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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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Bucking the trend of pollinator decline: the population genetics of a range expanding bumblebee. Evol Ecol 2021. [DOI: 10.1007/s10682-021-10111-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Bourdais D, Hance T. Consequence of emergence pattern on inbreeding risk in the aphid parasitoid Aphidius matricariae (Hymenoptera: Braconidae). Chronobiol Int 2019; 36:838-850. [PMID: 30950288 DOI: 10.1080/07420528.2019.1593190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
In insect parasitoids, mating strategy depends on mate availability and is influenced by the spatial and temporal emergence patterns of adults. For quasi-gregarious species, simultaneous emergence favors local mating and reduces search costs for partners while increasing the risk of inbreeding, particularly when only one female parasitizes the initial host patch. Consequently, in inbreeding sensitive species, mating on the place of adult emergence (patch mating) between siblings should be counter selected. In practice, the timing of male and female emergence and of their dispersal influences mate availability and can limit on patch mating. To test the role of these two factors, we analyzed the daily distribution of emergence and patch residence time of a cohort in the aphid parasitoid Aphidius matricariae (Hymenoptera: Braconidae). We observed that adult emergence is concentrated on the morning with males emerging on average before females with some overlaps. A more precise evaluation of emergence pattern within a brood suggests that brothers and sisters rarely emerge at the same time and rapid dispersal of males and females favors off-patch mating. The relationships between timing of emergence including differences between sex and consequences on inbreeding probability in these species are thus discussed.
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Affiliation(s)
- Delphine Bourdais
- a Earth and Life Institute, Biodiversity Research Centre , Université catholique de Louvain , Louvain-la-Neuve , Belgium
| | - Thierry Hance
- a Earth and Life Institute, Biodiversity Research Centre , Université catholique de Louvain , Louvain-la-Neuve , Belgium
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Corrà S, Salvadori R, Bee L, Barbieri V, Mognato M. Analysis of DNA-damage response to ionizing radiation in serum-shock synchronized human fibroblasts. Cell Biol Toxicol 2017; 33:373-388. [PMID: 28466226 PMCID: PMC5493713 DOI: 10.1007/s10565-017-9394-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 04/20/2017] [Indexed: 12/31/2022]
Abstract
Many aspects of cellular physiology, including cellular response to genotoxic stress, are related to the circadian rhythmicity induced by the molecular clock. The current study investigated if the cellular response to DNA damage is in relation to endogenous expression levels of the PER2 protein, a key component of the molecular regulatory system that confers rhythmicity in mammalian cells. Human normal fibroblasts (CCD-34Lu) were subjected to serum shock to induce circadian oscillations of the PER2 protein and then irradiated with γ- rays at times corresponding to the trough and peak expression of the PER2 protein. To better examine cellular response to DNA damage, the experiments performed in this study were carried out in non-proliferating CCD-34Lu fibroblasts in order to maintain the cell and circadian cycles separated while they were being exposed to genotoxic stress. Study results demonstrated that clonogenic cell survival, double-strand break repair kinetics, and TP53 protein levels were affected in the cells irradiated at the trough than in those irradiated at peak expression of the PER2 protein.
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Affiliation(s)
- Samantha Corrà
- Department of Biology, School of Sciences, University of Padova, via U. Bassi 58 B, 35131, Padova, Italy
| | - Riccardo Salvadori
- Department of Biology, School of Sciences, University of Padova, via U. Bassi 58 B, 35131, Padova, Italy
| | - Leonardo Bee
- Department of Biology, School of Sciences, University of Padova, via U. Bassi 58 B, 35131, Padova, Italy.,Menarini Silicon Biosystems, 10355 Science Center Dr #210, San Diego, CA, 92121, USA
| | - Vito Barbieri
- Department of Surgical, Oncological and Gastroenteric Sciences, University of Padova, via Giustiniani 2, Padova, Italy
| | - Maddalena Mognato
- Department of Biology, School of Sciences, University of Padova, via U. Bassi 58 B, 35131, Padova, Italy.
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Hänniger S, Dumas P, Schöfl G, Gebauer-Jung S, Vogel H, Unbehend M, Heckel DG, Groot AT. Genetic basis of allochronic differentiation in the fall armyworm. BMC Evol Biol 2017; 17:68. [PMID: 28264650 PMCID: PMC5339952 DOI: 10.1186/s12862-017-0911-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 02/14/2017] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Very little is known on how changes in circadian rhythms evolve. The noctuid moth Spodoptera frugiperda (Lepidoptera: Noctuidae) consists of two strains that exhibit allochronic differentiation in their mating time, which acts as a premating isolation barrier between the strains. We investigated the genetic basis of the strain-specific timing differences to identify the molecular mechanisms of differentiation in circadian rhythms. RESULTS Through QTL analyses we identified one major Quantitative trait chromosome (QTC) underlying differentiation in circadian timing of mating activity. Using RADtags, we identified this QTC to be homologous to Bombyx mori C27, on which the clock gene vrille is located, which thus became the major candidate gene. In S. frugiperda, vrille showed strain-specific polymorphisms. Also, vrille expression differed significantly between the strains, with the rice-strain showing higher expression levels than the corn-strain. In addition, RT-qPCR experiments with the other main clock genes showed that pdp1, antagonist of vrille in the modulatory feedback loop of the circadian clock, showed higher expression levels in the rice-strain than in the corn-strain. CONCLUSIONS Together, our results indicate that the allochronic differentiation in the two strains of S. frugiperda is associated with differential transcription of vrille or a cis-acting gene close to vrille, which contributes to the evolution of prezygotic isolation in S. frugiperda.
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Affiliation(s)
- Sabine Hänniger
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Pascaline Dumas
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Gerhard Schöfl
- DKMS Life Science Lab, Fiedlerstr, 34, 01307 Dresden, Germany
| | - Steffi Gebauer-Jung
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Heiko Vogel
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Melanie Unbehend
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - David G. Heckel
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
| | - Astrid T. Groot
- Max Planck Institute for Chemical Ecology, Entomology, Hans-Knöll-Str. 8, 07745 Jena, Germany
- DKMS Life Science Lab, Fiedlerstr, 34, 01307 Dresden, Germany
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O'Grady JF, Hoelters LS, Swain MT, Wilcockson DC. Identification and temporal expression of putative circadian clock transcripts in the amphipod crustacean Talitrus saltator. PeerJ 2016; 4:e2555. [PMID: 27761341 PMCID: PMC5068443 DOI: 10.7717/peerj.2555] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 09/11/2016] [Indexed: 11/20/2022] Open
Abstract
Background Talitrus saltator is an amphipod crustacean that inhabits the supralittoral zone on sandy beaches in the Northeast Atlantic and Mediterranean. T. saltator exhibits endogenous locomotor activity rhythms and time-compensated sun and moon orientation, both of which necessitate at least one chronometric mechanism. Whilst their behaviour is well studied, currently there are no descriptions of the underlying molecular components of a biological clock in this animal, and very few in other crustacean species. Methods We harvested brain tissue from animals expressing robust circadian activity rhythms and used homology cloning and Illumina RNAseq approaches to sequence and identify the core circadian clock and clock-related genes in these samples. We assessed the temporal expression of these genes in time-course samples from rhythmic animals using RNAseq. Results We identified a comprehensive suite of circadian clock gene homologues in T. saltator including the ‘core’ clock genes period (Talper), cryptochrome 2 (Talcry2), timeless (Taltim), clock (Talclk), and bmal1 (Talbmal1). In addition we describe the sequence and putative structures of 23 clock-associated genes including two unusual, extended isoforms of pigment dispersing hormone (Talpdh). We examined time-course RNAseq expression data, derived from tissues harvested from behaviourally rhythmic animals, to reveal rhythmic expression of these genes with approximately circadian period in Talper and Talbmal1. Of the clock-related genes, casein kinase IIβ (TalckIIβ), ebony (Talebony), jetlag (Taljetlag), pigment dispensing hormone (Talpdh), protein phosphatase 1 (Talpp1), shaggy (Talshaggy), sirt1 (Talsirt1), sirt7 (Talsirt7) and supernumerary limbs (Talslimb) show temporal changes in expression. Discussion We report the sequences of principle genes that comprise the circadian clock of T. saltator and highlight the conserved structural and functional domains of their deduced cognate proteins. Our sequencing data contribute to the growing inventory of described comparative clocks. Expression profiling of the identified clock genes illuminates tantalising targets for experimental manipulation to elucidate the molecular and cellular control of clock-driven phenotypes in this crustacean.
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Affiliation(s)
- Joseph F O'Grady
- Institute of Biological, Environmental and Rural Sciences, University of Wales , Aberystwyth , Ceredigion , United Kingdom
| | - Laura S Hoelters
- Institute of Biological, Environmental and Rural Sciences, University of Wales , Aberystwyth , Ceredigion , United Kingdom
| | - Martin T Swain
- Institute of Biological, Environmental and Rural Sciences, University of Wales , Aberystwyth , Ceredigion , United Kingdom
| | - David C Wilcockson
- Institute of Biological, Environmental and Rural Sciences, University of Wales , Aberystwyth , Ceredigion , United Kingdom
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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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Dor R, Cooper CB, Lovette IJ, Massoni V, Bulit F, Liljesthrom M, Winkler DW. Clock gene variation in Tachycineta swallows. Ecol Evol 2012; 2:95-105. [PMID: 22408729 PMCID: PMC3297181 DOI: 10.1002/ece3.73] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 10/14/2011] [Indexed: 11/07/2022] Open
Abstract
Many animals use photoperiod cues to synchronize reproduction with environmental conditions and thereby improve their reproductive success. The circadian clock, which creates endogenous behavioral and physiological rhythms typically entrained to photoperiod, is well characterized at the molecular level. Recent work provided evidence for an association between Clock poly-Q length polymorphism and latitude and, within a population, an association with the date of laying and the length of the incubation period. Despite relatively high overall breeding synchrony, the timing of clutch initiation has a large impact on the fitness of swallows in the genus Tachycineta. We compared length polymorphism in the Clock poly-Q region among five populations from five different Tachycineta species that breed across a hemisphere-wide latitudinal gradient (Fig. 1). Clock poly-Q variation was not associated with latitude; however, there was an association between Clock poly-Q allele diversity and the degree of clutch size decline within breeding seasons. We did not find evidence for an association between Clock poly-Q variation and date of clutch initiation in for any of the five Tachycineta species, nor did we found a relationship between incubation duration and Clock genotype. Thus, there is no general association between latitude, breeding phenology, and Clock polymorphism in this clade of closely related birds.Figure 1Photos of Tachycineta swallows that were used in this study: A) T. bicolor from Ithaca, New York, B) T. leucorrhoa from Chascomús, Argentina, C) T. albilinea from Hill Bank, Belize, D) T. meyeni from Puerto Varas, Chile, and E) T. thalassina from Mono Lake, California, Photographers: B: Valentina Ferretti; A, C-E: David Winkler.
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Affiliation(s)
- Roi Dor
- Cornell Lab of Ornithology, Cornell UniversityIthaca, New York 14850
| | - Caren B Cooper
- Cornell Lab of Ornithology, Cornell UniversityIthaca, New York 14850
| | - Irby J Lovette
- Cornell Lab of Ornithology, Cornell UniversityIthaca, New York 14850
- Department of Ecology and Evolutionary Biology, Cornell UniversityIthaca, New York 14853
| | - Viviana Massoni
- Departamento de Ecología, Genética y Evolución, Facultad de Cs. Exactas y Naturales, Universidad de Buenos AiresCABA, C1428EGA, Argentina
| | - Flor Bulit
- Departamento de Ecología, Genética y Evolución, Facultad de Cs. Exactas y Naturales, Universidad de Buenos AiresCABA, C1428EGA, Argentina
| | - Marcela Liljesthrom
- Centro Austral de Investigaciones CientíficasCADIC-CONICET, Bernardo Houssay 200, V9410BFD Ushuaia, Tierra del Fuego, Argentina
| | - David W Winkler
- Cornell Lab of Ornithology, Cornell UniversityIthaca, New York 14850
- Department of Ecology and Evolutionary Biology, Cornell UniversityIthaca, New York 14853
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Rodriguez-Zas SL, Southey BR, Shemesh Y, Rubin EB, Cohen M, Robinson GE, Bloch G. Microarray analysis of natural socially regulated plasticity in circadian rhythms of honey bees. J Biol Rhythms 2012; 27:12-24. [PMID: 22306970 DOI: 10.1177/0748730411431404] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Honey bee workers care for ("nurse") the brood around the clock without circadian rhythmicity, but then they forage outside with strong circadian rhythms and a consolidated nightly rest. This chronobiological plasticity is associated with variation in the expression of the canonical "clock genes" that regulate the circadian clock: nurse bees show no brain rhythms of expression, while foragers do. These results suggest that the circadian system is organized differently in nurses and foragers. Nurses switch to activity with circadian rhythms shortly after being removed from the hive, suggesting that at least some clock cells in their brain continue to measure time while in the hive. We performed a microarray genome-wide survey to determine general patterns of brain gene expression in nurses and foragers sampled around the clock. We found 160 and 541 transcripts that exhibited significant sinusoidal oscillations in nurses and foragers, respectively, with peaks of expression distributed throughout the day in both task groups. Consistent with earlier studies, transcripts of genes involved in circadian rhythms, including Clockwork Orange that has not been studied before in bees, oscillated in foragers but not in nurses. The oscillating transcripts also were enriched for genes involved in the visual system, "development" and "response to stimuli" (foragers), "muscle contraction" and "microfilament motor gene expression" (nurses), and "generation of precursor metabolites" and "energy" (both). Transcripts of genes encoding P450 enzymes oscillated in both nurses and foragers but with a different phase. This study identified new putative clock-controlled genes in the honey bee and suggests that some brain functions show circadian rhythmicity even in nurse bees that are active around the clock.
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Liedvogel M, Cornwallis CK, Sheldon BC. Integrating candidate gene and quantitative genetic approaches to understand variation in timing of breeding in wild tit populations. J Evol Biol 2012; 25:813-23. [PMID: 22409177 DOI: 10.1111/j.1420-9101.2012.02480.x] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two commonly used techniques for estimating the effect of genes on traits in wild populations are the candidate gene approach and quantitative genetic analyses. However, whether these two approaches measure the same underlying processes remains unresolved. Here, we use these two methods to test whether they are alternative or complementary approaches to understanding genetic variation in the timing of reproduction - a key trait involved in adaptation to climate change - in wild tit populations. Our analyses of the candidate gene Clock show weak correlates with timing variables in blue tits, but no association in great tits, confirming earlier results. Quantitative genetic analyses revealed very low levels of both direct (female) and indirect (male) additive genetic variation in timing traits for both species, in contrast to previous studies on these traits, and much lower than generally assumed. Hence, neither method suggests strong genetic effects on the timing of breeding in birds, and further work should seek to assess the generality of these conclusions. We discuss how differences in the genetic control of traits, species life-history and confounding environmental variables may determine how useful integrating these two techniques is to understand the phenotypic variation in wild populations.
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Affiliation(s)
- Miriam Liedvogel
- Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, UK.
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11
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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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12
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Hut RA, Beersma DGM. Evolution of time-keeping mechanisms: early emergence and adaptation to photoperiod. Philos Trans R Soc Lond B Biol Sci 2011; 366:2141-54. [PMID: 21690131 PMCID: PMC3130368 DOI: 10.1098/rstb.2010.0409] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Virtually all species have developed cellular oscillations and mechanisms that synchronize these cellular oscillations to environmental cycles. Such environmental cycles in biotic (e.g. food availability and predation risk) or abiotic (e.g. temperature and light) factors may occur on a daily, annual or tidal time scale. Internal timing mechanisms may facilitate behavioural or physiological adaptation to such changes in environmental conditions. These timing mechanisms commonly involve an internal molecular oscillator (a 'clock') that is synchronized ('entrained') to the environmental cycle by receptor mechanisms responding to relevant environmental signals ('Zeitgeber', i.e. German for time-giver). To understand the evolution of such timing mechanisms, we have to understand the mechanisms leading to selective advantage. Although major advances have been made in our understanding of the physiological and molecular mechanisms driving internal cycles (proximate questions), studies identifying mechanisms of natural selection on clock systems (ultimate questions) are rather limited. Here, we discuss the selective advantage of a circadian system and how its adaptation to day length variation may have a functional role in optimizing seasonal timing. We discuss various cases where selective advantages of circadian timing mechanisms have been shown and cases where temporarily loss of circadian timing may cause selective advantage. We suggest an explanation for why a circadian timing system has emerged in primitive life forms like cyanobacteria and we evaluate a possible molecular mechanism that enabled these bacteria to adapt to seasonal variation in day length. We further discuss how the role of the circadian system in photoperiodic time measurement may explain differential selection pressures on circadian period when species are exposed to changing climatic conditions (e.g. global warming) or when they expand their geographical range to different latitudes or altitudes.
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Affiliation(s)
- R A Hut
- University of Groningen, Chronobiology Research Unit, Life Science building, Nijenborgh 7, 9747AG Groningen, The Netherlands.
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Visser ME, Caro SP, van Oers K, Schaper SV, Helm B. Phenology, seasonal timing and circannual rhythms: towards a unified framework. Philos Trans R Soc Lond B Biol Sci 2010; 365:3113-27. [PMID: 20819807 PMCID: PMC2981940 DOI: 10.1098/rstb.2010.0111] [Citation(s) in RCA: 196] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Phenology refers to the periodic appearance of life-cycle events and currently receives abundant attention as the effects of global change on phenology are so apparent. Phenology as a discipline observes these events and relates their annual variation to variation in climate. But phenology is also studied in other disciplines, each with their own perspective. Evolutionary ecologists study variation in seasonal timing and its fitness consequences, whereas chronobiologists emphasize the periodic nature of life-cycle stages and their underlying timing programmes (e.g. circannual rhythms). The (neuro-) endocrine processes underlying these life-cycle events are studied by physiologists and need to be linked to genes that are explored by molecular geneticists. In order to fully understand variation in phenology, we need to integrate these different perspectives, in particular by combining evolutionary and mechanistic approaches. We use avian research to characterize different perspectives and to highlight integration that has already been achieved. Building on this work, we outline a route towards uniting the different disciplines in a single framework, which may be used to better understand and, more importantly, to forecast climate change impacts on phenology.
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Affiliation(s)
- Marcel E Visser
- Netherlands Institute of Ecology (NIOO-KNAW), PO Box 40, 6666 ZG Heteren, The Netherlands.
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14
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Abstract
Circadian (approximately 24 h) clock regulated biological rhythms have been identified in a wide range of organisms from prokaryotic unicellular cyanobacteria to higher mammals. These rhythms regulate an enormous variety of processes including gene expression, metabolic processes, activity and reproduction. Given the widespread occurrence of circadian systems it is not surprising that extensive efforts have been directed at understanding the adaptive significance of circadian rhythms. In this review we discuss the approaches and findings that have resulted. In studies on organisms in their natural environments, some species show adaptations in their circadian systems that correlate with living at different latitudes, such as clines in circadian clock properties. Additionally, some species show plasticity in their circadian systems suggested to match the demands of their physical and social environment. A number of experiments, both in the field and in the laboratory, have examined the effects of having a circadian system that does not resonate with the organism's environment. We conclude that the results of these studies suggest that having a circadian system that matches the oscillating environment is adaptive.
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Affiliation(s)
- Shai Yerushalmi
- Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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15
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LIEDVOGEL MIRIAM, SZULKIN MARTA, KNOWLES SARAHCL, WOOD MATTHEWJ, SHELDON BENC. Phenotypic correlates ofClockgene variation in a wild blue tit population: evidence for a role in seasonal timing of reproduction. Mol Ecol 2009; 18:2444-56. [DOI: 10.1111/j.1365-294x.2009.04204.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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16
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Johnsen A, Fidler AE, Kuhn S, Carter KL, Hoffmann A, Barr IR, Biard C, Charmantier A, Eens M, Korsten P, Siitari H, Tomiuk J, Kempenaers B. Avian Clock gene polymorphism: evidence for a latitudinal cline in allele frequencies. Mol Ecol 2007; 16:4867-80. [PMID: 17927702 DOI: 10.1111/j.1365-294x.2007.03552.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
In comparison with most animal behaviours, circadian rhythms have a well-characterized molecular genetic basis. Detailed studies of circadian clock genes in 'model' organisms provide a foundation for interpreting the functional and evolutionary significance of polymorphic circadian clock genes found within free-living animal populations. Here, we describe allelic variation in a region of the avian Clock orthologue which encodes a functionally significant polyglutamine repeat (ClkpolyQcds), within free-living populations of two passerine birds, the migratory bluethroat (Luscinia svecica) and the predominantly nonmigratory blue tit (Cyanistes caeruleus). Multiple ClkpolyQcds alleles were found within populations of both species (bluethroat: 12 populations, 7 alleles; blue tit: 14 populations, 9 alleles). Some populations of both species were differentiated at the ClkpolyQcds locus as measured by F(ST) and R(ST) values. Among the blue tit, but not bluethroat populations, we found evidence of latitudinal clines in (i) mean ClkpolyQcds repeat length, and (ii) the proportions of three ClkpolyQcds genotype groupings. Parallel analyses of microsatellite allele frequencies, which are considered to reflect selectively neutral processes, indicate that interpopulation allele frequency variation at the ClkpolyQcds and microsatellite loci does not reflect the same underlying demographic processes. The possibility that the observed interpopulation ClkpolyQcds allele frequency variation is, at least in part, maintained by selection for microevolutionary adaptation to photoperiodic parameters correlated with latitude warrants further study.
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Affiliation(s)
- A Johnsen
- Max Planck Institute for Ornithology, Department of Behavioural Ecology & Evolutionary Genetics, D-82305 Seewiesen, Germany
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