EPISTASIS AS A SOURCE OF INCREASED ADDITIVE GENETIC VARIANCE AT POPULATION BOTTLENECKS

The role of epistasis in evolution and speciation has remained controversial. We use a new parameterization of physiological epistasis to examine the effects of epistasis on levels of additive genetic variance during a population bottleneck. We found that all forms of epistasis increase average additive genetic variance in finite populations derived from initial populations with intermediate allele frequencies. Average additive variance continues to increase over many generations, especially at larger population sizes (N = 32 to 64). Additive-by-additive epistasis is the most potent source of additive genetic variance in this situation, whereas dominance-by-dominance epistasis contributes smaller amounts of additive genetic variance. With additive-by-dominance epistasis, additive genetic variance decreases at a relatively high rate immediately after a population bottleneck, rebounding to higher levels after several generations. Empirical examples of epistasis for murine adult body weight based on measured genotypes are provided illustrating the varying effects of epistasis on additive genetic variance during population bottlenecks.     

Effects of bottlenecks on quantitative genetic variation in the butterfly Bicyclus anynana

The effects of a single population bottleneck of differing severity on heritability and additive genetic variance was investigated experimentally using a butterfly. An outbred laboratory stock was used to found replicate lines with one pair, three pairs and 10 pairs of adults, as well as control lines with approximately 75 effective pairs. Heritability and additive genetic variance of eight wing pattern characters and wing size were estimated using parent-offspring covariances in the base population and in all daughter lines. Individual morphological characters and principal components of the nine characters showed a consistent pattern of treatment effects in which average heritability and additive genetic variance was lower in one pair and three pair lines than in 10 pair and control lines. Observed losses in heritability and additive genetic variance were significantly greater than predicted by the neutral additive model when calculated with coefficients of inbreeding estimated from demographic parameters alone. However, use of molecular markers revealed substantially more inbreeding, generated by increased variance in family size and background selection. Conservative interpretation of a statistical analysis incorporating this previously undetected inbreeding led to the conclusion that the response to inbreeding of the morphological traits studied showed no significant departure from the neutral additive model. This result is consistent with the evidence for minimal directional dominance for these traits. In contrast, egg hatching rate in the same experimental lines showed strong inbreeding depression, increased phenotypic variance and rapid response to selection, highly indicative of an increase in additive genetic variance due to dominance variance conversion.     

The effect of a population bottleneck on the evolution of genetic variance/covariance structure

It is well known that standard population genetic theory predicts decreased additive genetic variance (V(a) ) following a population bottleneck and that theoretical models including interallelic and intergenic interactions indicate such loss may be avoided. However, few empirical data from multicellular model systems are available, especially regarding variance/covariance (V/CV) relationships. Here, we compare the V/CV structure of seventeen traits related to body size and composition between control (60 mating pairs/generation) and bottlenecked (2 mating pairs/generation; average F = 0.39) strains of mice. Although results for individual traits vary considerably, multivariate analysis indicates that V(a) in the bottlenecked populations is greater than expected. Traits with patterns and amounts of epistasis predictive of enhanced V(a) also show the largest deviations from additive expectations. Finally, the correlation structure of weekly weights is not significantly different between control and experimental lines but correlations between necropsy traits do differ, especially those involving the heart, kidney and tail length.     

Do bottlenecks increase additive genetic variance?

Because of anthropogenic factors many populations have been at least temporarily reduced to a very small population size. Such reductions could potentially decrease genetic variation and increase the probability of extinction. Analysis of molecular markers has shown a decrease in genetic variation but in many cases this has not reduced the ability of the population to recover from the bottleneck. This apparent paradox is resolved by a consideration of how population bottlenecks can affect additive genetic variance, the relevant measure of ability to respond to selective factors. A bottleneck has the potential to increase additive genetic variance in a population. This may result in an increase in fitness, particularly in populations of conservation concern that are small and lack genetic variation. Here we present a meta-analysis of experimental tests of this prediction using models designed to fit data that is strictly additive and data that has non-additive components. This analysis shows that additive genetic variance in a dataset dominated by morphological traits increases, on average, after a bottleneck event when the inbreeding coefficient is less than 0.3, but neither of the theoretical models alone can adequately explain this result. Because of our inability at present to predict the results of a population bottleneck in a specific case and the probability of extinction associated with small population size we caution against using bottlenecks to increase genetic variance, and thus the fitness, of endangered populations.     

The changes in genetic and environmental variance with inbreeding in Drosophila melanogaster

We performed a large-scale experiment on the effects of inbreeding and population bottlenecks on the additive genetic and environmental variance for morphological traits in Drosophila melanogaster. Fifty-two inbred lines were created from the progeny of single pairs, and 90 parent-offspring families on average were measured in each of these lines for six wing size and shape traits, as well as 1945 families from the outbred population from which the lines were derived. The amount of additive genetic variance has been observed to increase after such population bottlenecks in other studies; in contrast here the mean change in additive genetic variance was in very good agreement with classical additive theory, decreasing proportionally to the inbreeding coefficient of the lines. The residual, probably environmental, variance increased on average after inbreeding. Both components of variance were highly variable among inbred lines, with increases and decreases recorded for both. The variance among lines in the residual variance provides some evidence for a genetic basis of developmental stability. Changes in the phenotypic variance of these traits are largely due to changes in the genetic variance.     

The Influence of the Mating System on the Maintenance of Genetic Variability in Polygenic Characters

The traditional models of the effect of assortative mating and inbreeding on the genetic variance of polygenic characters (Fisher 1918; Wright 1921) presume that there is no natural selection or mutation. In a large population, the genetic variance determined by additive genes may then increase by up to a factor of two with local inbreeding, and even more with assortative mating. The classical models are still used to interpret data from natural populations. But contrary to their assumptions, most metrical characters in natural populations are usually thought to be under a type of selection which depletes polygenic variation. Mutation is then necessary to maintain genetic variation. The present models show that with the additional features of mutation and selection, in a large population, the mating system has no influence on the amount of genetic variability maintained by additive genes.     

The Effect of an Experimental Bottleneck upon Quantitative Genetic Variation in the Housefly

Effects of a population bottleneck (founder-flush cycle) upon quantitative genetic variation of morphometric traits were examined in replicated experimental lines of the housefly founded with one, four or 16 pairs of flies. Heritability and additive genetic variances for eight morphometric traits generally increased as a result of the bottleneck, but the pattern of increase among bottleneck sizes differed among traits. Principal axes of the additive genetic correlation matrix for the control line yielded two suites of traits, one associated with general body size and another set largely independent of body size. In the former set containing five of the traits, additive genetic variance was greatest in the bottleneck size of four pairs, whereas in the latter set of two traits the largest additive genetic variance occurred in the smallest bottleneck size of one pair. One trait exhibited changes in additive genetic variance intermediate between these two major responses. These results were inconsistent with models of additive effects of alleles within loci or of additive effects among loci. An observed decline in viability measures and body size in the bottleneck lines also indicated that there was nonadditivity of allelic effects for these traits. Several possible nonadditive models were explored that increased additive genetic variance as a result of a bottleneck. These included a model with complete dominance, a model with overdominance and a model incorporating multiplicative epistasis.     

The role of founder effects on the evolution of reproductive isolation

Several theories argue that large changes in allele frequencies through genetic drift after a small founding population becomes allopatrically isolated can lead to significant changes in reproductive isolation and thus trigger the origin of new species. For this reason, founder speciation has been proposed as a potent force in the generation of new species. Nonetheless, the relative importance of such ‘founder effects’ remains largely untested. In this report, I used experimental evolution to create one thousand replicates that underwent an extreme bottleneck and to study whether founder effects can lead to an increase in reproductive isolation in Drosophila yakuba. Even though the most common outcome of inbreeding is extinction, founder effects can lead to increased premating reproductive isolation in a very small proportion of cases. Changes in reproductive isolation after a founding population bottleneck are similar to changes in other phenotypic traits, in which inbreeding might displace the mean phenotypic value and substantially increase the phenotypic variance. This increase in phenotypic variance does not confer an increase in the response to selection for reproductive isolation in artificial selection experiments, indicating that the increased phenotypic variance is not caused by increases in additive genetic variance. These results also demonstrate that, similar to morphological and life‐history traits, behavioural traits can be affected by inbreeding and genetic drift.     

MULTIVARIATE PHENOTYPIC DIFFERENTIATION AMONG BOTTLENECK LINES OF THE HOUSEFLY

Multivariate phenotypic differentiation in eight morphometric traits was examined in bottleneck lines of the housefly initiated with one, four, or 16 pairs of flies from a natural outbred population. Differentiation was assessed using a Mahalanobis' distance metric in units of additive genetic variance and covariance estimated from the ancestral population (i.e., generalized genetic distance). This distance metric was partitioned into contributions of size and shape to total distance. Bottleneck lines of all sizes diverged significantly from the ancestral line, but the direction of these shifts differed among the lines of different initial founding size. Those populations founded with single pairs diverged from the ancestral line mostly in shape; the 16-pair lines differentiated almost entirely in size, and the four-pair lines were intermediate in the relative contribution of shape to differentiation from the control. Bottlenecks serve to alter the genetic relationships among traits within the derived populations and in doing so could promote speciation by permitting differentiation of the populations along evolutionary trajectories less accessible to the base population.     

Past bottlenecks and current population fragmentation of endangered huemul deer (<Emphasis Type="Italic">Hippocamelus bisulcus</Emphasis>): implications for preservation of genetic diversity

Small populations in fragmented habitats can lose genetic variation through drift and inbreeding. The huemul (Hippocamelus bisulcus) is an endangered deer endemic to the southern Andes of Chile and Argentina. Huemul numbers have declined by 99% and its distribution by 50% since European settlement. The total population is estimated at less than 2,000 individuals and is highly fragmented. At one isolated population in Chilean Patagonia we sampled 56 individuals between 2005 and 2007 and genotyped them at 14 microsatellite loci. Despite low genetic variability (average 2.071 alleles/locus and average H _O of 0.341), a low inbreeding coefficient (F _IS) of 0.009 suggests nearly random mating. Population genetic bottleneck tests suggest both historical and contemporary reductions in population size. Simulations indicated that the population must be maintained at 75% of the current size of 120 individuals to maintain 90% of its current genetic diversity over the next 100 years. Potential management strategies to maintain genetic variability and limit future inbreeding include the conservation and establishment of habitat corridors to facilitate gene flow and the enlargement of protected areas to increase effective population size.     

Lack of nonadditive genetic effects on early fecundity in Drosophila melanogaster

Fecundity is usually considered as a trait closely connected to fitness and is expected to exhibit substantial nonadditive genetic variation and inbreeding depression. However, two independent experiments, using populations of different geographical origin, indicate that early fecundity in Drosophila melanogaster behaves as a typical additive trait of low heritability. The first experiment involved artificial selection in inbred and non-inbred lines, all of them started from a common base population previously maintained in the laboratory for about 35 generations. The realized heritability estimate was 0.151 +/- 0.075 and the inbreeding depression was very small and nonsignificant (0.09 +/- 0.09% of the non-inbred mean per 1% increase in inbreeding coefficient). With inbreeding, the observed decrease in the within-line additive genetic variance and the corresponding increase of the between-line variance were very close to their expected values for pure additive gene action. This result is at odds with previous studies showing inbreeding depression and, therefore, directional dominance for the same trait and species. All experiments, however, used laboratory populations, and it is possible that the original genetic architecture of the trait in nature was subsequently altered by the joint action of random drift and adaptation to captivity. Thus, we carried out a second experiment, involving inbreeding without artificial selection in a population recently collected from the wild. In this case we obtained, again, a maximum-likelihood heritability estimate of 0.210 +/- 0.027 and very little nonsignificant inbreeding depression (0.06 +/- 0.12%). The results suggest that, for fitness-component traits, low levels of additive genetic variance are not necessarily associated with large inbreeding depression or high levels of nonadditive genetic variance.     

Epistasis and the evolutionary dynamics of measured genotypic values during simulated serial bottlenecks

The evolutionary effects of epistasis have been primarily explored analytically and most empirical studies have utilized yeast, viral and bacterial populations. Empirical analyses in multi‐cellular organisms are rare because of experimental constraints. Here, we report the results of a genome‐wide scan for two‐way epistasis in 16 traits related to body size and composition in F₂ mice from the LG/J by SM/J intercross. We analyze two‐locus genotypic values at quantitative trait loci (QTL), which provides an especially detailed view of epistatic architectures, to evaluate their predicted evolutionary consequences via Monte Carlo simulations. Epistatic profiles vary, but all traits show complicated genetic architectures which are largely hidden in single locus QTL scans. On average, detected epistatic effects are comparable in size to marginal effects. Simulations demonstrate an expected preservation, and often inflation, of heritable variance across several generations of small effective population size for many identified epistatic pairs over a range of starting allele frequencies.     

GENETIC VARIANCE FOR RATE OF POPULATION INCREASE IN NATURAL POPULATIONS OF FLOUR BEETLES,TRIBOLIUM SPP.

The genetic and ecological effects of population subdividsion were investigated for two wild strains of Tribolium castaneum and two wild strains of T. confusum and compared with the effects of population subdivision on the synthetic laboratory strain of T. castaneum (c-SM), used extensively in earlier experiments. For the c-SM strain, it has been shown repeatedly, for a variety of different population structures (different combinations of effective numbers, N_e, and migration rates, m), that large heritable differences in population growth rate arise among demes during 10 to 15 generations of population subdivision. Because this laboratory strain was synthesized by mass mating several “inbred” strains in 1973 (80 to 100 generations ago), it is possible that it has genetic variation for fitness (measured as the heritable variance among demes in the rate of population increase) unusually large compared to natural populations of flour beetles. In this paper, I report that natural populations of flour beetle exhibit as much or more phenotypic and genetic variation in the effects of population structure on fitness than the laboratory strain, c-SM. The observation of substantial heritable variation for fitness in natural populations is unexpected under additive theory and may be indicative of nonadditive genetic variance.     

Maintenance of genetic variation in quantitative traits of a woodland rodent during generations of captive breeding

Breeding programs to conserve diversity are predicated on the assumption that genetic variation in adaptively important traits will be lost in parallel to the loss of variation at neutral loci. To test this assumption, we monitored quantitative traits across 18 generations of Peromyscus leucopus mice propagated with protocols that mirror breeding programs for threatened species. Ears, hind feet, and tails became shorter, but changes were reversible by outcrossing and therefore were due to accumulated inbreeding. Heritability of ear length decreased, because of an increase in phenotypic variance rather than the expected decrease in additive genetic variance. Additive genetic variance in hind foot length increased. This trait initially had low heritability but large dominance or common environmental variance contributing to resemblance among full-sibs. The increase in the additive component indicates that there was conversion of interaction variances to additive variance. For no trait did additive genetic variation decrease significantly across generations. These findings indicate that the restructuring of genetic variance that occurs with genetic drift and novel selection in captivity can prevent or delay the loss of phenotypic and heritable variation, providing variation on which selection can act to adapt populations to captivity and perhaps later to readapt to more natural habitats after release. Therefore, the importance of minimizing loss of gene diversity from conservation breeding programs for threatened wildlife species might lie in preventing immediate reduction in individual fitness due to inbreeding and protecting allelic diversity for long-term evolutionary change, more so than in protecting variation in quantitative traits for rapid re-adaptation to wild environments.     

Natural selection on the genetical component of variance in body condition in a wild bird population

Although there is substantial evidence that skeletal measures of body size are heritable in wild animal populations, it is frequently assumed that the nonskeletal component of body weight (or ‘condition’) is determined primarily by environmental factors, in particular nutritional state. We tested this assumption by quantifying the genetic and environmental components of variance in fledgling body condition index (=relative body weight) in a natural population of collared flycatchers (Ficedula albicollis), and compared the strength of natural selection on individual breeding values with that on phenotypic values. A mixed model analysis of the components of variance, based on an ‘animal model’ and using 18 years of data on 17 717 nestlings, revealed a significant additive genetic component of variance in body condition, which corresponded to a narrow sense heritability (h²) of 0.30 (SE=0.03). Nongenetic contributions to variation in body condition were large, but there was no evidence of dominance variance nor of contributions from early maternal or common environment effects (pre‐manipulation environment) in condition at fledging. Comparison of pre‐ and post‐selection samples revealed virtually identical h² of body condition index, despite the fact that there was a significant decrease (35%) in the levels of additive genetic variance from fledging to breeding. The similar h² in the two samples occurred because the environmental component of variance was also reduced by selection, suggesting that natural selection was acting on both genotypic and environmental variation. The effects of selection on genetic variance were confirmed by calculation of the selection differentials for both phenotypic values and best linear unbiased predictor (BLUP) estimates of breeding values: there was positive directional selection on condition index both at the phenotypic and the genotypic level. The significant h² of body condition index is consistent with data from human and rodent populations showing significant additive genetic variance in relative body mass and adiposity, but contrasts with the common assumption in ecology that body condition reflects an individual’s nongenetic nutritional state. Furthermore, the substantial reduction in the additive genetic component of variance in body condition index suggests that selection on environmental deviations cannot alone explain the maintenance of additive genetic variation in heritable traits, but that other mechanisms are needed to explain the moderate to high heritabilities of traits under consistent and strong directional selection.     

The Genetic Structure of Natural Populations of DROSOPHILA MELANOGASTER. Xviii. Clinal and Uniform Genetic Variation over Populations

It has been reported in the previous papers of this series that in the eastern United States and Japan there is a north-to-south cline of additive genetic variance of viability and that the amount of the additive genetic variance in the northern population can be explained by mutation-selection balance. To determine whether or not the difference in the genetic variation in northern and southern populations can be explained by the differences in mutation rate and/or effective population size, numerical calculations were made using population genetic parameters. In addition, the average heterozygosities of the northern and southern populations at ten of 19 polymorphic structural loci surveyed were estimated in relation to the cline of additive genetic variance of viability, and the following findings were obtained. (1) The changes in mutation rate and population size cannot simultaneously explain the difference in additive genetic variance and inbreeding decline between the northern and southern populations. Thus, the operation of some kind of balancing selection, most likely diversifying selection, was suggested to explain the observed excess of additive genetic variance. (2) Estimates of the average heterozygosities of the southern population were not significantly different from those of the northern population. Thus, it was strongly suggested that the excess of additive genetic variance in the southern population cannot be caused by structural loci, but by factors outside the structural loci, and that protein polymorphisms are selectively neutral or nearly neutral.     

The Theory of Speciation VIA the Founder Principle

The founder principle has been used to explain many instances of rapid speciation. Advances from theoretical population genetics are incorporated into Mayr''s original founder-effect genetic-revolution model to yield a newer model called the genetic transilience. The basic theoretical edifice lies upon the fact that founder event can sometimes lead to an accumulation of inbreeding and an induction of gametic disequilibrium. This, in turn, causes alleles to be selected more for their homozygous fitness effects and for their effects on a more stable genetic background. Selection occurring in multi-locus systems controlling integrated developmental, physiological, behavioral, etc., traits is particularly sensitive to these founder effects. If sufficient genetic variability exists in the founder population, such multilocus genetic systems can respond to drift and the altered selective forces by undergoing a rapid shift to a new adaptive peak known as the genetic transilience. A genetic transilience is, therefore, most likely to occur when the founder event causes a rapid accumulation of inbreeding without a severe reduction in genetic variability. The implications of this model are then examined for three aspects of the founder-effect genetic-transilience model: the attributes of the ancestral population, the nature of the sampling process used to generate the founders and the attributes of the founder population. The model is used to explain several features of the evolution of the Hawaiian Drosophila, and experimental designs are outlined to test the major predictions of the theory. Hence, this theory of speciation can be tested in the laboratory, using systems and techniques that already exist—a rare attribute of most models of speciation.     

A Building Block Model for Quantitative Genetics

We introduce a quantitative genetic model for multiple alleles which permits the parameterization of the degree, D, of dominance of favorable or unfavorable alleles. We assume gene effects to be random from some distribution and independent of the D's. We then fit the usual least-squares population genetic model of additive and dominance effects in an infinite equilibrium population to determine the five genetic components--additive variance sigma 2 a, dominance variance sigma 2 d, variance of homozygous dominance effects d2, covariance of additive and homozygous dominance effects d1, and the square of the inbreeding depression h--required to treat finite populations and large populations that have been through a bottleneck or in which there is inbreeding. The effects of dominance can be summarized as functions of the average, D, and the variance, sigma 2 D. An important distinction arises between symmetrical and nonsymmetrical distributions of gene effects. With symmetrical distributions d1 = -d2/2 which is always negative, and the contribution of dominance to sigma 2 a is equal to d2/2. With nonsymmetrical distributions there is an additional contribution H to sigma 2 a and -H/2 to d1, the sign of H being determined by D and the skew of the distribution. Some numerical evaluations are presented for the normal and exponential distributions of gene effects, illustrating the effects of the number of alleles and of the variation in allelic frequencies. Random additive by additive (a*a) epistatic effects contribute to sigma 2 a and to the a*a variance, sigma 2/aa, the relative contributions depending on the number of alleles and the variation in allelic frequencies.(ABSTRACT TRUNCATED AT 250 WORDS)     

Evidence of inbreeding depression on human height

Stature is a classical and highly heritable complex trait, with 80%-90% of variation explained by genetic factors. In recent years, genome-wide association studies (GWAS) have successfully identified many common additive variants influencing human height; however, little attention has been given to the potential role of recessive genetic effects. Here, we investigated genome-wide recessive effects by an analysis of inbreeding depression on adult height in over 35,000 people from 21 different population samples. We found a highly significant inverse association between height and genome-wide homozygosity, equivalent to a height reduction of up to 3 cm in the offspring of first cousins compared with the offspring of unrelated individuals, an effect which remained after controlling for the effects of socio-economic status, an important confounder (χ(2) = 83.89, df = 1; p = 5.2 × 10(-20)). There was, however, a high degree of heterogeneity among populations: whereas the direction of the effect was consistent across most population samples, the effect size differed significantly among populations. It is likely that this reflects true biological heterogeneity: whether or not an effect can be observed will depend on both the variance in homozygosity in the population and the chance inheritance of individual recessive genotypes. These results predict that multiple, rare, recessive variants influence human height. Although this exploratory work focuses on height alone, the methodology developed is generally applicable to heritable quantitative traits (QT), paving the way for an investigation into inbreeding effects, and therefore genetic architecture, on a range of QT of biomedical importance.     

SEVERE INBREEDING DEPRESSION AND RAPID FITNESS REBOUND IN THE BUTTERFLY BICYCLUS ANYNANA (SATYRIDAE)

We established inbred laboratory lines of the satyrid Bicyclus anynana with one, three and 10 pairs of butterflies, which were subsequently allowed to increase freely to a maximum size of 300 butterflies. Minimally inbred control lines were established with 300 randomly selected virgin butterflies of equal sex ratio. We measured fecundity, egg weight, egg hatching, adult emergence, adult size, and the proportion of crippled adults in generations F₂, F₃, F₅, and F₇ (the latter two for the one pair bottleneck lines only). The most striking result was an unexpectedly large decrease in egg hatching with increase in inbreeding (25% per 10% increase in inbreeding). Such a level of inbreeding depression has not been reported previously for any insect. The distribution of egg hatching rate for individual clutches within inbred lines was markedly skewed, with a large fraction of clutches producing no eggs at all. This is interpreted as a relatively lower ratio of detrimental to lethal (or sterile) mutation loads than is found in Drosophila, the only insects for which mutation loads have been well characterized. Possible explanations for this severe inbreeding depression include a relatively high rate of mutation to recessive alleles with substantial damaging effects and infrequent episodes of inbreeding in nature. In the experiments, average egg hatching rate recovered rapidly between F₂ and F₇ in three of the six one-pair lines. We discuss the implications of these results for survival of populations through extreme bottlenecks in nature and in captivity.