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Srikanthan P, Burg TM. Environmental drivers behind the genetic differentiation in mountain chickadees ( Poecile gambeli). Genome 2024; 67:53-63. [PMID: 37922513 DOI: 10.1139/gen-2023-0067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
Abstract
Anthropogenic climate change has a large impact on wildlife populations and the scale of the impacts has been increasing. In this study, we utilised 3dRAD sequence data to investigate genetic divergence and identify the environmental drivers of genetic differentiation between 12 populations of mountain chickadees, family Paridae, sampled across North America. To examine patterns of genetic variation across the range, we conducted a discriminant analysis of principal components (DAPC), admixture analysis, and calculated pairwise Fst values. The DAPC revealed four clusters: southern California, eastern Rocky Mountains, northwestern Rocky Mountains, and Oregon/northern California. We then used BayeScEnv to highlight significant outlier SNPs associated with the five environmental variables. We identified over 150 genes linked to outlier SNPs associated with more than 15 pathways, including stress response and circadian rhythm. We also found a strong signal of isolation by distance and local temperature was highly correlated with genetic distance. Maxent simulations showed a northward range shift over the next 50 years and a decrease in suitable habitat, highlighting the need for immediate conservation action.
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Affiliation(s)
- P Srikanthan
- Department of Biology, University of Lethbridge, 4401 University Dr., Lethbridge, AB T1K 3M4, Canada
| | - T M Burg
- Department of Biology, University of Lethbridge, 4401 University Dr., Lethbridge, AB T1K 3M4, Canada
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2
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Le Clercq LS, Bazzi G, Ferrer Obiol J, Cecere JG, Gianfranceschi L, Grobler JP, Kotzé A, Riutort León M, González-Solís J, Rubolini D, Liedvogel M, Dalton DL. Birds of a feather flock together: a dataset for Clock and Adcyap1 genes from migration genetics studies. Sci Data 2023; 10:787. [PMID: 37945571 PMCID: PMC10636037 DOI: 10.1038/s41597-023-02717-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Birds in seasonal habitats rely on intricate strategies for optimal timing of migrations. This is governed by environmental cues, including photoperiod. Genetic factors affecting intrinsic timekeeping mechanisms, such as circadian clock genes, have been explored, yielding inconsistent findings with potential lineage-dependency. To clarify this evidence, a systematic review and phylogenetic reanalysis was done. This descriptor outlines the methodology for sourcing, screening, and processing relevant literature and data. PRISMA guidelines were followed, ultimately including 66 studies, with 34 focusing on candidate genes at the genotype-phenotype interface. Studies were clustered using bibliographic coupling and citation network analysis, alongside scientometric analyses by publication year and location. Data was retrieved for allele data from databases, article supplements, and direct author communications. The dataset, version 1.0.2, encompasses data from 52 species, with 46 species for the Clock gene and 43 for the Adcyap1 gene. This dataset, featuring data from over 8000 birds, constitutes the most extensive cross-species collection for these candidate genes, used in studies investigating gene polymorphisms and seasonal bird migration.
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Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa.
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa.
| | - Gaia Bazzi
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale, via Ca' Fornacetta 9, I-40064, Ozzano Emilia, BO, Italy
| | - Joan Ferrer Obiol
- Departament de Genètica, Universitat de Barcelona, Gran Via de les Corts Catalanes, 585, 08007, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Gran Via de les Corts Catalanes, 585, 08007, Barcelona, Spain
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, Milan, I-20133, Italy
| | - Jacopo G Cecere
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale, via Ca' Fornacetta 9, I-40064, Ozzano Emilia, BO, Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan, I-20133, Italy
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Marta Riutort León
- Departament de Genètica, Universitat de Barcelona, Gran Via de les Corts Catalanes, 585, 08007, Barcelona, Spain
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Gran Via de les Corts Catalanes, 585, 08007, Barcelona, Spain
| | - Jacob González-Solís
- Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Gran Via de les Corts Catalanes, 585, 08007, Barcelona, Spain
- Departament de Biologia Evolutiva, Universitat de Barcelona, Gran Via de les Corts Catalanes, 585, 08007, Barcelona, Spain
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, Milan, I-20133, Italy
- Istituto di Ricerca sulle Acque, IRSA-CNR, Via del Mulino 19, I-20861, Brugherio, (MB), Italy
| | - Miriam Liedvogel
- Max Planck Research Group Behavioural Genomics, Max Planck Institute for Evolutionary Biology, 24306, Plön, Germany
- Institute of Avian Research, An der Vogelwarte 21, 26386, Wilhelmshaven, Germany
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BA, UK
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3
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Estandía A, Sendell-Price AT, Oatley G, Robertson F, Potvin D, Massaro M, Robertson BC, Clegg SM. Candidate gene polymorphisms are linked to dispersive and migratory behaviour: Searching for a mechanism behind the "paradox of the great speciators". J Evol Biol 2023; 36:1503-1516. [PMID: 37750610 DOI: 10.1111/jeb.14222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 07/22/2023] [Indexed: 09/27/2023]
Abstract
The "paradox of the great speciators" has puzzled evolutionary biologists for over half a century. A great speciator requires excellent dispersal propensity to explain its occurrence on multiple islands, but reduced dispersal ability to explain its high number of subspecies. A rapid reduction in dispersal ability is often invoked to solve this apparent paradox, but a proximate mechanism has not been identified yet. Here, we explored the role of six genes linked to migration and animal personality differences (CREB1, CLOCK, ADCYAP1, NPAS2, DRD4, and SERT) in 20 South Pacific populations of silvereye (Zosterops lateralis) that range from highly sedentary to partially migratory, to determine if genetic variation is associated with dispersal propensity and migration. We detected genetic associations in three of the six genes: (i) in a partial migrant population, migrant individuals had longer microsatellite alleles at the CLOCK gene compared to resident individuals from the same population; (ii) CREB1 displayed longer average microsatellite allele lengths in recently colonized island populations (<200 years), compared to evolutionarily older populations. Bayesian broken stick regression models supported a reduction in CREB1 length with time since colonization; and (iii) like CREB1, DRD4 showed differences in polymorphisms between recent and old colonizations but a larger sample is needed to confirm. ADCYAP1, SERT, and NPAS2 were variable but that variation was not associated with dispersal propensity. The association of genetic variants at three genes with migration and dispersal ability in silvereyes provides the impetus for further exploration of genetic mechanisms underlying dispersal shifts, and the prospect of resolving a long-running evolutionary paradox through a genetic lens.
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Affiliation(s)
- Andrea Estandía
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, Oxford, UK
| | - Ashley T Sendell-Price
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, Oxford, UK
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Graeme Oatley
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Fiona Robertson
- Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Dominique Potvin
- School of Science, Technology and Engineering, University of the Sunshine Coast, Petrie, Queensland, Australia
| | - Melanie Massaro
- Gulbali Institute and School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Albury, New South Wales, Australia
| | | | - Sonya M Clegg
- Edward Grey Institute of Field Ornithology, Department of Biology, University of Oxford, Oxford, UK
- Centre for Planetary Health and Food Security, Griffith University, Brisbane, Queensland, Australia
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4
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Chyb A, Włodarczyk R, Drzewińska‐Chańko J, Jedlikowski J, Walden KKO, Minias P. Urbanization is associated with non-coding polymorphisms in candidate behavioural genes in the Eurasian coot. Ecol Evol 2023; 13:e10572. [PMID: 37791294 PMCID: PMC10542476 DOI: 10.1002/ece3.10572] [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: 06/22/2023] [Revised: 09/15/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
Extensive transformation of natural land cover into urbanized areas enhances accumulation of phenotypic differences between animals from urban and nonurban populations, but there is little information on whether these changes, especially in terms of animal behaviour and circadian rhythm, have a genetic basis. The aim of this study was to investigate genetic background of behavioural differences between four pairs of urban and nonurban populations of a common waterbird, the Eurasian coot Fulica atra. For this purpose, we quantified polymorphisms in personality-related candidate genes, previously reported to be associated with avian circadian rhythms and behavioural traits that may be crucial for urban life. We found general associations between landscape urbanization level and polymorphisms in 3'UTR region of CREB1 gene encoding transcriptional factor, which participates in development of cognitive functions and regulation of circadian rhythm. We also found significant differentiation between urban and nonurban populations in the intronic region of CKIɛ gene responsible for regulation of circadian clock. Although we lacked evidence for linkage of this intronic variation with coding polymorphisms, genetic differentiation between urban populations was significantly stronger at CKIɛ intron compared with neutral microsatellite markers, suggesting possible local adaptations of CKIɛ expression regulation to specific urban sites. Our results indicate that behavioural differentiation between urban and nonurban coot populations may be the effect of habitat-specific selective pressure resulting in genetic adaptations to urban environment and supporting the microevolutionary scenario. These adaptations, however, prevailed in non-coding regulatory rather than coding gene regions and showed either general or local patterns, revealing high complexity of associations between behaviour and landscape urbanization in birds.
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Affiliation(s)
- Amelia Chyb
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Radosław Włodarczyk
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Joanna Drzewińska‐Chańko
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
| | - Jan Jedlikowski
- Faculty of Biology, Biological and Chemical Research CentreUniversity of WarsawWarsawPoland
| | - Kimberly K. O. Walden
- Roy J. Carver Biotechnology CenterUniversity of Illinois at Urbana‐ChampaignUrbanaIllinoisUSA
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental ProtectionUniversity of ŁódźŁódźPoland
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5
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Le Clercq LS, Bazzi G, Cecere JG, Gianfranceschi L, Grobler JP, Kotzé A, Rubolini D, Liedvogel M, Dalton DL. Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics. Biol Rev Camb Philos Soc 2023; 98:1051-1080. [PMID: 36879518 DOI: 10.1111/brv.12943] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023]
Abstract
Timing is a crucial aspect for survival and reproduction in seasonal environments leading to carefully scheduled annual programs of migration in many species. But what are the exact mechanisms through which birds (class: Aves) can keep track of time, anticipate seasonal changes, and adapt their behaviour? One proposed mechanism regulating annual behaviour is the circadian clock, controlled by a highly conserved set of genes, collectively called 'clock genes' which are well established in controlling the daily rhythmicity of physiology and behaviour. Due to diverse migration patterns observed within and among species, in a seemingly endogenously programmed manner, the field of migration genetics has sought and tested several candidate genes within the clock circuitry that may underlie the observed differences in breeding and migration behaviour. Among others, length polymorphisms within genes such as Clock and Adcyap1 have been hypothesised to play a putative role, although association and fitness studies in various species have yielded mixed results. To contextualise the existing body of data, here we conducted a systematic review of all published studies relating polymorphisms in clock genes to seasonality in a phylogenetically and taxonomically informed manner. This was complemented by a standardised comparative re-analysis of candidate gene polymorphisms of 76 bird species, of which 58 are migrants and 18 are residents, along with population genetics analyses for 40 species with available allele data. We tested genetic diversity estimates, used Mantel tests for spatial genetic analyses, and evaluated relationships between candidate gene allele length and population averages for geographic range (breeding- and non-breeding latitude), migration distance, timing of migration, taxonomic relationships, and divergence times. Our combined analysis provided evidence (i) of a putative association between Clock gene variation and autumn migration as well as a putative association between Adcyap1 gene variation and spring migration in migratory species; (ii) that these candidate genes are not diagnostic markers to distinguish migratory from sedentary birds; and (iii) of correlated variability in both genes with divergence time, potentially reflecting ancestrally inherited genotypes rather than contemporary changes driven by selection. These findings highlight a tentative association between these candidate genes and migration attributes as well as genetic constraints on evolutionary adaptation.
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Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
| | - Gaia Bazzi
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale, via Ca' Fornacetta 9, Ozzano Emilia (BO), I-40064, Italy
| | - Jacopo G Cecere
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale, via Ca' Fornacetta 9, Ozzano Emilia (BO), I-40064, Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan, I-20133, Italy
| | - Johannes Paul Grobler
- Department of Genetics, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, Milan, I-20133, Italy
- Istituto di Ricerca sulle Acque, IRSA-CNR, Via del Mulino 19, Brugherio (MB), I-20861, Italy
| | - Miriam Liedvogel
- Max Planck Research Group Behavioral Genomics, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
- Institute of Avian Research, An der Vogelwarte 21, Wilhelmshaven, 26386, Germany
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BA, UK
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6
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Schlicht L, Santema P, Kempenaers B. Start and end of daily activity predict extrapair siring success independently of age in male blue tits. Anim Behav 2023. [DOI: 10.1016/j.anbehav.2023.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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7
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Bossu CM, Heath JA, Kaltenecker GS, Helm B, Ruegg KC. Clock-linked genes underlie seasonal migratory timing in a diurnal raptor. Proc Biol Sci 2022; 289:20212507. [PMID: 35506230 PMCID: PMC9069262 DOI: 10.1098/rspb.2021.2507] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/07/2022] [Indexed: 01/04/2023] Open
Abstract
Seasonal migration is a dynamic natural phenomenon that allows organisms to exploit favourable habitats across the annual cycle. While the morphological, physiological and behavioural changes associated with migratory behaviour are well characterized, the genetic basis of migration and its link to endogenous biological time-keeping pathways are poorly understood. Historically, genome-wide research has focused on genes of large effect, whereas many genes of small effect may work together to regulate complex traits like migratory behaviour. Here, we explicitly relax stringent outlier detection thresholds and, as a result, discover how multiple biological time-keeping genes are important to migratory timing in an iconic raptor species, the American kestrel (Falco sparverius). To validate the role of candidate loci in migratory timing, we genotyped kestrels captured across autumn migration and found significant associations between migratory timing and genetic variation in metabolic and light-input pathway genes that modulate biological clocks (top1, phlpp1, cpne4 and peak1). Further, we demonstrate that migrating individuals originated from a single panmictic source population, suggesting the existence of distinct early and late migratory genotypes (i.e. chronotypes). Overall, our results provide empirical support for the existence of a within-population-level polymorphism in genes underlying migratory timing in a diurnally migrating raptor.
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Affiliation(s)
- Christen M. Bossu
- Biology Department, Colorado State University, Fort Collins, CO 80521, USA
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, CA 90095, USA
| | - Julie A. Heath
- Raptor Research Center and Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Gregory S. Kaltenecker
- Intermountain Bird Observatory, Department of Biological Sciences, Boise State University, Boise, ID 83725, USA
| | - Barbara Helm
- Department of Bird Migration, Swiss Ornithological Institute, 6204 Sempach, Switzerland
| | - Kristen C. Ruegg
- Biology Department, Colorado State University, Fort Collins, CO 80521, USA
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8
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de Almeida Miranda D, Araripe J, de Morais Magalhães NG, de Siqueira LS, de Abreu CC, Pereira PDC, Henrique EP, da Silva Chira PAC, de Melo MAD, do Rêgo PS, Diniz DG, Sherry DF, Diniz CWP, Guerreiro-Diniz C. Shorebirds' Longer Migratory Distances Are Associated With Larger ADCYAP1 Microsatellites and Greater Morphological Complexity of Hippocampal Astrocytes. Front Psychol 2022; 12:784372. [PMID: 35185684 PMCID: PMC8855117 DOI: 10.3389/fpsyg.2021.784372] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/29/2021] [Indexed: 12/12/2022] Open
Abstract
For the epic journey of autumn migration, long-distance migratory birds use innate and learned information and follow strict schedules imposed by genetic and epigenetic mechanisms, the details of which remain largely unknown. In addition, bird migration requires integrated action of different multisensory systems for learning and memory, and the hippocampus appears to be the integration center for this task. In previous studies we found that contrasting long-distance migratory flights differentially affected the morphological complexity of two types of hippocampus astrocytes. Recently, a significant association was found between the latitude of the reproductive site and the size of the ADCYAP1 allele in long distance migratory birds. We tested for correlations between astrocyte morphological complexity, migratory distances, and size of the ADCYAP1 allele in three long-distance migrant species of shorebird and one non-migrant. Significant differences among species were found in the number and morphological complexity of the astrocytes, as well as in the size of the microsatellites of the ADCYAP1 gene. We found significant associations between the size of the ADCYAP1 microsatellites, the migratory distances, and the degree of morphological complexity of the astrocytes. We suggest that associations between astrocyte number and morphological complexity, ADCYAP1 microsatellite size, and migratory behavior may be part of the adaptive response to the migratory process of shorebirds.
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Affiliation(s)
- Diego de Almeida Miranda
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil.,Laboratório de Genética e Conservação, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Juliana Araripe
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Nara G de Morais Magalhães
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Lucas Silva de Siqueira
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Cintya Castro de Abreu
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Patrick Douglas Corrêa Pereira
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Ediely Pereira Henrique
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Pedro Arthur Campos da Silva Chira
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Mauro A D de Melo
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
| | - Péricles Sena do Rêgo
- Laboratório de Genética e Conservação, Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará, Bragança, Brazil
| | - Daniel Guerreiro Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Universidade Federal do Pará, Hospital Universitário João de Barros Barreto, Belém, Brazil.,Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Brazil
| | - David Francis Sherry
- Department of Psychology, Advanced Facility for Avian Research, University of Western Ontario, London, ON, Canada
| | - Cristovam W P Diniz
- Laboratório de Investigações em Neurodegeneração e Infecção, Instituto de Ciências Biológicas, Universidade Federal do Pará, Hospital Universitário João de Barros Barreto, Belém, Brazil
| | - Cristovam Guerreiro-Diniz
- Instituto Federal de Educação Ciência e Tecnologia do Pará, Campus Bragança, Laboratório de Biologia Molecular e Neuroecologia, Bragança, Brazil
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Krietsch J, Cragnolini M, Kuhn S, Lanctot RB, Saalfeld ST, Valcu M, Kempenaers B. Extrapair paternity in a sequentially polyandrous shorebird: limited evidence for the sperm storage hypothesis. Anim Behav 2022. [DOI: 10.1016/j.anbehav.2021.10.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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10
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Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, Christmas MJ, Huang Y, Maldonado-Linares A, Puigcerver M, Jiménez-Blasco I, Andrade P, Gonçalves D, Friis G, Roig I, Webster MT, Leonard JA, Vilà C. Massive genome inversion drives coexistence of divergent morphs in common quails. Curr Biol 2021; 32:462-469.e6. [PMID: 34847353 DOI: 10.1016/j.cub.2021.11.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/25/2021] [Accepted: 11/08/2021] [Indexed: 12/31/2022]
Abstract
The presence of population-specific phenotypes often reflects local adaptation or barriers to gene flow. The co-occurrence of phenotypic polymorphisms that are restricted within the range of a highly mobile species is more difficult to explain. An example of such polymorphisms is in the common quail Coturnix coturnix, a small migratory bird that moves widely during the breeding season in search of new mating opportunities, following ephemeral habitats,1,2 and whose females may lay successive clutches at different locations while migrating.3 In spite of this vagility, previous studies reported a higher frequency of heavier males with darker throat coloration in the southwest of the distribution (I. Jiménez-Blasco et al., 2015, Int. Union Game Biol., conference). We used population genomics and cytogenetics to explore the basis of this polymorphism and discovered a large inversion in the genome of the common quail. This inversion extends 115 Mbp in length and encompasses more than 7,000 genes (about 12% of the genome), producing two very different forms. Birds with the inversion are larger, have darker throat coloration and rounder wings, are inferred to have poorer flight efficiency, and are geographically restricted despite the high mobility of the species. Stable isotope analyses confirmed that birds carrying the inversion have shorter migratory distances or do not migrate. However, we found no evidence of pre- or post-zygotic isolation, indicating the two forms commonly interbreed and that the polymorphism remains locally restricted because of the effect on behavior. This illustrates a genomic mechanism underlying maintenance of geographically structured polymorphisms despite interbreeding with a lineage with high mobility.
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Affiliation(s)
- Ines Sanchez-Donoso
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain.
| | - Sara Ravagni
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - J Domingo Rodríguez-Teijeiro
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Matthew J Christmas
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Yan Huang
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Andros Maldonado-Linares
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Manel Puigcerver
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Irene Jiménez-Blasco
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona 08028, Spain
| | - Pedro Andrade
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal
| | - David Gonçalves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, Vairão 4485-661, Portugal; BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, 4485-661 Vairão, Portugal; Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto 4169-007, Portugal
| | - Guillermo Friis
- Center for Genomics and Systems Biology, New York University-Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ignasi Roig
- Genome Integrity and Instability Group, Institut de Biotecnologia i Biomedicina, Departament de Biologia Cellular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès 08193, Spain
| | - Matthew T Webster
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala 75123, Sweden
| | - Jennifer A Leonard
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain
| | - Carles Vilà
- Conservation and Evolutionary Genetics Group, Estación Biológica de Doñana (EBD-CSIC), Seville 41092, Spain.
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11
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The genetic regulation of avian migration timing: combining candidate genes and quantitative genetic approaches in a long-distance migrant. Oecologia 2021; 196:373-387. [PMID: 33963450 DOI: 10.1007/s00442-021-04930-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
Plant and animal populations can adapt to prolonged environmental changes if they have sufficient genetic variation in important phenological traits. The genetic regulation of annual cycles can be studied either via candidate genes or through the decomposition of phenotypic variance by quantitative genetics. Here, we combined both approaches to study the timing of migration in a long-distance migrant, the collared flycatcher (Ficedula albicollis). We found that none of the four studied candidate genes (CLOCK, NPAS2, ADCYAP1 and CREB1) had any consistent effect on the timing of six annual cycle stages of geolocator-tracked individuals. This negative result was confirmed by direct observations of males arriving in spring to the breeding site over four consecutive years. Although male spring arrival date was significantly repeatable (R = 0.24 ± 0.08 SE), most was attributable to permanent environmental effects, while the additive genetic variance and heritability were very low (h2 = 0.03 ± 0.17 SE). This low value constrains species evolutionary adaptation, and our study adds to warnings that such populations may be threatened, e.g. by ongoing climate change.
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12
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Ralston J, Lorenc L, Montes M, DeLuca WV, Kirchman JJ, Woodworth BK, Mackenzie SA, Newman A, Cooke HA, Freeman NE, Sutton AO, Tauzer L, Norris DR. Length polymorphisms at two candidate genes explain variation of migratory behaviors in blackpoll warblers ( Setophaga striata). Ecol Evol 2019; 9:8840-8855. [PMID: 31410284 PMCID: PMC6686290 DOI: 10.1002/ece3.5436] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/30/2019] [Accepted: 06/15/2019] [Indexed: 12/12/2022] Open
Abstract
Migratory behaviors such as the timing and duration of migration are genetically inherited and can be under strong natural selection, yet we still know very little about the specific genes or molecular pathways that control these behaviors. Studies in candidate genes Clock and Adcyap1 have revealed that both of these loci can be significantly correlated with migratory behaviors in birds, though observed relationships appear to vary across species. We investigated geographic genetic structure of Clock and Adcyap1 in four populations of blackpoll warblers (Setophaga striata), a Neotropical-Nearctic migrant that exhibits geographic variation in migratory timing and duration across its boreal breeding distribution. Further, we used data on migratory timing and duration, obtained from light-level geolocator trackers to investigate candidate genotype-phenotype relationships at the individual level. While we found no geographic structure in either candidate gene, we did find evidence that candidate gene lengths are correlated with five of the six migratory traits. Maximum Clock allele length was significantly and negatively associated with spring arrival date. Minimum Adcyap1 allele length was significantly and negatively associated with spring departure date and positively associated with fall arrival date at the wintering grounds. Additionally, we found a significant interaction between Clock and Adcyap1 allele lengths on both spring and fall migratory duration. Adcyap1 heterozygotes also had significantly shorter migration duration in both spring and fall compared to homozygotes. Our results support the growing body of evidence that Clock and Adcyap1 allele lengths are correlated with migratory behaviors in birds.
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Affiliation(s)
- Joel Ralston
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - Lydia Lorenc
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - Melissa Montes
- Department of BiologySaint Mary's CollegeNotre DameINUSA
| | - William V. DeLuca
- Department of Environmental ConservationUniversity of MassachusettsAmherstMAUSA
| | | | - Bradley K. Woodworth
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
- School of Biological SciencesThe University of QueenslandBrisbaneQueenslandAustralia
| | | | - Amy Newman
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | | | | | - Alex O. Sutton
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
| | - Lila Tauzer
- Wildlife Conservation Society CanadaWhitehorseYTCanada
| | - D. Ryan Norris
- Department of Integrative BiologyUniversity of GuelphGuelphONCanada
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13
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Valcu CM, Scheltema RA, Schweiggert RM, Valcu M, Teltscher K, Walther DM, Carle R, Kempenaers B. Life history shapes variation in egg composition in the blue tit Cyanistes caeruleus. Commun Biol 2019; 2:6. [PMID: 30740542 PMCID: PMC6320336 DOI: 10.1038/s42003-018-0247-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 12/02/2018] [Indexed: 12/26/2022] Open
Abstract
Maternal investment directly shapes early developmental conditions and therefore has long-term fitness consequences for the offspring. In oviparous species prenatal maternal investment is fixed at the time of laying. To ensure the best survival chances for most of their offspring, females must equip their eggs with the resources required to perform well under various circumstances, yet the actual mechanisms remain unknown. Here we describe the blue tit egg albumen and yolk proteomes and evaluate their potential to mediate maternal effects. We show that variation in egg composition (proteins, lipids, carotenoids) primarily depends on laying order and female age. Egg proteomic profiles are mainly driven by laying order, and investment in the egg proteome is functionally biased among eggs. Our results suggest that maternal effects on egg composition result from both passive and active (partly compensatory) mechanisms, and that variation in egg composition creates diverse biochemical environments for embryonic development.
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Affiliation(s)
- Cristina-Maria Valcu
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Richard A. Scheltema
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - Ralf M. Schweiggert
- Plant Foodstuff Technology and Analysis, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany
| | - Mihai Valcu
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Kim Teltscher
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
| | - Dirk M. Walther
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Reinhold Carle
- Plant Foodstuff Technology and Analysis, Institute of Food Science and Biotechnology, University of Hohenheim, 70599 Stuttgart, Germany
- Biological Science Department, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Bart Kempenaers
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Seewiesen, Germany
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14
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Examination of Clock and Adcyap1 gene variation in a neotropical migratory passerine. PLoS One 2018; 13:e0190859. [PMID: 29324772 PMCID: PMC5764313 DOI: 10.1371/journal.pone.0190859] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 12/21/2017] [Indexed: 11/19/2022] Open
Abstract
Complex behavioral traits, such as those making up a migratory phenotype, are regulated by multiple environmental factors and multiple genes. We investigated possible relationships between microsatellite variation at two candidate genes implicated in the control of migratory behavior, Clock and Adcyap1, and several aspects of migratory life-history and evolutionary divergence in the Painted Bunting (Passerina ciris), a species that shows wide variation in migratory and molting strategies across a disjunct distribution. We focused on Clock and Adcyap1 microsatellite variation across three Painted Bunting populations in Oklahoma, Louisiana, and North Carolina, and for the Oklahoma breeding population we used published migration tracking data on adult males to explore phenotypic variation in individual migratory behavior. We found no correlation between microsatellite allele size within either Clock and Adcyap1 relative to the initiation or duration of fall migration in adult males breeding in Oklahoma. We also show the lack of significant correlations with aspects of the migratory phenotype for the Louisiana population. Our research highlights the limitations of studying microsatellite allelic mutations that are of undetermined functional influence relative to complex behavioral phenotypes.
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15
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Zhang S, Xu X, Wang W, Yang W, Liang W. Clock gene is associated with individual variation in the activation of reproductive endocrine and behavior of Asian short toed lark. Sci Rep 2017; 7:15002. [PMID: 29101400 PMCID: PMC5670178 DOI: 10.1038/s41598-017-15064-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/18/2017] [Indexed: 11/10/2022] Open
Abstract
Within year individual variation in the timing of seasonal reproduction within wild bird populations in highly seasonal environments can be pronounced, but the molecular and physiological mechanisms responsible for this variation are unclear. We investigated the relationship between Clock gene poly-Q length, activation of the HPG endocrine axis, and the timing of breeding behavior, in a wild population of the Asian short-toed lark (Calandrella cheleensis) in Inner Mongolia, China. Six variants of Clock gene poly-Q alleles were identified in this population. Clock poly-Q mean allele length was positively correlated with the mean peak date deviation of individual birds. The shorter an individual's Clock poly-Q mean allele length, the earlier its plasma LH, T and E2 values peaked. Mean Clock poly-Q allele length of nestlings in the same nest were positively correlated with the standardized laying date of the first egg in that nest. These results suggest that the Clock gene influences the reproductive timing of birds through its effect on the HPG endocrine axis, and that individual variation in the timing of reproduction may have a genetic basis.
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Affiliation(s)
- Shuping Zhang
- College of life and environment sciences, Minzu university of China, Beijing, 100081, China.
| | - Xianglong Xu
- College of life and environment sciences, Minzu university of China, Beijing, 100081, China.,Guangdong institute of applied biological resources, Guangzhou, 510260, China
| | - Weiwei Wang
- College of life and environment sciences, Minzu university of China, Beijing, 100081, China
| | - Wenyu Yang
- College of life and environment sciences, Minzu university of China, Beijing, 100081, China
| | - Wei Liang
- Ministry of education key laboratory for tropical animal and plant ecology, College of life sciences, Hainan normal university, Haikou, 571158, China
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16
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Romano A, Possenti CD, Caprioli M, Gatti E, Gianfranceschi L, Rubolini D, Saino N, Parolini M. Circadian genes polymorphism and breeding phenology in a resident bird, the yellow‐legged gull. J Zool (1987) 2017. [DOI: 10.1111/jzo.12501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- A. Romano
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - C. D. Possenti
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - M. Caprioli
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - E. Gatti
- Department of Biosciences University of Milan Milan Italy
| | | | - D. Rubolini
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - N. Saino
- Department of Environmental Science and Policy University of Milan Milan Italy
| | - M. Parolini
- Department of Environmental Science and Policy University of Milan Milan Italy
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17
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Costanzo A, Ambrosini R, Caprioli M, Gatti E, Parolini M, Canova L, Rubolini D, Romano A, Gianfranceschi L, Saino N. Lifetime reproductive success, selection on lifespan, and multiple sexual ornaments in male European barn swallows. Evolution 2017; 71:2457-2468. [DOI: 10.1111/evo.13312] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Accepted: 06/30/2017] [Indexed: 01/15/2023]
Affiliation(s)
- Alessandra Costanzo
- Department of Environmental Science and Policy; University of Milan; via Celoria 26, I-20133 Milan Italy
| | - Roberto Ambrosini
- Department of Earth and Environmental Sciences (DISAT); University of Milano Bicocca; Piazza della Scienza, 1, I-20126 Milan Italy
| | - Manuela Caprioli
- Department of Environmental Science and Policy; University of Milan; via Celoria 26, I-20133 Milan Italy
| | - Emanuele Gatti
- Department of Biosciences; University of Milan; via Celoria 26, I-20133 Milan Italy
| | - Marco Parolini
- Department of Environmental Science and Policy; University of Milan; via Celoria 26, I-20133 Milan Italy
| | - Luca Canova
- Department of Chemistry; Via Taramelli 12, I-27100 Pavia Italy
| | - Diego Rubolini
- Department of Environmental Science and Policy; University of Milan; via Celoria 26, I-20133 Milan Italy
| | - Andrea Romano
- Department of Environmental Science and Policy; University of Milan; via Celoria 26, I-20133 Milan Italy
| | - Luca Gianfranceschi
- Department of Earth and Environmental Sciences (DISAT); University of Milano Bicocca; Piazza della Scienza, 1, I-20126 Milan Italy
| | - Nicola Saino
- Department of Environmental Science and Policy; University of Milan; via Celoria 26, I-20133 Milan Italy
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18
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Bazzi G, Podofillini S, Gatti E, Gianfranceschi L, Cecere JG, Spina F, Saino N, Rubolini D. Candidate genes have sex-specific effects on timing of spring migration and moult speed in a long-distance migratory bird. Curr Zool 2016; 63:479-486. [PMID: 29492007 PMCID: PMC5804205 DOI: 10.1093/cz/zow103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 10/07/2016] [Indexed: 01/09/2023] Open
Abstract
The timing of major life-history events, such as migration and moult, is set by endogenous circadian and circannual clocks, that have been well characterized at the molecular level. Conversely, the genetic sources of variation in phenology and in other behavioral traits have been sparsely addressed. It has been proposed that inter-individual variability in the timing of seasonal events may arise from allelic polymorphism at phenological candidate genes involved in the signaling cascade of the endogenous clocks. In this study of a long-distance migratory passerine bird, the willow warbler Phylloscopus trochilus, we investigated whether allelic variation at 5 polymorphic loci of 4 candidate genes (Adcyap1, Clock, Creb1, and Npas2), predicted 2 major components of the annual schedule, namely timing of spring migration across the central Mediterranean sea and moult speed, the latter gauged from ptilochronological analyses of tail feathers moulted in the African winter quarters. We identified a novel Clock gene locus (Clock region 3) showing polyQ polymorphism, which was however not significantly associated with any phenotypic trait. Npas2 allele size predicted male (but not female) spring migration date, with males bearing longer alleles migrating significantly earlier than those bearing shorter alleles. Creb1 allele size significantly predicted male (but not female) moult speed, longer alleles being associated with faster moult. All other genotype-phenotype associations were statistically non-significant. These findings provide new evidence for a role of candidate genes in modulating the phenology of different circannual activities in long-distance migratory birds, and for the occurrence of sex-specific candidate gene effects.
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Affiliation(s)
- Gaia Bazzi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan I-20133, Italy
| | - Stefano Podofillini
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan I-20133, Italy
| | - Emanuele Gatti
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan I-20133, Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan I-20133, Italy
| | - Jacopo G Cecere
- ISPRA-Istituto Superiore per la Protezione e la Ricerca Ambientale, via Cà Fornacetta 9, Ozzano dell'Emilia, BO I-40064, Italy
| | - Fernando Spina
- ISPRA-Istituto Superiore per la Protezione e la Ricerca Ambientale, via Cà Fornacetta 9, Ozzano dell'Emilia, BO I-40064, Italy
| | - Nicola Saino
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan I-20133, Italy
| | - Diego Rubolini
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan I-20133, Italy
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19
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Bazzi G, Galimberti A, Hays QR, Bruni I, Cecere JG, Gianfranceschi L, Hobson KA, Morbey YE, Saino N, Guglielmo CG, Rubolini D. Adcyap1 polymorphism covaries with breeding latitude in a Nearctic migratory songbird, the Wilson's warbler (Cardellina pusilla). Ecol Evol 2016; 6:3226-39. [PMID: 27252831 PMCID: PMC4870208 DOI: 10.1002/ece3.2053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 02/12/2016] [Indexed: 12/14/2022] Open
Abstract
Understanding the genetic background of complex behavioral traits, showing multigenic control and extensive environmental effects, is a challenging task. Among such traits, migration is known to show a large additive genetic component. Yet, the identification of specific genes or gene regions explaining phenotypic variance in migratory behavior has received less attention. Migration ultimately depends on seasonal cycles, and polymorphism at phenological candidate genes may underlie variation in timing of migration or other aspects of migratory behavior. In this study of a Nearctic–Neotropical migratory songbird, the Wilson's warbler (Cardellina pusilla), we investigated the association between polymorphism at two phenological candidate genes, Clock and Adcyap1, and two aspects of the migratory phenotype, timing of spring migration through a stopover site and inferred latitude of the breeding destination. The breeding destination of migrating individuals was identified using feather deuterium ratio (δ2H), which reliably reflects breeding latitude throughout the species' western breeding range. Ninety‐eight percent of the individuals were homozygous at Clock, and the rare heterozygotes did not deviate from homozygous migration phenology. Adcyap1 was highly polymorphic, and allele size was not significantly associated with migration date. However, Adcyap1 allele size significantly positively predicted the inferred breeding latitude of males but not of females. Moreover, we found a strong positive association between inferred breeding latitude and Adcyap1 allele size in long‐distance migrating birds from the northern sector of the breeding range (western Canada), while this was not the case in short‐distance migrating birds from the southern sector of the breeding range (coastal California). Our findings support previous evidence for a role of Adcyap1 in shaping the avian migratory phenotype, while highlighting that patterns of phenological candidate gene–phenotype associations may be complex, significantly varying between geographically distinct populations and even between the sexes.
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Affiliation(s)
- Gaia Bazzi
- Dipartimento di Bioscienze Università degli Studi di Milano via Celoria 26 I-20133 Milan Italy
| | - Andrea Galimberti
- ZooPlantLab Dipartimento di Biotecnologie e Bioscienze Università degli Studi di Milano-Bicocca Piazza della Scienza 2 I-20126 Milan Italy
| | - Quentin R Hays
- Department of Biology Advanced Facility for Avian Research University of Western Ontario London Ontario N6A 5B7 Canada; Natural Resources Department Eastern New Mexico University - Ruidoso Ruidoso New Mexico 88345
| | - Ilaria Bruni
- ZooPlantLab Dipartimento di Biotecnologie e Bioscienze Università degli Studi di Milano-Bicocca Piazza della Scienza 2 I-20126 Milan Italy
| | - Jacopo G Cecere
- ISPRA - Istituto Superiore per la Protezione e la Ricerca Ambientale Via Cà Fornacetta 9 I-40064 Ozzano dell'Emilia (BO) Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze Università degli Studi di Milano via Celoria 26 I-20133 Milan Italy
| | - Keith A Hobson
- Department of Biology Advanced Facility for Avian Research University of Western Ontario London Ontario N6A 5B7 Canada; Environment Canada 11 Innovation Boulevard Saskatoon Saskatchewan S7N 3H5 Canada
| | - Yolanda E Morbey
- Department of Biology Advanced Facility for Avian Research University of Western Ontario London Ontario N6A 5B7 Canada
| | - Nicola Saino
- Dipartimento di Bioscienze Università degli Studi di Milano via Celoria 26 I-20133 Milan Italy
| | - Christopher G Guglielmo
- Department of Biology Advanced Facility for Avian Research University of Western Ontario London Ontario N6A 5B7 Canada
| | - Diego Rubolini
- Dipartimento di Bioscienze Università degli Studi di Milano via Celoria 26 I-20133 Milan Italy
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20
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Contina A, Bridge ES, Kelly JF. Exploring novel candidate genes from the Mouse Genome Informatics database: Potential implications for avian migration research. Integr Zool 2016; 11:240-9. [PMID: 27061206 DOI: 10.1111/1749-4877.12199] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
To search for genes associated with migratory phenotypes in songbirds, we selected candidate genes through annotations from the Mouse Genome Informatics database and assembled an extensive candidate-gene library. Then, we implemented a next-generation sequencing approach to obtain DNA sequences from the Painted Bunting genome. We focused on those sequences that were conserved across avian species and that aligned with candidate genes in our mouse library. We genotyped short sequence repeats from the following candidate genes: ADRA1d, ANKRD17, CISH and MYH7. We studied the possible correlations between allelic variations occurring in these novel candidate migration genes and avian migratory phenotypes available from the published literature. We found that allele variation at MYH7 correlated with a calculated index of speed of migration (km/day) across 11 species of songbirds. We highlight the potential of the Mouse Genome Informatics database in providing new candidate genes that might play a crucial role in regulating migration in birds and possibly in other taxa. Our research effort shows the benefits and limitations of working with extensive genomic datasets and offers a snapshot of the challenges related to cross-species validation in behavioral and molecular ecology studies.
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Affiliation(s)
- Andrea Contina
- Oklahoma Biological Survey, University of Oklahoma, Norman, Oklahoma, USA
| | - Eli S Bridge
- Oklahoma Biological Survey, University of Oklahoma, Norman, Oklahoma, USA
| | - Jeffrey F Kelly
- Oklahoma Biological Survey, University of Oklahoma, Norman, Oklahoma, USA.,Department of Biology, University of Oklahoma, Norman, Oklahoma, USA
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21
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Mettler R, Segelbacher G, Schaefer HM. Interactions between a Candidate Gene for Migration (ADCYAP1), Morphology and Sex Predict Spring Arrival in Blackcap Populations. PLoS One 2015; 10:e0144587. [PMID: 26684459 PMCID: PMC4684316 DOI: 10.1371/journal.pone.0144587] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 11/21/2015] [Indexed: 11/19/2022] Open
Abstract
Avian research has begun to reveal associations between candidate genes and migratory behaviors of captive birds, yet few studies utilize genotypic, morphometric, and phenological data from wild individuals. Previous studies have identified an association between ADCYAP1 polymorphism and autumn migratory behavior (restlessness, or zugunruhe), but little is known about the relationship between ADCYAP1 and spring migratory behavior. The timing of spring migration and arrival to the breeding ground are phenological traits which could be particularly favorable for establishing territories and acquiring mates, thus important to fitness and reproductive success. Here, we investigated how individual genotypic ADCYAP1 variation and phenotypic variation (wing length and shape) of blackcaps (Sylvia atricapilla) affect spring arrival date across nine natural populations in Europe. We hypothesized that longer alleles should be associated with earlier spring arrival dates and expected the effect on arrival date to be stronger for males as they arrive earlier. However, we found that longer wings were associated with earlier spring arrival to the breeding grounds for females, but not for males. Another female-specific effect indicated an interaction between ADCYAP1 allele size and wing pointedness on the response of spring arrival: greater allele size had a positive effect on spring arrival date for females with rounder wings, while a negative effect was apparent for females with more pointed wings. Also, female heterozygotes with pointed wing tips arrived significantly earlier than both homozygotes with pointed wings and heterozygotes with round wings. Stable isotope ratios (δ2H) of a subset of blackcaps captured in Freiburg in 2011 allowed us also to assign individuals to their main overwintering areas in northwest (NW) and southwest (SW) Europe. NW males arrived significantly earlier to the Freiburg breeding site than both SW males and females in 2011. NW females had more pointed wing tips compared to SW females, but no difference in ADCYAP1 allele size was found between the different migration routes.
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Affiliation(s)
- Raeann Mettler
- Department of Evolutionary Biology and Animal Ecology, University of Freiburg, Freiburg, Germany
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota, United States of America
- * E-mail:
| | - Gernot Segelbacher
- Wildlife Ecology and Management, University of Freiburg, Freiburg, Germany
| | - H. Martin Schaefer
- Department of Evolutionary Biology and Animal Ecology, University of Freiburg, Freiburg, Germany
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22
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Edwards HA, Hajduk GK, Durieux G, Burke T, Dugdale HL. No Association between Personality and Candidate Gene Polymorphisms in a Wild Bird Population. PLoS One 2015; 10:e0138439. [PMID: 26473495 PMCID: PMC4608812 DOI: 10.1371/journal.pone.0138439] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/31/2015] [Indexed: 02/06/2023] Open
Abstract
Consistency of between-individual differences in behaviour or personality is a phenomenon in populations that can have ecological consequences and evolutionary potential. One way that behaviour can evolve is to have a genetic basis. Identifying the molecular genetic basis of personality could therefore provide insight into how and why such variation is maintained, particularly in natural populations. Previously identified candidate genes for personality in birds include the dopamine receptor D4 (DRD4), and serotonin transporter (SERT). Studies of wild bird populations have shown that exploratory and bold behaviours are associated with polymorphisms in both DRD4 and SERT. Here we tested for polymorphisms in DRD4 and SERT in the Seychelles warbler (Acrocephalus sechellensis) population on Cousin Island, Seychelles, and then investigated correlations between personality and polymorphisms in these genes. We found no genetic variation in DRD4, but identified four polymorphisms in SERT that clustered into five haplotypes. There was no correlation between bold or exploratory behaviours and SERT polymorphisms/haplotypes. The null result was not due to lack of power, and indicates that there was no association between these behaviours and variation in the candidate genes tested in this population. These null findings provide important data to facilitate representative future meta-analyses on candidate personality genes.
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Affiliation(s)
- Hannah A. Edwards
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- * E-mail:
| | - Gabriela K. Hajduk
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Gillian Durieux
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Hannah L. Dugdale
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
- Groningen Institute for Evolutionary Life Sciences, University of Groningen, Groningen, The Netherlands
- Nature Seychelles, Mahe, Republic of Seychelles
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23
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Bourret A, Garant D. Candidate gene-environment interactions and their relationships with timing of breeding in a wild bird population. Ecol Evol 2015; 5:3628-41. [PMID: 26380692 PMCID: PMC4567867 DOI: 10.1002/ece3.1630] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/09/2015] [Accepted: 07/13/2015] [Indexed: 11/22/2022] Open
Abstract
Monitoring and predicting evolutionary changes underlying current environmental modifications are complex challenges. Recent approaches to achieve these objectives include assessing the genetic variation and effects of candidate genes on traits indicating adaptive potential. In birds, for example, short tandem repeat polymorphism at four candidate genes (CLOCK, NPAS2, ADCYAP1, and CREB1) has been linked to variation in phenological traits such as laying date and timing of migration. However, our understanding of their importance as evolutionary predictors is still limited, mainly because the extent of genotype–environment interactions (GxE) related to these genes has yet to be assessed. Here, we studied a population of Tree swallow (Tachycineta bicolor) over 4 years in southern Québec (Canada) to assess the relationships between those four candidate genes and two phenological traits related to reproduction (laying date and incubation duration) and also determine the importance of GxE in this system. Our results showed that NPAS2 female genotypes were nonrandomly distributed across the study system and formed a longitudinal cline with longer genotypes located to the east. We observed relationships between length polymorphism at all candidate genes and laying date and/or incubation duration, and most of these relationships were affected by environmental variables (breeding density, latitude, or temperature). In particular, the positive relationships detected between laying date and both CLOCK and NPAS2 female genotypes were variable depending on breeding density. Our results suggest that all four candidate genes potentially affect timing of breeding in birds and that GxE are more prevalent and important than previously reported in this context.
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Affiliation(s)
- Audrey Bourret
- Département de biologie, Université de Sherbrooke 2500 boulevard de l'Université, Sherbrooke, QC, J1K 2R1, Canada
| | - Dany Garant
- Département de biologie, Université de Sherbrooke 2500 boulevard de l'Université, Sherbrooke, QC, J1K 2R1, Canada
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24
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Saino N, Bazzi G, Gatti E, Caprioli M, Cecere JG, Possenti CD, Galimberti A, Orioli V, Bani L, Rubolini D, Gianfranceschi L, Spina F. Polymorphism at theClockgene predicts phenology of long-distance migration in birds. Mol Ecol 2015; 24:1758-73. [DOI: 10.1111/mec.13159] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 03/13/2015] [Accepted: 03/13/2015] [Indexed: 11/27/2022]
Affiliation(s)
- Nicola Saino
- Department of Biosciences; University of Milan; via Celoria 26 Milan I-20133 Italy
| | - Gaia Bazzi
- Department of Biosciences; University of Milan; via Celoria 26 Milan I-20133 Italy
| | - Emanuele Gatti
- Department of Biosciences; University of Milan; via Celoria 26 Milan I-20133 Italy
| | - Manuela Caprioli
- Department of Biosciences; University of Milan; via Celoria 26 Milan I-20133 Italy
| | - Jacopo G. Cecere
- ISPRA-Italian Institute for Environmental Protection and Research; Via Cà Fornacetta 9 Ozzano dell'Emilia I-40064 Italy
| | - Cristina D. Possenti
- Department of Biosciences; University of Milan; via Celoria 26 Milan I-20133 Italy
| | - Andrea Galimberti
- Department of Biotechnology and Biosciences; University of Milano-Bicocca; Piazza della Scienza 2 Milan I-20126 Italy
| | - Valerio Orioli
- Department of Earth and Environmental Sciences; University of Milano-Bicocca; Piazza della Scienza 1 Milan I-20126 Italy
| | - Luciano Bani
- Department of Earth and Environmental Sciences; University of Milano-Bicocca; Piazza della Scienza 1 Milan I-20126 Italy
| | - Diego Rubolini
- Department of Biosciences; University of Milan; via Celoria 26 Milan I-20133 Italy
| | - Luca Gianfranceschi
- Department of Biosciences; University of Milan; via Celoria 26 Milan I-20133 Italy
| | - Fernando Spina
- ISPRA-Italian Institute for Environmental Protection and Research; Via Cà Fornacetta 9 Ozzano dell'Emilia I-40064 Italy
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25
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Delmore KE, Hübner S, Kane NC, Schuster R, Andrew RL, Câmara F, Guigó R, Irwin DE. Genomic analysis of a migratory divide reveals candidate genes for migration and implicates selective sweeps in generating islands of differentiation. Mol Ecol 2015; 24:1873-88. [DOI: 10.1111/mec.13150] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 03/06/2015] [Accepted: 03/06/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Kira E. Delmore
- Department of Zoology; University of British Columbia; 6270 University Blvd Vancouver BC Canada V6T1Z4
| | - Sariel Hübner
- Department of Botany; University of British Columbia; 6270 University Blvd Vancouver BC Canada V6T1Z4
| | - Nolan C. Kane
- Ecology and Evolutionary Biology; University of Colorado at Boulder; Ramaley N122 Boulder CO 80309-0334 USA
| | - Richard Schuster
- Department of Forest and Conservation Sciences; University of British Columbia; 2424 Main Mall Vancouver BC Canada V6T1Z4
| | - Rose L. Andrew
- Molecular Ecology School of Environmental and Rural Science; University of New England Armidale; Armidale NSW 2351 Australia
| | - Francisco Câmara
- Centre for Genomic Regulation and UPF; Dr Aiguader 88 Barcelona 08003 Spain
| | - Roderic Guigó
- Centre for Genomic Regulation and UPF; Dr Aiguader 88 Barcelona 08003 Spain
| | - Darren E. Irwin
- Department of Zoology; University of British Columbia; 6270 University Blvd Vancouver BC Canada V6T1Z4
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26
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Influence of ecological and geological features on rangewide patterns of genetic structure in a widespread passerine. Heredity (Edinb) 2014; 114:143-54. [PMID: 25074576 DOI: 10.1038/hdy.2014.64] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2013] [Revised: 05/29/2014] [Accepted: 06/03/2014] [Indexed: 01/22/2023] Open
Abstract
Geological and ecological features restrict dispersal and gene flow, leading to isolated populations. Dispersal barriers can be obvious physical structures in the landscape; however microgeographic differences can also lead to genetic isolation. Our study examined dispersal barriers at both macro- and micro-geographical scales in the black-capped chickadee, a resident North American songbird. Although birds have high dispersal potential, evidence suggests dispersal is restricted by barriers. The chickadee's range encompasses a number of physiological features which may impede movement and lead to divergence. Analyses of 913 individuals from 34 sampling sites across the entire range using 11 microsatellite loci revealed as many as 13 genetic clusters. Populations in the east were largely panmictic whereas populations in the western portion of the range showed significant genetic structure, which often coincided with large mountain ranges, such as the Cascade and Rocky Mountains, as well as areas of unsuitable habitat. Unlike populations in the central and southern Rockies, populations on either side of the northern Rockies were not genetically distinct. Furthermore, Northeast Oregon represents a forested island within the Great Basin; genetically isolated from all other populations. Substructuring at the microgeographical scale was also evident within the Fraser Plateau of central British Columbia, and in the southeast Rockies where no obvious physical barriers are present, suggesting additional factors may be impeding dispersal and gene flow. Dispersal barriers are therefore not restricted to large physical structures, although mountain ranges and large water bodies do play a large role in structuring populations in this study.
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27
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Ruegg K, Anderson EC, Boone J, Pouls J, Smith TB. A role for migration-linked genes and genomic islands in divergence of a songbird. Mol Ecol 2014; 23:4757-69. [PMID: 24954641 DOI: 10.1111/mec.12842] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Revised: 06/13/2014] [Accepted: 06/18/2014] [Indexed: 02/02/2023]
Abstract
Next-generation sequencing has made it possible to begin asking questions about the process of divergence at the level of the genome. For example, recently, there has been a debate around the role of 'genomic islands of divergence' (i.e. blocks of outlier loci) in facilitating the process of speciation-with-gene-flow. The Swainson's thrush, Catharus ustulatus, is a migratory songbird with two genetically distinct subspecies that differ in a number of traits known to be involved in reproductive isolation in birds (plumage coloration, song and migratory behaviour), despite contemporary gene flow along a secondary contact zone. Here, we use RAD-PE sequencing to test emerging hypotheses about the process of divergence at the level of the genome and identify genes and gene regions involved in differentiation in this migratory songbird. Our analyses revealed distinct genomic islands on 15 of the 23 chromosomes and an accelerated rate of divergence on the Z chromosome, one of the avian sex chromosomes. Further, an analysis of loci linked to traits known to be involved in reproductive isolation in songbirds showed that genes linked to migration are significantly more differentiated than expected by chance, but that these genes lie primarily outside the genomic islands. Overall, our analysis supports the idea that genes linked to migration play an important role in divergence in migratory songbirds, but we find no compelling evidence that the observed genomic islands are facilitating adaptive divergence in migratory behaviour.
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Affiliation(s)
- Kristen Ruegg
- Center for Tropical Research, Institute of the Environment and Sustainability, University of California, Los Angeles, La Kretz Hall, Suite 300, 619 Charles E. Young Dr. East, Los Angeles, CA, 90095, USA; Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA, 95060, USA
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28
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Villavicencio CP, Apfelbeck B, Goymann W. Parental care, loss of paternity and circulating levels of testosterone and corticosterone in a socially monogamous song bird. Front Zool 2014; 11:11. [PMID: 24517241 PMCID: PMC3932846 DOI: 10.1186/1742-9994-11-11] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Accepted: 02/09/2014] [Indexed: 11/29/2022] Open
Abstract
Introduction In biparental birds testosterone levels of males are typically high during the mating phase and decrease during the parental phase. Testosterone implants may enhance mating behaviors, increase the likelihood of males to engage in extra-pair mating behavior and may reduce paternal care. Thus, sex steroids such as testosterone influence reproductive behaviors. Little is known, however, as to whether the more subtle differences in physiological concentrations of testosterone that occur between individuals are related to differences in paternal care, extra-pair behavior, and genetic paternity between those males. Here, we investigate these relationships in the male black redstart (Phoenicurus ochruros), a socially monogamous songbird with a low breeding synchrony. We used nestling provisioning as a proxy for parental care behavior and genetic paternity loss as a proxy for the efficiency of mate-guarding. Results There was no relationship between nestling provisioning and paternity loss of males. Baseline and gonadotropin releasing hormone (GnRH)-induced levels of testosterone, but not baseline corticosterone, were significantly higher during the mating than during the provisioning phase. Males fed more often when temperatures decreased and fed less when they sang more, but we found no correlation between parental behavior and baseline or GnRH-induced testosterone, and baseline corticosterone – both measured during either the mating or the parental phase. However, males that experienced loss of paternity had lower levels of testosterone during the provisioning phase than males that did not lose paternity. Further, males that lost paternity also expressed higher baseline levels of corticosterone. Conclusions Physiological differences in testosterone or baseline corticosterone were not related to differences in parental care, suggesting that the variation of testosterone within a physiological range may not relate to the degree of paternal care in this species. However, the profile of both hormones may indicate quality traits that influence the likelihood of the respective male to lose paternity.
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Affiliation(s)
- Camila P Villavicencio
- Abteilung für Verhaltensneurobiologie, Max-Planck-Institut für Ornithologie, Eberhard-Gwinner-Str, 6a, D-82319 Seewiesen, Germany.
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29
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Chakarov N, Jonker RM, Boerner M, Hoffman JI, Krüger O. Variation at phenological candidate genes correlates with timing of dispersal and plumage morph in a sedentary bird of prey. Mol Ecol 2013; 22:5430-40. [DOI: 10.1111/mec.12493] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 07/19/2013] [Accepted: 08/08/2013] [Indexed: 11/29/2022]
Affiliation(s)
- Nayden Chakarov
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
| | - Rudy M. Jonker
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
| | - Martina Boerner
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
| | - Joseph I. Hoffman
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
| | - Oliver Krüger
- Department of Animal Behaviour; Bielefeld University; PO Box 10 01 31 33501 Bielefeld Germany
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30
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Peterson MP, Abolins-Abols M, Atwell JW, Rice RJ, Milá B, Ketterson ED. Variation in candidate genes CLOCK and ADCYAP1 does not consistently predict differences in migratory behavior in the songbird genus Junco. F1000Res 2013; 2:115. [PMID: 24627781 PMCID: PMC3907158 DOI: 10.12688/f1000research.2-115.v1] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/22/2013] [Indexed: 11/20/2022] Open
Abstract
Recent studies exploring the molecular genetic basis for migratory variation in animals have identified polymorphisms in two genes (
CLOCK and ADCYAP1) that are linked to circadian rhythms and correlate with migratory propensity and phenology among individuals and populations. Results from these initial studies are mixed, however, and additional data are needed to assess the generality and diversity of the molecular mechanisms that regulate the biology of migration. We sequenced CLOCK and ADCYAP1 in 15 populations across the two species of the avian genus
Junco, a North American lineage in which multiple recently diverged subspecies and populations range from sedentary to long-distance migrants. We found no consistent associations between allele length and migratory status across the genus for either CLOCK or ADCYAP1. However, within two subspecies groups, populations that migrate longer distances have longer CLOCK alleles on average. Additionally, there was a positive relationship between ADCYAP1 allele length and migratory restlessness (zugunruhe) among individuals within one of two captive populations studied—a result similar to those reported previously within captive blackcaps (
Sylvia atricapilla). We conclude that, while both ADCYAP1 and CLOCK may correlate with migratory propensity within or among certain populations or species, previously identified relationships between migratory behavior and sequence variants cannot be easily generalized across taxa.
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Affiliation(s)
- Mark P Peterson
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington IN, 47408, USA
| | - Mikus Abolins-Abols
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington IN, 47408, USA
| | - Jonathan W Atwell
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington IN, 47408, USA
| | - Rebecca J Rice
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington IN, 47408, USA
| | - Borja Milá
- National Museum of Natural Sciences, Spanish Research Council (CSIC), Madrid, 28006, Spain
| | - Ellen D Ketterson
- Department of Biology and Center for the Integrative Study of Animal Behavior, Indiana University, Bloomington IN, 47408, USA
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31
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Mueller JC, Partecke J, Hatchwell BJ, Gaston KJ, Evans KL. Candidate gene polymorphisms for behavioural adaptations during urbanization in blackbirds. Mol Ecol 2013; 22:3629-37. [PMID: 23495914 DOI: 10.1111/mec.12288] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2012] [Revised: 02/04/2013] [Accepted: 02/04/2013] [Indexed: 02/06/2023]
Abstract
Successful urban colonization by formerly rural species represents an ideal situation in which to study adaptation to novel environments. We address this issue using candidate genes for behavioural traits that are expected to play a role in such colonization events. We identified and genotyped 16 polymorphisms in candidate genes for circadian rhythms, harm avoidance and migratory and exploratory behaviour in 12 paired urban and rural populations of the blackbird Turdus merula across the Western Palaearctic. An exonic microsatellite in the SERT gene, a candidate gene for harm avoidance behaviour, exhibited a highly significant association with habitat type in an analysis conducted across all populations. Genetic divergence at this locus was consistent in 10 of the 12 population pairs; this contrasts with previously reported stochastic genetic divergence between these populations at random markers. Our results indicate that behavioural traits related to harm avoidance and associated with the SERT polymorphism experience selection pressures during most blackbird urbanization events. These events thus appear to be influenced by homogeneous adaptive processes in addition to previously reported demographic founder events.
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Affiliation(s)
- J C Mueller
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany.
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32
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Testing for associations between candidate genes for circadian rhythms and individual variation in sleep behaviour in blue tits. Genetica 2012; 140:219-28. [PMID: 22922941 DOI: 10.1007/s10709-012-9673-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 08/07/2012] [Indexed: 12/25/2022]
Abstract
The regulation of sleep in animals is controlled by environmental factors, homeostatic mechanisms and endogenous circadian oscillators. The molecular mechanisms underlying such circadian oscillators have been described in detail and a variety of genes that are components of these molecular clocks have been reported. In addition to inter-specific variation in the temporal organization of sleep, there is significant intra-specific variation in different organisms. From numerous studies in humans it is known that polymorphisms in the regulatory clock genes are causing such variation but knowledge about associations between naturally occurring polymorphisms and sleep patterns in wild animals is scarce. In this study, we investigated the phenotypic sleep correlates of eleven previously described polymorphisms in seven candidate genes within a free-living blue tit Cyanistes caeruleus population. We detected associations between four single nucleotide polymorphisms and three of the nine tested sleep parameters representing temporal organization. Awakening time was associated with polymorphisms in AANAT and PERIOD2, morning latency with a polymorphism in CKIε and the duration of the longest sleep bout with a second polymorphism in AANAT. However, by a permutation procedure we showed that the number of significant results and the most significant association has a study-wide likelihood of 46.7 and 5.9 % respectively. Further replication studies are needed to evaluate the potential associations.
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33
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Dor R, Lovette IJ, Safran RJ, Billerman SM, Huber GH, Vortman Y, Lotem A, McGowan A, Evans MR, Cooper CB, Winkler DW. Low variation in the polymorphic Clock gene poly-Q region despite population genetic structure across barn swallow (Hirundo rustica) populations. PLoS One 2011; 6:e28843. [PMID: 22216124 PMCID: PMC3244424 DOI: 10.1371/journal.pone.0028843] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 11/16/2011] [Indexed: 01/17/2023] Open
Abstract
Recent studies of several species have reported a latitudinal cline in the circadian clock gene, Clock, which influences rhythms in both physiology and behavior. Latitudinal variation in this gene may hence reflect local adaptation to seasonal variation. In some bird populations, there is also an among-individual association between Clock poly-Q genotype and clutch initiation date and incubation period. We examined Clock poly-Q allele variation in the Barn Swallow (Hirundo rustica), a species with a cosmopolitan geographic distribution and considerable variation in life-history traits that may be influenced by the circadian clock. We genotyped Barn Swallows from five populations (from three subspecies) and compared variation at the Clock locus to that at microsatellite loci and mitochondrial DNA (mtDNA). We found very low variation in the Clock poly-Q region, as >96% of individuals were homozygous, and the two other alleles at this locus were globally rare. Genetic differentiation based on the Clock poly-Q locus was not correlated with genetic differentiation based on either microsatellite loci or mtDNA sequences. Our results show that high diversity in Clock poly-Q is not general across avian species. The low Clock variation in the background of heterogeneity in microsatellite and mtDNA loci in Barn Swallows may be an outcome of stabilizing selection on the Clock locus.
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Affiliation(s)
- Roi Dor
- Fuller Evolutionary Biology Program, Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA.
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34
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Mueller JC, Pulido F, Kempenaers B. Identification of a gene associated with avian migratory behaviour. Proc Biol Sci 2011; 278:2848-56. [PMID: 21325325 PMCID: PMC3145181 DOI: 10.1098/rspb.2010.2567] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Bird migration is one of the most spectacular and best-studied phenomena in behavioural biology. Yet, while the patterns of variation in migratory behaviour and its ecological causes have been intensively studied, its genetic, physiological and neurological control remains poorly understood. The lack of knowledge of the molecular basis of migration is currently not only limiting our insight into the proximate control of migration, but also into its evolution. We investigated polymorphisms in the exons of six candidate genes for key behavioural traits potentially linked to migration, which had previously been identified in several bird species, and eight control loci in 14 populations of blackcaps (Sylvia atricapilla), representing the whole range of geographical variation in migration patterns found in this species, with the aim of identifying genes controlling variation in migration. We found a consistent association between a microsatellite polymorphism and migratory behaviour only at one candidate locus: the ADCYAP1 gene. This polymorphism explained about 2.6 per cent of the variation in migratory tendency among populations, and 2.7–3.5% of variation in migratory restlessness among individuals within two independent populations. In all tests, longer alleles were associated with higher migratory activity. The consistency of results among different populations and levels of analysis suggests that ADCYAP1 is one of the genes controlling the expression of migratory behaviour. Moreover, the multiple described functions of the gene product indicate that this gene might act at multiple levels modifying the shift between migratory and non-migratory states.
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Affiliation(s)
- Jakob C Mueller
- Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319 Starnberg, Germany.
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35
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Korsten P, Mueller JC, Hermannstädter C, Bouwman KM, Dingemanse NJ, Drent PJ, Liedvogel M, Matthysen E, van Oers K, van Overveld T, Patrick SC, Quinn JL, Sheldon BC, Tinbergen JM, Kempenaers B. Association between DRD4 gene polymorphism and personality variation in great tits: a test across four wild populations. Mol Ecol 2010; 19:832-43. [PMID: 20070517 DOI: 10.1111/j.1365-294x.2009.04518.x] [Citation(s) in RCA: 85] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Polymorphisms in the dopamine receptor D4 gene (DRD4) have been related to individual variation in novelty-seeking or exploratory behaviour in a variety of animals, including humans. Recently, the human DRD4 orthologue was sequenced in a wild bird, the great tit (Parus major) and a single nucleotide polymorphism in exon 3 of this gene (SNP830) was shown to be associated with variation in exploratory behaviour of lab-raised individuals originating from a single wild population. Here we test the generality of this finding in a large sample of free-living individuals from four European great tit populations, including the originally sampled population. We demonstrate that the association between SNP830 genotype and exploratory behaviour also exists in free-living birds from the original population. However, in the other three populations we found only limited evidence for an association: in two populations the association appeared absent; while in one there was a nonsignificant tendency. We could not confirm a previously demonstrated interaction with another DRD4 polymorphism, a 15 bp indel in the promoter region (ID15). As yet unknown differences in genetic or environmental background could explain why the same genetic polymorphism (SNP830) has a substantial effect on exploratory behaviour in one population, explaining 4.5-5.8% of the total variance-a large effect for a single gene influencing a complex behavioural trait-but not in three others. The confirmation of an association between SNP830 genotype and personality-related behaviour in a wild bird population warrants further research into potential fitness effects of the polymorphism, while also the population differences in the strength of the association deserve further investigation. Another important future challenge is the identification of additional loci influencing avian personality traits in the wild.
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Affiliation(s)
- Peter Korsten
- Department of Behavioural Ecology & Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany
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36
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Olano-Marin J, Dawson DA, Girg A, Hansson B, Ljungqvist M, Kempenaers B, Mueller JC. A genome-wide set of 106 microsatellite markers for the blue tit (Cyanistes caeruleus). Mol Ecol Resour 2009; 10:516-32. [PMID: 21565051 DOI: 10.1111/j.1755-0998.2009.02777.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have characterized a set of 106 microsatellite markers in 26-127 individual blue tits (Cyanistes caeruleus), and assigned their location on the zebra finch (Taeniopygia guttata) and on the chicken (Gallus gallus) genome on the basis of sequence homology. Thirty-one markers are newly designed from zebra finch EST (expressed sequence tags) sequences, 22 markers were developed by others from EST sequences using different methods and the remaining 53 loci were previously designed or modified passerine markers. The 106 microsatellite markers are distributed over 26 and 24 chromosomes in the zebra finch and in the chicken genome respectively and the number of alleles varies between 2 and 49. Eight loci deviate significantly from Hardy-Weinberg equilibrium and show a high frequency of null alleles, and three pairs of markers located in the same chromosome appear to be in linkage disequilibrium. With the exception of these few loci, the polymorphic microsatellite markers presented here provide a useful genome-wide resource for population and evolutionary genetic studies of the blue tit, in addition to their potential utility in other passerine birds.
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Affiliation(s)
- Juanita Olano-Marin
- Department of Behavioral Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Postfach 1564, D-82305 Starnberg (Seewiesen), Germany Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK Department of Animal Ecology, Ecology Building, Lund University, SE-223 62 Lund, Sweden
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