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a Department of Ecology, Evolution, and Behavior, University of Minnesota, St. Paul
James W. Curtsinger, 100 Ecology, 1987 Upper Buford Circle, St. Paul, MN 55108 E-mail: jwcurt{at}tc.umn.edu.
Decision Editor: James R. Smith, PhD
| Abstract |
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QUANTITATIVE trait locus (QTL) mapping is a set of procedures for estimating the chromosomal locations of genes that contribute to variation in polygenic traits (1)(2). QTL mapping has been used to study many phenotypes in a variety of plant and animal species, often resulting in the detection of a small number of QTLs that, in combination, explain 2060% of the total phenotypic variance (2). These studies offer the hope that complex polygenic traits can be broken down into component genetic parts.
Experimental gerontologists have used QTL mapping to localize chromosomal regions responsible for variations in life span and related traits in Caenorhabditis elegans (3)(4)(5)(6), Drosophila melanogaster (7)(8)(9)(10)(11)(12)(13)(14), and Mus musculus (15)(16)(17)(18). A striking feature of life-span QTLs in flies and mice is the predominance of genetic effects that are limited to one sex. Nuzhdin and colleagues (7) detected five QTLs for life span in a set of recombinant inbred lines of D. melanogaster, four male specific and one female specific. Subsequent work on the same lines of flies reported three sex-specific QTLs out of six total (11) and 14 sex-specific QTLs out of 17 total (12). Miller and colleagues (16) reported genetic marker associations with life span among the progeny of a four-way cross between two F1 hybrid mouse stocks. Although none of the associations attained experimentwise levels of statistical significance, seven cases were suggestive, all sex specific. Subsequent work with the same population of mice has provided additional support for two life-span QTLs that do attain experimentwise levels of statistical significance, both sex specific (17). Taken as a whole, these observations support the novel and very interesting hypothesis that modification of life span frequently occurs by different cellular and genetic mechanisms in males and females.
Observations in my laboratory suggest that the detection of sex-limited QTLs is affected by the design of the mapping experiment. Curtsinger and colleagues (8) reported four autosomal life-span QTLs in a backcross population of D. melanogaster, two of which were specific to males and two of which were shared by the sexes. Subsequent work with the same genetic material in the same laboratory environment found life-span QTLs with genetic effects expressed in both sexes (14)(18). The first experiments were done on a small scale, with no replication of recombinant genotypes, whereas the later experiments were large, employing 56 recombinant inbred lines, over 1000 life-span measurements per line, and fivefold replication of life-span measurements. The difference between earlier and later results suggests that either the QTLs changed from sex specific to sex shared over a brief period of time, which seems very unlikely, or that the smaller and less powerful experiment gave only partial and misleading information about the properties of life-span QTLs.
One definition of statistical power is the probability that a test will reject the null hypothesis when it is false. In the context of QTL mapping, power is the probability of detecting a QTL when it is actually present. Many factors influence the power associated with a particular mapping experiment, including the magnitude of genetic effects, the density and distribution of marker loci, the breeding design, the number of recombinant genotypes studied, and the method of data analysis (2). The most powerful breeding designs involve replicated progeny genotypes, such as recombinant inbred lines. For such designs, power can depend on both the number of recombinant genotypes studied and on the number of individuals measured per line (19).
Here I consider the issue of statistical power in the context of conclusions about sex-specific QTLs. I show that the probability of detecting sex-specific QTLs is rather sensitive to sample size, and that even moderately large mapping experiments can frequently come to an erroneous conclusion regarding sex specificity. This argument is developed by randomly sampling data generated in a large experiment, and then asking how conclusions are affected by sample size. I also show that one method of data analysis increases the chances of detecting spurious sex-specific and sexually antagonistic effects.
| Sampling Experiments |
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Sampling experiments were executed as follows. For each fly in the original experiment there is a record of line, sex, and age at death. For each line and sex, flies were randomly sampled from the original data, without replacement, using the "RAN0" random number generator ((20), p. 195), which is essentially free of sequential correlations. Line means were computed for the sampled data separately for males and females, and then analyzed by interval mapping, using QTL Cartographer WinQTL version 1.2 (21)(22) with the Ri2 design, Kosambi map function, walking speed of 2 centimorgans (cM), and window size of 10 cM. QTL peaks were scored on the X chromosome and the left arm of chromosome 3 (in the interval between 15 and 45 cM from the left telomere) on the basis of likelihood ratios greater than 11.5. Normally, thresholds for statistical significance in QTL mapping are determined by permuting and reanalyzing the data 1000 times. However, because there are 3500 sampled data sets to analyze here, the full permutation analysis is not feasible, so an arbitrary, conservative value was chosen. The sampling procedure was repeated for sample sizes 5, 10, 25, 50, 100, 200, and 300 flies per sex and genotype, with 500 replications per sample size.
Results of the sampling experiments are shown in Fig. 1. Power curves are smoothed by distance-weighted least squares (23) to clarify trends. Power to detect the life-span QTL on the left arm of chromosome 3 is clearly sensitive to sample size, particularly below 100 animals per sex and genotype (11,600 animals total per experiment). From the estimated power curves it is possible to calculate the probability of executing an experiment in which the QTL is observed in one sex but not the other. If the probability of detecting a particular QTL in males when it is actually present is µ, and the probability of detecting it in females, given that it is present, is
, then the probability of detecting the QTL in just one sex is µ(1 -
) +
(1 - µ). The error rate calculated from estimates of µ and
is shown in Fig. 1. It is nearly 60% for very small sample sizes, declines to 20% at sample sizes of 100 individuals for each sex and genotype, and reaches the 5% level at approximately 200 flies per sex and genotype. For extremely low sample size, fewer than 10 animals per sex and genotype, the error rate is very low (not shown), but the "accuracy" of such experiments is entirely illusory, arising from the low probability of detecting the QTL in either sex.
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| Interval Mapping and Composite Interval Mapping |
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Although the CIM method is a significant advance in QTL methodology, there are unresolved problems in choosing the covariates. With too few covariates, CIM gives the same results as IM. With too many covariates, the results of CIM can become meaningless. Because it is not clear how the covariates should be chosen, CIM has been somewhat controversial. For example, Lynch and Walsh (2) support the method, but Broman (28) specifically recommends against its use.
All recent Drosophila experiments that report high levels of sex-specific life-span QTLs use CIM. This raises the possibility that the unresolved covariate problem might be influencing the interpretation of life-span QTL data. Nuzhdin and colleagues (7) were aware of this potential problem, which they addressed by comparing results obtained by CIM with regression of phenotypes on marker genotypes, a procedure that is very similar to IM when the marker map is dense. They found fairly good correspondence of results under the two methods. Subsequent studies with the same lines have addressed the possible biases of CIM by using additional, independent analyses for QTL mapping, including analyses of variance.
In order to further investigate the covariate problem, the data of Khazaeli and colleagues (unpublished data, 2002) have been reanalyzed by using both IM and CIM. IM was implemented as already described. CIM was implemented by using QTL Cartographer WinQTL version 1.2 (21)(22) with the Ri2 design, Kosambi map function, walking speed of 2 cM, forward regression, and a window size of 10 cM. CIM was executed with 5, 10, and 15 background covariates, spanning and exceeding the range normally reported in the literature. For each 2-cM segment of the genome, the additive effect on life span was estimated in both males and females, using both IM and CIM methods with all three levels of covariates. This procedure was repeated for five independent replicates of the mapping experiment, generating a total of 770 estimates of additive genetic effect in each sex by each method of data analysis.
Results of the different methods of data analysis are shown in Fig. 2, where additive effects in males are plotted against additive effects in females for each chromosomal segment. The IM method produces estimates that lie predominately in the upper right and lower left quadrants of Fig. 2, indicating similar genetic effects in males and females. There are three exceptional points in the lower right quadrant, suggesting a small degree of sex specificity. CIM with five covariates also produces estimates that are predominately positively correlated in males and females (Fig. 2), but more points lie in the lower right quadrant and along the axes far from the origin, suggesting a greater degree of sex-specific and sexually antagonistic genetic effects. CIM with 10 or 15 covariates (Fig. 2 and Fig. 2) produces many points in the lower right quadrant and many points along the y axis, suggesting a high degree of sex specificity and sexual antagonism. As the number of covariates increases from zero (equivalent to IM) to 5, 10, and then 15, the correlation of genetic effects across the sexes declines from 0.80 to 0.48, and the variance of estimated differences between male and female effects for each chromosomal segment increases more than threefold. Clearly, the degree of sex specificity detected by CIM is dependent on the number of covariates used in the analysis.
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| General Considerations and Conclusions |
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, and the probability of erroneously concluding that there is a sex-specific QTL when it is actually present in both sexes is µ(1 -
) +
(1 - µ). The three-dimensional error surface, which shows the error rate as a function of µ and
, is saddle shaped (Fig. 3). There is a saddle point at (0.5, 0.5) on the µ,
plane. That point is a local maximum along the main diagonal, running from (0, 0) to (1)(1), and is a local minimum along the off-diagonal, from (0, 1) to (1, 0). If statistical power were similar in the two sexes, then a weak experiment with a power of 50% in each sex would produce a 50% error rate. A moderately powerful experiment, one with 80% power in each sex, would have a 32% error rate; 95% power in each sex would produce a 9.5% error rate. The situation becomes worse when power varies inversely in the sexes, as could arise in situations in which the variance in one sex is larger than the other; then the 50% error rate at the saddle point is a minimum.
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There is no reason to think that these arguments apply only to Drosophila. Broman (28) discusses a backcross design appropriate for mice, and notes that with total sample sizes of 100200 animals, and a phenotypic standard deviation of 11.5 units, power varies from 97% for QTLs of large effect (11 units) to 2% for QTLs of small effect (5 units). Clearly, the magnitude of genetic effect of a particular QTL, which is beyond the control of the experimenter, can have dramatic effects on power. This fact, plus logistical limitations on the size of mapping experiments, is likely to make the detection of sex-limited QTLs in rodents exceptionally difficult, unless QTLs with large effect are discovered.
QTL mapping experiments of moderate or less statistical power can be misleading in several ways. It is well known that even very weak mapping experiments have a high probability of detecting at least one QTL if many are present, and that the variance explained by detected QTLs is dramatically and systematically overestimated (2)(29). For an experimentalist it is comforting that the Type I error rate is low (when a QTL is detected by IM, it is very likely that one is actually present) but disconcerting that the Type II error rate is high (real QTLs are often undetected in one sex or the other). Altering the criteria for significance could help with the latter problem but also lead to an unwelcome increase in false positives. The only solution that I can see is replication: artifacts do not have a high probability of replicating. Because any mapping experiment might have appreciably less than 100% power, the only conclusive demonstration of sex-limited QTLs for life span or any other trait must come from replicated observations with the same genotypes studied in the same environment.
Replication will have its own special challenges. With recombinant inbred lines of Drosophila it is straightforward to replicate whole genomes, provided that one ignores recent spontaneous mutations. With the intercross and four-way cross designs used in mouse studies, exact replication of entire genomes at the level of individual experimental animals is not possible. In those cases it is necessary to define genotypes solely by marker loci, implicitly assuming that there is no effect of genetic background in unmarked regions of the genome. Both fly and mouse studies will be subject to microenvironmental differences between replicate experiments that are beyond the control of the experimenter, and the possibility of significant genotype by replicate interaction that obscures main effects. There is no clear consensus in the QTL literature about the magnitude of interaction that one might expect ((2), Table 15.6), but it is potentially large. Statistical power will also matter; if there are many QTLs, then small experiments will have a large chance of detecting some QTL, but they will have little chance of detecting the same QTL in replicated experiments. Considering all of these factors, it is clear that making replicated observations of a particular QTL and its gender-specific properties is potentially a daunting task, but is nevertheless one that can be accomplished, as demonstrated by Khazaeli and colleagues (unpublished data, 2002).
| Acknowledgments |
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I thank A. Galecki, R. Miller, and S. Nuzhdin for their critical comments.
Received May 24, 2002
Accepted August 13, 2002
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This article has been cited by other articles:
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S. N. Forbes, R. K. Valenzuela, P. Keim, and P. M. Service Quantitative Trait Loci Affecting Life Span in Replicated Populations of Drosophila melanogaster. I. Composite Interval Mapping Genetics, September 1, 2004; 168(1): 301 - 311. [Abstract] [Full Text] [PDF] |
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