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Bustillo‐de la Rosa D, Barrero A, Traba J, García JT, Morales MB, Vázquez‐Domínguez E. Landscape features influencing gene flow and connectivity of an endangered passerine. Ecol Evol 2024; 14:e11078. [PMID: 38756688 PMCID: PMC11097005 DOI: 10.1002/ece3.11078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 01/10/2024] [Accepted: 02/12/2024] [Indexed: 05/18/2024] Open
Abstract
Dispersal of individuals and gene flow are crucial aspects to maintain genetic diversity and viability of populations, especially in the case of threatened species. Landscape composition and structure may facilitate or limit individual movement within and among populations. We used a landscape genetics approach to assess the connectivity patterns of the threatened Dupont's lark (Chersophilus duponti subsp. duponti), considering their genetic patterns and the landscape features associated with its gene flow in Spain. We analysed the genetic relatedness based on 11 species-specific polymorphic microsatellites on 416 Dupont's lark individuals sampled across peninsular Spain between 2017 and 2019, covering most of the European distribution of the species. To assess the relationship between the landscape composition and the species gene flow, we estimated genetic distance at the individual level (Dps). Next, we built a set of environmental surfaces from two time periods (years 1990 and 2018), based on factors such as land use and topography, influencing individuals' movement. We then obtained resistance surfaces from an optimization process on landscape variables. Landscape genetics analyses were done for single and composite surface models for each year separately. Our findings from both time points show that scatter or mosaic-structured vegetation composed by low agricultural and tree cover and high presence of sclerophyllous shrubs favoured Dupont's lark dispersal, while dense and continuous tree cover, as well as areas of intensive agriculture, were limiting factors. Our results suggest the importance of steppe habitat patches for the species' establishment and dispersal. In addition, our results provide key information to develop conservation measures, including conserving and restoring steppe habitats as scattered and/or mosaic-structured vegetation that could warrant the connectivity and persistence of Dupont's lark populations.
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Affiliation(s)
- Daniel Bustillo‐de la Rosa
- Terrestrial Ecology Group (TEG‐UAM). Department of EcologyUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Adrián Barrero
- Terrestrial Ecology Group (TEG‐UAM). Department of EcologyUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Juan Traba
- Terrestrial Ecology Group (TEG‐UAM). Department of EcologyUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Jesús T. García
- Instituto de Investigación en Recursos Cinegéticos (IREC, CSIC‐UCLM)Ciudad RealSpain
| | - Manuel B. Morales
- Terrestrial Ecology Group (TEG‐UAM). Department of EcologyUniversidad Autónoma de MadridMadridSpain
- Centro de Investigación en Biodiversidad y Cambio Global (CIBC‐UAM)Universidad Autónoma de MadridMadridSpain
| | - Ella Vázquez‐Domínguez
- Departamento de Ecología de la Biodiversidad, Instituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMexico
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Karabanina E, Lansink GMJ, Ponnikas S, Kvist L. A renewed glance at the Palearctic golden eagle: Genetic variation in space and time. Ecol Evol 2024; 14:e11109. [PMID: 38469039 PMCID: PMC10925523 DOI: 10.1002/ece3.11109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/16/2024] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
Anthropogenic pressures on nature have been causing population declines for centuries. Intensified persecution of apex predators, like the golden eagle, resulted in population bottlenecks during the 19th and 20th centuries. To study population genetics and demographic history of the golden eagle throughout its distribution, we collected museum samples from previously underrepresented regions, such as Russia and Central Asia. We used 12 microsatellite loci and a fragment of the mitochondrial DNA control region to re-evaluate phylogeography of Eurasian golden eagles and study the impacts of the population bottleneck. Our results revealed a north-south genetic gradient, expressed by the difference between Mediterranean and Holarctic lineages, as well as genetically distinct Northern Europe and Central Asia and Caucasus regions. Furthermore, Northern Europe exhibited the lowest, whereas Central Asia and Caucasus had the highest genetic diversity. Although golden eagles maintained relatively high genetic diversity, we detected genetic signatures of the recent bottleneck, including reduced genetic diversity and a decline in the effective female population size around the year 1975. Our study improves the knowledge of the genetic composition of Eurasian golden eagles and highlights the importance of understanding their historical population dynamics in the face of ongoing and future conservation efforts.
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Affiliation(s)
| | | | - Suvi Ponnikas
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
| | - Laura Kvist
- Ecology and Genetics Research UnitUniversity of OuluOuluFinland
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Genetic diversity and spatial genetic structure support the specialist-generalist variation hypothesis in two sympatric woodpecker species. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01451-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractSpecies are often arranged along a continuum from “specialists” to “generalists”. Specialists typically use fewer resources, occur in more patchily distributed habitats and have overall smaller population sizes than generalists. Accordingly, the specialist-generalist variation hypothesis (SGVH) proposes that populations of habitat specialists have lower genetic diversity and are genetically more differentiated due to reduced gene flow compared to populations of generalists. Here, expectations of the SGVH were tested by examining genetic diversity, spatial genetic structure and contemporary gene flow in two sympatric woodpecker species differing in habitat specialization. Compared to the generalist great spotted woodpecker (Dendrocopos major), lower genetic diversity was found in the specialist middle spotted woodpecker (Dendrocoptes medius). Evidence for recent bottlenecks was revealed in some populations of the middle spotted woodpecker, but in none of the great spotted woodpecker. Substantial spatial genetic structure and a significant correlation between genetic and geographic distances were found in the middle spotted woodpecker, but only weak spatial genetic structure and no significant correlation between genetic and geographic distances in the great spotted woodpecker. Finally, estimated levels of contemporary gene flow did not differ between the two species. Results are consistent with all but one expectations of the SGVH. This study adds to the relatively few investigations addressing the SGVH in terrestrial vertebrates.
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Gousy-Leblanc M, Yannic G, Therrien JF, Lecomte N. Mapping our knowledge on birds of prey population genetics. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01368-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Fine-scale genetic structure in the critically endangered red-fronted macaw in the absence of geographic and ecological barriers. Sci Rep 2021; 11:556. [PMID: 33436676 PMCID: PMC7804180 DOI: 10.1038/s41598-020-79575-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 12/07/2020] [Indexed: 02/01/2023] Open
Abstract
Behavioural and socio-cultural traits are recognized in the restriction of gene flow in species with high cognitive capacity and complex societies. This isolation by social barriers has been generally overlooked in threatened species by assuming disrupted gene flow due to population fragmentation and decline. We examine the genetic structure and ecology of the global population of the Critically Endangered red-fronted macaw (Ara rubrogenys), an endemic species to the inter-Andean valleys of Bolivia. We found a fine-scale genetic structuring in four genetic clusters. Genetic diversity was higher in wild compared to captive-bred macaws, but similar to that of captive wild-caught macaws. We found no clear evidence of severe genetic erosion in the population in recent decades, but it was patent in historic times, overlapping with drastic human habitat transformation and macaw persecution over millennia. We found no evidence of geographical and ecological barriers, owing to the high dispersal ability, nesting and foraging habits between genetic clusters. The lack of genetic intermixing despite long-distance foraging and seasonal movements suggests recruitment in natal colonies and other social factors reinforcing philopatry-related genetic structure. Conservation efforts should be specifically focussed on major threats in each genetic cluster as independent conservation units, and also considered in ex-situ management.
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Jensen AM, O'Neil NP, Iwaniuk AN, Burg TM. Landscape effects on the contemporary genetic structure of Ruffed Grouse ( Bonasa umbellus) populations. Ecol Evol 2019; 9:5572-5592. [PMID: 31160983 PMCID: PMC6540679 DOI: 10.1002/ece3.5112] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 01/28/2019] [Accepted: 02/08/2019] [Indexed: 01/01/2023] Open
Abstract
The amount of dispersal that occurs among populations can be limited by landscape heterogeneity, which is often due to both natural processes and anthropogenic activity leading to habitat loss or fragmentation. Understanding how populations are structured and mapping existing dispersal corridors among populations is imperative to both determining contemporary forces mediating population connectivity, and informing proper management of species with fragmented populations. Furthermore, the contemporary processes mediating gene flow across heterogeneous landscapes on a large scale are understudied, particularly with respect to widespread species. This study focuses on a widespread game bird, the Ruffed Grouse (Bonasa umbellus), for which we analyzed samples from the western extent of the range. Using three types of genetic markers, we uncovered multiple factors acting in concert that are responsible for mediating contemporary population connectivity in this species. Multiple genetically distinct groups were detected; microsatellite markers revealed six groups, and a mitochondrial marker revealed four. Many populations of Ruffed Grouse are genetically isolated, likely by macrogeographic barriers. Furthermore, the addition of landscape genetic methods not only corroborated genetic structure results, but also uncovered compelling evidence that dispersal resistance created by areas of unsuitable habitat is the most important factor mediating population connectivity among the sampled populations. This research has important implications for both our study species and other inhabitants of the early successional forest habitat preferred by Ruffed Grouse. Moreover, it adds to a growing body of evidence that isolation by resistance is more prevalent in shaping population structure of widespread species than previously thought.
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Affiliation(s)
- Ashley M. Jensen
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Nicholas P. O'Neil
- Canadian Centre for Behavioural NeuroscienceUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Andrew N. Iwaniuk
- Canadian Centre for Behavioural NeuroscienceUniversity of LethbridgeLethbridgeAlbertaCanada
| | - Theresa M. Burg
- Department of Biological SciencesUniversity of LethbridgeLethbridgeAlbertaCanada
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Kim B, Nakamura K, Tamura S, Lee BY, Kwak M. Genetic diversity and population structure of Lychnis wilfordii (Caryophyllaceae) with newly developed 17 microsatellite markers. Genes Genomics 2018; 41:381-387. [DOI: 10.1007/s13258-018-0759-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 10/29/2018] [Indexed: 01/16/2023]
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8
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Bounas A, Tsaparis D, Efrat R, Gradev G, Gustin M, Mikulic K, Rodríguez A, Sarà M, Kotoulas G, Sotiropoulos K. Genetic structure of a patchily distributed philopatric migrant: implications for management and conservation. Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Anastasios Bounas
- Molecular Ecology and Conservation Genetics Lab, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
- Hellenic Ornithological Society – BirdLife Greece, Themistokleous, Athens, Greece
| | - Dimitris Tsaparis
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Ron Efrat
- Mitrani Department of Desert Ecology, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, IL, Israel
| | | | - Marco Gustin
- LIPU (Lega Italiana Protezione Uccelli) – BirdLife Italia, Conservation Department, Via Udine, Parma, Italy
| | - Kresimir Mikulic
- Association BIOM – BirdLife Croatia, Preradoviceva, Zagreb, Croatia
| | - Airam Rodríguez
- Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Avda. Américo Vespucio, Seville, Spain
| | - Maurizio Sarà
- Section of Animal Biology, Department STEBICEF, University of Palermo, Via Archirafi, Palermo, Italy
| | - Georgios Kotoulas
- Institute of Marine Biology, Biotechnology and Aquaculture, Hellenic Centre for Marine Research, Heraklion, Greece
| | - Konstantinos Sotiropoulos
- Molecular Ecology and Conservation Genetics Lab, Department of Biological Applications and Technology, University of Ioannina, Ioannina, Greece
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Di Maggio R, Mengoni C, Mucci N, Campobello D, Randi E, Sarà M. Do not disturb the family: roles of colony size and human disturbance in the genetic structure of lesser kestrel. J Zool (1987) 2014. [DOI: 10.1111/jzo.12191] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- R. Di Maggio
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies University of Palermo Palermo Italy
| | - C. Mengoni
- Laboratorio di Genetica Istituto per la Protezione e la Ricerca Ambientale (ISPRA) Bologna Italy
| | - N. Mucci
- Laboratorio di Genetica Istituto per la Protezione e la Ricerca Ambientale (ISPRA) Bologna Italy
| | - D. Campobello
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies University of Palermo Palermo Italy
| | - E. Randi
- Laboratorio di Genetica Istituto per la Protezione e la Ricerca Ambientale (ISPRA) Bologna Italy
- Department 18/Section of Environmental Engineering Aalborg University Aalborg Denmark
| | - M. Sarà
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies University of Palermo Palermo Italy
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Ponnikas S, Kvist L, Ollila T, Stjernberg T, Orell M. Genetic structure of an endangered raptor at individual and population levels. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0501-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Gabrielsen CG, Kovach AI, Babbitt KJ, McDowell WH. Limited effects of suburbanization on the genetic structure of an abundant vernal pool-breeding amphibian. CONSERV GENET 2013. [DOI: 10.1007/s10592-013-0497-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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12
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Thimmayya AC, Buskirk SW. Genetic connectivity and diversity of pygmy rabbits (Brachylagus idahoensis) in southern Wyoming. J Mammal 2012. [DOI: 10.1644/11-mamm-a-045.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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RONNÅS CECILIA, CASSEL-LUNDHAGEN ANNA, BATTISTI ANDREA, WALLÉN JOHAN, LARSSON STIG. Limited emigration from an outbreak of a forest pest insect. Mol Ecol 2011; 20:4606-17. [DOI: 10.1111/j.1365-294x.2011.05312.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Lawton RJ, Messmer V, Pratchett MS, Bay LK. High gene flow across large geographic scales reduces extinction risk for a highly specialised coral feeding butterflyfish. Mol Ecol 2011; 20:3584-98. [PMID: 21806692 DOI: 10.1111/j.1365-294x.2011.05207.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The vulnerability of ecologically specialised species to environmental fluctuations has been well documented. However, population genetic structure can influence vulnerability to environmental change and recent studies have indicated that specialised species may have lower genetic diversity and greater population structuring compared to their generalist counterparts. To examine whether there were differences in population genetic structure between a dietary specialist (Chaetodon trifascialis) and a dietary generalist (Chaetodon lunulatus) we compared the demographic history and levels of gene flow of two related coral-feeding butterflyfishes. Using allele frequencies of ≥11 microsatellite loci and >350 bases of mitochondrial control region sequence our analyses of C. trifascialis and C. lunulatus from five locations across the Pacific Ocean revealed contrasting demographic histories and levels of genetic structure. Heterozygosity excess tests, neutrality tests and mismatch distributions were all highly significant in the dietary specialist C. trifascialis (all P < 0.01), suggesting genetic bottlenecks have occurred in all locations. In contrast, we found little evidence of genetic bottlenecks for the dietary generalist C. lunulatus. High gene flow and low genetic structuring was detected among locations for C. trifascialis (amova: R(ST) = 0.0027, P = 0.371; Φ(ST) = 0.068, P < 0.0001). Contrary to our expectations, a greater level of genetic structuring between locations was detected for C. lunulatus (amova: R(ST) = 0.0277, Φ(ST) = 0.166, both P < 0.0001). These results suggest that dietary specialisation may affect demographic history through reductions in population size following resource declines, without affecting population structure through reductions in gene flow in the same way that habitat specialisation appears to. Although C. trifascialis is highly vulnerable to coral loss, the high gene flow detected here suggests populations will be able to recover from local declines through the migration of individuals.
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Affiliation(s)
- Rebecca J Lawton
- ARC Centre of Excellence for Coral Reef Studies, James Cook University, Townsville, QLD 4811, Australia.
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Comparative and demographic analysis of orang-utan genomes. Nature 2011; 469:529-33. [PMID: 21270892 PMCID: PMC3060778 DOI: 10.1038/nature09687] [Citation(s) in RCA: 372] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 11/19/2010] [Indexed: 11/10/2022]
Abstract
“Orangutan” is derived from the Malay term “man of the forest” and aptly describes the Southeast Asian great apes native to Sumatra and Borneo. The orangutan species, Pongo abelii (Sumatran) and Pongo pygmaeus (Bornean), are the most phylogenetically distant great apes from humans, thereby providing an informative perspective on hominid evolution. Here we present a Sumatran orangutan draft genome assembly and short read sequence data from five Sumatran and five Bornean orangutan genomes. Our analyses reveal that, compared to other primates, the orangutan genome has many unique features. Structural evolution of the orangutan genome has proceeded much more slowly than other great apes, evidenced by fewer rearrangements, less segmental duplication, a lower rate of gene family turnover and surprisingly quiescent Alu repeats, which have played a major role in restructuring other primate genomes. We also describe the first primate polymorphic neocentromere, found in both Pongo species, emphasizing the gradual evolution of orangutan genome structure. Orangutans have extremely low energy usage for a eutherian mammal1, far lower than their hominid relatives. Adding their genome to the repertoire of sequenced primates illuminates new signals of positive selection in several pathways including glycolipid metabolism. From the population perspective, both Pongo species are deeply diverse; however, Sumatran individuals possess greater diversity than their Bornean counterparts, and more species-specific variation. Our estimate of Bornean/Sumatran speciation time, 400k years ago (ya), is more recent than most previous studies and underscores the complexity of the orangutan speciation process. Despite a smaller modern census population size, the Sumatran effective population size (Ne) expanded exponentially relative to the ancestral Ne after the split, while Bornean Ne declined over the same period. Overall, the resources and analyses presented here offer new opportunities in evolutionary genomics, insights into hominid biology, and an extensive database of variation for conservation efforts.
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Genetics and wolf conservation in the American West: lessons and challenges. Heredity (Edinb) 2010; 107:16-9. [PMID: 21119704 DOI: 10.1038/hdy.2010.147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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17
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ALCAIDE MIGUEL, LEMUS JESÚSA, BLANCO GUILLERMO, TELLA JOSÉL, SERRANO DAVID, NEGRO JUANJ, RODRÍGUEZ AIRAM, GARCÍA-MONTIJANO MARINO. Retracted:MHC diversity and differential exposure to pathogens in kestrels (Aves:Falconidae). Mol Ecol 2010; 19:691-705. [DOI: 10.1111/j.1365-294x.2009.04507.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Captive breeding and reintroduction of the lesser kestrel Falco naumanni: a genetic analysis using microsatellites. CONSERV GENET 2009. [DOI: 10.1007/s10592-009-9810-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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