Modes of Selection and Recombination Response in Drosophila melanogaster

Transcription

1 Journal of Heredity 2004:95(1):70 75 DOI: /jhered/esh016 ª 2004 The American Genetic Association Modes of Selection and Recombination Response in Drosophila melanogaster C. F. RODELL, M.R.SCHIPPER, AND D. K. KEENAN From the Department of Biology, College of St. Benedict/St. John s University, Collegeville, MN (Rodell), Tuff Cut Landscape, 115 Alabama St. SE, Lonsdale, MN (Schipper), and Department of Philosophy, Fairfield University, Fairfield, CT (Keenan). Address correspondence to Charles F. Rodell at the address above, or crodell@csbsju.edu. A selection experiment for sternopleural bristle number in Drosophila melanogaster was undertaken to analyze the correlated effects on recombination. Replicate lines were subjected to divergent directional selection and to stabilizing selection. Recombination rates for markers on chromosomes 2(dp-cn-bw) and 3 (se-ss-ro) were compared to those from a control. All lines responded as predicted for bristle number. Lines selected for both increased and decreased bristle number exhibited significantly increased recombination rates. The predicted recombination response from stabilizing selection is suggested by our data, but only one comparison is statistically significant. These results, taken with other studies, support the proposal that genetic recombination enhances individual fitness when populations are experiencing environmental change. Less conclusively, our results suggest that populations undergoing stabilizing selection may respond by reducing their rates of crossing over. Three types of data suggest that observed recombination rates are the result of natural selection. First, genetic control for both increased and decreased crossover rates between nonsister chromatids has been demonstrated by selection in laboratory populations of Drosophila melanogaster (Chinnici 1971; Kidwell 1972). Second, there is significant genetic variation for genes influencing recombination rates in natural populations of D. melanogaster (Brooks and Marks 1986). Finally, recombination rates in D. melanogaster can change as a correlated response to selection for other characters (Flexon and Rodell 1982; Korol and Iliadi 1994; Sismanidis 1942; Zhuchenko et al. 1985). These latter studies, which monitor the correlation between recombination rates and the selected character, illustrate that selection favoring individuals lying near the extremes of a phenotypic distribution causes a corresponding increase in the rate of recombination. Apparently alleles that enhance rates of crossing over generate more variation of the character under selection. Thus the response to directional selection, regardless of the direction, brings with it high recombination rate alleles. Conversely then, if this is the case, alleles that lower recombination rates should produce a greater proportion of offspring near the mean expression in the population. As a result, stabilizing selection should decrease recombination rates. To our knowledge, this response has not been demonstrated. In this study we assess the recombination rate response to both divergent directional selection and stabilizing selection on a polygenic trait. The selected character is sternopleural bristle number in D. melanogaster. Bristle number is influenced by many genetic loci distributed throughout the genome (Jan and Jan 1994), is highly heritable with largely additive genetic variation (Mackay 1995), and lends itself to all modes of selection. Quantitative effects on bristle number have been attributed to regions of all three major chromosomes (X, 2, 3) by both conventional Drosophila chromosome methods (Shrimpton and Robertson 1988; Thoday and Boam 1959; Thoday et al. 1964) and quantitative trait loci (QTL) mapping (Gurganus et al. 1999; Lai et al. 1994; Lyman et al. 1999; Nuzhdin et al. 1998). Likewise, all three major chromosomes of D. melanogaster have genes that influence the recombination rate (Charlesworth and Charlesworth 1985). Thus D. melanogaster provides a useful model organism with which to test our predictions on recombination rate and the mode of selection. Materials and Methods We established several isofemale lines from D. melanogaster collected in central Minnesota (Stearns County). From these, 10 inseminated females from each of 19 isofemale lines were pooled to establish the initial source population. All the selection lines were derived from this source population. Selected Lines Selection was based on sternopleural bristle number. We isolated 50 virgin females and 50 virgin males from the source population, scored the bristle number, and selected two pairs to initiate each selection line. We established three types of selection lines with two replicates for each. The high 70

2 Brief Communications lines (designated H1 and H2) were initiated from the four flies of each sex with the highest bristle numbers, low lines (L1 and L2) from the four males and four females with the lowest bristle numbers, and the median lines (M1 and M2) from four pairs of flies having a median bristle number of 18. The high and low lines simulated directional selection and the median lines represented stabilizing selection. Throughout the experiment we maintained cultures at C. In addition to the selection lines, we cultured a control line under identical conditions except that each generation was initiated with approximately 10 pairs of adults chosen at random. Selection At approximately 2-week intervals, we isolated 20 virgin females and 20 virgin males from each selection line. From these flies we scored the bristle number and selected the appropriate two pairs to parent the next generation. Selected parents for H1 and H2 were those flies with the highest bristle numbers, L1 and L2 the lowest bristle numbers, and M1 and M2 those with 18 bristles, or as close to 18 as possible. Selection continued for 25 generations except for L2, which was lost after the 16th generation. Recombination We measured recombination rates on the second and third chromosomes using stocks homozygous for the following loosely linked recessive alleles: chromosome 2/dumpy (dp, 13.0) cinnabar (cn, 57.5) brown (bw, 104.5); chromosome 3/sepia (se, 26.0) spineless (ss, 58.5) rough (ro, 91.1). The numbers are the standard map positions (Lindsley and Grell 1968). At generations 15 and 25, we crossed 20 males from each line individually to virgin females from each of the marker stocks. We then backcrossed one F 1 female from each of these single-pair crosses to marker stock males and scored the testcross offspring for recombinant phenotypes. The data are expressed as a recombination index, representing the observed number of recombination events divided by the total number of possible recombination events. Because each chromosome has three markers, the recombination index is computed by dividing the number of recombination events among testcross offspring by twice the total number of offspring, as it is possible to observe a maximum of two events per individual. These results were compared among selection lines and to the control population. Because we used loosely linked markers, we can assume that multiple crossover events were common. Between any two markers we score a single recombinant for an odd number of crossovers, whereas an even number of crossovers restores the parental arrangement. The sum of the odds will be greater than the sum of the evens. While a higherresolution analysis would be possible had we employed more markers with tighter linkage, our objective is simply to compare relative recombination frequency between selected lines and the control. Results Divergent Directional Selection The results indicate that directional selection was successful at both increasing and decreasing sternopleural bristle numbers. The source population had a mean sternopleural bristle number of (mean 6 95% confidence interval [CI]) and a range of 14 to 23. Each line selected for increased bristle number exhibited a steady increase throughout the 25 generations of selection, achieving mean bristle numbers of and for H1 and H2, respectively. Analysis of variance (ANOVA) indicates that these values are significantly greater than the bristle number of the source population (F 2,127 ¼ 887.2; P,.0001). Selection for low bristle number initially resulted in an increase; for example, at generation 2, L1 had a mean of and L2 had a mean number of Bristle numbers in L1 fell below the source population mean of 17.4 by generation 5 and continued to decrease to a mean value of by generation 25, which is significantly less than that of the source population (t 88 ¼ 13.6; P,.0001). L2 numbers momentarily fell below the base population mean at generation 5, but then bristle numbers were above this mean for six of the next seven generations. By generation 13, L2 s mean decreased to , and from this point it decreased to a mean value of at generation 16. However, as early as generation 9, L2 was not as productive as the other lines and it was lost after generation 16. At generation 15, the means of L1 ( ) and L2 ( ) are significantly less than the mean bristle number of the base population (F 2,127 ¼ 55.8; P,.0001). These response patterns are similar to those of other bristle selection experiments (Barker and Cummins 1969; Barnes and Kearsey 1970; Thoday 1958). This character responds well to selection, and response to an increased number of bristles is greater than is selection for a reduction in number. An asymmetrical response is common and may result from a number of different factors, including directional dominance and differential fitness between individuals at the distribution extremes (Hedrick 2000). Barnes and Kearsey (1970) did detect a dominance effect of approximately 0.45 in the direction of low bristle number when they employed divergent directional selection. In this experiment, L1 and L2 were generally less hardy than the other selection lines, suggesting lower fitness among individuals expressing fewer bristles in their phenotypes. Stabilizing Selection After 25 generations of selecting parents with 18 sternopleural bristles in our stabilizing selection lines, the means of M1 and M2 are and , respectively. Effective stabilizing selection is expected to decrease the variation about the mean. Figure 1 illustrates the standard deviation of bristle number each generation for populations M1 and M2. For each population, the negative slope is significantly less than zero, indicating effective stabilizing selection. 71

3 Journal of Heredity 2004:95(1) Figure 1. The relationship between standard deviation of sternopleural bristle number as a result of stabilizing selection in populations median 1 ( y ¼ x; t 24 ¼ 3.84, P,.001 for H o :b yx ¼ 0) and median 2 ( y ¼ x; t 24 ¼ 7.81, P,.001 for H o :b yx ¼ 0). Recombination Recombination indices for chromosomes 2 and 3 are presented for the control and selected populations (generations 15 and 25) in Table 1. For each chromosome at each generation tested, pooled heterogeneity G tests indicate significant recombination index differences among populations. For each selected population, the recombination index is compared to that of the control population by a contingency test. The most dramatic recombination responses are observed in H1 and H2, the lines that exhibited the greatest response to bristle selection. H2 has a significant increase in recombination frequency for chromosome 2 at both generations 15 and 25, while H1 shows no significant change in recombination activity for this chromosome. For chromosome 3, H1 has marked increases in its recombination index at generations 15 and 25, and H2 shows a significant increase at generation 15. At generation 25, H2 has an elevated recombination index, which flirts with the conventional level of significance (v 2 ¼ 3.70, df ¼ 1; P ¼.054). These results indicate that selection for increased bristle number, a polygenic, morphological character, brought about a corresponding increase in recombination rates on chromosome 3 in both H1 an H2, and on chromosome 2 in H2. Recombination effects in the low lines are less pronounced. While L2, the poor-viability line, exhibited a significant reduction in bristle number by generation 15, it did not experience any change in its recombination index compared to the control population (chromosome 2, P..70; chromosome 3, P..80). At generation 15, L1 had a significantly greater recombination index relative to the control population for both chromosome 2 and 3. By generation 25, this comparison is not significant. The selective response to bristle number corresponds to the recombination index pattern. L1 s mean bristle number went from at generation 0 to by generation 15, to at generation 25. While the bristle number difference between generations 0 and 15 is statistically significant, the difference between generations 15 and 25 is not (t ¼ 1.80, df ¼ 78; P ¼.075). It would appear that recombination increased as long as directional selection was effective, but when the population could no longer respond to selection for fewer bristles, there was a corresponding reduction in recombination, reverting to a frequency indistinguishable from that of the control population. The differences between replicates possibly result from a founder effect. Each population was initiated with two pairs (a total of eight genomes) drawn from the source population. 72

4 Brief Communications Table 1. Chromosome 2 and 3 recombination indices for selected populations (L1, L2, M1, M2, H1, H2) and the control Chromosome Generation Control L1 L2 M1 M2 H1 H a * ** (1,016) (1,311) (1,050) (847) (921) (943) (1,128) 2 25 b * (688) (966) (922) (1,035) (1,094) (1,201) 3 15 c * * 0.304** 0.297* (712) (1,224) (1,165) (1,026) (1,217) (943) (1,040) 3 25 d ** (975) (1,089) (980) (844) (1,155) (1,308) Numbers in parentheses represent the number of testcross offspring scored. * Significantly different from control at P,.05 (2 3 2 contingency chi-square); ** P,.01. a Pooled heterogeneity G test, G H ¼ 10.86, P,.05. b Pooled G H ¼ 15.38, P,.01. c Pooled G H ¼ 30.56, P,.001. d Pooled G H ¼ 30.12, P,.001. As a result, H1 and H2 exhibited similar recombination responses for chromosome 3, but not for chromosome 2. L2 did not do nearly as well as L1 in either selection response or recombination activity. Our working hypothesis predicted that the recombination index would decrease as a result of stabilizing selection. While only one comparison (M2, chromosome 3, generation 15) is statistically significantly different from the control, seven of the eight comparisons of M1 and M2 to the control have a lower recombination index than the control value. This distribution, seven of eight, has a probability equal to 0.03 if values less than or greater than the control are equally likely. These results suggest a reduction in recombination activity as a result of stabilizing selection on bristle number, but they are less conclusive than the results for directional selection. Stabilizing selection s less dramatic response compared to directional selection may reflect the fact that natural selection acts on sternopleural bristle number in a stabilizing manner (Barnes 1968; Mackay 1995; Simpson et al. 1999; Thoday 1958). Hence the recombination rate influences on this character have been selected naturally for lower rates and, as a result, there may be less potential for reduced recombination rates than for enhanced rates. For those comparisons where the recombination response is significantly different from that of the control, it is worth noting the chromosome location. Chromosome 2 in the source population had a recombination frequency of between markers dp-cn, and between cn-bw, that is, 46.6% of the observed recombinant events occurred between the first two markers and 53.4% between the second two. Likewise for chromosome 3, the source population has a recombination frequency of (50.4%) between se-ss, and a frequency of (49.6%) between ss-ro. Among selected populations, chromosome 2 changes occurred most significantly between cn-bw, with this region comprising 56.2%, 58.1%, and 57.0% of the total recombinant events for L1 generation 15, H2 generation 15, and H2 generation 25, respectively. Within chromosome 3, the region between se-ss displays the greatest response in all cases. Recombination responses in this region increase to 52.0% (L1), 54.1% (H1), and 53.2% (H2) in generation 15, and 55.3% (H1) in generation 25. Population M2 shows a marked decrease in this same region, with recombination events accounting for 47.7% of the total. These results are consistent with the positions of major sternopleural bristle loci identified by mapping (e.g., Nuzhdin et al. 1998; Shrimpton and Robertson 1988). Discussion The present study has two objectives. First is to test whether the response to divergent directional selection, both increased and decreased expression of a polygenic character, will alter recombination frequency among the offspring of favored individuals. Evolutionary theory postulates that populations must be genetically variable in order to evolve. With directional selection, the capacity of a population to respond is in large part dependent on its ability to release its latent variability and expose it to selective action. The most immediate source of genetic variation is that generated by the process of recombination. Individuals with the highest rates of recombination should, on average, produce genetically more variable offspring. When selection favors the population extremes, favored individuals are more likely to have descended from high recombination-rate parents. This result has been demonstrated by selection in one direction for increased scutellar bristle number (Sismanidis 1942), increased sternopleural bristle number (Thoday et al. 1964), and increased DDT resistance (Flexon and Rodell 1982); for divergent directional selection on geotaxis (Korol and Iliadi 1994); and for temperature fluctuations (Zhuchenko et al. 1985). The present study further confirms these results by employing selection for both increased and decreased sternopleural bristle numbers. The results from divergent directional selection show that increased recombination does not require gametic disequilibrium between genes affecting recombination rate 73

5 Journal of Heredity 2004:95(1) and genes influencing the selected character in order for high recombination-rate alleles to increase in frequency (Felsenstein 1965; Hedrick 1982). Rather, these data, along with the other divergent directional selection study (Korol and Iliadi 1994), argue that high rates of recombination produce a disproportionately greater proportion of individuals at the population extremes, and the recombination response is not due simply to hitchhiking. Our second objective tests whether stabilizing selection results in a corresponding decrease in recombination rate. Given the above discussion, it follows that individuals with lower recombination rates should produce less variable offspring. Mather (1943) suggested that selection for an intermediate optimum will cause gametic disequilibrium in such a way as to reduce the amount of genetic variation, that is, reduce recombination. It follows that mean fitness in a constant environment will be greatest when recombination is absent (Charlesworth 1993). Stabilizing selection should select a disproportionately greater number of individuals whose parents have low recombination rates. Our results show a general decline in recombination activity resulting from stabilizing selection, but just one of the eight comparative tests proved statistically significant. It is generally agreed that understanding the evolutionary cause of recombination is key to explaining the prevalence of sexual reproduction (Bell 1982; Maynard Smith 1978; Williams 1975). A recent experiment employing D. melanogaster compares the fate of beneficial mutants in sexual and asexual populations (Rice and Chippendale 2001). Their results support the explanation that recombination is advantageous because it allows populations to adapt more rapidly by accumulating beneficial mutants and by reducing the accumulation of harmful mutants. The results reported here add to those studies supporting the general conclusion that recombination persists to enhance individual fitness in response to changing environmental conditions. In contrast, an analysis of second chromosomes from collections of D. melanogaster indicates a negative correlation between recombination frequency and fitness (Tucic et al. 1981). This latter study differs from those previously mentioned in that the subjects were not subjected to further selection pressure. While many studies addressing this question utilize D. melanogaster, data from other organisms add relevance. For example, higher chiasma frequencies are observed when selecting for increased body size in mice (Gorlov et al. 1992). With yeast, increased sporulation rates are found in populations subjected to highly variable environments (Wolf et al. 1987). A survey of chiasma frequencies among 21 mammalian species suggests that recombination is necessary to keep pace with changing biotic relationships (Burt and Bell 1987). As in D. melanogaster, these studies support the contention that recombination rate is positively correlated to individual fitness when populations are subjected to selection. The extent, then, to which Mendelian populations respond to changing environmental conditions influences the rates of genetic recombination through crossing over. Recent studies support the interpretation that selection is a common force shaping patterns of variability in natural populations of Drosophila (Andolfatto and Przeworski 2000, 2001). Further, it appears as though biotic factors are of prime selective importance (Fay et al. 2002). Biotic interactions, coevolutionary forces, are likely to be persistent and directional, maintaining an advantage to recombination (Levin 1975). Additional studies on a wider range of organisms and on stabilizing selection s influence on crossing over should further enhance our understanding of genetic recombination and evolution. References Andolfatto P and Przeworski M, A genome-wide departure from the standard neutral model in natural populations of Drosophila. Genetics 156: Andolfatto P and Przeworski M, Regions of lower crossing over harbor more rare variants in African populations of Drosophila melanogaster. Genetics 158: Barker JSF and Cummins LJ, Disruptive selection for sternopleural bristle number in Drosophila melanogaster. Genetics 61: Barnes BW, Stabilising selection in Drosophila melanogaster. Heredity 23: Barnes BW and Kearsey MJ, Variation for metrical characters in Drosophila populations I. Genetic analysis. Heredity 25:1 10. Bell G, The masterpiece of nature: the evolution and genetics of sexuality. Berkeley: University of California Press. Brooks LD and Marks RW, The organization of genetic variation for recombination in Drosophila melanogaster. Genetics 114: Burt A and Bell G, Mammalian chiasma frequencies as a test of two theories of recombination. Nature 326: Charlesworth B, The evolution of sex and recombination in a varying environment. J Hered 84: Charlesworth B and Charlesworth D, Genetic variation in recombination in Drosophila. II. Genetic analysis of a high recombination stock. Heredity 54: Chinnici JP, Modification of recombination frequency in Drosophila. I. Selection for increased and decreased crossing over. Genetics 69: Fay JC, Wyckoff GJ, and Wu C-I, Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415: Felsenstein J, The effects of linkage on directional selection. Genetics 52: Flexon PB and Rodell CF, Genetic recombination and directional selection for DDT resistance in Drosophila melanogaster. Nature 298: Gorlov I, Schuler L, Bunger L, and Borodin P, Chiasma frequency in strains of mice selected for litter size and for birth weight. Theor Appl Genet 84: Gurganus MC, Nuzhdin SV, Leips JW, and Mackay TFC, Highresolution mapping of quantitative trait loci for sternopleural bristle number in Drosophila melanogaster. Genetics 152: Hedrick PW, Genetic hitchhiking: a new factor in evolution? BioScience 32: Hedrick PW, Genetics of populations, 2nd ed. Sudbury, MA: Jones and Bartlett. Jan YN and Jan LY, Genetic control of cell fate specification in Drosophila peripheral nervous system. Annu Rev Genet 28: Kidwell MG, Genetic change of recombination value in Drosophila melanogaster. I. Artificial selection for high and low recombination and some properties of recombination modifying genes. Genetics 70:

6 Brief Communications Korol AB and Iliadi KG, Increased recombination frequencies resulting from directional selection for geotaxis in Drosophila. Heredity 72: Lai C, Lyman RF, Long AD, Langley CH, and Mackay TFC, Naturally occurring variation in bristle number and DNA polymorphisms at the scabrous locus of Drosophila melanogaster. Science 266: Levin DA, Pest pressure and recombination systems in plants. Am Nat 109: Lindsley DL and Grell EH, Genetic variations of Drosophila melanogaster. Publication no. 627 Washington, DC: Carnegie Institution of Washington. Lyman RF, Lai C, and Mackay TFC, Linkage disequilibrium mapping of molecular polymorphisms at the scabrous locus associated with naturally occurring variation in bristle number in Drosophila melanogaster. Genet Res 74: Mackay TFC, The genetic basis of quantitative variation: numbers of sensory bristles of Drosophila melanogaster as a model system. Trends Genet 11: Mather K, Polygenic inheritance and natural selection. Biol Rev 18: Maynard Smith J, The evolution of sex. Cambridge: Cambridge University Press. Nuzhdin SV, Keightley PD, Pasyukova EG, and Morozova EA, Mapping quantitative trait loci affecting sternopleural bristle number in Drosophila melanogaster using changes of marker allele frequencies in divergently selected lines. Genet Res 72: Rice WR and Chippindale AK, Sexual recombination and the power of natural selection. Science 294: Shrimpton AE and Robertson A, The isolation of polygenic factors controlling bristle score in Drosophila melanogaster. I. Allocation of third chromosome sternopleural bristle effects to chromosome sections. Genetics 118: Simpson P, Woehl R, and Usui K, The development and evolution of bristle patterns in Diptera. Development 126: Sismanidis A, Selection for an almost invariable character in Drosophila. J Genet 44: Thoday JM, Homeostasis in a selection experiment. Heredity 12: Thoday JM and Boam TB, Effects of disruptive selection. II. Polymorphism and divergence without isolation. Heredity 13: Thoday JM, Gibson JB, and Spickett SG, Regular responses to selection. 2. Recombination and accelerated response. Genet Res 5: Tucic N, Ayala FJ, and Marinkovic D, Correlation between recombination frequency and fitness in Drosophila melanogaster. Genetica 56: Williams GC, Sex and evolution. Princeton, NJ: Princeton University Press. Wolf HG, Wohrmann K, and Tomiuk J, Experimental evidence for the adaptive value of sexual reproduction. Genetica 72: Zhuchenko AA, Korol AB, and Kovtyukh LP, Change in the crossing-over frequency in Drosophila during selection for resistance to temperature fluctuations. Genetica 67: Received April 2, 2003 Accepted September 1, 2003 Corresponding Editor: Rob DeSalle 75