [Indexed: 12/24/2022]
Abstract
The proteomic analysis of hairs, yarns or textiles has emerged as a powerful method to determine species of origin, mainly used in archaeozoological research and fraud control. Differentiation between the South American camelid (SAC) species (the wild guanaco and vicuña and their respective domesticates the llama and alpaca) is particularly challenging due to poor database information and significant hybridization between species. In this study, we analysed 41 modern and 4 archaeological samples from the four SACs species. Despite strong similarities with Old World Camelidae, we identified 7 peptides specific to SACs assigned to keratin K86 and the keratin-associated proteins KAP13-1 and KAP11-1. Untargeted multivariate analysis of the LC-MS data permitted to distinguish SAC species and propose discriminant features. MS/MS-based molecular networking combined with database-assisted de novo sequencing permitted to identify 5 new taxonomic peptides assigned to K33a, K81 and/or K83 keratins and KAP19-1. These peptides differentiate the two wild species, guanaco and vicuña. These results show the value of combining database search and untargeted metabolomic approaches for paleoproteomics, and reveal for the first time the potential of molecular networks to highlight deamidation related to diagenesis and cluster highly similar peptides related to interchain homologies or intra- or inter-specific polymorphism. SIGNIFICANCE: This study used an innovative approach combining multivariate analysis of LC-MS data together with molecular networking and database-assisted de novo sequencing to identify taxonomic peptides in palaeoproteomics. It constitutes the first attempt to differentiate between hair fibres from the four South American camelids (SACs) based on proteomic analysis of modern and archaeological samples. It provides different proteomic signatures for each of the four SAC species and proposes new SAC taxonomic peptides of interest in archaeozoology and fraud control. SACs have been extensively exploited since human colonization of South America but have not been studied to the extent of their economic, cultural and heritage importance. Applied to the analysis of ancient Andean textiles, our results should permit a better understanding of cultural and pastoral practices in South America. The wild SACs are endangered by poaching and black-market sale of their fibre. For the first time, our results provide discriminant features for the determination of species of origin of contraband fibre.
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Affiliation(s)
- Clara Azémard
- Unité Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 54, 63 rue Buffon, 75005 Paris, France; Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Elise Dufour
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Antoine Zazzo
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnements (AASPE), Muséum National d'Histoire Naturelle, CNRS, CP 56, 55 rue Buffon, 75005 Paris, France
| | - Jane C Wheeler
- CONOPA - Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Av. Reusche M4, Pachacamac, Lima 19, Peru
| | - Nicolas Goepfert
- Archéologie des Amériques, UMR 8096, CNRS - Université Paris 1 Panthéon-Sorbonne, MSH Mondes, 21 allée de l'université, 92023 Nanterre, France
| | - Arul Marie
- Unité Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 54, 63 rue Buffon, 75005 Paris, France
| | - Séverine Zirah
- Unité Molécules de Communication et Adaptations des Microorganismes (MCAM), Muséum National d'Histoire Naturelle, CNRS, CP 54, 63 rue Buffon, 75005 Paris, France.
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Fan R, Gu Z, Guang X, Marín JC, Varas V, González BA, Wheeler JC, Hu Y, Li E, Sun X, Yang X, Zhang C, Gao W, He J, Munch K, Corbett-Detig R, Barbato M, Pan S, Zhan X, Bruford MW, Dong C. Genomic analysis of the domestication and post-Spanish conquest evolution of the llama and alpaca. Genome Biol 2020; 21:159. [PMID: 32616020 PMCID: PMC7331169 DOI: 10.1186/s13059-020-02080-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/21/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Despite their regional economic importance and being increasingly reared globally, the origins and evolution of the llama and alpaca remain poorly understood. Here we report reference genomes for the llama, and for the guanaco and vicuña (their putative wild progenitors), compare these with the published alpaca genome, and resequence seven individuals of all four species to better understand domestication and introgression between the llama and alpaca. RESULTS Phylogenomic analysis confirms that the llama was domesticated from the guanaco and the alpaca from the vicuña. Introgression was much higher in the alpaca genome (36%) than the llama (5%) and could be dated close to the time of the Spanish conquest, approximately 500 years ago. Introgression patterns are at their most variable on the X-chromosome of the alpaca, featuring 53 genes known to have deleterious X-linked phenotypes in humans. Strong genome-wide introgression signatures include olfactory receptor complexes into both species, hypertension resistance into alpaca, and fleece/fiber traits into llama. Genomic signatures of domestication in the llama include male reproductive traits, while in alpaca feature fleece characteristics, olfaction-related and hypoxia adaptation traits. Expression analysis of the introgressed region that is syntenic to human HSA4q21, a gene cluster previously associated with hypertension in humans under hypoxic conditions, shows a previously undocumented role for PRDM8 downregulation as a potential transcriptional regulation mechanism, analogous to that previously reported at high altitude for hypoxia-inducible factor 1α. CONCLUSIONS The unprecedented introgression signatures within both domestic camelid genomes may reflect post-conquest changes in agriculture and the breakdown of traditional management practices.
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Affiliation(s)
- Ruiwen Fan
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Zhongru Gu
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | - Juan Carlos Marín
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bio Bio, Chillán, Chile
| | - Valeria Varas
- Programa de Doctorado en Ciencias mención Ecología y Evolución, Escuela de Graduados, Facultad de Ciencias., Universidad Austral de Chile, Valdivia, Chile
| | - Benito A. González
- Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
| | - Jane C. Wheeler
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Pachacamac, Lima, Peru
| | - Yafei Hu
- BGI Genomics, BGI, Shenzhen, China
| | - Erli Li
- BGI Genomics, BGI, Shenzhen, China
| | | | | | | | - Wenjun Gao
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Junping He
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
| | - Kasper Munch
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Russel Corbett-Detig
- Department of Biomolecular Engineering and Genomics Institute, UC Santa Cruz, Santa Cruz, CA USA
| | - Mario Barbato
- Department of Animal Science, Food and Technology – DIANA, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Shengkai Pan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
| | - Xiangjiang Zhan
- CAS Key Lab of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Michael W. Bruford
- Cardiff University – Institute of Zoology Joint Laboratory for Biocomplexity Research, Chinese Academy of Sciences, Beijing, China
- School of Biosciences and Sustainable Places Institute, Cardiff University, Cardiff, Wales UK
| | - Changsheng Dong
- College of Animal Science and Veterinary Medicine, Shanxi Agricultural University, Taigu, Shanxi China
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Paredes GF, Yalta-Macedo CE, Gutierrez GA, Veli-Rivera EA. Genetic Diversity and Population Structure of Llamas ( Lama glama) from the Camelid Germplasm Bank-Quimsachata. Genes (Basel) 2020; 11:E541. [PMID: 32408471 PMCID: PMC7291211 DOI: 10.3390/genes11050541] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/30/2020] [Accepted: 05/04/2020] [Indexed: 12/02/2022] Open
Abstract
Llamas (Lama glama) are invaluable resources of Peru. Despite their importance, their population is decreasing. The Camelid Germplasm Bank-Quimsachata was created as a guardian of this South American camelid (SAC) species and established a bank of llamas from their two types, Ch'aku and Q'ara. However, these populations need to present high genetic diversity to be considered suitable conservation stocks. Thus, in the present study, 13 microsatellites specific for the SAC were used to assess the current genetic variability and differentiation of the llama population from the Bank. The global population showed high genetic diversity with a total of 157 different alleles, with an average of 12.08 alleles per microsatellite, an expected and observed heterozygosity of 0.758 and 0.707, respectively, and an average polymorphic information content (PIC) of 0.723. Although considered as two different breeds and managed separately, the genetic differentiation between Ch'aku and Q'ara was low (FST = 0.01). Accordingly, the gene flow value was high (Nm = 30.5). Overall, our results indicate the existence of high genetic variation among individuals, and thus, this llama population could be considered a suitable genetic stock for their conservation and for sustainability programs. Additionally, the 13 microsatellites can be used to study other Peruvian llama populations and monitor the genetic variability of llamas from the Camelid Germplasm Bank-Quimsachata.
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Affiliation(s)
- Gabriela F. Paredes
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima, Peru;
| | - Claudia E. Yalta-Macedo
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima, Peru;
| | - Gustavo A. Gutierrez
- Facultad de Zootecnia, Universidad Nacional Agraria La Molina (UNALM), Av. La Molina s/n, 15024 Lima, Peru;
| | - Eudosio A. Veli-Rivera
- Laboratorio de Biología Molecular y Genómica, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA). Av. La Molina 1981, 15024 Lima, Peru;
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Alza L, Lavretsky P, Peters JL, Cerón G, Smith M, Kopuchian C, Astie A, McCracken KG. Old divergence and restricted gene flow between torrent duck ( Merganetta armata) subspecies in the Central and Southern Andes. Ecol Evol 2019; 9:9961-9976. [PMID: 31534707 PMCID: PMC6745679 DOI: 10.1002/ece3.5538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/16/2019] [Accepted: 07/19/2019] [Indexed: 12/03/2022] Open
Abstract
AIM To investigate the structure and rate of gene flow among populations of habitat-specialized species to understand the ecological and evolutionary processes underpinning their population dynamics and historical demography, including speciation and extinction. LOCATION Peruvian and Argentine Andes. TAXON Two subspecies of torrent duck (Merganetta armata). METHODS We sampled 156 individuals in Peru (M. a. leucogenis; Chillón River, n = 57 and Pachachaca River, n = 49) and Argentina (M. a. armata; Arroyo Grande River, n = 33 and Malargüe River, n = 17), and sequenced the mitochondrial DNA (mtDNA) control region to conduct coarse and fine-scale demographic analyses of population structure. Additionally, to test for differences between subspecies, and across genetic markers with distinct inheritance patterns, a subset of individuals (Peru, n = 10 and Argentina, n = 9) was subjected to partial genome resequencing, obtaining 4,027 autosomal and 189 Z-linked double-digest restriction-associated DNA sequences. RESULTS Haplotype and nucleotide diversities were higher in Peru than Argentina across all markers. Peruvian and Argentine subspecies showed concordant species-level differences (ΦST mtDNA = 0.82; ΦST autosomal = 0.30; ΦST Z chromosome = 0.45), including no shared mtDNA haplotypes. Demographic parameters estimated for mtDNA using IM and IMa2 analyses, and for autosomal markers using ∂a∂i (isolation-with-migration model), supported an old divergence (mtDNA = 600,000 years before present (ybp), 95% HPD range = 1.2 Mya to 200,000 ybp; and autosomal ∂a∂i = 782,490 ybp), between the two subspecies, characteristic of deeply diverged lineages. The populations were well-differentiated in Argentina but moderately differentiated in Peru, with low unidirectional gene flow in each country. MAIN CONCLUSIONS We suggest that the South American Arid Diagonal was preexisting and remains a current phylogeographic barrier between the ranges of the two torrent duck subspecies, and the adult territoriality and breeding site fidelity to the rivers define their population structure.
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Affiliation(s)
- Luis Alza
- Department of BiologyUniversity of MiamiCoral GablesFLUSA
- División de OrnitologíaCORBIDILimaPeru
- Institute of Arctic BiologyDepartment of Biology and WildlifeUniversity of Alaska FairbanksAKUSA
| | - Philip Lavretsky
- Department of Biological SciencesUniversity of Texas at El PasoEl PasoTXUSA
| | | | - Gerardo Cerón
- Laboratorio de Zoología‐CRUBUniversidad Nacional del ComahueBarilocheArgentina
| | - Matthew Smith
- Institute of Arctic BiologyDepartment of Biology and WildlifeUniversity of Alaska FairbanksAKUSA
| | - Cecilia Kopuchian
- Centro de Ecología Aplicada del Litoral (CECOAL‐CONICET)CorrientesArgentina
- División OrnitologíaMuseo Argentino de Ciencias Naturales (MACN‐CONICET)Buenos AiresArgentina
| | - Andrea Astie
- Instituto Argentino de Investigaciones de las Zonas Áridas (CCT Mendoza‐CONICET)MendozaArgentina
| | - Kevin G. McCracken
- Department of BiologyUniversity of MiamiCoral GablesFLUSA
- División de OrnitologíaCORBIDILimaPeru
- Institute of Arctic BiologyDepartment of Biology and WildlifeUniversity of Alaska FairbanksAKUSA
- Rosenstiel School of Marine and Atmospheric SciencesUniversity of MiamiCoral GablesFLUSA
- University of Alaska MuseumUniversity of Alaska FairbanksFairbanksAKUSA
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Demography of avian scavengers after Pleistocene megafaunal extinction. Sci Rep 2019; 9:9680. [PMID: 31273237 PMCID: PMC6609603 DOI: 10.1038/s41598-019-45769-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 06/07/2019] [Indexed: 11/08/2022] Open
Abstract
The late Quaternary megafauna extinctions reshaped species assemblages, yet we know little about how extant obligate scavengers responded to this abrupt ecological change. To explore whether obligate scavengers persisted by depending on contemporary community linkages or via foraging flexibility, we tested the importance of the trophic interaction between pumas (Puma concolor) and native camelids (Vicugna vicugna and Lama guanicoe) for the persistence of Andean condors (Vultur gryphus) in southern South America, and compared the demographic history of three vultures in different continents. We sequenced and compiled mtDNA to reconstruct past population dynamics. Our results suggest that Andean condors increased in population size >10 KYA, whereas vicuñas and pumas showed stable populations and guanacos a recent (<10 KYA) demographic expansion, suggesting independent trajectories between species. Further, vultures showed positive demographic trends: white-backed vultures (Gyps africanus) increased in population size, matching attenuated community changes in Africa, and California condors (Gymnogyps californianus) exhibited a steep demographic expansion ~20 KYA largely concurrent with North American megafaunal extinctions. Our results suggest that dietary plasticity of extant vulture lineages allowed them to thrive despite historical environmental changes. This dietary flexibility, however, is now detrimental as it enhances risk to toxicological compounds harbored by modern carrion resources.
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11
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González BA, Vásquez JP, Gómez-Uchida D, Cortés J, Rivera R, Aravena N, Chero AM, Agapito AM, Varas V, Wheleer JC, Orozco-terWengel P, Marín JC. Phylogeography and Population Genetics of Vicugna vicugna: Evolution in the Arid Andean High Plateau. Front Genet 2019; 10:445. [PMID: 31244880 PMCID: PMC6562099 DOI: 10.3389/fgene.2019.00445] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 04/29/2019] [Indexed: 11/13/2022] Open
Abstract
The vicuña (Vicugna vicugna) is the most representative wild ungulate of the high Andes of South America with two recognized morphological subspecies, V. v. mensalis in the north and V. v. vicugna in the south of its distribution. Current vicuña population size (460,000-520,000 animals) is the result of population recovery programs established in response to 500 years of overexploitation. Despite the vicuña's ecosystemic, economic and social importance, studies about their genetic variation and history are limited and geographically restricted. Here, we present a comprehensive assessment of the genetic diversity of vicuña based on samples collected throughout its distribution range corresponding to eleven localities in Peru and five in Chile representing V. v. mensalis, plus four localities each in Argentina and Chile representing V. v. vicugna. Analysis of mitochondrial DNA and microsatellite markers show contrasting results regarding differentiation between the two vicuña types with mitochondrial haplotypes supporting subspecies differentiation, albeit with only a few mutational steps separating the two subspecies. In contrast, microsatellite markers show that vicuña genetic variation is best explained as an isolation by distance pattern where populations on opposite ends of the distribution present different allelic compositions, but the intermediate populations present a variety of alleles shared by both extreme forms. Demographic characterization of the species evidenced a simultaneous and strong reduction in the effective population size in all localities supporting the existence of a unique, large ancestral population (effective size ∼50,000 individuals) as recently as the mid-Holocene. Furthermore, the genetic variation observed across all localities is better explained by a model of gene flow interconnecting them rather than only by genetic drift. Consequently, we propose space "continuous" Management Units for vicuña as populations exhibit differentiation by distance and spatial autocorrelation linked to sex biased dispersal instead of population fragmentation or geographical barriers across the distribution.
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Affiliation(s)
- Benito A. González
- Laboratorio de Ecología de Vida Silvestre, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santiago, Chile
- South American Camelid Specialist Group, Survival Species Commission, International Union for Conservation of Nature, Santiago, Chile
| | - Juan P. Vásquez
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
- GEECLAB, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Daniel Gómez-Uchida
- GEECLAB, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
- Núcleo Milenio INVASAL, Concepción, Chile
| | - Jorge Cortés
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
- GEECLAB, Departamento de Zoología, Facultad de Ciencias Naturales y Oceanográficas, Universidad de Concepción, Concepción, Chile
| | - Romina Rivera
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad Santo Tomás, Iquique, Chile
| | - Nicolas Aravena
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
| | - Ana M. Chero
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
| | - Ana M. Agapito
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
| | - Valeria Varas
- Doctorado en Ciencias, Mencioìn Ecologiìa y Evolucioìn, Instituto de Ciencias Ambientales and Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jane C. Wheleer
- South American Camelid Specialist Group, Survival Species Commission, International Union for Conservation of Nature, Santiago, Chile
- CONOPA-Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Lima, Peru
| | - Pablo Orozco-terWengel
- School of Biosciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff, United Kingdom
| | - Juan Carlos Marín
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Chillán, Chile
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12
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Shifts in habitat suitability and the conservation status of the Endangered Andean cat Leopardus jacobita under climate change scenarios. ORYX 2019. [DOI: 10.1017/s0030605317000503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractOrganisms adapted to life at high elevations are particularly threatened by climate change, which can cause them to become isolated on mountain tops, yet their responses may vary according to their position in the food chain and their ecological flexibility. Predicting the future distributions of such organisms requires fine-tuned species-specific models. Building on a previous ecological niche model, we explored shifts in the suitability of habitats for the Endangered Andean cat Leopardus jacobita, and assessed how these will be represented within existing protected areas in the future. Using a robust set of presence records and corrected climate surfaces, we applied the Maxent algorithm to model habitat suitability for this carnivore and for its preferred prey, the mountain viscacha Lagidium viscacia. Our predictions indicate that the areas climatically suitable for Andean cats could contract by up to 30% by 2080 under the most pessimistic scenario, with an overall upwards shift of 225 m and a polewards displacement of 98–180 km. The predicted range contraction was more pronounced in the species’ core range, in the Bolivian and Peruvian Andes, whereas suitable conditions may increase in the southern range in Patagonia. Bolivia and Peru are predicted to suffer the most marked decline in habitat representativeness within protected areas. The southern range appears to be less vulnerable to climate change, offering opportunities for the conservation of this genetically distinct population. We discuss the value and limitations of using species distribution modelling to assess changes in the potential distribution and conservation status of this and other Andean species.
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13
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Marín JC, Rivera R, Varas V, Cortés J, Agapito A, Chero A, Chávez A, Johnson WE, Orozco-terWengel P. Genetic Variation in Coat Colour Genes MC1R and ASIP Provides Insights Into Domestication and Management of South American Camelids. Front Genet 2018; 9:487. [PMID: 30483307 PMCID: PMC6242857 DOI: 10.3389/fgene.2018.00487] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2018] [Accepted: 10/01/2018] [Indexed: 01/15/2023] Open
Abstract
The domestication of wild vicuña and guanaco by early pre-Inca cultures is an iconic example of wildlife management and domestication in the Americas. Although domestic llamas and alpacas were clearly selected for key, yet distinct, phenotypic traits, the relative patterns and direction of selection and domestication have not been confirmed using genetic approaches. However, the detailed archaeological records from the region suggest that domestication was a process carried out under significant control and planning, which would have facilitated coordinated and thus extremely effective selective pressure to achieve and maintain desired phenotypic traits. Here we link patterns of sequence variation in two well-characterised genes coding for colour variation in vertebrates and interpret the results in the context of domestication in guanacos and vicuñas. We hypothesise that colour variation in wild populations of guanacos and vicunas were strongly selected against. In contrast, variation in coat colour variation in alpaca was strongly selected for and became rapidly fixed in alpacas. In contrast, coat colour variants in llamas were of less economic value, and thus were under less selective pressure. We report for the first time the full sequence of MC1R and 3 exons of ASIP in 171 wild specimens from throughout their distribution and which represented a range of commonly observed colour patterns. We found a significant difference in the number of non-synonymous substitutions, but not synonymous substitutions among wild and domestics species. The genetic variation in MC1R and ASIP did not differentiate alpaca from llama due to the high degree of reciprocal introgression, but the combination of 11 substitutions are sufficient to distinguish domestic from wild animals. Although there is gene flow among domestic and wild species, most of the non-synonymous variation in MC1R and ASIP was not observed in wild species, presumably because these substitutions and the associated colour phenotypes are not effectively transmitted back into wild populations. Therefore, this set of substitutions unequivocally differentiates wild from domestic animals, which will have important practical application in forensic cases involving the poaching of wild vicuñas and guanacos. These markers will also assist in identifying and studying archaeological remains pre- and post-domestication.
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Affiliation(s)
- Juan C. Marín
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Romina Rivera
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
- Departamento de Ciencias Básicas, Universidad Santo Tomas, Iquique, Chile
| | - Valeria Varas
- Doctorado en Ciencias, Mención Ecología y Evolución, Instituto de Ciencias Ambientales & Evolutivas, Facultad de Ciencias, Universidad Austral de Chile, Valdivia, Chile
| | - Jorge Cortés
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
- Departamento de Zoología, Universidad de Concepción, Concepción, Chile
| | - Ana Agapito
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Ana Chero
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Alexandra Chávez
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bío-Bío, Chillán, Chile
| | - Warren E. Johnson
- Smithsonian Conservation Biology Institute, Smithsonian Institution, Washington, DC, United States
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14
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Casey CS, Orozco-terWengel P, Yaya K, Kadwell M, Fernández M, Marín JC, Rosadio R, Maturrano L, Hoces D, Hu Y, Wheeler JC, Bruford MW. Comparing genetic diversity and demographic history in co-distributed wild South American camelids. Heredity (Edinb) 2018; 121:387-400. [PMID: 30061581 DOI: 10.1038/s41437-018-0120-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 05/11/2018] [Accepted: 05/28/2018] [Indexed: 11/09/2022] Open
Abstract
Vicuñas and guanacos are two species of wild South American camelids that are key ruminants in the ecosystems where they occur. Although closely related, these species feature differing ecologies and life history characters, which are expected to influence both their genetic diversity and population differentiation at different spatial scales. Here, using mitochondrial and microsatellite genetic markers, we show that vicuña display lower genetic diversity within populations than guanaco but exhibit more structure across their Peruvian range, which may reflect a combination of natural genetic differentiation linked to geographic isolation and recent anthropogenic population declines. Coalescent-based demographic analyses indicate that both species have passed through a strong bottleneck, reducing their effective population sizes from over 20,000 to less than 1000 individuals. For vicuña, this bottleneck is inferred to have taken place ~3300 years ago, but to have occurred more recently for guanaco at ~2000 years ago. These inferred dates are considerably later than the onset of domestication (when the alpaca was domesticated from the vicuña while the llama was domesticated from the guanaco), coinciding instead with a major human population expansion following the mid-Holocene cold period. As importantly, they imply earlier declines than the well-documented Spanish conquest, where major mass mortality events were recorded for Andean human and camelid populations. We argue that underlying species' differences and recent demographic perturbations have influenced genetic diversity in modern vicuña and guanaco populations, and these processes should be carefully evaluated in the development and implementation of management strategies for these important genetic resources.
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Affiliation(s)
- C S Casey
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, UK.,School of Life Sciences, University of Lincoln, Riseholme Park, Lincoln, LN2 2LG, UK
| | - P Orozco-terWengel
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, UK
| | - K Yaya
- CONOPA, Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Avenida Reusche Mz. M Lt. 4, Pachacamac, Lima 19, Peru
| | - M Kadwell
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - M Fernández
- CONOPA, Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Avenida Reusche Mz. M Lt. 4, Pachacamac, Lima 19, Peru
| | - J C Marín
- Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío - Bío, Casilla 447, Chillan, Chile
| | - R Rosadio
- CONOPA, Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Avenida Reusche Mz. M Lt. 4, Pachacamac, Lima 19, Peru.,Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - L Maturrano
- CONOPA, Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Avenida Reusche Mz. M Lt. 4, Pachacamac, Lima 19, Peru.,Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima, Peru
| | - D Hoces
- CONOPA, Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Avenida Reusche Mz. M Lt. 4, Pachacamac, Lima 19, Peru
| | - Y Hu
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, 1-5 Beichen West Road, 100101, Beijing, China
| | - J C Wheeler
- CONOPA, Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Avenida Reusche Mz. M Lt. 4, Pachacamac, Lima 19, Peru.
| | - M W Bruford
- School of Biosciences, Cardiff University, Cathays Park, Cardiff, CF10 3AX, UK. .,CONOPA, Instituto de Investigación y Desarrollo de Camélidos Sudamericanos, Avenida Reusche Mz. M Lt. 4, Pachacamac, Lima 19, Peru.
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15
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da Silva Santos A, Trigo TC, de Oliveira TG, Silveira L, Eizirik E. Phylogeographic analyses of the pampas cat (Leopardus colocola; Carnivora, Felidae) reveal a complex demographic history. Genet Mol Biol 2018; 41:273-287. [PMID: 29668017 PMCID: PMC5913729 DOI: 10.1590/1678-4685-gmb-2017-0079] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 06/07/2017] [Indexed: 11/22/2022] Open
Abstract
The pampas cat is a small felid that occurs in open habitats throughout much of South America. Previous studies have revealed intriguing patterns of morphological differentiation and genetic structure among its populations, as well as molecular evidence for hybridization with the closely related L. tigrinus. Here we report phylogeographic analyses encompassing most of its distribution (focusing particularly on Brazilian specimens, which had been poorly sampled in previous studies), using a novel dataset comprising 2,143 bp of the mitogenome, along with previously reported mtDNA sequences. Our data revealed strong population strutucture and supported a west-to-east colonization process in this species' history. We detected two population expansion events, one older (ca. 200 thousand years ago [kya]) in western South America and another more recent (ca. 60-50 kya) in eastern areas, coinciding with the expansion of savanna environments in Brazil. Analyses including L. tigrinus individuals bearing introgressed mtDNA from L. colocola showed a complete lack of shared haplotypes between species, indicating that their hybridization was ancient. Finally, we observed a close relationship between Brazilian/Uruguayan L. colocola haplotypes and those sampled in L. tigrinus, indicating that their hybridization was likely related to the demographic expansion of L. colocola into eastern South America.
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Affiliation(s)
- Anelisie da Silva Santos
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Tatiane Campos Trigo
- Setor de Mastozoologia, Museu de Ciências Naturais, Fundação Zoobotânica do Rio Grande do Sul. Porto Alegre, RS, Brazil
| | - Tadeu Gomes de Oliveira
- Universidade Estadual do Maranhão (UEMA), São Luís, MA, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil
| | | | - Eduardo Eizirik
- Laboratório de Biologia Genômica e Molecular, Escola de Ciências, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre, RS, Brazil.,Instituto Pró-Carnívoros, Atibaia, SP, Brazil
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16
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Marín JC, Romero K, Rivera R, Johnson WE, González BA. Y-chromosome and mtDNA variation confirms independent domestications and directional hybridization in South American camelids. Anim Genet 2017; 48:591-595. [DOI: 10.1111/age.12570] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2017] [Indexed: 11/29/2022]
Affiliation(s)
- J. C. Marín
- Laboratorio de Genómica y Biodiversidad; Departamento de Ciencias Básicas; Universidad del Bío-Bío; Av. Andres Bello 720 Chillán Chile
| | - K. Romero
- Laboratorio de Genómica y Biodiversidad; Departamento de Ciencias Básicas; Universidad del Bío-Bío; Av. Andres Bello 720 Chillán Chile
- Departamento de Zoología; Universidad de Concepción; Concepción Chile
| | - R. Rivera
- Laboratorio de Genómica y Biodiversidad; Departamento de Ciencias Básicas; Universidad del Bío-Bío; Av. Andres Bello 720 Chillán Chile
- Departamento de Ciencias Básicas; Universidad Santo Tomas; Av. Héroes de La Concepción 2885 Iquique Chile
| | - W. E. Johnson
- Smithsonian Conservation Biology Institute; Smithsonian Institution; Front Royal VA USA
| | - B. A. González
- Laboratorio de Ecología de Vida Silvestre; Facultad de Ciencias Forestales y de la Conservación de la Naturaleza; Universidad de Chile; Av. Santa Rosa 11315 Casilla 9206 Santiago Chile
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17
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Mata C, Malo JE, Galaz JL, Cadorzo C, Lagunas H. A three-step approach to minimise the impact of a mining site on vicuña (Vicugna vicugna) and to restore landscape connectivity. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2016; 23:13626-13636. [PMID: 27300165 DOI: 10.1007/s11356-016-7047-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/06/2016] [Indexed: 06/06/2023]
Abstract
Resource extraction projects generate a diversity of negative effects on the environment that are difficult to predict and mitigate. Consequently, adaptive management approaches have been advocated to develop effective responses to impacts that were not predicted. Mammal populations living in or around mine sites are frequently of management concern; yet, there is a dearth of published information on how to minimise the negative effects of different phases of mining operations on them. Here, we present the case study of a copper mine in the Chilean Altiplano, which caused roadkills of the protected vicuña (Vicugna vicugna). This issue led to a three-step solution being implemented: (1) the initial identification of the problem and implementation of an emergency response, (2) the scientific analysis for decision making and (3) the planning and informed implementation of responses for different future scenarios and timescales. The measures taken under each of these steps provide examples of environmental management approaches that make use of scientific information to develop integrated management responses. In brief, our case study showed how (1) the timescale and the necessity/urgency of the case were addressed, (2) the various stakeholders involved were taken into account and (3) changes were included into the physical, human and organisational elements of the company to achieve the stated objectives.
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Affiliation(s)
- Cristina Mata
- Terrestrial Ecology Group (TEG), Departamento de Ecología, Universidad Autónoma de Madrid, E-28049, Madrid, Spain.
| | - Juan E Malo
- Terrestrial Ecology Group (TEG), Departamento de Ecología, Universidad Autónoma de Madrid, E-28049, Madrid, Spain
| | - José Luis Galaz
- AMBIOS, El Liquidambar 149, Santa Cecilia, Colina, Santiago, Chile
| | - César Cadorzo
- Gerencia Medio Ambiente, Compañía Minera Doña Inés de Collahuasi, Peato Baquedano, 903, Iquique, Chile
| | - Héctor Lagunas
- Gerencia Medio Ambiente, Compañía Minera Doña Inés de Collahuasi, Peato Baquedano, 903, Iquique, Chile
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18
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Anello M, Daverio MS, Romero SR, Rigalt F, Silbestro MB, Vidal-Rioja L, Di Rocco F. Genetic diversity and conservation status of managed vicuña (Vicugna vicugna) populations in Argentina. Genetica 2016; 144:85-97. [PMID: 26842726 DOI: 10.1007/s10709-015-9880-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Accepted: 12/31/2015] [Indexed: 10/22/2022]
Abstract
The vicuña (Vicugna vicugna) was indiscriminately hunted for more than 400 years and, by the end of 1960s, it was seriously endangered. At that time, a captive breeding program was initiated in Argentina by the National Institute of Agricultural Technology (INTA) with the aim of preserving the species. Nowadays, vicuñas are managed in captivity and in the wild to obtain their valuable fiber. The current genetic status of Argentinean vicuña populations is virtually unknown. Using mitochondrial DNA and microsatellite markers, we assessed levels of genetic diversity of vicuña populations managed in the wild and compared it with a captive population from INTA. Furthermore, we examined levels of genetic structure and evidence for historical bottlenecks. Overall, all populations revealed high genetic variability with no signs of inbreeding. Levels of genetic diversity between captive and wild populations were not significantly different, although the captive population showed the lowest estimates of allelic richness, number of mitochondrial haplotypes, and haplotype diversity. Significant genetic differentiation at microsatellite markers was found between free-living populations from Jujuy and Catamarca provinces. Moreover, microsatellite data also revealed genetic structure within the Catamarca management area. Genetic signatures of past bottlenecks were detected in wild populations by the Garza Williamson test. Results from this study are discussed in relation to the conservation and management of the species.
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Affiliation(s)
- M Anello
- Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET-La Plata, CICPBA, Calle 526 e/10 y 11, PO Box 403, 1900, La Plata, Buenos Aires, Argentina.
| | - M S Daverio
- Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET-La Plata, CICPBA, Calle 526 e/10 y 11, PO Box 403, 1900, La Plata, Buenos Aires, Argentina
| | - S R Romero
- INTA-Estación Experimental Agropecuaria Abra Pampa, Ruta Provincial 11 km 17 (4640), Cochinoca, Abra Pampa, Jujuy, Argentina
| | - F Rigalt
- INTA-Estación Experimental Agropecuaria Catamarca, Ruta Provincial 33 km 4 (4705), Sumalao, Valle Viejo, Catamarca, Argentina
| | - M B Silbestro
- Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET-La Plata, CICPBA, Calle 526 e/10 y 11, PO Box 403, 1900, La Plata, Buenos Aires, Argentina
| | - L Vidal-Rioja
- Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET-La Plata, CICPBA, Calle 526 e/10 y 11, PO Box 403, 1900, La Plata, Buenos Aires, Argentina
| | - F Di Rocco
- Laboratorio de Genética Molecular, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT-CONICET-La Plata, CICPBA, Calle 526 e/10 y 11, PO Box 403, 1900, La Plata, Buenos Aires, Argentina.
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19
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Giarla TC, Jansa SA. The impact of Quaternary climate oscillations on divergence times and historical population sizes inThylamysopossums from the Andes. Mol Ecol 2015; 24:2495-506. [DOI: 10.1111/mec.13173] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 03/03/2015] [Accepted: 03/18/2015] [Indexed: 11/29/2022]
Affiliation(s)
- Thomas C. Giarla
- Department of Ecology, Evolution, and Behavior; University of Minnesota; St. Paul MN 55108 USA
- J.F. Bell Museum of Natural History; University of Minnesota; St. Paul MN 55108 USA
| | - Sharon A. Jansa
- Department of Ecology, Evolution, and Behavior; University of Minnesota; St. Paul MN 55108 USA
- J.F. Bell Museum of Natural History; University of Minnesota; St. Paul MN 55108 USA
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Roy T, Chang TH, Lan T, Lindqvist C. Phylogeny and biogeography of New World Stachydeae (Lamiaceae) with emphasis on the origin and diversification of Hawaiian and South American taxa. Mol Phylogenet Evol 2013; 69:218-38. [DOI: 10.1016/j.ympev.2013.05.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Revised: 05/25/2013] [Accepted: 05/30/2013] [Indexed: 12/15/2022]
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21
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Habitat use and preference by guanacos, vicuñas, and livestock in an altitudinal gradient in northwest Argentina. EUR J WILDLIFE RES 2013. [DOI: 10.1007/s10344-013-0748-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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22
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Marin JC, González BA, Poulin E, Casey CS, Johnson WE. The influence of the arid Andean high plateau on the phylogeography and population genetics of guanaco (Lama guanicoe) in South America. Mol Ecol 2013; 22:463-82. [PMID: 23206254 PMCID: PMC3549358 DOI: 10.1111/mec.12111] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 09/14/2012] [Accepted: 09/19/2012] [Indexed: 11/29/2022]
Abstract
A comprehensive study of the phylogeography and population genetics of the largest wild artiodactyl in the arid and cold-temperate South American environments, the guanaco (Lama guanicoe) was conducted. Patterns of molecular genetic structure were described using 514 bp of mtDNA sequence and 14 biparentally inherited microsatellite markers from 314 samples. These individuals originated from 17 localities throughout the current distribution across Peru, Bolivia, Argentina and Chile. This confirmed well-defined genetic differentiation and subspecies designation of populations geographically separated to the northwest (L. g. cacsilensis) and southeast (L. g. guanicoe) of the central Andes plateau. However, these populations are not completely isolated, as shown by admixture prevalent throughout a limited contact zone, and a strong signal of expansion from north to south in the beginning of the Holocene. Microsatellite analyses differentiated three northwestern and 4-5 southeastern populations, suggesting patterns of genetic contact among these populations. Possible genetic refuges were identified, as were source-sink patterns of gene flow at historical and recent time scales. Conservation and management of guanaco should be implemented with an understanding of these local population dynamics while also considering the preservation of broader adaptive variation and evolutionary processes.
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Affiliation(s)
- Juan C Marin
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Facultad de Ciencias, Universidad del Bío-Bío, Casilla 447, Chillán, Chile.
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23
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Barreta J, Gutiérrez-Gil B, Iñiguez V, Saavedra V, Chiri R, Latorre E, Arranz JJ. Analysis of mitochondrial DNA in Bolivian llama, alpaca and vicuna populations: a contribution to the phylogeny of the South American camelids. Anim Genet 2012; 44:158-68. [PMID: 22640259 DOI: 10.1111/j.1365-2052.2012.02376.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2012] [Indexed: 11/26/2022]
Abstract
The objectives of this work were to assess the mtDNA diversity of Bolivian South American camelid (SAC) populations and to shed light on the evolutionary relationships between the Bolivian camelids and other populations of SACs. We have analysed two different mtDNA regions: the complete coding region of the MT-CYB gene and 513 bp of the D-loop region. The populations sampled included Bolivian llamas, alpacas and vicunas, and Chilean guanacos. High levels of genetic diversity were observed in the studied populations. In general, MT-CYB was more variable than D-loop. On a species level, the vicunas showed the lowest genetic variability, followed by the guanacos, alpacas and llamas. Phylogenetic analyses performed by including additional available mtDNA sequences from the studied species confirmed the existence of the two monophyletic clades previously described by other authors for guanacos (G) and vicunas (V). Significant levels of mtDNA hybridization were found in the domestic species. Our sequence analyses revealed significant sequence divergence within clade G, and some of the Bolivian llamas grouped with the majority of the southern guanacos. This finding supports the existence of more than the one llama domestication centre in South America previously suggested on the basis of archaeozoological evidence. Additionally, analysis of D-loop sequences revealed two new matrilineal lineages that are distinct from the previously reported G and V clades. The results presented here represent the first report on the population structure and genetic variability of Bolivian camelids and may help to elucidate the complex and dynamic domestication process of SAC populations.
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Affiliation(s)
- J Barreta
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, 24071, León, Spain; Instituto de Biología Molecular y Biotecnología, Universidad Mayor de San Andrés, La Paz, Bolivia
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Cossíos ED, Walker RS, Lucherini M, Ruiz-García M, Angers B. Population structure and conservation of a high-altitude specialist, the Andean cat Leopardus jacobita. ENDANGER SPECIES RES 2012. [DOI: 10.3354/esr00402] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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25
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Marino J, Bennett M, Cossios D, Iriarte A, Lucherini M, Pliscoff P, Sillero-Zubiri C, Villalba L, Walker S. Bioclimatic constraints to Andean cat distribution: a modelling application for rare species. DIVERS DISTRIB 2011. [DOI: 10.1111/j.1472-4642.2011.00744.x] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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26
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Groeneveld LF, Lenstra JA, Eding H, Toro MA, Scherf B, Pilling D, Negrini R, Finlay EK, Jianlin H, Groeneveld E, Weigend S. Genetic diversity in farm animals--a review. Anim Genet 2010; 41 Suppl 1:6-31. [PMID: 20500753 DOI: 10.1111/j.1365-2052.2010.02038.x] [Citation(s) in RCA: 285] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.
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Affiliation(s)
- L F Groeneveld
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut, Hoeltystr. 10, 31535 Neustadt, Germany
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Silbermayr K, Orozco-terWengel P, Charruau P, Enkhbileg D, Walzer C, Vogl C, Schwarzenberger F, Kaczensky P, Burger PA. High mitochondrial differentiation levels between wild and domestic Bactrian camels: a basis for rapid detection of maternal hybridization. Anim Genet 2009; 41:315-8. [PMID: 19968638 DOI: 10.1111/j.1365-2052.2009.01993.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybridization between wild species and their domestic congeners often threatens the gene pool of the wild species. The last wild Bactrian camel (Camelus ferus) populations in Mongolia and China are examples of populations facing such a hybridization threat. To address this key issue in the conservation of wild camels, we analysed wild, hybrid and domestic Bactrian camels (Camelus bactrianus) originating from Mongolia, China and Austria. Through screening of an 804-base-pair mitochondrial fragment, we identified eight mitochondrial haplotypes and found high sequence divergence (1.9%) between C. ferus and C. bactrianus. On the basis of a mitochondrial DNA sequence fixed difference, we developed a diagnostic PCR restriction fragment length polymorphism (PCR-RFLP) assay to differentiate between wild and domestic camel samples. We applied the assay to 81 individuals and confirmed the origin of all samples including five hybrids with known maternal ancestry. The PCR-RFLP system was effective for both traditional (blood, skin) and non-invasive samples (faeces, hair), as well as for museum specimens. Our results demonstrate high levels of mitochondrial differentiation between wild and domestic Bactrian camels and that maternal hybridization can be detected by a rapid and reliable PCR-RFLP system.
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Affiliation(s)
- K Silbermayr
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna A-1210, Austria
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Marín JC, Saucedo CE, Corti P, González BA. Application of DNA forensic techniques for identifying poached guanacos (Lama guanicoe) in Chilean Patagonia*. J Forensic Sci 2009; 54:1073-6. [PMID: 19549029 DOI: 10.1111/j.1556-4029.2009.01087.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Guanaco (Lama guanicoe) is a protected and widely distributed ungulate in South America. A poacher, after killing guanacos in Valle Chacabuco, Chilean Patagonia, transported and stored the meat. Samples were retrieved by local police but the suspect argued that the meat was from a horse. Mitochondrial cytochrome b gene (774 pb), 15 loci microsatellites, and SRY gene were used to identify the species, number of animals and their population origin, and the sex of the animals, respectively. Analysis revealed that the samples came from a female (absence of SRY gene) Patagonian guanaco (assignment probability between 0.0075 and 0.0282), and clearly distinguishing it from sympatric ungulates (E-value = 0). Based on the evidence obtained in the field in addition to forensic data, the suspect was convicted of poaching and illegally carrying fire arms. This is the first report of molecular tools being used in forensic investigations of Chilean wildlife indicating its promising future application in guanaco management and conservation.
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Affiliation(s)
- Juan C Marín
- Departamento de Ciencias Básicas, Facultad de Ciencias, Laboratorio de Genómica y Biodiversidad, Universidad del Bío-Bío, Casilla 447, Chillán, Chile.
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Cossíos D, Lucherini M, Ruiz-García M, Angers B. Influence of ancient glacial periods on the Andean fauna: the case of the pampas cat (Leopardus colocolo). BMC Evol Biol 2009; 9:68. [PMID: 19331650 PMCID: PMC2669060 DOI: 10.1186/1471-2148-9-68] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Accepted: 03/30/2009] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND While numerous studies revealed the major role of environmental changes of the Quaternary on the evolution of biodiversity, research on the influence of that period on current South-American fauna is scarce and have usually focused on lowland regions. In this study, the genetic structure of the pampas cat (Leopardus colocolo), a widely distributed felid, was determined and linked to ancient climate fluctuations on the Andean region. RESULTS Using both mitochondrial sequences and nuclear microsatellites, we inferred the existence of at least four groups of populations in the central Andes, while other three localities, with little sample sizes (n = 3), presented differences in only one of these markers. The distribution of these groups is correlated to latitude, with a central area characterized by admixture of numerous mitochondrial clades. This suggests colonization from at least three glacial refuges and a contact zone between 20 degrees and 23 degrees S following a glaciation event. The similar coalescence times of the mitochondrial haplotypes indicated that the major clades split approximately one million years ago, likely during the Pre-Pastonian glacial period (0.80 - 1.30 MYA), followed by a demographic expansion in every clade during the Aftonian interglacial period (0.45 - 0.62 MYA). Interestingly, this structure roughly corresponds to the current recognised distribution of morphological subspecies. CONCLUSION The four groups of populations identified here must be considered different management units, and we propose the three localities showing differences in only mtDNA or ncDNA as provisional management units. The results revealed the influence of ancient climate fluctuations on the evolutionary history of this species. It is expected that the other species of land vertebrates with a smaller or similar mobility have been affected in the same manner by the glacial and interglacial periods in the central Andes.
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Affiliation(s)
- Daniel Cossíos
- Département de Sciences Biologiques, Université de Montréal, C.P.: 6128, Succ. Centre-Ville, Montréal, H3C 3J7, Canada
| | - Mauro Lucherini
- GECM, Cátedra de Fisiología Animal, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur-CONICET, San Juan 670, 8000 Bahía Blanca, Argentina
| | - Manuel Ruiz-García
- Departamento de Biología, Facultad de Ciencias, Pontificia Universidad Javeriana, Cra 7A No 43-82, Bogotá DC, Colombia
| | - Bernard Angers
- Département de Sciences Biologiques, Université de Montréal, C.P.: 6128, Succ. Centre-Ville, Montréal, H3C 3J7, Canada
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Marín JC, Spotorno AE, González BA, Bonacic C, Wheeler JC, Casey CS, Bruford MW, Palma RE, Poulin E. Mitochondrial DNA Variation and Systematics of the Guanaco (Lama guanicoe, Artiodactyla: Camelidae). J Mammal 2008. [DOI: 10.1644/06-mamm-a-385r.1] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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