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Recombination and Molecular Evolution
Recombination and Molecular Evolution AJ Betancourt, Vetmeduni Vienna, Vienna, Austria M Hartfield, University of Toronto, ON, Canada r 2016 Elsevier Inc. All rights reserved.
Glossary Adaptation The process of increasing in frequency a trait that is beneficial under natural selection. Allele A gene type that is present at a locus. Anisogamy The situation where male and female gametes are highly dimorphic; usually the male produces smaller gametes. Isogamous species are where males and females have similar-sized gametes. Background selection The loss of variation in the genome through purging deleterious mutation. Effective population size, Ne A quantity used to describe the genetic diversity present in a population; the principle being that an idealized population of size Ne would harbor the same level of diversity, if all mutations acted independently. Epistasis The effect where a collection of loci exhibit different fitness, compared to cases where each mutation acts independently.
Introduction Many organisms reproduce sexually – 99.9% of animal species, for instance (Vrijenhoek, 1998) – but the evolutionary reason for the widespread prevalence of sex is not immediately obvious. Sexual reproduction comes at a heavy price: mates must be found, fought for, and won; sexually transmitted diseases braved; and, after all these trials, sexually-produced offspring only carry half the genes of the parent. In fact, as
Males
Fitness Broadly, the ability of an individual to reproduce and leave descendants. Hitchhiking Where linked alleles (neutral or deleterious) fix with an adaptive allele. Interference When selection acts on mutations in a nonindependent manner (e.g., a deleterious allele hitchhikes to fixation with an adaptive mutant). Linkage disequilibrium Nonrandom association of mutations in the genome. Mutation A change made to the molecular sequence of a genome. Recombination Reciprocal exchange of genetic material. Segregation When two gene copies are separated and are passed at random during sexual reproduction.
John Maynard Smith pointed out (Maynard Smith, 1978), asexual reproduction should have a twofold advantage, all else being equal. That is, asexual females will reproduce at twice the rate of sexual ones, quickly outcompeting them, so that a mutation causing clonal reproduction in an anisogamous species is expected to quickly take over (Figure 1). Nevertheless, sex is pervasive in many taxa. In fact, phylogenetic analyses (Bell, 1982) show that sexual species tend to occur deeper in phylogenetic trees than asexual ones,
Sexuals Females
Asexuals Females
Figure 1 A cartoon describing Maynard Smith’s ‘twofold cos of sex’ argument. The sexual population, on the left, requires a male and a female pairing to reproduce; if one son and daughter are born every generation, the population is maintained at the same size. Asexual females, on the right, can produce two clonal offspring without needing a male partner. Adapted from Hartfield, M., Keightley, P.D., 2012. Current hypotheses for the evolution of sex and recombination. Integrative Zoology 7, 192–209.
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suggesting that only sexual species persist through time. For example, within the species Daphnia pulex, which has both sexual and asexual forms, the asexual lineages appear to be short-lived (Tucker et al., 2013). What, then, might account for the apparent advantage of sexual lineages? One possibility is that there are immediate advantages to sexual reproduction; for example, receiving care from two parents might improve the survival of offspring. That is, while the twofold cost of sex is useful as a thought experiment, it might rarely be realized in nature, as reproductive rates alone are not always the principal determinant of evolutionary fitness. However, this rationale depends on details of the life history of each species, and is therefore unsatisfying as a general explanation for the prevalence of sex. Instead, it is generally thought that sexual lineages have a long-term fitness advantage over asexual lineages. Sexual species are expected to adapt faster to changing environments, and to better maintain fitness in constant environments, compared to asexual organisms. The reason is that sex shuffles genomes, making new combinations of genotypes available for selection to act on. Mechanistically, this shuffling comes in two flavors: segregation and recombination between loci (Figure 2). Both are expected to promote the spread of beneficial mutations and the purging of deleterious ones. Without segregation, for example, the descendants of a heterozygous individual will remain heterozygous ad infinitum, or at least until a second mutation occurs at the same locus. A single beneficial mutation in such a population can increase from low frequency to 50%, but then faces a barrier to fixation. With segregation, there is no such barrier; homozygous individuals are easily generated from heterozygous ones, and the beneficial mutation can fully spread (Kirkpatrick and Jenkins, 1989). The overwhelming body of research, though, is directed toward the evolutionary benefits of genetic recombination. As we will discuss below, the implications of recombination have been spelled out in a large body of theory, some of which has been tested with molecular data.
Segregation
Recombination and Adaptation Theoretical Background Any selected allele, whether deleterious or beneficial, must begin as a mutation, either as a single or multiple copies. Each copy of the allele will arise on some genetic background, usually one randomly drawn from the population. Without recombination, the fate of the selected allele is strongly affected by whichever genetic background it arises on. For example, a beneficial allele unlucky enough to arise on an unfit genetic background may be lost, driven out of the population along with the deleterious alleles it is linked to. When the fates of selected alleles are non-independent, they are said to ‘interfere’ with one another. Felsenstein (1974), in an engaging review of the topic, termed this phenomenon 'Hill–Robertson interference,' after the seminal investigation into selection, linkage, and drift interactions by Hill and Robertson (1966). There are several flavors of Hill–Robertson interference, but all ultimately attribute the evolutionary advantage of recombination to its ability to uncouple selected alleles from their genetic backgrounds, so selection can act on them independently. 1. Fisher–Muller interference. Fisher (1930) and Muller (1932) pointed out how asexual populations suffer from interference between beneficial mutations. That is, in a non-recombining population, in order for two (or more) beneficial mutations to fix at the same time, they must occur in the same genetic background. This composition is unlikely, unless the first beneficial mutation to occur has already reached a high frequency. With recombination, two beneficial mutations can occur on different backgrounds, recombine onto the same genome, and sweep to fixation together (Figure 3). Thus, fixing two mutations takes roughly half the time that it does in an asexual population (Christiansen et al., 1998), unless mutation rates are high enough to create double mutants without Recombination
A
B
C
D
A
C
B
D
Figure 2 Segregation and recombination during sex. Segregation shuffles the manner in which gene copies (denoted here A–D and labeled with different colors) are organized within genomes. Recombination exchanges material between genomes.
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Asexual population aB Frequency of genotype in space
Ab
ab
AB
aB (a)
Generations Sexual population
Frequency of genotype in space
Ab AB
ab aB (b)
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Figure 3 Fisher–Muller argument for the evolution of sex. In asexuals (top), beneficial mutations have to arise and fix in sequence due to competition between them. In sexuals (bottom), however, recombination can form the optimal AB genotype much more rapidly. Adapted from Muller, H.J., 1932. Some genetic aspects of sex. American Naturalist 66, 118–138.
recombination (Kim and Orr, 2005). When applied to microbes, Fisher–Muller interference is sometimes called ‘clonal interference’ (Gerrish and Lenski, 1998), which can be tested experimentally (e.g., Lang et al. (2013)). 2. Muller’s ratchet. Muller’s (Muller, 1964) ratchet does not describe a failure to adapt to a changing environment, but instead a failure to maintain fitness even in a constant environment. In any population, particularly a small one, it is always possible to lose the fittest current genotype by chance. One way to model this phenomena is to consider deleterious mutations to be Poisson distributed over chromosomes essentially, distributed in the same way beans dropped onto a chessboard would be randomly spread over the squares. As Haigh (1978) showed, the mean number of mutations would be the ratio of the genomic mutation rate (U) to the average selection coefficient acting against these mutations (sd). The fraction of deleterious-mutation-free genomes is then just the size of the zero class for the Poisson distribution, exp(-U/sd). Thus, if the fraction of individuals carrying no deleterious mutations is expected to be one in a thousand, a population with a census size in the hundreds may not contain even one individual without deleterious mutations. In an asexual population, with no back mutation, there is also no way to regenerate a mutation-free genome the name ‘Muller’s ratchet’ comes from this irreversibility, as ratchets are wrenches that turn only one direction. Recombination, however, can reverse the process: as long as no particular deleterious mutation fixes, two genomes can recombine to form a reconstituted mutation-free genome. As the arguments above suggest, Muller’s ratchet is most important in small populations, with high genomic mutation rates (due to either high overall mutation rates, and/ or long genomes), or with weak selection (Felsenstein, 1974). Without these factors, the ratchet acts so slowly as to be unimportant; otherwise it can be a powerful
force, causing genomic degradation (Charlesworth and Charlesworth, 2000). 3. Ruby-in-the-rubbish interference. Ruby-in-the-rubbish interference (Peck, 1994) describes the loss of beneficial mutations that happen to arise on unfit backgrounds. The original ruby-in-the-rubbish model considers adaptation in an asexual population, where the beneficial mutations are not strong enough to overcome the effect of linked deleterious mutations. In this case, the only beneficial mutations with any chance of not going extinct must arise on deleterious-mutation-free genomes. In sexual populations, recombination can free the beneficial mutation from its loaded genetic background, improving its prospects for success. Cases in which the beneficial mutations are strongly selected for, and therefore override linked deleterious mutations, are more complex. If there are many deleterious mutations, adaptive alleles can still be lost in asexual populations if mutation rates are high (Johnson and Barton, 2002). With pairs of advantageous– deleterious mutations, sex can prevent the fixation of deleterious alleles. The benefit to recombination is greatest if deleterious mutations have slightly lower selection coefficients than their beneficial drivers (Hartfield and Otto, 2011). However, the case with many deleterious mutations affecting adaptive alleles in sexual populations has not yet been fully solved. In each of these cases, recombination counteracts interference by offering new allele combinations for selection to act on. This effect is only useful, though, when the fittest alleles are not already found together; otherwise, recombination breaks apart optimal genotypes. In technical terms, recombination only provides a benefit if there is negative linkage between beneficial mutations – when genomes more often have a mixture of beneficial and deleterious alleles at different loci, rather than possess only beneficial or only deleterious
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alleles. What, then, should give rise to these kinds of nonrandom associations? One answer is epistasis, where individuals carrying multiple mutations have better or worse fitness than expected based on the selective coefficients of the single mutations. However, only specific kinds of epistasis promote increased recombination (see Kondrashov (1988) and Kouyos et al. (2007)). A general explanation may simply be that population sizes are limited. As Fisher (1930) pointed out, in any finite population, all possible combinations of alleles never occur, so there will always be nonrandom associations between alleles. In cases where beneficial mutations are coupled, selection will quickly fix these genotypes (and, conversely, rapidly purge genotypes where deleterious mutations are coupled). The upshot is that the genotypes containing a mixture of beneficial and deleterious mutations would, on average, remain segregating for the longest amount of time. Over time, then, most linkage disequilibrium between beneficial mutations is negative, of just the sort to promote an advantage of recombination. Barton and Otto (2005) solidified this logic and showed how associations created in this manner select for increased recombination rates.
Empirical Evidence for an Advantage of Recombination If there is an advantage of recombination in aiding adaptation, can we see it in molecular population genetic data? Some of the earliest answers to this question come from sex chromosomes, which have evolved independently many times from autosomes. X and Y chromosomes proceed to diverge when recombination between them stops; as the Y only occurs while paired with the X, it can no longer recombine at all. What happens to this non-recombining chromosome? The longterm outcome can be seen on the Drosophila Y, for example. In terms of DNA content, this chromosome is huge – roughly twice the size of the X – but it harbors only a handful of genes, compared to thousands on the X. Initially, these chromosomes were identical, but the Y has lost most of its genes, and gained a large amount of ‘junk DNA.’ By studying young Y chromosomes, we can watch this process in action. For example, there is a very young Y chromosome in Drosophila miranda, which still retains many of its genes. Compared to their homologous on the X, however, these copies show less evidence of adaptation (Bachtrog and Charlesworth, 2000) as predicted by the theories outlined above. Similar surveys have been performed
in humans (Wilson Sayres et al., 2014), mice (Soh et al., 2014), and plants (Hough et al., 2014); see Bachtrog (2013) for a recent review. Other studies looking for an evolutionary advantage of recombination have been done within chromosomes, comparing low to high recombination regions. In Drosophila melanogaster, for example, there are long regions exhibiting very low recombination rates. Molecular evidence suggests that these regions show fewer substitutions of adaptive alleles and more substitutions of deleterious alleles, compared to regions of average recombination (Betancourt and Presgraves, 2002; Haddrill et al., 2007; Mackay et al., 2012). Gossmann et al. (2014) also found such a result in birds, by comparing chromosomes with different average recombination rates. Humans, in contrast, do not show a strong pattern of this type (Bullaughey et al., 2008), possibly due a low rate of adaptive protein evolution in our own species (Eyre-Walker and Keightley, 2009).
Recombination and Neutral Variation Even in sexual organisms, the amount of recombination can vary, for example, across sexes and individuals, and even across the genome. Studies of how evolutionary rates differ due to this variation have yielded fascinating insights into the effects of selection interference. D. melanogaster is an organism that shows a large amount of variation in recombination rates across its genome. In the early 1990s, Begun and Aquadro (1992) used this fact to show that, compared to highly recombination regions, low recombination regions had very little genetic diversity – in these regions, individual sequences of the same gene, which in D. melanogaster differ from each other at 1–2% of silent sites, showed only a small fraction of the normal level of variation. They invoked an explanation for which the theory had been worked out 20 years before: hitchhiking of neutral mutations (Maynard Smith and Haigh, 1974), based on Hill–Robertson interference caused by beneficial mutations. Briefly, hitchhiking argues that if selection fixes a single copy of a beneficial allele, it necessarily also fixes any neutral variants that arise on the same background (Figure 4). As a result, the nearby regions will be stripped of neutral variation. Recombination, however, allows the selected allele to move to other genetic backgrounds, and be linked to
Hitchhiking
Background selection
Before selection
Before selection
After selection
After selection
Figure 4 How selective effects reduce genetic variance. Hitchhiking (left) occurs when an adaptive allele, shown in red, spreads to all individuals in the population. Linked neutral mutations (blue dots) are driven with it to fixation as well, unifying the genetic signal around the adaptation. Background selection (right) occurs when deleterious mutations, the gray dots, are lost by selection, and are replaced by other neutral genotyped (after selection, the second genotype is replaced by the third, and the fifth by the fourth).
Recombination and Molecular Evolution
other neutral alleles; thus, the extent of the region affected by hitchhiking depends on the recombination rate. More formally, we can see why recombination should affect neutral sequence diversity if we first understand what affects it, namely, mutation rate (u), and the number of ancestors contributing genetic material to a population, quantified as effective population size (Ne). Diversity increases as mutation rate increases, because, as more mutations are introduced into a population, more sites can contain differences. Diversity also increases as Ne increases – if the number of genetic ancestors is small, individuals will be closely related, and therefore genetically similar to one another. Begun and Aquadro were able to eliminate an effect of recombination on mutation rate, and therefore concluded that recombination affects Ne. As diversity is measured across the genome of a single species of fly, it is unlikely that there are different numbers of actual ancestors contributing to different regions of the genome. Instead, it may be that the fixation of beneficial mutations reduces the number of genetic ancestors for long regions in low recombination regions via the hitchhiking effect (Figure 4). Hitchhiking, then, appears to explain the relationship between diversity and recombination, which also implies that adaptive evolution is frequent enough to change levels of neutral diversity. However, Charlesworth et al. (1993) almost immediately challenged this explanation, pointing out that hitchhiking is not the only possible cause for a relationship between neutral diversity and recombination, recurrent deleterious mutations is another. The reason is that deleterious mutations also reduce the effective population size of linked regions: as they are removed from the population, so is any neutral linked variation (Figure 4). Without recombination, the only genomes that ultimately contribute ancestry to the population are those deleterious-mutation-free genomes; that is, the zero class of the Muller's ratchet model. With recombination, some of the genetic material that would have otherwise been lost can recombine onto mutation-free backgrounds. As a result, the effect of background selection, like that of hitchhiking, varies with the recombination rate. Trying to disentangle the two effects still motivates current research, since the two phenomena can be difficult to tease apart (Cutter and Payseur, 2013). Begun and Aquadro’s observations were based on a limited amount of data (appropriate for the time), so it is worth asking how their findings have held up. For Drosophila, the answer is quite well, as shown using whole-genome polymorphism datasets (Mackay et al., 2012). Besides Drosophila, these effects have been examined in a broad range of taxa (Cutter and Payseur, 2013); though the results are mixed, most other taxa show similar patterns to those in Drosophila, with recombination rate positively correlated with neutral genetic diversity. The effect of recombination on Ne is also reflected in patterns seen for weakly selected alleles: alleles whose selection coefficients hover near the value of 1/Ne, rendering them borderline neutral. A local reduction in Ne can push them under this threshold, so that they act effectively neutrally. In Drosophila, sites evolving under weak selection do, in fact, show reduced adaptation in regions of very low recombination. However, this effect appears to be restricted to these regions, rather than scaling with increased recombination rate
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(Marais et al., 2001; Haddrill et al., 2007; Campos et al., 2014). The reason is likely historical: weakly selected sites will take a long time to reach their equilibrium level of adaptation, while most reduced recombination regions in D. melanogaster seem to have only recently suffered from a reduction in recombination rate (Campos et al., 2014). Further, with whole-genome polymorphism data, we have been able to refine our picture of the local effect of selection on linked neutral sites. In the immediate vicinity of putatively adaptive substitutions, there is a dip in average neutral diversity, just as expected under hitchhiking (Sattath et al., 2011), though not in humans (Hernandez et al., 2011). In our own species, the role of background selection is well-established; in fact, the effect of linkage to selected sites has been quantified in a ‘background selection map’ (McVicker et al., 2009). The contrast between Drosophila, which shows evidence consistent with adaptive evolution, and humans, where deleterious mutations appear to play a bigger role, may be due to their contrasting effective population sizes. All else being equal, larger populations may experience higher overall rates of adaptive substitutions: in support of this, mice, which are mammals like humans but have larger population sizes (Phifer-Rixey et al., 2012), show a Drosophila-like pattern near substitutions (Halligan et al., 2013).
Conclusion Here, we have seen how recombination frees organisms to adapt at multiple sites, allows them to preserve the integrity of their genomes, and conserves genetic variation. With reduced sequencing costs, these questions can now be addressed in new species and in new ways. Future results will refine our picture on how recombination shapes genomes, and hopefully throw up unexpected outcomes, generating new avenues of research.
See also: Effective Population Size. Recombination and Selection. Selective Sweeps. Sex, Evolution and Maintenance of
References Bachtrog, D., 2013. Y-chromosome evolution: Emerging insights into processes of Y-chromosome degeneration. Nature Reviews Genetics 14, 113–124. Bachtrog, D., Charlesworth, B., 2000. Reduced levels of microsatellite variability on the neo-Y chromosome of Drosophila miranda. Current Biology 10, 1025–1031. Barton, N.H., Otto, S.P., 2005. Evolution of rRecombination due to random drift. Genetics 169, 2353–2370. Begun, D.J., Aquadro, C.F., 1992. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature 356, 519–520. Bell, G., 1982. The Masterpiece of Nature: The Evolution and Genetics of Sexuality. Berkeley: University of California Press. Betancourt, A.J., Presgraves, D.C., 2002. Linkage limits the power of natural selection in Drosophila. Proceedings of the National Academy of Sciences of the United States of America 99, 13616–13620. Bullaughey, K., Przeworski, M., Coop, G., 2008. No effect of recombination on the efficacy of natural selection in primates. Genome Research 18, 544–554. Campos, J.L., Halligan, D.L., Haddrill, P.R., Charlesworth, B., 2014. The relation between recombination rate and patterns of molecular evolution and variation in Drosophila melanogaster. Molecular Biology & Evolution 31, 1010–1028.
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Charlesworth, B., Charlesworth, D., 2000. The degeneration of Y chromosomes. Philosophical Transactions of the Royal Society of London, B: Biological Sciences 355, 1563–1572. Charlesworth, B., Morgan, M.T., Charlesworth, D., 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134, 1289–1303. Christiansen, F.B., Otto, S.P., Bergman, A., Feldman, M.W., 1998. Waiting with and without recombination: The time to production of a double mutant. Theoretical Population Biology 53, 199–215. Cutter, A.D., Payseur, B.A., 2013. Genomic signatures of selection at linked sites: Unifying the disparity among species. Nature Review Genetics 14, 262–274. Eyre-Walker, A., Keightley, P.D., 2009. Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Molecular Biology & Evolution 26, 2097–2108. Felsenstein, J., 1974. The evolutionary advantage of recombination. Genetics 78, 737–756. Fisher, R.A., 1930. The Genetical Theory of Natural Selection. Oxford: The Clarendon Press. Gerrish, P., Lenski, R., 1998. The fate of competing beneficial mutations in an asexual population. Genetica 102−103, 127–144. Gossmann, T.I., Santure, A.W., Sheldon, B.C., Slate, J., Zeng, K., 2014. Highly variable recombinational landscape modulates efficacy of natural selection in birds. Genome Biology & Evolution 6, 2061–2075. Haddrill, P., Halligan, D., Tomaras, D., Charlesworth, B., 2007. Reduced efficacy of selection in regions of the Drosophila genome that lack crossing over. Genome Biology 8, R18. Haigh, J., 1978. The accumulation of deleterious genes in a population − Muller's Ratchet. Theoretical Population Biology 14, 251–267. Halligan, D.L., Kousathanas, A., Ness, R.W., et al., 2013. Contributions of proteincoding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genetics 9, e1003995. Hartfield, M., Otto, S.P., 2011. Recombination and hitchhiking of deleterious alleles. Evolution 65, 2421–2434. Hernandez, R.D., Kelley, J.L., Elyashiv, E., et al., 2011. Classic selective sweeps were rare in recent human evolution. Science 331, 920–924. Hill, W.G., Robertson, A., 1966. The effect of linkage on limits to artificial selection. Genetic Research 8, 269–294. Hough, J., Hollister, J.D., Wang, W., Barrett, S.C.H., Wright, S.I., 2014. Genetic degeneration of old and young Y chromosomes in the flowering plant Rumex hastatulus. Proceedings of the National Academy of Sciences of the United States of America 111, 7713–7718. Johnson, T., Barton, N.H., 2002. The effect of deleterious alleles on adaptation in asexual populations. Genetics 162, 395–411. Kim, Y., Orr, H.A., 2005. Adaptation in sexuals vs. asexuals: Clonal interference and the Fisher−Muller model. Genetics 171, 1377–1386.
Kirkpatrick, M., Jenkins, C.D., 1989. Genetic segregation and the maintenance of sexual reproduction. Nature 339, 300–301. Kondrashov, A.S., 1988. Deleterious mutations and the evolution of sexual reproduction. Nature 336, 435–440. Kouyos, R.D., Silander, O.K., Bonhoeffer, S., 2007. Epistasis between deleterious mutations and the evolution of recombination. Trends in Ecology & Evolution 22, 308–315. Lang, G.I., Rice, D.P., Hickman, M.J., et al., 2013. Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 500, 571–574. Mackay, T.F.C., Richards, S., Stone, E.A., et al., 2012. The Drosophila melanogaster Genetic Reference Panel. Nature 482, 173–178. Marais, G., Mouchiroud, D., Duret, L., 2001. Does recombination improve selection on codon usage? Lessons from nematode and fly complete genomes. Proceedings of the National Academy of Sciences of the United States of America 98, 5688–5692. Maynard Smith, J., 1978. The Evolution of Sex. Cambridge; New York: Cambridge University Press. Maynard Smith, J., Haigh, J., 1974. The hitch-hiking effect of a favourable gene. Genetics Research 23, 23–35. McVicker, G., Gordon, D., Davis, C., Green, P., 2009. Widespread genomic signatures of natural selection in hominid evolution. PLoS Genetics 5, e1000471. Muller, H.J., 1932. Some genetic aspects of sex. American Naturalist 66, 118–138. Muller, H.J., 1964. The relation of recombination to mutational advance. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 1, 2–9. Peck, J.R., 1994. A ruby in the rubbish: Beneficial mutations, deleterious mutations and the evolution of sex. Genetics 137, 597–606. Phifer-Rixey, M., Bonhomme, F., Boursot, P., et al., 2012. Adaptive evolution and effective population size in wild house mice. Molecular Biology & Evolution 29, 2949–2955. Sattath, S., Elyashiv, E., Kolodny, O., Rinott, Y., Sella, G., 2011. Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans. PLoS Genetics 7, e1001302. Soh, Y.Q.S., Alföldi, J., Pyntikova, T., et al., 2014. Sequencing the mouse Y chromosome reveals convergent gene acquisition and amplification on both sex chromosomes. Cell 159, 800–813. Tucker, A.E., Ackerman, M.S., Eads, B.D., Xu, S., Lynch, M., 2013. Populationgenomic insights into the evolutionary origin and fate of obligately asexual Daphnia pulex. Proceedings of the National Academy of Sciences of the United States of America 110, 15740–15745. Vrijenhoek, R.C., 1998. Animal clones and diversity. BioScience 48, 617–628. Wilson Sayres, M.A., Lohmueller, K.E., Nielsen, R., 2014. Natural selection reduced diversity on human Y chromosomes. PLoS Genetics 10, e1004064.
Glossary Adaptation The process of increasing in frequency a trait that is beneficial under natural selection. Allele A gene type that is present at a locus. Anisogamy The situation where male and female gametes are highly dimorphic; usually the male produces smaller gametes. Isogamous species are where males and females have similar-sized gametes. Background selection The loss of variation in the genome through purging deleterious mutation. Effective population size, Ne A quantity used to describe the genetic diversity present in a population; the principle being that an idealized population of size Ne would harbor the same level of diversity, if all mutations acted independently. Epistasis The effect where a collection of loci exhibit different fitness, compared to cases where each mutation acts independently.
Introduction Many organisms reproduce sexually – 99.9% of animal species, for instance (Vrijenhoek, 1998) – but the evolutionary reason for the widespread prevalence of sex is not immediately obvious. Sexual reproduction comes at a heavy price: mates must be found, fought for, and won; sexually transmitted diseases braved; and, after all these trials, sexually-produced offspring only carry half the genes of the parent. In fact, as
Males
Fitness Broadly, the ability of an individual to reproduce and leave descendants. Hitchhiking Where linked alleles (neutral or deleterious) fix with an adaptive allele. Interference When selection acts on mutations in a nonindependent manner (e.g., a deleterious allele hitchhikes to fixation with an adaptive mutant). Linkage disequilibrium Nonrandom association of mutations in the genome. Mutation A change made to the molecular sequence of a genome. Recombination Reciprocal exchange of genetic material. Segregation When two gene copies are separated and are passed at random during sexual reproduction.
John Maynard Smith pointed out (Maynard Smith, 1978), asexual reproduction should have a twofold advantage, all else being equal. That is, asexual females will reproduce at twice the rate of sexual ones, quickly outcompeting them, so that a mutation causing clonal reproduction in an anisogamous species is expected to quickly take over (Figure 1). Nevertheless, sex is pervasive in many taxa. In fact, phylogenetic analyses (Bell, 1982) show that sexual species tend to occur deeper in phylogenetic trees than asexual ones,
Sexuals Females
Asexuals Females
Figure 1 A cartoon describing Maynard Smith’s ‘twofold cos of sex’ argument. The sexual population, on the left, requires a male and a female pairing to reproduce; if one son and daughter are born every generation, the population is maintained at the same size. Asexual females, on the right, can produce two clonal offspring without needing a male partner. Adapted from Hartfield, M., Keightley, P.D., 2012. Current hypotheses for the evolution of sex and recombination. Integrative Zoology 7, 192–209.
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suggesting that only sexual species persist through time. For example, within the species Daphnia pulex, which has both sexual and asexual forms, the asexual lineages appear to be short-lived (Tucker et al., 2013). What, then, might account for the apparent advantage of sexual lineages? One possibility is that there are immediate advantages to sexual reproduction; for example, receiving care from two parents might improve the survival of offspring. That is, while the twofold cost of sex is useful as a thought experiment, it might rarely be realized in nature, as reproductive rates alone are not always the principal determinant of evolutionary fitness. However, this rationale depends on details of the life history of each species, and is therefore unsatisfying as a general explanation for the prevalence of sex. Instead, it is generally thought that sexual lineages have a long-term fitness advantage over asexual lineages. Sexual species are expected to adapt faster to changing environments, and to better maintain fitness in constant environments, compared to asexual organisms. The reason is that sex shuffles genomes, making new combinations of genotypes available for selection to act on. Mechanistically, this shuffling comes in two flavors: segregation and recombination between loci (Figure 2). Both are expected to promote the spread of beneficial mutations and the purging of deleterious ones. Without segregation, for example, the descendants of a heterozygous individual will remain heterozygous ad infinitum, or at least until a second mutation occurs at the same locus. A single beneficial mutation in such a population can increase from low frequency to 50%, but then faces a barrier to fixation. With segregation, there is no such barrier; homozygous individuals are easily generated from heterozygous ones, and the beneficial mutation can fully spread (Kirkpatrick and Jenkins, 1989). The overwhelming body of research, though, is directed toward the evolutionary benefits of genetic recombination. As we will discuss below, the implications of recombination have been spelled out in a large body of theory, some of which has been tested with molecular data.
Segregation
Recombination and Adaptation Theoretical Background Any selected allele, whether deleterious or beneficial, must begin as a mutation, either as a single or multiple copies. Each copy of the allele will arise on some genetic background, usually one randomly drawn from the population. Without recombination, the fate of the selected allele is strongly affected by whichever genetic background it arises on. For example, a beneficial allele unlucky enough to arise on an unfit genetic background may be lost, driven out of the population along with the deleterious alleles it is linked to. When the fates of selected alleles are non-independent, they are said to ‘interfere’ with one another. Felsenstein (1974), in an engaging review of the topic, termed this phenomenon 'Hill–Robertson interference,' after the seminal investigation into selection, linkage, and drift interactions by Hill and Robertson (1966). There are several flavors of Hill–Robertson interference, but all ultimately attribute the evolutionary advantage of recombination to its ability to uncouple selected alleles from their genetic backgrounds, so selection can act on them independently. 1. Fisher–Muller interference. Fisher (1930) and Muller (1932) pointed out how asexual populations suffer from interference between beneficial mutations. That is, in a non-recombining population, in order for two (or more) beneficial mutations to fix at the same time, they must occur in the same genetic background. This composition is unlikely, unless the first beneficial mutation to occur has already reached a high frequency. With recombination, two beneficial mutations can occur on different backgrounds, recombine onto the same genome, and sweep to fixation together (Figure 3). Thus, fixing two mutations takes roughly half the time that it does in an asexual population (Christiansen et al., 1998), unless mutation rates are high enough to create double mutants without Recombination
A
B
C
D
A
C
B
D
Figure 2 Segregation and recombination during sex. Segregation shuffles the manner in which gene copies (denoted here A–D and labeled with different colors) are organized within genomes. Recombination exchanges material between genomes.
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Asexual population aB Frequency of genotype in space
Ab
ab
AB
aB (a)
Generations Sexual population
Frequency of genotype in space
Ab AB
ab aB (b)
Generations
Figure 3 Fisher–Muller argument for the evolution of sex. In asexuals (top), beneficial mutations have to arise and fix in sequence due to competition between them. In sexuals (bottom), however, recombination can form the optimal AB genotype much more rapidly. Adapted from Muller, H.J., 1932. Some genetic aspects of sex. American Naturalist 66, 118–138.
recombination (Kim and Orr, 2005). When applied to microbes, Fisher–Muller interference is sometimes called ‘clonal interference’ (Gerrish and Lenski, 1998), which can be tested experimentally (e.g., Lang et al. (2013)). 2. Muller’s ratchet. Muller’s (Muller, 1964) ratchet does not describe a failure to adapt to a changing environment, but instead a failure to maintain fitness even in a constant environment. In any population, particularly a small one, it is always possible to lose the fittest current genotype by chance. One way to model this phenomena is to consider deleterious mutations to be Poisson distributed over chromosomes essentially, distributed in the same way beans dropped onto a chessboard would be randomly spread over the squares. As Haigh (1978) showed, the mean number of mutations would be the ratio of the genomic mutation rate (U) to the average selection coefficient acting against these mutations (sd). The fraction of deleterious-mutation-free genomes is then just the size of the zero class for the Poisson distribution, exp(-U/sd). Thus, if the fraction of individuals carrying no deleterious mutations is expected to be one in a thousand, a population with a census size in the hundreds may not contain even one individual without deleterious mutations. In an asexual population, with no back mutation, there is also no way to regenerate a mutation-free genome the name ‘Muller’s ratchet’ comes from this irreversibility, as ratchets are wrenches that turn only one direction. Recombination, however, can reverse the process: as long as no particular deleterious mutation fixes, two genomes can recombine to form a reconstituted mutation-free genome. As the arguments above suggest, Muller’s ratchet is most important in small populations, with high genomic mutation rates (due to either high overall mutation rates, and/ or long genomes), or with weak selection (Felsenstein, 1974). Without these factors, the ratchet acts so slowly as to be unimportant; otherwise it can be a powerful
force, causing genomic degradation (Charlesworth and Charlesworth, 2000). 3. Ruby-in-the-rubbish interference. Ruby-in-the-rubbish interference (Peck, 1994) describes the loss of beneficial mutations that happen to arise on unfit backgrounds. The original ruby-in-the-rubbish model considers adaptation in an asexual population, where the beneficial mutations are not strong enough to overcome the effect of linked deleterious mutations. In this case, the only beneficial mutations with any chance of not going extinct must arise on deleterious-mutation-free genomes. In sexual populations, recombination can free the beneficial mutation from its loaded genetic background, improving its prospects for success. Cases in which the beneficial mutations are strongly selected for, and therefore override linked deleterious mutations, are more complex. If there are many deleterious mutations, adaptive alleles can still be lost in asexual populations if mutation rates are high (Johnson and Barton, 2002). With pairs of advantageous– deleterious mutations, sex can prevent the fixation of deleterious alleles. The benefit to recombination is greatest if deleterious mutations have slightly lower selection coefficients than their beneficial drivers (Hartfield and Otto, 2011). However, the case with many deleterious mutations affecting adaptive alleles in sexual populations has not yet been fully solved. In each of these cases, recombination counteracts interference by offering new allele combinations for selection to act on. This effect is only useful, though, when the fittest alleles are not already found together; otherwise, recombination breaks apart optimal genotypes. In technical terms, recombination only provides a benefit if there is negative linkage between beneficial mutations – when genomes more often have a mixture of beneficial and deleterious alleles at different loci, rather than possess only beneficial or only deleterious
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alleles. What, then, should give rise to these kinds of nonrandom associations? One answer is epistasis, where individuals carrying multiple mutations have better or worse fitness than expected based on the selective coefficients of the single mutations. However, only specific kinds of epistasis promote increased recombination (see Kondrashov (1988) and Kouyos et al. (2007)). A general explanation may simply be that population sizes are limited. As Fisher (1930) pointed out, in any finite population, all possible combinations of alleles never occur, so there will always be nonrandom associations between alleles. In cases where beneficial mutations are coupled, selection will quickly fix these genotypes (and, conversely, rapidly purge genotypes where deleterious mutations are coupled). The upshot is that the genotypes containing a mixture of beneficial and deleterious mutations would, on average, remain segregating for the longest amount of time. Over time, then, most linkage disequilibrium between beneficial mutations is negative, of just the sort to promote an advantage of recombination. Barton and Otto (2005) solidified this logic and showed how associations created in this manner select for increased recombination rates.
Empirical Evidence for an Advantage of Recombination If there is an advantage of recombination in aiding adaptation, can we see it in molecular population genetic data? Some of the earliest answers to this question come from sex chromosomes, which have evolved independently many times from autosomes. X and Y chromosomes proceed to diverge when recombination between them stops; as the Y only occurs while paired with the X, it can no longer recombine at all. What happens to this non-recombining chromosome? The longterm outcome can be seen on the Drosophila Y, for example. In terms of DNA content, this chromosome is huge – roughly twice the size of the X – but it harbors only a handful of genes, compared to thousands on the X. Initially, these chromosomes were identical, but the Y has lost most of its genes, and gained a large amount of ‘junk DNA.’ By studying young Y chromosomes, we can watch this process in action. For example, there is a very young Y chromosome in Drosophila miranda, which still retains many of its genes. Compared to their homologous on the X, however, these copies show less evidence of adaptation (Bachtrog and Charlesworth, 2000) as predicted by the theories outlined above. Similar surveys have been performed
in humans (Wilson Sayres et al., 2014), mice (Soh et al., 2014), and plants (Hough et al., 2014); see Bachtrog (2013) for a recent review. Other studies looking for an evolutionary advantage of recombination have been done within chromosomes, comparing low to high recombination regions. In Drosophila melanogaster, for example, there are long regions exhibiting very low recombination rates. Molecular evidence suggests that these regions show fewer substitutions of adaptive alleles and more substitutions of deleterious alleles, compared to regions of average recombination (Betancourt and Presgraves, 2002; Haddrill et al., 2007; Mackay et al., 2012). Gossmann et al. (2014) also found such a result in birds, by comparing chromosomes with different average recombination rates. Humans, in contrast, do not show a strong pattern of this type (Bullaughey et al., 2008), possibly due a low rate of adaptive protein evolution in our own species (Eyre-Walker and Keightley, 2009).
Recombination and Neutral Variation Even in sexual organisms, the amount of recombination can vary, for example, across sexes and individuals, and even across the genome. Studies of how evolutionary rates differ due to this variation have yielded fascinating insights into the effects of selection interference. D. melanogaster is an organism that shows a large amount of variation in recombination rates across its genome. In the early 1990s, Begun and Aquadro (1992) used this fact to show that, compared to highly recombination regions, low recombination regions had very little genetic diversity – in these regions, individual sequences of the same gene, which in D. melanogaster differ from each other at 1–2% of silent sites, showed only a small fraction of the normal level of variation. They invoked an explanation for which the theory had been worked out 20 years before: hitchhiking of neutral mutations (Maynard Smith and Haigh, 1974), based on Hill–Robertson interference caused by beneficial mutations. Briefly, hitchhiking argues that if selection fixes a single copy of a beneficial allele, it necessarily also fixes any neutral variants that arise on the same background (Figure 4). As a result, the nearby regions will be stripped of neutral variation. Recombination, however, allows the selected allele to move to other genetic backgrounds, and be linked to
Hitchhiking
Background selection
Before selection
Before selection
After selection
After selection
Figure 4 How selective effects reduce genetic variance. Hitchhiking (left) occurs when an adaptive allele, shown in red, spreads to all individuals in the population. Linked neutral mutations (blue dots) are driven with it to fixation as well, unifying the genetic signal around the adaptation. Background selection (right) occurs when deleterious mutations, the gray dots, are lost by selection, and are replaced by other neutral genotyped (after selection, the second genotype is replaced by the third, and the fifth by the fourth).
Recombination and Molecular Evolution
other neutral alleles; thus, the extent of the region affected by hitchhiking depends on the recombination rate. More formally, we can see why recombination should affect neutral sequence diversity if we first understand what affects it, namely, mutation rate (u), and the number of ancestors contributing genetic material to a population, quantified as effective population size (Ne). Diversity increases as mutation rate increases, because, as more mutations are introduced into a population, more sites can contain differences. Diversity also increases as Ne increases – if the number of genetic ancestors is small, individuals will be closely related, and therefore genetically similar to one another. Begun and Aquadro were able to eliminate an effect of recombination on mutation rate, and therefore concluded that recombination affects Ne. As diversity is measured across the genome of a single species of fly, it is unlikely that there are different numbers of actual ancestors contributing to different regions of the genome. Instead, it may be that the fixation of beneficial mutations reduces the number of genetic ancestors for long regions in low recombination regions via the hitchhiking effect (Figure 4). Hitchhiking, then, appears to explain the relationship between diversity and recombination, which also implies that adaptive evolution is frequent enough to change levels of neutral diversity. However, Charlesworth et al. (1993) almost immediately challenged this explanation, pointing out that hitchhiking is not the only possible cause for a relationship between neutral diversity and recombination, recurrent deleterious mutations is another. The reason is that deleterious mutations also reduce the effective population size of linked regions: as they are removed from the population, so is any neutral linked variation (Figure 4). Without recombination, the only genomes that ultimately contribute ancestry to the population are those deleterious-mutation-free genomes; that is, the zero class of the Muller's ratchet model. With recombination, some of the genetic material that would have otherwise been lost can recombine onto mutation-free backgrounds. As a result, the effect of background selection, like that of hitchhiking, varies with the recombination rate. Trying to disentangle the two effects still motivates current research, since the two phenomena can be difficult to tease apart (Cutter and Payseur, 2013). Begun and Aquadro’s observations were based on a limited amount of data (appropriate for the time), so it is worth asking how their findings have held up. For Drosophila, the answer is quite well, as shown using whole-genome polymorphism datasets (Mackay et al., 2012). Besides Drosophila, these effects have been examined in a broad range of taxa (Cutter and Payseur, 2013); though the results are mixed, most other taxa show similar patterns to those in Drosophila, with recombination rate positively correlated with neutral genetic diversity. The effect of recombination on Ne is also reflected in patterns seen for weakly selected alleles: alleles whose selection coefficients hover near the value of 1/Ne, rendering them borderline neutral. A local reduction in Ne can push them under this threshold, so that they act effectively neutrally. In Drosophila, sites evolving under weak selection do, in fact, show reduced adaptation in regions of very low recombination. However, this effect appears to be restricted to these regions, rather than scaling with increased recombination rate
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(Marais et al., 2001; Haddrill et al., 2007; Campos et al., 2014). The reason is likely historical: weakly selected sites will take a long time to reach their equilibrium level of adaptation, while most reduced recombination regions in D. melanogaster seem to have only recently suffered from a reduction in recombination rate (Campos et al., 2014). Further, with whole-genome polymorphism data, we have been able to refine our picture of the local effect of selection on linked neutral sites. In the immediate vicinity of putatively adaptive substitutions, there is a dip in average neutral diversity, just as expected under hitchhiking (Sattath et al., 2011), though not in humans (Hernandez et al., 2011). In our own species, the role of background selection is well-established; in fact, the effect of linkage to selected sites has been quantified in a ‘background selection map’ (McVicker et al., 2009). The contrast between Drosophila, which shows evidence consistent with adaptive evolution, and humans, where deleterious mutations appear to play a bigger role, may be due to their contrasting effective population sizes. All else being equal, larger populations may experience higher overall rates of adaptive substitutions: in support of this, mice, which are mammals like humans but have larger population sizes (Phifer-Rixey et al., 2012), show a Drosophila-like pattern near substitutions (Halligan et al., 2013).
Conclusion Here, we have seen how recombination frees organisms to adapt at multiple sites, allows them to preserve the integrity of their genomes, and conserves genetic variation. With reduced sequencing costs, these questions can now be addressed in new species and in new ways. Future results will refine our picture on how recombination shapes genomes, and hopefully throw up unexpected outcomes, generating new avenues of research.
See also: Effective Population Size. Recombination and Selection. Selective Sweeps. Sex, Evolution and Maintenance of
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