1
|
Murray M, Wright J, Araya-Ajoy YG. Evolutionary rescue from climate change: male indirect genetic effects on lay-dates and their consequences for population persistence. Evol Lett 2024; 8:137-148. [PMID: 38487362 PMCID: PMC10939382 DOI: 10.1093/evlett/qrad022] [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: 08/30/2022] [Revised: 04/15/2023] [Accepted: 05/03/2023] [Indexed: 03/17/2024] Open
Abstract
Changes in avian breeding phenology are among the most apparent responses to climate change in free-ranging populations. A key question is whether populations will be able to keep up with the expected rates of environmental change. There is a large body of research on the mechanisms by which avian lay-dates track temperature change and the consequences of (mal)adaptation on population persistence. Often overlooked is the role of males, which can influence the lay-date of their mate through their effect on the prelaying environment. We explore how social plasticity causing male indirect genetic effects can help or hinder population persistence when female genes underpinning lay-date and male genes influencing female's timing of reproduction both respond to climate-mediated selection. We extend quantitative genetic moving optimum models to predict the consequences of social plasticity on the maximum sustainable rate of temperature change, and evaluate our model using a combination of simulated data and empirical estimates from the literature. Our results suggest that predictions for population persistence may be biased if indirect genetic effects and cross-sex genetic correlations are not considered and that the extent of this bias depends on sex differences in how environmental change affects the optimal timing of reproduction. Our model highlights that more empirical work is needed to understand sex-specific effects of environmental change on phenology and the fitness consequences for population dynamics. While we discuss our results exclusively in the context of avian breeding phenology, the approach we take here can be generalized to many different contexts and types of social interaction.
Collapse
Affiliation(s)
- Myranda Murray
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Jonathan Wright
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Yimen G Araya-Ajoy
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Birchard K, Driver HG, Ademidun D, Bedolla-Guzmán Y, Birt T, Chown EE, Deane P, Harkness BAS, Morrin A, Masello JF, Taylor RS, Friesen VL. Circadian gene variation in relation to breeding season and latitude in allochronic populations of two pelagic seabird species complexes. Sci Rep 2023; 13:13692. [PMID: 37608061 PMCID: PMC10444859 DOI: 10.1038/s41598-023-40702-8] [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: 10/16/2022] [Accepted: 08/16/2023] [Indexed: 08/24/2023] Open
Abstract
Annual cues in the environment result in physiological changes that allow organisms to time reproduction during periods of optimal resource availability. Understanding how circadian rhythm genes sense these environmental cues and stimulate the appropriate physiological changes in response is important for determining the adaptability of species, especially in the advent of changing climate. A first step involves characterizing the environmental correlates of natural variation in these genes. Band-rumped and Leach's storm-petrels (Hydrobates spp.) are pelagic seabirds that breed across a wide range of latitudes. Importantly, some populations have undergone allochronic divergence, in which sympatric populations use the same breeding sites at different times of year. We investigated the relationship between variation in key functional regions of four genes that play an integral role in the cellular clock mechanism-Clock, Bmal1, Cry2 and Per2-with both breeding season and absolute latitude in these two species complexes. We discovered that allele frequencies in two genes, Clock and Bmal1, differed between seasonal populations in one archipelago, and also correlated with absolute latitude of breeding colonies. These results indicate that variation in these circadian rhythm genes may be involved in allochronic speciation, as well as adaptation to photoperiod at breeding locations.
Collapse
Affiliation(s)
- Katie Birchard
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Apex Resource Management Solutions, Ottawa, ON, K2A 3K2, Canada
| | - Hannah G Driver
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, K1H 8L1, Canada
| | - Dami Ademidun
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
| | | | - Tim Birt
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Erin E Chown
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
| | - Petra Deane
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Mascoma LLC, Lallemand Inc., Lebanon, NH, 03766, USA
| | - Bronwyn A S Harkness
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Environment and Climate Change Canada, Wildlife Research Division, Ottawa, ON, K1S 5B6, Canada
| | - Austin Morrin
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Sims Animal Hospital, Kingston, ON, K7K 7E9, Canada
| | - Juan F Masello
- Department of Animal Behaviour, University of Bielefeld, 33615, Bielefeld, Germany
| | - Rebecca S Taylor
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada
- Environment and Climate Change Canada, Landscape Science and Technology Division, Ottawa, ON, K1S 5R1, Canada
| | - Vicki L Friesen
- Biology Department, Queen's University, Kingston, ON, K7L 3N6, Canada.
| |
Collapse
|
4
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
5
|
de Greef E, Suh A, Thorstensen MJ, Delmore KE, Fraser KC. Genomic architecture of migration timing in a long-distance migratory songbird. Sci Rep 2023; 13:2437. [PMID: 36765096 PMCID: PMC9918537 DOI: 10.1038/s41598-023-29470-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
The impact of climate change on spring phenology poses risks to migratory birds, as migration timing is controlled predominantly by endogenous mechanisms. Despite recent advances in our understanding of the underlying genetic basis of migration timing, the ways that migration timing phenotypes in wild individuals may map to specific genomic regions requires further investigation. We examined the genetic architecture of migration timing in a long-distance migratory songbird (purple martin, Progne subis subis) by integrating genomic data with an extensive dataset of direct migratory tracks. A moderate to large amount of variance in spring migration arrival timing was explained by genomics (proportion of phenotypic variation explained by genomics = 0.74; polygenic score R2 = 0.24). On chromosome 1, a region that was differentiated between migration timing phenotypes contained genes that could facilitate nocturnal flights and act as epigenetic modifiers. Overall, these results advance our understanding of the genomic underpinnings of migration timing.
Collapse
Affiliation(s)
- Evelien de Greef
- Department of Biological Sciences, University of Manitoba, Winnipeg, R3T 2N2, Canada.
| | - Alexander Suh
- Department of Organismal Biology, Uppsala University, 752 36, Uppsala, Sweden
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TU, UK
| | - Matt J Thorstensen
- Department of Biological Sciences, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Kira E Delmore
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Kevin C Fraser
- Department of Biological Sciences, University of Manitoba, Winnipeg, R3T 2N2, Canada
| |
Collapse
|
6
|
Hoban S, Bruford MW, da Silva JM, Funk WC, Frankham R, Gill MJ, Grueber CE, Heuertz M, Hunter ME, Kershaw F, Lacy RC, Lees C, Lopes-Fernandes M, MacDonald AJ, Mastretta-Yanes A, McGowan PJK, Meek MH, Mergeay J, Millette KL, Mittan-Moreau CS, Navarro LM, O'Brien D, Ogden R, Segelbacher G, Paz-Vinas I, Vernesi C, Laikre L. Genetic diversity goals and targets have improved, but remain insufficient for clear implementation of the post-2020 global biodiversity framework. CONSERV GENET 2023; 24:181-191. [PMID: 36683963 PMCID: PMC9841145 DOI: 10.1007/s10592-022-01492-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 11/30/2022] [Indexed: 01/18/2023]
Abstract
Genetic diversity among and within populations of all species is necessary for people and nature to survive and thrive in a changing world. Over the past three years, commitments for conserving genetic diversity have become more ambitious and specific under the Convention on Biological Diversity's (CBD) draft post-2020 global biodiversity framework (GBF). This Perspective article comments on how goals and targets of the GBF have evolved, the improvements that are still needed, lessons learned from this process, and connections between goals and targets and the actions and reporting that will be needed to maintain, protect, manage and monitor genetic diversity. It is possible and necessary that the GBF strives to maintain genetic diversity within and among populations of all species, to restore genetic connectivity, and to develop national genetic conservation strategies, and to report on these using proposed, feasible indicators.
Collapse
Affiliation(s)
- Sean Hoban
- The Morton Arboretum, Center for Tree Science, Lisle, USA.,The University of Chicago, Chicago, USA
| | | | - Jessica M da Silva
- South African National Biodiversity Institute, Pretoria, South Africa.,Centre for Ecological Genomics and Wildlife Conservation, University of Johannesburg, Johannesburg, South Africa
| | - W Chris Funk
- Department of Biology, Colorado State University, Fort Collins, USA
| | - Richard Frankham
- School of Natural Sciences, Macquarie University, Sydney, NSW Australia
| | - Michael J Gill
- NatureServe, Biodiversity Indicators Program, Arlington, USA
| | - Catherine E Grueber
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
| | | | - Margaret E Hunter
- U.S. Geological Survey, Wetland and Aquatic Research Center, Gainesville, USA
| | - Francine Kershaw
- Oceans Division, Natural Resources Defense Council, NewYork, USA
| | - Robert C Lacy
- Chicago Zoological Society, Species Conservation Toolkit Initiative, Brookfield, USA
| | - Caroline Lees
- Conservation Planning Specialist Group, IUCN SSC, Auckland, New Zealand
| | | | - Anna J MacDonald
- Australian Antarctic Division, Department of Climate Change, Energy, the Environment and Water, Kingston, Australia
| | - Alicia Mastretta-Yanes
- Comisión Nacional para el Conocimiento y Uso de la Biodiversidad (CONABIO), Mexico City, Mexico.,Consejo Nacional de Ciencia Y Tecnología (CONACYT), Mexico City, Mexico
| | - Philip J K McGowan
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - Mariah H Meek
- Department of Integrative Biology; Ecology, Evolution, and Behavior Program, Michigan State University, AgBio Research, Lansing, USA
| | - Joachim Mergeay
- Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Katie L Millette
- Group on Earth Observations Biodiversity Observation Network (GEO BON), McGill University, Montreal, Canada
| | - Cinnamon S Mittan-Moreau
- Kellogg Biological Station; Ecology and Evolutionary Biology, Michigan State University, Lansing, USA
| | | | | | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin Institute, University of Edinburgh, EH25 9RG, Midlothian, United Kingdom
| | | | - Ivan Paz-Vinas
- Department of Biology, Colorado State University, Fort Collins, USA
| | | | - Linda Laikre
- Department of Zoology, Stockholm University, Stockholm, Sweden
| |
Collapse
|
7
|
Sharma A, Tripathi V, Kumar V. Control and adaptability of seasonal changes in behavior and physiology of latitudinal avian migrants: Insights from laboratory studies in Palearctic-Indian migratory buntings. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2022; 337:902-918. [PMID: 35677956 DOI: 10.1002/jez.2631] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 06/15/2023]
Abstract
Twice-a-year migrations, one in autumn and the other in spring, occur within a discrete time window with striking alterations in the behavior and physiology, as regulated by the interaction of endogenous rhythms with prevailing photoperiod. These seasonal voyages are not isolated events; rather, they are part of an overall annual itinerary and remain closely coupled to the other annual subcycles, called seasonal life history states (LHSs). The success of migration depends on appropriate timing of the initiation and termination of each LHS, for example, reproduction, molt, summer nonmigratory, preautumn migratory (fattening and weight gain), autumn migratory, winter nonmigratory (wnM), prevernal (spring) migratory (fattening and weight gain), and spring migratory LHSs. Migration-linked photoperiod-induced changes include the body fattening and weight gain, nocturnal Zugunruhe (migratory restlessness), elevated triglycerides and free fatty acids, triiodothyronine and corticosterone levels. Hypothalamic expression of the thyroid hormone-responsive dio2 and dio3, light-responsive per2, cry1, and adcyap1 and th (tyrosine hydroxylase, involved in dopamine biosynthesis) genes also show significant changes with transition from wnM to the vernal migratory LHS. Concurrent changes in the expression of genes associated with lipid metabolism and its transport also occur in the liver and flight muscles, respectively. Interestingly, there are clear differences in the behavioral and physiological phenotypes, and associated molecular changes, between the autumn and vernal migrations. In this review, we discuss seasonal changes in the behavior and physiology, and present molecular insights into the development of migratory phenotypes in latitudinal avian migrants, with special reference to Palearctic-Indian migratory buntings.
Collapse
Affiliation(s)
- Aakansha Sharma
- Department of Zoology, IndoUS Center in Chronobiology, University of Delhi, Delhi, India
| | - Vatsala Tripathi
- Department of Zoology, Dyal Singh College, University of Delhi, Delhi, India
| | - Vinod Kumar
- Department of Zoology, IndoUS Center in Chronobiology, University of Delhi, Delhi, India
| |
Collapse
|
8
|
Williams CT, Chmura HE, Deal CK, Wilsterman K. Sex-differences in Phenology: A Tinbergian Perspective. Integr Comp Biol 2022; 62:980-997. [PMID: 35587379 DOI: 10.1093/icb/icac035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/18/2022] [Accepted: 04/23/2022] [Indexed: 11/13/2022] Open
Abstract
Shifts in the timing of cyclic seasonal life-history events are among the most commonly reported responses to climate change, with differences in response rates among interacting species leading to phenological mismatches. Within a species, however, males and females can also exhibit differential sensitivity to environmental cues and may therefore differ in their responsiveness to climate change, potentially leading to phenological mismatches between the sexes. This occurs because males differ from females in when and how energy is allocated to reproduction, resulting in marked sex-differences in life-history timing across the annual cycle. In this review, we take a Tinbergian perspective and examine sex differences in timing of vertebrates from adaptive, ontogenetic, mechanistic, and phylogenetic viewpoints with the goal of informing and motivating more integrative research on sexually dimorphic phenologies. We argue that sexual and natural selection lead to sex-differences in life-history-timing and that understanding the ecological and evolutionary drivers of these differences is critical for connecting climate-driven phenological shifts to population resilience. Ontogeny may influence how and when sex differences in life-history timing arise because the early-life environment can profoundly affect developmental trajectory, rates of reproductive maturation, and seasonal timing. The molecular mechanisms underlying these organismal traits are relevant to identifying the diversity and genetic basis of population- and species-level responses to climate change, and promisingly, the molecular basis of phenology is becoming increasingly well-understood. However, because most studies focus on a single sex, the causes of sex-differences in phenology critical to population resilience often remain unclear. New sequencing tools and analyses informed by phylogeny may help generate hypotheses about mechanism as well as insight into the general "evolvability" of sex differences across phylogenetic scales, especially as trait and genome resources grow. We recommend that greater attention be placed on determining sex-differences in timing mechanisms and monitoring climate change responses in both sexes, and we discuss how new tools may provide key insights into sex-differences in phenology from all four Tinbergian domains.
Collapse
Affiliation(s)
- Cory T Williams
- Department of Biology, Colorado State University, 1878 Campus Delivery Fort Collins, CO 80523, USA
| | - Helen E Chmura
- Institute of Arctic Biology, University of Alaska Fairbanks, 2140 Koyukuk Drive, Fairbanks, AK 99775, USA.,Rocky Mountain Research Station, United States Forest Service, 800 E. Beckwith Ave, Missoula, MT 59801, USA
| | - Cole K Deal
- Department of Biology, Colorado State University, 1878 Campus Delivery Fort Collins, CO 80523, USA
| | - Kathryn Wilsterman
- Department of Biology, Colorado State University, 1878 Campus Delivery Fort Collins, CO 80523, USA
| |
Collapse
|
9
|
Population-specific association of Clock gene polymorphism with annual cycle timing in stonechats. Sci Rep 2022; 12:7947. [PMID: 35562382 PMCID: PMC9106710 DOI: 10.1038/s41598-022-11158-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 04/19/2022] [Indexed: 11/28/2022] Open
Abstract
Timing is essential for survival and reproduction of organisms across the tree of life. The core circadian clock gene Clk is involved in the regulation of annual timing events and shows highly conserved sequence homology across vertebrates except for one variable region of poly-glutamine repeats. Clk genotype varies in some species with latitude, seasonal timing and migration. However, findings are inconsistent, difficult to disentangle from environmental responses, and biased towards high latitudes. Here we combine field data with a common-garden experiment to study associations of Clk polymorphism with latitude, migration and annual-cycle timing within the stonechat species complex across its trans-equatorial distribution range. Our dataset includes 950 records from 717 individuals from nine populations with diverse migratory strategies. Gene diversity was lowest in resident African and Canary Island populations and increased with latitude, independently of migration distance. Repeat length and annual-cycle timing was linked in a population-specific way. Specifically, equatorial African stonechats showed delayed timing with longer repeat length for all annual-cycle stages. Our data suggest that at low latitudes with nearly constant photoperiod, Clk genotype might orchestrate a range of consistent, individual chronotypes. In contrast, the influence of Clk on annual-cycle timing at higher latitudes might be mediated by its interactions with genes involved in (circadian) photoperiodic pathways.
Collapse
|
10
|
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.
Collapse
|
11
|
A New Census of Protein Tandem Repeats and Their Relationship with Intrinsic Disorder. Genes (Basel) 2020; 11:genes11040407. [PMID: 32283633 PMCID: PMC7230257 DOI: 10.3390/genes11040407] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 12/31/2022] Open
Abstract
Protein tandem repeats (TRs) are often associated with immunity-related functions and diseases. Since that last census of protein TRs in 1999, the number of curated proteins increased more than seven-fold and new TR prediction methods were published. TRs appear to be enriched with intrinsic disorder and vice versa. The significance and the biological reasons for this association are unknown. Here, we characterize protein TRs across all kingdoms of life and their overlap with intrinsic disorder in unprecedented detail. Using state-of-the-art prediction methods, we estimate that 50.9% of proteins contain at least one TR, often located at the sequence flanks. Positive linear correlation between the proportion of TRs and the protein length was observed universally, with Eukaryotes in general having more TRs, but when the difference in length is taken into account the difference is quite small. TRs were enriched with disorder-promoting amino acids and were inside intrinsically disordered regions. Many such TRs were homorepeats. Our results support that TRs mostly originate by duplication and are involved in essential functions such as transcription processes, structural organization, electron transport and iron-binding. In viruses, TRs are found in proteins essential for virulence.
Collapse
|
12
|
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.
Collapse
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
| |
Collapse
|
13
|
Rittenhouse JL, Robart AR, Watts HE. Variation in chronotype is associated with migratory timing in a songbird. Biol Lett 2019; 15:20190453. [PMID: 31455169 DOI: 10.1098/rsbl.2019.0453] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Like many organisms, birds exhibit daily (circadian) and seasonal biological rhythms, and within populations both daily and seasonal timing often vary among individuals. Because photoperiod interacts with the circadian rhythms of many organisms to induce seasonal changes in behaviour and physiology, it is hypothesized that differences in daily timing, called chronotypes, underpin differences among individuals in the timing of seasonal events. For seasonal events stimulated by increasing daylength, this hypothesis predicts a positive relationship between the timing of daily and seasonal activities of individuals, with advanced chronotypes expressing events earlier in the year. The few previous tests of this hypothesis have focused on seasonal reproductive timing in birds. However, the hypothesis predicts that this relationship should extend to other photoinduced seasonal events. Therefore, we tested whether variation in chronotype was associated with variation in spring migratory timing in a captive songbird model, the pine siskin (Spinus pinus). We found that pine siskins expressing migratory restlessness exhibited repeatable chronotypes in their timing of nocturnal activity. Further, chronotype was significantly associated with the onset date of migratory behaviour, consistent with the hypothesized relationship between chronotype and seasonal timing.
Collapse
Affiliation(s)
| | - Ashley R Robart
- School of Biological Sciences, Washington State University, Pullman, WA, USA
| | - Heather E Watts
- School of Biological Sciences, Washington State University, Pullman, WA, USA.,Center for Reproductive Biology, Washington State University, Pullman, WA, USA
| |
Collapse
|
14
|
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.
Collapse
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
| |
Collapse
|
15
|
Saino N, Albetti B, Ambrosini R, Caprioli M, Costanzo A, Mariani J, Parolini M, Romano A, Rubolini D, Formenti G, Gianfranceschi L, Bollati V. Inter-generational resemblance of methylation levels at circadian genes and associations with phenology in the barn swallow. Sci Rep 2019; 9:6505. [PMID: 31019206 PMCID: PMC6482194 DOI: 10.1038/s41598-019-42798-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/25/2019] [Indexed: 12/16/2022] Open
Abstract
Regulation of gene expression can occur via epigenetic effects as mediated by DNA methylation. The potential for epigenetic effects to be transmitted across generations, thus modulating phenotypic variation and affecting ecological and evolutionary processes, is increasingly appreciated. However, the study of variation in epigenomes and inter-generational transmission of epigenetic alterations in wild populations is at its very infancy. We studied sex- and age-related variation in DNA methylation and parent-offspring resemblance in methylation profiles in the barn swallows. We focused on a class of highly conserved ‘clock’ genes (clock, cry1, per2, per3, timeless) relevant in the timing of activities of major ecological importance. In addition, we considerably expanded previous analyses on the relationship between methylation at clock genes and breeding date, a key fitness trait in barn swallows. We found positive assortative mating for methylation at one clock locus. Methylation varied between the nestling and the adult stage, and according to sex. Individuals with relatively high methylation as nestlings also had high methylation levels when adults. Extensive parent-nestling resemblance in methylation levels was observed. Occurrence of extra-pair fertilizations allowed to disclose evidence hinting at a prevalence of paternal germline or sperm quality effects over common environment effects in generating father-offspring resemblance in methylation. Finally, we found an association between methylation at the clock poly-Q region, but not at other loci, and breeding date. We thus provided evidence for sex-dependent variation and the first account of parent-offspring resemblance in methylation in any wild vertebrate. We also showed that epigenetics may influence phenotypic plasticity of timing of life cycle events, thus having a major impact on fitness.
Collapse
Affiliation(s)
- Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy.
| | - Benedetta Albetti
- Department of Clinical Sciences and Community Health, via S. Barnaba 8, I-20122, Milan, Italy
| | - Roberto Ambrosini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Manuela Caprioli
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Alessandra Costanzo
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Jacopo Mariani
- Department of Clinical Sciences and Community Health, via S. Barnaba 8, I-20122, Milan, Italy
| | - Marco Parolini
- 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.,Department of Ecology and Evolution, University of Lausanne, Building Biophore, CH-1015, Lausanne, Switzerland
| | - Diego Rubolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via Celoria 26, I-20133, Milan, Italy
| | - Valentina Bollati
- Department of Clinical Sciences and Community Health, via S. Barnaba 8, I-20122, Milan, Italy.
| |
Collapse
|
16
|
Formenti G, Chiara M, Poveda L, Francoijs KJ, Bonisoli-Alquati A, Canova L, Gianfranceschi L, Horner DS, Saino N. SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica). Gigascience 2019; 8:5202456. [PMID: 30496513 PMCID: PMC6324554 DOI: 10.1093/gigascience/giy142] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 11/14/2018] [Indexed: 11/12/2022] Open
Abstract
Background The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica). Findings As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp. Conclusions This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
Collapse
Affiliation(s)
- Giulio Formenti
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| | - Matteo Chiara
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Lucy Poveda
- Functional Genomics Center of Zurich, University of Zurich, Winterthurerstrasse 190, Zürich, 8057, Switzerland
| | | | - Andrea Bonisoli-Alquati
- Department of Biological Sciences, California State Polytechnic University, 3801 West Temple Avenue, Pomona, California, 91768, USA
| | - Luca Canova
- Department of Biochemistry, University of Pavia, Via Taramelli 12, Pavia, 27100, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - David Stephen Horner
- Department of Biosciences, University of Milan, via celoria 26, Milan, 20133, Italy
| | - Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via celoria 2, Milan, 20133, Italy
| |
Collapse
|
17
|
A Variable Polyglutamine Repeat Affects Subcellular Localization and Regulatory Activity of a Populus ANGUSTIFOLIA Protein. G3-GENES GENOMES GENETICS 2018; 8:2631-2641. [PMID: 29884614 PMCID: PMC6071607 DOI: 10.1534/g3.118.200188] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Polyglutamine (polyQ) stretches have been reported to occur in proteins across many organisms including animals, fungi and plants. Expansion of these repeats has attracted much attention due their associations with numerous human diseases including Huntington’s and other neurological maladies. This suggests that the relative length of polyQ stretches is an important modulator of their function. Here, we report the identification of a Populus C-terminus binding protein (CtBP) ANGUSTIFOLIA (PtAN1) which contains a polyQ stretch whose functional relevance had not been established. Analysis of 917 resequenced Populus trichocarpa genotypes revealed three allelic variants at this locus encoding 11-, 13- and 15-glutamine residues. Transient expression assays using Populus leaf mesophyll protoplasts revealed that the 11Q variant exhibited strong nuclear localization whereas the 15Q variant was only found in the cytosol, with the 13Q variant exhibiting localization in both subcellular compartments. We assessed functional implications by evaluating expression changes of putative PtAN1 targets in response to overexpression of the three allelic variants and observed allele-specific differences in expression levels of putative targets. Our results provide evidence that variation in polyQ length modulates PtAN1 function by altering subcellular localization.
Collapse
|
18
|
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'.
Collapse
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
| |
Collapse
|
19
|
Salmela MJ, McMinn RL, Guadagno CR, Ewers BE, Weinig C. Circadian Rhythms and Reproductive Phenology Covary in a Natural Plant Population. J Biol Rhythms 2018; 33:245-254. [DOI: 10.1177/0748730418764525] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
| | - Robby L. McMinn
- Department of Botany, University of Wyoming, Laramie, Wyoming
- Program in Ecology, University of Wyoming, Laramie, Wyoming
| | | | - Brent E. Ewers
- Department of Botany, University of Wyoming, Laramie, Wyoming
- Program in Ecology, University of Wyoming, Laramie, Wyoming
| | - Cynthia Weinig
- Department of Botany, University of Wyoming, Laramie, Wyoming
- Program in Ecology, University of Wyoming, Laramie, Wyoming
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
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
| |
Collapse
|
22
|
Mishra I, Kumar V. Circadian basis of seasonal timing in higher vertebrates. BIOL RHYTHM RES 2017. [DOI: 10.1080/09291016.2017.1345447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ila Mishra
- Department of Zoology, University of Delhi, Delhi, India
| | - Vinod Kumar
- Department of Zoology, University of Delhi, Delhi, India
| |
Collapse
|
23
|
Chahad-Ehlers S, Arthur LP, Lima ALA, Gesto JSM, Torres FR, Peixoto AA, de Brito RA. Expanding the view of Clock and cycle gene evolution in Diptera. INSECT MOLECULAR BIOLOGY 2017; 26:317-331. [PMID: 28234413 DOI: 10.1111/imb.12296] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We expanded the view of Clock (Clk) and cycle (cyc) gene evolution in Diptera by studying the fruit fly Anastrepha fraterculus (Afra), a Brachycera. Despite the high conservation of clock genes amongst insect groups, striking structural and functional differences of some clocks have appeared throughout evolution. Clk and cyc nucleotide sequences and corresponding proteins were characterized, along with their mRNA expression data, to provide an evolutionary overview in the two major groups of Diptera: Lower Diptera and Higher Brachycera. We found that AfraCYC lacks the BMAL (Brain and muscle ARNT-like) C-terminus region (BCTR) domain and is constitutively expressed, suggesting that AfraCLK has the main transactivation function, which is corroborated by the presence of poly-Q repeats and an oscillatory pattern. Our analysis suggests that the loss of BCTR in CYC is not exclusive of drosophilids, as it also occurs in other Acalyptratae flies such as tephritids and drosophilids, however, but it is also present in some Calyptratae, such as Muscidae, Calliphoridae and Sarcophagidae. This indicates that BCTR is missing from CYC of all higher-level Brachycera and that it was lost during the evolution of Lower Brachycera. Thus, we can infer that CLK protein may play the main role in the CLK\CYC transcription complex in these flies, like in its Drosophila orthologues.
Collapse
Affiliation(s)
- S Chahad-Ehlers
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - L P Arthur
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A L A Lima
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - J S M Gesto
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - F R Torres
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - A A Peixoto
- Laboratório de Biologia Molecular de Insetos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, RJ, Brazil
| | - R A de Brito
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| |
Collapse
|
24
|
Saino N, Ambrosini R, Albetti B, Caprioli M, De Giorgio B, Gatti E, Liechti F, Parolini M, Romano A, Romano M, Scandolara C, Gianfranceschi L, Bollati V, Rubolini D. Migration phenology and breeding success are predicted by methylation of a photoperiodic gene in the barn swallow. Sci Rep 2017; 7:45412. [PMID: 28361883 PMCID: PMC5374444 DOI: 10.1038/srep45412] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 02/16/2017] [Indexed: 02/07/2023] Open
Abstract
Individuals often considerably differ in the timing of their life-cycle events, with major consequences for individual fitness, and, ultimately, for population dynamics. Phenological variation can arise from genetic effects but also from epigenetic modifications in DNA expression and translation. Here, we tested if CpG methylation at the poly-Q and 5'-UTR loci of the photoperiodic Clock gene predicted migration and breeding phenology of long-distance migratory barn swallows (Hirundo rustica) that were tracked year-round using light-level geolocators. Increasing methylation at Clock poly-Q was associated with earlier spring departure from the African wintering area, arrival date at the European breeding site, and breeding date. Higher methylation levels also predicted increased breeding success. Thus, we showed for the first time in any species that CpG methylation at a candidate gene may affect phenology and breeding performance. Methylation at Clock may be a candidate mechanism mediating phenological responses of migratory birds to ongoing climate change.
Collapse
Affiliation(s)
- Nicola Saino
- Department of Biosciences, 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
| | - Benedetta Albetti
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Manuela Caprioli
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Barbara De Giorgio
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Emanuele Gatti
- Department of Earth and Environmental Sciences (DISAT), University of Milano Bicocca, Piazza della Scienza, 1, I-20126 Milan, Italy
| | - Felix Liechti
- Swiss Ornithological Insititute, Seerose 1, CH-6204, Sempach, Switzerland
| | - Marco Parolini
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Andrea Romano
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Maria Romano
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Chiara Scandolara
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Valentina Bollati
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Diego Rubolini
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| |
Collapse
|
25
|
Saino N, Ambrosini R, Caprioli M, Romano A, Romano M, Rubolini D, Scandolara C, Liechti F. Sex-dependent carry-over effects on timing of reproduction and fecundity of a migratory bird. J Anim Ecol 2017; 86:239-249. [DOI: 10.1111/1365-2656.12625] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/04/2016] [Indexed: 11/29/2022]
Affiliation(s)
- Nicola Saino
- Department of Biosciences; University of Milan; Via Celoria 26 I-20133 Milan Italy
| | - Roberto Ambrosini
- Department of Earth and Environmental Sciences; University of Milano-Bicocca; Piazza della Scienza 2 I-20126 Milan Italy
| | - Manuela Caprioli
- Department of Biosciences; University of Milan; Via Celoria 26 I-20133 Milan Italy
| | - Andrea Romano
- Department of Biosciences; University of Milan; Via Celoria 26 I-20133 Milan Italy
| | - Maria Romano
- Department of Biosciences; University of Milan; Via Celoria 26 I-20133 Milan Italy
| | - Diego Rubolini
- Department of Biosciences; University of Milan; Via Celoria 26 I-20133 Milan Italy
| | - Chiara Scandolara
- Department of Biosciences; University of Milan; Via Celoria 26 I-20133 Milan Italy
- Swiss Ornithological Insititute; Seerose 1 CH-6204 Sempach Switzerland
| | - Felix Liechti
- Swiss Ornithological Insititute; Seerose 1 CH-6204 Sempach Switzerland
| |
Collapse
|
26
|
Romano A, De Giorgio B, Parolini M, Favero C, Possenti CD, Iodice S, Caprioli M, Rubolini D, Ambrosini R, Gianfranceschi L, Saino N, Bollati V. Methylation of the circadian Clock gene in the offspring of a free-living passerine bird increases with maternal and individual exposure to PM 10. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2017; 220:29-37. [PMID: 27712846 DOI: 10.1016/j.envpol.2016.08.060] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 08/01/2016] [Accepted: 08/24/2016] [Indexed: 06/06/2023]
Abstract
The consequences of exposure to particulate matter (PM) have been thoroughly investigated in humans and other model species, but there is a dearth of studies of the effects of PM on physiology and life-history traits of non-human organisms living in natural or semi-natural environments. Besides toxicological relevance, PM has been recently suggested to exert epigenetic effects by altering DNA methylation patterns. Here, we investigated for the first time the association between the exposure to free-air PM10 and DNA methylation at two loci ('poly-Q exon' and '5'-UTR') of the Clock gene in blood cells of the nestlings of a synanthropic passerine bird, the barn swallow (Hirundo rustica). The Clock gene is a phylogenetically highly conserved gene playing a major role in governing circadian rhythms and circannual life cycles of animals, implying that change in its level of methylation can impact on important fitness traits. We found that methylation at both loci significantly increased with PM10 levels recorded few days before blood sampling, and also with PM10 exposure experienced by the mother during or shortly before egg laying. This study is the first where methylation at a functionally important gene has been shown to vary according to the concentration of anthropogenic pollutants in any animal species in the wild. Since early-life environmental conditions produce epigenetic effects that can transgenerationally be transmitted, DNA methylation of genes controlling photoperiodic response can have far reaching consequences for the ecology and the evolution of wild animal populations.
Collapse
Affiliation(s)
- Andrea Romano
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Barbara De Giorgio
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Marco Parolini
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Chiara Favero
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | | | - Simona Iodice
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy
| | - Manuela Caprioli
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Diego Rubolini
- Department of Biosciences, 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
| | - Luca Gianfranceschi
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy.
| | - Nicola Saino
- Department of Biosciences, University of Milan, via Celoria 26, I-20133 Milan, Italy
| | - Valentina Bollati
- EPIGET - Epidemiology, Epigenetics and Toxicology Lab - Department of Clinical Sciences and Community Health, University of Milan, via San Barnaba 8, I-20122 Milan, Italy.
| |
Collapse
|
27
|
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.
Collapse
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
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
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: 10] [Impact Index Per Article: 1.3] [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.
Collapse
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
| |
Collapse
|
30
|
Delmore KE, Liedvogel M. Investigating Factors that Generate and Maintain Variation in Migratory Orientation: A Primer for Recent and Future Work. Front Behav Neurosci 2016; 10:3. [PMID: 26834592 PMCID: PMC4720750 DOI: 10.3389/fnbeh.2016.00003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/04/2016] [Indexed: 01/24/2023] Open
Abstract
The amazing accuracy of migratory orientation performance across the animal kingdom is facilitated by the use of magnetic and celestial compass systems that provide individuals with both directional and positional information. Quantitative genetics analyses in several animal systems suggests that migratory orientation has a strong genetic component. Nevertheless, the exact identity of genes controlling orientation remains largely unknown, making it difficult to obtain an accurate understanding of this fascinating behavior on the molecular level. Here, we provide an overview of molecular genetic techniques employed thus far, highlight the pros and cons of various approaches, generalize results from species-specific studies whenever possible, and evaluate how far the field has come since early quantitative genetics studies. We emphasize the importance of examining different levels of molecular control, and outline how future studies can take advantage of high-resolution tracking and sequencing techniques to characterize the genomic architecture of migratory orientation.
Collapse
Affiliation(s)
- Kira E Delmore
- Behavioural Genomics Department, Max Planck Institute for Evolutionary Biology Plön, Germany
| | - Miriam Liedvogel
- Behavioural Genomics Department, Max Planck Institute for Evolutionary Biology Plön, Germany
| |
Collapse
|
31
|
Genetic Correlates of Individual Differences in Sleep Behavior of Free-Living Great Tits (Parus major). G3-GENES GENOMES GENETICS 2016; 6:599-607. [PMID: 26739645 PMCID: PMC4777123 DOI: 10.1534/g3.115.024216] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Within populations, free-living birds display considerable variation in observable sleep behaviors, reflecting dynamic interactions between individuals and their environment. Genes are expected to contribute to repeatable between-individual differences in sleep behaviors, which may be associated with individual fitness. We identified and genotyped polymorphisms in nine candidate genes for sleep, and measured five repeatable sleep behaviors in free-living great tits (Parus major), partly replicating a previous study in blue tits (Cyanistes caeruleus). Microsatellites in the CLOCK and NPAS2 clock genes exhibited an association with sleep duration relative to night length, and morning latency to exit the nest box, respectively. Furthermore, microsatellites in the NPSR1 and PCSK2 genes associated with relative sleep duration and proportion of time spent awake at night, respectively. Given the detection rate of associations in the same models run with random markers instead of candidate genes, we expected two associations to arise by chance. The detection of four associations between candidate genes and sleep, however, suggests that clock genes, a clock-related gene, or a gene involved in the melanocortin system, could play key roles in maintaining phenotypic variation in sleep behavior in avian populations. Knowledge of the genetic architecture underlying sleep behavior in the wild is important because it will enable ecologists to assess the evolution of sleep in response to selection.
Collapse
|
32
|
Ketterson ED, Fudickar AM, Atwell JW, Greives TJ. Seasonal timing and population divergence: when to breed, when to migrate. Curr Opin Behav Sci 2015. [DOI: 10.1016/j.cobeha.2015.09.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
|
33
|
Charmantier A, Doutrelant C, Dubuc-Messier G, Fargevieille A, Szulkin M. Mediterranean blue tits as a case study of local adaptation. Evol Appl 2015; 9:135-52. [PMID: 27087844 PMCID: PMC4780380 DOI: 10.1111/eva.12282] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/27/2015] [Indexed: 02/01/2023] Open
Abstract
While the study of the origins of biological diversity across species has provided numerous examples of adaptive divergence, the realization that it can occur at microgeographic scales despite gene flow is recent, and scarcely illustrated. We review here evidence suggesting that the striking phenotypic differentiation in ecologically relevant traits exhibited by blue tits Cyanistes caeruleus in their southern range‐edge putatively reflects adaptation to the heterogeneity of the Mediterranean habitats. We first summarize the phenotypic divergence for a series of life history, morphological, behavioural, acoustic and colour ornament traits in blue tit populations of evergreen and deciduous forests. For each divergent trait, we review the evidence obtained from common garden experiments regarding a possible genetic origin of the observed phenotypic differentiation as well as evidence for heterogeneous selection. Second, we argue that most phenotypically differentiated traits display heritable variation, a fundamental requirement for evolution to occur. Third, we discuss nonrandom dispersal, selective barriers and assortative mating as processes that could reinforce local adaptation. Finally, we show how population genomics supports isolation – by – environment across landscapes. Overall, the combination of approaches converges to the conclusion that the strong phenotypic differentiation observed in Mediterranean blue tits is a fascinating case of local adaptation.
Collapse
Affiliation(s)
- Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
| | - Claire Doutrelant
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
| | - Gabrielle Dubuc-Messier
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France; Département des sciences biologiques Université du Québec à Montréal Succursalle centre-ville QC Canada
| | | | - Marta Szulkin
- Centre d'Ecologie Fonctionnelle et Evolutive Campus CNRS Montpellier France
| |
Collapse
|
34
|
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.
Collapse
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
| |
Collapse
|
35
|
Clock gene polymorphism and scheduling of migration: a geolocator study of the barn swallow Hirundo rustica. Sci Rep 2015. [PMID: 26197782 PMCID: PMC4510496 DOI: 10.1038/srep12443] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Circannual rhythms often rely on endogenous seasonal photoperiodic timers involving ‘clock’ genes, and Clock gene polymorphism has been associated to variation in phenology in some bird species. In the long-distance migratory barn swallow Hirundo rustica, individuals bearing the rare Clock allele with the largest number of C-terminal polyglutamine repeats found in this species (Q8) show a delayed reproduction and moult later. We explored the association between Clock polymorphism and migration scheduling, as gauged by light-level geolocators, in two barn swallow populations (Switzerland; Po Plain, Italy). Genetic polymorphism was low: 91% of the 64 individuals tracked year-round were Q7/Q7 homozygotes. We compared the phenology of the rare genotypes with the phenotypic distribution of Q7/Q7 homozygotes within each population. In Switzerland, compared to Q7/Q7, two Q6/Q7 males departed earlier from the wintering grounds and arrived earlier to their colony in spring, while a single Q7/Q8 female was delayed for both phenophases. On the other hand, in the Po Plain, three Q6/Q7 individuals had a similar phenology compared to Q7/Q7. The Swiss data are suggestive for a role of genetic polymorphism at a candidate phenological gene in shaping migration traits, and support the idea that Clock polymorphism underlies phenological variation in birds.
Collapse
|
36
|
Singh D, Trivedi AK, Rani S, Panda S, Kumar V. Circadian timing in central and peripheral tissues in a migratory songbird: dependence on annual life-history states. FASEB J 2015; 29:4248-55. [PMID: 26103987 DOI: 10.1096/fj.15-275339] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/15/2015] [Indexed: 01/07/2023]
Abstract
Predictable seasonal change in photoperiod triggers a sequential change in the daily activity-rest pattern, adaptive for migration in several bird species. The night-migratory black-headed bunting (Emberiza melanocephala) is day active under short photoperiods (8 h light:16 h dark, short day sensitive). Under long photoperiods (16 h light:8 h dark), the buntings are initially day active (long day premigratory) but subsequently become intensely night active (long day migratory) and after few weeks again return to a day active pattern (long day refractory). However, it is unclear how the daily expression of circadian genes changes during photoperiod-induced seasonal life-history states (LHSs). We measured period 2 (Per2), cryptochrome 1 (Cry1), brain and muscle arnt-like protein 1 (Bmal1), and circadian locomotor output cycles kaput (Clock) mRNA expressions in various neural and peripheral tissues of buntings in different LHSs and discovered differences of ∼2 to 6 h in the phase and 2- to 4-fold in amplitude of circadian oscillations of Per2, Cry1, and Bmal1 between photoperiod-induced LHSs. Phase relationship in mRNA oscillations was altered between oscillator components in the circadian pacemaker system (retina, pineal, hypothalamus) as well as in the peripheral (liver, muscle) tissues. These results show for the first time altered waveforms of clock gene expressions in all tissues in parallel with behavioral shifts and suggest the involvement of circadian system in photoperiod induction of seasonal LHSs in a migratory species.
Collapse
Affiliation(s)
- Devraj Singh
- *Department of Science and Technology-Intensification of Research in High Priority Areas Center for Excellence in Biological Rhythms Research and Indo-U.S. Center for Biological Timing, Department of Zoology, University of Delhi, Delhi, India; Department of Zoology, University of Lucknow, Lucknow, India; and Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Amit Kumar Trivedi
- *Department of Science and Technology-Intensification of Research in High Priority Areas Center for Excellence in Biological Rhythms Research and Indo-U.S. Center for Biological Timing, Department of Zoology, University of Delhi, Delhi, India; Department of Zoology, University of Lucknow, Lucknow, India; and Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Sangeeta Rani
- *Department of Science and Technology-Intensification of Research in High Priority Areas Center for Excellence in Biological Rhythms Research and Indo-U.S. Center for Biological Timing, Department of Zoology, University of Delhi, Delhi, India; Department of Zoology, University of Lucknow, Lucknow, India; and Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Satchidananda Panda
- *Department of Science and Technology-Intensification of Research in High Priority Areas Center for Excellence in Biological Rhythms Research and Indo-U.S. Center for Biological Timing, Department of Zoology, University of Delhi, Delhi, India; Department of Zoology, University of Lucknow, Lucknow, India; and Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| | - Vinod Kumar
- *Department of Science and Technology-Intensification of Research in High Priority Areas Center for Excellence in Biological Rhythms Research and Indo-U.S. Center for Biological Timing, Department of Zoology, University of Delhi, Delhi, India; Department of Zoology, University of Lucknow, Lucknow, India; and Regulatory Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California, USA
| |
Collapse
|
37
|
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
| |
Collapse
|
38
|
Lemay MA, Russello MA. Latitudinal cline in allele length provides evidence for selection in a circadian rhythm gene. Biol J Linn Soc Lond 2014. [DOI: 10.1111/bij.12267] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Matthew A. Lemay
- Okanagan Campus; University of British Columbia; 3333 University Way Kelowna BC V1V 1V7 Canada
| | - Michael A. Russello
- Okanagan Campus; University of British Columbia; 3333 University Way Kelowna BC V1V 1V7 Canada
| |
Collapse
|
39
|
Abstract
A significant body of evidence shows that polyglutamine (polyQ) tracts are important for various biological functions. The characteristic polymorphism of polyQ length is thought to play an important role in the adaptation of organisms to their environment. However, proteins with expanded polyQ are prone to form amyloids, which cause diseases in humans and animals and toxicity in yeast. Saccharomyces cerevisiae contain at least 8 proteins which can form heritable amyloids, called prions, and most of them are proteins with glutamine- and asparagine-enriched domains. Yeast prion amyloids are susceptible to fragmentation by the protein disaggregase Hsp104, which allows them to propagate and be transmitted to daughter cells during cell divisions. We have previously shown that interspersion of polyQ domains with some non-glutamine residues stimulates fragmentation of polyQ amyloids in yeast and that yeast prion domains are often enriched in one of these residues. These findings indicate that yeast prion domains may have derived from polyQ tracts via accumulation and amplification of mutations. The same hypothesis may be applied to polyasparagine (polyN) tracts, since they display similar properties to polyQ, such as length polymorphism, amyloid formation and toxicity. We propose that mutations in polyQ/N may be favored by natural selection thus making prion domains likely by-products of the evolution of polyQ/N.
Collapse
|
40
|
Charmantier A, Gienapp P. Climate change and timing of avian breeding and migration: evolutionary versus plastic changes. Evol Appl 2014; 7:15-28. [PMID: 24454545 PMCID: PMC3894895 DOI: 10.1111/eva.12126] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Accepted: 09/26/2013] [Indexed: 11/27/2022] Open
Abstract
There are multiple observations around the globe showing that in many avian species, both the timing of migration and breeding have advanced, due to warmer springs. Here, we review the literature to disentangle the actions of evolutionary changes in response to selection induced by climate change versus changes due to individual plasticity, that is, the capacity of an individual to adjust its phenology to environmental variables. Within the abundant literature on climate change effects on bird phenology, only a small fraction of studies are based on individual data, yet individual data are required to quantify the relative importance of plastic versus evolutionary responses. While plasticity seems common and often adaptive, no study so far has provided direct evidence for an evolutionary response of bird phenology to current climate change. This assessment leads us to notice the alarming lack of tests for microevolutionary changes in bird phenology in response to climate change, in contrast with the abundant claims on this issue. In short, at present we cannot draw reliable conclusions on the processes underlying the observed patterns of advanced phenology in birds. Rapid improvements in techniques for gathering and analysing individual data offer exciting possibilities that should encourage research activity to fill this knowledge gap.
Collapse
Affiliation(s)
- Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive, UMR 5175 Campus CNRSMontpellier Cedex 5, France
| | - Phillip Gienapp
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW)Wageningen, The Netherlands
| |
Collapse
|
41
|
Cassone VM. Avian circadian organization: a chorus of clocks. Front Neuroendocrinol 2014; 35:76-88. [PMID: 24157655 PMCID: PMC3946898 DOI: 10.1016/j.yfrne.2013.10.002] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/18/2013] [Accepted: 10/09/2013] [Indexed: 12/24/2022]
Abstract
In birds, biological clock function pervades all aspects of biology, controlling daily changes in sleep: wake, visual function, song, migratory patterns and orientation, as well as seasonal patterns of reproduction, song and migration. The molecular bases for circadian clocks are highly conserved, and it is likely the avian molecular mechanisms are similar to those expressed in mammals, including humans. The central pacemakers in the avian pineal gland, retinae and SCN dynamically interact to maintain stable phase relationships and then influence downstream rhythms through entrainment of peripheral oscillators in the brain controlling behavior and peripheral tissues. Birds represent an excellent model for the role played by biological clocks in human neurobiology; unlike most rodent models, they are diurnal, they exhibit cognitively complex social interactions, and their circadian clocks are more sensitive to the hormone melatonin than are those of nocturnal rodents.
Collapse
Affiliation(s)
- Vincent M Cassone
- Department of Biology, University of Kentucky, Lexington, KY 40506, United States.
| |
Collapse
|
42
|
Kuhn K, Schwenk K, Both C, Canal D, Johansson US, van der Mije S, Töpfer T, Päckert M. Differentiation in neutral genes and a candidate gene in the pied flycatcher: using biological archives to track global climate change. Ecol Evol 2013; 3:4799-814. [PMID: 24363905 PMCID: PMC3867912 DOI: 10.1002/ece3.855] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/25/2013] [Accepted: 09/25/2013] [Indexed: 11/11/2022] Open
Abstract
Global climate change is one of the major driving forces for adaptive shifts in migration and breeding phenology and possibly impacts demographic changes if a species fails to adapt sufficiently. In Western Europe, pied flycatchers (Ficedula hypoleuca) have insufficiently adapted their breeding phenology to the ongoing advance of food peaks within their breeding area and consequently suffered local population declines. We address the question whether this population decline led to a loss of genetic variation, using two neutral marker sets (mitochondrial control region and microsatellites), and one potentially selectively non-neutral marker (avian Clock gene). We report temporal changes in genetic diversity in extant populations and biological archives over more than a century, using samples from sites differing in the extent of climate change. Comparing genetic differentiation over this period revealed that only the recent Dutch population, which underwent population declines, showed slightly lower genetic variation than the historic Dutch population. As that loss of variation was only moderate and not observed in all markers, current gene flow across Western and Central European populations might have compensated local loss of variation over the last decades. A comparison of genetic differentiation in neutral loci versus the Clock gene locus provided evidence for stabilizing selection. Furthermore, in all genetic markers, we found a greater genetic differentiation in space than in time. This pattern suggests that local adaptation or historic processes might have a stronger effect on the population structure and genetic variation in the pied flycatcher than recent global climate changes.
Collapse
Affiliation(s)
- Kerstin Kuhn
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Ecology and Evolution, Johann Wolfgang Goethe-UniversitätMax-von-Laue-Straße 13, Frankfurt am Main, D-60438, Germany
| | - Klaus Schwenk
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Institute of Environmental Sciences, University of Koblenz-LandauFortstraße 7, Landau in der Pfalz, 76829, Germany
| | - Christiaan Both
- Centre for Ecological and Evolutionary Studies (CEES), University of GroningenPO Box 11103, Groningen, 9700 CC, The Netherlands
| | - David Canal
- Department of Evolutionary Ecology, Estación Biológica de Doñana, CSICAv. Américo Vespucio s/n, Sevilla, 41092, Spain
| | - Ulf S Johansson
- Department of Zoology, Swedish Museum of Natural HistoryPO Box 50007, Stockholm, SE 10405, Sweden
| | | | - Till Töpfer
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
| | - Martin Päckert
- Biodiversity and Climate Research CentreSenckenberganlage 25, Frankfurt a. Main, D-60325, Germany
- Museum of Zoology, Senckenberg Natural History CollectionsKönigsbrücker Landstraße 159, Dresden, D-01109, Germany
| |
Collapse
|
43
|
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
| |
Collapse
|
44
|
Helm B, Ben-Shlomo R, Sheriff MJ, Hut RA, Foster R, Barnes BM, Dominoni D. Annual rhythms that underlie phenology: biological time-keeping meets environmental change. Proc Biol Sci 2013; 280:20130016. [PMID: 23825201 DOI: 10.1098/rspb.2013.0016] [Citation(s) in RCA: 122] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Seasonal recurrence of biological processes (phenology) and its relationship to environmental change is recognized as being of key scientific and public concern, but its current study largely overlooks the extent to which phenology is based on biological time-keeping mechanisms. We highlight the relevance of physiological and neurobiological regulation for organisms' responsiveness to environmental conditions. Focusing on avian and mammalian examples, we describe circannual rhythmicity of reproduction, migration and hibernation, and address responses of animals to photic and thermal conditions. Climate change and urbanization are used as urgent examples of anthropogenic influences that put biological timing systems under pressure. We furthermore propose that consideration of Homo sapiens as principally a 'seasonal animal' can inspire new perspectives for understanding medical and psychological problems.
Collapse
Affiliation(s)
- Barbara Helm
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK.
| | | | | | | | | | | | | |
Collapse
|
45
|
Kovach RP, Gharrett AJ, Tallmon DA. Temporal patterns of genetic variation in a salmon population undergoing rapid change in migration timing. Evol Appl 2013; 6:795-807. [PMID: 29387166 PMCID: PMC5779130 DOI: 10.1111/eva.12066] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2012] [Accepted: 03/04/2013] [Indexed: 01/17/2023] Open
Abstract
Though genetic diversity is necessary for population persistence in rapidly changing environments, little is known about how climate-warming influences patterns of intra-population genetic variation. For a pink salmon population experiencing increasing temperatures, we used temporal genetic data (microsatellite = 1993, 2001, 2009; allozyme = 1979, 1981, 1983) to quantify the genetic effective population size (Ne ) and genetic divergence due to differences in migration timing and to estimate whether these quantities have changed over time. We predicted that temporal trends toward earlier migration timing and a corresponding loss of phenotypic variation would decrease genetic divergence based on migration timing and Ne . We observed significant genetic divergence based on migration timing and genetic heterogeneity between early- and late-migrating fish. There was also some evidence for divergent selection between early- and late-migrating fish at circadian rhythm genes, but results varied over time. Estimates of Ne from multiple methods were large (>1200) and Ne /Nc generally exceeded 0.2. Despite shifts in migration timing and loss of phenotypic variation, there was no evidence for changes in within-population genetic divergence or Ne over the course of this study. These results suggest that in instances of population stability, genetic diversity may be resistant to climate-induced changes in migration timing.
Collapse
Affiliation(s)
- Ryan P Kovach
- Biology and Wildlife Department Institute of Arctic Biology University of Alaska Fairbanks Fairbanks AK USA
| | - Anthony J Gharrett
- School of Fisheries and Oceanic Sciences University of Alaska Fairbanks Juneau AK USA
| | - David A Tallmon
- Biology and Wildlife Department Institute of Arctic Biology University of Alaska Fairbanks Fairbanks AK USA
- School of Fisheries and Oceanic Sciences University of Alaska Fairbanks Juneau AK USA
- Biology and Marine Biology Program University of Alaska Southeast Juneau AK USA
| |
Collapse
|
46
|
Saino N, Romano M, Caprioli M, Fasola M, Lardelli R, Micheloni P, Scandolara C, Rubolini D, Gianfranceschi L. Timing of molt of barn swallows is delayed in a rare Clock genotype. PeerJ 2013; 1:e17. [PMID: 23638351 PMCID: PMC3629011 DOI: 10.7717/peerj.17] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/04/2013] [Indexed: 11/20/2022] Open
Abstract
Photoperiodic responses are major factors entraining circannual life-cycles, functioning to adaptively synchronize annual routines to seasonal fluctuations in ecological conditions. Photoperiodism in physiology and behaviour is enforced by genes, including the vertebrate Clock orthologues, which are associated, for example, with phenology of migration in fish and breeding in birds. However, the role of Clock in photoperiodic plumage molt processes is unknown. We analyzed variation in molt schedules in relation to Clock genotype, using the long-distance migratory barn swallow (Hirundo rustica) as a model and by identifying males and females using molecular sexing techniques. Consistently with previous studies, we found one very common (Q7) and two rare (Q6, Q8) variants of a functionally significant Clock polyglutamine repeat. Molt schedules of primary wing feathers of swallows during their wintering period in Nigeria differed among Clock genotypes: rare (1.1%) Q7/Q8 heterozygotes had significantly delayed molt compared to the other genotypes. Molt schedules did not differ between males and females, and no differential association between molt and Clock in relation to sex emerged. The same rare Clock genotype that exhibited delayed breeding in Europe was here found to delay molt in Africa. Though based on a limited number of Q7/Q8 individuals from an otherwise very large sample, these novel results suggest that Clock is involved in the photoperiodic control of both molt and breeding, potentially also via reciprocal carry-over effects. If confirmed in species with higher Clock polymorphism, present results may have far-reaching consequences for the study of photoperiodic control of molt and expression of annual routines.
Collapse
Affiliation(s)
- Nicola Saino
- Department of Biosciences , University of Milan , Milan , Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Schwartz C, Andrews MT. Circannual transitions in gene expression: lessons from seasonal adaptations. Curr Top Dev Biol 2013; 105:247-73. [PMID: 23962845 DOI: 10.1016/b978-0-12-396968-2.00009-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Circannual timing is important for the coordination of seasonal activities, particularly promoting the survival of individuals in adverse conditions through adaptive physiological and behavioral changes. This includes optimizing the survival of offspring by coordinating reproductive efforts at appropriate times. Thus, timing is very important for overall fitness. In this chapter, we provide several examples of circannually timed events, including mammalian hibernation, discussing the physiological changes that accompany these events, and some of the known genes and pathways underlying these changes. We then describe five candidate systems that are potentially involved in circannual timing. Finally, we discuss several recent advances in molecular biology and animal husbandry that have made the use of nonmodel organisms for research more feasible, which will hopefully promote and encourage further advancement in the knowledge of circannual timing.
Collapse
Affiliation(s)
- Christine Schwartz
- Department of Biology, University of Minnesota Duluth, Duluth, Minnesota, USA
| | | |
Collapse
|