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Kasinsky T, Rosciano N, A. Vianna J, Yorio P, Campagna L. Population structure and connectivity among coastal and freshwater Kelp Gull (Larus dominicanus) populations from Patagonia. PLoS One 2024; 19:e0301004. [PMID: 38635529 PMCID: PMC11025793 DOI: 10.1371/journal.pone.0301004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 03/09/2024] [Indexed: 04/20/2024] Open
Abstract
The genetic identification of evolutionary significant units and information on their connectivity can be used to design effective management and conservation plans for species of concern. Despite having high dispersal capacity, several seabird species show population structure due to both abiotic and biotic barriers to gene flow. The Kelp Gull is the most abundant species of gull in the southern hemisphere. In Argentina it reproduces in both marine and freshwater environments, with more than 100,000 breeding pairs following a metapopulation dynamic across 140 colonies in the Atlantic coast of Patagonia. However, little is known about the demography and connectivity of inland populations. We aim to provide information on the connectivity of the largest freshwater colonies (those from Nahuel Huapi Lake) with the closest Pacific and Atlantic populations to evaluate if these freshwater colonies are receiving immigrants from the larger coastal populations. We sampled three geographic regions (Nahuel Huapi Lake and the Atlantic and Pacific coasts) and employed a reduced-representation genomic approach to genotype individuals for single-nucleotide polymorphisms (SNPs). Using clustering and phylogenetic analyses we found three genetic groups, each corresponding to one of our sampled regions. Individuals from marine environments are more closely related to each other than to those from Nahuel Huapi Lake, indicating that the latter population constitutes the first freshwater Kelp Gull colony to be identified as an evolutionary significant unit in Patagonia.
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Affiliation(s)
- Tatiana Kasinsky
- Centro Para El Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut, Argentina
| | - Natalia Rosciano
- Instituto de Investigaciones en Biodiversidad y Medio Ambiente, CONICET, Universidad Nacional del Comahue, San Carlos de Bariloche, Río Negro, Argentina
| | - Juliana A. Vianna
- Departamento de Ecología, Facultad de Ciencias Biológicas, Instituto para el Desarrollo Sustentable, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Institute Center for Genome Regulation (CRG), Millennium Institute of Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Millennium Nucleus of Patagonian Limit of Life (LiLi), Valdivia, Chile
| | - Pablo Yorio
- Centro Para El Estudio de Sistemas Marinos, CONICET, Puerto Madryn, Chubut, Argentina
- Wildlife Conservation Society Argentina, Ciudad Autónoma de Buenos Aires, Argentina
| | - Leonardo Campagna
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY, United States of America
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Ithaca, NY, United States of America
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2
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Trevine VC, Grazziotin FG, Giraudo A, Sallesbery‐Pinchera N, Vianna JA, Zaher H. The systematics of Tachymenini (Serpentes, Dipsadidae): An updated classification based on molecular and morphological evidence. ZOOL SCR 2022. [DOI: 10.1111/zsc.12565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Vivian C. Trevine
- Laboratório de Coleções Zoológicas Instituto Butantan São Paulo Brazil
- Programa de Pós‐Graduação de Zoologia, Insituto de Biociências Universidade de São Paulo São Paulo Brazil
| | | | - Alejandro Giraudo
- Instituto Nacional de Limnología (CONICET – UNL) Ciudad Universitaria Santa Fe Argentina
- Facultad de Humanidades y Ciencias (FHUC – UNL) Ciudad Universitaria Santa Fe Argentina
| | - Nicole Sallesbery‐Pinchera
- Escuela Medicina Veterinaria, Facultad Ecología y Recursos Naturales Universidad Andrés Bello Santiago Chile
| | - Juliana A. Vianna
- Millennium Institute Center for Genome Regulation (CRG), Departamento de Ecosistemas y Medio Ambiente Pontificia Universidad Católica de Chile Santiago Chile
| | - Hussam Zaher
- Laboratório de Herpetologia, Museu de Zoologia da Universidade de São Paulo São Paulo Brazil
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3
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de Ferran V, Figueiró HV, de Jesus Trindade F, Smith O, Sinding MHS, Trinca CS, Lazzari GZ, Veron G, Vianna JA, Barbanera F, Kliver S, Serdyukova N, Bulyonkova T, Ryder OA, Gilbert MTP, Koepfli KP, Eizirik E. Phylogenomics of the world's otters. Curr Biol 2022; 32:3650-3658.e4. [PMID: 35779528 DOI: 10.1016/j.cub.2022.06.036] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/18/2022] [Accepted: 06/13/2022] [Indexed: 10/17/2022]
Abstract
Comparative whole-genome analyses hold great power to illuminate commonalities and differences in the evolution of related species that share similar ecologies. The mustelid subfamily Lutrinae includes 13 currently recognized extant species of otters,1-5 a semiaquatic group whose evolutionary history is incompletely understood. We assembled a dataset comprising 24 genomes from all living otter species, 14 of which were newly sequenced. We used this dataset to infer phylogenetic relationships and divergence times, to characterize patterns of genome-wide genealogical discordance, and to investigate demographic history and current genomic diversity. We found that genera Lutra, Aonyx, Amblonyx, and Lutrogale form a coherent clade that should be synonymized under Lutra, simplifying the taxonomic structure of the subfamily. The poorly known tropical African Aonyx congicus and the more widespread Aonyx capensis were found to be reciprocally monophyletic (having diverged 440,000 years ago), supporting the validity of the former as a distinct species. We observed variable changes in effective population sizes over time among otters within and among continents, although several species showed similar trends of expansions and declines during the last 100,000 years. This has led to different levels of genomic diversity assessed by overall heterozygosity, genome-wide SNV density, and run of homozygosity burden. Interestingly, there were cases in which diversity metrics were consistent with the current threat status (mostly based on census size), highlighting the potential of genomic data for conservation assessment. Overall, our results shed light on otter evolutionary history and provide a framework for further in-depth comparative genomic studies targeting this group.
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Affiliation(s)
- Vera de Ferran
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Henrique Vieira Figueiró
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA
| | - Fernanda de Jesus Trindade
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Oliver Smith
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Mikkel-Holger S Sinding
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark
| | - Cristine S Trinca
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Gabriele Zenato Lazzari
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil
| | - Géraldine Veron
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 57 rue Cuvier, CP 51, 75231 Paris Cedex 5, France
| | - Juliana A Vianna
- Millennium Institute Center for Genome Regulation (CRG), Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuna Mackenna 4860, Santiago 782-0436, Chile
| | - Filippo Barbanera
- Department of Biology, University of Pisa, Via A. Volta 4, 56126 Pisa, Italy
| | - Sergei Kliver
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Natalia Serdyukova
- Institute of Molecular and Cellular Biology SB RAS, 8/2 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Tatiana Bulyonkova
- A. P. Ershov Institute of Informatics Systems SB RAS, 6 Acad. Lavrentiev Ave, 630090 Novosibirsk, Russia
| | - Oliver A Ryder
- San Diego Zoo Institute for Conservation Research, Escondido, CA 92027, USA; Department of Evolution, Behavior, and Ecology, Division of Biology, University of California, San Diego, La Jolla, CA 92093, USA
| | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, The GLOBE Institute - University of Copenhagen, Øster Farimagsgade 5A, Copenhagen 1353, Denmark; University Museum, NTNU, Trondheim, Norway
| | - Klaus-Peter Koepfli
- Smithsonian Conservation Biology Institute, Center for Species Survival, National Zoological Park, 3001 Connecticut Avenue NW, Washington, DC 20008, USA; Smithsonian-Mason School of Conservation, George Mason University, Front Royal, VA 22630, USA.
| | - Eduardo Eizirik
- School of Health and Life Sciences, Pontifical Catholic University of Rio Grande do Sul, Av. Ipiranga, 6681, prédio 12C, sala 134, Porto Alegre, Rio Grande do Sul 90619-900, Brazil; Instituto Pró-Carnívoros, Av. Horácio Netto, 1030 - Parque Edmundo Zanoni, Atibaia, São Paulo 12945-010, Brazil.
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Álvarez-Varas R, Medrano C, Benítez HA, Guerrero F, León Miranda F, Vianna JA, González C, Véliz D. Genetics, Morphometrics and Health Characterization of Green Turtle Foraging Grounds in Mainland and Insular Chile. Animals (Basel) 2022; 12:ani12121473. [PMID: 35739811 PMCID: PMC9219523 DOI: 10.3390/ani12121473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/28/2022] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Chilean waters constitute a foraging habitat for the endangered green turtle. Information about this species in the country has increased in recent years; nevertheless, little is known of its ecology and health status. Additionally, some populations have drastically decreased, probably due to human factors. Here, we studied the proportion of sex, age, morphological variation, genetic characteristics, origin, and health status of green turtles in mainland and insular Chile. We found that turtles from both regions are morphologically and genetically different. Individuals from the mainland territory are juveniles and probably originated from Galapagos. In contrast, the insular territory hosts juveniles and adults that probably originated from Galapagos and French Polynesia. We also found that turtles from both regions are facing numerous anthropic threats that must be controlled. We suggest the creation of protected areas for mainland foraging grounds, and strengthen the administrative plan of the insular region to ensure sea turtle population health. Abstract Two divergent genetic lineages have been described for the endangered green turtle in the Pacific Ocean, occurring sympatrically in some foraging grounds. Chile has seven known green turtle foraging grounds, hosting mainly juveniles of different lineages. Unfortunately, anthropic factors have led to the decline or disappearance of most foraging aggregations. We investigated age-class/sex structure, morphological variation, genetic diversity and structure, and health status of turtles from two mainland (Bahia Salado and Playa Chinchorro) and one insular (Easter Island) Chilean foraging grounds. Bahia Salado is composed of juveniles, and with Playa Chinchorro, exclusively harbors individuals of the north-central/eastern Pacific lineage, with Galapagos as the major genetic contributor. Conversely, Easter Island hosts juveniles and adults from both the eastern Pacific and French Polynesia. Morphological variation was found between lineages and foraging grounds, suggesting an underlying genetic component but also an environmental influence. Turtles from Easter Island, unlike Bahia Salado, exhibited injuries/alterations probably related to anthropic threats. Our findings point to establishing legal protection for mainland Chile’s foraging grounds, and to ensure that the administrative plan for Easter Island’s marine protected area maintains ecosystem health, turtle population viability, and related cultural and touristic activities.
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Affiliation(s)
- Rocío Álvarez-Varas
- Center for Ecology and Sustainable Management of Oceanic Islands (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo 1780000, Chile;
- Qarapara Tortugas Marinas Chile NGO, Santiago 7750000, Chile; (C.M.); (F.G.)
- Correspondence:
| | - Carol Medrano
- Qarapara Tortugas Marinas Chile NGO, Santiago 7750000, Chile; (C.M.); (F.G.)
| | - Hugo A. Benítez
- Laboratorio de Ecología y Morfometría Evolutiva, Centro de Investigación de Estudios Avanzados del Maule, Universidad Católica del Maule, Talca 3466706, Chile;
- Centro de Investigación en Recursos Naturales y Sustentabilidad (CIRENYS), Universidad Bernardo O’Higgins, Santiago 8370993, Chile
| | - Felipe Guerrero
- Qarapara Tortugas Marinas Chile NGO, Santiago 7750000, Chile; (C.M.); (F.G.)
| | - Fabiola León Miranda
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 8940000, Chile; (F.L.M.); (J.A.V.)
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 8940000, Chile; (F.L.M.); (J.A.V.)
- Millennium Institute Center for Genomic Regulation (CRG), Santiago 7800003, Chile
| | - Camila González
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Coquimbo 1780000, Chile;
| | - David Véliz
- Center for Ecology and Sustainable Management of Oceanic Islands (ESMOI), Departamento de Biología Marina, Universidad Católica del Norte, Coquimbo 1780000, Chile;
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago 7800003, Chile
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5
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Noll D, Leon F, Brandt D, Pistorius P, Le Bohec C, Bonadonna F, Trathan PN, Barbosa A, Rey AR, Dantas GPM, Bowie RCK, Poulin E, Vianna JA. Positive selection over the mitochondrial genome and its role in the diversification of gentoo penguins in response to adaptation in isolation. Sci Rep 2022; 12:3767. [PMID: 35260629 PMCID: PMC8904570 DOI: 10.1038/s41598-022-07562-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 02/21/2022] [Indexed: 12/21/2022] Open
Abstract
Although mitochondrial DNA has been widely used in phylogeography, evidence has emerged that factors such as climate, food availability, and environmental pressures that produce high levels of stress can exert a strong influence on mitochondrial genomes, to the point of promoting the persistence of certain genotypes in order to compensate for the metabolic requirements of the local environment. As recently discovered, the gentoo penguins (Pygoscelis papua) comprise four highly divergent lineages across their distribution spanning the Antarctic and sub-Antarctic regions. Gentoo penguins therefore represent a suitable animal model to study adaptive processes across divergent environments. Based on 62 mitogenomes that we obtained from nine locations spanning all four gentoo penguin lineages, we demonstrated lineage-specific nucleotide substitutions for various genes, but only lineage-specific amino acid replacements for the ND1 and ND5 protein-coding genes. Purifying selection (dN/dS < 1) is the main driving force in the protein-coding genes that shape the diversity of mitogenomes in gentoo penguins. Positive selection (dN/dS > 1) was mostly present in codons of the Complex I (NADH genes), supported by two different codon-based methods at the ND1 and ND4 in the most divergent lineages, the eastern gentoo penguin from Crozet and Marion Islands and the southern gentoo penguin from Antarctica respectively. Additionally, ND5 and ATP6 were under selection in the branches of the phylogeny involving all gentoo penguins except the eastern lineage. Our study suggests that local adaptation of gentoo penguins has emerged as a response to environmental variability promoting the fixation of mitochondrial haplotypes in a non-random manner. Mitogenome adaptation is thus likely to have been associated with gentoo penguin diversification across the Southern Ocean and to have promoted their survival in extreme environments such as Antarctica. Such selective processes on the mitochondrial genome may also be responsible for the discordance detected between nuclear- and mitochondrial-based phylogenies of gentoo penguin lineages.
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Affiliation(s)
- D Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile.,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile.,Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - F Leon
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - D Brandt
- Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720, USA
| | - P Pistorius
- Department of Zoology, 11DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Nelson Mandela University, Port Elizabeth, South Africa
| | - C Le Bohec
- CNRS, IPHC UMR 7178, Université de Strasbourg, 67000, Strasbourg, France.,Département de Biologie Polaire, Centre Scientifique de Monaco, 98000, Monaco City, Monaco
| | - F Bonadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier Cedex 5, France
| | | | - A Barbosa
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - A Raya Rey
- Centro Austral de Investigaciones Científicas - Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Argentina.,Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Argentina.,Wildlife Conservation Society, Buenos Aires, Argentina
| | - G P M Dantas
- PPG in Vertebrate Biology, Pontificia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - R C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, University of California, 3101 Valley Life Science Building, Berkeley, CA, 94720, USA
| | - E Poulin
- Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile.,Facultad de Ciencias, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - J A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Vicuña Mackenna 4860, Macul, Santiago, Chile. .,Millennium Institute Biodiversity of Antarctic and Subantarctic Ecosystems (BASE), Santiago, Chile. .,Fondo de Desarrollo de Áreas Prioritarias (FONDAP), Center for Genome Regulation (CRG), Santiago, Chile.
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6
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Fiddaman SR, Vinkler M, Spiro SG, Levy H, Emerling CA, Boyd AC, Dimopoulos EA, Vianna JA, Cole TL, Pan H, Fang M, Zhang G, Hart T, Frantz LAF, Smith AL. Adaptation and cryptic pseudogenization in penguin Toll-like Receptors. Mol Biol Evol 2021; 39:6460345. [PMID: 34897511 PMCID: PMC8788240 DOI: 10.1093/molbev/msab354] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Penguins (Sphenisciformes) are an iconic order of flightless, diving seabirds distributed across a large latitudinal range in the Southern Hemisphere. The extensive area over which penguins are endemic is likely to have fostered variation in pathogen pressure, which in turn will have imposed differential selective pressures on the penguin immune system. At the front line of pathogen detection and response, the Toll-like receptors (TLRs) provide insight into host evolution in the face of microbial challenge. TLRs respond to conserved pathogen-associated molecular patterns and are frequently found to be under positive selection, despite retaining specificity for defined agonist classes. We undertook a comparative immunogenetics analysis of TLRs for all penguin species and found evidence of adaptive evolution that was largely restricted to the cell surface-expressed TLRs, with evidence of positive selection at, or near, key agonist-binding sites in TLR1B, TLR4, and TLR5. Intriguingly, TLR15, which is activated by fungal products, appeared to have been pseudogenized multiple times in the Eudyptes spp., but a full-length form was present as a rare haplotype at the population level. However, in vitro analysis revealed that even the full-length form of Eudyptes TLR15 was nonfunctional, indicating an ancestral cryptic pseudogenization prior to its eventual disruption multiple times in the Eudyptes lineage. This unusual pseudogenization event could provide an insight into immune adaptation to fungal pathogens such as Aspergillus, which is responsible for significant mortality in wild and captive bird populations.
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Affiliation(s)
- Steven R Fiddaman
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | - Michal Vinkler
- Department of Zoology, Faculty of Science, Charles University Prague, Czech Republic
| | - Simon G Spiro
- Wildlife Health Services, Zoological Society of London Regent's Park, London, UK
| | - Hila Levy
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | | | - Amy C Boyd
- Jenner Institute, University of Oxford Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford Oxford, UK
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ecosistemas y Medio Ambiente Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Theresa L Cole
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen DK2100, Copenhagen, Denmark
| | - Hailin Pan
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China
| | - Miaoquan Fang
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China
| | - Guojie Zhang
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen DK2100, Copenhagen, Denmark.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District Shenzhen 518083, China.,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
| | - Tom Hart
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Fogg Building, Queen Mary University of London Mile End Rd, Bethnal Green, London E1 4DQ, UK.,Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Faculty of Veterinary Medicine, Ludwig Maximilian University of Munich, Germany
| | - Adrian L Smith
- Department of Zoology, University of Oxford South Parks Road, Oxford, OX1 3PS, UK
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7
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Lagos N, Villalobos R, Vianna JA, Espinosa-Miranda C, Rau JR, Iriarte A. The spatial and trophic ecology of culpeo foxes (Lycalopex culpaeus) in the high Andes of northern Chile. Studies on Neotropical Fauna and Environment 2021. [DOI: 10.1080/01650521.2021.2005393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Nicolás Lagos
- Consultora Ambiental Flora y Fauna Chile Limitada, Santiago, Chile
| | - Rodrigo Villalobos
- Consultora Ambiental Flora y Fauna Chile Limitada, Santiago, Chile
- Conservation Biology Graduate Program, University of Minnesota, USA
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Jaime R. Rau
- Laboratorio de Ecología, Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Osorno, Chile
| | - Agustín Iriarte
- Consultora Ambiental Flora y Fauna Chile Limitada, Santiago, Chile
- Consultora Ambiental Flora y Fauna Chile Limitada y Center of Applied Ecology and Sustainbility (CAPES), Pontificia Universidad Católica de Chile, Santiago, Chile
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8
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Weinberger CS, Vianna JA, Faugeron S, Marquet PA. Inferring the impact of past climate changes and hunting on the South American sea lion. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Affiliation(s)
- Constanza S. Weinberger
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente Facultad de Agronomía e Ingeniería Forestal Pontifícia Universidad Católica de Chile Santiago Chile
- Centro Cambio Global UC Pontificia Universidad Católica de Chile Santiago Chile
| | - Sylvain Faugeron
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
- IRL3614 Evolutionary Biology and Ecology of Algae CNRS Sorbonne Université Pontificia Universidad Católica de ChileUniversidad Austral de ChileStation Biologique Roscoff France
| | - Pablo A. Marquet
- Departamento de Ecología Facultad de Ciencias Biológicas Pontificia Universidad Católica de Chile Santiago Chile
- Centro Cambio Global UC Pontificia Universidad Católica de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
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9
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Raj Kolora SR, Owens GL, Vazquez JM, Stubbs A, Chatla K, Jainese C, Seeto K, McCrea M, Sandel MW, Vianna JA, Maslenikov K, Bachtrog D, Orr JW, Love M, Sudmant PH. Origins and evolution of extreme life span in Pacific Ocean rockfishes. Science 2021; 374:842-847. [PMID: 34762458 PMCID: PMC8923369 DOI: 10.1126/science.abg5332] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Pacific Ocean rockfishes (genus Sebastes) exhibit extreme variation in life span, with some species being among the most long-lived extant vertebrates. We de novo assembled the genomes of 88 rockfish species and from these identified repeated signatures of positive selection in DNA repair pathways in long-lived taxa and 137 longevity-associated genes with direct effects on life span through insulin signaling and with pleiotropic effects through size and environmental adaptations. A genome-wide screen of structural variation reveals copy number expansions in the immune modulatory butyrophilin gene family in long-lived species. The evolution of different rockfish life histories is coupled to genetic diversity and reshapes the mutational spectrum driving segregating CpG→TpG variants in long-lived species. These analyses highlight the genetic innovations that underlie life history trait adaptations and, in turn, how they shape genomic diversity.
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Affiliation(s)
| | - Gregory L. Owens
- University of California Berkeley Department of Integrative Biology
- University of Victoria Department of Biology
| | | | - Alexander Stubbs
- University of California Berkeley Department of Integrative Biology
| | - Kamalakar Chatla
- University of California Berkeley Department of Integrative Biology
| | - Conner Jainese
- University of California Santa Barbara Marine Sciences Institute
| | - Katelin Seeto
- University of California Santa Barbara Marine Sciences Institute
| | - Merit McCrea
- University of California Santa Barbara Marine Sciences Institute
| | | | - Juliana A. Vianna
- Pontificia Universidad Católica de Chile, Departamento de Ecosistemas y Medio Ambiente
| | - Katherine Maslenikov
- University of Washington, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture
| | - Doris Bachtrog
- University of California Berkeley Department of Integrative Biology
| | - James W. Orr
- University of Washington, School of Aquatic and Fishery Sciences and Burke Museum of Natural History and Culture
| | - Milton Love
- University of California Santa Barbara Marine Sciences Institute
| | - Peter H. Sudmant
- University of California Berkeley Department of Integrative Biology
- University of California Berkeley Center for Computational Biology
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10
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Frugone MJ, Cole TL, López ME, Clucas G, Matos‐Maraví P, Lois NA, Pistorius P, Bonadonna F, Trathan P, Polanowski A, Wienecke B, Raya‐Rey A, Pütz K, Steinfurth A, Bi K, Wang‐Claypool CY, Waters JM, Bowie RCK, Poulin E, Vianna JA. Front Cover. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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11
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Frugone MJ, Cole TL, López ME, Clucas G, Matos‐Maraví P, Lois NA, Pistorius P, Bonadonna F, Trathan P, Polanowski A, Wienecke B, Raya‐Rey A, Pütz K, Steinfurth A, Bi K, Wang‐Claypool CY, Waters JM, Bowie RCK, Poulin E, Vianna JA. Taxonomy based on limited genomic markers may underestimate species diversity of rockhopper penguins and threaten their conservation. DIVERS DISTRIB 2021. [DOI: 10.1111/ddi.13399] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- María José Frugone
- Laboratorio de Ecología Molecular Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
- Instituto de Ciencias Ambientales y EvolutivasFacultad de CienciasUniversidad Austral de Chile Valdivia Chile
| | - Theresa L. Cole
- Department of Zoology University of Otago Dunedin New Zealand
- Department of Biology, Ecology and Evolution University of Copenhagen Copenhagen Denmark
| | - María Eugenia López
- Department of Aquatic Resources Swedish University of Agricultural Sciences Drottningholm Sweden
| | - Gemma Clucas
- Atkinson Center for a Sustainable Future Cornell University Ithaca NY USA
- Cornell Lab of Ornithology Cornell University Ithaca NY USA
| | - Pável Matos‐Maraví
- Biology Centre of the Czech Academy of SciencesInstitute of Entomology České Budějovice Czech Republic
| | - Nicolás A. Lois
- Departamento de Ecología Genética y Evolución Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires Buenos Aires Argentina
- Instituto de Ecología Genética y Evolución de Buenos AiresConsejo Nacional de Investigaciones Científicas y Técnicas Buenos Aires Argentina
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology Department of Zoology Nelson Mandela University Port Elizabeth South Africa
| | | | | | | | | | - Andrea Raya‐Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC‐CONICET) Ushuaia Argentina
- Wildlife Conservation Society Bronx NY USA
- Instituto de Ciencias Polares, Ambiente y Recursos NaturalesUniversidad Nacional de Tierra del Fuego Ushuaia Argentina
| | | | - Antje Steinfurth
- FitzPatrick Institute of African Ornithology University of Cape Town Rondebosch South Africa
- RSPB Centre for Conservation Science Cambridge UK
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | - Cynthia Y. Wang‐Claypool
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | | | - Rauri C. K. Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology University of California Berkeley CA USA
| | - Elie Poulin
- Laboratorio de Ecología Molecular Departamento de Ciencias Ecológicas Facultad de Ciencias Universidad de Chile Santiago Chile
- Instituto de Ecología y Biodiversidad (IEB) Santiago Chile
| | - Juliana A. Vianna
- Pontificia Universidad Católica de ChileCenter for Genome RegulationFacultad de Agronomía e Ingeniería ForestalDepartamento de Ecosistemas y Medio Ambiente Santiago Chile
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12
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Pütz K, Gherardi-Fuentes C, García-Borboroglu P, Godoy C, Flagg M, Pedrana J, Vianna JA, Simeone A, Lüthi B. Exceptional foraging plasticity in King Penguins (Aptenodytes patagonicus) from a recently established breeding site in Tierra del Fuego, Chile. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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13
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Álvarez-Varas R, Rojas-Hernández N, Heidemeyer M, Riginos C, Benítez HA, Araya-Donoso R, Reséndiz E, Lara-Uc M, Godoy DA, Muñoz-Pérez JP, Alarcón-Ruales DE, Alfaro-Shigueto J, Ortiz-Alvarez C, Mangel JC, Vianna JA, Véliz D. Green, yellow or black? Genetic differentiation and adaptation signatures in a highly migratory marine turtle. Proc Biol Sci 2021; 288:20210754. [PMID: 34229490 DOI: 10.1098/rspb.2021.0754] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Marine species may exhibit genetic structure accompanied by phenotypic differentiation related to adaptation despite their high mobility. Two shape-based morphotypes have been identified for the green turtle (Chelonia mydas) in the Pacific Ocean: the south-central/western or yellow turtle and north-central/eastern or black turtle. The genetic differentiation between these morphotypes and the adaptation of the black turtle to environmentally contrasting conditions of the eastern Pacific region has remained a mystery for decades. Here we addressed both questions using a reduced-representation genome approach (Dartseq; 9473 neutral SNPs) and identifying candidate outlier loci (67 outlier SNPs) of biological relevance between shape-based morphotypes from eight Pacific foraging grounds (n = 158). Our results support genetic divergence between morphotypes, probably arising from strong natal homing behaviour. Genes and enriched biological functions linked to thermoregulation, hypoxia, melanism, morphogenesis, osmoregulation, diet and reproduction were found to be outliers for differentiation, providing evidence for adaptation of C. mydas to the eastern Pacific region and suggesting independent evolutionary trajectories of the shape-based morphotypes. Our findings support the evolutionary distinctness of the enigmatic black turtle and contribute to the adaptive research and conservation genomics of a long-lived and highly mobile vertebrate.
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Affiliation(s)
- Rocío Álvarez-Varas
- 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.,Qarapara Tortugas Marinas Chile NGO, Santiago, Chile
| | - Noemi Rojas-Hernández
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Maike Heidemeyer
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, Costa Rica
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Hugo A Benítez
- Laboratorio de Ecología y Morfometría Evolutiva, Centro de Investigación de Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | | | - Eduardo Reséndiz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Mexico
| | - Mónica Lara-Uc
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, Mexico
| | - Daniel A Godoy
- Coastal-Marine Research Group, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Juan Pablo Muñoz-Pérez
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galápagos, Ecuador.,University of the Sunshine Coast USC, 90 Sippy Downs Dr, Sippy Downs, Queensland 4556, Australia
| | - Daniela E Alarcón-Ruales
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galápagos, Ecuador
| | - Joanna Alfaro-Shigueto
- ProDelphinus, Lima, Peru.,Facultad de Biología Marina, Universidad Científica del Perú, Lima, Peru
| | | | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica 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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14
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Doussang D, Sallaberry-Pincheira N, Cabanne GS, Lijtmaer DA, González-Acuña D, Vianna JA. Specialist versus generalist parasites: the interactions between host diversity, environment and geographic barriers in avian malaria. Int J Parasitol 2021; 51:899-911. [PMID: 34044005 DOI: 10.1016/j.ijpara.2021.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/03/2021] [Accepted: 04/12/2021] [Indexed: 10/21/2022]
Abstract
The specialist versus generalist strategies of hemoparasites in relation to their avian host, as well as environmental factors, can influence their prevalence, diversity and distribution. In this paper we investigated the influence of avian host species, as well as the environmental and geographical factors, on the strategies of Haemoproteus and Plasmodium hemoparasites. We determined prevalence and diversity by targeting their cytochrome b (Cytb) in a total of 2,590 passerine samples from 138 localities of Central and South America, and analysed biogeographic patterns and host-parasite relationships. We found a total prevalence of 23.2%. Haemoproteus presented a higher prevalence (15.3%) than Plasmodium (4.3%), as well as a higher diversity and host specificity. We determined that Plasmodium and Haemoproteus prevalences correlated positively with host diversity (Shannon index) and were significantly influenced by bird diversity, demonstrating a possible "amplification effect". We found an effect of locality and the avian family for prevalences of Haemoproteus and Plasmodium. These results suggest that Haemoproteus is more specialist than Plasmodium and could be mostly influenced by its avian host and the Andes Mountains.
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Affiliation(s)
- Daniela Doussang
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Casilla 537, Chillán, Chile; Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Chile
| | | | - Gustavo S Cabanne
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Darío A Lijtmaer
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia", Buenos Aires, Argentina
| | - Daniel González-Acuña
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Casilla 537, Chillán, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Código Postal, 6904411, Casilla 306, Correo 22, Santiago, Chile.
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15
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Álvarez-Varas R, Heidemeyer M, Riginos C, Benítez HA, Reséndiz E, Lara-Uc M, Godoy DA, Muñoz-Pérez JP, Alarcón-Ruales DE, Vélez-Rubio GM, Fallabrino A, Piovano S, Alfaro-Shigueto J, Ortiz-Alvarez C, Mangel JC, Esquerré D, Zárate P, Medrano C, León Miranda F, Guerrero F, Vianna JA, Véliz D. Integrating morphological and genetic data at different spatial scales in a cosmopolitan marine turtle species: challenges for management and conservation. Zool J Linn Soc 2020. [DOI: 10.1093/zoolinnean/zlaa066] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
AbstractPatterns of genetic structure in highly mobile marine vertebrates may be accompanied by phenotypic variation. Most studies in marine turtles focused on population genetic structure have been performed at rookeries. We studied whether genetic and morphological variation of the endangered green turtle (Chelonia mydas) is consistent geographically, focusing on foraging grounds. An association between population genetic structure and body shape variation at broad (inter-lineage) and fine (foraging grounds) scales was predicted and analysed using mitochondrial DNA and geometric morphometrics. Although genetic and phenotypic differentiation patterns were congruent between lineages, no fine-scale association was found, suggesting adaptive divergence. Connectivity among Pacific foraging grounds found here suggests that temperatures of ocean surface currents may influence the genetic structure of C. mydas on a broad scale. Our results suggest that vicariance, dispersal, life-history traits and ecological conditions operating in foraging grounds have shaped the intraspecific morphology and genetic diversity of this species. Considering a range of geographic and temporal scales is useful when management strategies are required for cosmopolitan species. Integrating morphological and genetic tools at different spatial scales, conservation management is proposed based on protection of neutral and adaptive diversity. This approach opens new questions and challenges, especially regarding conservation genetics in cosmopolitan species.
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Affiliation(s)
- Rocío Álvarez-Varas
- 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
- Qarapara Tortugas Marinas Chile Non-governmental Organization, Santiago, Chile
| | - Maike Heidemeyer
- Centro de Investigación en Biología Celular y Molecular (CIBCM), Universidad de Costa Rica, San José, Costa Rica
| | - Cynthia Riginos
- School of Biological Sciences, The University of Queensland, Brisbane, Australia
| | - Hugo A Benítez
- Centro de Investigación de Estudios Avanzados del Maule, Universidad Católica del Maule, Talca, Chile
| | - Eduardo Reséndiz
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, México
| | - Mónica Lara-Uc
- Departamento Académico de Ciencias Marinas y Costeras, Universidad Autónoma de Baja California Sur, México
| | - Daniel A Godoy
- Coastal-Marine Research Group, Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Juan Pablo Muñoz-Pérez
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galapagos, Ecuador
- University of the Sunshine Coast USC, Queensland, Australia
| | - Daniela E Alarcón-Ruales
- Galapagos Science Center GSC (Universidad San Francisco de Quito USFQ-University of North Carolina at Chapel Hill UNC), Isla San Cristobal, Galapagos, Ecuador
| | | | | | - Susanna Piovano
- School of Marine Studies, The University of the South Pacific, Suva, Fiji
| | - Joanna Alfaro-Shigueto
- ProDelphinus, Lima, Peru
- Facultad de Biología Marina, Universidad Científica del Sur, Lima, Peru
| | | | | | - Damien Esquerré
- Division of Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australia
| | - Patricia Zárate
- Departamento de Oceanografía y Medio Ambiente, Instituto de Fomento Pesquero, Valparaíso, Chile
| | - Carol Medrano
- Qarapara Tortugas Marinas Chile Non-governmental Organization, Santiago, Chile
| | - Fabiola León Miranda
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Felipe Guerrero
- Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Qarapara Tortugas Marinas Chile Non-governmental Organization, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica 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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16
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Levy H, Fiddaman SR, Vianna JA, Noll D, Clucas GV, Sidhu JKH, Polito MJ, Bost CA, Phillips RA, Crofts S, Miller GD, Pistorius P, Bonnadonna F, Le Bohec C, Barbosa A, Trathan P, Raya Rey A, Frantz LAF, Hart T, Smith AL. Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird. Mol Biol Evol 2020; 37:1708-1726. [PMID: 32096861 PMCID: PMC7253215 DOI: 10.1093/molbev/msaa040] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.
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Affiliation(s)
- Hila Levy
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
| | - Daly Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Macul, Santiago, Chile
- Departamento de Ciencias Ecológicas, Instituto de Ecología y Biodiversidad, Universidad de Chile, Santiago, Chile
| | - Gemma V Clucas
- Cornell Atkinson Center for a Sustainable Future, Cornell University, Ithaca, NY
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY
| | | | - Michael J Polito
- Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, LA
| | - Charles A Bost
- Centre d’Etudes Biologiques de Chizé (CEBC), UMR 7372 du CNRS‐Université de La Rochelle, Villiers‐en‐Bois, France
| | | | - Sarah Crofts
- Falklands Conservation, Stanley, Falkland Islands, United Kingdom
| | - Gary D Miller
- Microbiology and Immunology, PALM, University of Western Australia, Crawley, Western Australia, Australia
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Department of Zoology, Nelson Mandela University, Port Elizabeth, South Africa
| | - Francesco Bonnadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Montpellier, France
| | - Céline Le Bohec
- Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, France
- Département de Biologie Polaire, Centre Scientifique de Monaco, Monaco, Principality of Monaco
| | - Andrés Barbosa
- Museo Nacional de Ciencias Naturales, Departamento de Ecología Evolutiva, CSIC, Madrid, Spain
| | - Phil Trathan
- British Antarctic Survey, Cambridge, United Kingdom
| | - Andrea Raya Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET), Ushuaia, Tierra del Fuego, Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales, Universidad Nacional de Tierra del Fuego, Ushuaia, Tierra del Fuego, Argentina
- Wildlife Conservation Society, Buenos Aires, Argentina
| | - Laurent A F Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Tom Hart
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Adrian L Smith
- Department of Zoology, University of Oxford, Oxford, United Kingdom
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17
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Pertierra LR, Segovia NI, Noll D, Martinez PA, Pliscoff P, Barbosa A, Aragón P, Raya Rey A, Pistorius P, Trathan P, Polanowski A, Bonadonna F, Le Bohec C, Bi K, Wang‐Claypool CY, González‐Acuña D, Dantas GPM, Bowie RCK, Poulin E, Vianna JA. Cryptic speciation in gentoo penguins is driven by geographic isolation and regional marine conditions: Unforeseen vulnerabilities to global change. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13072] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Luis R. Pertierra
- Departamento de Ecología Evolutiva Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
| | - Nicolás I. Segovia
- Departamento de Ciencias Ecológicas Instituto de Ecología y Biodiversidad Universidad de Chile Santiago Chile
- Departamento de Biología Marina Facultad de Ciencias del Mar Universidad Católica del Norte Coquimbo Chile
| | - Daly Noll
- Departamento de Ciencias Ecológicas Instituto de Ecología y Biodiversidad Universidad de Chile Santiago Chile
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal Pontificia Universidad Católica de Chile Santiago Chile
| | - Pablo A. Martinez
- PIBi‐Lab Departamento de Biologia Universidade Federal de Sergipe São Cristóvão Brazil
| | - Patricio Pliscoff
- Departamento de Ecología Instituto de Geografía Pontificia Universidad Católica de Chile Santiago Chile
| | - Andrés Barbosa
- Departamento de Ecología Evolutiva Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
| | - Pedro Aragón
- Departamento de Ecología Evolutiva Museo Nacional de Ciencias NaturalesCSIC Madrid Spain
- Facultad de Ciecias Biológicas Departamento de Biodiversidad, Ecología y Evolución Universidad Complutense de Madrid Madrid Spain
| | - Andrea Raya Rey
- Centro Austral de Investigaciones Científicas – Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC‐CONICET) Ushuaia Argentina
- Instituto de Ciencias Polares, Ambiente y Recursos Naturales Universidad Nacional de Tierra del Fuego Ushuaia Argentina
- Wildlife Conservation Society Buenos Aires Argentina
| | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology Department of Zoology Nelson Mandela University Port Elizabeth South Africa
| | | | | | - Francesco Bonadonna
- CEFE UMR 5175CNRSUniversité de MontpellierUniversité Paul‐Valéry MontpellierEPHE Montpellier Cedex 5 France
| | - Céline Le Bohec
- Universit de Strasbourg, CNRSIPHC UMR 7178F-67000 Strasbourg France
- Centre Scientifique de Monaco Département de Biologie Polaire Monaco City Monaco
| | - Ke Bi
- Department of Integrative Biology Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Cynthia Y. Wang‐Claypool
- Department of Integrative Biology Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Daniel González‐Acuña
- Laboratorio de Parásitos y Enfermedades de Fauna Silvestre Facultad de Ciencias Veterinarias Universidad de Concepción Chillán Santiago Chile
| | - Gisele P. M. Dantas
- PPG in Vertebrate Zoology Pontificia Universidade Católica de Minas Gerais Belo Horizonte Brazil
| | - Rauri C. K. Bowie
- Department of Integrative Biology Museum of Vertebrate Zoology University of California Berkeley CA USA
| | - Elie Poulin
- Departamento de Ciencias Ecológicas Instituto de Ecología y Biodiversidad Universidad de Chile Santiago Chile
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal Pontificia Universidad Católica de Chile Santiago Chile
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18
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Lois NA, Campagna L, Balza U, Polito MJ, Pütz K, Vianna JA, Morgenthaler A, Frere E, Sáenz-Samaniego R, Raya Rey A, Mahler B. Metapopulation dynamics and foraging plasticity in a highly vagile seabird, the southern rockhopper penguin. Ecol Evol 2020; 10:3346-3355. [PMID: 32273992 PMCID: PMC7141044 DOI: 10.1002/ece3.6127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 01/29/2020] [Accepted: 02/04/2020] [Indexed: 12/25/2022] Open
Abstract
Population connectivity is driven by individual dispersal potential and modulated by natal philopatry. In seabirds, high vagility facilitates dispersal yet philopatry is also common, with foraging area overlap often correlated with population connectivity. We assess the interplay between these processes by studying past and current connectivity and foraging niche overlap among southern rockhopper penguin colonies of the coast of southern South America using genomic and stable isotope analyses. We found two distinct genetic clusters and detected low admixture between northern and southern colonies. Stable isotope analysis indicated niche variability between colonies, with Malvinas/Falklands colonies encompassing the species entire isotopic foraging niche, while the remaining colonies had smaller, nonoverlapping niches. A recently founded colony in continental Patagonia differed in isotopic niche width and position with Malvinas/Falklands colonies, its genetically identified founder population, suggesting the exploitation of novel foraging areas and/or prey items. Additionally, dispersing individuals found dead across the Patagonian shore in an unusual mortality event were also assigned to the northern cluster, suggesting northern individuals reach southern localities, but do not breed in these colonies. Facilitated by variability in foraging strategies, and especially during unfavorable conditions, the number of dispersing individuals may increase and enhance the probability of founding new colonies. Metapopulation demographic dynamics in seabirds should account for interannual variability in dispersal behavior and pay special attention to extreme climatic events, classically related to negative effects on population trends.
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Affiliation(s)
- Nicolás A Lois
- Instituto de Ecología, Genética y Evolución de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas (IEGEBA-CONICET) Buenos Aires Argentina
- Departamento de Ecología, Genética y Evolución Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires (DEGE-FCEyN-UBA) Buenos Aires Argentina
- Centro Austral de Investigaciones Científicas Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET) Ushuaia Argentina
| | - Leonardo Campagna
- Fuller Evolutionary Biology Program Cornell Lab of Ornithology Cornell University Ithaca NY USA
- Department of Ecology and Evolutionary Biology Cornell University Ithaca NY USA
| | - Ulises Balza
- Departamento de Ecología, Genética y Evolución Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires (DEGE-FCEyN-UBA) Buenos Aires Argentina
- Centro Austral de Investigaciones Científicas Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET) Ushuaia Argentina
| | - Michael J Polito
- Department of Oceanography and Coastal Sciences Louisiana State University Baton Rouge LA USA
| | | | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente Facultad de Agronomía e Ingeniería Forestal Pontificia Universidad Católica de Chile Santiago Chile
| | - Annick Morgenthaler
- Centro de Investigaciones Puerto Deseado UACO Universidad Nacional de la Patagonia Austral Puerto Deseado, Santa Cruz Argentina
| | - Esteban Frere
- Centro de Investigaciones Puerto Deseado UACO Universidad Nacional de la Patagonia Austral Puerto Deseado, Santa Cruz Argentina
- Wildlife Conservation Society Buenos Aires Argentina
| | - Ricardo Sáenz-Samaniego
- Centro Austral de Investigaciones Científicas Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET) Ushuaia Argentina
| | - Andrea Raya Rey
- Centro Austral de Investigaciones Científicas Consejo Nacional de Investigaciones Científicas y Técnicas (CADIC-CONICET) Ushuaia Argentina
- Instituto de Ciencias Polares Ambiente y Recursos Naturales Universidad Nacional de Tierra del Fuego (ICPA-UNTdF) Ushuaia Argentina
- Wildlife Conservation Society Buenos Aires Argentina
| | - Bettina Mahler
- Instituto de Ecología, Genética y Evolución de Buenos Aires Consejo Nacional de Investigaciones Científicas y Técnicas (IEGEBA-CONICET) Buenos Aires Argentina
- Departamento de Ecología, Genética y Evolución Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires (DEGE-FCEyN-UBA) Buenos Aires Argentina
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19
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Cuevas E, Vianna JA, Botero-Delgadillo E, Doussang D, González-Acuña D, Barroso O, Rozzi R, Vásquez RA, Quirici V. Latitudinal gradients of haemosporidian parasites: Prevalence, diversity and drivers of infection in the Thorn-tailed Rayadito ( Aphrastura spinicauda). Int J Parasitol Parasites Wildl 2019; 11:1-11. [PMID: 31879589 PMCID: PMC6920315 DOI: 10.1016/j.ijppaw.2019.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 11/02/2019] [Accepted: 11/03/2019] [Indexed: 01/15/2023]
Abstract
Latitudinal gradients are well-suited systems that may be helpful explaining distribution of haemosporidian parasites and host susceptibility. We studied the prevalence, diversity and drivers of haemosporidian parasites (Leucocytozoon, Plasmodium and Haemoproteus) along a latitudinal gradient (30°–56° S), that encompass the total distribution (~3,000 km) of the Thorn-tailed Rayadito (Aphrastura spinicauda) in the South American temperate forests from Chile. We analyzed 516 individuals from 18 localities between 2010 and 2017 and observed an overall prevalence of 28.3% for haemosporidian parasites. Leucocytozoon was the most prevalent parasite (25.8%). We recorded 19 distinct lineages (13 for Leucocytozoon, five for Plasmodium, and one for Haemoproteus). Differences in haemosporidian prevalence and diversity by genus and type of habitat were observed in the latitudinal gradient. Further, we support the existence of a latitudinal associate distribution of Leucocytozoids in South America, where prevalence and diversity increase toward higher latitudes. Distribution of Leucocytozoon was associated with sub-antarctic habitat (higher latitude) and explained by cold temperature and high precipitation. On the other hand, we lacked to find a latitudinal associate pattern for Plasmodium and Haemoproteus, however low prevalence and high diversity were recorded in areas considered as a hotspot of biodiversity in Central Chile. Our findings confirmed the importance of habitat and climatic variables explaining prevalence, diversity and distribution of haemosporidian parasites in a huge latitudinal gradient, belonging the distribution of the Thorn-tailed Rayadito in the world's southernmost forests ecosystems. Prevalence and diversity differed between haemosporidian genera and habitats in the latitudinal gradient. Leucocytozoon was the most prevalent genus in the latitudinal distribution. Leucocytozoon prevalence and diversity were associated to higher latitudes. Distribution of Leucocytozoon was explained by cold temperature and high precipitation.
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Affiliation(s)
- Elfego Cuevas
- Programa de Doctorado en Medicina de la Conservación, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago, Chile.,Centro de Investigación para la Sustentabilidad (CIS), Universidad Andres Bello, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Esteban Botero-Delgadillo
- Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,SELVA: Research for Conservation in the Neotropics, Bogotá, Colombia.,Department of Behavioral Ecology and Evolutionary Genetics, Max Plank Institute for Ornithology, Seewiesen, Germany
| | - Daniela Doussang
- Laboratorio de Parásitos y Enfermedades de Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile.,Facultad de Ciencias de la Vida, Universidad Andres Bello, Viña Del Mar, Chile
| | - Daniel González-Acuña
- Laboratorio de Parásitos y Enfermedades de Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Omar Barroso
- Instituto de Ecología y Biodiversidad, Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Ricardo Rozzi
- Instituto de Ecología y Biodiversidad, Parque Etnobotánico Omora, Universidad de Magallanes, Puerto Williams, Chile
| | - Rodrigo A Vásquez
- Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Verónica Quirici
- Centro de Investigación para la Sustentabilidad (CIS), Universidad Andres Bello, Santiago, Chile.,Departamento de Ecología y Biodiversidad, Universidad Andres Bello, Santiago, Chile
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20
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Frugone MJ, López ME, Segovia NI, Cole TL, Lowther A, Pistorius P, Dantas GPM, Petry MV, Bonadonna F, Trathan P, Polanowski A, Wienecke B, Bi K, Wang-Claypool CY, Waters JM, Bowie RCK, Poulin E, Vianna JA. More than the eye can see: Genomic insights into the drivers of genetic differentiation in Royal/Macaroni penguins across the Southern Ocean. Mol Phylogenet Evol 2019; 139:106563. [PMID: 31323335 DOI: 10.1016/j.ympev.2019.106563] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 07/12/2019] [Accepted: 07/15/2019] [Indexed: 01/31/2023]
Abstract
The study of systematics in wide-ranging seabirds can be challenging due to the vast geographic scales involved, as well as the possible discordance between molecular, morphological and behavioral data. In the Southern Ocean, macaroni penguins (Eudyptes chrysolophus) are distributed over a circumpolar range including populations in Antarctic and sub-Antarctic areas. Macquarie Island, in its relative isolation, is home to a closely related endemic taxon - the royal penguin (Eudyptes schlegeli), which is distinguishable from E. chrysolophus mainly by facial coloration. Although these sister taxa are widely accepted as representing distinct species based on morphological grounds, the extent of their genome-wide differentiation remains uncertain. In this study, we use genome-wide Single Nucleotide Polymorphisms to test genetic differentiation between these geographically isolated taxa and evaluate the main drivers of population structure among breeding colonies of macaroni/royal penguins. Genetic similarity observed between macaroni and royal penguins suggests they constitute a single evolutionary unit. Nevertheless, royal penguins exhibited a tendency to cluster only with macaroni individuals from Kerguelen Island, suggesting that dispersal occurs mainly between these neighboring colonies. A stepping stone model of differentiation of macaroni/royal populations was further supported by a strong pattern of isolation by distance detected across its whole distribution range, possibly driven by large geographic distances between colonies as well as natal philopatry. However, we also detected intraspecific genomic differentiation between Antarctic and sub-Antarctic populations of macaroni penguins, highlighting the role of environmental factors together with geographic distance in the processes of genetic differentiation between Antarctic and sub-Antarctic waters.
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Affiliation(s)
- María José Frugone
- Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras # 3425, Ñuñoa, Santiago, Chile; Instituto de Ecología y Biodiversidad (IEB), Las Palmeras # 3425, Ñuñoa, Santiago, Chile; Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ecosistemas y Medio Ambiente, Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - María Eugenia López
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago 8820808, Chile
| | - Nicolás I Segovia
- Instituto de Ecología y Biodiversidad (IEB), Las Palmeras # 3425, Ñuñoa, Santiago, Chile; Universidad Católica del Norte, Facultad de Ciencias del Mar, Departamento de Biología Marina, Coquimbo, Chile
| | - Theresa L Cole
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand; Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, Canterbury 7640, New Zealand
| | | | - Pierre Pistorius
- DST/NRF Centre of Excellence at the Percy FitzPatrick Institute for African Ornithology, Department of Zoology, Nelson Mandela University, Port Elizabeth 6031, South Africa
| | - Gisele P M Dantas
- Pontificia Universidade Católica de Minas Gerais, PPG in Vertebrate Biology, Belo Horizonte, Brazil
| | - Maria Virginia Petry
- Universidade do Vale do Rio dos Sinos, Laboratório de Ornitologia e Animais Marinhos, Av. Unisinos, 950, São Leopoldo, RS, Brazil
| | - Francesco Bonadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Phil Trathan
- British Antarctic Survey, High Cross, Madingley Road, Cambridge CB3 0ET, UK
| | - Andrea Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania 7050, Australia
| | - Barbara Wienecke
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tasmania 7050, Australia
| | - Ke Bi
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Science Building, University of California, Berkeley, CA 94720-3160, USA
| | - Cynthia Y Wang-Claypool
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Science Building, University of California, Berkeley, CA 94720-3160, USA
| | - Jonathan M Waters
- Department of Zoology, University of Otago, P.O. Box 56, Dunedin 9054, New Zealand
| | - Rauri C K Bowie
- Museum of Vertebrate Zoology and Department of Integrative Biology, 3101 Valley Life Science Building, University of California, Berkeley, CA 94720-3160, USA
| | - Elie Poulin
- Laboratorio de Ecología Molecular, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras # 3425, Ñuñoa, Santiago, Chile; Instituto de Ecología y Biodiversidad (IEB), Las Palmeras # 3425, Ñuñoa, Santiago, Chile
| | - Juliana A Vianna
- Pontificia Universidad Católica de Chile, Facultad de Agronomía e Ingeniería Forestal, Departamento de Ecosistemas y Medio Ambiente, Vicuña Mackenna 4860, Macul, Santiago, Chile.
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21
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Dantas GPM, Oliveira LR, Santos AM, Flores MD, de Melo DR, Simeone A, González-Acuña D, Luna-Jorquera G, Le Bohec C, Valdés-Velásquez A, Cardeña M, Morgante JS, Vianna JA. Uncovering population structure in the Humboldt penguin (Spheniscus humboldti) along the Pacific coast at South America. PLoS One 2019; 14:e0215293. [PMID: 31075106 PMCID: PMC6510429 DOI: 10.1371/journal.pone.0215293] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/31/2019] [Indexed: 12/04/2022] Open
Abstract
The upwelling hypothesis has been proposed to explain reduced or lack of population structure in seabird species specialized in food resources available at cold-water upwellings. However, population genetic structure may be challenging to detect in species with large population sizes, since variation in allele frequencies are more robust under genetic drift. High gene flow among populations, that can be constant or pulses of migration in a short period, may also decrease power of algorithms to detect genetic structure. Penguin species usually have large population sizes, high migratory ability but philopatric behavior, and recent investigations debate the existence of subtle population structure for some species not detected before. Previous study on Humboldt penguins found lack of population genetic structure for colonies of Punta San Juan and from South Chile. Here, we used mtDNA and nuclear markers (10 microsatellites and RAG1 intron) to evaluate population structure for 11 main breeding colonies of Humboldt penguins, covering the whole spatial distribution of this species. Although mtDNA failed to detect population structure, microsatellite loci and nuclear intron detected population structure along its latitudinal distribution. Microsatellite showed significant Rst values between most of pairwise locations (44 of 56 locations, Rst = 0.003 to 0.081) and 86% of individuals were assigned to their sampled colony, suggesting philopatry. STRUCTURE detected three main genetic clusters according to geographical locations: i) Peru; ii) North of Chile; and iii) Central-South of Chile. The Humboldt penguin shows signal population expansion after the Last Glacial Maximum (LGM), suggesting that the genetic structure of the species is a result of population dynamics and foraging colder water upwelling that favor gene flow and phylopatric rate. Our findings thus highlight that variable markers and wide sampling along the species distribution are crucial to better understand genetic population structure in animals with high dispersal ability.
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Affiliation(s)
- Gisele P. M. Dantas
- PPG Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
- Instituto de Biologia, Universidade de São Paulo (IB-USP), São Paulo, Brazil
- * E-mail:
| | - Larissa R. Oliveira
- Universidade do Vale do Rio dos Sinos (UNISINOS), São Leopoldo, Rio Grande do Sul, Brazil
| | - Amanda M. Santos
- Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | | | - Daniella R. de Melo
- PPG Biologia de Vertebrados, Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, Brazil
| | - Alejandro Simeone
- Universidad Andrés Bello, Facultad de Ecología y Recursos Naturales, Santiago, Chile
| | | | - Guillermo Luna-Jorquera
- Departamento de Biología Marina, Facultad de Ciencias del Mar, Universidad Católica del Norte, Coquimbo, Chile
| | - Céline Le Bohec
- Université de Strasbourg, Centre National de la Recherche Scientifique (CNRS); Institut Pluridisciplinaire Hubert Curien (IPHC), Strasbourg, France
- Département de Biologie PolaireCentre Scientifique de Monaco (CSM), Principality of Monaco, Monaco
| | - Armando Valdés-Velásquez
- Centro de Investigación para el Desarrollo Integral y Sostenible (CIDIS) and Facultad de Ciencias y Filosofía, Universidad Cayetano Heredia, Lima, Perú
| | - Marco Cardeña
- Programa Punta San Juan (CSA-UPCH), Universidad Peruana Cayetano Heredia, Lima, Perú
| | - João S. Morgante
- Instituto de Biologia, Universidade de São Paulo (IB-USP), São Paulo, Brazil
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile
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22
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Doussang D, González-Acuña D, Torres-Fuentes LG, Lougheed SC, Clemente-Carvalho RB, Greene KC, Vianna JA. Spatial distribution, prevalence and diversity of haemosporidians in the rufous-collared sparrow, Zonotrichia capensis. Parasit Vectors 2019; 12:2. [PMID: 30606248 PMCID: PMC6318949 DOI: 10.1186/s13071-018-3243-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 11/29/2018] [Indexed: 12/30/2022] Open
Abstract
Background Parasite prevalence and diversity are determined by the distribution of hosts and vectors and by the interplay among a suite of environmental factors. Distributions of parasite lineages vary based on host susceptibility and geographical barriers. Hemoparasites of the genera Haemoproteus and Plasmodium have wide distributions, and high prevalence and genetic diversity within perching birds (Order Passeriformes). The rufous-collared sparrow (Zonotrichia capensis) is widely distributed in Central and South America across an immense diversity of environments from sea level to more than 4000 meters above sea level. It therefore provides an excellent model to investigate whether altitudinal and latitudinal gradients influence the distribution, prevalence and diversity of haemosporidian parasites, their population structure and the biogeographical boundaries of distinct parasite lineages. Results We assembled samples from 1317 rufous-collared sparrows spanning 75 locales from across Central and South America (between 9.5°N and 54°S; 10–4655 meters above sea level). We used DNA sequence data from a fragment of the mitochondrial cytochrome b gene (cytb) of Haemoproteus and Plasmodium from 325 positive samples and found prevalences of 22 and 3%, respectively. Haemoproteus exhibited a higher prevalence than Plasmodium but with comparatively lower genetic diversity. We detected a relationship of Plasmodium and Haemoproteus prevalence with altitude and latitude; however, altitude and latitude did not influence parasite diversity. Conclusions Parasite lineages showed a phylogeographical boundary coincident with the Andes Mountains, although we also observed a north-south disjunction in Peru for Haemoproteus. Haemosporidian distribution was not homogeneous but differed based on latitude and altitude. This is most probably due to environmental factors that have influenced both vector distribution and abundance, as well as parasite development. Our study provides key insights on the distribution of haemoparasite lineages and parasite dynamics within hosts. Electronic supplementary material The online version of this article (10.1186/s13071-018-3243-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Daniela Doussang
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Casilla, 537, Chillán, Chile.,Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Código Postal: 6904411, Casilla 306, Correo, 22, Santiago, Chile
| | - Daniel González-Acuña
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Casilla, 537, Chillán, Chile
| | | | - Stephen C Lougheed
- Department of Biology, Queen's University, Kingston, ON, K7L 3N6, Canada
| | | | - Kian Connelly Greene
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Código Postal: 6904411, Casilla 306, Correo, 22, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Código Postal: 6904411, Casilla 306, Correo, 22, Santiago, Chile.
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23
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Mura-Jornet I, Pimentel C, Dantas GPM, Petry MV, González-Acuña D, Barbosa A, Lowther AD, Kovacs KM, Poulin E, Vianna JA. Correction to: Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean? BMC Evol Biol 2018; 18:117. [PMID: 30045693 PMCID: PMC6060512 DOI: 10.1186/s12862-018-1231-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Correction to: BMC Evolutionary Biology (2018) 18:90 https://doi.org/10.1186/s12862-018-1207-0 .
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Affiliation(s)
- Isidora Mura-Jornet
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Carolina Pimentel
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Gisele P M Dantas
- Pontifícia Universidade Católica de Minas Gerais, PPG in Biology of Vertebrate Av, Dom Jose Gaspar, 500, prédio 41, Belo Horizonte, 30535901, Brazil
| | - Maria Virginia Petry
- Laboratório de Ornitologia e Animais Marinhos, Universidade do Vale do Rio dos Sinos, Av. Unisinos, São Leopoldo, RS, 950, Brazil
| | - Daniel González-Acuña
- Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Méndez 595, 3780000, Chillán, CP, Chile
| | - Andrés Barbosa
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, C/José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Andrew D Lowther
- Norwegian Polar Institute, Hjalmar Johansensgata, Tromsø, Norway
| | - Kit M Kovacs
- Norwegian Polar Institute, Hjalmar Johansensgata, Tromsø, Norway
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile. .,Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile.
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24
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Álvarez-Varas R, Morales-Moraga D, González-Acuña D, Klarian SA, Vianna JA. Mercury Exposure in Humboldt (Spheniscus humboldti) and Chinstrap (Pygoscelis antarcticus) Penguins Throughout the Chilean Coast and Antarctica. Arch Environ Contam Toxicol 2018; 75:75-86. [PMID: 29725722 DOI: 10.1007/s00244-018-0529-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 04/21/2018] [Indexed: 06/08/2023]
Abstract
Penguins are reliable sentinels for environmental assessments of mercury (Hg) due to their longevity, abundance, high trophic level, and relatively small foraging areas. We analyzed Hg concentrations from blood and feathers of adult Humboldt penguins (Spheniscus humboldti) and feathers of chinstrap penguins (Pygoscelis antarcticus) from different reproductive colonies with variable degrees of urbanization and industrialization along the Chilean and Antarctic coasts. We evaluated Hg concentration differences between species, sexes (Humboldt penguins), and localities. Our results showed significantly greater levels in Humboldt penguins than in chinstrap penguins and nonsignificant differences between sexes among Humboldts. Penguin Hg concentrations showed a latitudinal pattern, with greater values of the metal at lower latitudes, independent of the species. Both studied penguin species showed elevated Hg concentrations compared to their congeners, highlighting the necessity to investigate potential negative effects on their populations. Although differences between species are possibly due to variation in diet and trophic level, our results suggest an important effect of the degree of Hg pollution adjacent to foraging areas. Further research on Hg content in prey species and environmental samples, together with a larger overall sample size, and investigation on penguin's diet and trophic level are needed to elucidate Hg bioavailability in each location and the role of local Hg pollution levels. Likewise, it is important to monitor Hg and other heavy metals of ecotoxicological importance in penguin populations in vulnerable regions of Chile.
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Affiliation(s)
- Rocío Álvarez-Varas
- Laboratorio de Biodiversidad Molecular, Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile
| | - David Morales-Moraga
- Centro de Cambio Global, Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306, Correo 22, Santiago, Chile
| | - Daniel González-Acuña
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Casilla 537, Chillán, Chile
| | - Sebastián A Klarian
- Centro de Investigación Marina Quintay, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Av. Quillota #980, Viña del Mar, Chile
- Centro de Investigación para la Sustentabilidad, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Av. Republica 440, Santiago, Chile
- Laboratorio de Análisis Isotópico, Universidad Andrés Bello, Av. Quillota #980, Viña del Mar, Chile
| | - Juliana A Vianna
- Laboratorio de Biodiversidad Molecular, Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Casilla 306, Correo 22, Santiago, Chile.
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25
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Mura-Jornet I, Pimentel C, Dantas GPM, Petry MV, González-Acuña D, Barbosa A, Lowther AD, Kovacs KM, Poulin E, Vianna JA. Chinstrap penguin population genetic structure: one or more populations along the Southern Ocean? BMC Evol Biol 2018; 18:90. [PMID: 29898661 PMCID: PMC6001010 DOI: 10.1186/s12862-018-1207-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 06/03/2018] [Indexed: 11/16/2022] Open
Abstract
Background Historical factors, demography, reproduction and dispersal are crucial in determining the genetic structure of seabirds. In the Antarctic marine environment, penguins are a major component of the avian biomass, dominant predators and important bioindicators of ecological change. Populations of chinstrap penguins have decreased in nearly all their breeding sites, and their range is expanding throughout the Antarctic Peninsula. Population genetic structure of this species has been studied in some colonies, but not between breeding colonies in the Antarctic Peninsula or at the species’ easternmost breeding colony (Bouvetøya). Results Connectivity, sex-biased dispersal, diversity, genetic structure and demographic history were studied using 12 microsatellite loci and a mitochondrial DNA region (HVRI) in 12 breeding colonies in the South Shetland Islands (SSI) and the Western Antarctic Peninsula (WAP), and one previously unstudied sub-Antarctic island, 3600 km away from the WAP (Bouvetøya). High genetic diversity, evidence of female bias-dispersal and a sign of population expansion after the last glacial maximum around 10,000 mya were detected. Limited population genetic structure and lack of isolation by distance throughout the region were found, along with no differentiation between the WAP and Bouvetøya (overall microsatellite FST = 0.002, p = 0.273; mtDNA FST = − 0.004, p = 0.766), indicating long distance dispersal. Therefore, genetic assignment tests could not assign individuals to their population(s) of origin. The most differentiated location was Georges Point, one of the southernmost breeding colonies of this species in the WAP. Conclusions The subtle differentiation found may be explained by some combination of low natal philopatric behavior, high rates of dispersal and/or generally high mobility among colonies of chinstrap penguins compared to other Pygoscelis species. Electronic supplementary material The online version of this article (10.1186/s12862-018-1207-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Isidora Mura-Jornet
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Carolina Pimentel
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Gisele P M Dantas
- Pontifícia Universidade Católica de Minas Gerais, PPG in Biology of Vertebrate Av, Dom Jose Gaspar, 500, prédio 41, Belo Horizonte, 30535901, Brasil
| | - Maria Virginia Petry
- Laboratório de Ornitologia e Animais Marinhos, Universidade do Vale do Rio dos Sinos, Av. Unisinos, São Leopoldo, RS, 950, Brazil
| | - Daniel González-Acuña
- Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Méndez 595, 3780000, Chillán, CP, Chile
| | - Andrés Barbosa
- Departamento de Ecología Evolutiva, Museo Nacional de Ciencias Naturales, CSIC, C/José Gutiérrez Abascal, 2, 28006, Madrid, Spain
| | - Andrew D Lowther
- Norwegian Polar Institute, Hjalmar Johansensgata, Tromsø, Norway
| | - Kit M Kovacs
- Norwegian Polar Institute, Hjalmar Johansensgata, Tromsø, Norway
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Macul, Santiago, Chile.
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26
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Ramos B, González-Acuña D, Loyola DE, Johnson WE, Parker PG, Massaro M, Dantas GPM, Miranda MD, Vianna JA. Landscape genomics: natural selection drives the evolution of mitogenome in penguins. BMC Genomics 2018; 19:53. [PMID: 29338715 PMCID: PMC5771141 DOI: 10.1186/s12864-017-4424-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 12/28/2017] [Indexed: 12/21/2022] Open
Abstract
Background Mitochondria play a key role in the balance of energy and heat production, and therefore the mitochondrial genome is under natural selection by environmental temperature and food availability, since starvation can generate more efficient coupling of energy production. However, selection over mitochondrial DNA (mtDNA) genes has usually been evaluated at the population level. We sequenced by NGS 12 mitogenomes and with four published genomes, assessed genetic variation in ten penguin species distributed from the equator to Antarctica. Signatures of selection of 13 mitochondrial protein-coding genes were evaluated by comparing among species within and among genera (Spheniscus, Pygoscelis, Eudyptula, Eudyptes and Aptenodytes). The genetic data were correlated with environmental data obtained through remote sensing (sea surface temperature [SST], chlorophyll levels [Chl] and a combination of SST and Chl [COM]) through the distribution of these species. Results We identified the complete mtDNA genomes of several penguin species, including ND6 and 8 tRNAs on the light strand and 12 protein coding genes, 14 tRNAs and two rRNAs positioned on the heavy strand. The highest diversity was found in NADH dehydrogenase genes and the lowest in COX genes. The lowest evolutionary divergence among species was between Humboldt (Spheniscus humboldti) and Galapagos (S. mendiculus) penguins (0.004), while the highest was observed between little penguin (Eudyptula minor) and Adélie penguin (Pygoscelis adeliae) (0.097). We identified a signature of purifying selection (Ka/Ks < 1) across the mitochondrial genome, which is consistent with the hypothesis that purifying selection is constraining mitogenome evolution to maintain Oxidative phosphorylation (OXPHOS) proteins and functionality. Pairwise species maximum-likelihood analyses of selection at codon sites suggest positive selection has occurred on ATP8 (Fixed-Effects Likelihood, FEL) and ND4 (Single Likelihood Ancestral Counting, SLAC) in all penguins. In contrast, COX1 had a signature of strong negative selection. ND4 Ka/Ks ratios were highly correlated with SST (Mantel, p-value: 0.0001; GLM, p-value: 0.00001) and thus may be related to climate adaptation throughout penguin speciation. Conclusions These results identify mtDNA candidate genes under selection which could be involved in broad-scale adaptations of penguins to their environment. Such knowledge may be particularly useful for developing predictive models of how these species may respond to severe climatic changes in the future. Electronic supplementary material The online version of this article (10.1186/s12864-017-4424-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Barbara Ramos
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile.,Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Republica 252, Santiago, Chile
| | - Daniel González-Acuña
- Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Universidad de Concepción, Av. Vicente Méndez 595, 3780000, Chillán, CP, Chile
| | - David E Loyola
- Centro Nacional de Genómica y Bioinformática, Portugal 49, Santiago, Chile.,I+DEA Biotech, Av. Central 3413, Padre Hurtado, Santiago, Chile
| | - Warren E Johnson
- Smithsonian Conservation Biology Institute, National Zoological Park, 1500 Remount Road, Front Royal, VA, 22630, USA
| | - Patricia G Parker
- University of Missouri St Louis and Saint Louis Zoo, One University Blvd., St. Louis, MO, 63121-4400, USA
| | - Melanie Massaro
- School of Environmental Sciences and Institute for Land, Water and Society, Charles Sturt University, PO Box 789, Albury, NSW, Australia
| | - Gisele P M Dantas
- Pontifícia Universidade Católica de Minas Gerais, Av. Dom José Gaspar 500, Coração Eucarístico, Belo Horizonte, MG, Brazil
| | - Marcelo D Miranda
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile
| | - Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna, 4860, Santiago, Chile. .,Centro de Cambio Global UC, Santiago, Chile.
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27
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Mora M, Medina-Vogel G, Sepúlveda MA, Noll D, Álvarez-Varas R, Vianna JA. Genetic structure of introduced American mink (Neovison vison) in Patagonia: colonisation insights and implications for control and management strategies. Wildl Res 2018. [DOI: 10.1071/wr18026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Context
Biological invasions have caused dramatic changes in native biodiversity and ecosystem function. Studies of genetic variation and evolutionary changes are useful for understanding population dynamics during biological invasions, and shed light on management, prevention and restoration strategies.
Aims
This study aimed to investigate the structure and genetic variability of American mink (Neovison vison), an invasive species in southern South America, introduced for fur farming in the 1930s.
Methods
Samples from 153 mink were obtained from 12 locations in southern Chile to sequence the mitochondrial DNA (mtDNA) control region and to genotype 11 polymorphic microsatellite loci.
Key results
The highest mtDNA diversity was detected in Puerto Cisnes, suggesting multiple introductions and/or the most probable area where mink was first introduced. The latter is also supported by microsatellite data, because a high percentage of individuals from different locations were assigned to this location. All other locations showed low or no mtDNA diversity, possibly due to founder effect. The results also indicate marked population structure, with three genetic clusters coincident with the main historical introduction points, with low dispersal among them.
Conclusions
The results suggest that control strategies for American mink in southern Chile should be concentrated on these three genetically differentiated management units, and particularly on source populations and locations with low effective population size and restricted connectivity.
Implications
Genetic approaches have been used for the management of numerous alien species worldwide. Recommendations delivered here for American mink control could also be implemented in other regions and for other invasive species with similar genetic diversity distribution and connectivity.
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Vianna JA, Noll D, Mura-Jornet I, Valenzuela-Guerra P, González-Acuña D, Navarro C, Loyola DE, Dantas GPM. Comparative genome-wide polymorphic microsatellite markers in Antarctic penguins through next generation sequencing. Genet Mol Biol 2017; 40:676-687. [PMID: 28898354 PMCID: PMC5596379 DOI: 10.1590/1678-4685-gmb-2016-0224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 03/17/2017] [Indexed: 12/01/2022] Open
Abstract
Microsatellites are valuable molecular markers for evolutionary and ecological
studies. Next generation sequencing is responsible for the increasing number of
microsatellites for non-model species. Penguins of the Pygoscelis
genus are comprised of three species: Adélie (P. adeliae), Chinstrap
(P. antarcticus) and Gentoo penguin (P. papua),
all distributed around Antarctica and the sub-Antarctic. The species have been
affected differently by climate change, and the use of microsatellite markers will be
crucial to monitor population dynamics. We characterized a large set of genome-wide
microsatellites and evaluated polymorphisms in all three species. SOLiD reads were
generated from the libraries of each species, identifying a large amount of
microsatellite loci: 33,677, 35,265 and 42,057 for P. adeliae, P.
antarcticus and P. papua, respectively. A large number
of dinucleotide (66,139), trinucleotide (29,490) and tetranucleotide (11,849)
microsatellites are described. Microsatellite abundance, diversity and orthology were
characterized in penguin genomes. We evaluated polymorphisms in 170 tetranucleotide
loci, obtaining 34 polymorphic loci in at least one species and 15 polymorphic loci
in all three species, which allow to perform comparative studies. Polymorphic markers
presented here enable a number of ecological, population, individual identification,
parentage and evolutionary studies of Pygoscelis, with potential use
in other penguin species.
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Affiliation(s)
- Juliana A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Chile.,Centro de Cambio Global UC, Santiago, Chile
| | - Daly Noll
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isidora Mura-Jornet
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Paulina Valenzuela-Guerra
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Daniel González-Acuña
- Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | | | - David E Loyola
- Centro Nacional de Genómica y Bioinformática, Santiago, Chile
| | - Gisele P M Dantas
- Pontifícia Universidade Católica de Minas Gerais, Belo Horizonte, MG, Brazil
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Vianna JA, Noll D, Moreno L, Silva C, Muñoz-Leal S, Najle M, González-Acuña D. Record of an alleged extinct rodent: molecular analyses of the endemicOctodon pacificusfrom Chile. J Mammal 2017. [DOI: 10.1093/jmammal/gyw193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Vianna JA, Noll D, Dantas GPM, Petry MV, Barbosa A, González-Acuña D, Le Bohec C, Bonadonna F, Poulin E. Marked phylogeographic structure of Gentoo penguin reveals an ongoing diversification process along the Southern Ocean. Mol Phylogenet Evol 2016; 107:486-498. [PMID: 27940333 DOI: 10.1016/j.ympev.2016.12.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Revised: 12/01/2016] [Accepted: 12/06/2016] [Indexed: 11/28/2022]
Abstract
Two main hypotheses have been debated about the biogeography of the Southern Ocean: (1) the Antarctic Polar Front (APF), acting as a barrier between Antarctic and sub-Antarctic provinces, and (2) the Antarctic Circumpolar Current (ACC), promoting gene flow among sub-Antarctic areas. The Gentoo penguin is distributed throughout these two provinces, separated by the APF. We analyzed mtDNA (HVR1) and 12 microsatellite loci of 264 Gentoo penguins, Pygoscelis papua, from 12 colonies spanning from the Western Antarctic Peninsula and the South Shetland Islands (WAP) to the sub-Antarctic Islands (SAI). While low genetic structure was detected among WAP colonies (mtDNA ФST=0.037-0.133; microsatellite FST=0.009-0.063), high differentiation was found between all SAI and WAP populations (mtDNA ФST=0.678-0.930; microsatellite FST=0.110-0.290). These results suggest that contemporary dispersal around the Southern Ocean is very limited or absent. As predicted, the APF appears to be a significant biogeographical boundary for Gentoo penguin populations; however, the ACC does not promote connectivity in this species. Our data suggest demographic expansion in the WAP during the last glacial maximum (LGM, about 20kya), but stability in SAI. Phylogenetic analyses showed a deep divergence between populations from the WAP and those from the SAI. Therefore, taxonomy should be further revised. The Crozet Islands resulted as a basal clade (3.57Mya), followed by the Kerguelen Islands (2.32Mya) as well as a more recent divergence between the Falkland/Malvinas Islands and the WAP (1.27Mya). Historical isolation, local adaptation, and past climate scenarios of those Evolutionarily Significant Units may have led to different potentials to respond to climate changes.
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Affiliation(s)
- Juliana A Vianna
- Pontificia Universidad Católica de Chile, Departamento de Ecosistemas y Medio Ambiente, Vicuña Mackenna 4860, Macul, Santiago, Chile.
| | - Daly Noll
- Pontificia Universidad Católica de Chile, Departamento de Ecosistemas y Medio Ambiente, Vicuña Mackenna 4860, Macul, Santiago, Chile
| | - Gisele P M Dantas
- Pontificia Universidade Católica de Minas Gerais, PPG in Vertebrate Zoology, Belo Horizonte, Brazil
| | - Maria Virginia Petry
- Universidade do Vale do Rio dos Sinos, Laboratório de Ornitologia e Animais Marinhos, Av. Unisinos, 950, São Leopoldo, RS, Brazil
| | - Andrés Barbosa
- Museo Nacional de Ciencias Naturales, Departamento de Ecología Evolutiva, CSIC, C/José Gutiérrez Abascal, 2, 28006 Madrid, Spain
| | - Daniel González-Acuña
- Universidad de Concepción, Departamento de Ciencias Pecuarias, Facultad de Ciencias Veterinarias, Av. Vicente Méndez 595, CP 3780000 Chillán, Chile
| | - Céline Le Bohec
- Université de Strasbourg (UdS), Institut Pluridisciplinaire Hubert Curien, Laboratoire International Associé LIA-647 BioSensib (CSM-CNRS-UdS), 23 rue Becquerel, 67087 Strasbourg Cedex 02, France; Centre National de la Recherche Scientifique (CNRS), UMR 7178, LIA-647 BioSensib, 23 rue Becquerel, 67087 Strasbourg Cedex 02, France; Centre Scientifique de Monaco (CSM), LIA-647 BioSensib, 8 quai Antoine 1er, MC 98000, Monaco
| | - Francesco Bonadonna
- CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, 1919 route de Mende, 34293 Montpellier cedex 5, France
| | - Elie Poulin
- Instituto de Ecología y Biodiversidad, Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Chile
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Sallaberry‐Pincheira N, González‐Acuña D, Padilla P, Dantas GPM, Luna‐Jorquera G, Frere E, Valdés‐Velásquez A, Vianna JA. Contrasting patterns of selection between MHC I and II across populations of Humboldt and Magellanic penguins. Ecol Evol 2016; 6:7498-7510. [PMID: 28725416 PMCID: PMC5513272 DOI: 10.1002/ece3.2502] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 08/18/2016] [Accepted: 08/28/2016] [Indexed: 12/21/2022] Open
Abstract
The evolutionary and adaptive potential of populations or species facing an emerging infectious disease depends on their genetic diversity in genes, such as the major histocompatibility complex (MHC). In birds, MHC class I deals predominantly with intracellular infections (e.g., viruses) and MHC class II with extracellular infections (e.g., bacteria). Therefore, patterns of MHC I and II diversity may differ between species and across populations of species depending on the relative effect of local and global environmental selective pressures, genetic drift, and gene flow. We hypothesize that high gene flow among populations of Humboldt and Magellanic penguins limits local adaptation in MHC I and MHC II, and signatures of selection differ between markers, locations, and species. We evaluated the MHC I and II diversity using 454 next-generation sequencing of 100 Humboldt and 75 Magellanic penguins from seven different breeding colonies. Higher genetic diversity was observed in MHC I than MHC II for both species, explained by more than one MHC I loci identified. Large population sizes, high gene flow, and/or similar selection pressures maintain diversity but limit local adaptation in MHC I. A pattern of isolation by distance was observed for MHC II for Humboldt penguin suggesting local adaptation, mainly on the northernmost studied locality. Furthermore, trans-species alleles were found due to a recent speciation for the genus or convergent evolution. High MHC I and MHC II gene diversity described is extremely advantageous for the long-term survival of the species.
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Affiliation(s)
- Nicole Sallaberry‐Pincheira
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
- Escuela de Medicina VeterinariaFacultad Ecología y Recursos NaturalesUniversidad Andrés BelloSantiagoChile
| | | | - Pamela Padilla
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
| | | | - Guillermo Luna‐Jorquera
- Universidad Católica del NorteMillenium Nucleus of Ecology and Sustainable Management of Oceanic Islands ESMOICentro de Estudios Avanzados en Zonas Áridas CEAZACoquimboChile
| | - Esteban Frere
- Centro de Investigaciones de Puerto DeseadoUniversidad Nacional de la Patagonia AustralPuerto DeseadoArgentina
| | - Armando Valdés‐Velásquez
- Laboratorio de Estudios en BiodiversidadFacultad de Ciencias Biológicas y FisiológicasUniversidad Peruana Cayetano HerediaLimaPeru
| | - Juliana A. Vianna
- Laboratorio de Biodiversidad MolecularDepartamento de Ecosistemas y Medio AmbienteFacultad de Agronomía e Ingeniería ForestalPontificia Universidad Católica de ChileSantiagoChile
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Sallaberry-Pincheira N, Gonzalez-Acuña D, Herrera-Tello Y, Dantas GPM, Luna-Jorquera G, Frere E, Valdés-Velasquez A, Simeone A, Vianna JA. Molecular Epidemiology of Avian Malaria in Wild Breeding Colonies of Humboldt and Magellanic Penguins in South America. Ecohealth 2015; 12:267-277. [PMID: 25492695 DOI: 10.1007/s10393-014-0995-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 09/21/2014] [Accepted: 10/25/2014] [Indexed: 06/04/2023]
Abstract
Avian malaria is a disease caused by species of the genera Haemoproteus, Leucocytozoon, and Plasmodium. It affects hundreds of bird species, causing varied clinical signs depending on the susceptibility of the host species. Although high mortality has been reported in captive penguins, limited epidemiological studies have been conducted in wild colonies, and isolated records of avian malaria have been reported mostly from individuals referred to rehabilitation centers. For this epidemiological study, we obtained blood samples from 501 adult Humboldt and 360 adult Magellanic penguins from 13 colonies throughout South America. To identify malaria parasitaemia, we amplified the mtDNA cytochrome b for all three parasite genera. Avian malaria was absent in most of the analyzed colonies, with exception of the Punta San Juan Humboldt penguin colony, in Peru, where we detected at least two new Haemoproteus lineages in three positive samples, resulting in a prevalence of 0.6% for the species. The low prevalence of avian malaria detected in wild penguins could be due to two possible causes: A low incidence, with high morbidity and mortality in wild penguins or alternatively, penguins sampled in the chronic stage of the disease (during which parasitaemia in peripheral blood samples is unlikely) would be detected as false negatives.
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Affiliation(s)
- Nicole Sallaberry-Pincheira
- Laboratorio Fauna Australis, Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile
- Escuela Medicina Veterinaria, Facultad Ecología y Recursos Naturales, Universidad Andrés Bello, Santiago, Chile
| | | | - Yertiza Herrera-Tello
- Laboratorio Fauna Australis, Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile
| | - Gisele P M Dantas
- Pontificia Universidade Catolica de Minas Gerais, Belo Horizonte, Brazil
| | - Guillermo Luna-Jorquera
- Universidad Católica del Norte, Millenium Nucleus of Ecology and Sustainable Management of Oceanic Islands ESMOI, Centro de Estudios Avanzados en Zonas Áridas CEAZA, Coquimbo, Chile
| | - Esteban Frere
- Centro de Investigaciones de Puerto Deseado, Universidad Nacional de la Patagonia Austral, Puerto Deseado, Argentina
| | - Armando Valdés-Velasquez
- Laboratorio de Estudios en Biodiversidad, Facultad de Ciencias Biológicas y Fisiológicas, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Alejandro Simeone
- Departamento de Ecología y Biodiversidad, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Santiago, Chile
| | - Juliana A Vianna
- Laboratorio Fauna Australis, Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago, Chile.
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Álvarez-Varas R, González-Acuña D, Vianna JA. Comparative phylogeography of co-distributed Phrygilus species (Aves, Thraupidae) from the Central Andes. Mol Phylogenet Evol 2015; 90:150-63. [PMID: 25987531 DOI: 10.1016/j.ympev.2015.04.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 04/10/2015] [Accepted: 04/13/2015] [Indexed: 02/01/2023]
Abstract
The Neotropical ecoregion has been an important place of avian diversification where dispersal and allopatric events coupled with periods of active orogeny and climate change (Late Pliocene-Pleistocene) have shaped the biogeography of the region. In the Neotropics, avian population structure has been sculpted not only by geographical barriers, but also by non-allopatric factors such as natural selection and local adaptation. We analyzed the genetic variation of six co-distributed Phrygilus species from the Central Andes, based on mitochondrial and nuclear markers in conjunction with morphological differentiation. We examined if Phrygilus species share patterns of population structure and historical demography, and reviewed the intraspecific taxonomy in part of their geographic range. Our results showed different phylogeographic patterns between species, even among those belonging to the same phylogenetic clade. P. alaudinus, P. atriceps, and P. unicolor showed genetic differentiation mediated by allopatric mechanisms in response to specific geographic barriers; P. gayi showed sympatric lineages in northern Chile, while P. plebejus and P. fruticeti showed a single genetic group. We found no relationship between geographic range size and genetic structure. Additionally, a signature of expansion was found in three species related to the expansion of paleolakes in the Altiplano region and the drying phase of the Atacama Desert. Morphological analysis showed congruence with molecular data and intraspecific taxonomy in most species. While we detected genetic and phenotypic patterns that could be related to natural selection and local adaptation, our results indicate that allopatric events acted as a major factor in the population differentiation of Phrygilus species.
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Affiliation(s)
- R Álvarez-Varas
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Código Postal: 6904411, Casilla 306, Correo 22, Santiago, Chile.
| | - D González-Acuña
- Facultad de Ciencias Veterinarias, Universidad de Concepción, Casilla 537, Chillán, Chile.
| | - J A Vianna
- Departamento de Ecosistemas y Medio Ambiente, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Código Postal: 6904411, Casilla 306, Correo 22, Santiago, Chile.
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Marín JC, Orozco-terWengel P, Romero K, Vásquez JP, Varas V, Vianna JA. Cross-amplification of nonspecific microsatellites markers: a useful tool to study endangered/vulnerable species of southern Andes deer. Genet Mol Res 2014; 13:3193-200. [PMID: 24841651 DOI: 10.4238/2014.april.25.4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Thirty-nine microsatellite loci that are highly conserved in red deer, sika deer, reindeer, Soay sheep, and other artiodactyls were tested in two vulnerable and endangered Neotropical deer (pudu: Pudu puda and huemul: Hippocamelus bisulcus) with the aim of producing a standardized set of markers that can be used successfully in noninvasive samples from these species. We also compared these nonspecific loci against eight polymorphic loci that were recently developed for huemul to determine whether the nonspecific markers could reflect the huemul's genetic variation that was observed with the specific loci. We identified 10 suitable loci, six of which constitute a standardized set for the two species and can be used to identify them in the absence of phenotypic data. The expected heterozygosity per locus for the panel of six loci ranged from 0.461 to 0.889 (average 0.665), and the maximum probability of identity value was 6.9x10(-6) and 3.2x10(-4) in pudu and huemul, respectively. This set of loci has potential applications in evolutionary, ecological, forensic, and conservation studies in pudu and huemul.
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Affiliation(s)
- J C Marín
- Laboratory of Genomic and Biodiversity, Department of Basic Sciences, University of Bío-Bío, Chillán, Chile
| | | | - K Romero
- Laboratory of Genomic and Biodiversity, Department of Basic Sciences, University of Bío-Bío, Chillán, Chile
| | - J P Vásquez
- Laboratory of Genomic and Biodiversity, Department of Basic Sciences, University of Bío-Bío, Chillán, Chile
| | - V Varas
- Institute of Environmental Science and Evolution, Faculty of Sciences, Austral University of Chile, Valdivia, Chile
| | - J A Vianna
- Departament of Ecosystem and Environment, Pontifical Catholic University of Chile, Santiago, Chile
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Peña M. F, Poulin E, Dantas GPM, González-Acuña D, Petry MV, Vianna JA. Have historical climate changes affected Gentoo penguin (Pygoscelis papua) populations in Antarctica? PLoS One 2014; 9:e95375. [PMID: 24759777 PMCID: PMC3997368 DOI: 10.1371/journal.pone.0095375] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/25/2014] [Indexed: 01/30/2023] Open
Abstract
The West Antarctic Peninsula (WAP) has been suffering an increase in its atmospheric temperature during the last 50 years, mainly associated with global warming. This increment of temperature trend associated with changes in sea-ice dynamics has an impact on organisms, affecting their phenology, physiology and distribution range. For instance, rapid demographic changes in Pygoscelis penguins have been reported over the last 50 years in WAP, resulting in population expansion of sub-Antarctic Gentoo penguin (P. papua) and retreat of Antarctic Adelie penguin (P. adeliae). Current global warming has been mainly associated with human activities; however these climate trends are framed in a historical context of climate changes, particularly during the Pleistocene, characterized by an alternation between glacial and interglacial periods. During the last maximal glacial (LGM∼21,000 BP) the ice sheet cover reached its maximum extension on the West Antarctic Peninsula (WAP), causing local extinction of Antarctic taxa, migration to lower latitudes and/or survival in glacial refugia. We studied the HRVI of mtDNA and the nuclear intron βfibint7 of 150 individuals of the WAP to understand the demographic history and population structure of P. papua. We found high genetic diversity, reduced population genetic structure and a signature of population expansion estimated around 13,000 BP, much before the first paleocolony fossil records (∼1,100 BP). Our results suggest that the species may have survived in peri-Antarctic refugia such as South Georgia and North Sandwich islands and recolonized the Antarctic Peninsula and South Shetland Islands after the ice sheet retreat.
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Affiliation(s)
- Fabiola Peña M.
- Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Metropolitan Region, Chile
| | - Elie Poulin
- Departamento de Ciencias Ecológicas, Universidad de Chile, Santiago, Metropolitan Region, Chile
| | - Gisele P. M. Dantas
- Pós-Graduação em Zoologia de Vertebrados, Pontificia Universidade Catolica de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Maria Virginia Petry
- Laboratório de Ornitologia e Animais Marinhos, Universidade do Vale do Rio dos Sinos, São Leopoldo, Rio Grande do Sul, Brazil
| | - Juliana A. Vianna
- Departamento de Ecosistemas y Medio Ambiente, Pontificia Universidad Católica de Chile, Santiago, Metropolitan Region, Chile
- * E-mail:
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Trinca CS, de Thoisy B, Rosas FCW, Waldemarin HF, Koepfli KP, Vianna JA, Eizirik E. Phylogeography and demographic history of the neotropical otter (Lontra longicaudis). J Hered 2012; 103:479-92. [PMID: 22589556 DOI: 10.1093/jhered/ess001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Neotropical otter (Lontra longicaudis) is a medium-sized semiaquatic carnivore with a broad distribution in the Neotropical region. Despite being apparently common in many areas, it is one of the least known otters, and genetic studies on this species are scarce. Here, we have investigated its genetic diversity, population structure, and demographic history across a large portion of its geographic range by analyzing 1471 base pairs (bp) of mitochondrial DNA from 52 individuals. Our results indicate that L. longicaudis presents high levels of genetic diversity and a consistent phylogeographic pattern, suggesting the existence of at least 4 distinct evolutionary lineages in South America. The observed phylogeographic partitions are partially congruent with the subspecies classification previously proposed for this species. Coalescence-based analyses indicate that Neotropical otter mitochondrial DNA lineages have shared a rather recent common ancestor, approximately 0.5 Ma, and have subsequently diversified into the observed phylogroups. A consistent scenario of recent population expansion was identified in Eastern South America based on several complementary analyses of historical demography. The results obtained here provide novel insights on the evolutionary history of this largely unknown Neotropical mustelid and should be useful to design conservation and management policies on behalf of this species and its habitats.
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Affiliation(s)
- Cristine S Trinca
- Departamento de Genética, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves, 9500, prédio 43323, Porto Alegre, Rio Grande do Sul, Brazil
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Fuentes-Hurtado M, Marín JC, González-Acuña D, Verdugo C, Vidal F, Vianna JA. Molecular divergence between insular and continental Pudu deer (Pudu puda) populations in the Chilean Patagonia. Studies on Neotropical Fauna and Environment 2011. [DOI: 10.1080/01650521.2010.537906] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Silva-Rodríguez EA, Aleuy OA, Fuentes-Hurtado M, Vianna JA, Vidal F, Jiménez JE. Priorities for the conservation of the pudu (Pudu puda) in southern South America. Anim Prod Sci 2011. [DOI: 10.1071/an10286] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The southern pudu (Pudu puda) is a threatened deer that is endemic to the South American temperate forests. Despite its assumed threatened status, there is relatively little understanding on the ecology and conservation of this species. Considering this situation and the fact that there are some research groups currently working on this species, we organised a symposium to discuss research and management priorities – as well as to coordinate efforts – to move forward on the conservation of the pudu. We agreed that main research priorities should be to increase the understanding of the threats that jeopardize the viability of pudu populations, with a strong emphasis on research questions that will provide information for the management of these threats. The main management recommendations were to implement monitoring of pudu populations at least in protected areas, to implement specific actions to remove threats from protected areas and to start following internationally-accepted guidelines for the management of rescued and confiscated animals.
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Vianna JA, Ayerdi P, Medina-Vogel G, Mangel JC, Zeballos H, Apaza M, Faugeron S. Phylogeography of the Marine Otter (Lontra felina): historical and contemporary factors determining its distribution. ACTA ACUST UNITED AC 2010; 101:676-89. [PMID: 20688888 DOI: 10.1093/jhered/esq088] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The evolutionary history of a species can be revealed by phylogeographical analysis; nevertheless, not only historical but also contemporary processes can imprint on the distribution of genetic diversity. We report on the phylogeny of Lontra ssp. in South America, and the role of spatial heterogeneity in shaping the distribution and population structure of the endangered marine otter, Lontra felina. Analyzing a total of 2261 bp of mitochondrial DNA (mtDNA) revealed the recent divergence of L. felina from L. provocax. A strong population structure (Φ(st) = 0.83, P < 0.0001) and a significant pattern of isolation by distance were described for L. felina (n = 168) across a wide geographical distribution (13°53'S to 43°36'S). Lontra felina mtDNA phylogeny is composed of 2 main clades: a clade from Peru and another composed of Chilean haplotypes. Northern populations show different divergent lineages and higher genetic diversity when compared with more recently colonized southern populations. Furthermore, long sandy beaches seem to act as barriers to dispersal, creating 2 evolutionary significant units in agreement with subspecies previous description, and at least 5 different management units (MUs). At a fine spatial scale, the size of rocky seashore patches, the distance between patches and anthropogenic factors also play important roles in species gene flow.
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Affiliation(s)
- Juliana A Vianna
- Departamento de Ecología y Biodiversidad, Facultad de Ecología y Recursos Naturales, Universidad Andrés Bello, Republica 440, código postal 8370251, Santiago, Chile
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Vianna JA, Bonde RK, Caballero S, Giraldo JP, Lima RP, Clark A, Marmontel M, Morales-Vela B, De Souza MJ, Parr L, Rodríguez-Lopez MA, Mignucci-Giannoni AA, Powell JA, Santos FR. Phylogeography, phylogeny and hybridization in trichechid sirenians: implications for manatee conservation. Mol Ecol 2006; 15:433-47. [PMID: 16448411 DOI: 10.1111/j.1365-294x.2005.02771.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Abstract The three living species of manatees, West Indian (Trichechus manatus), Amazonian (Trichechus inunguis) and West African (Trichechus senegalensis), are distributed across the shallow tropical and subtropical waters of America and the western coast of Africa. We have sequenced the mitochondrial DNA control region in 330 Trichechus to compare their phylogeographic patterns. In T. manatus we observed a marked population structure with the identification of three haplotype clusters showing a distinct spatial distribution. A geographic barrier represented by the continuity of the Lesser Antilles to Trinidad Island, near the mouth of the Orinoco River in Venezuela, appears to have restricted the gene flow historically in T. manatus. However, for T. inunguis we observed a single expanding population cluster, with a high diversity of very closely related haplotypes. A marked geographic population structure is likely present in T. senegalensis with at least two distinct clusters. Phylogenetic analyses with the mtDNA cytochrome b gene suggest a clade of the marine Trichechus species, with T. inunguis as the most basal trichechid. This is in agreement with previous morphological analyses. Mitochondrial DNA, autosomal microsatellites and cytogenetic analyses revealed the presence of hybrids between the T. manatus and T. inunguis species at the mouth of the Amazon River in Brazil, extending to the Guyanas and probably as far as the mouth of the Orinoco River. Future conservation strategies should consider the distinct population structure of manatee species, as well as the historical barriers to gene flow and the likely occurrence of interspecific hybridization.
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Affiliation(s)
- Juliana A Vianna
- Laboratory of Biodiversity and Molecular Evolution (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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