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Inbreeding Changes the Shape of the Genetic Covariance Matrix in Drosophila melanogaster
Patrick C. Phillipsa, Michael C. Whitlockb, and Kevin Fowlerca Program in Ecology and Evolution, Department of Biology, University of Oregon, Eugene, Oregon 97403-1210,
b Department of Zoology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada and
c Department of Biology, University College, London NW1 2HE, United Kingdom
Corresponding author: Patrick C. Phillips, Program in Ecology and Evolution, Department of Biology, University of Oregon, Eugene, OR 97403-1210., pphil{at}darkwing.uoregon.edu (E-mail)
Communicating editor: Z-B. ZENG
| ABSTRACT |
|---|
The pattern of genetic covariation among traits (the G matrix) plays a central role in determining the pattern of evolutionary change from both natural selection and random genetic drift. Here we measure the effect of genetic drift on the shape of the G matrix using a large data set on the inheritance of wing characteristics in Drosophila melanogaster. Fifty-two inbred lines with a total of 4680 parent-offspring families were generated by one generation of brother-sister mating and compared to an outbred control population of 1945 families. In keeping with the theoretical expectation for a correlated set of additively determined traits, the average G matrix of the inbred lines remained proportional to the outbred control G matrix with a proportionality constant approximately equal to (1 - F), where F is the inbreeding coefficient. Further, the pattern of covariance among the means of the inbred lines induced by inbreeding was also proportional to the within-line G matrix of the control population with a constant very close to the expectation of 2F. Although the average G of the inbred lines did not show change in overall structure relative to the outbred controls, separate analysis revealed a great deal of variation among inbred lines around this expectation, including changes in the sign of genetic correlations. Since any given line can be quite different from the outbred control, it is likely that in nature unreplicated drift will lead to changes in the G matrix. Thus, the shape of G is malleable under genetic drift, and the evolutionary response of any particular population is likely to depend on the specifics of its evolutionary history.
THE short-term response to both artificial and natural selection is influenced primarily by two factors: the amount of genetic variation for a trait and the strength of selection on that trait (![]()
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This theoretical result, however, refers only to the average changes in G that result from drift. Currently there are no theoretical predictions about the distribution of changes in the G matrix caused by drift. It is well known that the additive genetic variances (the diagonal elements of G) change on average in predictable ways, but the distribution of such changes can be quite broad (![]()
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The expectation of overall proportional change in the elements of G is a change in matrix "size." Variation in the orientation of the covariances among the traits, or element-specific changes, can then be referred to as changes in matrix "shape." Matrix shape is frequently described using the principal component or eigen structure of the matrix (![]()
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Various lines of empirical evidence suggest that the G matrix is not constant, but how much does it change over time? For example, ![]()
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In addition to causing an average reduction in genetic variance within populations, genetic drift also tends to increase the genetic variance among populations. Under a strictly additive model of genetic variation, the amount of genetic variance among populations is expected to be 2F times the genetic variance of the base population (![]()
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In a large study of the changes in variance due to population bottlenecks in Drosophila melanogaster, we found that on average the additive genetic variance within lines for a set of six wing characters declined quantitatively as expected by the additive theory. However, changes in genetic variance varied considerably among the lines (![]()
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In this article we investigate the changes in genetic and environmental covariance matrices that may result from the inbreeding during a population bottleneck. We use a recent innovation in matrix comparison that allows simultaneous investigation of the changes in both the size and shape of these matrices (![]()
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| MATERIALS AND METHODS |
|---|
Strains and derivation of inbred lines:
The stocks, culture maintenance, and measurement procedures are described in ![]()
3 months. At each time point two independent sets of
400 randomly mated pairs were used to form outbred control populations, totaling 1945 families over the six control lines. Over this same time period, 52 inbred lines were derived from the outbred base population via one generation of brother-sister mating, with
90 families per inbred line being analyzed (4680 total families in the inbred lines). For each control and inbred line family, the wings of eight daughters were mounted on microscope slides and measured using a digitizing tablet attached to a computer. Ten landmarks on each wing were determined and used to measure one size and five shape characters on the basis of the angles made by the intersection of the wing veins (Fig 1).
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Calculation of phenotypic, genetic, and environmental matrices:
Values for the outbred controls were normalized to their replicate mean before calculations. Before calculating the pooled estimates for the inbred lines, values for each line were normalized to the line mean to keep the among-line variance from biasing the average within-line estimates. The among-line variances and covariances were calculated from the line means after they had been normalized to the mean value of the control line in their batch to eliminate inclusion of any among-batch variance in these estimates.
Quantitative genetic parameters were estimated from the regression of the mean trait value of all measured offspring in a family on the midparent value. Additive genetic variances were estimated as twice the parent-offspring covariance (![]()
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Comparison of matrices:
Matrix comparisons were conducted using the approach outlined by ![]()
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Patterns of two-trait covariance were visualized by constructing 95% confidence ellipses of the bivariate variance-covariance matrix under the assumption of normality. Principal components of the matrix were calculated and used to orient the ellipse in the plane. Distance along each principal axis was calculated as 1.96 times the eigenvalue associated with that particular axis. These ellipses are useful for comparing the covariance patterns of two matrices (![]()
| RESULTS |
|---|
Patterns of genetic covariance:
The average G matrices for the control and inbred lines are shown in Table 1. In the control lines, phenotypic correlations varied from -0.44 to 0.54, while genetic correlations varied from -0.27 to 0.60. Environmental correlations tended to be smaller and more variable (Table 2). As was found in ![]()
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Comparison of inbred and outbred genetic covariance matrices:
First, let us consider the changes in the average (i.e., pooled) G matrix in the inbred lines. Using the randomization test of the Flury hierarchy, comparison of the outbred and pooled inbred matrices suggests a great deal of shared structure. In particular, the hypothesis of proportionality could not be ruled out (P = 0.1450) whereas equality was clearly rejected (P < 0.0001). As can be seen in Fig 2, the average G matrix is proportional to that of the outbred population. All of the genetic covariances maintained their relative orientation in multivariate space following genetic drift, with the entire matrix simply shrinking by a nearly constant proportion. Bootstrapping across families (![]()
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0.3 (![]()
0.7. The estimated value is not significantly different from this expectation. The change in average genetic covariance structure observed here is therefore consistent with the theoretical prediction of the change expected for drift of a set of correlated additive traits.
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Variance among inbred genetic covariance matrices:
Although, on average, genetic drift maintained proportionality between the outbred and bottlenecked G matrices, when one looks at the variation around this average, a very different picture emerges. Fig 3 highlights the covariance pattern estimated within the 52 inbred lines for one of the two-trait combinations. Although most matrices are seen to wobble around the expected orientation (as represented by the control population), some of the covariance patterns can be extremely divergent, with the genetic correlation occasionally even changing sign (see also ![]()
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Phenotypic and environmental covariance matrices:
The pooled environmental covariance matrices (E) of the inbred lines were somewhat less similar to the outbred controls than were the genetic covariance matrices (Table 2). The hypothesis of shared common principal components was not ruled out (P = 0.1948), the hypothesis of proportionality was marginally rejected (P = 0.0508), and equality was more clearly rejected (P = 0.0155). Although this analysis suggests that it is probably not the appropriate model, if the environmental covariance matrices are constrained to be proportional, their estimated proportionality constant is 1.10 ± 0.04. This indicates that the environmental covariance matrix increased slightly in overall variance. This increase in environmental variance is comparable to that found in ![]()
Interestingly, the similarities observed in the outbred and average inbred genetic and environmental covariance do not hold with the phenotypic covariance matrices (P). Here, the average inbred P matrices do not share more than one principal component in common with the controls (test of common principal component CPC[1], P = 0.2901; while for CPC[2], P = 0.0020). Since P is the sum of the G and E matrices, if each of these latter matrices is affected by drift in different ways, then P will necessarily be more divergent than the other matrices. As was found for the G matrices, when the inbred lines are compared to one another, there is no indication that any principal components are shared in common for either the P or E matrices (P < 0.0001).
Covariance among line means:
The among-line covariance matrix cannot be statistically compared to the within-line G matrix because they are sampled from different classes of covariance estimates (Table 3). The among-line covariances are estimated using a product-moment covariance among the population means, while the elements of the G matrix are estimated as the covariance components derived from the parent-offspring regression. These two types of covariances have very different sampling properties (![]()
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| DISCUSSION |
|---|
Genetic drift affects genetic variances and covariances, but in complex ways. With traits determined by additively interacting genetic effects, on average the additive genetic variance for each trait will decrease in proportion to the inbreeding coefficient of the population. ![]()
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These theoretical predictions are expectations, the mean over all possible outcomes. Any particular population need not be at this expectation; in fact, under certain circumstances the variance around the expectation can be very large (![]()
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Divergence among populations:
Drift has two separate but important consequences for the divergence of isolated populations. First, drift generates variance among the means of each population so that they each start at different points in phenotypic space. The results of this study are consistent with the theoretical expectations about the pattern of divergence among means by drift (![]()
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Second, drift causes idiosyncratic changes in the variance-covariance structure of particular populations. If similar patterns of directional selection were to act on all populations following isolation, the response to selection within some populations could be quite variable. For example, if selection were to act on just one trait (say wing size) in a uniform manner, the correlated response to selection on the other traits would follow the lines of divergence shown in the top row of Fig 4. Again, the expected change under selection will follow the path predicted by the average G, but individual populations could be evolving in very different wayseven in the opposite direction. Drift-induced variation in G, even with samples derived from the same base population, may explain variation in correlated responses to selection frequently observed in replicated selection experiments (reviewed in ![]()
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Under more complex patterns of selection, the consequences of drift in covariance structure become more complicated. If selection leads to the existence of two separate evolutionary equilibria (![]()
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Trait-specific variation in covariance structure:
The covariance between different traits is variable to different extents, and that variability is weakly correlated with the magnitude of the covariance in the outbred population. To some extent it takes initial covariance to generate divergence in covariance structure. However, it is possible for traits that are influenced by pleiotropic alleles to not display any genetic covariance (if, for instance, positive and negative effects balance one another; ![]()
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Long-term evolution of G:
Over longer periods of time, the structure of G will be determined by some combination of mutation, genetic drift, migration, and natural selection (![]()
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| ACKNOWLEDGMENTS |
|---|
Giselle Geddes, Jing Tu, and James Bayle provided excellent support in the laboratory, for which we are grateful. We thank Dolph Schluter, Jenny Boughman, Cort Griswold, Sally Otto, Art Poon, Howard Rundle, Steve Vamosi, and other members of the SOWD group at UBC for useful comments on the manuscript. An anonymous reviewer contributed strongly to the clarity of the presentation. This work was supported by the Natural Environment Research Council (United Kingdom), Natural Sciences and Engineering Research Council (Canada), the Royal Society, and the National Science Foundation (United States, grants BIR-9612469 and DBI-9722921).
Manuscript received November 1, 2000; Accepted for publication April 11, 2001.
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