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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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Araya-Donoso R, San Juan E, Tamburrino Í, Lamborot M, Veloso C, Véliz D. Integrating genetics, physiology and morphology to study desert adaptation in a lizard species. J Anim Ecol 2021; 91:1148-1162. [PMID: 34048024 DOI: 10.1111/1365-2656.13546] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 05/24/2021] [Indexed: 11/28/2022]
Abstract
Integration of multiple approaches is key to understand the evolutionary processes of local adaptation and speciation. Reptiles have successfully colonized desert environments, that is, extreme and arid conditions that constitute a strong selective pressure on organisms. Here, we studied genomic, physiological and morphological variations of the lizard Liolaemus fuscus to detect adaptations to the Atacama Desert. By comparing populations of L. fuscus inhabiting the Atacama Desert with populations from the Mediterranean forests from central Chile, we aimed at characterizing features related to desert adaptation. We combined ddRAD sequencing with physiological (evaporative water loss, metabolic rate and selected temperature) and morphological (linear and geometric morphometrics) measurements. We integrated the genomic and phenotypic data using redundancy analyses. Results showed strong genetic divergence, along with a high number of fixed loci between desert and forest populations. Analyses detected 110 fixed and 30 outlier loci located within genes, from which 43 were in coding regions, and 12 presented non-synonymous mutations. The candidate genes were associated with cellular membrane and development. Desert lizards presented lower evaporative water loss than those from the forest. Morphological data showed that desert lizards had smaller body size, different allometry, larger eyeballs and more dorsoventrally compressed heads. Our results suggest incipient speciation between desert and forest populations. The adaptive signal must be cautiously interpreted since genetic drift could also contribute to the divergence pattern. Nonetheless, we propose water and resource availability, and changes in habitat structure, as the most relevant challenges for desert reptiles. This study provides insights of the mechanisms that allow speciation as well as desert adaptation in reptiles at multiple levels, and highlights the benefit of integrating independent evidence.
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Affiliation(s)
- Raúl Araya-Donoso
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile.,School of Life Sciences, Arizona State University, Tempe, AZ, USA
| | - Esteban San Juan
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Ítalo Tamburrino
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Madeleine Lamborot
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Claudio Veloso
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - David Véliz
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Núcleo Milenio de Ecología y Manejo Sustentable de Islas Oceánicas (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo, Chile
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Colihueque N, Gantz A, Parraguez M. Revealing the biodiversity of Chilean birds through the COI barcode approach. Zookeys 2021; 1016:143-161. [PMID: 33628081 PMCID: PMC7892532 DOI: 10.3897/zookeys.1016.51866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 12/20/2020] [Indexed: 11/12/2022] Open
Abstract
The mitochondrial cytochrome c oxidase subunit I (COI) gene is an effective molecular tool for the estimation of genetic variation and the identification of bird species. This molecular marker is used to differentiate among Chilean bird species by analyzing barcodes for 76 species (197 individuals), comprising 28 species with no previous barcode data and 48 species with sequences retrieved from the BOLD and GenBank databases. The DNA barcodes correctly identified 94.7% of the species analyzed (72 of 76 species). Mean intraspecific K2P distance was 0.3% (range 0-8.7%). Within the intraspecific divergence range, three species, Phrygilus gayi, Sephanoides sephanoides and Curaeus curaeus, showed relatively high intraspecific divergence (1.5-8.7%), possibly due to the presence of a species complex or geographic isolation of sub-populations. Mean interspecific K2P distance was 24.7% (range 1.3-43.5%). Consequently, the intraspecific K2P distance showed limited overlap with interspecific K2P distance. The mean intraspecific divergence in our study was similar to that found in temperate regions of South America (0.24%). However, it was approximately one order of magnitude lower than values reported for bird species in tropical regions of northern South America (1.8-2.13%). This result suggests that bird species from Chile show low levels of genetic structure and divergence. The small overlap between intra- and inter-specific distances implies that COI barcodes could be used as an effective tool to identify nearly all the Chilean bird species analyzed.
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Affiliation(s)
- Nelson Colihueque
- Laboratorio de Biología Molecular y Citogenética, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Avenida Alcalde Fuchslocher 1305, Casilla 933, Osorno, Chile Universidad de Los Lagos Osorno Chile
| | - Alberto Gantz
- Laboratorio de Ecología, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile Universidad de Los Lagos Osorno Chile
| | - Margarita Parraguez
- Laboratorio de Genética, Acuicultura y Biodiversidad, Universidad de Los Lagos, Osorno, Chile Universidad de Los Lagos Osorno Chile
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Colihueque N, Gantz A. Molecular genetic studies of Chilean avifauna: an overview about current progress. NEOTROPICAL BIOLOGY AND CONSERVATION 2019. [DOI: 10.3897/neotropical.14.e48588] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The biodiversity of Chilean avifauna has been shaped by geological events, geographical factors and extreme climatic regimens. Molecular genetic studies developed to date have begun to provide valuable information to elucidate the effect of these factors on the evolutionary history of Chilean birds. We conducted a search in two bibliographic databases (PubMed and Scopus) over the period between 1998 and 2018 to identify the number and class of articles published in this research field. The quantification of specific research categories was also performed to assess progress in different molecular genetic issues of Chilean birds. Representative studies of the more active research areas: population structure, phylogeography, systematics and taxonomy and genetic diversity, were briefly commented on. Studies on genetic divergence analysis of cryptic species and the underlying genetics at molecular level of adaptive phenotypes in populations, were very scarce. Several types of mitochondrial and nuclear markers have been used, with COI plus D-loop and microsatellite loci, respectively, being the most widely-used markers. However, high-throughput analyses based on complete mitochondrial genomes have also been published. More than one hundred species have been analyzed; the most studied groups being penguins, followed by New World swallows. Although, to date, molecular genetic studies of Chilean birds still require further analysis, the studies available on some species or groups have provided important data to improve our understanding of the origin and evolution of this avifauna.
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Gutiérrez‐Pinto N, McCracken KG, Tubaro P, Kopuchian C, Astie A, Cadena CD. Molecular and morphological differentiation among Torrent Duck (
Merganetta armata
) populations in the Andes. ZOOL SCR 2019. [DOI: 10.1111/zsc.12367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Natalia Gutiérrez‐Pinto
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
- School of Biological Sciences University of Nebraska Lincoln Nebraska
| | - Kevin G. McCracken
- Department of Biology University of Miami Coral Gables Florida
- Department of Marine Biology and Ecology Rosenstiel School of Marine and Atmospheric Sciences Miami Florida
- Institute of Arctic Biology University of Alaska Museum Fairbanks Alaska
- Department of Biology and Wildlife University of Alaska Fairbanks Fairbanks Alaska
| | - Pablo Tubaro
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
| | - Cecilia Kopuchian
- División Ornitología Museo Argentino de Ciencias Naturales “Bernardino Rivadavia” (MACN ‐ CONICET) Buenos Aires Argentina
- Centro de Ecología Aplicada del Litoral (CECOAL‐CONICET) Corrientes Argentina
| | - Andrea Astie
- Instituto Argentino de Investigaciones de las Zonas Áridas (CONICET‐CCT Mendoza) Mendoza Argentina
| | - Carlos Daniel Cadena
- Laboratorio de Biología Evolutiva de Vertebrados, Departamento de Ciencias Biológicas Universidad de los Andes Bogotá Colombia
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Lecocq T, Michez D, Gérard M, Vereecken NJ, Delangre J, Rasmont P, Vray S, Dufrêne M, Mardulyn P, Dellicour S. Divergent geographic patterns of genetic diversity among wild bees: Conservation implications. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12819] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Thomas Lecocq
- Université de Lorraine; INRA; URAFPA; Nancy France
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Denis Michez
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Maxence Gérard
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Nicolas J. Vereecken
- Agroecology & Pollination; Landscape Ecology & Plant Production Systems; Université libre de Bruxelles (ULB); Brussels Belgium
| | - Jessica Delangre
- Biodiversity & Landscape; Gembloux Agro-Bio Tech; University of Liège; Gembloux Belgium
| | - Pierre Rasmont
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
| | - Sarah Vray
- Laboratoire de Zoologie; Research Institute of Biosciences; University of Mons; Mons Belgium
- Department of Geography; University of Namur; Namur Belgium
| | - Marc Dufrêne
- Biodiversity & Landscape; Gembloux Agro-Bio Tech; University of Liège; Gembloux Belgium
| | - Patrick Mardulyn
- Evolutionary Biology and Ecology; Université libre de Bruxelles (ULB); Bruxelles Belgium
| | - Simon Dellicour
- KU Leuven Department of Microbiology and Immunology; Rega Institute; Laboratory for Clinical and Epidemiological Virology; Leuven Belgium
- Spatial Epidemiology Lab (SpELL); Université Libre de Bruxelles; CP160/12 50, av. FD Roosevelt; 1050 Bruxelles Belgium
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Rivera DS, Vianna JA, Ebensperger LA, Eduardo Palma R. Phylogeography and demographic history of the Andean degu,Octodontomys gliroides(Rodentia: Octodontidae). Zool J Linn Soc 2016. [DOI: 10.1111/zoj.12412] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Daniela S. Rivera
- Departamento de Ecología; Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Casilla 114-D Santiago Chile
- Centro de Biodiversidad y Genética; Facultad de Ciencias y Tecnología; Universidad Mayor de San Simón; Cochabamba Bolivia
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente; Facultad de Agronomía e Ingeniería Forestal; Pontificia Universidad Católica de Chile; Santiago Chile
| | - Luis A. Ebensperger
- Departamento de Ecología; Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Casilla 114-D Santiago Chile
| | - R. Eduardo Palma
- Departamento de Ecología; Facultad de Ciencias Biológicas; Pontificia Universidad Católica de Chile; Casilla 114-D Santiago Chile
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