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Lindner M, Verhagen I, Mateman AC, van Oers K, Laine VN, Visser ME. Genetic and epigenetic differentiation in response to genomic selection for avian lay date. Evol Appl 2024; 17:e13703. [PMID: 38948539 PMCID: PMC11211926 DOI: 10.1111/eva.13703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 04/20/2024] [Accepted: 04/29/2024] [Indexed: 07/02/2024] Open
Abstract
Anthropogenic climate change has led to globally increasing temperatures at an unprecedented pace and, to persist, wild species have to adapt to their changing world. We, however, often fail to derive reliable predictions of species' adaptive potential. Genomic selection represents a powerful tool to investigate the adaptive potential of a species, but constitutes a 'blind process' with regard to the underlying genomic architecture of the relevant phenotypes. Here, we used great tit (Parus major) females from a genomic selection experiment for avian lay date to zoom into this blind process. We aimed to identify the genetic variants that responded to genomic selection and epigenetic variants that accompanied this response and, this way, might reflect heritable genetic variation at the epigenetic level. We applied whole genome bisulfite sequencing to blood samples of individual great tit females from the third generation of bidirectional genomic selection lines for early and late lay date. Genomic selection resulted in differences at both the genetic and epigenetic level. Genetic variants that showed signatures of selection were located within genes mostly linked to brain development and functioning, including LOC107203824 (SOX3-like). SOX3 is a transcription factor that is required for normal hypothalamo-pituitary axis development and functioning, an essential part of the reproductive axis. As for epigenetic differentiation, the early selection line showed hypomethylation relative to the late selection line. Sites with differential DNA methylation were located in genes important for various biological processes, including gonadal functioning (e.g., MSTN and PIK3CB). Overall, genomic selection for avian lay date provided insights into where within the genome the heritable genetic variation for lay date, on which selection can operate, resides and indicates that some of this variation might be reflected by epigenetic variants.
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Affiliation(s)
- Melanie Lindner
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
| | - Irene Verhagen
- Wageningen University & Research (WUR)WageningenThe Netherlands
| | - A. Christa Mateman
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
| | - Kees van Oers
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Behavioural Ecology GroupWageningen University & Research (WUR)WageningenThe Netherlands
| | - Veronika N. Laine
- Finnish Museum of Natural HistoryUniversity of HelsinkiHelsinkiFinland
| | - Marcel E. Visser
- Department of Animal EcologyNetherlands Institute of Ecology (NIOO‐KNAW)WageningenThe Netherlands
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES)University of GroningenGroningenThe Netherlands
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2
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Mittell EA, Morrissey MB. The missing fraction problem as an episodes of selection problem. Evolution 2024; 78:601-611. [PMID: 38374726 DOI: 10.1093/evolut/qpae022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 11/10/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
In evolutionary quantitative genetics, the missing fraction problem refers to a specific kind of bias in parameters estimated later in life that occurs when nonrandom subsets of phenotypes are missing from the population due to prior viability selection on correlated traits. The missing fraction problem thus arises when the following hold: (a) viability selection and (b) correlation between later-life traits and traits important for early-life survival. Although it is plausible that these conditions are widespread in wild populations, this problem has received little empirical attention. This may be natural: the problem could appear intractable, given that it is impossible to measure phenotypes of individuals that have previously died. However, it is not impossible to correctly measure lifetime selection, or correctly predict evolutionary trajectories, of later-life traits in the presence of the missing fraction. Two basic strategies are available. First, given phenotypic data on selected early life traits, well established but underused episodes of selection theory can yield correct values of evolutionary parameters throughout life. Second, when traits subjected to early-life viability selection are not known and/or measured, it is possible to use the genetic association of later-life traits with early-life viability to correctly infer important information about the consequences of prior viability selection for later-life traits. By carefully reviewing the basic nature of the missing fraction problem, and describing the tractable solutions to the problem, we hope that future studies will be able to be better designed to cope with the (likely pervasive) consequences of early-life viability selection.
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Affiliation(s)
- Elizabeth A Mittell
- Centre for Biodiversity, School of Biology, University of St. Andrews, St. Andrews, United Kingdom
- Institute for Evolutionary Ecology, School of Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Michael B Morrissey
- Centre for Biodiversity, School of Biology, University of St. Andrews, St. Andrews, United Kingdom
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3
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González-Forero M. A mathematical framework for evo-devo dynamics. Theor Popul Biol 2024; 155:24-50. [PMID: 38043588 DOI: 10.1016/j.tpb.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/10/2023] [Accepted: 11/28/2023] [Indexed: 12/05/2023]
Abstract
Natural selection acts on phenotypes constructed over development, which raises the question of how development affects evolution. Classic evolutionary theory indicates that development affects evolution by modulating the genetic covariation upon which selection acts, thus affecting genetic constraints. However, whether genetic constraints are relative, thus diverting adaptation from the direction of steepest fitness ascent, or absolute, thus blocking adaptation in certain directions, remains uncertain. This limits understanding of long-term evolution of developmentally constructed phenotypes. Here we formulate a general, tractable mathematical framework that integrates age progression, explicit development (i.e., the construction of the phenotype across life subject to developmental constraints), and evolutionary dynamics, thus describing the evolutionary and developmental (evo-devo) dynamics. The framework yields simple equations that can be arranged in a layered structure that we call the evo-devo process, whereby five core elementary components generate all equations including those mechanistically describing genetic covariation and the evo-devo dynamics. The framework recovers evolutionary dynamic equations in gradient form and describes the evolution of genetic covariation from the evolution of genotype, phenotype, environment, and mutational covariation. This shows that genotypic and phenotypic evolution must be followed simultaneously to yield a dynamically sufficient description of long-term phenotypic evolution in gradient form, such that evolution described as the climbing of a fitness landscape occurs in "geno-phenotype" space. Genetic constraints in geno-phenotype space are necessarily absolute because the phenotype is related to the genotype by development. Thus, the long-term evolutionary dynamics of developed phenotypes is strongly non-standard: (1) evolutionary equilibria are either absent or infinite in number and depend on genetic covariation and hence on development; (2) developmental constraints determine the admissible evolutionary path and hence which evolutionary equilibria are admissible; and (3) evolutionary outcomes occur at admissible evolutionary equilibria, which do not generally occur at fitness landscape peaks in geno-phenotype space, but at peaks in the admissible evolutionary path where "total genotypic selection" vanishes if exogenous plastic response vanishes and mutational variation exists in all directions of genotype space. Hence, selection and development jointly define the evolutionary outcomes if absolute mutational constraints and exogenous plastic response are absent, rather than the outcomes being defined only by selection. Moreover, our framework provides formulas for the sensitivities of a recurrence and an alternative method to dynamic optimization (i.e., dynamic programming or optimal control) to identify evolutionary outcomes in models with developmentally dynamic traits. These results show that development has major evolutionary effects.
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Murray M, Wright J, Araya-Ajoy YG. Evolutionary rescue from climate change: male indirect genetic effects on lay-dates and their consequences for population persistence. Evol Lett 2024; 8:137-148. [PMID: 38487362 PMCID: PMC10939382 DOI: 10.1093/evlett/qrad022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 04/15/2023] [Accepted: 05/03/2023] [Indexed: 03/17/2024] Open
Abstract
Changes in avian breeding phenology are among the most apparent responses to climate change in free-ranging populations. A key question is whether populations will be able to keep up with the expected rates of environmental change. There is a large body of research on the mechanisms by which avian lay-dates track temperature change and the consequences of (mal)adaptation on population persistence. Often overlooked is the role of males, which can influence the lay-date of their mate through their effect on the prelaying environment. We explore how social plasticity causing male indirect genetic effects can help or hinder population persistence when female genes underpinning lay-date and male genes influencing female's timing of reproduction both respond to climate-mediated selection. We extend quantitative genetic moving optimum models to predict the consequences of social plasticity on the maximum sustainable rate of temperature change, and evaluate our model using a combination of simulated data and empirical estimates from the literature. Our results suggest that predictions for population persistence may be biased if indirect genetic effects and cross-sex genetic correlations are not considered and that the extent of this bias depends on sex differences in how environmental change affects the optimal timing of reproduction. Our model highlights that more empirical work is needed to understand sex-specific effects of environmental change on phenology and the fitness consequences for population dynamics. While we discuss our results exclusively in the context of avian breeding phenology, the approach we take here can be generalized to many different contexts and types of social interaction.
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Affiliation(s)
- Myranda Murray
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Jonathan Wright
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
| | - Yimen G Araya-Ajoy
- Centre for Biodiversity Dynamics (CBD), Department of Biology, Norwegian University of Science and Technology (NTNU), N-7491 Trondheim, Norway
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5
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Edelsparre AH, Fitzpatrick MJ, Saastamoinen M, Teplitsky C. Evolutionary adaptation to climate change. Evol Lett 2024; 8:1-7. [PMID: 38370543 PMCID: PMC10872154 DOI: 10.1093/evlett/qrad070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/14/2023] [Accepted: 12/18/2023] [Indexed: 02/20/2024] Open
Abstract
When the notion of climate change emerged over 200 years ago, few speculated as to the impact of rising atmospheric temperatures on biological life. Tens of decades later, research clearly demonstrates that the impact of climate change on life on Earth is enormous, ongoing, and with foreseen effects lasting well into the next century. Responses to climate change have been widely documented. However, the breadth of phenotypic traits involved with evolutionary adaptation to climate change remains unclear. In addition, it is difficult to identify the genetic and/or epigenetic bases of phenotypes adaptive to climate change, in part because it often is not clear whether this change is plastic, genetic, or some combination of the two. Adaptive responses to climate-driven selection also interact with other processes driving genetic changes in general, including demography as well as selection driven by other factors. In this Special Issue, we explore the factors that will impact the overall outcome of climate change adaptation. Our contributions explain that traits involved in climate change adaptation include not only classic phenomena, such as range shifts and environmentally dependent sex determination, but also often overlooked phenomena such as social and sexual conflicts and the expression of stress hormones. We learn how climate-driven selection can be mediated via both natural and sexual selection, effectively influencing key fitness-related traits such as offspring growth and fertility as well as evolutionary potential. Finally, we explore the limits and opportunities for predicting adaptive responses to climate change. This contribution forms the basis of 10 actions that we believe will improve predictions of when and how organisms may adapt genetically to climate change. We anticipate that this Special Issue will inform novel investigations into how the effects of climate change unfold from phenotypes to genotypes, particularly as methodologies increasingly allow researchers to study selection in field experiments.
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Affiliation(s)
- Allan H Edelsparre
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada
| | - Mark J Fitzpatrick
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, ON, Canada
| | - Marjo Saastamoinen
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Institute of Life Sciences, University of Helsinki, Helsinki, Finland
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6
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Baverstock K. The Gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2024; 186:e73-e88. [PMID: 38044248 DOI: 10.1016/j.pbiomolbio.2023.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics, and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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7
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Westergren M, Archambeau J, Bajc M, Damjanić R, Theraroz A, Kraigher H, Oddou-Muratorio S, González-Martínez SC. Low but significant evolutionary potential for growth, phenology and reproduction traits in European beech. Mol Ecol 2023. [PMID: 37962106 DOI: 10.1111/mec.17196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/23/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
Local survival of forest tree populations under climate change depends on existing genetic variation and their adaptability to changing environments. Responses to selection were studied in European beech (Fagus sylvatica) under field conditions. A total of 1087 adult trees, seeds, 1-year-old seedlings and established multiyear saplings were genotyped with 16 nuSSRs. Adult trees were assessed for phenotypic traits related to growth, phenology and reproduction. Parentage and paternity analyses were used to estimate effective female and male fecundity as a proxy of fitness and showed that few parents contributed to successful regeneration. Selection gradients were estimated from the relationship between traits and fecundity, while heritability and evolvability were estimated using mixed models and the breeder's equation. Larger trees bearing more fruit and early male flowering had higher total fecundity, while trees with longer growth season had lower total fecundity (directional selection). Stabilizing selection on spring phenology was found for female fecundity, highlighting the role of late frosts as a selection driver. Selection gradients for other traits varied between measurement years and the offspring cohort used to estimate parental fecundity. Compared to other studies in natural populations, we found low to moderate heritability and evolvability for most traits. Response to selection was higher for growth than for budburst, leaf senescence or reproduction traits, reflecting more consistent selection gradients across years and sex functions, and higher phenotypic variability in the population. Our study provides empirical evidence suggesting that populations of long-lived organisms such as forest trees can adapt locally, even at short-time scales.
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Affiliation(s)
| | | | - Marko Bajc
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | - Rok Damjanić
- Slovenian Forestry Institute, Ljubljana, Slovenia
| | | | | | - Sylvie Oddou-Muratorio
- INRAE, URFM, Avignon, France
- INRAE, Univ. de Pau et des Pays de l'Adour, E2S UPPA, ECOBIOP, Saint-Pée-sur-Nivelle, France
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8
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Godineau C, Fririon V, Beudez N, de Coligny F, Courbet F, Ligot G, Oddou‐Muratorio S, Sanchez L, Lefèvre F. A demo-genetic model shows how silviculture reduces natural density-dependent selection in tree populations. Evol Appl 2023; 16:1830-1844. [PMID: 38029065 PMCID: PMC10681482 DOI: 10.1111/eva.13606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 12/01/2023] Open
Abstract
Biological production systems and conservation programs benefit from and should care for evolutionary processes. Developing evolution-oriented strategies requires knowledge of the evolutionary consequences of management across timescales. Here, we used an individual-based demo-genetic modelling approach to study the interactions and feedback between tree thinning, genetic evolution, and forest stand dynamics. The model combines processes that jointly drive survival and mating success-tree growth, competition and regeneration-with genetic variation of quantitative traits related to these processes. In various management and disturbance scenarios, the evolutionary rates predicted by the coupled demo-genetic model for a growth-related trait, vigor, fit within the range of empirical estimates found in the literature for wild plant and animal populations. We used this model to simulate non-selective silviculture and disturbance scenarios over four generations of trees. We characterized and quantified the effect of thinning frequencies and intensities and length of the management cycle on viability selection driven by competition and fecundity selection. The thinning regimes had a drastic long-term effect on the evolutionary rate of vigor over generations, potentially reaching 84% reduction, depending on management intensity, cycle length and disturbance regime. The reduction of genetic variance by viability selection within each generation was driven by changes in genotypic frequencies rather than by gene diversity, resulting in low-long-term erosion of the variance across generations, despite short-term fluctuations within generations. The comparison among silviculture and disturbance scenarios was qualitatively robust to assumptions on the genetic architecture of the trait. Thus, the evolutionary consequences of management result from the interference between human interventions and natural evolutionary processes. Non-selective thinning, as considered here, reduces the intensity of natural selection, while selective thinning (on tree size or other criteria) might reduce or reinforce it depending on the forester's tree choice and thinning intensity.
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Affiliation(s)
| | | | - Nicolas Beudez
- AMAP, Univ Montpellier, CIRAD, CNRS, INRAE, IRDMontpellierFrance
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9
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Walter GM, McGuigan K. Predicting the future. eLife 2023; 12:e91450. [PMID: 37671937 PMCID: PMC10482426 DOI: 10.7554/elife.91450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2023] Open
Abstract
Experiments on worms suggest that a statistical measure called the G matrix can accurately predict how phenotypes will adapt to a novel environment over multiple generations.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, Monash UniversityMelbourneAustralia
| | - Katrina McGuigan
- School of the Environment, University of QueenslandBrisbaneAustralia
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10
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Mallard F, Afonso B, Teotónio H. Selection and the direction of phenotypic evolution. eLife 2023; 12:e80993. [PMID: 37650381 PMCID: PMC10564456 DOI: 10.7554/elife.80993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/14/2023] [Indexed: 09/01/2023] Open
Abstract
Predicting adaptive phenotypic evolution depends on invariable selection gradients and on the stability of the genetic covariances between the component traits of the multivariate phenotype. We describe the evolution of six traits of locomotion behavior and body size in the nematode Caenorhabditis elegans for 50 generations of adaptation to a novel environment. We show that the direction of adaptive multivariate phenotypic evolution can be predicted from the ancestral selection differentials, particularly when the traits were measured in the new environment. Interestingly, the evolution of individual traits does not always occur in the direction of selection, nor are trait responses to selection always homogeneous among replicate populations. These observations are explained because the phenotypic dimension with most of the ancestral standing genetic variation only partially aligns with the phenotypic dimension under directional selection. These findings validate selection theory and suggest that the direction of multivariate adaptive phenotypic evolution is predictable for tens of generations.
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Affiliation(s)
- François Mallard
- Institut de Biologie de l’École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research UniversityParisFrance
| | - Bruno Afonso
- Institut de Biologie de l’École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research UniversityParisFrance
| | - Henrique Teotónio
- Institut de Biologie de l’École Normale Supérieure, CNRS UMR 8197, Inserm U1024, PSL Research UniversityParisFrance
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11
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Rolland J, Henao-Diaz LF, Doebeli M, Germain R, Harmon LJ, Knowles LL, Liow LH, Mank JE, Machac A, Otto SP, Pennell M, Salamin N, Silvestro D, Sugawara M, Uyeda J, Wagner CE, Schluter D. Conceptual and empirical bridges between micro- and macroevolution. Nat Ecol Evol 2023; 7:1181-1193. [PMID: 37429904 DOI: 10.1038/s41559-023-02116-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 06/13/2023] [Indexed: 07/12/2023]
Abstract
Explaining broad molecular, phenotypic and species biodiversity patterns necessitates a unifying framework spanning multiple evolutionary scales. Here we argue that although substantial effort has been made to reconcile microevolution and macroevolution, much work remains to identify the links between biological processes at play. We highlight four major questions of evolutionary biology whose solutions require conceptual bridges between micro and macroevolution. We review potential avenues for future research to establish how mechanisms at one scale (drift, mutation, migration, selection) translate to processes at the other scale (speciation, extinction, biogeographic dispersal) and vice versa. We propose ways in which current comparative methods to infer molecular evolution, phenotypic evolution and species diversification could be improved to specifically address these questions. We conclude that researchers are in a better position than ever before to build a synthesis to understand how microevolutionary dynamics unfold over millions of years.
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Affiliation(s)
- Jonathan Rolland
- CNRS, UMR5174, Laboratoire Evolution et Diversité Biologique, Université Toulouse 3 Paul Sabatier, Toulouse, France.
| | - L Francisco Henao-Diaz
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA
| | - Michael Doebeli
- Department of Zoology, and Department of Mathematics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rachel Germain
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Luke J Harmon
- Dept. of Biological Sciences, University of Idaho, Moscow, ID, USA
| | - L Lacey Knowles
- Department of Ecology and Evolutionary Biology, Museum of Zoology, University of Michigan, Ann Arbor, MI, USA
| | | | - Judith E Mank
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Antonin Machac
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Laboratory of Environmental Microbiology, Institute of Microbiology of the CAS, Prague, Czech Republic
| | - Sarah P Otto
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matt Pennell
- Departments of Quantitative and Computational Biology and Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, University of Gothenburg, Gothenburg, Sweden
| | - Mauro Sugawara
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
- Mário Schenberg Institute, São Paulo, Brazil
| | - Josef Uyeda
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Catherine E Wagner
- Department of Botany, and Program in Ecology and Evolution, University of Wyoming, Laramie, WY, USA
| | - Dolph Schluter
- Department of Zoology, and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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12
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Lindner M, Ramakers JJ, Verhagen I, Tomotani BM, Mateman AC, Gienapp P, Visser ME. Genotypes selected for early and late avian lay date differ in their phenotype, but not fitness, in the wild. SCIENCE ADVANCES 2023; 9:eade6350. [PMID: 37285433 DOI: 10.1126/sciadv.ade6350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 05/01/2023] [Indexed: 06/09/2023]
Abstract
Global warming has shifted phenological traits in many species, but whether species are able to track further increasing temperatures depends on the fitness consequences of additional shifts in phenological traits. To test this, we measured phenology and fitness of great tits (Parus major) with genotypes for extremely early and late egg lay dates, obtained from a genomic selection experiment. Females with early genotypes advanced lay dates relative to females with late genotypes, but not relative to nonselected females. Females with early and late genotypes did not differ in the number of fledglings produced, in line with the weak effect of lay date on the number of fledglings produced by nonselected females in the years of the experiment. Our study is the first application of genomic selection in the wild and led to an asymmetric phenotypic response that indicates the presence of constraints toward early, but not late, lay dates.
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Affiliation(s)
- Melanie Lindner
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, Netherlands
| | - Jip Jc Ramakers
- Mathematical and Statistical Methods-Biometris, Wageningen University & Research (WUR), Wageningen, Netherlands
| | - Irene Verhagen
- Wageningen University & Research (WUR) Library, Wageningen, Netherlands
| | - Barbara M Tomotani
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - A Christa Mateman
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | | | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
- Chronobiology Unit, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Groningen, Netherlands
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13
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Castellanos MC, Montero-Pau J, Ziarsolo P, Blanca JM, Cañizares J, Pausas JG. Quantitative genetic analysis of floral traits shows current limits but potential evolution in the wild. Proc Biol Sci 2023; 290:20230141. [PMID: 37122252 PMCID: PMC10130720 DOI: 10.1098/rspb.2023.0141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/22/2023] [Indexed: 05/02/2023] Open
Abstract
The vast variation in floral traits across angiosperms is often interpreted as the result of adaptation to pollinators. However, studies in wild populations often find no evidence of pollinator-mediated selection on flowers. Evolutionary theory predicts this could be the outcome of periods of stasis under stable conditions, followed by shorter periods of pollinator change that provide selection for innovative phenotypes. We asked if periods of stasis are caused by stabilizing selection, absence of other forms of selection or by low trait ability to respond even if selection is present. We studied a plant predominantly pollinated by one bee species across its range. We measured heritability and evolvability of traits, using genome-wide relatedness in a large wild population, and combined this with estimates of selection on the same individuals. We found evidence for both stabilizing selection and low trait heritability as potential explanations for stasis in flowers. The area of the standard petal is under stabilizing selection, but the variability is not heritable. A separate trait, floral weight, presents high heritability, but is not currently under selection. We show how a simple pollination environment coincides with the absence of current prerequisites for adaptive evolutionary change, while heritable variation remains to respond to future selection pressures.
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Affiliation(s)
- Maria Clara Castellanos
- School of Life Sciences, Universityof Sussex, Brighton BN1 9QG, UK
- CIDE-CSIC, Montcada, Valencia, Spain
| | - Javier Montero-Pau
- COMAV, Universitat Politècnica de València, Valencia, Spain
- Cavanilles Institute of Biodiversity and Evolutionary Biology, Universitat de València, Valencia, Spain
| | - Peio Ziarsolo
- COMAV, Universitat Politècnica de València, Valencia, Spain
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14
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Nicolaus M, Ubels R, Both C. Eco-Evolutionary Consequences of Dispersal Syndromes during Colonization in a Passerine Bird. Am Nat 2023; 201:523-536. [PMID: 36958003 DOI: 10.1086/723214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
AbstractIn most animal species, dispersing individuals possess phenotypic attributes that mitigate the costs of colonization and/or increase settlement success in new areas (dispersal syndromes). This phenotypic integration likely affects population dynamics and the direction of selection, but data are lacking for natural populations. Using an approach that combines population dynamics, quantitative genetics, and phenotypic selection analyses, we reveal the existence of dispersal syndromes in a pied flycatcher (Ficedula hypoleuca) population in the Netherlands: immigrants were larger, tended to have darker plumage, bred earlier, and produced larger clutches than local recruits, and some of these traits were genetically correlated. Over time, the phenotypic profile of the population gradually changed: each generation advanced arrival and breeding and exhibited longer wings as a result of direct and indirect selection on these correlated traits. Although phenotypic attributes of immigrants were favored by selection during the early phase of colonization, observed phenotypic changes were similar for immigrants and local recruits. We propose that immigrants facilitated initial population establishment but that temporal changes likely resulted from climate change-induced large-scale selection. This study highlights that newly established populations are of nonrandom composition and that phenotypic architecture affects evolutionary population trajectories.
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15
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Pepke ML, Kvalnes T, Rønning B, Jensen H, Boner W, Saether BE, Monaghan P, Ringsby TH. Artificial size selection experiment reveals telomere length dynamics and fitness consequences in a wild passerine. Mol Ecol 2022; 31:6224-6238. [PMID: 34997994 DOI: 10.1111/mec.16340] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 12/10/2021] [Accepted: 12/23/2021] [Indexed: 01/31/2023]
Abstract
Telomere dynamics could underlie life-history trade-offs among growth, size and longevity, but our ability to quantify such processes in natural, unmanipulated populations is limited. We investigated how 4 years of artificial selection for either larger or smaller tarsus length, a proxy for body size, affected early-life telomere length (TL) and several components of fitness in two insular populations of wild house sparrows over a study period of 11 years. The artificial selection was expected to shift the populations away from their optimal body size and increase the phenotypic variance in body size. Artificial selection for larger individuals caused TL to decrease, but there was little evidence that TL increased when selecting for smaller individuals. There was a negative correlation between nestling TL and tarsus length under both selection regimes. Males had longer telomeres than females and there was a negative effect of harsh weather on TL. We then investigated whether changes in TL might underpin fitness effects due to the deviation from the optimal body size. Mortality analyses indicated disruptive selection on TL because both short and long early-life telomeres tended to be associated with the lowest mortality rates. In addition, there was a tendency for a negative association between TL and annual reproductive success, but only in the population where body size was increased experimentally. Our results suggest that natural selection for optimal body size in the wild may be associated with changes in TL during growth, which is known to be linked to longevity in some bird species.
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Affiliation(s)
- Michael Le Pepke
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Thomas Kvalnes
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Bernt Rønning
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Henrik Jensen
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Winnie Boner
- Institute of Biodiversity, Animal Health and Comparative Medicine (IBAHCM), University of Glasgow, Glasgow, UK
| | - Bernt-Erik Saether
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Pat Monaghan
- Institute of Biodiversity, Animal Health and Comparative Medicine (IBAHCM), University of Glasgow, Glasgow, UK
| | - Thor Harald Ringsby
- Department of Biology, Centre for Biodiversity Dynamics (CBD), Norwegian University of Science and Technology (NTNU), Trondheim, Norway
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16
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Gauzere J, Pemberton JM, Kruuk LEB, Morris A, Morris S, Walling CA. Maternal effects do not resolve the paradox of stasis in birth weight in a wild red deer populaton. Evolution 2022; 76:2605-2617. [PMID: 36111977 PMCID: PMC9828841 DOI: 10.1111/evo.14622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/14/2022] [Indexed: 01/22/2023]
Abstract
In natural populations, quantitative traits seldom show short-term evolution at the rate predicted by evolutionary models. Resolving this "paradox of stasis" is a key goal in evolutionary biology, as it directly challenges our capacity to predict evolutionary change. One particularly promising hypothesis to explain the lack of evolutionary responses in a key offspring trait, body weight, is that positive selection on juveniles is counterbalanced by selection against maternal investment in offspring growth, given that reproduction is costly for the mothers. Here, we used data from one of the longest individual-based studies of a wild mammal population to test this hypothesis. We first showed that despite positive directional selection on birth weight, and heritable variation for this trait, no genetic change has been observed for birth weight over the past 47 years in the study population. Contrarily to our expectation, we found no evidence of selection against maternal investment in birth weight-if anything, selection favors mothers that produce large calves. Accordingly, we show that genetic change in birth weight over the study period is actually lower than that predicted from models including selection on maternal performance; ultimately our analysis here only deepens rather than resolves the paradox of stasis.
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Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Josephine M. Pemberton
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Loeske E. B. Kruuk
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK,Research School of BiologyThe Australian National UniversityCanberraACT 0200Australia
| | - Alison Morris
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Sean Morris
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
| | - Craig A. Walling
- Institute of Evolutionary Biology, School of Biological SciencesUniversity of EdinburghEdinburghEH9 3FLUK
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17
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Fritz ML. Utility and challenges of using whole‐genome resequencing to detect emerging insect and mite resistance in agroecosystems. Evol Appl 2022; 15:1505-1520. [PMID: 36330307 PMCID: PMC9624086 DOI: 10.1111/eva.13484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 11/29/2022] Open
Abstract
Arthropods that invade agricultural ecosystems systematically evolve resistance to the control measures used against them, and this remains a significant and ongoing challenge for sustainable food production systems. Early detection of resistance evolution could prompt remedial action to slow the spread of resistance alleles in the landscape. Historical approaches used to detect emerging resistance included phenotypic monitoring of agricultural pest populations, as well as monitoring of allele frequency changes at one or a few candidate pesticide resistance genes. In this article, I discuss the successes and limitations of these traditional monitoring approaches and then consider whether whole‐genome scanning could be applied to samples collected from agroecosystems over time for resistance monitoring. I examine the qualities of agroecosystems that could impact application of this approach to pesticide resistance monitoring and describe a recent retrospective analysis where genome scanning successfully detected an oligogenic response to selection by pesticides years prior to pest management failure. I conclude by considering areas of further study that will shed light on the feasibility of applying whole‐genome scanning for resistance risk monitoring in agricultural pest species.
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Affiliation(s)
- Megan L. Fritz
- Department of Entomology University of Maryland College Park Maryland USA
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18
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A method to predict the response to directional selection using a Kalman filter. Proc Natl Acad Sci U S A 2022; 119:e2117916119. [PMID: 35867739 DOI: 10.1073/pnas.2117916119] [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: 11/18/2022] Open
Abstract
Predicting evolution remains challenging. The field of quantitative genetics provides predictions for the response to directional selection through the breeder's equation, but these predictions can have errors. The sources of these errors include omission of traits under selection, inaccurate estimates of genetic variance, and nonlinearities in the relationship between genetic and phenotypic variation. Previous research showed that the expected value of these prediction errors is often not zero, so predictions are systematically biased. Here, we propose that this bias, rather than being a nuisance, can be used to improve the predictions. We use this to develop a method to predict evolution, which is built on three key innovations. First, the method predicts change as the breeder's equation plus a bias term. Second, the method combines information from the breeder's equation and from the record of past changes in the mean to predict change using a Kalman filter. Third, the parameters of the filter are fitted in each generation using a learning algorithm on the record of past changes. We compare the method to the breeder's equation in two artificial selection experiments, one using the wing of the fruit fly and another using simulations that include a complex mapping of genotypes to phenotypes. The proposed method outperforms the breeder's equation, particularly when traits under selection are omitted from the analysis, when data are noisy, and when additive genetic variance is estimated inaccurately or not estimated at all. The proposed method is easy to apply, requiring only the trait means over past generations.
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19
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Bonnet T, Morrissey MB, de Villemereuil P, Alberts SC, Arcese P, Bailey LD, Boutin S, Brekke P, Brent LJN, Camenisch G, Charmantier A, Clutton-Brock TH, Cockburn A, Coltman DW, Courtiol A, Davidian E, Evans SR, Ewen JG, Festa-Bianchet M, de Franceschi C, Gustafsson L, Höner OP, Houslay TM, Keller LF, Manser M, McAdam AG, McLean E, Nietlisbach P, Osmond HL, Pemberton JM, Postma E, Reid JM, Rutschmann A, Santure AW, Sheldon BC, Slate J, Teplitsky C, Visser ME, Wachter B, Kruuk LEB. Genetic variance in fitness indicates rapid contemporary adaptive evolution in wild animals. Science 2022; 376:1012-1016. [PMID: 35617403 DOI: 10.1126/science.abk0853] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The rate of adaptive evolution, the contribution of selection to genetic changes that increase mean fitness, is determined by the additive genetic variance in individual relative fitness. To date, there are few robust estimates of this parameter for natural populations, and it is therefore unclear whether adaptive evolution can play a meaningful role in short-term population dynamics. We developed and applied quantitative genetic methods to long-term datasets from 19 wild bird and mammal populations and found that, while estimates vary between populations, additive genetic variance in relative fitness is often substantial and, on average, twice that of previous estimates. We show that these rates of contemporary adaptive evolution can affect population dynamics and hence that natural selection has the potential to partly mitigate effects of current environmental change.
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Affiliation(s)
- Timothée Bonnet
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Pierre de Villemereuil
- Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études, PSL, MNHN, CNRS, SU, UA, Paris, France.,School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Susan C Alberts
- Departments of Biology and Evolutionary Anthropology, Duke University, Durham, NC, USA
| | - Peter Arcese
- Forest and Conservation Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Liam D Bailey
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Stan Boutin
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Patricia Brekke
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | - Lauren J N Brent
- Centre for Research in Animal Behaviour, University of Exeter, Penryn, UK
| | - Glauco Camenisch
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Anne Charmantier
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Tim H Clutton-Brock
- Department of Zoology, University of Cambridge, Cambridge, UK.,Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Andrew Cockburn
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | - David W Coltman
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Alexandre Courtiol
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Eve Davidian
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Simon R Evans
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK.,Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - John G Ewen
- Institute of Zoology, Zoological Society of London, Regents Park, London, UK
| | | | - Christophe de Franceschi
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Lars Gustafsson
- Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden
| | - Oliver P Höner
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Thomas M Houslay
- Department of Zoology, University of Cambridge, Cambridge, UK.,Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Lukas F Keller
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Zoological Museum, University of Zurich,, Zurich, Switzerland
| | - Marta Manser
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.,Mammal Research Institute, University of Pretoria, Pretoria, South Africa
| | - Andrew G McAdam
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Emily McLean
- Biology Department, Oxford College, Emory University, Oxford, GA, USA
| | - Pirmin Nietlisbach
- School of Biological Sciences, Illinois State University, Normal, IL, USA
| | - Helen L Osmond
- Research School of Biology, Australian National University, Canberra, ACT, Australia
| | | | - Erik Postma
- Centre for Ecology and Conservation, University of Exeter, Penryn, UK
| | - Jane M Reid
- Centre for Biodiversity Dynamics, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,School of Biological Sciences, University of Aberdeen, Aberdeen, UK
| | - Alexis Rutschmann
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Ben C Sheldon
- Edward Grey Institute, Department of Zoology, University of Oxford, Oxford, UK
| | - Jon Slate
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Céline Teplitsky
- Centre d'Écologie Fonctionnelle et Évolutive, Université de Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, Netherlands
| | - Bettina Wachter
- Departments of Evolutionary Ecology and Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Loeske E B Kruuk
- Research School of Biology, Australian National University, Canberra, ACT, Australia.,Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
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20
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Bridle J, Hoffmann A. Understanding the biology of species' ranges: when and how does evolution change the rules of ecological engagement? Philos Trans R Soc Lond B Biol Sci 2022; 377:20210027. [PMID: 35184590 PMCID: PMC8859517 DOI: 10.1098/rstb.2021.0027] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Understanding processes that limit species' ranges has been a core issue in ecology and evolutionary biology for many decades, and has become increasingly important given the need to predict the responses of biological communities to rapid environmental change. However, we still have a poor understanding of evolution at range limits and its capacity to change the ecological 'rules of engagement' that define these communities, as well as the time frame over which this occurs. Here we link papers in the current volume to some key concepts involved in the interactions between evolutionary and ecological processes at species' margins. In particular, we separate hypotheses about species' margins that focus on hard evolutionary limits, which determine how genotypes interact with their environment, from those concerned with soft evolutionary limits, which determine where and when local adaptation can persist in space and time. We show how theoretical models and empirical studies highlight conditions under which gene flow can expand local limits as well as contain them. In doing so, we emphasize the complex interplay between selection, demography and population structure throughout a species' geographical and ecological range that determines its persistence in biological communities. However, despite some impressively detailed studies on range limits, particularly in invertebrates and plants, few generalizations have emerged that can predict evolutionary responses at ecological margins. We outline some directions for future work such as considering the impact of structural genetic variants and metapopulation structure on limits, and the interaction between range limits and the evolution of mating systems and non-random dispersal. This article is part of the theme issue 'Species' ranges in the face of changing environments (Part II)'.
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Affiliation(s)
- Jon Bridle
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Ary Hoffmann
- School of BioSciences, Bio21 Institute, The University of Melbourne, Melbourne, Australia
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21
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Reid JM, Acker P. Conceptualizing the evolutionary quantitative genetics of phenological life‐history events: Breeding time as a plastic threshold trait. Evol Lett 2022; 6:220-233. [PMID: 35784452 PMCID: PMC9233176 DOI: 10.1002/evl3.278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 01/22/2022] [Accepted: 01/30/2022] [Indexed: 11/06/2022] Open
Affiliation(s)
- Jane M. Reid
- Centre for Biodiversity Dynamics NTNU Trondheim 7491 Norway
- School of Biological Sciences University of Aberdeen Aberdeen AB24 2TZ United Kingdom
| | - Paul Acker
- Centre for Biodiversity Dynamics NTNU Trondheim 7491 Norway
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22
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Morales-Mata JI, Potti J, Camacho C, Martínez-Padilla J, Canal D. Phenotypic selection on an ornamental trait is not modulated by breeding density in a pied flycatcher population. J Evol Biol 2022; 35:610-620. [PMID: 35293060 PMCID: PMC9311403 DOI: 10.1111/jeb.13993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 01/25/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
Most studies of phenotypic selection in the wild have focussed on morphological and life‐history traits and looked at abiotic (climatic) variation as the main driver of selection. Consequently, our knowledge of the effects of biotic environmental variation on phenotypic selection on sexual traits is scarce. Population density can be considered a proxy for the intensity of intrasexual and intersexual competition and could therefore be a key factor influencing the covariation between individual fitness and the expression of sexual traits. Here, we used an individual‐based data set from a population of pied flycatchers (Ficedula hypoleuca) monitored over 24 years to analyze the effect of breeding density on phenotypic selection on dorsal plumage colouration, a heritable and sexually selected ornament in males of this species. Using the number of recruits as a fitness proxy, our results showed overall stabilizing selection on male dorsal colouration, with intermediate phenotypes being favoured over extremely dark and dull individuals. However, our results did not support the hypothesis that breeding density mediates phenotypic selection on this sexual trait. We discuss the possible role of other biotic factors influencing selection on ornamental plumage.
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Affiliation(s)
| | - Jaime Potti
- Department of Evolutionary Ecology, Estación Biológica de Doñana (CSIC), Seville, Spain
| | - Carlos Camacho
- Department of Biological Conservation and Ecosystem Restoration, Pyrenean Institute of Ecology (IPE-CSIC), Jaca, Spain
| | - Jesús Martínez-Padilla
- Department of Biological Conservation and Ecosystem Restoration, Pyrenean Institute of Ecology (IPE-CSIC), Jaca, Spain
| | - David Canal
- Centre for Ecological Research, Institute of Ecology and Botany, Vácrátót, Hungary
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23
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Assis APA, Guimarães PR. Organisms as complex structures wrapped in a complex web of life. Am Nat 2022; 199:804-807. [DOI: 10.1086/719657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Cubry P, Oddou-Muratorio S, Scotti I, Lefèvre F. Interactions between microenvironment, selection and genetic architecture drive multiscale adaptation in a simulation experiment. J Evol Biol 2022; 35:451-466. [PMID: 35170114 PMCID: PMC9306464 DOI: 10.1111/jeb.13988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 02/05/2022] [Accepted: 02/08/2022] [Indexed: 11/28/2022]
Abstract
When environmental conditions differ both within and among populations, multiscale adaptation results from processes at both scales and interference across scales. We hypothesize that within-population environmental heterogeneity influences the chance of success of migration events, both within and among populations, and maintains within-population adaptive differentiation. We used a simulation approach to analyze the joint effects of environmental heterogeneity patterns, selection intensity and number of QTL controlling a selected trait on local adaptation in a hierarchical metapopulation design. We show the general effects of within-population environmental heterogeneity: (i) it increases occupancy rate at the margins of distribution ranges, under extreme environments and high levels of selection; (ii) it increases the adaptation lag in all environments; (iii) it impacts the genetic variance in each environment, depending on the ratio of within- to between-populations environmental heterogeneity; (iv) it reduces the selection-induced erosion of adaptive gene diversity. Most often, the smaller the number of QTL involved, the stronger are these effects. We also show that both within- and between-populations phenotypic differentiation (QST ) mainly results from covariance of QTL effects rather than QTL differentiation (FSTq ), that within-population QTL differentiation is negligible, and that stronger divergent selection is required to produce adaptive differentiation within populations than among populations. With a high number of QTL, when the difference between environments within populations exceeds the smallest difference between environments across populations, high levels of within-population differentiation can be reached, reducing differentiation among populations. Our study stresses the need to account for within-population environmental heterogeneity when investigating local adaptation.
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Affiliation(s)
- Philippe Cubry
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France.,DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France
| | - Sylvie Oddou-Muratorio
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France.,ECOBIOP, Université de Pau et des Pays de l'Adour, E2S UPPA, INRAE, Saint-Pée-sur-Nivelle, France
| | - Ivan Scotti
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France
| | - François Lefèvre
- Ecologie des Forêts Méditerranéennes, URFM, INRAE, Avignon, France
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25
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Pélissié B, Chen YH, Cohen ZP, Crossley MS, Hawthorne DJ, Izzo V, Schoville SD. Genome resequencing reveals rapid, repeated evolution in the Colorado potato beetle. Mol Biol Evol 2022; 39:6511499. [PMID: 35044459 PMCID: PMC8826761 DOI: 10.1093/molbev/msac016] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Insecticide resistance and rapid pest evolution threatens food security and the development of sustainable agricultural practices, yet the evolutionary mechanisms that allow pests to rapidly adapt to control tactics remains unclear. Here we examine how a global super-pest, the Colorado potato beetle (CPB), Leptinotarsa decemlineata, rapidly evolves resistance to insecticides. Using whole genome resequencing and transcriptomic data focused on its ancestral and pest range in North America, we assess evidence for three, non-mutually exclusive models of rapid evolution: pervasive selection on novel mutations, rapid regulatory evolution, and repeated selection on standing genetic variation. Population genomic analysis demonstrates that CPB is geographically structured, even among recently established pest populations. Pest populations exhibit similar levels of nucleotide diversity, relative to non-pest populations, and show evidence of recent expansion. Genome scans provide clear signatures of repeated adaptation across CPB populations, with especially strong evidence of selection on insecticide resistance genes in different populations. Analyses of gene expression show that constitutive upregulation of candidate insecticide resistance genes drives distinctive population patterns. CPB evolves insecticide resistance repeatedly across agricultural regions, leveraging similar genetic pathways but different genes, demonstrating a polygenic trait architecture for insecticide resistance that can evolve from standing genetic variation. Despite expectations, we do not find support for strong selection on novel mutations, or rapid evolution from selection on regulatory genes. These results suggest that integrated pest management practices must mitigate the evolution of polygenic resistance phenotypes among local pest populations, in order to maintain the efficacy and sustainability of novel control techniques.
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Affiliation(s)
- Benjamin Pélissié
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yolanda H Chen
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA
| | - Zachary P Cohen
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Michael S Crossley
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - David J Hawthorne
- Department of Entomology, University of Maryland, College Park, MD 20742, USA
| | - Victor Izzo
- Department of Plant and Soil Science, University of Vermont, Burlington, VT 05405, USA
| | - Sean D Schoville
- Department of Entomology, University of Wisconsin-Madison, Madison, WI 53706, USA
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26
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Biquet J, Bonamour S, de Villemereuil P, de Franceschi C, Teplitsky C. Phenotypic plasticity drives phenological changes in a Mediterranean blue tit population. J Evol Biol 2021; 35:347-359. [PMID: 34669221 DOI: 10.1111/jeb.13950] [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: 07/23/2021] [Revised: 10/05/2021] [Accepted: 10/08/2021] [Indexed: 01/14/2023]
Abstract
Earlier phenology induced by climate change, such as the passerines' breeding time, is observed in many natural populations. Understanding the nature of such changes is key to predict the responses of wild populations to climate change. Genetic changes have been rarely investigated for laying date, though it has been shown to be heritable and under directional selection, suggesting that the trait could evolve. In a Corsican blue tit population, the birds' laying date has significantly advanced over 40 years, and we here determine whether this response is of plastic or evolutionary origin, by comparing the predictions of the breeder's and the Robertson-Price (STS) equations, to the observed genetic changes. We compare the results obtained for two fitness proxies (fledgling and recruitment success), using models accounting for their zero inflation. Because the trait appears heritable and under directional selection, the breeder's equation predicts that genetic changes could drive a significant part of the phenological change observed. We, however, found that fitness proxies and laying date are not genetically correlated. The STS, therefore, predicts no evolution of the breeding time, predicting correctly the absence of trend in breeding values. Our results also emphasize that when investigating selection on a plastic trait under fluctuating selection, part of the fitness-trait phenotypic covariance can be due to within individual covariance. In the case of repeated measurements, splitting within and between individual covariance can shift our perspective on the actual intensity of selection over multiple selection episodes, shedding light on the potential for the trait to evolve.
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Affiliation(s)
- Juliette Biquet
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - Suzanne Bonamour
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Centre d'Ecologie et des Sciences de la Conservation (CESCO, UMR 7204), Muséum national d'histoire naturelle, CNRS, Sorbonne Université, Paris, France
| | - Pierre de Villemereuil
- CEFE, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France.,Institut de Systématique, Évolution, Biodiversité (ISYEB), École Pratique des Hautes Études, PSL, MNHN, CNRS, SU, UA, Paris, France
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27
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Baverstock K. The gene: An appraisal. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2021; 164:46-62. [PMID: 33979646 DOI: 10.1016/j.pbiomolbio.2021.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/14/2021] [Accepted: 04/22/2021] [Indexed: 11/29/2022]
Abstract
The gene can be described as the foundational concept of modern biology. As such, it has spilled over into daily discourse, yet it is acknowledged among biologists to be ill-defined. Here, following a short history of the gene, I analyse critically its role in inheritance, evolution, development, and morphogenesis. Wilhelm Johannsen's genotype-conception, formulated in 1910, has been adopted as the foundation stone of genetics, giving the gene a higher degree of prominence than is justified by the evidence. An analysis of the results of the Long-Term Evolution Experiment (LTEE) with E. coli bacteria, grown over 60,000 generations, does not support spontaneous gene mutation as the source of variance for natural selection. From this it follows that the gene is not Mendel's unit of inheritance: that must be Johannsen's transmission-conception at the gamete phenotype level, a form of inheritance that Johannsen did not consider. Alternatively, I contend that biology viewed on the bases of thermodynamics, complex system dynamics and self-organisation, provides a new framework for the foundations of biology. In this framework, the gene plays a passive role as a vital information store: it is the phenotype that plays the active role in inheritance, evolution, development, and morphogenesis.
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Affiliation(s)
- Keith Baverstock
- Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio Campus, Kuopio, Finland.
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28
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Henry LP, Bruijning M, Forsberg SKG, Ayroles JF. The microbiome extends host evolutionary potential. Nat Commun 2021; 12:5141. [PMID: 34446709 PMCID: PMC8390463 DOI: 10.1038/s41467-021-25315-x] [Citation(s) in RCA: 113] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 08/03/2021] [Indexed: 02/07/2023] Open
Abstract
The microbiome shapes many host traits, yet the biology of microbiomes challenges traditional evolutionary models. Here, we illustrate how integrating the microbiome into quantitative genetics can help untangle complexities of host-microbiome evolution. We describe two general ways in which the microbiome may affect host evolutionary potential: by shifting the mean host phenotype and by changing the variance in host phenotype in the population. We synthesize the literature across diverse taxa and discuss how these scenarios could shape the host response to selection. We conclude by outlining key avenues of research to improve our understanding of the complex interplay between hosts and microbiomes.
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Affiliation(s)
- Lucas P. Henry
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
| | - Marjolein Bruijning
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA
| | - Simon K. G. Forsberg
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA ,grid.8993.b0000 0004 1936 9457Dept. of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Julien F. Ayroles
- grid.16750.350000 0001 2097 5006Dept. of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ USA ,grid.16750.350000 0001 2097 5006Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
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29
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Le Vaillant J, Potti J, Camacho C, Canal D, Martínez-Padilla J. Fluctuating selection driven by global and local climatic conditions leads to stasis in breeding time in a migratory bird. J Evol Biol 2021; 34:1541-1553. [PMID: 34415649 DOI: 10.1111/jeb.13916] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 07/26/2021] [Accepted: 08/04/2021] [Indexed: 11/30/2022]
Abstract
The origin of natural selection is linked to environmental heterogeneity, which influences variation in relative fitness among phenotypes. However, individuals in wild populations are exposed to a plethora of biotic and abiotic environmental factors. Surprisingly, the relative influence of multiple environmental conditions on the relative fitness of phenotypes has rarely been tested in wild populations. Identifying the main selection agent(s) is crucial when the target phenotype is tightly linked to reproduction and when temporal variation in selection is expected to affect evolutionary responses. By using individual-based data from a 29-year study of a short-lived migratory songbird, the pied flycatcher (Ficedula hypoleuca), we studied the relative influence of 28 temperature- and precipitation-based factors at local and global scales on selection on breeding time (egg laying) at the phenotypic level. Selection, estimated using the number of recruits as a proxy for fitness, penalized late breeders. Minimum temperatures in April and May were the environmental drivers that best explained selection on laying date. In particular, there was negative directional selection on laying date mediated by minimum temperature in April, being strongest in cold years. In addition, nonlinear selection on laying date was influenced by minimum temperatures in May, with selection on laying date changing from null to negative as the breeding season progressed. The intensity of selection on late breeders increased when minimum temperatures in May were highest. Our results illustrate the complex influence of environmental factors on selection on laying date in wild bird populations. Despite minimum temperature in April being the only variable that changed over time, its increase did not induce a shift in laying date in the population. In this songbird population, stabilizing selection has led to a three-decade stasis in breeding time. We suggest that variation in the effects of multiple climatic variables on selection may constrain phenotypic change.
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Affiliation(s)
- Justine Le Vaillant
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Sevilla, Spain
| | - Jaime Potti
- Department of Evolutionary Ecology, Estación Biológica de Doñana-CSIC, Sevilla, Spain
| | - Carlos Camacho
- Department of Biological Conservation and Ecosystem Restoration, Pyrenean Institute of Ecology (CSIC), Jaca, Spain
| | - David Canal
- Institute of Ecology and Botany, Centre for Ecological Research, Vácrátót, Hungary
| | - Jesús Martínez-Padilla
- Department of Biological Conservation and Ecosystem Restoration, Pyrenean Institute of Ecology (CSIC), Jaca, Spain
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30
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Fokkema RW, Korsten P, Schmoll T, Wilson AJ. Social competition as a driver of phenotype-environment correlations: implications for ecology and evolution. Biol Rev Camb Philos Soc 2021; 96:2561-2572. [PMID: 34145714 PMCID: PMC9290562 DOI: 10.1111/brv.12768] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 12/27/2022]
Abstract
While it is universally recognised that environmental factors can cause phenotypic trait variation via phenotypic plasticity, the extent to which causal processes operate in the reverse direction has received less consideration. In fact individuals are often active agents in determining the environments, and hence the selective regimes, they experience. There are several important mechanisms by which this can occur, including habitat selection and niche construction, that are expected to result in phenotype–environment correlations (i.e. non‐random assortment of phenotypes across heterogeneous environments). Here we highlight an additional mechanism – intraspecific competition for preferred environments – that may be widespread, and has implications for phenotypic evolution that are currently underappreciated. Under this mechanism, variation among individuals in traits determining their competitive ability leads to phenotype–environment correlation; more competitive phenotypes are able to acquire better patches. Based on a concise review of the empirical evidence we argue that competition‐induced phenotype–environment correlations are likely to be common in natural populations before highlighting the major implications of this for studies of natural selection and microevolution. We focus particularly on two central issues. First, competition‐induced phenotype–environment correlation leads to the expectation that positive feedback loops will amplify phenotypic and fitness variation among competing individuals. As a result of being able to acquire a better environment, winners gain more resources and even better phenotypes – at the expense of losers. The distinction between individual quality and environmental quality that is commonly made by researchers in evolutionary ecology thus becomes untenable. Second, if differences among individuals in competitive ability are underpinned by heritable traits, competition results in both genotype–environment correlations and an expectation of indirect genetic effects (IGEs) on resource‐dependent life‐history traits. Theory tells us that these IGEs will act as (partial) constraints, reducing the amount of genetic variance available to facilitate evolutionary adaptation. Failure to recognise this will lead to systematic overestimation of the adaptive potential of populations. To understand the importance of these issues for ecological and evolutionary processes in natural populations we therefore need to identify and quantify competition‐induced phenotype–environment correlations in our study systems. We conclude that both fundamental and applied research will benefit from an improved understanding of when and how social competition causes non‐random distribution of phenotypes, and genotypes, across heterogeneous environments.
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Affiliation(s)
- Rienk W Fokkema
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany.,Evolutionary Biology, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany.,Conservation Ecology Group, Groningen Institute for Evolutionary Life Sciences (GELIFES), University of Groningen, Nijenborgh 7, Groningen, 9747AG, The Netherlands
| | - Peter Korsten
- Department of Animal Behaviour, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
| | - Tim Schmoll
- Evolutionary Biology, Bielefeld University, Konsequenz 45, Bielefeld, 33615, Germany
| | - Alastair J Wilson
- Centre for Ecology and Conservation, University of Exeter (Penryn Campus), Penryn, Cornwall, TR10 9FE, United Kingdom
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31
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Waters JM, McCulloch GA. Reinventing the wheel? Reassessing the roles of gene flow, sorting and convergence in repeated evolution. Mol Ecol 2021; 30:4162-4172. [PMID: 34133810 DOI: 10.1111/mec.16018] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/31/2022]
Abstract
Biologists have long been intrigued by apparently predictable and repetitive evolutionary trajectories inferred across a variety of lineages and systems. In recent years, high-throughput sequencing analyses have started to transform our understanding of such repetitive shifts. While researchers have traditionally categorized such shifts as either "convergent" or "parallel," based on relatedness of the lineages involved, emerging genomic insights provide an opportunity to better describe the actual evolutionary mechanisms at play. A synthesis of recent genomic analyses confirms that convergence is the predominant driver of repetitive evolution among species, whereas repeated sorting of standing variation is the major driver of repeated shifts within species. However, emerging data reveal numerous notable exceptions to these expectations, with recent examples of de novo mutations underpinning convergent shifts among even very closely related lineages, while repetitive sorting processes have occurred among even deeply divergent taxa, sometimes via introgression. A number of very recent analyses have found evidence for both processes occurring on different scales within taxa. We suggest that the relative importance of convergent versus sorting processes depends on the interplay between gene flow among populations, and phylogenetic relatedness of the lineages involved.
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32
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Chirgwin E, Connallon T, Monro K. The thermal environment at fertilization mediates adaptive potential in the sea. Evol Lett 2021; 5:154-163. [PMID: 33868711 PMCID: PMC8045945 DOI: 10.1002/evl3.215] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 12/04/2020] [Accepted: 01/15/2021] [Indexed: 12/11/2022] Open
Abstract
Additive genetic variation for fitness at vulnerable life stages governs the adaptive potential of populations facing stressful conditions under climate change, and can depend on current conditions as well as those experienced by past stages or generations. For sexual populations, fertilization is the key stage that links one generation to the next, yet the effects of fertilization environment on the adaptive potential at the vulnerable stages that then unfold during development are rarely considered, despite climatic stress posing risks for gamete function and fertility in many taxa and external fertilizers especially. Here, we develop a simple fitness landscape model exploring the effects of environmental stress at fertilization and development on the adaptive potential in early life. We then test our model with a quantitative genetic breeding design exposing family groups of a marine external fertilizer, the tubeworm Galeolaria caespitosa, to a factorial manipulation of current and projected temperatures at fertilization and development. We find that adaptive potential in early life is substantially reduced, to the point of being no longer detectable, by genotype‐specific carryover effects of fertilization under projected warming. We interpret these results in light of our fitness landscape model, and argue that the thermal environment at fertilization deserves more attention than it currently receives when forecasting the adaptive potential of populations confronting climate change.
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Affiliation(s)
- Evatt Chirgwin
- School of Biological Sciences Monash University Clayton Victoria Australia.,Cesar Australia Parkville Victoria Australia
| | - Tim Connallon
- School of Biological Sciences Monash University Clayton Victoria Australia
| | - Keyne Monro
- School of Biological Sciences Monash University Clayton Victoria Australia
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33
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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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34
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Feiner N, Brun-Usan M, Uller T. Evolvability and evolutionary rescue. Evol Dev 2021; 23:308-319. [PMID: 33528902 DOI: 10.1111/ede.12374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 11/22/2020] [Accepted: 01/13/2021] [Indexed: 11/29/2022]
Abstract
The survival prospects of threatened species or populations can sometimes be improved by adaptive change. Such evolutionary rescue is particularly relevant when the threat comes from changing environments, or when long-term population persistence requires range expansion into new habitats. Conservation biologists are therefore often interested in whether or not populations or lineages show a disposition for adaptive evolution, that is, if they are evolvable. Here, we discuss four alternative perspectives that target different causes of evolvability and outline some of the key challenges those perspectives are designed to address. Standing genetic variation provides one familiar estimate of evolvability. Yet, the mere presence of genetic variation is often insufficient to predict if a population will adapt, or how it will adapt. The reason is that adaptive change not only depends on genetic variation, but also on the extent to which this genetic variation can be realized as adaptive phenotypic variation. This requires attention to developmental systems and how plasticity influences evolutionary potential. Finally, we discuss how a better understanding of the different factors that contribute to evolvability can be exploited in conservation practice.
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Affiliation(s)
| | | | - Tobias Uller
- Department of Biology, Lund University, Lund, Sweden
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35
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Reid JM, Arcese P, Nietlisbach P, Wolak ME, Muff S, Dickel L, Keller LF. Immigration counter-acts local micro-evolution of a major fitness component: Migration-selection balance in free-living song sparrows. Evol Lett 2021; 5:48-60. [PMID: 33552535 PMCID: PMC7857281 DOI: 10.1002/evl3.214] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/28/2020] [Accepted: 12/18/2020] [Indexed: 01/11/2023] Open
Abstract
Ongoing adaptive evolution, and resulting “evolutionary rescue” of declining populations, requires additive genetic variation in fitness. Such variation can be increased by gene flow resulting from immigration, potentially facilitating evolution. But, gene flow could in fact constrain rather than facilitate local adaptive evolution if immigrants have low additive genetic values for local fitness. Local migration‐selection balance and micro‐evolutionary stasis could then result. However, key quantitative genetic effects of natural immigration, comprising the degrees to which gene flow increases the total local additive genetic variance yet counteracts local adaptive evolutionary change, have not been explicitly quantified in wild populations. Key implications of gene flow for population and evolutionary dynamics consequently remain unclear. Our quantitative genetic analyses of long‐term data from free‐living song sparrows (Melospiza melodia) show that mean breeding value for local juvenile survival to adulthood, a major component of fitness, increased across cohorts more than expected solely due to drift. Such micro‐evolutionary change should be expected given nonzero additive genetic variance and consistent directional selection. However, this evolutionary increase was counteracted by negative additive genetic effects of recent immigrants, which increased total additive genetic variance but prevented a net directional evolutionary increase in total additive genetic value. These analyses imply an approximate quantitative genetic migration‐selection balance in a major fitness component, and hence demonstrate a key mechanism by which substantial additive genetic variation can be maintained yet decoupled from local adaptive evolutionary change.
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Affiliation(s)
- Jane M Reid
- Centre for Biodiversity Dynamics NTNU Trondheim Norway.,School of Biological Sciences University of Aberdeen Aberdeen UK
| | - Peter Arcese
- Forest & Conservation Sciences University of British Columbia Vancouver British Columbia Canada
| | - Pirmin Nietlisbach
- School of Biological Sciences Illinois State University Normal Illinois USA
| | - Matthew E Wolak
- Department of Biological Sciences Auburn University Auburn Alaska USA
| | - Stefanie Muff
- Centre for Biodiversity Dynamics NTNU Trondheim Norway.,Department of Mathematical Sciences NTNU Trondheim Norway
| | - Lisa Dickel
- Centre for Biodiversity Dynamics NTNU Trondheim Norway
| | - Lukas F Keller
- Department of Evolutionary Biology & Environmental Studies University of Zurich Zurich Switzerland.,Zoological Museum University of Zurich Zurich Switzerland
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36
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Potter T, Bassar RD, Bentzen P, Ruell EW, Torres-Dowdall J, Handelsman CA, Ghalambor CK, Travis J, Reznick DN, Coulson T. Environmental Change, If Unaccounted, Prevents Detection of Cryptic Evolution in a Wild Population. Am Nat 2021; 197:29-46. [PMID: 33417522 DOI: 10.1086/711874] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractDetecting contemporary evolution requires demonstrating that genetic change has occurred. Mixed effects models allow estimation of quantitative genetic parameters and are widely used to study evolution in wild populations. However, predictions of evolution based on these parameters frequently fail to match observations. Here, we applied three commonly used quantitative genetic approaches to predict the evolution of size at maturity in a wild population of Trinidadian guppies. Crucially, we tested our predictions against evolutionary change observed in common-garden experiments performed on samples from the same population. We show that standard quantitative genetic models underestimated or failed to detect the cryptic evolution of this trait as demonstrated by the common-garden experiments. The models failed because (1) size at maturity and fitness both decreased with increases in population density, (2) offspring experienced higher population densities than their parents, and (3) selection on size was strongest at high densities. When we accounted for environmental change, predictions better matched observations in the common-garden experiments, although substantial uncertainty remained. Our results demonstrate that predictions of evolution are unreliable if environmental change is not appropriately captured in models.
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37
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Suárez-Vidal E, Sampedro L, Climent J, Voltas J, Sin E, Notivol E, Zas R. Direct and correlated responses to artificial selection for growth and water-use efficiency in a Mediterranean pine. AMERICAN JOURNAL OF BOTANY 2021; 108:102-112. [PMID: 33512710 DOI: 10.1002/ajb2.1599] [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: 05/20/2020] [Accepted: 09/22/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Persistence of tree populations in the face of global change relies on their capacity to respond to biotic and abiotic stressors through plastic or adaptive changes. Genetic adaptation will depend on the additive genetic variation within populations and the heritability of traits related to stress tolerance. Because traits can be genetically linked, selective pressure acting on one trait may lead to correlated responses in other traits. METHODS To test direct and correlated responses to selection for growth and drought tolerance in Pinus halepensis, we selected trees in a parental population for higher growth and greater water-use efficiency (WUE) and compared their offspring with the offspring of random trees from the parental population in two contrasting common gardens. We estimated direct responses to selection for growth and WUE and correlated responses for growth and tolerance to abiotic and biotic stressors. RESULTS We found a strong response to selection and high realized heritability for WUE, but no response to selection for growth. Correlated responses to selection in other life-history traits were not significant, except for concentration of some chemical defenses, which was greater in the offspring of mother trees selected for growth than in the offspring of unselected control trees. CONCLUSIONS The empirical evidence of direct responses to selection for high WUE suggests that P. halepensis has the potential to evolve in response to increasing drought stress. Contrary to expectations, the results are not conclusive of a potential negative impact of WUE and growth selection on other key life-history traits.
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Affiliation(s)
| | - Luis Sampedro
- Misión Biológica de Galicia (MBG-CSIC), Apdo. 28, 36143, Pontevedra, Spain
| | - Jose Climent
- INIA-CIFOR, Department of Ecology and Forest Genetics, Ctra. Coruña km 7.5, 28040, Madrid, Spain
| | - Jordi Voltas
- Joint Research Unit CTFC - AGROTECNIO, Rovira Roure 191, E25198, Lleida, Spain
- Department of Crop and Forest Sciences, University of Lleida, Rovira Roure 191, E25198, Lleida, Spain
| | - Ester Sin
- Department of Crop and Forest Sciences, University of Lleida, Rovira Roure 191, E25198, Lleida, Spain
| | - Eduardo Notivol
- Forest Resources Unit, CITA & IA2, Av. Montañana 930, 50059, Zaragoza, Spain
| | - Rafael Zas
- Misión Biológica de Galicia (MBG-CSIC), Apdo. 28, 36143, Pontevedra, Spain
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38
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Alexandre H, Truffaut L, Klein E, Ducousso A, Chancerel E, Lesur I, Dencausse B, Louvet J, Nepveu G, Torres‐Ruiz JM, Lagane F, Musch B, Delzon S, Kremer A. How does contemporary selection shape oak phenotypes? Evol Appl 2020; 13:2772-2790. [PMID: 33294022 PMCID: PMC7691464 DOI: 10.1111/eva.13082] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 06/09/2020] [Accepted: 07/13/2020] [Indexed: 01/12/2023] Open
Abstract
Most existing forests are subjected to natural and human-mediated selection pressures, which have increased due to climate change and the increasing needs of human societies for wood, fibre and fuel resources. It remains largely unknown how these pressures trigger evolutionary changes. We address this issue here for temperate European oaks (Quercus petraea and Q. robur), which grow in mixed stands, under even-aged management regimes. We screened numerous functional traits for univariate selection gradients and for expected and observed genetic changes over two successive generations. In both species, growth, leaf morphology and physiology, and defence-related traits displayed significant selection gradients and predicted shifts, whereas phenology, water metabolism, structure and resilience-related traits did not. However, the direction of the selection response and the potential for adaptive evolution differed between the two species. Quercus petraea had a much larger phenotypic and genetic variance of fitness than Q. robur. This difference raises concerns about the adaptive response of Q. robur to contemporary selection pressures. Our investigations suggest that Q. robur will probably decline steadily, particularly in mixed stands with Q. petraea, consistent with the contrasting demographic dynamics of the two species.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - José M. Torres‐Ruiz
- INRAEUniversity of BordeauxBIOGECOCestasFrance
- INRAEUniversity of Clermont‐AuvergnePIAFClermont‐FerrandFrance
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39
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De Lisle SP, Punzalan D, Rollinson N, Rowe L. Extinction and the temporal distribution of macroevolutionary bursts. J Evol Biol 2020; 34:380-390. [PMID: 33205504 PMCID: PMC7983991 DOI: 10.1111/jeb.13741] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/29/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022]
Abstract
Phenotypic evolution through deep time is slower than expected from microevolutionary rates. This is the paradox of stasis. Previous models suggest stasis occurs because populations track adaptive peaks that remain relatively stable on million‐year intervals, raising the equally perplexing question of why these large changes are so rare. Here, we consider the possibility that peaks can move more rapidly than populations can adapt, resulting in extinction. We model peak movement with explicit population dynamics, parameterized with published microevolutionary estimates. Allowing extinction greatly increases the parameter space of peak movements that yield the appearance of stasis observed in real data through deep time. Extreme peak displacements, regardless of their frequency, will rarely result in an equivalent degree of trait evolution because of extinction. Thus, larger peak displacements will rarely be inferred using trait data from extant species or observed in fossil records. Our work highlights population ecology as an important contributor to macroevolutionary dynamics, presenting an alternative perspective on the paradox of stasis, where apparent constraint on phenotypic evolution in deep time reflects our restricted view of the subset of earth's lineages that were fortunate enough to reside on relatively stable peaks.
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Affiliation(s)
- Stephen P De Lisle
- Evolutionary Ecology Unit, Department of Biology, Lund University, Lund, Sweden
| | - David Punzalan
- Department of Biology, University of Victoria, Victoria, BC, Canada
| | - Njal Rollinson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,School of the Environment, University of Toronto, Toronto, ON, Canada
| | - Locke Rowe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada.,Swedish Collegium for Advanced Study, Uppsala, Sweden
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40
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Taylor-Cox ED, Macgregor CJ, Corthine A, Hill JK, Hodgson JA, Saccheri IJ. Wing morphological responses to latitude and colonisation in a range expanding butterfly. PeerJ 2020; 8:e10352. [PMID: 33240660 PMCID: PMC7680626 DOI: 10.7717/peerj.10352] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/22/2020] [Indexed: 11/20/2022] Open
Abstract
Populations undergoing rapid climate-driven range expansion experience distinct selection regimes dominated both by increased dispersal at the leading edges and steep environmental gradients. Characterisation of traits associated with such expansions provides insight into the selection pressures and evolutionary constraints that shape demographic and evolutionary responses. Here we investigate patterns in three components of wing morphology (size, shape, colour) often linked to dispersal ability and thermoregulation, along latitudinal gradients of range expansion in the Speckled Wood butterfly (Pararge aegeria) in Britain (two regions of expansion in England and Scotland). We measured 774 males from 54 sites spanning 799 km with a 10-year mean average temperature gradient of 4 °C. A geometric morphometric method was used to investigate variation in size and shape of forewings and hindwings; colour, pattern, and contrast of the wings were examined using a measure of lightness (inverse degree of melanism). Overall, wing size increased with latitude by ∼2% per 100 km, consistent with Bergmann’s rule. Forewings became more rounded and hindwings more elongated with history of colonisation, possibly reflecting selection for increased dispersal ability. Contrary to thermal melanism expectations, wing colour was lighter where larvae developed at cooler temperatures and unrelated to long-term temperature. Changes in wing spot pattern were also detected. High heterogeneity in variance among sites for all of the traits studied may reflect evolutionary time-lags and genetic drift due to colonisation of new habitats. Our study suggests that temperature-sensitive plastic responses for size and colour interact with selection for dispersal traits (wing size and shape). Whilst the plastic and evolutionary responses may in some cases act antagonistically, the rapid expansion of P. aegeria implies an overall reinforcing effect between these two mechanisms.
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Affiliation(s)
- Evelyn D Taylor-Cox
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Callum J Macgregor
- Leverhulme Centre for Anthropocene Biodiversity, Department of Biology, University of York, York, United Kingdom.,Energy and Environment Institute, University of Hull, Hull, United Kingdom
| | - Amy Corthine
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Jane K Hill
- Leverhulme Centre for Anthropocene Biodiversity, Department of Biology, University of York, York, United Kingdom
| | - Jenny A Hodgson
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, United Kingdom
| | - Ilik J Saccheri
- Department of Evolution, Ecology and Behaviour, University of Liverpool, Liverpool, United Kingdom
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41
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Landscape and Climate Influence the Patterns of Genetic Diversity and Inbreeding in Cerrado Plant Species. DIVERSITY 2020. [DOI: 10.3390/d12110421] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The anthropization of the landscape of the Cerrado biome that has occurred over the past few decades has fragmented its natural environments, impacting the connectivity of the plant populations and altering their gene flow. Plant species may also reduce population size in response to sub-optimal climatic and environmental conditions, and observed distribution patterns may align with theoretical schemes, such as the center–periphery model, that is, it is possible that populations on the edge have lower genetic diversity than center populations, theoretically submitted to environmental conditions closer to the optimum. In this context, we evaluate whether the genetic diversity and inbreeding coefficients of Cerrado plant species are affected by landscape features and climate characteristics, and in particular, if the distribution of the genetic diversity of these plants is consistent with the center–periphery model. To do this, we conducted a literature search for genetic studies of Cerrado plant populations using Scopus, Web of Science, and Scielo databases and the species found were used as a proxy to explore patterns throughout the biome. The data were analyzed using generalized linear mixed models (GLMM) and multiple matrix regressions (MMRRs) to evaluate the effects of landscape features and climatic variables on the observed (HO) and expected heterozygosity (HE), allelic richness (AR) and inbreeding (Fis) patterns of the local populations. The landscape was evaluated in terms of the percentage land cover of agriculture (AG), forestry (FO), remnant vegetation (RV), urban areas (UA), pasture (PA), and water (WA) within buffers of 1 km, 3 km, and 5 km around the study populations. We analyzed 121 populations of 31 plant species. The GLMMs showed that HO was affected by FO regardless of buffer size, while HE was also affected by FO, but also by WA and UA. AR was affected by WA and UA in all three buffer zones while the Fis was affected by FO and AU. The MMRRs showed that WA may affect HO, HE, and Fis within the 1 km buffer, while FO affects HO and UA affects AR within the 5 km buffer. In the case of the 1 km and 3 km buffers, however, the geographic distance between populations was identified as a factor determining the genetic diversity and inbreeding indices, indicating that isolation by distance may be an important factor defining the breeding patterns of the Cerrado plant populations. The GLMMs and MMRRs also showed that the mean annual temperature (MAT) and, to a lesser extent, isothermality (ISO) can explain the variation in genetic diversity observed in the Cerrado plant populations. We also found that the center–periphery model fits the distribution pattern observed in most of the species evaluated, including Annona crassiflora,Annona coriacea, Copaifera langsdorffii, and Eugenia dysenterica. Our results indicate that changes in the climate and the landscape of Brazilian Cerrado must be considered carefully to guarantee minimizing the impacts of these processes on the genetic diversity of Cerrado plant species and ensuring the long-term conservation of these species in this biome.
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42
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Brousseau L, Fine PVA, Dreyer E, Vendramin GG, Scotti I. Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae). Mol Ecol 2020; 30:1136-1154. [PMID: 32786115 DOI: 10.1111/mec.15595] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 06/19/2020] [Accepted: 07/31/2020] [Indexed: 01/04/2023]
Abstract
Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees-whose large and undisturbed populations often span a variety of environmental conditions and local habitats-are particularly good models to study this process. Here, we explore patterns of adaptive divergence from large (i.e., regional) to small (i.e., microgeographic) spatial scales in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae) under a replicated design involving two microhabitats (~300 m apart) in two study sites (~300 km apart). A three-year reciprocal transplant illustrates that, beyond strong maternal effects and phenotypic plasticity, genetically driven divergence in seedling growth and leaf traits was detected both between seedlings originating from different regions, and between seedlings from different microhabitats. In parallel, a complementary genome scan for selection was carried out through whole-genome sequencing of tree population pools. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier-surrounding genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence of microgeographic divergence in functional traits, the discovery of genomic candidates for microgeographic adaptive divergence represents a promising advance in our understanding of local adaptation, which probably operates across multiple spatial scales and underpins divergence and diversification in Neotropical trees.
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Affiliation(s)
- Louise Brousseau
- UMR EcoFoG, AgroParisTech, CIRAD, CNRS, INRAE, Université de Guyane, Université des Antilles, Kourou Cedex, France.,AMAP, Univ. Montpellier, CIRAD, CNRS, INRAE, IRD, Montpellier, France
| | - Paul V A Fine
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Erwin Dreyer
- Université de Lorraine, AgroParisTech, INRAE, Silva, Nancy, France
| | - Giovanni G Vendramin
- Institute of Biosciences and BioResources (IBBR-CNR), National Research Council, Division of Florence, Sesto Fiorentino, Italy
| | - Ivan Scotti
- UR629 Ecologie des Forêts Méditerranéennes (URFM), INRAE, Avignon, France
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43
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Scopece G, Palma-Silva C, Cafasso D, Lexer C, Cozzolino S. Phenotypic expression of floral traits in hybrid zones provides insights into their genetic architecture. THE NEW PHYTOLOGIST 2020; 227:967-975. [PMID: 32237254 DOI: 10.1111/nph.16566] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Accepted: 03/15/2020] [Indexed: 06/11/2023]
Abstract
Information on the genetic architecture of phenotypic traits is helpful for constructing and testing models of the ecoevolutionary dynamics of natural populations. For plant groups with long life cycles there is a lack of line cross experiments that can unravel the genetic architecture of loci underlying quantitative traits. To fill this gap, we propose the use of variation for phenotypic traits expressed in natural hybrid zones as an alternative approach. We used data from orchid hybrid zones and compared expected and observed patterns of phenotypic trait expression in different early-generation hybrid classes identified by molecular genetic markers. We found evidence of additivity, dominance, and epistatic interactions for different phenotypic traits. We discuss the potential of this approach along with its limitations and suggest that it may represent a realistic way to gain an initial insight into the heritability and genomic architecture of traits in organismal groups with complex life history, such as orchids and many others.
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Affiliation(s)
- Giovanni Scopece
- Department of Biology, University of Naples 'Federico II', Complesso Universitario MSA, I-80126, Naples, Italy
| | - Clarisse Palma-Silva
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, 13083-862, Campinas, Brazil
| | - Donata Cafasso
- Department of Biology, University of Naples 'Federico II', Complesso Universitario MSA, I-80126, Naples, Italy
| | - Christian Lexer
- Department of Botany and Biodiversity Research, University of Vienna, Rennweg 14, 1030, Wien, Austria
| | - Salvatore Cozzolino
- Department of Biology, University of Naples 'Federico II', Complesso Universitario MSA, I-80126, Naples, Italy
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44
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Garant D. Natural and human-induced environmental changes and their effects on adaptive potential of wild animal populations. Evol Appl 2020; 13:1117-1127. [PMID: 32684950 PMCID: PMC7359845 DOI: 10.1111/eva.12928] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Revised: 01/23/2020] [Accepted: 01/24/2020] [Indexed: 12/26/2022] Open
Abstract
A major challenge of evolutionary ecology over the next decades is to understand and predict the consequences of the current rapid and important environmental changes on wild populations. Extinction risk of species is linked to populations' evolutionary potential and to their ability to express adaptive phenotypic plasticity. There is thus a vital need to quantify how selective pressures, quantitative genetics parameters, and phenotypic plasticity, for multiple traits in wild animal populations, may vary with changes in the environment. Here I review our previous research that integrated ecological and evolutionary theories with molecular ecology, quantitative genetics, and long-term monitoring of individually marked wild animals. Our results showed that assessing evolutionary and plastic changes over time and space, using multi-trait approaches, under a realistic range of environmental conditions are crucial steps toward improving our understanding of the evolution and adaptation of natural populations. Our current and future work focusses on assessing the limits of adaptive potential by determining the factors constraining the evolvability of plasticity, those generating covariation among genetic variance and selection, as well as indirect genetic effects, which can affect population's capacity to adjust to environmental changes. In doing so, we aim to provide an improved assessment of the spatial and temporal scale of evolutionary processes in wild animal populations.
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Affiliation(s)
- Dany Garant
- Département de biologieFaculté des SciencesUniversité de SherbrookeSherbrookeQCCanada
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45
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Class B, Brommer JE. Can dominance genetic variance be ignored in evolutionary quantitative genetic analyses of wild populations? Evolution 2020; 74:1540-1550. [PMID: 32510608 DOI: 10.1111/evo.14034] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 05/06/2020] [Accepted: 05/30/2020] [Indexed: 12/21/2022]
Abstract
Accurately estimating genetic variance components is important for studying evolution in the wild. Empirical work on domesticated and wild outbred populations suggests that dominance genetic variance represents a substantial part of genetic variance, and theoretical work predicts that ignoring dominance can inflate estimates of additive genetic variance. Whether this issue is pervasive in natural systems is unknown, because we lack estimates of dominance variance in wild populations obtained in situ. Here, we estimate dominance and additive genetic variance, maternal variance, and other sources of nongenetic variance in eight traits measured in over 9000 wild nestlings linked through a genetically resolved pedigree. We find that dominance variance, when estimable, does not statistically differ from zero and represents a modest amount (2-36%) of genetic variance. Simulations show that (1) inferences of all variance components for an average trait are unbiased; (2) the power to detect dominance variance is low; (3) ignoring dominance can mildly inflate additive genetic variance and heritability estimates but such inflation becomes substantial when maternal effects are also ignored. These findings hence suggest that dominance is a small source of phenotypic variance in the wild and highlight the importance of proper model construction for accurately estimating evolutionary potential.
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Affiliation(s)
- Barbara Class
- Global Change Ecology Research Group, University of the Sunshine Coast, 90 Sippy Downs Drive, Sippy Downs, QLD, 4556, Australia.,Department of Biology, University of Turku, University Hill, Turku, 20014, Finland
| | - Jon E Brommer
- Department of Biology, University of Turku, University Hill, Turku, 20014, Finland
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46
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Gauzere J, Pemberton JM, Morris S, Morris A, Kruuk LEB, Walling CA. The genetic architecture of maternal effects across ontogeny in the red deer. Evolution 2020; 74:1378-1391. [DOI: 10.1111/evo.14000] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/24/2020] [Accepted: 05/04/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Julie Gauzere
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
| | - Josephine M. Pemberton
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
| | - Sean Morris
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
| | - Alison Morris
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
| | - Loeske E. B. Kruuk
- Research School of Biology The Australian National University ACT 0200 Canberra Australia
| | - Craig A. Walling
- Institute of Evolutionary Biology, School of Biological Sciences University of Edinburgh Edinburgh EH9 3FL United Kingdom
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47
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Walter GM, Abbott RJ, Brennan AC, Bridle JR, Chapman M, Clark J, Filatov D, Nevado B, Ortiz-Barrientos D, Hiscock SJ. Senecio as a model system for integrating studies of genotype, phenotype and fitness. THE NEW PHYTOLOGIST 2020; 226:326-344. [PMID: 31951018 DOI: 10.1111/nph.16434] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 12/17/2019] [Indexed: 05/24/2023]
Abstract
Two major developments have made it possible to use examples of ecological radiations as model systems to understand evolution and ecology. First, the integration of quantitative genetics with ecological experiments allows detailed connections to be made between genotype, phenotype, and fitness in the field. Second, dramatic advances in molecular genetics have created new possibilities for integrating field and laboratory experiments with detailed genetic sequencing. Combining these approaches allows evolutionary biologists to better study the interplay between genotype, phenotype, and fitness to explore a wide range of evolutionary processes. Here, we present the genus Senecio (Asteraceae) as an excellent system to integrate these developments, and to address fundamental questions in ecology and evolution. Senecio is one of the largest and most phenotypically diverse genera of flowering plants, containing species ranging from woody perennials to herbaceous annuals. These Senecio species exhibit many growth habits, life histories, and morphologies, and they occupy a multitude of environments. Common within the genus are species that have hybridized naturally, undergone polyploidization, and colonized diverse environments, often through rapid phenotypic divergence and adaptive radiation. These diverse experimental attributes make Senecio an attractive model system in which to address a broad range of questions in evolution and ecology.
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Affiliation(s)
- Greg M Walter
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Richard J Abbott
- School of Biology, University of St Andrews, St Andrews, Fife, KY16 9TH, UK
| | - Adrian C Brennan
- School of Biological and Biomedical Sciences, University of Durham, Durham, DH1 3LE, UK
| | - Jon R Bridle
- School of Biological Sciences, University of Bristol, Bristol, BS8 1TQ, UK
| | - Mark Chapman
- School of Biological Sciences, University of Southampton, Southampton, SO17 1BJ, UK
| | - James Clark
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Bruno Nevado
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | | | - Simon J Hiscock
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
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48
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Helanterä H, Uller T. Different perspectives on non-genetic inheritance illustrate the versatile utility of the Price equation in evolutionary biology. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190366. [PMID: 32146886 DOI: 10.1098/rstb.2019.0366] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The diversity of genetic and non-genetic processes that make offspring resemble their parents are increasingly well understood. In addition to genetic inheritance, parent-offspring similarity is affected by epigenetic, behavioural and cultural mechanisms that collectively can be referred to as non-genetic inheritance. Given the generality of the Price equation as a description of evolutionary change, is it not surprising that the Price equation has been adopted to model the evolutionary implications of non-genetic inheritance. In this paper, we briefly introduce the heredity perspectives on which those models rely, discuss the extent to which these perspectives make different assumptions and place different emphases on the roles of heredity and development in evolution, and the types of empirical research programmes they motivate. The existence of multiple perspectives and explanatory aims highlight, on the one hand, the versatility of the Price equation and, on the other hand, the importance of understanding how heredity and development can be conceptualized in evolutionary studies. This article is part of the theme issue 'Fifty years of the Price equation'.
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Affiliation(s)
- Heikki Helanterä
- Ecology and Genetics Research Unit, University of Oulu, Pentti Kaiteran katu 1, 90014 Oulu, Finland
| | - Tobias Uller
- Department of Biology, Lund University, Sölvegatan 37, 22362 Lund, Sweden
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49
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Gervais L, Hewison AJM, Morellet N, Bernard M, Merlet J, Cargnelutti B, Chaval Y, Pujol B, Quéméré E. Pedigree-free quantitative genetic approach provides evidence for heritability of movement tactics in wild roe deer. J Evol Biol 2020; 33:595-607. [PMID: 31985133 DOI: 10.1111/jeb.13594] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 01/07/2020] [Accepted: 01/13/2020] [Indexed: 11/30/2022]
Abstract
Assessing the evolutionary potential of animal populations in the wild is crucial to understanding how they may respond to selection mediated by rapid environmental change (e.g. habitat loss and fragmentation). A growing number of studies have investigated the adaptive role of behaviour, but assessments of its genetic basis in a natural setting remain scarce. We combined intensive biologging technology with genome-wide data and a pedigree-free quantitative genetic approach to quantify repeatability, heritability and evolvability for a suite of behaviours related to the risk avoidance-resource acquisition trade-off in a wild roe deer (Capreolus capreolus) population inhabiting a heterogeneous, human-dominated landscape. These traits, linked to the stress response, movement and space-use behaviour, were all moderately to highly repeatable. Furthermore, the repeatable among-individual component of variation in these traits was partly due to additive genetic variance, with heritability estimates ranging from 0.21 ± 0.08 to 0.70 ± 0.11 and evolvability ranging from 1.1% to 4.3%. Changes in the trait mean can therefore occur under hypothetical directional selection over just a few generations. To the best of our knowledge, this is the first empirical demonstration of additive genetic variation in space-use behaviour in a free-ranging population based on genomic relatedness data. We conclude that wild animal populations may have the potential to adjust their spatial behaviour to human-driven environmental modifications through microevolutionary change.
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Affiliation(s)
- Laura Gervais
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France.,Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), CNRS, IRD, UPS, Université Fédérale de Toulouse Midi-Pyrénées, Toulouse, France
| | - Aidan J M Hewison
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Nicolas Morellet
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Maria Bernard
- INRAE, GABI, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,INRAE, SIGENAE, Jouy-en-Josas, France
| | - Joël Merlet
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Bruno Cargnelutti
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Yannick Chaval
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France
| | - Benoit Pujol
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), CNRS, IRD, UPS, Université Fédérale de Toulouse Midi-Pyrénées, Toulouse, France.,USR 3278 CRIOBE, PSL Université Paris: EPHE-UPVD-CNRS, Université de Perpignan, Perpignan Cedex, France
| | - Erwan Quéméré
- CEFS, INRAE, Université de Toulouse, Castanet-Tolosan, France.,LTSER ZA PYRénées GARonne, Auzeville-Tolosane, France.,ESE, Ecology and Ecosystems Health, Ouest, INRAE, Rennes, France
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50
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Salles OC, Almany GR, Berumen ML, Jones GP, Saenz‐Agudelo P, Srinivasan M, Thorrold SR, Pujol B, Planes S. Strong habitat and weak genetic effects shape the lifetime reproductive success in a wild clownfish population. Ecol Lett 2019; 23:265-273. [DOI: 10.1111/ele.13428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 10/11/2019] [Accepted: 10/24/2019] [Indexed: 12/19/2022]
Affiliation(s)
- Océane C. Salles
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan 52 Avenue Paul Alduy 66860 Perpignan Cedex France
- Laboratoire d’Excellence ‘CORAIL’ 58 avenue Paul Alduy F‐66360 Perpignan France
| | - Glenn R. Almany
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan 52 Avenue Paul Alduy 66860 Perpignan Cedex France
- Laboratoire d’Excellence ‘CORAIL’ 58 avenue Paul Alduy F‐66360 Perpignan France
| | - Michael L. Berumen
- Red Sea Research Center Division of Biological and Environmental Sciences and Engineering King Abdullah University of Science and Technology Thuwal 23955 Saudi Arabia
| | - Geoffrey P. Jones
- ARC Centre of Excellence for Coral Reef Studies, and College of Science and Engineering James Cook University Townsville Qld 4811 Australia
| | - Pablo Saenz‐Agudelo
- Instituto de Ciencias Ambientales y Evolutivas Universidad Austral de Chile 5090000 Valvidia Chile
| | - Maya Srinivasan
- ARC Centre of Excellence for Coral Reef Studies, and College of Science and Engineering James Cook University Townsville Qld 4811 Australia
| | - Simon R. Thorrold
- Biology Department Woods Hole Oceanographic Institution Woods Hole MA 02543 USA
| | - Benoit Pujol
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan 52 Avenue Paul Alduy 66860 Perpignan Cedex France
- Laboratoire d’Excellence ‘CORAIL’ 58 avenue Paul Alduy F‐66360 Perpignan France
| | - Serge Planes
- PSL Université Paris: EPHE‐UPVD‐CNRS USR 3278 CRIOBE Université de Perpignan 52 Avenue Paul Alduy 66860 Perpignan Cedex France
- Laboratoire d’Excellence ‘CORAIL’ 58 avenue Paul Alduy F‐66360 Perpignan France
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