The Evolutionary Interplay between Adaptation and Self-Fertilization
Authors: Matthew Hartfield, Thomas Bataillon, Sylvain Glémin
Journal: Trends in Genetics (2017)

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. 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. 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. Adaptive mutations are the fuel of evolution. Appearance of novel genotypes with reproductive advantages allows populations to persist in the face of continual and threatening changes. The ubiquity of cheap genome sequencing makes it possible to uncover a greater number of adaptive mutations than before. In addition, many researchers are enacting large-scale sequencing projects of organisms capable of self-fertilization (see Glossary), especially plants. For example, in the Ensembl database, 17 of 36 angiosperm species and four of 11 nematodes are listed as preferentially selfing. As these organisms are spread across large geographic ranges, genomic studies of self-fertilizing organisms are proving fruitful in determining the evolutionary history of species following ancient climatic events (such as the last glacial maximum), and how they respond to local geographic and climatic changes [1Savolainen O. et al.Ecological genomics of local adaptation.Nat. Rev. Genet. 2013; 14: 807-820Crossref PubMed Scopus (735) Google Scholar, 2Tiffin P. Ross-Ibarra J. Advances and limits of using population genetics to understand local adaptation.Trends Ecol. Evol. 2014; 29: 673-680Abstract Full Text Full Text PDF PubMed Scopus (204) Google Scholar]. The majority of crop plants also self-fertilize to some degree [3Zohary D. et al.Domestication of Plants in the Old World: The Origin and Spread of Domesticated Plants in South-West Asia, Europe, and the Mediterranean Basin. Oxford University Press, 2012Crossref Scopus (935) Google Scholar]; finding adaptive variants in them plays a key role in agricultural genomic studies. Many theoretical predictions regarding the genetic basis of adaptation, and the majority of statistical methods used to detect loci that have been subject to selection, were developed for populations assumed to be completely outcrossing. Yet self-fertilization strongly affects the setting on which adaptation takes place. Under selfing, two gametes are inherited from the same parent, increasing homozygosity and reducing haploid gene flow (e.g., pollen gene flow in plants). Increased homozygosity also weakens the mixing effects of recombination because it takes place between highly similar chromosomes [4Nordborg M. Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization.Genetics. 2000; 154: 923-929Crossref PubMed Google Scholar]. Selfing also increases genetic drift as it reduces the number of independent alleles sampled at reproduction [5Nordborg M. Donnelly P. The coalescent process with selfing.Genetics. 1997; 146: 1185-1195PubMed Google Scholar]. Dominance values of mutations contributing to adaptation will also depend on the mating system [6Charlesworth B. Evolutionary rates in partially self-fertilizing species.Am. Nat. 1992; 140: 126-148Crossref PubMed Scopus (177) Google Scholar], yet most selection inference methods implicitly assume additive selection. In some cases, predictions on the dynamics of adaptation under selfing can be obtained by rescaling relevant population genetics parameters to incorporate these effects (see mathematical details in Box 1). Yet under more complex scenarios (such as polygenic adaptation), selfing also qualitatively changes adaptation dynamics compared to outcrossing.Box 1How Self-Fertilization Affects Genetic EvolutionReduction in Effective Population Size, NeThe selective strength acting on mutations is proportional to Ne × s, where Ne is the effective population size and s the selective advantage of a beneficial variant [66Ewens W.J. Mathematical Population Genetics: 1. Theoretical Introduction. Springer, 2004Crossref Google Scholar]. Ne in self-fertilizing organisms is generally scaled by a factor α/(1 + F). Here F = σ/(2 −σ) is the inbreeding rate, given self-fertilization occurs with probability σ [5Nordborg M. Donnelly P. The coalescent process with selfing.Genetics. 1997; 146: 1185-1195PubMed Google Scholar], and α accounts for the effect of background selection. Hence Ne is reduced by at least a half with complete self-fertilization [67Nordborg M. Structured coalescent processes on different time scales.Genetics. 1997; 146: 1501-1514PubMed Google Scholar], weakening selection overall. A lower Ne can also inhibit adaptation from standing variation through limiting neutral diversity from which beneficial variants could arise from [34Glémin S. Ronfort J. Adaptation and maladaptation in selfing and outcrossing species: new mutations versus standing variation.Evolution. 2013; 67: 225-240Crossref PubMed Scopus (92) Google Scholar].Reduced RecombinationSelf-fertilization also lessens the impact of recombination in generating novel haplotypes, if identical haplotypes were inherited from the same parent. For tightly linked loci, the recombination rate is reduced by a factor (1 −F) [4Nordborg M. Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization.Genetics. 2000; 154: 923-929Crossref PubMed Google Scholar]. The exact rescaling becomes more complex over long map distances with high self-fertilization [68Roze D. Effects of interference between selected loci on the mutation load, inbreeding depression, and heterosis.Genetics. 2015; 201: 745-757Crossref PubMed Scopus (29) Google Scholar].Altered Emergence ProbabilitiesIf the beneficial variant is initially present as a single copy, it is most likely to go extinct by genetic drift [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]. If the selective advantage of homozygote mutations is 1 + s for s≪ 1, and heterozygote mutations have advantage 1 + hs (h being the dominance coefficient), the emergence probability for a mutation to escape early extinction by drift equals [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]:2s(h+F−hF)1+F(I) With complete outcrossing (F = 0), the emergence probability equals 2hs and thus increases with higher dominance, h. In contrast, with complete self-fertilization (F = 1) the fixation probability equals s; dominance does not affect emergence. Recessive mutations (h < 0.5) are thus more likely to fix with higher rates of self-fertilization, while dominant mutations (h > 0.5) are less likely to fix.Different Adaptation TrajectoriesFor weak selection coefficients, the rate of change in variant frequency p over time can be given by [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]:dpdt=s p(1−p)[F+h−Fh+(1−F)(1−2h)p](II) Hence the level of self-fertilization affects the fixation time [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]. The level of dominance and self-fertilization also interact to affect the genetic history of the adaptive variant, which can influence how its properties are inferred (see Figure 1 in main text). Reduction in Effective Population Size, Ne The selective strength acting on mutations is proportional to Ne × s, where Ne is the effective population size and s the selective advantage of a beneficial variant [66Ewens W.J. Mathematical Population Genetics: 1. Theoretical Introduction. Springer, 2004Crossref Google Scholar]. Ne in self-fertilizing organisms is generally scaled by a factor α/(1 + F). Here F = σ/(2 −σ) is the inbreeding rate, given self-fertilization occurs with probability σ [5Nordborg M. Donnelly P. The coalescent process with selfing.Genetics. 1997; 146: 1185-1195PubMed Google Scholar], and α accounts for the effect of background selection. Hence Ne is reduced by at least a half with complete self-fertilization [67Nordborg M. Structured coalescent processes on different time scales.Genetics. 1997; 146: 1501-1514PubMed Google Scholar], weakening selection overall. A lower Ne can also inhibit adaptation from standing variation through limiting neutral diversity from which beneficial variants could arise from [34Glémin S. Ronfort J. Adaptation and maladaptation in selfing and outcrossing species: new mutations versus standing variation.Evolution. 2013; 67: 225-240Crossref PubMed Scopus (92) Google Scholar]. Reduced Recombination Self-fertilization also lessens the impact of recombination in generating novel haplotypes, if identical haplotypes were inherited from the same parent. For tightly linked loci, the recombination rate is reduced by a factor (1 −F) [4Nordborg M. Linkage disequilibrium, gene trees and selfing: an ancestral recombination graph with partial self-fertilization.Genetics. 2000; 154: 923-929Crossref PubMed Google Scholar]. The exact rescaling becomes more complex over long map distances with high self-fertilization [68Roze D. Effects of interference between selected loci on the mutation load, inbreeding depression, and heterosis.Genetics. 2015; 201: 745-757Crossref PubMed Scopus (29) Google Scholar]. Altered Emergence Probabilities If the beneficial variant is initially present as a single copy, it is most likely to go extinct by genetic drift [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]. If the selective advantage of homozygote mutations is 1 + s for s≪ 1, and heterozygote mutations have advantage 1 + hs (h being the dominance coefficient), the emergence probability for a mutation to escape early extinction by drift equals [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]:2s(h+F−hF)1+F(I) With complete outcrossing (F = 0), the emergence probability equals 2hs and thus increases with higher dominance, h. In contrast, with complete self-fertilization (F = 1) the fixation probability equals s; dominance does not affect emergence. Recessive mutations (h < 0.5) are thus more likely to fix with higher rates of self-fertilization, while dominant mutations (h > 0.5) are less likely to fix. Different Adaptation Trajectories For weak selection coefficients, the rate of change in variant frequency p over time can be given by [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]:dpdt=s p(1−p)[F+h−Fh+(1−F)(1−2h)p](II) Hence the level of self-fertilization affects the fixation time [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]. The level of dominance and self-fertilization also interact to affect the genetic history of the adaptive variant, which can influence how its properties are inferred (see Figure 1 in main text). Looking beyond genetic consequences, selfing species often exhibit specific biological and ecological traits that affect a species' demography. In particular, 'Baker's Law' states that organisms capable of self-fertilization (or any other uniparental reproduction) are more likely to establish new populations following long-distance dispersal than outcrossing relatives [7Baker H.G. Support for Baker's law – as a rule.Evolution. 1967; 21: 853-856Crossref PubMed Google Scholar, 8Pannell J.R. The scope of Baker's law.New Phytol. 2015; 208: 656-667Crossref PubMed Scopus (124) Google Scholar]. Selfing is thus often associated with weedy habitats [9Clements D.R. et al.Adaptability of plants invading North American cropland.Agric. Ecosyst. Environ. 2004; 104: 379-398Crossref Scopus (92) Google Scholar], invasiveness [10van Kleunen M. et al.Phylogenetically independent associations between autonomous self-fertilization and plant invasiveness.Am. Nat. 2008; 171: 195-201Crossref PubMed Scopus (111) Google Scholar], and range expansions [11Grossenbacher D. Geographic range size is predicted by plant mating system.Ecol. 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Here we review and discuss empirical population genomics studies of adaptation in self-fertilizing species, in the light of classical and recent theory predicting how self-fertilization affects the genetic basis, rates, and genomic signatures of adaptation. This synthesis highlights the specificities of selfing species in studying adaptation, and how future research can best utilise emerging sequence data to accurately quantify adaptation in organisms undergoing self-fertilization. In outcrossing organisms, beneficial variants are more likely to emerge in a population from low frequency if dominant (h> ½). This is the original formulation of 'Haldane's Sieve' [18Haldane J.B.S. A mathematical theory of natural and artificial selection, Part V: selection and mutation.Math. Proc. Camb. Philos. Soc. 1927; 23: 838-844Crossref Scopus (609) Google Scholar]. Higher rates of self-fertilization are more likely to create homozygote copies of beneficial alleles, meaning recessive types have a higher fixation probability compared to outcrossers [19Glémin S. Extinction and fixation times with dominance and inbreeding.Theor. Popul. Biol. 2012; 81: 310-316Crossref PubMed Scopus (17) Google Scholar]. However, this prediction only holds at a single locus when genetic drift is solely affected by selfing (Box 1). Additional drift, due to demographic history or background selection (see below), should reduce the dominance threshold for which selfing favours the fixation of beneficial alleles. Selection interference can further reduce the efficacy of selection in low-recombining genetic regions [20Charlesworth B. Genetic recombination and molecular evolution.Cold Spring Harb. Symp. Quant. Biol. 2009; 74: 177-186Crossref PubMed Scopus (77) Google Scholar, 21Betancourt A.J. Hartfield M. Recombination and molecular evolution.Encyclopedia of Evolutionary Biology. Academic Press, 2016: 411-416Crossref Scopus (1) Google Scholar] and is expected to be pervasive in self-fertilizing organisms that exhibit reduced effective recombination rates (Box 1). High rates of self-fertilization makes it likelier that linked deleterious alleles hitch-hike to fixation with selective sweeps, compared to outcrossing populations [22Hartfield M. Glémin S. Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species.Genetics. 2014; 196: 281-293Crossref PubMed Scopus (24) Google Scholar]. This phenomenon is a consequence of a reduction in both the net recombination rate, and a weakened overall efficacy of selection due to a reduced effective population size. For similar reasons, an adaptive allele will also be less likely to fix if a first sweeping allele is already present, if self-fertilization is more frequent [23Hartfield M. Glémin S. Limits to adaptation in partially selfing species.Genetics. 2016; 203: 959-974Crossref PubMed Scopus (25) Google Scholar]. Multilocus models similarly show that high selfing rates amplifies background selection, reducing the effective population size by one or possibly several orders of magnitude, adversely affecting the fixation probability of beneficial mutations [24Kamran-Disfani A. Agrawal A.F. Selfing, adaptation and background selection in finite populations.J. Evol. Biol. 2014; 27: 1360-1371Crossref PubMed Scopus (54) Google Scholar]. Except for strongly beneficial recessive mutations, self-fertilization should reduce the overall efficacy of selection acting on individual mutations. However, while there have been many comparative studies between outcrossing and self-fertilizing sister species focusing on background selection [25Glémin S. Galtier N. Genome evolution in outcrossing versus selfing versus asexual species.Methods Mol. 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Furthermore, demography associated with the species split, such as bottlenecks, could remove diversity that would otherwise be under selection [26Hough J. Patterns of selection in plant genomes.Annu. Rev. Ecol. Evol. Syst. 2013; 44: 31-49Crossref Scopus (37) Google Scholar, 29Wright S.I. Gaut B.S. Molecular population genetics and the search for adaptive evolution in plants.Mol. Biol. Evol. 2005; 22: 506-519Crossref PubMed Scopus (264) Google Scholar]. Another problem is that the stronger effects of linked selection in selfers, caused by reduced recombination, should be accounted for as they are expected to substantially bias estimates of adaptation rates. Despite these challenges, comparisons were obtained between the outcrossing snail Physa acuta, which displayed evidence of adaptive substitution (as measured using the McDonald–Kreitman test) and the self-fertilizer Galba truncatula, which showed no evidence for adaptation [30Burgarella C. Molecular evolution of freshwater snails with contrasting mating systems.Mol. Biol. Evol. 2015; 32: 2403-2416Crossref PubMed Scopus (32) Google Scholar]. Selection interference models also predict different outcomes than those expected by 'Haldane's Sieve' [22Hartfield M. Glémin S. Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species.Genetics. 2014; 196: 281-293Crossref PubMed Scopus (24) Google Scholar, 23Hartfield M. Glémin S. Limits to adaptation in partially selfing species.Genetics. 2016; 203: 959-974Crossref PubMed Scopus (25) Google Scholar]. In particular, if adaptive mutations are recessive (h< 0.5) then intermediate self-fertilization rates, as opposed to complete selfing, leads to the highest emergence probabilities of novel beneficial alleles. Here, partial selfing combines the best of both worlds: some degree of outcrossing and recombination reduces selection interference, while selfing reveals recessive beneficial mutations when rare. To our knowledge, these predictions have not yet been tested. Model species exhibiting varying degrees of selfing, such as Mimulus [31Wu C.A. Mimulus is an emerging model system for the integration of ecological and genomic studies.Heredity. 2007; 100: 220-230Crossref PubMed Scopus (203) Google Scholar] and Arabis alpina [32Tedder A. et al.Sporophytic self-incompatibility genes and mating system variation in Arabis alpina.Ann. Bot. 2011; 108: 699-713Crossref PubMed Scopus (38) Google Scholar], would be ideal candidates to test these theories. It has become apparent in recent years that many adaptations arise from pre-existing neutral (or deleterious) variation, or from recurrent mutation, so adaptive variants are initially found on multiple genetic backgrounds [33Messer P.W. Petrov D.A. Population genomics of rapid adaptation by soft selective sweeps.Trends Ecol. Evol. 2013; 28: 659-669Abstract Full Text Full Text PDF PubMed Scopus (297) Google Scholar]. Adaptation from standing variation can be less likely with selfing, since both neutral diversity and population-wide mutations rates are reduced as a consequence of a lower effective population size [34Glémin S. Ronfort J. Adaptation and maladaptation in selfing and outcrossing species: new mutations versus standing variation.Evolution. 2013; 67: 225-240Crossref PubMed Scopus (92) Google Scholar]. In addition, Haldane's sieve applies less strongly when adaptation proceeds from pre-existing variation, because both homozygote and heterozygote genotypes can segregate in the population when the beneficial allele is already present in several copies [35Orr H.A. Betancourt A.J. Haldane's sieve and adaptation from the standing genetic variation.Genetics. 2001; 157: 875-884PubMed Google Scholar, 36Hermisson J. Pennings P.S. Soft sweeps: molecular population genetics of adaptation from standing genetic variation.Genetics. 2005; 169: 2335-2352Crossref PubMed Scopus (662) Google Scholar]. As a consequence, even recessive mutations are more likely to fix in outcrossers than in selfers [27Hartfield M. Evolutionary genetic consequences of facultative sex and outcrossing.J. Evol. Biol. 2016; 29: 5-22Crossref PubMed Scopus (48) Google Scholar]. Reduction in genetic diversity can also prevent self-fertilizing organisms from adapting quickly in an unfavourable environment. Yet if the mutations needed for evolutionary rescue are present before the harmful environment arose, these rescuing mutations can be more readily selected under selfing by quickly creating fitter homozygote genotypes [37Uecker H. Evolutionary rescue in randomly mating, selfing, and clonal populations.Evolution. 2017; 71: 845-858Crossref PubMed Scopus (16) Google Scholar]. Numerous statistical tests exist for inferring adaptation from genomic data. Table 1 outlines some key methods used, along with how their outcomes can be altered under self-fertilization. One popular method for detecting recent adaptation involves tracking footprints of selective sweeps, where the spread of a beneficial variant reduces sequence diversity at neutral markers linked to the selected site. Box 2 outlines the basic theory used to predict patterns of diversity around a selective sweep. Selective sweeps can be easier to detect in selfers than outcrossers for two reasons. First, self-fertilization reduces fixation times of beneficial alleles, as homozygote mutations arise earlier, exposing the mutant to selection [6Charlesworth B. Evolutionary rates in partially self-fertilizing species.Am. Nat. 1992; 140: 126-148Crossref PubMed Scopus (177) Google Scholar]. Second, reduced effective recombination under selfing means that recombinant haplotypes are less common, making it easier to detect sweeps [38Maynard Smith J. Haigh J. The hitch-hiking effect of a favourable gene.Genet. Res. 1974; 23: 23-35Crossref PubMed Scopus (2225) Google Scholar]. Unfortunately, the exact locus undergoing adaptation will be less easy to pinpoint as large genomic regions fix alongside targets of selection.Table 1Overview of Methods for Detecting Selection Footprints in Data from Genome-wide Re-sequencing StudiesType of methodSummary of methodData neededHow does selfing affect the method?RefsMcDonald–Kreitman (MK) testDetects abnormally high nonsynonymous over synonymous divergence ratio, relative to nonsynonymous over synonymous polymorphism ratioSNP data, unlinked, and divergence to an outgroup (e.g., a related sister-species)Linked selection could be more prevalent with selfing, which can alter estimates of the distribution of fitness effects of deleterious mutations. This distribution usually has to be accurately calculated to correctly infer the proportion of adaptive substitutions.74Messer P.W. Petrov D.A. Frequent adaptation and the McDonald–Kreitman test.Proc. Natl. Acad. Sci. U. S. A. 2013; 110: 8615-8620Crossref PubMed Scopus (136) Google ScholarSite–frequency spectrum (SFS) testsSFS in sweep regions consists of elevated low- and high-frequency variants compared to neutral caseSNPs data, unlinked, unphasedSelfing will affect expectation for SFS under soft and hard sweeps (Figure 1). SFS methods inferring selection assume invariably unlinked SNPs; this assumption is much more likely to be violated in selfers.75Kim Y. Stephan W. Detecting a local signature of genetic hitchhiking along a recombining chromosome.Genetics. 2002; 160: 765-777PubMed Google Scholar, 76Nielsen R. Genomic scans for selective sweeps using SNP data.Genome Res. 2005; 15: 1566-1575Crossref PubMed Scopus (652) Google ScholarNeutrality tests based on SFS (Tajima's D, Fay and Wu's H, etc.)These tests measure the excess or deficit of rare alleles in the SFS compared to neutral expectationsSNPs data, unlinked, unphasedShould work; selfing per se unlikely to sway these tests. Yet they are sensitive to demography, whose effect could be more difficult to remove in selfing species (Box 2).77Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.Genetics. 1989; 123: 585-595Crossref PubMed Google ScholarLinkage disequilibrium (LD)Increase in linkage disequilibrium at loci flanking a sweepSNPs data, linked and phasedA decrease in effective recombination rate might further amplify the effect of selective sweeps and expand the width of high LD regions.78McVean G.A.T. The structure of linkage disequilibrium around a selective sweep.Genetics. 2007; 175: 1395-1406Crossref PubMed Scopus (106) Google ScholarFst-based testsTracks local adaptation between two geographic regions by finding highly differentiated loci, as measured using the Fst statisticSNP frequencies from two or more populationsFst scans for excess differentiation will be robust to selfing when usin