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Le Clercq LS, Kotzé A, Grobler JP, Dalton DL. Biological clocks as age estimation markers in animals: a systematic review and meta-analysis. Biol Rev Camb Philos Soc 2023; 98:1972-2011. [PMID: 37356823 DOI: 10.1111/brv.12992] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 06/04/2023] [Accepted: 06/08/2023] [Indexed: 06/27/2023]
Abstract
Various biological attributes associated with individual fitness in animals change predictably over the lifespan of an organism. Therefore, the study of animal ecology and the work of conservationists frequently relies upon the ability to assign animals to functionally relevant age classes to model population fitness. Several approaches have been applied to determining individual age and, while these methods have proved useful, they are not without limitations and often lack standardisation or are only applicable to specific species. For these reasons, scientists have explored the potential use of biological clocks towards creating a universal age-determination method. Two biological clocks, tooth layer annulation and otolith layering have found universal appeal. Both methods are highly invasive and most appropriate for post-mortem age-at-death estimation. More recently, attributes of cellular ageing previously explored in humans have been adapted to studying ageing in animals for the use of less-invasive molecular methods for determining age. Here, we review two such methods, assessment of methylation and telomere length, describing (i) what they are, (ii) how they change with age, and providing (iii) a summary and meta-analysis of studies that have explored their utility in animal age determination. We found that both attributes have been studied across multiple vertebrate classes, however, telomere studies were used before methylation studies and telomere length has been modelled in nearly twice as many studies. Telomere length studies included in the review often related changes to stress responses and illustrated that telomere length is sensitive to environmental and social stressors and, in the absence of repair mechanisms such as telomerase or alternative lengthening modes, lacks the ability to recover. Methylation studies, however, while also detecting sensitivity to stressors and toxins, illustrated the ability to recover from such stresses after a period of accelerated ageing, likely due to constitutive expression or reactivation of repair enzymes such as DNA methyl transferases. We also found that both studied attributes have parentally heritable features, but the mode of inheritance differs among taxa and may relate to heterogamy. Our meta-analysis included more than 40 species in common for methylation and telomere length, although both analyses included at least 60 age-estimation models. We found that methylation outperforms telomere length in terms of predictive power evidenced from effect sizes (more than double that observed for telomeres) and smaller prediction intervals. Both methods produced age correlation models using similar sample sizes and were able to classify individuals into young, middle, or old age classes with high accuracy. Our review and meta-analysis illustrate that both methods are well suited to studying age in animals and do not suffer significantly from variation due to differences in the lifespan of the species, genome size, karyotype, or tissue type but rather that quantitative method, patterns of inheritance, and environmental factors should be the main considerations. Thus, provided that complex factors affecting the measured trait can be accounted for, both methylation and telomere length are promising targets to develop as biomarkers for age determination in animals.
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Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, P.O. Box 339, Bloemfontein, 9300, South Africa
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BA, UK
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Le Clercq LS, Bazzi G, Cecere JG, Gianfranceschi L, Grobler JP, Kotzé A, Rubolini D, Liedvogel M, Dalton DL. Time trees and clock genes: a systematic review and comparative analysis of contemporary avian migration genetics. Biol Rev Camb Philos Soc 2023; 98:1051-1080. [PMID: 36879518 DOI: 10.1111/brv.12943] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 03/08/2023]
Abstract
Timing is a crucial aspect for survival and reproduction in seasonal environments leading to carefully scheduled annual programs of migration in many species. But what are the exact mechanisms through which birds (class: Aves) can keep track of time, anticipate seasonal changes, and adapt their behaviour? One proposed mechanism regulating annual behaviour is the circadian clock, controlled by a highly conserved set of genes, collectively called 'clock genes' which are well established in controlling the daily rhythmicity of physiology and behaviour. Due to diverse migration patterns observed within and among species, in a seemingly endogenously programmed manner, the field of migration genetics has sought and tested several candidate genes within the clock circuitry that may underlie the observed differences in breeding and migration behaviour. Among others, length polymorphisms within genes such as Clock and Adcyap1 have been hypothesised to play a putative role, although association and fitness studies in various species have yielded mixed results. To contextualise the existing body of data, here we conducted a systematic review of all published studies relating polymorphisms in clock genes to seasonality in a phylogenetically and taxonomically informed manner. This was complemented by a standardised comparative re-analysis of candidate gene polymorphisms of 76 bird species, of which 58 are migrants and 18 are residents, along with population genetics analyses for 40 species with available allele data. We tested genetic diversity estimates, used Mantel tests for spatial genetic analyses, and evaluated relationships between candidate gene allele length and population averages for geographic range (breeding- and non-breeding latitude), migration distance, timing of migration, taxonomic relationships, and divergence times. Our combined analysis provided evidence (i) of a putative association between Clock gene variation and autumn migration as well as a putative association between Adcyap1 gene variation and spring migration in migratory species; (ii) that these candidate genes are not diagnostic markers to distinguish migratory from sedentary birds; and (iii) of correlated variability in both genes with divergence time, potentially reflecting ancestrally inherited genotypes rather than contemporary changes driven by selection. These findings highlight a tentative association between these candidate genes and migration attributes as well as genetic constraints on evolutionary adaptation.
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Affiliation(s)
- Louis-Stéphane Le Clercq
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
| | - Gaia Bazzi
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale, via Ca' Fornacetta 9, Ozzano Emilia (BO), I-40064, Italy
| | - Jacopo G Cecere
- Area Avifauna Migratrice, Istituto Superiore per la Protezione e la Ricerca Ambientale, via Ca' Fornacetta 9, Ozzano Emilia (BO), I-40064, Italy
| | - Luca Gianfranceschi
- Dipartimento di Bioscienze, Università degli Studi di Milano, via Celoria 26, Milan, I-20133, Italy
| | - Johannes Paul Grobler
- Department of Genetics, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
| | - Antoinette Kotzé
- South African National Biodiversity Institute, P.O. Box 754, Pretoria, 0001, South Africa
- Department of Genetics, University of the Free State, PO Box 339, Bloemfontein, 9300, South Africa
| | - Diego Rubolini
- Dipartimento di Scienze e Politiche Ambientali, Università degli Studi di Milano, via Celoria 26, Milan, I-20133, Italy
- Istituto di Ricerca sulle Acque, IRSA-CNR, Via del Mulino 19, Brugherio (MB), I-20861, Italy
| | - Miriam Liedvogel
- Max Planck Research Group Behavioral Genomics, Max Planck Institute for Evolutionary Biology, Plön, 24306, Germany
- Institute of Avian Research, An der Vogelwarte 21, Wilhelmshaven, 26386, Germany
| | - Desiré Lee Dalton
- School of Health and Life Sciences, Teesside University, Middlesbrough, TS1 3BA, UK
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Beltran RS, Burns JM, Breed GA. Convergence of biannual moulting strategies across birds and mammals. Proc Biol Sci 2019; 285:rspb.2018.0318. [PMID: 29769361 DOI: 10.1098/rspb.2018.0318] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/16/2018] [Indexed: 12/31/2022] Open
Abstract
Birds and mammals have developed numerous strategies for replacing worn feathers and hair. Moulting usually occurs on an annual basis; however, moults that take place twice per year (biannual moults) also occur. Here, we review the forces driving the evolution of various moult strategies, focusing on the special case of the complete biannual moult as a convergence of selection pressures across birds and mammals. Current evidence suggests that harsh environmental conditions or seasonality (e.g. larger variation in temperatures) drive evolution of a biannual moult. In turn, the biannual moult can respond to secondary selection that results in phenotypic alteration such as colour changes for mate choice dynamics (sexual selection) or camouflage requirements (natural selection). We discuss the contributions of natural and sexual selection to the evolution of biannual moulting strategies in the contexts of energetics, niche selection, functionality and physiological mechanisms. Finally, we suggest that moult strategies are directly related to species niche because environmental attributes drive the utility (e.g. thermoregulation, camouflage, social dynamics) of the hair or feathers. Functional efficiency of moult may be undermined if the pace of evolution fails to match that of the changing climate. Thus, future research should seek to understand the plasticity of moult duration and phenology, especially in the context of annual cycles.
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Affiliation(s)
- Roxanne S Beltran
- Department of Biology and Wildlife, University of Alaska Fairbanks, 101 Murie Building, 982 Koyukuk Drive, Fairbanks, AK 99775, USA .,Department of Biological Sciences, University of Alaska Anchorage, 3101 Science Circle, Anchorage, AK 99508, USA
| | - Jennifer M Burns
- Department of Biological Sciences, University of Alaska Anchorage, 3101 Science Circle, Anchorage, AK 99508, USA
| | - Greg A Breed
- Department of Biology and Wildlife, University of Alaska Fairbanks, 101 Murie Building, 982 Koyukuk Drive, Fairbanks, AK 99775, USA.,Institute of Arctic Biology, University of Alaska Fairbanks, 311 Irving I, Fairbanks, AK 99775, USA
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Costanzo A, Ambrosini R, Caprioli M, Gatti E, Parolini M, Romano A, Rubolini D, Gianfranceschi L, Saino N. Extrapair fertilizations vary with female traits and pair composition, besides male attractiveness, in barn swallows. Anim Behav 2017. [DOI: 10.1016/j.anbehav.2017.10.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Saino N, Ambrosini R, Caprioli M, Liechti F, Romano A, Rubolini D, Scandolara C. Wing morphology, winter ecology, and fecundity selection: evidence for sex-dependence in barn swallows (Hirundo rustica). Oecologia 2017; 184:799-812. [PMID: 28741127 DOI: 10.1007/s00442-017-3918-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 07/14/2017] [Indexed: 11/29/2022]
Affiliation(s)
- Nicola Saino
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133, Milan, Italy.
| | - Roberto Ambrosini
- Department of Earth and Environmental Sciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milan, Italy
| | - Manuela Caprioli
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Felix Liechti
- Swiss Ornithological Institute, Seerose 1, 6204, Sempach, Switzerland
| | - Andrea Romano
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Diego Rubolini
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133, Milan, Italy
| | - Chiara Scandolara
- Department of Environmental Science and Policy, University of Milan, via Celoria 26, 20133, Milan, Italy
- Swiss Ornithological Institute, Seerose 1, 6204, Sempach, Switzerland
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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
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