1
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Ono J, Kuzmin A, Miller L, Otto SP. The limit to evolutionary rescue depends on ploidy in yeast exposed to nystatin. Can J Microbiol 2024; 70:394-404. [PMID: 38875715 DOI: 10.1139/cjm-2023-0235] [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: 06/16/2024]
Abstract
The number of copies of each chromosome, or ploidy, of an organism is a major genomic factor affecting adaptation. We set out to determine how ploidy can impact the outcome of evolution, as well as the likelihood of evolutionary rescue, using short-term experiments with yeast (Saccharomyces cerevisiae) in a high concentration of the fungicide nystatin. In similar experiments using haploid yeast, the genetic changes underlying evolutionary rescue were highly repeatable, with all rescued lines containing a single mutation in the ergosterol biosynthetic pathway. All of these beneficial mutations were recessive, which led to the expectation that diploids would find alternative genetic routes to adaptation. To test this, we repeated the experiment using both haploid and diploid strains and found that diploid populations did not evolve resistance. Although diploids are able to adapt at the same rate as haploids to a lower, not fully inhibitory, concentration of nystatin, the present study suggests that diploids are limited in their ability to adapt to an inhibitory concentration of nystatin, while haploids may undergo evolutionary rescue. These results demonstrate that ploidy can tip the balance between adaptation and extinction when organisms face an extreme environmental change.
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Affiliation(s)
- Jasmine Ono
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Centre for Ecology and Evolution & Environment and Sustainability Institute, University of Exeter, Penryn, Cornwall TR10 9FE, United Kingdom
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, United Kingdom
| | - Anastasia Kuzmin
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Lesley Miller
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Sarah P Otto
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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2
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Zaffaroni M, Rimbaud L, Rey J, Papaïx J, Fabre F. Effects of pathogen reproduction system on the evolutionary and epidemiological control provided by deployment strategies for two major resistance genes in agricultural landscapes. Evol Appl 2024; 17:e13627. [PMID: 38283600 PMCID: PMC10810173 DOI: 10.1111/eva.13627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 10/27/2023] [Accepted: 11/20/2023] [Indexed: 01/30/2024] Open
Abstract
Resistant cultivars are of value for protecting crops from disease, but can be rapidly overcome by pathogens. Several strategies have been proposed to delay pathogen adaptation (evolutionary control), while maintaining effective protection (epidemiological control). Resistance genes can be (i) combined in the same cultivar (pyramiding), (ii) deployed in different cultivars sown in the same field (mixtures) or in different fields (mosaics), or (iii) alternated over time (rotations). The outcomes of these strategies have been investigated principally in pathogens displaying pure clonal reproduction, but many pathogens have at least one sexual event in their annual life cycles. Sexual reproduction may promote the emergence of superpathogens adapted to all the resistance genes deployed. Here, we improved the spatially explicit stochastic model landsepi to include pathogen sexual reproduction, and we used the improved model to investigate the effect of sexual reproduction on evolutionary and epidemiological outcomes across deployment strategies for two major resistance genes. Sexual reproduction favours the establishment of a superpathogen when single mutant pathogens are present together at a sufficiently high frequency, as in mosaic and mixture strategies. However, sexual reproduction did not affect the strategy recommendations for a wide range of mutation probabilities, associated fitness costs, and landscape organisations.
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Affiliation(s)
- Marta Zaffaroni
- INRAE, Bordeaux Sciences Agro, SAVEVillenave d'OrnonFrance
- INRAE, BioSPAvignonFrance
| | | | | | | | - Frédéric Fabre
- INRAE, Bordeaux Sciences Agro, SAVEVillenave d'OrnonFrance
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3
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Ahmadi N, Barry MB, Frouin J, de Navascués M, Toure MA. Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes' Selective Footprints in the Genes Network Regulating Flowering Time. RICE (NEW YORK, N.Y.) 2023; 16:15. [PMID: 36947285 PMCID: PMC10033818 DOI: 10.1186/s12284-023-00633-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/11/2023] [Indexed: 06/18/2023]
Abstract
Analyses of the genetic bases of plant adaptation to climate changes, using genome-scan approaches, are often conducted on natural populations, under hypothesis of out-crossing reproductive regime. We report here on a study based on diachronic sampling (1980 and 2011) of the autogamous crop species, Oryza sativa and Oryza glaberrima, in the tropical forest and the Sudanian savannah of West Africa. First, using historical meteorological data we confirmed changes in temperatures (+ 1 °C on average) and rainfall regime (less predictable and reduced amount) in the target areas. Second, phenotyping the populations for phenology, we observed significantly earlier heading time in the 2010 samples. Third, implementing two genome-scan methods (one of which specially developed for selfing species) on genotyping by sequencing genotypic data of the two populations, we detected 31 independent selection footprints. Gene ontology analysis detected significant enrichment of these selection footprints in genes involved in reproductive processes. Some of them bore known heading time QTLs and genes, including OsGI, Hd1 and OsphyB. This rapid adaptive evolution, originated from subtle changes in the standing variation in genetic network regulating heading time, did not translate into predominance of multilocus genotypes, as it is often the case in selfing plants, and into notable selective sweeps. The high adaptive potential observed results from the multiline genetic structure of the rice landraces, and the rather large and imbricated genetic diversity of the rice meta-population at the farm, the village and the region levels, that hosted the adaptive variants in multiple genetic backgrounds before the advent of the environmental selective pressure. Our results illustrate the evolution of in situ diversity through processes of human and natural selection, and provide a model for rice breeding and cultivars deployment strategies aiming resilience to climate changes. It also calls for further development of population genetic models for adaptation of plant populations to environmental changes. To our best knowledge, this is the first study dealing with climate-changes' selective footprint in crops.
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Affiliation(s)
- Nourollah Ahmadi
- UMR AGAP, CIRAD, TA-A 108/03, Avenue Agropolis, 34398, Montpellier Cedex 5, France.
- AGAP, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France.
| | | | - Julien Frouin
- UMR AGAP, CIRAD, TA-A 108/03, Avenue Agropolis, 34398, Montpellier Cedex 5, France
- AGAP, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Miguel de Navascués
- CBGP, CIRAD, INRAE, IRD, Montpellier SupAgro, Univ Montpellier, Montpellier, France
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4
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Tanaka MM, Wahl LM. Surviving environmental change: when increasing population size can increase extinction risk. Proc Biol Sci 2022; 289:20220439. [PMID: 35642362 PMCID: PMC9156903 DOI: 10.1098/rspb.2022.0439] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Populations threatened by an abrupt environmental change-due to rapid climate change, pathogens or invasive competitors-may survive if they possess or generate genetic combinations adapted to the novel, challenging condition. If these genotypes are initially rare or non-existent, the emergence of lineages that allow a declining population to survive is known as 'evolutionary rescue'. By contrast, the genotypes required for survival could, by chance, be common before the environmental change. Here, considering both of these possibilities, we find that the risk of extinction can be lower in very small or very large populations, but peaks at intermediate population sizes. This pattern occurs when the survival genotype has a small deleterious effect before the environmental change. Since mildly deleterious mutations constitute a large fraction of empirically measured fitness effects, we suggest that this unexpected result-an intermediate size that puts a population at a greater risk of extinction-may not be unusual in the face of environmental change.
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Affiliation(s)
- Mark M. Tanaka
- University of New South Wales, Sydney, NSW 2052, Australia
| | - Lindi M. Wahl
- Western University, London, Ontario, Canada, N6A 5B7
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5
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Yamamichi M. How does genetic architecture affect eco-evolutionary dynamics? A theoretical perspective. Philos Trans R Soc Lond B Biol Sci 2022; 377:20200504. [PMID: 35634922 PMCID: PMC9149794 DOI: 10.1098/rstb.2020.0504] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Recent studies have revealed the importance of feedbacks between contemporary rapid evolution (i.e. evolution that occurs through changes in allele frequencies) and ecological dynamics. Despite its inherent interdisciplinary nature, however, studies on eco-evolutionary feedbacks have been mostly ecological and tended to focus on adaptation at the phenotypic level without considering the genetic architecture of evolutionary processes. In empirical studies, researchers have often compared ecological dynamics when the focal species under selection has a single genotype with dynamics when it has multiple genotypes. In theoretical studies, common approaches are models of quantitative traits where mean trait values change adaptively along the fitness gradient and Mendelian traits with two alleles at a single locus. On the other hand, it is well known that genetic architecture can affect short-term evolutionary dynamics in population genetics. Indeed, recent theoretical studies have demonstrated that genetic architecture (e.g. the number of loci, linkage disequilibrium and ploidy) matters in eco-evolutionary dynamics (e.g. evolutionary rescue where rapid evolution prevents extinction and population cycles driven by (co)evolution). I propose that theoretical approaches will promote the synthesis of functional genomics and eco-evolutionary dynamics through models that combine population genetics and ecology as well as nonlinear time-series analyses using emerging big data.
This article is part of the theme issue ‘Genetic basis of adaptation and speciation: from loci to causative mutations’.
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Affiliation(s)
- Masato Yamamichi
- School of Biological Sciences, The University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
- Department of International Health and Medical Anthropology, Institute of Tropical Medicine, Nagasaki University, Nagasaki 852-8523, Japan
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6
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Czuppon P, Blanquart F, Uecker H, Débarre F. The Effect of Habitat Choice on Evolutionary Rescue in Subdivided Populations. Am Nat 2021; 197:625-643. [PMID: 33989144 DOI: 10.1086/714034] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractEvolutionary rescue is the process by which a population, in response to an environmental change, successfully avoids extinction through adaptation. In spatially structured environments, dispersal can affect the probability of rescue. Here, we model an environment consisting of patches that degrade one after another, and we investigate the probability of rescue by a mutant adapted to the degraded habitat. We focus on the effects of dispersal and of immigration biases. We identify up to three regions delimiting the effect of dispersal on the probability of evolutionary rescue: (i) starting from low dispersal rates, the probability of rescue increases with dispersal; (ii) at intermediate dispersal rates, it decreases; and (iii) at large dispersal rates, it increases again with dispersal, except if mutants are too counterselected in not-yet-degraded patches. The probability of rescue is generally highest when mutant and wild-type individuals preferentially immigrate into patches that have already undergone environmental change. Additionally, we find that mutants that will eventually rescue the population most likely first appear in nondegraded patches. Overall, our results show that habitat choice, compared with the often-studied unbiased immigration scheme, can substantially alter the dynamics of population survival and adaptation to new environments.
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7
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Osmond MM, Coop G. Genetic Signatures of Evolutionary Rescue by a Selective Sweep. Genetics 2020; 215:813-829. [PMID: 32398227 PMCID: PMC7337082 DOI: 10.1534/genetics.120.303173] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 05/06/2020] [Indexed: 12/31/2022] Open
Abstract
One of the most useful models in population genetics is that of a selective sweep and the consequent hitch-hiking of linked neutral alleles. While variations on this model typically assume constant population size, many instances of strong selection and rapid adaptation in nature may co-occur with complex demography. Here, we extend the hitch-hiking model to evolutionary rescue, where adaptation and demography not only co-occur but are intimately entwined. Our results show how this feedback between demography and evolution determines-and restricts-the genetic signatures of evolutionary rescue, and how these differ from the signatures of sweeps in populations of constant size. In particular, we find rescue to harden sweeps from standing variance or new mutation (but not from migration), reduce genetic diversity both at the selected site and genome-wide, and increase the range of observed Tajima's D values. For a given initial rate of population decline, the feedback between demography and evolution makes all of these differences more dramatic under weaker selection, where bottlenecks are prolonged. Nevertheless, it is likely difficult to infer the co-incident timing of the sweep and bottleneck from these simple signatures, never mind a feedback between them. Temporal samples spanning contemporary rescue events may offer one way forward.
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Affiliation(s)
- Matthew M Osmond
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California 95616
| | - Graham Coop
- Center for Population Biology and Department of Evolution and Ecology, University of California, Davis, California 95616
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8
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Tomasini M, Peischl S. When does gene flow facilitate evolutionary rescue? Evolution 2020; 74:1640-1653. [DOI: 10.1111/evo.14038] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/03/2020] [Accepted: 06/06/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Matteo Tomasini
- Interfaculty Bioinformatics UnitUniversity of Bern Bern 3012 Switzerland
- Computational and Molecular Population Genetics Laboratory, Institute of Ecology and EvolutionUniversity of Bern Bern 3012 Switzerland
- Swiss Institute for Bioinformatics Lausanne 1015 Switzerland
- Current Address: Department of Integrative BiologyMichigan State University East Lansing Michigan 48824
| | - Stephan Peischl
- Interfaculty Bioinformatics UnitUniversity of Bern Bern 3012 Switzerland
- Swiss Institute for Bioinformatics Lausanne 1015 Switzerland
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9
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Vinton AC, Vasseur DA. Evolutionary tracking is determined by differential selection on demographic rates and density dependence. Ecol Evol 2020; 10:5725-5736. [PMID: 32607186 PMCID: PMC7319176 DOI: 10.1002/ece3.6311] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 03/27/2020] [Accepted: 04/01/2020] [Indexed: 11/11/2022] Open
Abstract
Recent ecological forecasts predict that ~25% of species worldwide will go extinct by 2050. However, these estimates are primarily based on environmental changes alone and fail to incorporate important biological mechanisms such as genetic adaptation via evolution. Thus, environmental change can affect population dynamics in ways that classical frameworks can neither describe nor predict. Furthermore, often due to a lack of data, forecasting models commonly describe changes in population demography by summarizing changes in fecundity and survival concurrently with the intrinsic growth rate (r). This has been shown to be an oversimplification as the environment may impose selective pressure on specific demographic rates (birth and death) rather than directly on r (the difference between the birth and death rates). This differential pressure may alter population response to density, in each demographic rate, further diluting the information combined to produce r. Thus, when we consider the potential for persistence via adaptive evolution, populations with the same r can have different abilities to persist amidst environmental change. Therefore, we cannot adequately forecast population response to climate change without accounting for demography and selection on density dependence. Using a continuous-time Markov chain model to describe the stochastic dynamics of the logistic model of population growth and allow for trait evolution via mutations arising during birth events, we find persistence via evolutionary tracking more likely when environmental change alters birth rather than the death rate. Furthermore, species that evolve responses to changes in the strength of density dependence due to environmental change are less vulnerable to extinction than species that undergo selection independent of population density. By incorporating these key demographic considerations into our predictive models, we can better understand how species will respond to climate change.
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Affiliation(s)
| | - David Alan Vasseur
- Department of Ecology and Evolutionary BiologyYale UniversityNew HavenConnecticut
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10
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Evolutionary Rescue and Drug Resistance on Multicopy Plasmids. Genetics 2020; 215:847-868. [PMID: 32461266 DOI: 10.1534/genetics.119.303012] [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: 12/23/2019] [Accepted: 05/15/2020] [Indexed: 11/18/2022] Open
Abstract
Bacteria often carry "extra DNA" in the form of plasmids in addition to their chromosome. Many plasmids have a copy number greater than one such that the genes encoded on these plasmids are present in multiple copies per cell. This has evolutionary consequences by increasing the mutational target size, by prompting the (transitory) co-occurrence of mutant and wild-type alleles within the same cell, and by allowing for gene dosage effects. We develop and analyze a mathematical model for bacterial adaptation to harsh environmental change if adaptation is driven by beneficial alleles on multicopy plasmids. Successful adaptation depends on the availability of advantageous alleles and on their establishment probability. The establishment process involves the segregation of mutant and wild-type plasmids to the two daughter cells, allowing for the emergence of mutant homozygous cells over the course of several generations. To model this process, we use the theory of multitype branching processes, where a type is defined by the genetic composition of the cell. Both factors-the availability of advantageous alleles and their establishment probability-depend on the plasmid copy number, and they often do so antagonistically. We find that in the interplay of various effects, a lower or higher copy number may maximize the probability of evolutionary rescue. The decisive factor is the dominance relationship between mutant and wild-type plasmids and potential gene dosage effects. Results from a simple model of antibiotic degradation indicate that the optimal plasmid copy number may depend on the specific environment encountered by the population.
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11
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Dubé CE, Boissin E, Mercière A, Planes S. Parentage analyses identify local dispersal events and sibling aggregations in a natural population of Millepora hydrocorals, a free-spawning marine invertebrate. Mol Ecol 2020; 29:1508-1522. [PMID: 32227655 DOI: 10.1111/mec.15418] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 03/13/2020] [Accepted: 03/19/2020] [Indexed: 01/03/2023]
Abstract
Dispersal is a critical process for the persistence and productivity of marine populations. For many reef species, there is increasing evidence that local demography and self-recruitment have major consequences on their genetic diversity and adaptation to environmental change. Yet empirical data of dispersal patterns in reef-building species remain scarce. Here, we document the first genetic estimates of self-recruitment and dispersal distances in a free-spawning marine invertebrate, the hydrocoral Millepora cf. platyphylla. Using twelve microsatellite markers, we gathered genotypic information from 3,160 georeferenced colonies collected over 27,000 m2 of a single reef in three adjacent habitats in Moorea, French Polynesia; the mid slope, upper slope, and back reef. Although the adult population was predominantly clonal (85% were clones), our parentage analysis revealed a moderate self-recruitment rate with a minimum of 8% of sexual propagules produced locally. Assigned offspring often settled at <10 m from their parents and dispersal events decrease with increasing geographic distance. There were no discrepancies between the dispersal distances of offspring assigned to parents belonging to clonal versus nonclonal genotypes. Interhabitat dispersal events via cross-reef transport were also detected for sexual and asexual propagules. Sibship analysis showed that full siblings recruit nearby on the reef (more than 40% settled at <30 m), resulting in sibling aggregations. Our findings highlight the importance of self-recruitment together with clonality in stabilizing population dynamics, which may ultimately enhance local sustainability and resilience to disturbance.
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Affiliation(s)
- Caroline E Dubé
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.,Laboratoire d'Excellence "CORAIL", Papetoai, Moorea, French Polynesia
| | - Emilie Boissin
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.,Laboratoire d'Excellence "CORAIL", Papetoai, Moorea, French Polynesia
| | - Alexandre Mercière
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.,Laboratoire d'Excellence "CORAIL", Papetoai, Moorea, French Polynesia
| | - Serge Planes
- PSL Research University: EPHE-UPVD-CNRS, USR 3278 CRIOBE, Université de Perpignan, Perpignan Cedex, France.,Laboratoire d'Excellence "CORAIL", Papetoai, Moorea, French Polynesia
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12
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Hartfield M, Bataillon T. Selective Sweeps Under Dominance and Inbreeding. G3 (BETHESDA, MD.) 2020; 10:1063-1075. [PMID: 31974096 PMCID: PMC7056974 DOI: 10.1534/g3.119.400919] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 01/18/2020] [Indexed: 12/26/2022]
Abstract
A major research goal in evolutionary genetics is to uncover loci experiencing positive selection. One approach involves finding 'selective sweeps' patterns, which can either be 'hard sweeps' formed by de novo mutation, or 'soft sweeps' arising from recurrent mutation or existing standing variation. Existing theory generally assumes outcrossing populations, and it is unclear how dominance affects soft sweeps. We consider how arbitrary dominance and inbreeding via self-fertilization affect hard and soft sweep signatures. With increased self-fertilization, they are maintained over longer map distances due to reduced effective recombination and faster beneficial allele fixation times. Dominance can affect sweep patterns in outcrossers if the derived variant originates from either a single novel allele, or from recurrent mutation. These models highlight the challenges in distinguishing hard and soft sweeps, and propose methods to differentiate between scenarios.
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Affiliation(s)
- Matthew Hartfield
- Department of Ecology and Evolutionary Biology, University of Toronto, Ontario M5S 3B2, Canada,
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, and
- Institute of Evolutionary Biology, The University of Edinburgh, Edinburgh EH9 3FL, United Kingdom
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, Aarhus 8000, Denmark, and
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13
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Unckless RL, Orr HA. The Population Genetics of Evolutionary Rescue in Diploids: X Chromosomal versus Autosomal Rescue. Am Nat 2020; 195:561-568. [PMID: 32097044 DOI: 10.1086/707139] [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] [Indexed: 11/03/2022]
Abstract
Most population genetic theory assumes that populations adapt to an environmental change without a change in population size. However, environmental changes might be so severe that populations decline in size and, without adaptation, become extinct. This "evolutionary rescue" scenario differs from traditional models of adaptation in that rescue involves a race between adaptation and extinction. While most previous work has usually focused on models of evolutionary rescue in haploids, here we consider diploids. In many species, diploidy introduces a novel feature into adaptation: adaptive evolution might occur either on sex chromosomes or on autosomes. Previous studies of nonrescue adaptation revealed that the relative rates of adaptation on the X chromosome versus autosomes depend on the dominance of beneficial mutations, reflecting differences in effective population size and the efficacy of selection. Here, we extend these results to evolutionary rescue and find that, given equal-sized chromosomes, there is greater parameter space in which the X is more likely to contribute to adaptation than the autosomes relative to standard nonrescue models. We also discuss how subtle effects of dominance can increase the chance of evolutionary rescue in diploids when absolute heterozygote fitness is close to 1. These effects do not arise in standard nonrescue models.
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14
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Sachdeva H. Effect of partial selfing and polygenic selection on establishment in a new habitat. Evolution 2019; 73:1729-1745. [PMID: 31339550 PMCID: PMC6771878 DOI: 10.1111/evo.13812] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 07/11/2019] [Indexed: 01/30/2023]
Abstract
This article analyzes how partial selfing in a large source population influences its ability to colonize a new habitat via the introduction of a few founder individuals. Founders experience inbreeding depression due to partially recessive deleterious alleles as well as maladaptation to the new environment due to selection on a large number of additive loci. I first introduce a simplified version of the inbreeding history model to characterize mutation‐selection balance in a large, partially selfing source population under selection involving multiple nonidentical loci. I then use individual‐based simulations to study the eco‐evolutionary dynamics of founders establishing in the new habitat under a model of hard selection. The study explores how selfing rate shapes establishment probabilities of founders via effects on both inbreeding depression and adaptability to the new environment, and also distinguishes the effects of selfing on the initial fitness of founders from its effects on the long‐term adaptive response of the populations they found. A high rate of (but not complete) selfing is found to aid establishment over a wide range of parameters, even in the absence of mate limitation. The sensitivity of the results to assumptions about the nature of polygenic selection is discussed.
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Affiliation(s)
- Himani Sachdeva
- Institute of Science and Technology Austria (IST Austria), Klosterneuburg, 3400, Austria
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15
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Anciaux Y, Lambert A, Ronce O, Roques L, Martin G. Population persistence under high mutation rate: From evolutionary rescue to lethal mutagenesis. Evolution 2019; 73:1517-1532. [DOI: 10.1111/evo.13771] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 04/24/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Yoann Anciaux
- Bioinformatics Research Center (BiRC)Aarhus University C.F. Møllers Allé 8 8000 Aarhus Denmark
| | - Amaury Lambert
- Center for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS UMR 7241, INSERM U1050PSL Research University Paris France
- Laboratoire de Probabilités, Statistique et Modélisation (LPSM)Sorbonne Université CNRS UMR 8001 Paris France
| | - Ophélie Ronce
- Institut des Sciences de l'Evolution de MontpellierUniversité de Montpellier, CNRS, IRD, EPHE Montpellier France
| | | | - Guillaume Martin
- Institut des Sciences de l'Evolution de MontpellierUniversité de Montpellier, CNRS, IRD, EPHE Montpellier France
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16
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Abstract
A major current molecular evolution challenge is to link comparative genomic patterns to species' biology and ecology. Breeding systems are pivotal because they affect many population genetic processes and thus genome evolution. We review theoretical predictions and empirical evidence about molecular evolutionary processes under three distinct breeding systems-outcrossing, selfing, and asexuality. Breeding systems may have a profound impact on genome evolution, including molecular evolutionary rates, base composition, genomic conflict, and possibly genome size. We present and discuss the similarities and differences between the effects of selfing and clonality. In reverse, comparative and population genomic data and approaches help revisiting old questions on the long-term evolution of breeding systems.
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Affiliation(s)
- Sylvain Glémin
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Clémentine M François
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France
| | - Nicolas Galtier
- Institut des Sciences de l'Evolution, UMR5554, Université Montpellier II, Montpellier, France.
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17
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Govaert L, Fronhofer EA, Lion S, Eizaguirre C, Bonte D, Egas M, Hendry AP, De Brito Martins A, Melián CJ, Raeymaekers JAM, Ratikainen II, Saether B, Schweitzer JA, Matthews B. Eco‐evolutionary feedbacks—Theoretical models and perspectives. Funct Ecol 2018. [DOI: 10.1111/1365-2435.13241] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Lynn Govaert
- Laboratory of Aquatic Ecology, Evolution and Conservation KU Leuven Leuven Belgium
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
- Department of Evolutionary Biology and Environmental Studies University of Zurich Zürich Switzerland
| | | | - Sébastien Lion
- Centre d'Ecologie Fonctionnelle et Evolutive CNRS, IRD, EPHE Université de Montpellier Montpellier France
| | | | - Dries Bonte
- Department of Biology Ghent University Ghent Belgium
| | - Martijn Egas
- Institute for Biodiversity and Ecosystem Dynamics University of Amsterdam Amsterdam The Netherlands
| | - Andrew P. Hendry
- Redpath Museum and Department of Biology McGill University Montreal Quebec Canada
| | - Ayana De Brito Martins
- Fish Ecology and Evolution DepartmentCenter for Ecology, Evolution and BiogeochemistryEawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
| | - Carlos J. Melián
- Fish Ecology and Evolution DepartmentCenter for Ecology, Evolution and BiogeochemistryEawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
| | | | - Irja I. Ratikainen
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
- Institute of Biodiversity, Animal Health and Comparative Medicine University of Glasgow Glasgow UK
| | - Bernt‐Erik Saether
- Department of Biology Centre for Biodiversity Dynamics Norwegian University of Science and Technology Trondheim Norway
| | - Jennifer A. Schweitzer
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee
| | - Blake Matthews
- Department of Aquatic Ecology Eawag: Swiss Federal Institute of Aquatic Science and Technology Dübendorf Switzerland
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Underwood JN, Richards ZT, Miller KJ, Puotinen ML, Gilmour JP. Genetic signatures through space, time and multiple disturbances in a ubiquitous brooding coral. Mol Ecol 2018; 27:1586-1602. [DOI: 10.1111/mec.14559] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 02/22/2018] [Accepted: 02/24/2018] [Indexed: 12/17/2022]
Affiliation(s)
- Jim N. Underwood
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Zoe T. Richards
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences Curtin University Bentley WA Australia
- Department of Aquatic Zoology Western Australian Museum Perth WA Australia
| | - Karen J. Miller
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - Marji L. Puotinen
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
| | - James P. Gilmour
- Indian Oceans Marine Research Centre Australian Institute of Marine Science Crawley WA Australia
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19
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Hartfield M, Bataillon T, Glémin S. The Evolutionary Interplay between Adaptation and Self-Fertilization. Trends Genet 2017; 33:420-431. [PMID: 28495267 PMCID: PMC5450926 DOI: 10.1016/j.tig.2017.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 03/31/2017] [Accepted: 04/03/2017] [Indexed: 11/29/2022]
Abstract
Genome-wide surveys of nucleotide polymorphisms, obtained from next-generation sequencing, have uncovered numerous examples of adaptation in self-fertilizing organisms, especially regarding changes to climate, geography, and reproductive systems. Yet existing models for inferring attributes of adaptive mutations often assume idealized outcrossing populations, which risks mischaracterizing properties of these variants. Recent theoretical work is emphasizing how various aspects of self-fertilization affects adaptation, yet empirical data on these properties are lacking. We review theoretical and empirical studies demonstrating how self-fertilization alters the process of adaptation, illustrated using examples from current sequencing projects. We propose ideas for how future research can more accurately quantify aspects of adaptation in self-fertilizers, including incorporating the effects of standing variation, demographic history, and polygenic adaptation. Analysis of large-scale next-generation sequencing datasets are finding more examples of adaptive evolution at the genomic level. Advances in theoretical work has demonstrated how self-fertilisation affects different aspects of adaptation in these organisms, compared to outcrossers. Current software and statistical methods do not take different mating systems into account, which risks mischaracterising the presence or strength of adaptive mutations from genome scans. Development of new mathematical and statistical methods that explicitly consider self-fertilization and associated demographic effects will enable researchers to more accurately quantify adaptation in these organisms.
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Affiliation(s)
- Matthew Hartfield
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto ON, Canada M5S 3B2; Bioinformatics Research Centre, Aarhus University, 8000C, Aarhus, Denmark.
| | - Thomas Bataillon
- Bioinformatics Research Centre, Aarhus University, 8000C, Aarhus, Denmark
| | - Sylvain Glémin
- Institut des Sciences de l'Evolution (ISEM - UMR 5554 Universite de Montpellier-CNRS-IRD-EPHE), Place Eugene Bataillon, 34075 Montpellier, France; Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
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