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Conditions for Positive and Negative Correlations Between Fitness and Heterozygosity in Equilibrium Populations
Hong-Wen Denga and Yun-Xin Fuba Osteoporosis Research Center, Creighton University, Omaha, Nebraska 68131
b Human Genetics Center, SPH, University of Texas, Houston, Texas 77225
Corresponding author: Hong-Wen Deng, Osteoporosis Research Center, Creighton University, 601 N. 30th St., Suite 6787, Omaha, NE 68131, deng{at}creighton.edu (E-mail).
Communicating editor: Z-B. ZENG
| ABSTRACT |
|---|
The past decades have witnessed extensive efforts to correlate fitness traits with genomic heterozygosity. While positive correlations are revealed in most of the organisms studied, results of no/negative correlations are not uncommon. There has been little effort to reveal the genetic causes of these negative correlations. The positive correlations are regarded either as evidence for functional overdominance in large, randomly mating populations at equilibrium, or the results of populations at disequilibrium under dominance. More often, the positive correlations are viewed as a phenomenon of heterosis, so that it cannot possibly occur under within-locus additive allelic effects. Here we give exact genetic conditions that give rise to positive and negative correlations in populations at Hardy-Weinberg and linkage equilibria, thus offering a genetic explanation for the observed negative correlations. Our results demonstrate that the above interpretations concerning the positive correlations are not complete or even necessary. Such a positive correlation can result under dominance and potentially under additivity, even in populations where associated overdominance due to linked alleles at different loci is not significant. Additionally, negative correlations and heterosis can co-occur in a single population. Although our emphasis is on equilibrium populations and for biallelic genetic systems, the basic conclusions are generalized to non-equilibrium populations and for multi-allelic situations.
DURING the past three decades, numerous efforts have attempted to correlate fitness (or related characters) with genomic heterozygosity as reflected by molecular marker heterozygosity in natural populations (![]()
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One explanation is that (![]()
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Another explanation is that the populations studied may not be strictly panmictic but instead have local inbreeding. Nonrandom mating may cause correlations between homozygosity in the genome, even with unlinked loci (![]()
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The correlation approach for fitness and genomic heterozygosity and the different explanations for the observed data are highly relevant to one fundamental and long-standing issue in population genetics: How is genetic variation maintained in natural populations? Overdominance essentially encompasses all forms of balancing selection at the allelic level and dominance is compatible with mutation-selection balance. The following two inferences are common to the above two genetic explanations. First, the positive correlation reflects the phenomenon of heterosis. Hence in large randomly mating populations, it cannot possibly exist under within-locus additive allelic effects. In addition, heterosis should be incompatible with the negative correlations and they cannot co-occur within individual populations. Second, in populations at genetic equilibria, the positive correlations cannot exist with dominance. These concepts have been widely held among the researchers in this field. However, are they always true? Throughout, unless otherwise specified, (genetic) equilibria refer to Hardy-Weinberg and/or linkage equilibria.
Employing a multilocus biallelic model, and by theoretical analyses supplemented by computer simulations, we show that these two concepts are not true. Moreover, we demonstrate that negative correlations between fitness and genomic heterozygosity are not unexpected, and we give explicit genetic conditions for both positive and negative correlations to occur. Our focus is on equilibrium populations. However, the conclusions derived for multiple loci under equilibrium are generalized to nonequilibrium populations and multi-allelic systems through one locus model.
There are extensive data existing for the discovered correlations. There are also some potential limitations of the correlation approach for fitness and genomic heterozygosity (see DISCUSSION). Therefore, our focus here is to show when correlations do indeed exist in equilibrium populations, and how to interpret them when they are detected. Hence, some practical issues are not dealt with here, such as what sample sizes are needed and how many loci need to be assayed in order to detect a correlation when it indeed exists. Some of these, or related practical problems, have been addressed before (e.g., ![]()
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| THEORY |
|---|
Consider a simplified situation, in which there are N polymorphic loci underlying fitness, each having two alleles A and a. The allelic effects across loci may vary so that the equilibrium frequencies for the ith locus is pi and qi, respectively. Let the three genotypic values be:
Then for the ith locus, hi < 0.0 implies overdominance, hi = 0.5 implies additivity, 0 < hi < 1.0 (hi
0.5) implies dominance and hi > 1.0 implies underdominance. For the time being, we will assume hi = h, si = s, and that mutation-selection balance has been established so that qi = q where qi is the frequency of the less fit allele a at the ith locus. We will, later in the discussion section, consider the situation where hi , si and qi vary across loci. qi may vary across loci either due to variable hi and si in populations at mutation-selection balance, or in populations experiencing recent expansion after a population bottleneck (even with constant h and s), where genetic disequilibria could be negligible but mutation-selection balance has not been reached.
The multiplicative fitness function is biologically plausible by direct and indirect evidence (![]()
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(1) |
n1 + n2
N.
Under random mating and linkage equilibrium, genomic genotypes for individuals, as determined by n1 and n2, follow a trinomial distribution:
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(2) |
Conditional on having n1 heterozygous loci, the probability of having n2 homozygous loci for the a allele in the genome is a binomial distribution:
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(3) |
Thus, conditional on having n1 heterozygous loci in the genome, the expected fitness of a genotype [E(W/n1)] is:
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(4) |
Note that the quantities
and
in the above equation are, respectively, the probabilities of being aa and AA genotypes, conditional on that the genotype is homozygous.
+
is the weighted mean fitness of the two homozygotes, with the weight being their conditional probabilities as above.
Equation 4 can be re-written as:
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(5) |
It is then easy to see that E(W/n1) is a monotonically increasing function of n1, if
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(6) |
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(7) |
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(8) |
In other words, if the heterozygote fitness is larger than the weighted mean fitness of the two homozygotes (Equation 6), or if h satisfies Equation 8, then the expected fitness of a genotype increases monotonically with the number of heterozygous loci (n1) in the genome; otherwise it decreases monotonically with n1. This result may be easier to understand when we only consider, later in this section, the simplest case of a single locus with two alleles.
Therefore, both positive and negative relationships between fitness and genomic heterozygosity can exist. Which one exists critically depends on the above condition (Equation 6 or Equation 8) under our assumptions of random mating, no significant linkage disequilibrium, and multiplicative fitness function. Figure 1 depicts the parameter space of h and q that gives rise to positive and negative correlations between fitness and genomic heterozygosity. Note that Figure 1 does not imply any true relationship of h and q. It just graphically depicts the outcome regions of the relationship of fitness and heterozygosity given the true relationship of h and q. It can be seen that negative correlations are possible under a large range of parameter space of h and q. In particular, when q is small (<0.1), negative correlations are almost always expected under dominance and additivity. Additionally, positive correlations could potentially exist under additivity, if q is larger than 0.5 (see DISCUSSION).
|
To corroborate our analytical derivations, computer simulations were performed. The population was at Hardy-Weinberg and linkage equilibria. A total of 1000 polymorphic genomic loci of constant effects h and s with the same equilibrium allele frequencies p and q were assumed to be underlying fitness. At each locus, the genotype of an individual was determined by a uniform random variable
(0 <
< 1.0). Genotype AA was chosen if
< p2, else Aa if
< p2 + 2pq, otherwise aa was chosen. An individual's fitness was determined by Equation 1. One hundred genotypes were sampled from the population in our simulations. As stated in the introduction, our objective here was to find the genetic conditions for the existence of a true correlation. Additionally, the purpose of our simulation was to corroborate our analytical results. Therefore, the genotypic values of the 100 sampled genotypes were assumed to be measured without error, and are plotted in Figure 2. Regression analysis was performed; the regression slope was positive and highly significant (P = 0.0006). The simulation corroborates very well with our analytical derivations, i.e., the regression line based on the simulated genotypic data coincides with the expected theoretical line (Figure 2).
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The above conclusion, which was derived from a multiple-locus system where linkage equilibrium and mutation-selection balance were assumed, may be made more intuitive and general. In the rest of this section, we are going to progressively relax the assumptions concerning the genetic systems. First, we consider the simplest case of one locus with two alleles A and a as defined before. The essential question is then: Which has a higher fitness, a heterozygote or a homozygote? With the heterozygote, the fitness is 1 - hs. With a homozygote, it can be either AA or aa with respective frequencies in the population under Hardy-Weinberg equilibrium being p2 and q2. Thus the expected fitness of a homozygote in the population is
Therefore, if
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(9) |
0.5) or additive (h = 0.5). Note that Equation 9 is actually equivalent to Equation 7 and Equation 8. This is exactly the condition we found earlier when we considered multiple loci under a multiplicative fitness function (Equation 6, Equation 7 and Equation 8), where we assumed constant h, s, q, linkage equilibrium and mutation-selection balance. However, in the one locus case, no assumption needs to be made about the linkage disequilibrium and mutation-selection balance. Therefore, regardless of linkage disequilibrium and mutation-selection balance, as long as Equation 9 is satisfied at each locus, a positive correlation will exist.
Now, let us relax our assumptions even further and assume a general population where even Hardy-Weinberg equilibrium may not hold. A population resulting from the mixing of different populations may represent such a scenario. The essential question still is: At each polymorphic locus, which has a higher fitness, a heterozygote or a homozygote? For a biallelic locus as above, let us denote the genotype frequencies as PAA, PAa, and Paa respectively. The expected fitness of a genotype conditional on that it is homozygous is:
Again, this is the weighted fitness of the homozygotes, with the weight being their conditional genotype frequencies. Therefore, if
![]() |
(10) |
Note there is no assumption concerning the (Hardy-Weinberg/linkage disequilibrium) equilibrium in the above derivation. It can be easily seen that if Hardy-Weinberg equilibrium is assumed, Equation 10 can be reduced to Equation 9. If h > hc , a negative correlation will exist.
All the above analyses are for biallelic genetic systems, which are applicable for many allozyme loci and restriction fragment polymorphisms (RFLPs). However, some allozyme loci have more than two alleles and the increasingly employed micro-satellite marker loci are even more polymorphic. In the following, we are going to give the general genetic conditions of the correlation relationships for multi-allelic systems. We will use the tri-allelic genetic system as an example; extensions to genetic systems with more alleles are straightforward and can be obtained similarly.
Let the genotypic values and frequencies of a tri-allelic locus be:
The essential question is again the same as before: Which has a higher fitness, a heterozygote or a homozygote? The expected fitness of a genotype given that it is homozygous is:
Let
=
. That is,
is the weighted homozygous effect of the less fit alleles, with the weight being the conditional probabilities
Let
=
. That is,
is the weighted dominance coefficient, with the weight being the product of the corresponding selection coefficients (s1, s2 and s3) and the conditional probabilities
Therefore, if
![]() |
(11) |
and
as above, Equation 11 can be reduced to Equation 10 for the biallelic situations by just setting PCC = 0, PAC = 0, PBC = 0 (since only two alleles A and B exist at the locus). | DISCUSSION |
|---|
Under the simplified model of two alleles at each locus, in randomly mating populations with genetic equilibria, a positive correlation between genomic heterozygosity and fitness with dominance seems to be counterintuitive and has not been revealed before (Figure 1 and Figure 2). A more counterintuitive conclusion is that a positive correlation could potentially exist even under within-locus additive allelic effects, without any dominance or overdominance in equilibrium populations (Figure 1, Equation 6Equation 7Equation 8Equation 9). However, our analyses clearly demonstrate that these are entirely possible for a range of parameter space under Hardy-Weinberg and linkage equilibria. Importantly, negative correlations between fitness and genomic heterozygosity are actually not unexpected under a wide range of plausible parameter space of h and q in equilibrium populations (Figure 1). Additionally, in nonequilibrium populations, a positive correlation can also exist with dominance, overdominance, and additive allelic effects if Equation 10 holds at polymorphic loci; otherwise a negative correlation may exist. Furthermore, with no assumption about the genetic equilibrium, the exact genetic conditions for the positive and negative correlations for general multi-allelic systems are also given. All of these results are new in that they give genetic conditions for the correlations, which directly link the genetic effect h (and s) with the population property of gene (or genotype) frequencies.
The conditions for these counterintuitive phenomena to exist do not seem to be prohibitive given some level of biological knowledge. For a positive correlation to exist, q does not have to be very common in the dominance case (Figure 1). In the additive case, in order for hc > 0.5 so that a positive correlation could possibly exist (Equation 6, Equation 8 and Equation 9), q has to be greater than 0.5 in populations at genetic equilibrium or PAA < Paa in populations at disequilibrium (Equation 10). Are these entirely impossible? Our knowledge is very limited on fitness effects at polymorphic loci such as those revealed by molecular markers (![]()
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The second situation where q may exceed 0.5 may be in populations experiencing recent expansion, where mutation-selection balance is not established yet but Hardy-Weinberg and linkage disequilibria are not significant. We focus on considering the conditions for different correlations under Hardy-Weinberg and linkage equilibria. In order to assume constant q under constant h and s across loci, mutation-selection balance is assumed when we derive Equation 8 for the case of multiple loci. However, mutation-selection may not be an essential assumption for our conclusions. This can be easily seen, since the same basic conclusion (Equation 8) is derived for the single locus case (Equation 9) without assuming mutation-selection balance. It is known that Hardy-Weinberg equilibrium can be established by just one generation of random mating; linkage disequilibrium decays at a rate of r. r is the recombination rate between two loci at disequilibrium. However, to reach a mutation-selection balance, roughly, for those mutants with s greater than 10/N e, where Ne is the effective population size, the population has to have an annual population size in excess of Ne for a time span (in generations) of at least a few Ne (![]()
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The observed negative correlations between fitness traits and heterozygosity in a number of studies (![]()
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The potentially common negative correlations are not inconsistent with the widely observed inbreeding depression. For a single locus with two alleles, the necessary and sufficient condition for population inbreeding depression to occur is that the heterozygote has fitness greater than the arithmetic mean fitness of the two corresponding homozygotes, not weighted by their population frequencies as in Equation 6 and Equation 10 (![]()
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It should be pointed out that although the derivation for multiple-loci in the THEORY section is based on the assumptions of constant effects (h and s) and multiplicative fitness function, these assumptions are not essential for our main conclusions. In the THEORY section, for the one locus model, we also showed the same basic results as the multilocus model. If hi and si are variable across loci, each locus will have its own peculiar qi , and thus a peculiar hic , at mutation-selection balance. At the ith locus, hic is determined by the equilibrium qi (Equation 7), which in turn depends on the specific allelic effects hi and si for equilibrium populations at mutation-selection balance (![]()
The explanation for the commonly observed positive correlations between fitness (or its related traits such as developmental stability) and molecular marker loci may be complex. In populations that are not strictly panmictic with local inbreeding present, the genomic heterozygosity may be correlated with individual levels of inbreeding. Therefore, the associations between heterozygosity and fitness are largely the consequence of variation in the level of inbreeding among individuals (![]()
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An implication of our results is that there is probably a limitation of the correlation approach for distinguishing the genetic mechanisms responsible for the maintenance of genetic variability. This is because of the following reasons. First, in equilibrium populations, a positive correlation can be explained by both dominance (0 < h < 1.0) and overdominance (h < 0) as long as h < hc (Equation 6Equation 7Equation 8Equation 9Equation 10). Second, the negative correlations and heterosis can co-occur under the same genetic conditions (Figure 1). Third, even for the same genetic effect (i.e., the same h) in one species, both correlations could be revealed in different populations if these populations have different genotype frequencies due to different population origins and histories (Equation 10). The limitation of the correlation approach in inferring the mechanisms responsible for the maintenance of genetic variability was also pointed out before on different grounds (e.g., ![]()
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A potential application of the theoretical result here is that, for diallelic makers (such as those from RFLP), inference of the upper/lower bounds of h may be made given significant positive/negative correlations being found (Equation 6Equation 7Equation 8Equation 9Equation 10). h is an important genetic parameter in population and evolutionary genetics and has been difficult to estimate (even for its bounds, DENG 1997; DENG et al. 1997), especially for those organisms for which controlled breeding is difficult. Whereas, using Equation 6Equation 7Equation 8Equation 9Equation 10, the bounds of h may be estimated without controlled breeding with the application of the traditional correlation approach for fitness and genomic heterozygosity in natural populations.
| ACKNOWLEDGMENTS |
|---|
We thank Drs. D. CHARLESWORTH, M. LYNCH, R. CHAKROBARTY, and M. JOHNSON for discussions and comments. We are also grateful to Dr. Z-B. ZENG and three anonymous reviewers for their helpful comments that improved the paper. H.-W. DENG would like to thank Dr. M. LYNCH for years of advice, and Dr. D. HEDGECOCK for providing support to attend the conference "Genetic and Physiological Basis of Heterosis," which stimulated the development of this work. The work was in part supported by a FIRST AWARD from National Institutes of Health to Dr. Y.-X. FU. H.-W. DENG was supported by a grant from Health Future Foundation to Drs. R. RECKER and D. KIMMEL while finalizing this paper.
Manuscript received August 12, 1997; Accepted for publication November 7, 1997.
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