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Garrido-Bautista J, Comas M, Jowers MJ, Smith S, Penn DJ, Bakkali M, Moreno-Rueda G. Fine-scale genetic structure and phenotypic divergence of a passerine bird population inhabiting a continuous Mediterranean woodland. ROYAL SOCIETY OPEN SCIENCE 2024; 11:240601. [PMID: 39253402 PMCID: PMC11382889 DOI: 10.1098/rsos.240601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 05/04/2024] [Accepted: 05/08/2024] [Indexed: 09/11/2024]
Abstract
Genetic differentiation between populations inhabiting ecologically different habitats might appear because of limited dispersal and gene flow, which may lead to patterns of phenotypic divergence and local adaptation. In this study, we use dispersal, genotypic (24 microsatellite loci) and phenotypic (body size and clutch size) data to analyse patterns of genetic structuring and phenotypic divergence in a blue tit (Cyanistes caeruleus) population inhabiting a continuous and heterogeneous woodland along a valley. The two slopes of the valley differ in their forest formations and environmental conditions. Findings showed that most blue tits reproduced within their natal slope. Accordingly, microsatellite analyses revealed that populations of blue tits established in the two slopes show subtle genetic differentiation. The two genetic populations diverged in clutch size, exceeding the level of differentiation expected based on genetic drift, hence suggesting divergent selection (or other processes promoting divergence) on this life-history trait. Our findings reveal that restricted dispersal and spatial heterogeneity may lead to genetic differentiation among bird populations at a surprisingly small scale. In this respect, it is worth highlighting that such differentiation occurs for an organism with high dispersal capacity and within a continuous woodland. Moreover, we show that small-scale ecological differences, together with limited gene flow, can result in selection favouring different phenotypes even within the same continuum population.
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Affiliation(s)
| | - Mar Comas
- Department of Zoology, University of Granada, Granada 18071, Spain
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
| | - Michael J Jowers
- Department of Zoology, University of Granada, Granada 18071, Spain
| | - Steve Smith
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna 1160, Austria
| | - Dustin J Penn
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna 1160, Austria
| | - Mohammed Bakkali
- Department of Genetics, Faculty of Sciences, University of Granada, Granada 18071, Spain
| | - Gregorio Moreno-Rueda
- Department of Zoology, University of Granada, Granada 18071, Spain
- Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
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2
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Chatelain M, Da Silva A, Celej M, Kurek E, Bulska E, Corsini M, Szulkin M. Replicated, urban-driven exposure to metallic trace elements in two passerines. Sci Rep 2021; 11:19662. [PMID: 34608262 PMCID: PMC8490372 DOI: 10.1038/s41598-021-99329-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
While there are increasing examples of phenotypic and genotypic differences between urban and non-urban populations of plants and animals, few studies identified the mechanisms explaining those dissimilarities. The characterization of the urban landscape, which can only be achieved by measuring variability in relevant environmental factors within and between cities, is a keystone prerequisite to understand the effects of urbanization on wildlife. Here, we measured variation in bird exposure to metal pollution within 8 replicated urbanization gradients and within 2 flagship bird species in urban evolutionary ecology: the blue tit (Cyanistes caeruleus) and the great tit (Parus major). We report on a highly significant, positive linear relationship between the magnitude of urbanization-inferred as either tree cover, impervious surface cover, or an urbanization score computed from several environmental variables, and copper, zinc and lead concentrations in bird feathers. The reverse relationship was measured in the case of mercury, while cadmium and arsenic did not vary in response to the urbanization level. This result, replicated across multiple cities and two passerine species, strongly suggests that copper, zinc, lead and mercury pollution is likely to trigger the emergence of parallel responses at the phenotypic and/or genotypic level between urban environments worldwide.
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Affiliation(s)
- Marion Chatelain
- Centre of New Technologies, University of Warsaw, 02-097, Warsaw, Poland. .,Department of Zoology, University of Innsbruck, Technikerstraße 25, 6020, Innsbruck, Austria.
| | - Arnaud Da Silva
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marta Celej
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Eliza Kurek
- grid.12847.380000 0004 1937 1290Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | - Ewa Bulska
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland ,grid.12847.380000 0004 1937 1290Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 02-089 Warsaw, Poland
| | - Michela Corsini
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
| | - Marta Szulkin
- grid.12847.380000 0004 1937 1290Centre of New Technologies, University of Warsaw, 02-097 Warsaw, Poland
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3
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Markowski M, Minias P, Bańbura M, Glądalski M, Kaliński A, Skwarska J, Wawrzyniak J, Zieliński P, Bańbura J. Genetic structure of urban and non-urban populations differs between two common parid species. Sci Rep 2021; 11:10428. [PMID: 34001959 PMCID: PMC8128859 DOI: 10.1038/s41598-021-89847-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 04/30/2021] [Indexed: 02/03/2023] Open
Abstract
Landscape conversions induced by human activities can affect dispersal patterns of various bird species and, as a result, affect genetic structure of their populations. Genetic differentiation of bird populations may be enhanced by habitat variation, especially in urban-non-urban systems. The majority of population genetic studies focus on single species, which inflicts limitations for direct comparisons of genetic responses of avian populations to urbanization. Here, we used a set of microsatellite markers to examine genetic diversity, gene flow and population structure in two common parid species, great tits Parus major and blue tits Cyanistes caeruleus occupying three sites in habitats with contrasting urbanization level in central Poland. We found low but significant divergence of urban park population with both suburban and non-urban forest great tit populations, while no differentiation was found between suburban forest and non-urban forest populations. In contrast, no evidence for genetic differentiation was found between blue tit populations from the urban park, suburban forest and non-urban forest sites. We conclude that great tits and blue tits respond to urbanization-related changes in a different way, which may be a result of different rates of migration and/or dispersal, likely higher in blue tits. Some impact may be also induced by interspecific competition. We suggest that changing the focus of urban genetic research from single to multiple species may provide novel insights into how natural populations respond to the processes of urbanization.
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Affiliation(s)
- Marcin Markowski
- grid.10789.370000 0000 9730 2769Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90–237 Łódź, Poland
| | - Piotr Minias
- grid.10789.370000 0000 9730 2769Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 1/3, 90–237 Łódź, Poland
| | - Mirosława Bańbura
- grid.10789.370000 0000 9730 2769Museum of Natural History, Faculty of Biology and Environmental Protection, University of Łódź, Kilińskiego 101, 90-011 Łódź, Poland
| | - Michał Glądalski
- grid.10789.370000 0000 9730 2769Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90–237 Łódź, Poland
| | - Adam Kaliński
- grid.10789.370000 0000 9730 2769Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90–237 Łódź, Poland
| | - Joanna Skwarska
- grid.10789.370000 0000 9730 2769Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90–237 Łódź, Poland
| | - Jarosław Wawrzyniak
- grid.10789.370000 0000 9730 2769Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90–237 Łódź, Poland
| | - Piotr Zieliński
- grid.10789.370000 0000 9730 2769Department of Ecology and Vertebrate Zoology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland
| | - Jerzy Bańbura
- grid.10789.370000 0000 9730 2769Department of Experimental Zoology and Evolutionary Biology, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90–237 Łódź, Poland
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4
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Perrier C, Rougemont Q, Charmantier A. Demographic history and genomics of local adaptation in blue tit populations. Evol Appl 2020; 13:1145-1165. [PMID: 32684952 PMCID: PMC7359843 DOI: 10.1111/eva.13035] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 05/11/2020] [Accepted: 05/18/2020] [Indexed: 12/24/2022] Open
Abstract
Understanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio‐temporal variations in population demography and variations in recombination rate and in diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests, and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.003 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long‐lasting gene flow between populations inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migration, followed by isolation since the end of the last glaciation. Effective population sizes were large, yet smaller on the island than on the mainland. Weak and nonparallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds and were more often found in regions of low recombination, as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8 Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.
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Affiliation(s)
- Charles Perrier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France.,Centre de Biologie pour la Gestion des Populations UMR CBGP INRAE CIRAD IRD Montpellier SupAgro Univ Montpellier Montpellier France
| | - Quentin Rougemont
- Département de Biologie Institut de Biologie Intégrative et des Systèmes (IBIS) Université Laval Québec Québec Canada
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive UMR 5175 CNRS Univ Montpellier CNRS EPHE IRD Univ Paul Valéry Montpellier 3 Montpellier France
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5
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Gilsenan C, Valcu M, Kempenaers B. Timing of arrival in the breeding area is repeatable and affects reproductive success in a non‐migratory population of blue tits. J Anim Ecol 2020; 89:1017-1031. [DOI: 10.1111/1365-2656.13160] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 10/20/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Carol Gilsenan
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
| | - Mihai Valcu
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics Max Planck Institute for Ornithology Seewiesen Germany
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6
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Slagsvold T, Wiebe KL. Immigrants and locally recruited birds differ in prey delivered to their offspring in blue tits and great tits. Anim Behav 2018. [DOI: 10.1016/j.anbehav.2018.01.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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7
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Rojas ER, Sueur C, Henry PY, Doligez B, Wey G, Dehorter O, Massemin S. Network Analysis Shows Asymmetrical Flows within a Bird Metapopulation. PLoS One 2016; 11:e0166701. [PMID: 27893770 PMCID: PMC5125599 DOI: 10.1371/journal.pone.0166701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 11/02/2016] [Indexed: 11/19/2022] Open
Abstract
How the spatial expansion of a species changes at a human time scale is a process difficult to determine. We studied the dispersal pattern of the French white stork population, using a 21-year ringing/resighting dataset. We used the graph-theory to investigate the strength of links between 5 populations (North-East, North-West, Centre, West, and South) and to determine factors important for the birds’ movements. Two clusters of populations were identified within the metapopulation, with most frequent movements of individuals between North-Eastern and Centre populations, and between North-Western and Western populations. Exchanges of individuals between populations were asymmetrical, where North-Eastern and North-Western populations provided more emigrants than they received immigrants. Neither the geographical distance between populations, nor the difference in densities influenced the number of individuals exchanging between populations. The graph-theory approach provides a dynamic view of individual movements within a metapopulation and might be useful for future population studies in the context of conservation.
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Affiliation(s)
| | | | - Pierre-Yves Henry
- Mécanismes adaptatifs et Evolution (MECADEV UMR7179), Sorbonne Universités, MNHN, CNRS, Muséum National d'Histoire Naturelle, 1 avenue du Petit Château, Brunoy, France
- Centre de Recherches sur la Biologie des Populations d’Oiseaux (CRBPO), Centre d’Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, Muséum National d’Histoire Naturelle, Paris, France
| | - Blandine Doligez
- UMR CNRS 5558 –LBBE, "Biométrie et Biologie Évolutive", Villeurbanne cedex, France
| | - Gérard Wey
- Groupe Cigognes France & APRECIAL, Colmar, France
| | - Olivier Dehorter
- Centre de Recherches sur la Biologie des Populations d’Oiseaux (CRBPO), Centre d’Ecologie et des Sciences de la Conservation (CESCO UMR7204), Sorbonne Universités, MNHN, CNRS, UPMC, Muséum National d’Histoire Naturelle, Paris, France
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8
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Ferrer ES, García-Navas V, Sanz JJ, Ortego J. The strength of the association between heterozygosity and probability of interannual local recruitment increases with environmental harshness in blue tits. Ecol Evol 2016; 6:8857-8869. [PMID: 28035274 PMCID: PMC5192745 DOI: 10.1002/ece3.2591] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/10/2016] [Accepted: 10/17/2016] [Indexed: 02/02/2023] Open
Abstract
The extent of inbreeding depression and the magnitude of heterozygosity–fitness correlations (HFC) have been suggested to depend on the environmental context in which they are assayed, but little evidence is available for wild populations. We combine extensive molecular and capture–mark–recapture data from a blue tit (Cyanistes caeruleus) population to (1) analyze the relationship between heterozygosity and probability of interannual adult local recruitment and (2) test whether environmental stress imposed by physiologically suboptimal temperatures and rainfall influence the magnitude of HFC. To address these questions, we used two different arrays of microsatellite markers: 14 loci classified as neutral and 12 loci classified as putatively functional. We found significant relationships between heterozygosity and probability of interannual local recruitment that were most likely explained by variation in genomewide heterozygosity. The strength of the association between heterozygosity and probability of interannual local recruitment was positively associated with annual accumulated precipitation. Annual mean heterozygosity increased over time, which may have resulted from an overall positive selection on heterozygosity over the course of the study period. Finally, neutral and putatively functional loci showed similar trends, but the former had stronger effect sizes and seemed to better reflect genomewide heterozygosity. Overall, our results show that HFC can be context dependent, emphasizing the need to consider the role of environmental heterogeneity as a key factor when exploring the consequences of individual genetic diversity on fitness in natural populations.
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Affiliation(s)
- Esperanza S Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM) Ciudad Real Spain; Departamento de Ciencias Ambientales Facultad de Ciencias Ambientales y Bioquímica Universidad de Castilla-La Mancha Toledo Spain
| | - Vicente García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM) Ciudad Real Spain; Departamento de Ciencias Ambientales Facultad de Ciencias Ambientales y Bioquímica Universidad de Castilla-La Mancha Toledo Spain; Institute of Evolutionary Biology and Environmental Studies University of Zurich Zurich Switzerland; Department of Integrative Ecology Estación Biológica de Doñana (EBD-CSIC) Seville Spain
| | - Juan José Sanz
- Departamento de Ecología Evolutiva Museo Nacional de Ciencias Naturales (CSIC) Madrid Spain
| | - Joaquín Ortego
- Department of Integrative Ecology Estación Biológica de Doñana (EBD-CSIC) Seville Spain
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9
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Grilo C, Del Cerro I, Centeno-Cuadros A, Ramiro V, Román J, Molina-Vacas G, Fernández-Aguilar X, Rodríguez J, Porto-Peter F, Fonseca C, Revilla E, Godoy JA. Heterogeneous road networks have no apparent effect on the genetic structure of small mammal populations. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 565:706-713. [PMID: 27219505 DOI: 10.1016/j.scitotenv.2016.05.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2016] [Revised: 05/11/2016] [Accepted: 05/11/2016] [Indexed: 06/05/2023]
Abstract
Roads are widely recognized to represent a barrier to individual movements and, conversely, verges can act as potential corridors for the dispersal of many small mammals. Both barrier and corridor effects should generate a clear spatial pattern in genetic structure. Nevertheless, the effect of roads on the genetic structure of small mammal populations still remains unclear. In this study, we examine the barrier effect that different road types (4-lane highway, 2-lane roads and single-lane unpaved roads) may have on the population genetic structure of three species differing in relevant life history traits: southern water vole Arvicola sapidus, the Mediterranean pine vole Microtus duodecimcostatus and the Algerian mouse Mus spretus. We also examine the corridor effect of highway verges on the Mediterranean pine vole and the Algerian mouse. We analysed the population structure through pairwise estimates of FST among subpopulations bisected by roads, identified genetic clusters through Bayesian assignment approaches, and used simple and partial Mantel tests to evaluate the relative barrier or corridor effect of roads. No strong evidences were found for an effect of roads on population structure of these three species. The barrier effect of roads seems to be site-specific and no corridor effect of verges was found for the pine vole and Algerian mouse populations. The lack of consistent results among species and for each road type lead us to believe that the ability of individual dispersers to use those crossing structures or the habitat quality in the highway verges may have a relatively higher influence on gene flow among populations than the presence of crossing structures per se. Further research should include microhabitat analysis and the estimates of species abundance to understand the mechanisms that underlie the genetic structure observed at some sites.
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Affiliation(s)
- Clara Grilo
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (EBD-CSIC), Calle Américo Vespucio s/n, E-41092 Sevilla, Spain; Centro Brasileiro de Estudos em Ecologia de Estradas/Setor Ecologia, Departamento de Biologia, Universidade Federal de Lavras, Campus Universitário, 37200-000 Lavras, Minas Gerais, Brazil.
| | - Irene Del Cerro
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
| | - Alejandro Centeno-Cuadros
- Department of Molecular Biology and Biochemical Engineering, University Pablo de Olavide, Sevilla, Spain.
| | - Victor Ramiro
- Universidade de Lisboa, Fundação da Faculdade de Ciências, C2 5º 1749-016 Lisboa, Portugal.
| | - Jacinto Román
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (EBD-CSIC), Calle Américo Vespucio s/n, E-41092 Sevilla, Spain.
| | - Guillem Molina-Vacas
- Universidade de Lisboa, Fundação da Faculdade de Ciências, C2 5º 1749-016 Lisboa, Portugal.
| | | | - Juan Rodríguez
- Universidade de Lisboa, Fundação da Faculdade de Ciências, C2 5º 1749-016 Lisboa, Portugal.
| | - Flávia Porto-Peter
- Universidade de Lisboa, Fundação da Faculdade de Ciências, C2 5º 1749-016 Lisboa, Portugal.
| | - Carlos Fonseca
- Department of Biology & CESAM, University of Aveiro, Campus de Santiago, Aveiro, Portugal.
| | - Eloy Revilla
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (EBD-CSIC), Calle Américo Vespucio s/n, E-41092 Sevilla, Spain.
| | - José A Godoy
- Departamento de Biología de la Conservación, Estación Biológica de Doñana (EBD-CSIC), Calle Américo Vespucio s/n, E-41092 Sevilla, Spain.
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10
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Szulkin M, Gagnaire PA, Bierne N, Charmantier A. Population genomic footprints of fine-scale differentiation between habitats in Mediterranean blue tits. Mol Ecol 2016; 25:542-58. [PMID: 26800038 DOI: 10.1111/mec.13486] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 12/20/2022]
Abstract
Linking population genetic variation to the spatial heterogeneity of the environment is of fundamental interest to evolutionary biology and ecology, in particular when phenotypic differences between populations are observed at biologically small spatial scales. Here, we applied restriction-site associated DNA sequencing (RAD-Seq) to test whether phenotypically differentiated populations of wild blue tits (Cyanistes caeruleus) breeding in a highly heterogeneous environment exhibit genetic structure related to habitat type. Using 12 106 SNPs in 197 individuals from deciduous and evergreen oak woodlands, we applied complementary population genomic analyses, which revealed that genetic variation is influenced by both geographical distance and habitat type. A fine-scale genetic differentiation supported by genome- and transcriptome-wide analyses was found within Corsica, between two adjacent habitats where blue tits exhibit marked differences in breeding time while nesting < 6 km apart. Using redundancy analysis (RDA), we show that genomic variation remains associated with habitat type when controlling for spatial and temporal effects. Finally, our results suggest that the observed patterns of genomic differentiation were not driven by a small proportion of highly differentiated loci, but rather emerged through a process such as habitat choice, which reduces gene flow between habitats across the entire genome. The pattern of genomic isolation-by-environment closely matches differentiation observed at the phenotypic level, thereby offering significant potential for future inference of phenotype-genotype associations in a heterogeneous environment.
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Affiliation(s)
- M Szulkin
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
| | - P-A Gagnaire
- Université Montpellier 2, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, 34200, Sète, France
| | - N Bierne
- Université Montpellier 2, Place Eugène Bataillon, 34095, Montpellier Cedex 5, France.,ISEM - CNRS, UMR 5554, SMEL, 2 rue des Chantiers, 34200, Sète, France
| | - A Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRS, 1919 Route de Mende, 34293, Montpellier Cedex 5, France
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11
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Ferrer ES, García-Navas V, Bueno-Enciso J, Barrientos R, Serrano-Davies E, Cáliz-Campal C, Sanz JJ, Ortego J. The influence of landscape configuration and environment on population genetic structure in a sedentary passerine: insights from loci located in different genomic regions. J Evol Biol 2015; 29:205-19. [DOI: 10.1111/jeb.12776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- E. S. Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - V. García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - J. Bueno-Enciso
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - R. Barrientos
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - E. Serrano-Davies
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - C. Cáliz-Campal
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - J. J. Sanz
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
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Charmantier A, Doutrelant C, Dubuc-Messier G, Fargevieille A, Szulkin M. Mediterranean blue tits as a case study of local adaptation. Evol Appl 2015; 9:135-52. [PMID: 27087844 PMCID: PMC4780380 DOI: 10.1111/eva.12282] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/27/2015] [Indexed: 02/01/2023] Open
Abstract
While the study of the origins of biological diversity across species has provided numerous examples of adaptive divergence, the realization that it can occur at microgeographic scales despite gene flow is recent, and scarcely illustrated. We review here evidence suggesting that the striking phenotypic differentiation in ecologically relevant traits exhibited by blue tits Cyanistes caeruleus in their southern range‐edge putatively reflects adaptation to the heterogeneity of the Mediterranean habitats. We first summarize the phenotypic divergence for a series of life history, morphological, behavioural, acoustic and colour ornament traits in blue tit populations of evergreen and deciduous forests. For each divergent trait, we review the evidence obtained from common garden experiments regarding a possible genetic origin of the observed phenotypic differentiation as well as evidence for heterogeneous selection. Second, we argue that most phenotypically differentiated traits display heritable variation, a fundamental requirement for evolution to occur. Third, we discuss nonrandom dispersal, selective barriers and assortative mating as processes that could reinforce local adaptation. Finally, we show how population genomics supports isolation – by – environment across landscapes. Overall, the combination of approaches converges to the conclusion that the strong phenotypic differentiation observed in Mediterranean blue tits is a fascinating case of local adaptation.
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Affiliation(s)
- Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
| | - Claire Doutrelant
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
| | - Gabrielle Dubuc-Messier
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France; Département des sciences biologiques Université du Québec à Montréal Succursalle centre-ville QC Canada
| | | | - Marta Szulkin
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
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Ferrer ES, García-Navas V, Sanz JJ, Ortego J. Individual genetic diversity and probability of infection by avian malaria parasites in blue tits (Cyanistes caeruleus). J Evol Biol 2014; 27:2468-82. [PMID: 25264126 DOI: 10.1111/jeb.12489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Accepted: 09/01/2014] [Indexed: 11/30/2022]
Abstract
Understanding the importance of host genetic diversity for coping with parasites and infectious diseases is a long-standing goal in evolutionary biology. Here, we study the association between probability of infection by avian malaria (Plasmodium relictum) and individual genetic diversity in three blue tit (Cyanistes caeruleus) populations that strongly differ in prevalence of this parasite. For this purpose, we screened avian malaria infections and genotyped 789 blue tits across 26 microsatellite markers. We used two different arrays of markers: 14 loci classified as neutral and 12 loci classified as putatively functional. We found a significant relationship between probability of infection and host genetic diversity estimated at the subset of neutral markers that was not explained by strong local effects and did not differ among the studied populations. This relationship was not linear, and probability of infection increased up to values of homozygosity by locus (HL) around 0.15, reached a plateau at values of HL from 0.15 to 0.40 and finally declined among a small proportion of highly homozygous individuals (HL > 0.4). We did not find evidence for significant identity disequilibrium, which may have resulted from a low variance of inbreeding in the study populations and/or the small power of our set of markers to detect it. A combination of subtle positive and negative local effects and/or a saturation threshold in the association between probability of infection and host genetic diversity in combination with increased resistance to parasites in highly homozygous individuals may explain the observed negative quadratic relationship. Overall, our study highlights that parasites play an important role in shaping host genetic variation and suggests that the use of large sets of neutral markers may be more appropriate for the study of heterozygosity-fitness correlations.
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Affiliation(s)
- E S Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural, Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM), Ciudad Real, Spain; Departamento de Ciencias Ambientales, Facultad de Ciencias Ambientales y Bioquímica, Universidad de Castilla-La Mancha, Toledo, Spain
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14
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Guerrini M, Gennai C, Panayides P, Crabtree A, Zuberogoitia I, Copland AS, Babushkina O, Politi PM, Giunchi D, Barbanera F. Large-scale patterns of genetic variation in a female-biased dispersing passerine: the importance of sex-based analyses. PLoS One 2014; 9:e98574. [PMID: 24886720 PMCID: PMC4041750 DOI: 10.1371/journal.pone.0098574] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 05/05/2014] [Indexed: 11/19/2022] Open
Abstract
Dispersal affects the distribution, dynamics and genetic structure of natural populations, and can be significantly different between sexes. However, literature records dealing with the dispersal of migratory birds are scarce, as migratory behaviour can notably complicate the study of dispersal. We used the barn swallow Hirundo rustica as model taxon to investigate patterns of genetic variability in males and in females of a migratory species showing sex-biased dispersal. We collected blood samples (n = 186) over the period 2006 to 2011 from adults (H. r. rustica subspecies) nesting in the same breeding site at either high (Ireland, Germany and Russia) or low (Spain, Italy and Cyprus) latitude across Europe. We amplified the Chromo Helicase DNA gene in all birds in order to warrant a sex-balanced sample size (92 males, 94 females). We investigated both uniparental (mitochondrial ND2 gene) and biparental (microsatellite DNA: 10 loci) genetic systems. The mtDNA provided evidence for demographic expansion yet no significant partition of the genetic variability was disclosed. Nevertheless, a comparatively distant Russian population investigated in another study, whose sequences were included in the present dataset, significantly diverged from all other ones. Different to previous studies, microsatellites highlighted remarkable genetic structure among the studied populations, and pointed to the occurrence of differences between male and female barn swallows. We produced evidence for non-random patterns of gene flow among barn swallow populations probably mediated by female natal dispersal, and we found significant variability in the philopatry of males of different populations. Our data emphasize the importance of taking into account the sex of sampled individuals in order to obtain reliable inferences on species characterized by different patterns of dispersal between males and females.
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Affiliation(s)
- Monica Guerrini
- Department of Biology, Zoology and Anthropology Unit, University of Pisa, Pisa, Italy
| | - Clizia Gennai
- Department of Biology, Zoology and Anthropology Unit, University of Pisa, Pisa, Italy
| | | | | | | | | | - Olga Babushkina
- Laboratory of Avian Ecology and Bird Protection, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Paolo M. Politi
- Orti-Bottagone Nature Reserve, World Wildlife Fund, Piombino, Italy
| | - Dimitri Giunchi
- Department of Biology, Ethology Unit, University of Pisa, Pisa, Italy
| | - Filippo Barbanera
- Department of Biology, Zoology and Anthropology Unit, University of Pisa, Pisa, Italy
- * E-mail:
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15
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García-Navas V, Ferrer ES, Sanz JJ, Ortego J. The role of immigration and local adaptation on fine-scale genotypic and phenotypic population divergence in a less mobile passerine. J Evol Biol 2014; 27:1590-603. [DOI: 10.1111/jeb.12412] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/18/2014] [Accepted: 04/11/2014] [Indexed: 11/28/2022]
Affiliation(s)
- V. García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - E. S. Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - J. J. Sanz
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Ortego
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Conservation and Evolutionary Genetics Group; Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
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García-Navas V, Ferrer ES, Bueno-Enciso J, Barrientos R, Sanz JJ, Ortego J. Extrapair paternity in Mediterranean blue tits: socioecological factors and the opportunity for sexual selection. Behav Ecol 2013. [DOI: 10.1093/beheco/art111] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Pierson JC, Allendorf FW, Drapeau P, Schwartz MK. Breed locally, disperse globally: fine-scale genetic structure despite landscape-scale panmixia in a fire-specialist. PLoS One 2013; 8:e67248. [PMID: 23825646 PMCID: PMC3692495 DOI: 10.1371/journal.pone.0067248] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 05/14/2013] [Indexed: 12/02/2022] Open
Abstract
An exciting advance in the understanding of metapopulation dynamics has been the investigation of how populations respond to ephemeral patches that go 'extinct' during the lifetime of an individual. Previous research has shown that this scenario leads to genetic homogenization across large spatial scales. However, little is known about fine-scale genetic structuring or how this changes over time in ephemeral patches. We predicted that species that specialize on ephemeral habitats will delay dispersal to exploit natal habitat patches while resources are plentiful and thus display fine-scale structure. To investigate this idea, we evaluated the effect of frequent colonization of ephemeral habitats on the fine-scale genetic structure of a fire specialist, the black-backed woodpecker (Picoides arcticus) and found a pattern of fine-scale genetic structure. We then tested for differences in spatial structure between sexes and detected a pattern consistent with male-biased dispersal. We also detected a temporal increase in relatedness among individuals within newly burned forest patches. Our results indicate that specialist species that outlive their ephemeral patches can accrue significant fine-scale spatial structure that does not necessarily affect spatial structure at larger scales. This highlights the importance of both spatial and temporal scale considerations in both sampling and data interpretation of molecular genetic results.
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Affiliation(s)
- Jennifer C Pierson
- Wildlife Biology Program, University of Montana, Missoula, Montana, United States of America.
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18
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Porlier M, Garant D, Perret P, Charmantier A. Habitat-linked population genetic differentiation in the blue tit Cyanistes caeruleus. ACTA ACUST UNITED AC 2012; 103:781-91. [PMID: 23087385 DOI: 10.1093/jhered/ess064] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Although the recent emergence of the field of landscape genetics has led to several studies investigating the effects of habitat composition between populations on genetic differentiation, much less is known on the impact of within-habitat ecological characteristics on levels of gene flow and genetic differentiation among populations. Using data on 840 individuals sampled in 8 sites in Corsica and 1 in southern France and analyzed at 10 microsatellite loci, we assessed the spatial and temporal population genetic structure of blue tits (Cyanistes caeruleus) in Corsica and identified the ecological factors, both between- and within-sampling sites, responsible for the observed genetic structure. We found temporally stable fine-scale genetic structure within Corsica, with genetic differentiation values among populations corresponding to ~25% of levels observed between Corsica and the mainland. This structure was not explained by the geographic distance among populations or by the presence of physical barriers but was instead related to local habitat types (deciduous or evergreen oaks). Our results are thus consistent with previously documented phenotypic differences among habitats in morphological and reproductive traits. These findings suggest that although individuals have high dispersal ability, local adaptation might reduce gene flow among populations located in different habitats.
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Affiliation(s)
- Melody Porlier
- Département de Biologie, Faculté des Sciences, Université de Sherbrooke, Sherbrooke, Qc, J1K 2R1 Canada.
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Ferrer ES, García-Navas V, Sanz JJ, Ortego J. Molecular characterization of avian malaria parasites in three Mediterranean blue tit (Cyanistes caeruleus) populations. Parasitol Res 2012; 111:2137-42. [DOI: 10.1007/s00436-012-3062-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 07/20/2012] [Indexed: 10/28/2022]
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