- THIS ARTICLE
-
Abstract
- Full Text (PDF)
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Gessler, D. D. G.
- Articles by Xu, S.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Gessler, D. D. G.
- Articles by Xu, S.
Meiosis and the Evolution of Recombination at Low Mutation Rates
Damian D. G. Gesslera and Shizhong Xuaa Department of Botany and Plant Sciences, University of California, Riverside, California 92521
Corresponding author: Damian D. G. Gessler, National Center for Genome Resources, 2935 Rodeo Park Dr. East, Santa Fe, NM 87505., ddg{at}ncgr.org (E-mail)
Communicating editor: W. STEPHAN
| ABSTRACT |
|---|
The classical understanding of recombination is that in large asexual populations with multiplicative fitness, linkage disequilibrium is negligible, and thus there is no selective agent driving an allele for recombination. This has led researchers to recognize the importance of synergistic epistatic selection in generating negative linkage disequilibrium that thereby renders an advantage to recombination. Yet data on such selection is equivocal, and various works have shown that synergistic epistasis per se, when left unquantified in its magnitude or operation, is not sufficient to drive the evolution of recombination. Here we show that neither it, nor any mechanism generating negative linkage disequilibrium among fitness-related loci, is necessary. We demonstrate that a neutral gene for recombination can increase in frequency in a large population under a low mutation rate and strict multiplicative fitness. We work in a parameter range where individuals have, on average, less than one mutation each, yet recombination can still evolve. We demonstrate this in two ways: first, by examining the consequences of recombination correlated with misrepaired DNA damage and, second, by increasing the probability of recombination with declining fitness. Interestingly, the allele spreads without repairing even a single DNA mutation.
THE evolution of recombination has historically been dominated by two main understandings. The first is that recombination destroys linkage disequilibrium; thus, if there is no linkage disequilibrium among fitness-related loci, there is no mechanism other than drift driving an allele for recombination. The second is that concurrent with the destruction of such linkage disequilibrium, there is a commensurate change in population mean fitness. A rise in mean fitness is often inferred, though is not sufficient, to conclude an adaptive advantage of recombination. These properties are based on well-established and well-verified analyses (e.g., ![]()
![]()
![]()
![]()
![]()
![]()
To begin, consider that in any population heritable differences in fitness mean that some individuals leave more offspring than others and that this bias is transmitted with some degree of error from generation to generation. This means that without recombination, the probability of fixation for all loci on the best haplotypes is disproportionately biased toward unity (![]()
|
|
Inspection of Table 1 shows that asexual populations create an inherent selective pressure on genes in inferior haplotypes to escape their genetic background. Only among the best individuals is it advantageous for loci to remain linked. This is a direct and inescapable consequence of inheritance in asexual populations. To the degree that the best individuals constitute a subclass of the population (even if not necessarily few in number), this selection can be strong, since virtually all haplotypes save the best are destined for extinction (![]()
![]()
![]()
In natural systems, the idealized probabilities in Table 1 will be obfuscated by recurrent mutation, compensatory and beneficial mutations, and environmental changes. Yet since nonrecombining genomes have dynamics analogous to single-locus models with temporally varying selection coefficients, and since such models predict that haplotypes deterministically differ in their fixation probabilities so long as differences in their geometric mean fitness exceed N-1e, it is inescapable that asexual populationsat least as we currently understand themwill incorporate some bias in their distribution of fixation probabilities. The question then becomes, Is there sufficient genetic variance for alleles to exploit this variance in fixation probabilities to increase their own probabilities of fixation? Clearly, if inferior haplotypes are destined to extinction, then it is advantageous for their alleles to destroy their current association.
| MUTATION AND RECOMBINATION |
|---|
Currently, and with the exception of examples such as Weigle reactivation [i.e., SOS-induced viral reactivation via recombinatoric pathways (![]()
![]()
There is strong evidence that ionizing radiation, mutagens, and cellular processes themselves cause double-strand breaks (DSBs); these act as initiation sites for recombination (![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
![]()
In addition to the link between DNA damage and recombination, it would be pertinent to know if damage increased the likelihood of recombination even among undamaged sites. Again, there is supportive evidence: ![]()
![]()
The preceding studies do not show that inferior haplotypes are more likely to recombine. But they do suggest that biases in recombinatoric propensity exist: when we consider recombination theoretically, we should consider its differential induction. Currently, recombination within a cell is often viewed in terms of DNA repairthat is, for the benefit of the cell (though see ![]()
| THE MODEL |
|---|
To examine the consequences of the latter for the evolution of meiosis, we use a model of early eukaryotic, proto-meiotic, haploid organisms. We introduce genetic variance for recombination in the form of an invading allele that instigates homologous reciprocal recombination between unicellulars upon coupling. But the allele, instead of inducing recombination arbitrarily and being oblivious to the state of the cell within which it resides, is integrated into its cellular mechanisms: it is more likely to be activated in cells that have recently acquired deleterious mutations. We then relax this mutation/recombination link in a more general model that negatively correlates recombination with fitness.
In a computer, we construct a population of N = 105 asexual individuals. The computer keeps track of each mutation's position and deleterious effect on a single haploid chromosome for each individual. Actual positions approximate an infinite-sites model. Each generation, individuals go through a stochastic process of mutation, selection, and reproduction. Mutations occur randomly throughout the genome with a Poisson mean of µ = 0.0034 individual-1 generation-1 (![]()
![]()
![]()
![]()
![]()
= 1 and ß = s-1 - 1 = 49. There is currently much discussion in the literature about appropriate values and distributions of µ and s, but the important point in this parameterization is that both Nµ and N
exceed unity (where
is the average segregating selection coefficient in the population), while µ is in the range believable for DNA microbes. We do not explicitly model DSBs, in large part because we have little or no data on how their resolution generates a mutational spectrum of selection coefficients. We do know, though, that cells experience thousands of lesions per generation (![]()
![]()
![]()
Selection in the model is strictly multiplicative, with individuals that pass selection becoming the adults of the next generation. Before invading alleles are introduced, each population first comes to approximate mutation-selection balance such that mean fitness equals e-µ (generation 0 on graph). Variance for recombination is introduced by mutating an allele at a randomly chosen neutral locus, such that individuals with this allele may instigate coupling with another randomly chosen individual. Coupling is defined loosely, meaning two individuals unite, recombine their genomes, and dissociate. For the first set of runs (mutational-induction runs), an individual instigates recombination only if it both has the allele and has acquired a mutation in the current generation. Since the probability of a mutation is 1 - e-0.0034
0.0034, this is a rare event. For the second set of runs (fitness-conditional runs), for each generation, each individual's fitness is compared to a 01 uniform variate. If its fitness is less than the variate and it has the recombination allele, then it instigates recombination. Since mean fitness is high (e-0.0034
0.9966), this also is a rare event. In contrast to the mutational-induction runs, induction of recombination is independent of mutational events per se and thus can be instigated by members of the best class. In additional runs, noise is added to reduce the correlation between fitness and recombination. Each individual's fitness is mapped to an indicator variable (a 0/1 random variate) such that the correlation coefficient between it and an individual's fitness is
-0.01. Individuals need both the correct state of the variate and the allele to instigate recombination.
Because of the low mean number of mutations per individual (
0.55), recombination is modeled as free recombination. We did additional simulations with the number of chiasma as a Poisson random variate. As expected, one could demonstrate a decrease in the strength of selection on driving the recombination allele to fixation as the mean number of chiasma (
) approached 0 (for
< 1, data not shown), but the qualitative results are the same as those reported here.
In all treatments, the invading allele acts dominantly such that only one individual of a conjugating pair needs the allele for recombination to proceed. For controls, the computer also monitors an invading neutral allele. We ran three controls: (1) an invading recombination allele (but recombination is unconditional); (2) a neutral allele in a strictly asexual population; and (3) a neutral allele in a population already fixed for recombination. To most efficiently measure the realized strength of selection on the invading allele, the allele is introduced at a frequency of 0.5 and monitored for 1000 generations.
| RESULTS |
|---|
Fig 2 shows that in all treatment cases, the invading recombination allele sweeps rapidly toward fixation, converting the populations from asexual to sexual. The strength of selection is estimated from the deterministic prediction that
pf0.5(
) = 1000 generations implies s =
, where pf is the final frequency. Accordingly, the estimated strengths of selection are 1.2 x 10-3 ± 2.8 x 10-4 SD (P = 1.5 x 10-7), 1.1 x 10-3 ± 3.3 x 10-4 SD (P = 1.3 x 10-6), and 3.3 x 10-4 ± 1.6 x 10-4 SD (P = 1.1 x 10-4) for the mutational induction, fitness correlation, and fitness correlation with noise runs, respectively. P values are two-tailed Behrens-Fisher probabilities for deviations from 0. No control runs differed significantly from 0 or each other.
|
When we modify the mutation-induction runs such that recombination is randomly induced on only 10% of mutations entering at the net deleterious rate, the allele still spreads. [After 10,000 generations, 10 out of 10 runs had frequencies >0.5 with 1 run reaching fixation. Of the 9 still segregating, mean frequency was 0.780 ± 0.136 SD (P = 2.5 x 10-4); not shown in Fig 2.]
Since there is no linkage disequilibrium in the populations before the introduction of the alleles, there is no change in the standard population-wide measures and there is no significant difference in either mean fitness or the coefficient of variation in fitness between any combination of treatments and controls (P > 0.05). We did additional simulations with alleles at high frequency to verify that mean fitness remained time invariant.
| DISCUSSION |
|---|
The allele modeled above purposefully does not "repair" mutations, and thus its advantage is not explained by an alteration of the segregating load; it merely recombines out of inferior haplotypes as they tend to become mutated. This makes its mechanism of spread distinct from, yet not antagonistic to, traditional repair/recombination hypotheses (![]()
![]()
We modeled these simulations in terms of the induction of recombination, yet the process can be equivalently viewed as the suppression of recombination by the best haplotypes. All genes on the best haplotypesincluding the recombination allele itselfbenefit by a coordinated induction/suppression rule as this is in the best interest of all linked alleles. ![]()
The simulations that negatively correlate recombination and fitness show that the mutation-recombination link is only a special case of a more general relationship. For example, we could have modeled a basal probability of recombination for all cells, with more mutated cells more likely to recombine. Any factor sufficiently increasing recombination with decreasing fitness will bias the probability of fixation for a background-sensitive recombination allele. The numerically small variance in fitness in these simulations (
2w = e-2µ[eµs - 1] = 6.75 x 10-5) means that conditional induction and suppression cues can capitalize on subtle differences in fitness to produce a marked qualitative result.
Evolutionarily, the reliance on induction cues, while important, is a weak requirement. For recombination to spread, the haplotype need only (imperfectly) decide if it is likely to be the best or not the best. We assume this is never available per se, and thus the mutation-induction model is a hypothesis of how haplotypes could achieve this independent of any direct knowledge. But as µ increases, it becomes exponentially more likely that haplotypes will make the right decision by recombining regardless of the state of their genomes. The relationship is exponential because when stable, the relative size of the best class is e
(1 - e
)-1 (![]()
falls below unity (![]()
![]()
In all of the above cases, the allele spreads because it alters its probability of fixation (Table 1) by biasing the alteration of its genetic background. This generates positive linkage disequilibrium between the allele and its background, though not among fitness-related loci. At first, this absence of linkage disequilibrium among fitness-related loci may seem somewhat disquieting when extended as an explanation for the ubiquity of recombination. Our best evidence so far is that haploid genome-wide mutation rates of single-celled eukaryotes are on the order of 0.0034 (![]()
![]()
That gene assortment is actively maintained is supported by molecular examinations in yeast. The yeast Saccharomyces cerevisiae create DSBs before meiosis in a strikingly nonrandom manner: 89% of DSBs on chromosome III are intergenic, and these DSBs correspond well with sites of crossing over (![]()
![]()
![]()
![]()
< 1, the subsequent generation of negative linkage disequilibrium yields an unconditional advantage to recombination across the genome (![]()
The evolution of meiosis:
Fig 3 shows how the spread of a recombination allele as modeled in these simulations immediately generates a model of meiosis; i.e., the conversion of intracellular recombination to intercellular recombination can be considered the creative step in meiotic evolution (see also ![]()
![]()
|
Part of the difficulty in understanding meiosis has been that hypotheses have had to first advocate advantages to diploidy and have then needed to explain the subsequent and repetitive return of cells to haploidy (![]()
Fig 3 addresses two simple yet common questions: (1) In meiosis, why does the cell double its DNA only to cut it in half twice again, and (2) how could a process as complicated as meiosisone involving dozens to hundreds of genesever evolve? The hypothesis implied here is that meiosis has only become a gametogenic process, but it did not evolve that way. The duplication of DNA is inherently mutagenic, as is the correction of lesions prior to replication (![]()
![]()
We have long known that background trapping affects the rate of adaptation between asexual and sexual populations (![]()
| ACKNOWLEDGMENTS |
|---|
We warmly thank two anonymous reviewers, especially a reviewer who kindly directed our attention to supporting articles in the literature, some of which are cited herein.
Manuscript received September 1, 1999; Accepted for publication May 26, 2000.
| LITERATURE CITED |
|---|
BARTON, N. H., 1995 A general model for the evolution of recombination. Genet. Res. 65:123-144[Medline].
BAUDAT, F. and A. NICOLAS, 1997 Clustering of meiotic double-strand breaks on yeast chromosome III. Proc. Natl. Acad. Sci. USA 94:5213-5218
BERNSTEIN, H., H. C. BYERLY, F. A. HOPF, and R. E. MICHOD, 1985 Genetic damage, mutation, and the evolution of sex. Science 229:1277-1281
BIRKY, C. W., JR. and J. B. WALSH, 1988 Effects of linkage on rates of molecular evolution. Proc. Natl. Acad. Sci. USA 85:6414-6418
CALSOU, P. and B. SALLES, 1991 Heat-inducible reactivation of UV-damaged bacteriophage
. Mol. Gen. Genet. 226:113-119[Medline].
CHARLESWORTH, B., 1990 Mutation-selection balance and the evolutionary advantage of sex and recombination. Genet. Res. 55:199-221[Medline].
COX, M. M., 1997 Recombinational crossroads: eukaryotic enzymes and the limits of bacterial precedents. Proc. Natl. Acad. Sci. USA 94:11764-11766
DE MASSY, B., F. BAUDAT, and A. NICOLAS, 1994 Initiation of recombination in Saccharomyces cerevisiae haploid meiosis. Proc. Natl. Acad. Sci. USA 91:11929-11933
DERNBURG, A. F., K. MCDONALD, G. MOULDER, R. BARSTEAD, and M. DRESSER et al., 1998 Meiotic recombination in C. elegans initiates by a conserved mechanism and is dispensable for homologous chromosome synapsis. Cell 94:387-398[Medline].
DRAKE, J. W., B. CHARLESWORTH, D. CHARLESWORTH, and J. F. CROW, 1998 Rates of spontaneous mutation. Genetics 148:1667-1686
ECKARDT-SCHUPP, F. and C. KLAUS, 1999 Radiation inducible DNA repair processes in eukaryotes. Biochimie 81:161-171[Medline].
FABRE, F. and H. ROMAN, 1977 Genetic evidence for inducibility of recombination competence in yeast. Proc. Natl. Acad. Sci. USA 74:1667-1671
FELSENSTEIN, J., 1965 The effect of linkage on directional selection. Genetics 52:349-363
FISHER, R. A., 1930 The Genetical Theory of Natural Selection, pp. 121123. Clarendon Press, Oxford.
FRIEDBERG, E. C., G. C. WALKER and W. SIEDE, 1995 DNA Repair and Mutagenesis, pp. 453455. ASM Press, Washington, DC.
GESSLER, D. D. G., 1995 The constraints of finite size in asexual populations and the rate of the ratchet. Genet. Res. 66:241-253.
GESSLER, D. D. G. and S. XU, 1999 On the evolution of recombination and meiosis. Genet. Res. 73:119-131[Medline].
GILBERTSON, L. A. and F. W. STAHL, 1994 Initiation of meiotic recombination is independent of interhomologue interactions. Proc. Natl. Acad. Sci. USA 91:11934-11937
GILLESPIE, J. H., 1991 The Causes of Molecular Evolution, pp. 262266. Oxford University Press, New York.
GOLUB, E. I. and K. B. LOW, 1983 Indirect stimulation of genetic recombination. Proc. Natl. Acad. Sci. USA 80:1401-1405
GUPTA, R. C. and W. K. LUTZ, 1999 Background DNA damage from endogenous and unavoidable exogenous carcinogens: a basis for spontaneous cancer incidence? Mutat. Res. 424:1-8[Medline].
HAAF, T., E. I. GOLUB, G. REDDY, C. M. RADDING, and D. C. WARD, 1995 Nuclear foci of mammalian Rad51 recombination protein in somatic cells after DNA damage and its localization in synaptonemal complexes. Proc. Natl. Acad. Sci. USA 92:2298-2302
HAIGH, J., 1978 The accumulation of deleterious genes in a populationMuller's ratchet. Theor. Popul. Biol. 14:251-267[Medline].
HOLBECK, S. L. and J. N. STRATHERN, 1997 A role for REV3 in mutagenesis during double-strand-break repair in Saccharomyces cerevisiae.. Genetics 147:1017-1024[Abstract].
KANAAR, R., J. H. HOEIJMAKERS, and D. C. VAN GENT, 1998 Molecular mechanisms of DNA double strand break repair. Trends Cell Biol. 8:483-489[Medline].
KIMURA, M. and T. MARUYAMA, 1966 The mutational load with epistatic gene interactions in fitness. Genetics 54:1337-1351
KONDRASHOV, A. S., 1982 Selection against harmful mutations in large sexual and asexual populations. Genet. Res. 40:325-332[Medline].
KUZMINOV, A., 1999 Recombinational repair of DNA damage in Escherichia coli and bacteriophage
. Microbiol. Mol. Biol. Rev. 63:751-813
LIANG, F., M. HAN, P. J. ROMANIENKO, and M. JASIN, 1998 Homology-directed repair is a major double-strand break repair pathway in mammalian cells. Proc. Natl. Acad. Sci. USA 95:5172-5177
LICHTEN, M. and A. S. H. GOLDMAN, 1995 Meiotic recombination hotspots. Annu. Rev. Genet. 29:423-444[Medline].
LYNCH, M., J. CONERY, and R. BÜRGER, 1995 Mutation accumulation and the extinction of small populations. Am. Nat. 146:489-518.
LYNCH, M., J. BLANCHARD, D. HOULE, T. KIBOTA, and S. SCHULTZ et al., 1999 Perspective: spontaneous deleterious mutation. Evolution 53:645-663.
MAYNARD-SMITH, J., 1968 Evolution in sexual and asexual populations. Am. Nat. 102:469-473.
MAYNARD-SMITH, J., 1978 The Evolution of Sex. Cambridge University Press, Cambridge, UK.
NICOLAS, A., 1998 Relationship between transcription and initiation of meiotic recombination: toward chromatin accessibility. Proc. Natl. Acad. Sci. USA 95:87-89
OHTA, T., 1977 Extension to the neutral mutation random drift hypothesis, pp. 148167 in Molecular Evolution and Polymorphism, edited by M. KIMURA. National Institutes of Genetics, Mishima, Japan.
PECK, J. R., 1994 A ruby in the rubbish: beneficial mutations, deleterious mutations and the evolution of sex. Genetics 137:597-606[Abstract].
RADERSCHALL, E., E. I. GOLUB, and T. HAAF, 1999 Nuclear foci of mammalian recombination proteins are located at single-stranded DNA regions formed after DNA damage. Proc. Natl. Acad. Sci. USA 96:1921-1926
REDFIELD, R. J., 1988 Evolution of bacterial transformation: is sex with dead cells ever better than no sex at all? Genetics 119:213-221
RESNICK, M. A., 1976 The repair of double-strand breaks in DNA: a model involving recombination. J. Theor. Biol. 59:97-106[Medline].
RUVINSKY, A., 1997 Sex, meiosis and multicellularity. Acta Biotheoretica 45:127-141[Medline].
SHINOHARA, A. and T. OGAWA, 1995 Homologous recombination and the roles of double-strand breaks. Trends Biochem. Sci. 20:387-391[Medline].
SONODA, E., M. S. SASAKI, J. M. BUERSTEDDE, O. BEZZUBOVA, and A. SHINOHARA et al., 1998 Rad51-deficient vertebrate cells accumulate chromosomal breaks prior to cell death. EMBO J. 17:598-608[Medline].
STAHL, F., 1996 Meiotic recombination in yeast: coronation of the double-strand-break repair model. Cell 87:965-968[Medline].
STRATHERN, J. N., B. K. SHAFER, and C. B. MCGILL, 1995 DNA synthesis errors associated with double-strand-break repair. Genetics 140:965-972[Abstract].
SZOSTAK, J. W., T. L. ORR-WEAVER, R. J. ROTHSTEIN, and F. W. STAHL, 1983 The double-strand break repair model for recombination. Cell 33:25-35[Medline].
THACKER, J., 1999 Repair of ionizing radiation damage in mammalian cells: alternative pathways and their fidelity. C. R. Acad. Sci. III 322:103-108[Medline].
THALER, D. S., 1994 Sex is for sisters: intragenomic recombination and homology-dependent mutation as sources of evolutionary variation. Trends Ecol. Evol. 9:108-110.
THALER, D. S. and F. W. STAHL, 1988 DNA double-chain breaks in recombination of phage
and of yeast. Annu. Rev. Genet. 22:169-197[Medline].
VISPE, S., C. CAZAUX, C. LESCA, and M. DEFAIS, 1998 Overexpression of Rad51 protein stimulates homologous recombination and increases resistance of mammalian cells to ionizing radiation. Nucleic Acids Res. 26:2859-2864
WEIGLE, J. J., 1953 Induction of mutation in a bacterial virus. Proc. Natl. Acad. Sci. USA 39:628-636
WILLIAMS, G. C., 1975 Sex and Evolution, p. 28. Princeton University Press, Princeton, NJ.
WU, T. C. and M. LICHTEN, 1994 Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science 263:515-518
This article has been cited by other articles:
![]() |
L. Hadany and S. P. Otto The Evolution of Condition-Dependent Sex in the Face of High Costs Genetics, July 1, 2007; 176(3): 1713 - 1727. [Abstract] [Full Text] [PDF] |
||||
![]() |
A. F. Agrawal, L. Hadany, and S. P. Otto The Evolution of Plastic Recombination Genetics, October 1, 2005; 171(2): 803 - 812. [Abstract] [Full Text] [PDF] |
||||
![]() |
L. Hadany and T. Beker On the Evolutionary Advantage of Fitness-Associated Recombination Genetics, December 1, 2003; 165(4): 2167 - 2179. [Abstract] [Full Text] [PDF] |
||||
![]() |
D. M. Wloch, K. Szafraniec, R. H. Borts, and R. Korona Direct Estimate of the Mutation Rate and the Distribution of Fitness Effects in the Yeast Saccharomyces cerevisiae Genetics, October 1, 2001; 159(2): 441 - 452. [Abstract] [Full Text] [PDF] |
||||
- THIS ARTICLE
-
Abstract
- Full Text (PDF)
- Alert me when this article is cited
- Alert me if a correction is posted
- SERVICES
- Email this article to a friend
- Similar articles in this journal
- Similar articles in PubMed
- Alert me to new issues of the journal
- Download to citation manager
- Reprints & Permissions
- CITING ARTICLES
- Citing Articles via HighWire
- Citing Articles via Google Scholar
- GOOGLE SCHOLAR
- Articles by Gessler, D. D. G.
- Articles by Xu, S.
- Search for Related Content
- PUBMED
- PubMed Citation
- Articles by Gessler, D. D. G.
- Articles by Xu, S.



