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Genetic Components of Variation in Nemophila menziesii Undergoing Inbreeding: Morphology and Flowering Time
Ruth G. Shawa, Diane L. Byersa, and Frank H. Shawaa Department of Ecology, Evolution, and Behavior, University of Minnesota, Saint Paul, Minnesota 55108
Corresponding author: Ruth G. Shaw, Department of Ecology, Evolution and Behavior, University of Minnesota, 1987 Upper Buford Circle, 100 Ecology, Saint Paul, MN 55108., rshaw{at}superb.ecology.umn.edu (E-mail).
Communicating editor: M. K. UYENOYAMA
| ABSTRACT |
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The standard approaches to estimation of quantitative genetic parameters and prediction of response to selection on quantitative traits are based on theory derived for populations undergoing random mating. Many studies demonstrate, however, that mating systems in natural populations often involve inbreeding in various degrees (i.e., self matings and matings between relatives). Here we apply theory developed for estimating quantitative genetic parameters for partially inbreeding populations to a population of Nemophila menziesii recently obtained from nature and experimentally inbred. Two measures of overall plant size and two of floral size expressed highly significant inbreeding depression. Of three dominance components of phenotypic variance that are defined under partial inbreeding, one was found to contribute significantly to phenotypic variance in flower size and flowering time, while the remaining two components contributed only negligibly to variation in each of the five traits considered. Computer simulations investigating selection response under the more complete genetic model for populations undergoing mixed mating indicate that, for parameter values estimated in this study, selection response can be substantially slowed relative to predictions for a random mating population. Moreover, inbreeding depression alone does not generally account for the reduction in selection response.
WIDESPREAD interest in assessing the potential for response to either artificial or natural selection has motivated numerous studies of quantitative genetic variation within populations of plants and animals. These studies have generally employed experimental designs in which traits are measured on progeny ob-tained from controlled crosses, where parents are chosen and assigned mates at random (![]()
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Investigations of mating systems of numerous wild populations have, however, indicated that deviations from random mating are the rule and that inbreeding is common (reviewed in ![]()
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These findings of substantial rates of inbreeding in many taxa have motivated studies to assess consequences of inbreeding. Many of these focus on detecting and quantifying inbreeding depression, the rate of reduction in the mean value of a trait in a population relative to the increase in the degree of inbreeding. Inbreeding depression has long been recognized (e.g., ![]()
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The common finding of partial inbreeding in natural populations suggests that quantitative genetic predictions of R, the per-generation response to selection, may often be misleading when, as is typical, they use the breeder's equation,
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(1) |
These methods for partitioning genetic variation of quantitative traits in inbreeding populations paved the way for prediction of selection response with inbreeding, and interest in the interplay between selection and inbreeding has been growing over the past decade. ![]()
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Considering the converse effects of selection on rates of inbreeding, ![]()
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Despite these developments, little empirical work has taken advantage of theory addressing the effects of inbreeding on the structure of quantitative genetic variation and on response to selection. Two such studies concern domesticated populations (maize, ![]()
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| THEORY, MATERIALS AND METHODS |
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Theory:
Considering effects on a trait, y, measured in an individual bearing alleles i and j at a single segregating locus, we can use a general model to separate genetic effects from effects due to environmental conditions:

Here, ß is a column vector of fixed effects (most simply, having a single element, the overall mean, but more generally, including as additional elements effects of specified levels of factors potentially influencing the trait, for example, blocks or nutrient treatments), and X is a row vector, with elements of 1 to represent exposure of this individual to a given effect and 0 otherwise. Thus, Xß is a sum of fixed effects pertaining to the individual's observed phenotype y, including the overall mean and effects of specified environments. Genetic effects ai and dij are defined with reference to a random mating population; ai are additive effects of allele i, ai + aj is the breeding value, and dij is the dominance deviation for the interaction between the alleles i and j (i.e., the difference between the genotypic value and the breeding value for the genotype bearing the i and j alleles; ![]()
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In a random mating population, Hardy-Weinberg frequencies ensure that
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(2) |

of the additive and dominance genetic variances and the environmental or residual variance.
Compared to a random mating population, inbreeding increases the frequencies of homozygous genotypes, or more specifically, of autozygous genotypes, in which paris of homologous alleles are IBD. In this case, the expectation of the dominance deviations does not remain zero. The expected trait value E(y) of an individual inbred to degree F then includes inbreeding depression µF, i.e., the (nonzero) expectation of the autozygous dominance effects, expressed in inbreds,
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(3) |
Apart from its widely recognized effect on the population mean, inbreeding alters the population variance, in part because inbreeding destroys the simplifications given in Equation 2 and also because the variance of autozygous dominance deviations may differ from the variance of dominance deviations under random mating (VD, above). In the framework developed by ![]()
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- VDI = E(d2ii) - (E(dii))2, the total variance due to autozygous dominance effects. This is the dominance variance of a completely inbred population.
- H* = (E(dii))2, the squared per-locus inbreeding depression, summed over loci.
- Cov(a, dI) = E(aidii), the covariance between the additive effect of alleles and their autozygous dominance deviations.
Thus, the variance of autozygous dominance deviations can differ from that of "random" dominance deviations (i.e., dominance deviations attributable to allelic combinations that are not IBD). To emphasize this, we relabel VD, the dominance variance in a randomly mating population, to VDR. Using these definitions, the variance of individual phenotypes can be written as
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(4) |
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Study species:
N. menziessi is a self-compatible annual plant of the family Hydrophyllaceae. It is native to California and Oregon. ![]()
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Genetic design and trait assays:
Estimation of the components of genetic variance that arise with inbreeding requires observations on groups of individuals in which pairs can be predicted (from the pedigree) to share alleles in autozygous form (thus contributing information for VDI and H*) or with one individual autozygous and the other heterozygous [contributing information for Cov(a, dI); COCKERHAM and WEIR 1984]. On the basis of a simulation study (F. H. SHAW, unpublished results; see also ![]()
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To obtain parents for the initial crosses, seedlings were collected in January 1990 from an uncultivated area of the University of California at Riverside (UCR) Botanic Gardens. Seedlings were sampled at 2-m intervals along parallel transects 2 m apart to reduce the chance of sampling close relatives. These plants were grown to maturity in a greenhouse at UCR. A total of 52 plants chosen at random served as paternal parents (sires) and 156 as maternal parents (dams) in a nested crossing design (a distinct set of 3 dams crossed with each sire). The progeny of these crosses, termed generation 1, are considered the reference generation, with inbreeding coefficients (F) of zero [ ![]()
In January 1994, 40 of these 52 progeny groups (half-sibships, each comprising three full-sibships) were chosen at random as sources of parents in the next series of crosses; a distinct set of eight progeny groups was chosen at random for each of five crossing blocks (Figure 1). Within each block, five progeny groups were designated at random as sources of sires in further matings, while the remaining three progeny groups provided individuals to be used as dams. Individuals randomly chosen from these progeny groups were grown, and measures of petal length and width were obtained for each. Within each crossing block, plants were mated factorially, yielding progeny in generation 2 with F = 0 [a study based on these crosses is reported in ![]()
Assays of generation 2 and a further series of crosses were initiated in December 1994. Generation 2 was subsampled to establish 10 crossing blocks, 2 from each of the crossing blocks of the previous generation. In generation 2, each crossing block consisted of nine individuals descended from one pair of grandsires in the founding generation (Figure 1). This group was composed of three trios, each comprising a pair of full-sibs and a self-sib (maternal half-sib produced by selfing the maternal parent). These trios were chosen such that they had in common the maternal grandsire and also, in the case of the noninbred individuals, the sire. In addition, two plants within each trio (in Figure 1, plants 2 and 3, with F = 0 and F = 0.5, respectively) were each crossed to a randomly chosen plant that shared no ancestors in the known pedigree. Individuals chosen for the next series of crosses according to the above scheme, together with an additional five full-sibs of each, were grown and measured (see below). The crosses produced seeds with the following array of inbreeding coefficients: 0, 0.06, 0.25, 0.5, and 0.75. All crosses were carried out reciprocally. We refer to the offspring from this set of crosses as generation 3.
Assays of generation 3 and a further series of crosses were initiated in August 1995. Five plants from each set of progeny (e.g., AJ in Figure 1) were grown and measured. One individual from each full-sib group was selfed to produce progeny not considered further here.
Summarizing the available observations, petal length and width were measured on the 114 individuals representing generation 1, and five traits, date of first flower, size (height and number of nodes) at first flower, and petal length and width for the first opened flowers, were measured on 450 and 1226 individuals in generations 2 and 3, respectively. Single petals of each of 35 flowers were measured in millimeters with digital calipers. Height was measured with a meter rule in centimeters. Progeny from every level of inbreeding planned were measured, but not every lineage was represented fully according to the design given above, as a result of germination failure, mortality, or sterility (Table 2). To the extent that deviations from the intended design are due to selection, they are likely to bias estimates of inbreeding depression (i.e., indicating weaker inbreeding depression than the actual), but to have negligible influence on maximum likelihood estimates of the variance components, according to a simulation study of ![]()
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Analysis:
Restricted maximum likelihood (REML) was used to estimate the parameters of the full model (Equation 3 and Equation 4) of trait determination and to test hypotheses (![]()
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Likelihood ratios (![]()
= 0.05. This is appropriate when the null hypothesis coincides with the feasible limit for the parameter (i.e., variance components less than zero are not allowed; ![]()
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Estimates for the component H* were all negative, but their substantial sampling variances and very small likelihood ratio test statistics suggest that these are attributable to sampling error. If inbreeding depression is due to the composite effects of many loci, H*, which is the sum of the squares of these single locus effects, should be near zero. The component H* is not reported in our analyses because it was invariably constrained to zero to satisfy feasibility.
Simulations:
To assess the impact of the complete dominance model (Equation 3 and Equation 4) and partial inbreeding on projected short-term response to selection on a quantitative trait, we simulated finite populations undergoing five generations of selection on a single trait with genetic determination corresponding to that estimated for height and for petal width. Populations of size 100 were simulated as noninbred progeny of 20 unrelated founders. Each founder was assigned 2 unique alleles at each of 30 loci (1200 alleles in all). This contrasts with previous simulations of this model that use only two alleles per locus in different frequencies (![]()
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where nloc is the number of loci, and id is the inbreeding depression. Each non-IBD combination of alleles within a locus was given a random dominance deviation (dij for alleles i and j) drawn from a normal distribution with mean zero and variance VDR. From these elements, genotypic values were obtained for each combination of alleles at each locus. For comparison, two simpler models were also simulated: Model 1 with VP composed of only the components of variance defined for random mating populations and Model 2, as Model 1, but including inbreeding depression. In both these simpler models, VDI is set equal to VDR; i.e., the variance of dominance deviations for autozygous genotypes is assumed the same as for heterozygous genotypes. Transmission of alleles at each locus from one generation to the next was simulated by Mendelian segregation and free recombination into gametes. Phenotypic values were then obtained as the sum of the genotypic values over loci and an independent environmental effect simulated from a normal distribution with mean zero and variance VE.
Distinct mating systems were simulated: random mating, 20% selfing, and 50% selfing (with the remaining matings at random in the latter two cases). In each case, 100 offspring were produced from the individuals in the mating pool for each generation. For five initial generations, transmission proceeded by the specified mating system, in the absence of selection. Thereafter, we imposed linear directional selection on the phenotype for five generations, according to the following scheme: individuals in generation k joined the mating pool with probability

where y is the potential parent's phenotype, µ and VP are mean and variance of the phenotypic values in generation k (respectively), w is the mean probability of mating (fixed at 0.5 for all simulations), and s is the selection differential, i.e., the covariance between fitness (here determined by mating probability p) and the character under selection (y). We specified s as 0.44. Altogether 1000 simulations were conducted for each combination of the three genetic models and three mating schemes.
| RESULTS |
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Morphological traits:
For each of the morphological traits, additive genetic variance (VA) made highly significant contributions to the phenotypic variance. Narrow-sense heritabilities of the traits (computed with VP as for a random mating population, as the sum of VA, VE, VDR, and VM; Table 3) ranged from 16% for petal length to 26% for height, while additive genetic coefficients of variation, CVA, ranged from 5% for petal length to 15% for node number. Highly significant inbreeding depression was also consistently found (Table 3), indicating that, with inbreeding, plants tended to decline in size with respect to each of these characters.
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The estimates of variance components associated with dominance differed among traits far more strikingly. In the case of whole-plant size traits (plant height and node number), although inbreeding depression was detected as significant for both traits and the random component of dominance variance, VDR, was significant for node number, VDI appeared to be negligible. In the case of node number, the likelihood was maximized at a very small negative value for this variance component, indicating that the best estimate for both VDI and Cov(a, dI) is zero; under this constraint, the estimates of the remaining components and their standard errors differed little from the values given. Thus, for both overall size traits, the phenotypic variance was largely accounted for by the components, VA, VE, VDR, and VM.
For the petal size traits, VDR of petal width was significant, but that for petal length, similar in magnitude but substantially smaller in relation to the remaining components, was not. The estimates of VDR were substantially exceeded by the estimates for VDI. These were up to four times as large as VDR and contributed significantly to VP (petal length, P < 0.025; petal width, P < 0.05), despite their large standard errors in the full model (Table 3). The differences between VDI and VDR were not detected as significant. The covariance between additive effects and autozygous dominance deviations [Cov(a, dI)] was estimated as positive for petal length and negative for petal width; in neither case was it significantly different from zero (P > 0.5 and 0.15, respectively). Thus, the additive effects of alleles associated with these traits appear to be weakly correlated with their autozygous dominance deviations.
Although the design had sufficient power to detect VDI for floral size traits as significant, it tended to yield lower precision for estimates of VDI and Cov(a, dI) than for the other components of variation (Table 3). Moreover, the sampling covariance between these two parameters was substantial and negative (see Appendix 1; e.g., sampling correlation was -0.76 and -0.83 for petal length and width, respectively), as was that between Cov(a, dI) and VA (sampling correlation was -0.61 and -0.73 for petal length and width). Thus, the inclusion in the model of Cov(a, dI) can substantially affect the estimates of VA and VDI. Under a model omitting Cov(a, dI), the estimates of VA for petal length and width were 0.35 ± 0.11 and 0.17 ± 0.06, respectively, and the estimates of VDI were 0.56 ± 0.33 and 0.25 ± 0.18, respectively.
Other contributions to variation in these morphological traits were also substantial. Differences between generations were detected (not shown), with plants in later generations tending to be larger in whole plant measures, but smaller in size of petals. These generation effects are distinct from effects of inbreeding. Maternal variance (VM) was detected as highly significant for two traits, number of nodes and petal length, and accounted for 8 and 3% of the variance in those traits, respectively.
Flowering date:
The effect of inbreeding on mean time to flowering was positive, indicating that more inbred plants tend to flower later, but this effect was not statistically significant. Considering estimates of genetic components of variance, both VA and VDR were substantial, with h2 computed as for a random mating population of ~30% and CVA of 12.3%. VDI was extremely large, greatly surpassing VE, and highly significant. In comparison, Cov(a, dI) was relatively small (ra,dI =-0.3) and did not differ significantly from zero. The weakness of both this covariance and the inbreeding depression for this trait suggests that dominance at the loci influencing this trait is not strongly directional. VM accounted for ~7% of the random mating phenotypic variance and was highly significant.
Simulations of selection response:
Before the onset of selection, the simulated populations accumulate inbreeding approximately according to predictions accounting for the numbers of individuals (![]()
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Inbreeding depression affecting the mean of the trait in opposition to the direction of selection (Model 2), as found for plant height and petal width, can dramatically slow response to selection in all three mating schemes. In the case of the random mating population, this reduction results from inbreeding caused by finite population size alone. With partial selfing, the population mean can quickly decline below its initial value and not regain it, despite gradual increases due to selection (e.g., Figure 2B and Figure C). The observed reductions in trait mean relative to means observed in the absence of inbreeding depression (Model 1) closely match the predictions from standard theory [ ![]()
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Under the full model (Model 3), when the estimate of VDI is substantial and that of Cov(a, dI) is small and negative, as for petal width, selection response can be reduced substantially further, with somewhat greater reduction the higher the selfing rate (Figure 3). For plant height, where VDI makes a far smaller contribution to variation, the reduction of selection response under Model 3, relative to Model 2, is relatively slight. The discrepancy between the responses under Models 2 and 3 is essentially eliminated when Cov(a, dI) is absent (not shown; means for each generation coincide with those for Model 2 within 1.5%).
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| DISCUSSION |
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In keeping with many previous studies of inbreeding in diverse organisms (see Introduction), this work has demonstrated strong inbreeding depression in a population of N. menziesii recently collected from nature. Matings between more closely related individuals produced progeny that were smaller overall and bore smaller flowers. Beyond this, we have quantified the novel components of genetic variance expected to arise with inbreeding, VDI, H*, and Cov(a, dI). Although the study gave no evidence that these components contribute to variation in two measures of plant size (height and number of nodes), it demonstrated that VDI contributes substantially to genetic variation in three reproductive traits (petal length and width and flowering date).
In the petal size traits, significant inbreeding depression is accompanied by significant VDI, although not by significant Cov(a, dI). Thus, inbreeding increases the genetic variance for the trait, but this increase in variance is accompanied by a reduction in the mean, opposing selection favoring larger flower size. For both petal size traits, estimates of VDI appreciably exceeded those for VDR, although the difference was not detected as significant; in the case of petal length, VDR was not significant. These findings may illuminate earlier ones in which VD was not detected in progeny resulting from random mating, despite apparent inbreeding depression (e.g., of seed mass; ![]()
A surprising pattern of genetic determination was found for the two size traits, height and node number at flowering. These traits showed clear inbreeding depression, yet no detectable homozygous dominance variance (VDI). Similarly, ![]()
In only one of the traits studied, flowering time, was the estimate of inbreeding depression not significant. This trait exhibited substantial VDR and VDI, however. Taken together, these results indicate that, for this trait, the homozygous dominance deviations are not strongly directional. Inbreeding thus enhances the variance for flowering time without significantly affecting the mean.
Under partial inbreeding, prediction of selection response is problematic, in part because individuals are expected to vary in their degree of inbreeding, because the covariance between parent and offspring, on which selection response depends, involves all the dominance components in addition to VA and because allele frequencies and linkage disequilibrium, and hence the components of variance, change more rapidly with inbreeding and selection than with selection alone. Although special cases of selection with inbreeding have been considered (![]()
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Results for Model 2, involving inbreeding depression alone (with VDI = VDR), showed reductions in selection response of up to 70% per generation, depending on the mating scheme. Our simulations further showed that when this genetic model applies, short-term selection in partially inbreeding populations can be well predicted by summing the response expected from the breeder's equation (Equation 1) and the effect on the mean due to inbreeding depression. We found, moreover, that this approach to predicting selection response closely approximated the average response in our simulations, even with the much larger values of VDI that we found for petal width, as long as Cov(a, dI) was specified as zero. However, when additive effects of alleles are not independent of autozygous dominance deviations (Model 3), striking differences from these predictions arise. Even with the small, negative estimates of Cov(a, dI) we obtained for petal width, response to selection toward larger petals is reduced substantially more than can be simply accounted for by inbreeding depression. Negative Cov(a, dI) implies that the higher the effect of an individual allele, the more extreme tends to be its contribution, in autozygous state, to inbreeding depression, and thus, selection exacerbates inbreeding depression. The simulations show that even the moderate values of Cov(a, dI) we estimated can strongly affect selection response. Given the precision of our estimates, however, we cannot reject the null hypothesis that the true value of this parameter is zero for any trait. If future work consistently fails to demonstrate definitively that Cov(a, dI) contributes to genetic variance in inbreeding populations, then it appears that valid short-term predictions can be obtained by the composite method above, requiring only estimates of VA and inbreeding depression, both of which can be estimated from genetic designs far simpler than the cumbersome pedigrees required to estimate all the parameters of Model 3.
These dominance effects on selection can be viewed as distinct causes of selection decline in addition to those modeled by ![]()
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We know of few empirical studies in which effects of nonrandom mating on the structure of genetic variation have been assessed. ![]()
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Taking a distinct approach in a study of Plantago lanceolata, ![]()
Our findings of substantial VDI contributing to variation in three traits expressed under inbreeding suggest that further studies of the components of genetic variance in partially inbreeding populations would be of value. An accumulation of evidence that, apart from VDI, inbred dominance components are negligible could justify appreciable simplification in experimental designs used to study genetic variation under inbreeding. However, it is premature to rule out the importance of the remaining components even in the population of N. menziesii we studied. It remains to be seen whether expression of variation in other characters or under field conditions is subject to gene action involving the remaining components not detected in the present study.
| ACKNOWLEDGMENTS |
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Discussions with M. Lynch and D. Houle stimulated our initial work, funded by Pioneer Hi-Bred International; collaboration with J. Woolliams with support from the Biotechnology and Biological Sciences Research Council (BBSRC), U.K. greatly enhanced our progress and understanding. We thank J. Larson for invaluable assistance in many forms and A. Caballero, D. Charlesworth, J.-L. Jannink, J. Kelly, R. Miller, A. Montalvo, J. Stone, B. Walsh, N. Waser, and an anonymous reviewer, all of whose comments greatly improved the manuscript. We appreciate support from the National Science Foundation, which funded portions of this project.
Manuscript received January 26, 1998; Accepted for publication September 8, 1998.
| APPENDIX 1 |
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