1
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Burch J, Nava C, Blackmon H. Assessing the opportunity for selection to impact morphological traits in crosses between two Solanum species. PeerJ 2024; 12:e17985. [PMID: 39221264 PMCID: PMC11365482 DOI: 10.7717/peerj.17985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Accepted: 08/06/2024] [Indexed: 09/04/2024] Open
Abstract
Within biology, there have been long-standing goals to understand how traits impact fitness, determine the degree of adaptation, and predict responses to selection. One key step in answering these questions is to study the mode of gene action or genetic architecture of traits. The genetic architecture underlying a trait will ultimately determine whether selection can lead to a change in the phenotype. Theoretical and empirical research have shown that additive architectures are most responsive to selection. The genus Solanum offers a unique system to quantify the genetic architecture of traits. Crosses between Solanum pennellii and S. lycopersicum, which have evolved unique adaptive traits for very different environments, offer an opportunity to investigate the genetic architecture of a variety of morphological traits that often are not variable within species. We generated cohorts between strains of these two Solanum species and collected phenotypic data for eight morphological traits. The genetic architectures underlying these traits were estimated using an information-theoretic approach to line cross analysis. By estimating the genetic architectures of these traits, we were able to show a key role for maternal and epistatic effects and infer the accessibility of these traits to selection.
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Affiliation(s)
- Jorja Burch
- Biology, Texas A&M University, College Station, Texas, United States
| | - Crystal Nava
- Biology, Texas A&M University, College Station, Texas, United States
| | - Heath Blackmon
- Biology, Texas A&M University, College Station, Texas, United States
- Interdisciplinary Program in Ecology and Evolutionary Biology, Texas A&M University, College Station, Texas, United States
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2
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Dickel L, Arcese P, Keller LF, Nietlisbach P, Goedert D, Jensen H, Reid JM. Multigenerational Fitness Effects of Natural Immigration Indicate Strong Heterosis and Epistatic Breakdown in a Wild Bird Population. Am Nat 2024; 203:411-431. [PMID: 38358807 DOI: 10.1086/728669] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractThe fitness of immigrants and their descendants produced within recipient populations fundamentally underpins the genetic and population dynamic consequences of immigration. Immigrants can in principle induce contrasting genetic effects on fitness across generations, reflecting multifaceted additive, dominance, and epistatic effects. Yet full multigenerational and sex-specific fitness effects of regular immigration have not been quantified within naturally structured systems, precluding inference on underlying genetic architectures and population outcomes. We used four decades of song sparrow (Melospiza melodia) life history and pedigree data to quantify fitness of natural immigrants, natives, and their F1, F2, and backcross descendants and test for evidence of nonadditive genetic effects. Values of key fitness components (including adult lifetime reproductive success and zygote survival) of F1 offspring of immigrant-native matings substantially exceeded their parent mean, indicating strong heterosis. Meanwhile, F2 offspring of F1-F1 matings had notably low values, indicating surprisingly strong epistatic breakdown. Furthermore, magnitudes of effects varied among fitness components and differed between female and male descendants. These results demonstrate that strong nonadditive genetic effects on fitness can arise within weakly structured and fragmented populations experiencing frequent natural immigration. Such effects will substantially affect the net degree of effective gene flow and resulting local genetic introgression and adaptation.
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3
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Faraji-Arough H, Maghsoudi A, Ghazaghi M, Rokouei M. Additive and non-additive genetic effects of humoral immune traits in Japanese quail. J APPL POULTRY RES 2022. [DOI: 10.1016/j.japr.2022.100287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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4
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Mularo AJ, Bernal XE, DeWoody JA. Dominance can increase genetic variance after a population bottleneck: a synthesis of the theoretical and empirical evidence. J Hered 2022; 113:257-271. [PMID: 35143665 DOI: 10.1093/jhered/esac007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 02/07/2022] [Indexed: 11/13/2022] Open
Abstract
Drastic reductions in population size, or population bottlenecks, can lead to a reduction in additive genetic variance and adaptive potential. Genetic variance for some quantitative genetic traits, however, can increase after a population reduction. Empirical evaluations of quantitative traits following experimental bottlenecks indicate that non-additive genetic effects, including both allelic dominance at a given locus and epistatic interactions among loci, may impact the additive variance contributed by alleles that ultimately influences phenotypic expression and fitness. The dramatic effects of bottlenecks on overall genetic diversity have been well studied, but relatively little is known about how dominance and demographic events like bottlenecks can impact additive genetic variance. Herein, we critically examine how the degree of dominance among alleles affects additive genetic variance after a bottleneck. We first review and synthesize studies that document the impact of empirical bottlenecks on dominance variance. We then extend earlier work by elaborating on two theoretical models that illustrate the relationship between dominance and the potential increase in additive genetic variance immediately following a bottleneck. Furthermore, we investigate the parameters that influence the maximum level of genetic variation (associated with adaptive potential) after a bottleneck, including the number of founding individuals. Finally, we validated our methods using forward-time population genetic simulations of loci with varying dominance and selection levels. The fate of non-additive genetic variation following bottlenecks could have important implications for conservation and management efforts in a wide variety of taxa, and our work should help contextualize future studies (e.g., epistatic variance) in population genomics.
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Affiliation(s)
- Andrew J Mularo
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
| | - Ximena E Bernal
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Smithsonian Tropical Research Institute, Balboa, Republic of Panamá
| | - J Andrew DeWoody
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA.,Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
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5
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Xiao L, Man L, Yang L, Zhang J, Liu B, Quan M, Lu W, Fang Y, Wang D, Du Q, Zhang D. Association Study and Mendelian Randomization Analysis Reveal Effects of the Genetic Interaction Between PtoMIR403b and PtoGT31B-1 on Wood Formation in Populus tomentosa. FRONTIERS IN PLANT SCIENCE 2021; 12:704941. [PMID: 34527007 PMCID: PMC8435637 DOI: 10.3389/fpls.2021.704941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
MicroRNAs (miRNAs), important posttranscriptional regulators of gene expression, play a crucial role in plant growth and development. A single miRNA can regulate numerous target genes, making the determination of its function and interaction with targets challenging. We identified PtomiR403b target to PtoGT31B-1, which encodes a galactosyltransferase responsible for the biosynthesis of cell wall polysaccharides. We performed an association study and epistasis and Mendelian randomization (MR) analyses to explore how the genetic interaction between PtoMIR403b and its target PtoGT31B-1 underlies wood formation. Single nucleotide polymorphism (SNP)-based association studies identified 25 significant associations (P < 0.01, Q < 0.05), and PtoMIR403b and PtoGT31B-1 were associated with five traits, suggesting a role for PtomiR403b and PtoGT31B-1 in wood formation. Epistasis analysis identified 93 significant pairwise epistatic associations with 10 wood formation traits, and 37.89% of the SNP-SNP pairs indicated interactions between PtoMIR403b and PtoGT31B-1. We performed an MR analysis to demonstrate the causality of the relationships between SNPs in PtoMIR403b and wood property traits and that PtoMIR403b modulates wood formation by regulating expression of PtoGT31B-1. Therefore, our findings will facilitate dissection of the functions and interactions with miRNA-targets.
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Affiliation(s)
- Liang Xiao
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Liting Man
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Xining Forestry Science Research Institute, Xining, China
| | - Lina Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jinmei Zhang
- Xining Forestry Science Research Institute, Xining, China
| | - Baoyao Liu
- Xining Forestry Science Research Institute, Xining, China
| | - Mingyang Quan
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Wenjie Lu
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yuanyuan Fang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Dan Wang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qingzhang Du
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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6
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Chicco D, Faultless T. Brief Survey on Machine Learning in Epistasis. Methods Mol Biol 2021; 2212:169-179. [PMID: 33733356 DOI: 10.1007/978-1-0716-0947-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
In biology, the term "epistasis" indicates the effect of the interaction of a gene with another gene. A gene can interact with an independently sorted gene, located far away on the chromosome or on an entirely different chromosome, and this interaction can have a strong effect on the function of the two genes. These changes then can alter the consequences of the biological processes, influencing the organism's phenotype. Machine learning is an area of computer science that develops statistical methods able to recognize patterns from data. A typical machine learning algorithm consists of a training phase, where the model learns to recognize specific trends in the data, and a test phase, where the trained model applies its learned intelligence to recognize trends in external data. Scientists have applied machine learning to epistasis problems multiple times, especially to identify gene-gene interactions from genome-wide association study (GWAS) data. In this brief survey, we report and describe the main scientific articles published in data mining and epistasis. Our article confirms the effectiveness of machine learning in this genetics subfield.
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Affiliation(s)
- Davide Chicco
- Krembil Research Institute, Toronto, Ontario, Canada.
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7
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Engen S, Sæther BE. Structure of the G-matrix in relation to phenotypic contributions to fitness. Theor Popul Biol 2021; 138:43-56. [PMID: 33610661 DOI: 10.1016/j.tpb.2021.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 01/20/2021] [Accepted: 01/21/2021] [Indexed: 10/22/2022]
Abstract
Classical theory in population genetics includes derivation of the stationary distribution of allele frequencies under balance between selection, genetic drift, and mutation. Here we investigate the simplest generalization of these single locus models to quantitative genetics with many loci, assuming simple additive effects on a set of phenotypes and a linear approximation to the fitness function. Genetic effects and pleiotropy are simulated by a prescribed stochastic model. Our goal is to analyze the structure of the G-matrix at stasis when the model is not very close to being neutral. The smallest eigenvalue of the G-matrix is practically zero by Fisher's fundamental theorem for natural selection and the fitness function is approximately a linear function of the corresponding eigenvector. Evolution of genetic trade-offs is closely linked to the fitness function. If a single locus never codes for more than two traits, then additive genetic covariance between two phenotype components always has the opposite sign of the product of their coefficients in the fitness function under no mutation, a pattern that is likely to occur frequently also in more complex models. In our major examples only 1-2 percent of the loci are over-dominant for fitness, but they still account for practically all dominance variance in fitness as well as all contributions to the G-matrix. These analyses show that the structure of the G-matrix reveals important information about the contribution of different traits to fitness.
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Affiliation(s)
- Steinar Engen
- Centre for Biodiversity Dynamics, Department of Mathematical Sciences, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
| | - Bernt-Erik Sæther
- Centre for Biodiversity Dynamics, Department of Biology, Norwegian University of Science and Technology, NO-7491 Trondheim, Norway.
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8
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Baškiera S, Gvoždík L. Repeatability and heritability of resting metabolic rate in a long-lived amphibian. Comp Biochem Physiol A Mol Integr Physiol 2020; 253:110858. [PMID: 33276133 DOI: 10.1016/j.cbpa.2020.110858] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/28/2020] [Accepted: 11/28/2020] [Indexed: 11/25/2022]
Abstract
Resting metabolic rate (RMR), i.e. spent energy necessary to maintain basic life functions, is a basic component of energy budget in ectotherms. The evolution of RMR through natural selection rests on the premise of its non-zero repeatability and heritability, i.e. consistent variation within individual lifetimes and resemblance between parents and their offspring, respectively. Joint estimates of RMR repeatability and heritability are missing in ectotherms, however, which precludes estimations of the evolutionary potential of this trait. We examined RMR repeatability and heritability in a long-lived ectotherm, the alpine newt (Ichthyosaura alpestris). Individual RMR was repeatable over both six-month (0.28 ± 0.09 [SE]) and five-year (0.16 ± 0.07) periods. While there was no resemblance between parent and offspring RMR (0.21 ± 0.34), the trait showed similarity among offspring within families (broad-sense heritability; 0.25 ± 0.09). Similar repeatability and broad-sense heritability values in parental and offspring generations, respectively, and non-conclusive narrow-sense heritability suggest the contribution of non-additive genetic factors to total phenotypic variance in this trait. We conclude that RMR evolutionary trajectories are shaped by other processes than natural selection in this long-lived ectotherm.
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Affiliation(s)
- Senka Baškiera
- Department of Botany and Zoology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lumír Gvoždík
- Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic.
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9
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Koch EL, Sbilordo SH, Guillaume F. Genetic variance in fitness and its cross‐sex covariance predict adaptation during experimental evolution. Evolution 2020; 74:2725-2740. [DOI: 10.1111/evo.14119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 09/29/2020] [Accepted: 10/25/2020] [Indexed: 01/05/2023]
Affiliation(s)
- Eva L. Koch
- Department of Evolutionary Biology and Environmental Studies University of Zürich Winterthurerstr. 190 Zürich 8057 Switzerland
- Department of Animal and Plant Science University of Sheffield Western Bank Sheffield S10 2TN United Kingdom
| | - Sonja H. Sbilordo
- Department of Evolutionary Biology and Environmental Studies University of Zürich Winterthurerstr. 190 Zürich 8057 Switzerland
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies University of Zürich Winterthurerstr. 190 Zürich 8057 Switzerland
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10
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Ruckman SN, Blackmon H. The March of the Beetles: Epistatic Components Dominate Divergence in Dispersal Tendency in Tribolium castaneum. J Hered 2020; 111:498-505. [PMID: 32798223 PMCID: PMC7525825 DOI: 10.1093/jhered/esaa030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 08/12/2020] [Indexed: 11/14/2022] Open
Abstract
The genetic underpinnings of traits are rarely simple. Most traits of interest are instead the product of multiple genes acting in concert to determine the phenotype. This is particularly true for behavioral traits, like dispersal. Our investigation focuses on the genetic architecture of dispersal tendency in the red flour beetle, Tribolium castaneum. We used artificial selection to generate lines with either high or low dispersal tendency. Our populations responded quickly in the first generations of selection and almost all replicates had higher dispersal tendency in males than in females. These selection lines were used to create a total of 6 additional lines: F1 and reciprocal F1, as well as 4 types of backcrosses. We estimated the composite genetic effects that contribute to divergence in dispersal tendency among lines using line cross-analysis. We found variation in the dispersal tendency of our lines was best explained by autosomal additive and 3 epistatic components. Our results indicate that dispersal tendency is heritable, but much of the divergence in our selection lines was due to epistatic effects. These results are consistent with other life-history traits that are predicted to maintain more epistatic variance than additive variance and highlight the potential for epistatic variation to act as an adaptive reserve that may become visible to selection when a population is subdivided.
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Affiliation(s)
- Sarah N Ruckman
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX.,Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, 2475 TAMU, College Station, TX
| | - Heath Blackmon
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, TX.,Ecology and Evolutionary Biology Interdisciplinary Program, Texas A&M University, 2475 TAMU, College Station, TX
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11
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Armstrong A, Anderson NW, Blackmon H. Inferring the potentially complex genetic architectures of adaptation, sexual dimorphism and genotype by environment interactions by partitioning of mean phenotypes. J Evol Biol 2019; 32:369-379. [PMID: 30698300 DOI: 10.1111/jeb.13421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 12/23/2018] [Accepted: 01/23/2019] [Indexed: 01/18/2023]
Abstract
Genetic architecture fundamentally affects the way that traits evolve. However, the mapping of genotype to phenotype includes complex interactions with the environment or even the sex of an organism that can modulate the expressed phenotype. Line-cross analysis is a powerful quantitative genetics method to infer genetic architecture by analysing the mean phenotype value of two diverged strains and a series of subsequent crosses and backcrosses. However, it has been difficult to account for complex interactions with the environment or sex within this framework. We have developed extensions to line-cross analysis that allow for gene by environment and gene by sex interactions. Using extensive simulation studies and reanalysis of empirical data, we show that our approach can account for both unintended environmental variation when crosses cannot be reared in a common garden and can be used to test for the presence of gene by environment or gene by sex interactions. In analyses that fail to account for environmental variation between crosses, we find that line-cross analysis has low power and high false-positive rates. However, we illustrate that accounting for environmental variation allows for the inference of adaptive divergence, and that accounting for sex differences in phenotypes allows practitioners to infer the genetic architecture of sexual dimorphism.
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Affiliation(s)
- Andrew Armstrong
- Department of Mathematics, Texas A&M University, College Station, Texas
| | - Nathan W Anderson
- Department of Mathematics, Texas A&M University, College Station, Texas
| | - Heath Blackmon
- Department of Biology, Texas A&M University, College Station, Texas
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12
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Hendry AP, Schoen DJ, Wolak ME, Reid JM. The Contemporary Evolution of Fitness. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2018. [DOI: 10.1146/annurev-ecolsys-110617-062358] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The rate of evolution of population mean fitness informs how selection acting in contemporary populations can counteract environmental change and genetic degradation (mutation, gene flow, drift, recombination). This rate influences population increases (e.g., range expansion), population stability (e.g., cryptic eco-evolutionary dynamics), and population recovery (i.e., evolutionary rescue). We review approaches for estimating such rates, especially in wild populations. We then review empirical estimates derived from two approaches: mutation accumulation (MA) and additive genetic variance in fitness (IAw). MA studies inform how selection counters genetic degradation arising from deleterious mutations, typically generating estimates of <1% per generation. IAw studies provide an integrated prediction of proportional change per generation, nearly always generating estimates of <20% and, more typically, <10%. Overall, considerable, but not unlimited, evolutionary potential exists in populations facing detrimental environmental or genetic change. However, further studies with diverse methods and species are required for more robust and general insights.
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Affiliation(s)
- Andrew P. Hendry
- Redpath Museum, McGill University, Montréal, Québec H3A 0C4, Canada
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Daniel J. Schoen
- Department of Biology, McGill University, Montréal, Québec H3A 1B1, Canada
| | - Matthew E. Wolak
- Department of Biological Sciences, Auburn University, Auburn, Alabama 36849, USA
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
| | - Jane M. Reid
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, United Kingdom
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13
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Pujol B, Blanchet S, Charmantier A, Danchin E, Facon B, Marrot P, Roux F, Scotti I, Teplitsky C, Thomson CE, Winney I. The Missing Response to Selection in the Wild. Trends Ecol Evol 2018; 33:337-346. [PMID: 29628266 PMCID: PMC5937857 DOI: 10.1016/j.tree.2018.02.007] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 02/26/2018] [Accepted: 02/28/2018] [Indexed: 01/28/2023]
Abstract
Although there are many examples of contemporary directional selection, evidence for responses to selection that match predictions are often missing in quantitative genetic studies of wild populations. This is despite the presence of genetic variation and selection pressures – theoretical prerequisites for the response to selection. This conundrum can be explained by statistical issues with accurate parameter estimation, and by biological mechanisms that interfere with the response to selection. These biological mechanisms can accelerate or constrain this response. These mechanisms are generally studied independently but might act simultaneously. We therefore integrated these mechanisms to explore their potential combined effect. This has implications for explaining the apparent evolutionary stasis of wild populations and the conservation of wildlife. Recent discoveries at the intersection of quantitative genetics and evolutionary ecology are challenging our views on the potential of wild populations to respond to selection. Multiple biological mechanisms can disconnect genetic variation from the response to selection in the wild. We highlight areas for future research. We provide an integrative framework that can be used to qualitatively assess the combined influence of these mechanisms on the response to selection.
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Affiliation(s)
- Benoit Pujol
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 31062 Toulouse, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France.
| | - Simon Blanchet
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 31062 Toulouse, France; Station d'Ecologie Théorique Expérimentale (SETE), CNRS UMR 5321, Université Paul Sabatier, 09200 Moulis, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Anne Charmantier
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), CNRS UMR 5175, 34293 Montpellier, France; Département des Sciences Biologiques, Université du Québec à Montréal, CP 888 Succursale Centre-Ville, H3P 3P8 QC, Canada; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Etienne Danchin
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 31062 Toulouse, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Benoit Facon
- UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical (PVBMT), Institut National de la Recherche Agronomique (INRA), Saint Pierre, Réunion, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Pascal Marrot
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 31062 Toulouse, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Fabrice Roux
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, CNRS, Université de Toulouse, 31326 Castanet-Tolosan, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Ivan Scotti
- INRA Unité de Recherche 0629 Ecologie des Forêts Méditerranéennes, 84914 Avignon, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Céline Teplitsky
- Centre d'Ecologie Fonctionnelle et Evolutive (CEFE), CNRS UMR 5175, 34293 Montpellier, France; Muséum National d'Histoire Naturelle, CNRS UMR 7204 Centre d'Écologie et des Sciences de la Conservation (CESCO), 75005 Paris, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Caroline E Thomson
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 31062 Toulouse, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
| | - Isabel Winney
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université Fédérale de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 31062 Toulouse, France; Groupement de Recherche de l'Institut Ecologie et Environnement 6448, Génétique Quantitative dans les Populations Naturelles (GQPN), c/o EDB, 31062 Toulouse, France
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14
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van Heerwaarden B, Sgrò CM. The quantitative genetic basis of clinal divergence in phenotypic plasticity. Evolution 2017; 71:2618-2633. [PMID: 28857153 DOI: 10.1111/evo.13342] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 08/14/2017] [Accepted: 08/16/2017] [Indexed: 01/18/2023]
Abstract
Phenotypic plasticity is thought to be an important mechanism for adapting to environmental heterogeneity. Nonetheless, the genetic basis of plasticity is still not well understood. In Drosophila melanogaster and D. simulans, body size and thermal stress resistance show clinal patterns along the east coast of Australia, and exhibit plastic responses to different developmental temperatures. The genetic basis of thermal plasticity, and whether the genetic effects underlying clinal variation in traits and their plasticity are similar, remains unknown. Here, we use line-cross analyses between a tropical and temperate population of Drosophila melanogaster and D. simulans developed at three constant temperatures (18°C, 25°C, and 29°C) to investigate the quantitative genetic basis of clinal divergence in mean thermal response (elevation) and plasticity (slope and curvature) for thermal stress and body size traits. Generally, the genetic effects underlying divergence in mean response and plasticity differed, suggesting that different genetic models may be required to understand the evolution of trait means and plasticity. Furthermore, our results suggest that nonadditive genetic effects, in particular epistasis, may commonly underlie plastic responses, indicating that current models that ignore epistasis may be insufficient to understand and predict evolutionary responses to environmental change.
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Affiliation(s)
| | - Carla M Sgrò
- School of Biological Sciences, Monash University, Clayton 3800, Victoria, Australia
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15
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Marsh JN, Vega-Trejo R, Jennions MD, Head ML. Why does inbreeding reduce male paternity? Effects on sexually selected traits. Evolution 2017; 71:2728-2737. [PMID: 28857148 DOI: 10.1111/evo.13339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 08/16/2017] [Indexed: 01/17/2023]
Abstract
Mating with relatives has often been shown to negatively affect offspring fitness (inbreeding depression). There is considerable evidence for inbreeding depression due to effects on naturally selected traits, particularly those expressed early in life, but there is less evidence of it for sexually selected traits. This is surprising because sexually selected traits are expected to exhibit strong inbreeding depression. Here, we experimentally created inbred and outbred male mosquitofish (Gambusia holbrooki). Inbred males were the offspring of matings between full siblings. We then investigated how inbreeding influenced a number of sexually selected male traits, specifically: attractiveness, sperm number and velocity, as well as sperm competitiveness based on a male's share of paternity. We found no inbreeding depression for male attractiveness or sperm traits. There was, however, evidence that lower heterozygosity decreased paternity due to reduced sperm competitiveness. Our results add to the growing evidence that competitive interactions exacerbate the negative effects of the increased homozygosity that arises when there is inbreeding.
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Affiliation(s)
- Jason N Marsh
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Regina Vega-Trejo
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Michael D Jennions
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia.,Wissenschaftskolleg zu Berlin, Wallotstaße 19, 14193 Berlin, Germany
| | - Megan L Head
- Division of Evolution, Ecology and Genetics, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
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16
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Saastamoinen M, Bocedi G, Cote J, Legrand D, Guillaume F, Wheat CW, Fronhofer EA, Garcia C, Henry R, Husby A, Baguette M, Bonte D, Coulon A, Kokko H, Matthysen E, Niitepõld K, Nonaka E, Stevens VM, Travis JMJ, Donohue K, Bullock JM, Del Mar Delgado M. Genetics of dispersal. Biol Rev Camb Philos Soc 2017; 93:574-599. [PMID: 28776950 PMCID: PMC5811798 DOI: 10.1111/brv.12356] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 07/03/2017] [Accepted: 07/05/2017] [Indexed: 12/12/2022]
Abstract
Dispersal is a process of central importance for the ecological and evolutionary dynamics of populations and communities, because of its diverse consequences for gene flow and demography. It is subject to evolutionary change, which begs the question, what is the genetic basis of this potentially complex trait? To address this question, we (i) review the empirical literature on the genetic basis of dispersal, (ii) explore how theoretical investigations of the evolution of dispersal have represented the genetics of dispersal, and (iii) discuss how the genetic basis of dispersal influences theoretical predictions of the evolution of dispersal and potential consequences. Dispersal has a detectable genetic basis in many organisms, from bacteria to plants and animals. Generally, there is evidence for significant genetic variation for dispersal or dispersal‐related phenotypes or evidence for the micro‐evolution of dispersal in natural populations. Dispersal is typically the outcome of several interacting traits, and this complexity is reflected in its genetic architecture: while some genes of moderate to large effect can influence certain aspects of dispersal, dispersal traits are typically polygenic. Correlations among dispersal traits as well as between dispersal traits and other traits under selection are common, and the genetic basis of dispersal can be highly environment‐dependent. By contrast, models have historically considered a highly simplified genetic architecture of dispersal. It is only recently that models have started to consider multiple loci influencing dispersal, as well as non‐additive effects such as dominance and epistasis, showing that the genetic basis of dispersal can influence evolutionary rates and outcomes, especially under non‐equilibrium conditions. For example, the number of loci controlling dispersal can influence projected rates of dispersal evolution during range shifts and corresponding demographic impacts. Incorporating more realism in the genetic architecture of dispersal is thus necessary to enable models to move beyond the purely theoretical towards making more useful predictions of evolutionary and ecological dynamics under current and future environmental conditions. To inform these advances, empirical studies need to answer outstanding questions concerning whether specific genes underlie dispersal variation, the genetic architecture of context‐dependent dispersal phenotypes and behaviours, and correlations among dispersal and other traits.
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Affiliation(s)
- Marjo Saastamoinen
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Greta Bocedi
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K
| | - Julien Cote
- Laboratoire Évolution & Diversité Biologique UMR5174, CNRS, Université Toulouse III Paul Sabatier, 31062 Toulouse, France
| | - Delphine Legrand
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France
| | - Frédéric Guillaume
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Christopher W Wheat
- Population Genetics, Department of Zoology, Stockholm University, S-10691 Stockholm, Sweden
| | - Emanuel A Fronhofer
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland.,Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dubendorf, Switzerland
| | - Cristina Garcia
- CIBIO-InBIO, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Roslyn Henry
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K.,School of GeoSciences, University of Edinburgh, Edinburgh EH89XP, U.K
| | - Arild Husby
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Michel Baguette
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France.,Museum National d'Histoire Naturelle, Institut Systématique, Evolution, Biodiversité, UMR 7205, F-75005 Paris, France
| | - Dries Bonte
- Department of Biology, Ghent University, B-9000 Ghent, Belgium
| | - Aurélie Coulon
- PSL Research University, CEFE UMR 5175, CNRS, Université de Montpellier, Université Paul-Valéry Montpellier, EPHE, Biogéographie et Ecologie des Vertébrés, 34293 Montpellier, France.,CESCO UMR 7204, Bases écologiques de la conservation, Muséum national d'Histoire naturelle, 75005 Paris, France
| | - Hanna Kokko
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, CH-8057 Zurich, Switzerland
| | - Erik Matthysen
- Evolutionary Ecology Group, Department of Biology, University of Antwerp, Universiteitsplein 1, 2610 Wilrijk, Belgium
| | - Kristjan Niitepõld
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Etsuko Nonaka
- Department of Biosciences, Metapopulation Research Centre, University of Helsinki, P.O. Box 65, 00014 Helsinki, Finland
| | - Virginie M Stevens
- Centre National de la Recherche Scientifique and Université Paul Sabatier Toulouse III, SETE Station d'Ecologie Théorique et Expérimentale, UMR 5321, 09200 Moulis, France
| | - Justin M J Travis
- School of Biological Sciences, University of Aberdeen, Aberdeen AB24 2TZ, U.K
| | | | - James M Bullock
- NERC Centre for Ecology & Hydrology, Wallingford OX10 8BB, U.K
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17
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Guinand B, Vandeputte M, Dupont-Nivet M, Vergnet A, Haffray P, Chavanne H, Chatain B. Metapopulation patterns of additive and nonadditive genetic variance in the sea bass ( Dicentrarchus labrax). Ecol Evol 2017; 7:2777-2790. [PMID: 28428868 PMCID: PMC5395432 DOI: 10.1002/ece3.2832] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 12/19/2016] [Accepted: 01/28/2017] [Indexed: 01/30/2023] Open
Abstract
Describing and explaining the geographic within‐species variation in phenotypes (“phenogeography”) in the sea over a species distribution range is central to our understanding of a variety of eco‐evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full‐sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria‐Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.
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Affiliation(s)
- Bruno Guinand
- Département Biologie-Ecologie Université de Montpellier Montpellier France.,UMR CNRS IRD EPHE UM Institut des Sciences de l'Evolution de Montpellier Montpellier France
| | - Marc Vandeputte
- INRA UMR 1313 GABI Domaine de Vilvert Jouy-en-Josas France.,Ifremer UMR 9190 Marine Biodiversity, Exploitation and Conservation Palavas-les-Flots France
| | | | - Alain Vergnet
- Ifremer UMR 9190 Marine Biodiversity, Exploitation and Conservation Palavas-les-Flots France
| | | | - Hervé Chavanne
- Istituto Sperimentale Lazzaro Spallanzani Rivolta d'Adda Italy
| | - Béatrice Chatain
- Ifremer UMR 9190 Marine Biodiversity, Exploitation and Conservation Palavas-les-Flots France
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18
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Chirgwin E, Marshall DJ, Sgrò CM, Monro K. The other 96%: Can neglected sources of fitness variation offer new insights into adaptation to global change? Evol Appl 2017; 10:267-275. [PMID: 28250811 PMCID: PMC5322406 DOI: 10.1111/eva.12447] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/31/2016] [Indexed: 01/07/2023] Open
Abstract
Mounting research considers whether populations may adapt to global change based on additive genetic variance in fitness. Yet selection acts on phenotypes, not additive genetic variance alone, meaning that persistence and evolutionary potential in the near term, at least, may be influenced by other sources of fitness variation, including nonadditive genetic and maternal environmental effects. The fitness consequences of these effects, and their environmental sensitivity, are largely unknown. Here, applying a quantitative genetic breeding design to an ecologically important marine tubeworm, we examined nonadditive genetic and maternal environmental effects on fitness (larval survival) across three thermal environments. We found that these effects are nontrivial and environment dependent, explaining at least 44% of all parentally derived effects on survival at any temperature and 96% of parental effects at the most stressful temperature. Unlike maternal environmental effects, which manifested at the latter temperature only, nonadditive genetic effects were consistently significant and covaried positively across temperatures (i.e., parental combinations that enhanced survival at one temperature also enhanced survival at elevated temperatures). Thus, while nonadditive genetic and maternal environmental effects have long been neglected because their evolutionary consequences are complex, unpredictable, or seen as transient, we argue that they warrant further attention in a rapidly warming world.
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Affiliation(s)
- Evatt Chirgwin
- Centre for Geometric BiologyMonash UniversityMelbourneVICAustralia
- School of Biological SciencesMonash UniversityMelbourneVICAustralia
| | - Dustin J. Marshall
- Centre for Geometric BiologyMonash UniversityMelbourneVICAustralia
- School of Biological SciencesMonash UniversityMelbourneVICAustralia
| | - Carla M. Sgrò
- School of Biological SciencesMonash UniversityMelbourneVICAustralia
| | - Keyne Monro
- Centre for Geometric BiologyMonash UniversityMelbourneVICAustralia
- School of Biological SciencesMonash UniversityMelbourneVICAustralia
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19
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Houde ALS, Wilson CC, Pitcher TE. Genetic architecture and maternal contributions of early-life survival in lake trout Salvelinus namaycush. JOURNAL OF FISH BIOLOGY 2016; 88:2088-2094. [PMID: 27097972 DOI: 10.1111/jfb.12965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 02/22/2016] [Indexed: 06/05/2023]
Abstract
The influences of additive, non-additive and maternal effects on early survival (uneyed embryo survival, eyed embryo survival, alevin survival and overall survival to first feeding) were quantified in lake trout Salvelinus namaycush using a 7 × 7 full-factorial breeding design. Maternal effects followed by non-additive genetic effects explained around one third of the phenotypic variance of the survival traits. Although the amount of additive genetic effects were low (<1%), suggesting a limited potential of the traits to respond to new selection pressures, how maternal and non-additive genetic effects may respond to selection under certain circumstances are discussed.
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Affiliation(s)
- A L S Houde
- Department of Biological Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
| | - C C Wilson
- Aquatic Research and Monitoring Section, Ontario Ministry of Natural Resources and Forestry, Trent University, Peterborough, ON, K9J 7B8, Canada
| | - T E Pitcher
- Department of Biological Sciences, University of Windsor, Windsor, ON, N9B 3P4, Canada
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, ON, N9B 3P4, Canada
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20
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Etterson JR, Franks SJ, Mazer SJ, Shaw RG, Gorden NLS, Schneider HE, Weber JJ, Winkler KJ, Weis AE. Project Baseline: An unprecedented resource to study plant evolution across space and time. AMERICAN JOURNAL OF BOTANY 2016; 103:164-173. [PMID: 26772308 DOI: 10.3732/ajb.1500313] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 10/07/2015] [Indexed: 06/05/2023]
Abstract
PREMISE OF THE STUDY Project Baseline is a seed bank that offers an unprecedented opportunity to examine spatial and temporal dimensions of microevolution during an era of rapid environmental change. Over the upcoming 50 years, biologists will withdraw genetically representative samples of past populations from this time capsule of seeds and grow them contemporaneously with modern samples to detect any phenotypic and molecular evolution that has occurred during the intervening time. METHODS We carefully developed this living genome bank using protocols to enhance its experimental value by collecting from multiple populations and species across a broad geographical range in sites that are likely to be preserved into the future. Seeds are accessioned with site and population data and are stored by maternal line under conditions that maximize seed longevity. This open-access resource will be available to researchers at regular intervals to evaluate contemporary evolution. KEY RESULTS To date, the Project Baseline collection includes 100-200 maternal lines of each of 61 species collected from over 831 populations on sites that are likely to be preserved into the future across the United States (∼78,000 maternal lines). Our strategically designed collection circumvents some problems that can cloud the results of "resurrection" studies involving naturally preserved or existing seed collections that are available fortuitously. CONCLUSIONS The resurrection approach can be coupled with long-established and newer techniques over the next five decades to elucidate genetic change and thereby vastly improve our understanding of temporal and spatial changes in phenotype and the evolutionary processes underlying it.
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Affiliation(s)
- Julie R Etterson
- Department of Biology, University of Minnesota Duluth, 207A Swenson Science Building, 1035 Kirby Drive, Duluth, Minnesota 55812 USA
| | - Steven J Franks
- Department of Biological Sciences, 441 East Fordham Road, Fordham University, Bronx, New York 10458 USA
| | - Susan J Mazer
- Department of Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, California 93106 USA
| | - Ruth G Shaw
- Department of Ecology, Evolution and Behavior, 1479 Gortner Avenue, University of Minnesota Twin Cities, St. Paul, Minnesota 55108 USA
| | - Nicole L Soper Gorden
- Department of Biology, University of Minnesota Duluth, 207A Swenson Science Building, 1035 Kirby Drive, Duluth, Minnesota 55812 USA
| | - Heather E Schneider
- Department of Ecology, Evolution & Marine Biology, University of California, Santa Barbara, Santa Barbara, California 93106 USA
| | - Jennifer J Weber
- Department of Biological Sciences, 441 East Fordham Road, Fordham University, Bronx, New York 10458 USA
| | - Katharine J Winkler
- Department of Biology, University of Minnesota Duluth, 207A Swenson Science Building, 1035 Kirby Drive, Duluth, Minnesota 55812 USA
| | - Arthur E Weis
- Department of Ecology and Evolutionary Biology, and Koffler Scientific Reserve at Jokers Hill, 25 Willcocks Street, University of Toronto, Toronto, Ontario, Canada M5S 3B2
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21
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Response of body size and developmental time of Tribolium castaneum to constant versus fluctuating thermal conditions. J Therm Biol 2015; 51:110-8. [PMID: 25965024 DOI: 10.1016/j.jtherbio.2015.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 03/26/2015] [Accepted: 04/06/2015] [Indexed: 11/21/2022]
Abstract
Temperature has profound effects on biological functions at all levels of organization. In ectotherms, body size is usually negatively correlated with ambient temperature during development, a phenomenon known as The Temperature-Size Rule (TSR). However, a growing number of studies have indicated that temperature fluctuations have a large influence on life history traits and the implications of such fluctuations for the TSR are unknown. Our study investigated the effect of different constant and fluctuating temperatures on the body mass and development time of red flour beetles (Tribolium castaneum Herbst, 1797); we also examined whether the sexes differed in their responses to thermal conditions. We exposed the progeny of half-sib families of a T. castaneum laboratory strain to one of four temperature regimes: constant 30°C, constant 25°C, fluctuating with a daily mean of 30°C, or fluctuating with a daily mean of 25°C. Sex-specific development time and body mass at emergence were determined. Beetles developed the fastest and had the greatest body mass upon emergence when they were exposed to a constant temperature of 30°C. This pattern was reversed when beetles experienced a constant temperature of 25°C: slowest development and lowest body mass upon emergence were observed. Fluctuations changed those effects significantly - impact of temperature on development time was smaller, while differences in body mass disappeared completely. Our results do not fit TSR predictions. Furthermore, regardless of the temperature regime, females acquired more mass, while there were no differences between sexes in development time to eclosion. This finding fails to support one of the explanations for smaller male size: that selection favors the early emergence of males. We found no evidence of genotype × environment interactions for selected set of traits.
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22
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Vijendravarma RK, Kawecki TJ. Idiosyncratic evolution of maternal effects in response to juvenile malnutrition in Drosophila. J Evol Biol 2015; 28:876-84. [PMID: 25716891 DOI: 10.1111/jeb.12611] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 11/30/2022]
Abstract
Maternal effects often affect fitness traits, but there is little experimental evidence pertaining to their contribution to response to selection imposed by novel environments. We studied the evolution of maternal effects in Drosophila populations selected for tolerance to chronic larval malnutrition. To this end, we performed pairwise reciprocal F1 crosses between six selected (malnutrition tolerant) populations and six unselected control populations and assessed the effect of cross direction on larval growth and developmental rate, adult weight and egg-to-adult viability expressed under the malnutrition regime. Each pair of reciprocal crosses revealed large maternal effects (possibly including cytoplasmic genetic effects) on at least one trait, but the magnitude, sign and which traits were affected varied among populations. Thus, maternal effects contributed significantly to the response to selection imposed by the malnutrition regime, but these changes were idiosyncratic, suggesting a rugged adaptive landscape. Furthermore, although the selected populations evolved both faster growth and higher viability, the maternal effects on growth rate and viability were negatively correlated across populations. Thus, genes mediating maternal effects can evolve to partially counteract the response to selection mediated by the effects of alleles on their own carriers' phenotype, and maternal effects may contribute to evolutionary trade-offs between components of offspring fitness.
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Affiliation(s)
- R K Vijendravarma
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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23
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Dominance genetic variance for traits under directional selection in Drosophila serrata. Genetics 2015; 200:371-84. [PMID: 25783700 DOI: 10.1534/genetics.115.175489] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 03/11/2015] [Indexed: 01/10/2023] Open
Abstract
In contrast to our growing understanding of patterns of additive genetic variance in single- and multi-trait combinations, the relative contribution of nonadditive genetic variance, particularly dominance variance, to multivariate phenotypes is largely unknown. While mechanisms for the evolution of dominance genetic variance have been, and to some degree remain, subject to debate, the pervasiveness of dominance is widely recognized and may play a key role in several evolutionary processes. Theoretical and empirical evidence suggests that the contribution of dominance variance to phenotypic variance may increase with the correlation between a trait and fitness; however, direct tests of this hypothesis are few. Using a multigenerational breeding design in an unmanipulated population of Drosophila serrata, we estimated additive and dominance genetic covariance matrices for multivariate wing-shape phenotypes, together with a comprehensive measure of fitness, to determine whether there is an association between directional selection and dominance variance. Fitness, a trait unequivocally under directional selection, had no detectable additive genetic variance, but significant dominance genetic variance contributing 32% of the phenotypic variance. For single and multivariate morphological traits, however, no relationship was observed between trait-fitness correlations and dominance variance. A similar proportion of additive and dominance variance was found to contribute to phenotypic variance for single traits, and double the amount of additive compared to dominance variance was found for the multivariate trait combination under directional selection. These data suggest that for many fitness components a positive association between directional selection and dominance genetic variance may not be expected.
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24
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Nepoux V, Babin A, Haag C, Kawecki TJ, Le Rouzic A. Quantitative genetics of learning ability and resistance to stress in Drosophila melanogaster. Ecol Evol 2015; 5:543-56. [PMID: 25691979 PMCID: PMC4328760 DOI: 10.1002/ece3.1379] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 11/19/2014] [Accepted: 11/21/2014] [Indexed: 11/12/2022] Open
Abstract
Even though laboratory evolution experiments have demonstrated genetic variation for learning ability, we know little about the underlying genetic architecture and genetic relationships with other ecologically relevant traits. With a full diallel cross among twelve inbred lines of Drosophila melanogaster originating from a natural population (0.75 < F < 0.93), we investigated the genetic architecture of olfactory learning ability and compared it to that for another behavioral trait (unconditional preference for odors), as well as three traits quantifying the ability to deal with environmental challenges: egg-to-adult survival and developmental rate on a low-quality food, and resistance to a bacterial pathogen. Substantial additive genetic variation was detected for each trait, highlighting their potential to evolve. Genetic effects contributed more than nongenetic parental effects to variation in traits measured at the adult stage: learning, odorant perception, and resistance to infection. In contrast, the two traits quantifying larval tolerance to low-quality food were more strongly affected by parental effects. We found no evidence for genetic correlations between traits, suggesting that these traits could evolve at least to some degree independently of one another. Finally, inbreeding adversely affected all traits.
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Affiliation(s)
- Virginie Nepoux
- Department of Ecology and Evolution, University of Lausanne Lausanne, CH-1015, Switzerland
| | - Aurélie Babin
- Department of Ecology and Evolution, University of Lausanne Lausanne, CH-1015, Switzerland
| | - Christoph Haag
- Centre d'Écologie Fonctionnelle et Évolutive, UMR 5175, CNRS - Université de Montpellier - Université Paul-Valéry Montpellier - EPHA Montpellier 5, FR-34293, France
| | - Tadeusz J Kawecki
- Department of Ecology and Evolution, University of Lausanne Lausanne, CH-1015, Switzerland
| | - Arnaud Le Rouzic
- Laboratoire Evolution Génome et Spéciation, UPR 9034, CNRS Gif-sur-Yvette, FR-91198, France
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25
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Avila V, Pérez-Figueroa A, Caballero A, Hill WG, García-Dorado A, López-Fanjul C. The action of stabilizing selection, mutation, and drift on epistatic quantitative traits. Evolution 2014; 68:1974-87. [PMID: 24689841 DOI: 10.1111/evo.12413] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 03/05/2014] [Indexed: 01/14/2023]
Abstract
For a quantitative trait under stabilizing selection, the effect of epistasis on its genetic architecture and on the changes of genetic variance caused by bottlenecking were investigated using theory and simulation. Assuming empirical estimates of the rate and effects of mutations and the intensity of selection, we assessed the impact of two-locus epistasis (synergistic/antagonistic) among linked or unlinked loci on the distribution of effects and frequencies of segregating loci in populations at the mutation-selection-drift balance. Strong pervasive epistasis did not modify substantially the genetic properties of the trait and, therefore, the most likely explanation for the low amount of variation usually accounted by the loci detected in genome-wide association analyses is that many causal loci will pass undetected. We investigated the impact of epistasis on the changes in genetic variance components when large populations were subjected to successive bottlenecks of different sizes, considering the action of genetic drift, operating singly (D), or jointly with mutation (MD) and selection (MSD). An initial increase of the different components of the genetic variance, as well as a dramatic acceleration of the between-line divergence, were always associated with synergistic epistasis but were strongly constrained by selection.
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Affiliation(s)
- Victoria Avila
- Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain; Institute of Evolutionary Biology, School of Biological Sciences, University of Edinburgh, West Mains Road, Edinburgh EH9 3JT, United Kingdom.
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Fragata I, Simões P, Lopes-Cunha M, Lima M, Kellen B, Bárbaro M, Santos J, Rose MR, Santos M, Matos M. Laboratory selection quickly erases historical differentiation. PLoS One 2014; 9:e96227. [PMID: 24788553 PMCID: PMC4008540 DOI: 10.1371/journal.pone.0096227] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 04/04/2014] [Indexed: 11/19/2022] Open
Abstract
The roles of history, chance and selection have long been debated in evolutionary biology. Though uniform selection is expected to lead to convergent evolution between populations, contrasting histories and chance events might prevent them from attaining the same adaptive state, rendering evolution somewhat unpredictable. The predictability of evolution has been supported by several studies documenting repeatable adaptive radiations and convergence in both nature and laboratory. However, other studies suggest divergence among populations adapting to the same environment. Despite the relevance of this issue, empirical data is lacking for real-time adaptation of sexual populations with deeply divergent histories and ample standing genetic variation across fitness-related traits. Here we analyse the real-time evolutionary dynamics of Drosophila subobscura populations, previously differentiated along the European cline, when colonizing a new common environment. By analysing several life-history, physiological and morphological traits, we show that populations quickly converge to the same adaptive state through different evolutionary paths. In contrast with other studies, all analysed traits fully converged regardless of their association with fitness. Selection was able to erase the signature of history in highly differentiated populations after just a short number of generations, leading to consistent patterns of convergent evolution.
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Affiliation(s)
- Inês Fragata
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail: (IF); (PS)
| | - Pedro Simões
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
- * E-mail: (IF); (PS)
| | - Miguel Lopes-Cunha
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Margarida Lima
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Bárbara Kellen
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Margarida Bárbaro
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Josiane Santos
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Michael R. Rose
- Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America
| | - Mauro Santos
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Margarida Matos
- Centro de Biologia Ambiental and Departamento de Biologia Animal, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
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The between-population genetic architecture of growth, maturation, and plasticity in Atlantic salmon. Genetics 2014; 196:1277-91. [PMID: 24473933 DOI: 10.1534/genetics.114.161729] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The between-population genetic architecture for growth and maturation has not been examined in detail for many animal species despite its central importance in understanding hybrid fitness. We studied the genetic architecture of population divergence in: (i) maturation probabilities at the same age; (ii) size at age and growth, while accounting for maturity status and sex; and (iii) growth plasticity in response to environmental factors, using divergent wild and domesticated Atlantic salmon (Salmo salar). Our work examined two populations and their multigenerational hybrids in a common experimental arrangement in which salinity and quantity of suspended sediments were manipulated to mimic naturally occurring environmental variation. Average specific growth rates across environments differed among crosses, maturity groups, and cross-by-maturity groups, but a growth-rate reduction in the presence of suspended sediments was equal for all groups. Our results revealed both additive and nonadditive outbreeding effects for size at age and for growth rates that differed with life stage, as well as the presence of different sex- and size-specific maturation probabilities between populations. The major implication of our work is that estimates of the genetic architecture of growth and maturation can be biased if one does not simultaneously account for temporal changes in growth and for different maturation probabilities between populations. Namely, these correlated traits interact differently within each population and between sexes and among generations, due to nonadditive effects and a level of independence in the genetic control for traits. Our results emphasize the challenges to investigating and predicting phenotypic changes resulting from between-population outbreeding.
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The Deleterious Effects of High Inbreeding on Male Drosophila melanogaster Attractiveness are Observed Under Competitive but not Under Non-competitive Conditions. Behav Genet 2014; 44:144-54. [DOI: 10.1007/s10519-013-9639-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 12/24/2013] [Indexed: 01/22/2023]
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Nespolo RF, Bartheld JL, González A, Bruning A, Roff DA, Bacigalupe LD, Gaitán‐Espitia JD. The quantitative genetics of physiological and morphological traits in an invasive terrestrial snail: additive vs. non‐additive genetic variation. Funct Ecol 2013. [DOI: 10.1111/1365-2435.12203] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Roberto F. Nespolo
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
| | - José L. Bartheld
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
| | - Avia González
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
| | - Andrea Bruning
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
| | - Derek A. Roff
- Department of Biology University of California Riverside CaliforniaUSA
| | - Leonardo D. Bacigalupe
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
| | - Juan D. Gaitán‐Espitia
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile Valdivia Chile
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Body composition and gene expression QTL mapping in mice reveals imprinting and interaction effects. BMC Genet 2013; 14:103. [PMID: 24165562 PMCID: PMC4233306 DOI: 10.1186/1471-2156-14-103] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 10/22/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Shifts in body composition, such as accumulation of body fat, can be a symptom of many chronic human diseases; hence, efforts have been made to investigate the genetic mechanisms that underlie body composition. For example, a few quantitative trait loci (QTL) have been discovered using genome-wide association studies, which will eventually lead to the discovery of causal mutations that are associated with tissue traits. Although some body composition QTL have been identified in mice, limited research has been focused on the imprinting and interaction effects that are involved in these traits. Previously, we found that Myostatin genotype, reciprocal cross, and sex interacted with numerous chromosomal regions to affect growth traits. RESULTS Here, we report on the identification of muscle, adipose, and morphometric phenotypic QTL (pQTL), translation and transcription QTL (tQTL) and expression QTL (eQTL) by applying a QTL model with additive, dominance, imprinting, and interaction effects. Using an F2 population of 1000 mice derived from the Myostatin-null C57BL/6 and M16i mouse lines, six imprinted pQTL were discovered on chromosomes 6, 9, 10, 11, and 18. We also identified two IGF1 and two Atp2a2 eQTL, which could be important trans-regulatory elements. pQTL, tQTL and eQTL that interacted with Myostatin, reciprocal cross, and sex were detected as well. Combining with the additive and dominance effect, these variants accounted for a large amount of phenotypic variation in this study. CONCLUSIONS Our study indicates that both imprinting and interaction effects are important components of the genetic model of body composition traits. Furthermore, the integration of eQTL and traditional QTL mapping may help to explain more phenotypic variation than either alone, thereby uncovering more molecular details of how tissue traits are regulated.
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Vijendravarma RK, Kawecki TJ. Epistasis and maternal effects in experimental adaptation to chronic nutritional stress in Drosophila. J Evol Biol 2013; 26:2566-80. [PMID: 24118120 DOI: 10.1111/jeb.12248] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Revised: 08/12/2013] [Accepted: 08/13/2013] [Indexed: 11/30/2022]
Abstract
Based on ecological and metabolic arguments, some authors predict that adaptation to novel, harsh environments should involve alleles showing negative (diminishing return) epistasis and/or that it should be mediated in part by evolution of maternal effects. Although the first prediction has been supported in microbes, there has been little experimental support for either prediction in multicellular eukaryotes. Here we use a line-cross design to study the genetic architecture of adaptation to chronic larval malnutrition in a population of Drosophila melanogaster that evolved on an extremely nutrient-poor larval food for 84 generations. We assayed three fitness-related traits (developmental rate, adult female weight and egg-to-adult viability) under the malnutrition conditions in 14 crosses between this selected population and a nonadapted control population originally derived from the same base population. All traits showed a pattern of negative epistasis between alleles improving performance under malnutrition. Furthermore, evolutionary changes in maternal traits accounted for half of the 68% increase in viability and for the whole of 8% reduction in adult female body weight in the selected population (relative to unselected controls). These results thus support both of the above predictions and point to the importance of nonadditive effects in adaptive microevolution.
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Affiliation(s)
- R K Vijendravarma
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Bruning A, Gaitán-Espitia JD, González A, Bartheld JL, Nespolo RF. Metabolism, Growth, and the Energetic Definition of Fitness: A Quantitative Genetic Study in the Land Snail Cornu aspersum. Physiol Biochem Zool 2013; 86:538-46. [DOI: 10.1086/672092] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Breckels RD, Garner SR, Neff BD. Rapid evolution in response to increased temperature maintains population viability despite genetic erosion in a tropical ectotherm. Evol Ecol 2013. [DOI: 10.1007/s10682-013-9668-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Key questions in the genetics and genomics of eco-evolutionary dynamics. Heredity (Edinb) 2013; 111:456-66. [PMID: 23963343 DOI: 10.1038/hdy.2013.75] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2012] [Revised: 05/07/2013] [Accepted: 05/28/2013] [Indexed: 11/09/2022] Open
Abstract
Increasing acceptance that evolution can be 'rapid' (or 'contemporary') has generated growing interest in the consequences for ecology. The genetics and genomics of these 'eco-evolutionary dynamics' will be--to a large extent--the genetics and genomics of organismal phenotypes. In the hope of stimulating research in this area, I review empirical data from natural populations and draw the following conclusions. (1) Considerable additive genetic variance is present for most traits in most populations. (2) Trait correlations do not consistently oppose selection. (3) Adaptive differences between populations often involve dominance and epistasis. (4) Most adaptation is the result of genes of small-to-modest effect, although (5) some genes certainly have larger effects than the others. (6) Adaptation by independent lineages to similar environments is mostly driven by different alleles/genes. (7) Adaptation to new environments is mostly driven by standing genetic variation, although new mutations can be important in some instances. (8) Adaptation is driven by both structural and regulatory genetic variation, with recent studies emphasizing the latter. (9) The ecological effects of organisms, considered as extended phenotypes, are often heritable. Overall, the study of eco-evolutionary dynamics will benefit from perspectives and approaches that emphasize standing genetic variation in many genes of small-to-modest effect acting across multiple traits and that analyze overall adaptation or 'fitness'. In addition, increasing attention should be paid to dominance, epistasis and regulatory variation.
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35
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Genetic architecture of survival and fitness-related traits in two populations of Atlantic salmon. Heredity (Edinb) 2013; 111:513-9. [PMID: 23942281 DOI: 10.1038/hdy.2013.74] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2013] [Revised: 06/14/2013] [Accepted: 06/27/2013] [Indexed: 11/08/2022] Open
Abstract
The additive genetic effects of traits can be used to predict evolutionary trajectories, such as responses to selection. Non-additive genetic and maternal environmental effects can also change evolutionary trajectories and influence phenotypes, but these effects have received less attention by researchers. We partitioned the phenotypic variance of survival and fitness-related traits into additive genetic, non-additive genetic and maternal environmental effects using a full-factorial breeding design within two allopatric populations of Atlantic salmon (Salmo salar). Maternal environmental effects were large at early life stages, but decreased during development, with non-additive genetic effects being most significant at later juvenile stages (alevin and fry). Non-additive genetic effects were also, on average, larger than additive genetic effects. The populations, generally, did not differ in the trait values or inferred genetic architecture of the traits. Any differences between the populations for trait values could be explained by maternal environmental effects. We discuss whether the similarities in architectures of these populations is the result of natural selection across a common juvenile environment.
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36
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van Bergen E, Brakefield PM, Heuskin S, Zwaan BJ, Nieberding CM. The scent of inbreeding: a male sex pheromone betrays inbred males. Proc Biol Sci 2013; 280:20130102. [PMID: 23466986 PMCID: PMC3619463 DOI: 10.1098/rspb.2013.0102] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Accepted: 02/08/2013] [Indexed: 11/12/2022] Open
Abstract
Inbreeding depression results from mating among genetically related individuals and impairs reproductive success. The decrease in male mating success is usually attributed to an impact on multiple fitness-related traits that reduce the general condition of inbred males. Here, we find that the production of the male sex pheromone is reduced significantly by inbreeding in the butterfly Bicyclus anynana. Other traits indicative of the general condition, including flight performance, are also negatively affected in male butterflies by inbreeding. Yet, we unambiguously show that only the production of male pheromones affects mating success. Thus, this pheromone signal informs females about the inbreeding status of their mating partners. We also identify the specific chemical component (hexadecanal) probably responsible for the decrease in male mating success. Our results advocate giving increased attention to olfactory communication as a major causal factor of mate-choice decisions and sexual selection.
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Affiliation(s)
- Erik van Bergen
- Evolutionary Biology, Institute of Biology Leiden, Leiden University, RA 2300 Leiden, The Netherlands.
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37
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Breno M, Bots J, Van Dongen S. Between-family variation and quantitative genetics of developmental instability of long bones in rabbit foetuses. Biol J Linn Soc Lond 2013. [DOI: 10.1111/bij.12051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Matteo Breno
- Evolutionary Ecology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171; B-2020; Antwerp; Belgium
| | - Jessica Bots
- Evolutionary Ecology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171; B-2020; Antwerp; Belgium
| | - Stefan Van Dongen
- Evolutionary Ecology Group; Department of Biology; University of Antwerp; Groenenborgerlaan 171; B-2020; Antwerp; Belgium
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HANGARTNER S, LAURILA A, RÄSÄNEN K. The quantitative genetic basis of adaptive divergence in the moor frog (Rana arvalis) and its implications for gene flow. J Evol Biol 2012; 25:1587-99. [DOI: 10.1111/j.1420-9101.2012.02546.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Affiliation(s)
- Anneke Dierks
- Zoological Institute and Museum, University of Greifswald, J.-S.-Bachstraße 11/12, D-17489 Greifswald, Germany.
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41
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KETOLA TARMO, KOTIAHO JANNES. Inbreeding depression in the effects of body mass on energy use. Biol J Linn Soc Lond 2011. [DOI: 10.1111/j.1095-8312.2011.01790.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Shi J, Li R, Zou J, Long Y, Meng J. A dynamic and complex network regulates the heterosis of yield-correlated traits in rapeseed (Brassica napus L.). PLoS One 2011; 6:e21645. [PMID: 21747942 PMCID: PMC3128606 DOI: 10.1371/journal.pone.0021645] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2010] [Accepted: 06/07/2011] [Indexed: 01/12/2023] Open
Abstract
Although much research has been conducted, the genetic architecture of heterosis remains ambiguous. To unravel the genetic architecture of heterosis, a reconstructed F2 population was produced by random intercross among 202 lines of a double haploid population in rapeseed (Brassica napus L.). Both populations were planted in three environments and 15 yield-correlated traits were measured, and only seed yield and eight yield-correlated traits showed significant mid-parent heterosis, with the mean ranging from 8.7% (branch number) to 31.4% (seed yield). Hundreds of QTL and epistatic interactions were identified for the 15 yield-correlated traits, involving numerous variable loci with moderate effect, genome-wide distribution and obvious hotspots. All kinds of mode-of-inheritance of QTL (additive, A; partial-dominant, PD; full-dominant, D; over-dominant, OD) and epistatic interactions (additive × additive, AA; additive × dominant/dominant × additive, AD/DA; dominant × dominant, DD) were observed and epistasis, especially AA epistasis, seemed to be the major genetic basis of heterosis in rapeseed. Consistent with the low correlation between marker heterozygosity and mid-parent heterosis/hybrid performance, a considerable proportion of dominant and DD epistatic effects were negative, indicating heterozygosity was not always advantageous for heterosis/hybrid performance. The implications of our results on evolution and crop breeding are discussed.
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Affiliation(s)
- Jiaqin Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Ruiyuan Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
- * E-mail:
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44
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Berner D, Kaeuffer R, Grandchamp AC, Raeymaekers JAM, Räsänen K, Hendry AP. Quantitative genetic inheritance of morphological divergence in a lake-stream stickleback ecotype pair: implications for reproductive isolation. J Evol Biol 2011; 24:1975-83. [PMID: 21649765 DOI: 10.1111/j.1420-9101.2011.02330.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ecological selection against hybrids between populations occupying different habitats might be an important component of reproductive isolation during the initial stages of speciation. The strength and directionality of this barrier to gene flow depends on the genetic architecture underlying divergence in ecologically relevant phenotypes. We here present line cross analyses of inheritance for two key foraging-related morphological traits involved in adaptive divergence between stickleback ecotypes residing parapatrically in lake and stream habitats within the Misty Lake watershed (Vancouver Island, Canada). One main finding is the striking genetic dominance of the lake phenotype for body depth. Selection associated with this phenotype against first- and later-generation hybrids should therefore be asymmetric, hindering introgression from the lake to the stream population but not vice versa. Another main finding is that divergence in gill raker number is inherited additively and should therefore contribute symmetrically to reproductive isolation. Our study suggests that traits involved in adaptation might contribute to reproductive isolation qualitatively differently, depending on their mode of inheritance.
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Affiliation(s)
- D Berner
- Zoological Institute, University of Basel, Basel, Switzerland.
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45
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Analysis of the effects of inbreeding on lifespan and starvation resistance in Drosophila melanogaster. Genetica 2011; 139:525-33. [PMID: 21505760 DOI: 10.1007/s10709-011-9574-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Accepted: 04/02/2011] [Indexed: 10/18/2022]
Abstract
Because of their decreased overall fitness and genetic variability inbred individuals are expected to show reduced survival and lifespan under most environmental conditions as compared with outbred individuals. Whereas evidence for the deleterious effects of inbreeding on lifespan has been previously provided, only a few studies have investigated effects of inbreeding on survival under starved conditions. In the present study we compared the abilities of inbred and outbred adult Drosophila melanogaster to survive under starved and fed conditions. We found that inbreeding reduced lifespan but had no effect on starvation resistance. The results indicate highly trait specific consequences of inbreeding. Possible mechanisms behind the observed results are discussed.
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46
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Genetic architecture and phenotypic plasticity of thermally-regulated traits in an eruptive species, Dendroctonus ponderosae. Evol Ecol 2011. [DOI: 10.1007/s10682-011-9474-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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47
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Reid JM, Arcese P, Sardell RJ, Keller LF. Additive Genetic Variance, Heritability, and Inbreeding Depression in Male Extra-Pair Reproductive Success. Am Nat 2011; 177:177-87. [DOI: 10.1086/657977] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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48
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van Heerwaarden B, Sgrò CM. THE EFFECT OF DEVELOPMENTAL TEMPERATURE ON THE GENETIC ARCHITECTURE UNDERLYING SIZE AND THERMAL CLINES IN DROSOPHILA MELANOGASTER AND D. SIMULANS FROM THE EAST COAST OF AUSTRALIA. Evolution 2010; 65:1048-67. [DOI: 10.1111/j.1558-5646.2010.01196.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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49
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Affiliation(s)
- L W Simmons
- Centre for Evolutionary Biology, School of Animal Biology (M092), University of Western Australia, Crawley, Australia.
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50
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Reid JM, Arcese P, Sardell RJ, Keller LF. Heritability of female extra-pair paternity rate in song sparrows (Melospiza melodia). Proc Biol Sci 2010; 278:1114-20. [PMID: 20980302 PMCID: PMC3049030 DOI: 10.1098/rspb.2010.1704] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
The forces driving the evolution of extra-pair reproduction in socially monogamous animals remain widely debated and unresolved. One key hypothesis is that female extra-pair reproduction evolves through indirect genetic benefits, reflecting increased additive genetic value of extra-pair offspring. Such evolution requires that a female's propensity to produce offspring that are sired by an extra-pair male is heritable. However, additive genetic variance and heritability in female extra-pair paternity (EPP) rate have not been quantified, precluding accurate estimation of the force of indirect selection. Sixteen years of comprehensive paternity and pedigree data from socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia) showed significant additive genetic variance and heritability in the proportion of a female's offspring that was sired by an extra-pair male, constituting major components of the genetic architecture required for extra-pair reproduction to evolve through indirect additive genetic benefits. However, estimated heritabilities were moderately small (0.12 and 0.18 on the observed and underlying latent scales, respectively). The force of selection on extra-pair reproduction through indirect additive genetic benefits may consequently be relatively weak. However, the additive genetic variance and non-zero heritability observed in female EPP rate allow for multiple further genetic mechanisms to drive and constrain mating system evolution.
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Affiliation(s)
- Jane M Reid
- Institute of Biological and Environmental Sciences, School of Biological Sciences, University of Aberdeen, Zoology Building, Tillydrone Avenue, Aberdeen AB24 2TZ, UK.
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