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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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Hedlund J, Fransson T, Kullberg C, Persson J, Jakobsson S. Increase in protandry over time in a long‐distance migratory bird. Ecol Evol 2022; 12:e9037. [PMID: 35813931 PMCID: PMC9257377 DOI: 10.1002/ece3.9037] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 05/20/2022] [Accepted: 05/25/2022] [Indexed: 11/15/2022] Open
Abstract
Protandry is a widespread life‐history phenomenon describing how males precede females at the site or state of reproduction. In migratory birds, protandry has an important influence on individual fitness, the migratory syndrome, and phenological response to climate change. Despite its significance, accurate analyses on the dynamics of protandry using data sets collected at the breeding site, are lacking. Basing our study on records collected during two time periods, 1979 to 1988 and 2006 to 2016, we aim to investigate protandry dynamics over 38 years in a breeding population of willow warblers (Phylloscopus trochilus). Change in the timing of arrival was analyzed in males and females, and protandry (number of days between male and female arrival) was investigated both at population level and within breeding pairs. Our results show advancement in the arrival time at the breeding site in both sexes, but male arrival has advanced to a greater extent, leading to an increase in protandry both at the population level and within breeding pairs. We did not observe any change in sex ratio that could explain the protandry increase, but pronounced temperature change has occurred and been reported in the breeding area and along the migratory route. Typically, natural selection opposes too early arrival in males, but given warmer springs, this counteracting force may be relaxing, enabling an increase in protandry. We discuss whether our results suggest that climate change has induced sex‐specific effects, if these could be evolutionary and whether the timing of important life‐history stages such as arrival at the breeding site may change at different rates in males and females following environmental shifts.
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Affiliation(s)
- Johanna Hedlund
- Centre for Ecology and Conservation, College of Life and Environmental Sciences University of Exeter Penryn UK
- Lund University Lund Sweden
| | - Thord Fransson
- Department of Environmental Research and Monitoring Swedish Museum of Natural History Stockholm Sweden
| | | | | | - Sven Jakobsson
- Department of Zoology Stockholm University Stockholm Sweden
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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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Parody-Merino ÁM, Battley PF, Conklin JR, Fidler AE. No evidence for an association between Clock gene allelic variation and migration timing in a long-distance migratory shorebird (Limosa lapponica baueri). Oecologia 2019; 191:843-859. [PMID: 31659437 DOI: 10.1007/s00442-019-04524-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 10/01/2019] [Indexed: 01/09/2023]
Abstract
The gene Clock is a key part of the Core Circadian Oscillator, and the length of the polyglutamine (poly-Q) repeat sequence in Clock (ClkpolyQcds) has been proposed to be associated with the timing of annual cycle events in birds. We tested whether variation in ClkpolyQcds corresponds to variation in migration timing in the bar-tailed godwit (Limosa lapponica baueri), a species in which individuals show strong annual consistency in their migration timing despite the New Zealand population migrating across a 5-week period. We describe allelic variation of the ClkpolyQcds in 135 godwits over-wintering in New Zealand (N.Z.) and investigate whether polymorphism in this region is associated with northward migration timing (chronophenotype) from N.Z. or (for 32 birds tracked by geolocator) after the primary stopover in Asia. Six Clock alleles were detected (Q7‒Q12) and there was substantial variation between individuals (heterozygosity of 0.79). There was no association between ClkpolyQcds polymorphism and migration timing from N.Z. The length of the shorter Clock allele was related to migration timing from Asia, though this relationship arose largely from just a few northern-breeding birds with longer alleles. Other studies show no consistent associations between ClkpolyQcds and migration timing in birds, although Clock may be associated with breeding latitude in some species (as an adaptation to photoperiodic regime). Apparent relationships with migration timing could reflect latitude-related variation in migration timing, rather than Clock directly affecting migration timing. On current evidence, ClkpolyQcds is not a strong candidate for driving migration timing in migratory birds generally.
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Affiliation(s)
- Ángela M Parody-Merino
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand.
| | - Phil F Battley
- Wildlife and Ecology Group, School of Agriculture and Environment, Massey University, Palmerston North, 4442, New Zealand
| | - Jesse R Conklin
- Conservation Ecology Group, University of Groningen, 9700 AB, Groningen, The Netherlands
| | - Andrew E Fidler
- Institute of Marine Science, University of Auckland, Auckland, 1142, New Zealand
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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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Hau M, Dominoni D, Casagrande S, Buck CL, Wagner G, Hazlerigg D, Greives T, Hut RA. Timing as a sexually selected trait: the right mate at the right moment. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0249. [PMID: 28993493 DOI: 10.1098/rstb.2016.0249] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2017] [Indexed: 12/20/2022] Open
Abstract
Sexual selection favours the expression of traits in one sex that attract members of the opposite sex for mating. The nature of sexually selected traits such as vocalization, colour and ornamentation, their fitness benefits as well as their costs have received ample attention in field and laboratory studies. However, sexually selected traits may not always be expressed: coloration and ornaments often follow a seasonal pattern and behaviours may be displayed only at specific times of the day. Despite the widely recognized differences in the daily and seasonal timing of traits and their consequences for reproductive success, the actions of sexual selection on the temporal organization of traits has received only scant attention. Drawing on selected examples from bird and mammal studies, here we summarize the current evidence for the daily and seasonal timing of traits. We highlight that molecular advances in chronobiology have opened exciting new opportunities for identifying the genetic targets that sexual selection may act on to shape the timing of trait expression. Furthermore, known genetic links between daily and seasonal timing mechanisms lead to the hypothesis that selection on one timescale may simultaneously also affect the other. We emphasize that studies on the timing of sexual displays of both males and females from wild populations will be invaluable for understanding the nature of sexual selection and its potential to act on differences within and between the sexes in timing. Molecular approaches will be important for pinpointing genetic components of biological rhythms that are targeted by sexual selection, and to clarify whether these represent core or peripheral components of endogenous clocks. Finally, we call for a renewed integration of the fields of evolution, behavioural ecology and chronobiology to tackle the exciting question of how sexual selection contributes to the evolution of biological clocks.This article is part of the themed issue 'Wild clocks: integrating chronobiology and ecology to understand timekeeping in free-living animals'.
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Affiliation(s)
- Michaela Hau
- Max Planck Institute for Ornithology, Seewiesen, Germany .,Department of Biology, University of Konstanz, Konstanz, Germany
| | - Davide Dominoni
- Department of Animal Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.,Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow, UK
| | | | - C Loren Buck
- Department of Biological Sciences and Center for Bioengineering Innovation, Northern Arizona University, Flagstaff, AZ, USA
| | - Gabriela Wagner
- Department of Arctic and Marine Biology, UiT: the Arctic University of Norway, Tromsø, Norway
| | - David Hazlerigg
- Department of Arctic and Marine Biology, UiT: the Arctic University of Norway, Tromsø, Norway
| | - Timothy Greives
- Department of Biological Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Roelof A Hut
- Chronobiology unit, Groningen Institute for Evolutionary Life Sciences, University of Groningen, The Netherlands
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Bazzi G, Cecere JG, Caprioli M, Gatti E, Gianfranceschi L, Podofillini S, Possenti CD, Ambrosini R, Saino N, Spina F, Rubolini D. Clock gene polymorphism, migratory behaviour and geographic distribution: a comparative study of trans-Saharan migratory birds. Mol Ecol 2016; 25:6077-6091. [PMID: 27862517 DOI: 10.1111/mec.13913] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 10/25/2016] [Accepted: 10/27/2016] [Indexed: 12/18/2022]
Abstract
Migratory behaviour is controlled by endogenous circannual rhythms that are synchronized by external cues, such as photoperiod. Investigations on the genetic basis of circannual rhythmicity in vertebrates have highlighted that variation at candidate 'circadian clock' genes may play a major role in regulating photoperiodic responses and timing of life cycle events, such as reproduction and migration. In this comparative study of 23 trans-Saharan migratory bird species, we investigated the relationships between species-level genetic variation at two candidate genes, Clock and Adcyap1, and species' traits related to migration and geographic distribution, including timing of spring migration across the Mediterranean Sea, migration distance and breeding latitude. Consistently with previous evidence showing latitudinal clines in 'circadian clock' genotype frequencies, Clock allele size increased with breeding latitude across species. However, early- and late-migrating species had similar Clock allele size. Species migrating over longer distances, showing delayed spring migration and smaller phenotypic variance in spring migration timing, had significantly reduced Clock (but not Adcyap1) gene diversity. Phylogenetic confirmatory path analysis suggested that migration date and distance were the most important variables directly affecting Clock gene diversity. Hence, our study supports the hypothesis that Clock allele size increases poleward as a consequence of adaptation to the photoperiodic regime of the breeding areas. Moreover, we show that long-distance migration is associated with lower Clock diversity, coherently with strong stabilizing selection acting on timing of life cycle events in long-distance migratory species, likely resulting from the time constraints imposed by late spring migration.
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Affiliation(s)
- Gaia Bazzi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133, 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
| | - Manuela Caprioli
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133, Milan, Italy
| | - Emanuele Gatti
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133, Milan, Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133, Milan, Italy
| | - Stefano Podofillini
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133, Milan, Italy
| | - Cristina D Possenti
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133, Milan, Italy
| | - Roberto Ambrosini
- Dipartimento di Scienze dell'Ambiente e della Terra (DISAT), Università degli Studi di Milano Bicocca, Piazza della Scienza 1, I-20126, Milan, Italy
| | - Nicola Saino
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133, Milan, Italy
| | - Fernando Spina
- ISPRA - Istituto Superiore per la Protezione e la Ricerca Ambientale, via Cà Fornacetta 9, I-40064, Ozzano dell'Emilia (BO), Italy
| | - Diego Rubolini
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, I-20133, Milan, Italy
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