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León F, Pizarro EJ, Noll D, Pertierra LR, Gonzalez BA, Johnson WE, Marín JC, Vianna JA. History of Diversification and Adaptation from North to South Revealed by Genomic Data: Guanacos from the Desert to Sub-Antarctica. Genome Biol Evol 2024; 16:evae085. [PMID: 38761112 PMCID: PMC11102080 DOI: 10.1093/gbe/evae085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2024] [Indexed: 05/20/2024] Open
Abstract
The increased availability of quality genomic data has greatly improved the scope and resolution of our understanding of the recent evolutionary history of wild species adapted to extreme environments and their susceptibility to anthropogenic impacts. The guanaco (Lama guanicoe), the largest wild ungulate in South America, is a good example. The guanaco is well adapted to a wide range of habitats, including the Sechura Desert, the high Andes Mountains to the north, and the extreme temperatures and conditions of Navarino Island to the south. Guanacos also have a long history of overexploitation by humans. To assess the evolutionary impact of these challenging habitats on the genomic diversity, we analyzed 38 genomes (∼10 to 16×) throughout their extensive latitudinal distribution from the Sechura and Atacama Desert to southward into Tierra del Fuego Island. These included analyses of patterns of unique differentiation in the north and geographic region further south with admixture among L. g. cacsilensis and L. g. guanicoe. Our findings provide new insights on the divergence of the subspecies ∼800,000 yr BP and document two divergent demographic trajectories and to the initial expansion of guanaco into the more southern portions of the Atacama Desert. Patagonian guanacos have experienced contemporary reductions in effective population sizes, likely the consequence of anthropogenic impacts. The lowest levels of genetic diversity corresponded to their northern and western limits of distribution and some varying degrees of genetic differentiation. Adaptive genomic diversity was strongly linked with environmental variables and was linked with colonization toward the south followed by adaptation.
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Affiliation(s)
- Fabiola León
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Eduardo J Pizarro
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Daly Noll
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
| | - Luis R Pertierra
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
| | - Benito A Gonzalez
- Laboratorio de Ecología de Vida Silvestre, Facultad de Ciencias Forestales y de la Conservación de la Naturaleza, Universidad de Chile, Santigo, Chile
| | | | - Juan Carlos Marín
- Laboratorio de Genómica y Biodiversidad, Departamento de Ciencias Básicas, Universidad del Bio-Bío, Chillán, Chile
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Santiago, Chile
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile
- Millennium Nucleus of Patagonian Limit of Life (LiLi), Santiago, Chile
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Figueroa D, Corredor FA, Mamani-Cato RH, Gallegos-Acero RF, Condori-Rojas N, Estrada R, Heredia L, Salazar W, Quilcate C, Arbizu CI. Microsatellite-Based Genetic Diversity and Population Structure of Huacaya Alpacas ( Vicugna pacos) in Southern Peru. Animals (Basel) 2023; 13:ani13091552. [PMID: 37174589 PMCID: PMC10177232 DOI: 10.3390/ani13091552] [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: 12/29/2022] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 05/15/2023] Open
Abstract
The alpaca population mostly consists of the Huacaya phenotype and is widely distributed in Southern Peru. This study aimed to estimate the genetic diversity and population structure of two Huacaya alpaca populations (Ajoyani and Quimsachata) using fourteen and twelve microsatellite markers for each population, respectively. A total of 168 alpaca biological samples were outsourced to Peruvian laboratories for DNA extraction and genotyping. For genetic diversity, observed heterozygosity (Ho), expected heterozygosity (He), polymorphism information content (PIC), and fixation indices values were estimated. An admixture analysis was performed for the population structure analysis. Different programs were used for these estimations. In total, 133 (Ajoyani) and 129 (Quimsachata) alleles were found, with a range of 4 to 17 by locus. The mean HO, HE, and PIC per marker for Ajoyani were 0.764 ± 0.112, 0.771 ± 0.1, and 0.736; for Quimsachata, they were 0.783 ± 0.087, 0.773 ± 0.095, and 0.738, respectively. The population structure showed no structure with K = 2. This study provides useful indicators for the creation of appropriate alpaca conservation programs.
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Affiliation(s)
- Deyanira Figueroa
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Flor-Anita Corredor
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Ruben H Mamani-Cato
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Estación Experimental Agraria Illpa, Puno 21002, Peru
| | - Roberto F Gallegos-Acero
- Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional del Altiplano, Av. Floral 1153, Puno 21001, Peru
| | - Nicoll Condori-Rojas
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Estación Experimental Agraria Illpa, Puno 21002, Peru
| | - Richard Estrada
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Lizeth Heredia
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Wilian Salazar
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos Quilcate
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
| | - Carlos I Arbizu
- Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Av. La Molina 1981, Lima 15024, Peru
- Facultad de Ingeniería y Ciencias Agrarias, Universidad Nacional Toribio Rodríguez de Mendoza de Amazonas (UNTRM), Cl. Higos Urco 342, Chachapoyas 01001, Peru
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