THE FITNESS CONSEQUENCES OF MULTIPLE-LOCUS HETEROZYGOSITY UNDER THE MULTIPLICATIVE OVERDOMINANCE AND INBREEDING DEPRESSION MODELS

There is a growing body of literature suggesting that the fitness of an individual increases with the observed number of heterozygous loci. Broad theoretical considerations indicate that under various sorts of balancing selection, this is what one should generally expect in a population of multiple-locus genotypes. To date, however, it has not been possible to distinguish between two potential explanations of the phenomenon. The first explanation is that the loci examined are themselves responsible for the fitness differences observed (or, equivalents, are very closely linked to those that do). The genetic variation in question is thought to be maintained in polymorphic equilibrium by some form of balancing selection. The second explanation assumes that the observed loci are themselves selectively irrelevant but that their heterozygosity reflects that of the total genome. Genomic heterozygosity is thought to be predictive of fitness, being an obverse measure of generalized inbreeding depression. We provide a formal derivation of an explicit relationship between fitness and multiple-locus genotype for a simple form of the first explanation, the multiplicative overdominance model. The inbreeding depression model is a degenerate special case of this more general formulation. A formal estimation and testing framework is constructed that should facilitate evaluation of the two models with empiric data on heterozygosity and fitness.     

Warming and drought alter C and N concentration,allocation and accumulation in a Mediterranean shrubland

We investigated the effects of warming and drought on C and N concentrations, nitrogen use efficiency (NUE), and C and N accumulation in different ecosystem compartments. We conducted a 6-year (1999–2005) field experiment to simulate the climate conditions projected by IPCC models for the coming decades in a Mediterranean shrubland. We studied the two dominant species, Globularia alypum and Erica multiflora, and an N-fixing species, Dorycnium pentaphyllum, also abundant in this shrubland. Warming (1 °C) decreased N leaf concentrations by 25% and increased N stem concentrations by 40% in G. alypum. Although warming changed the available ammonium in soil in some seasons, it did not increase total soil N contents. Drought (19% average reduction in soil moisture) decreased leaf N concentrations in the two dominant shrub species, E. multiflora and G. alypum by 16% and 19%, respectively, and increased stem N concentrations by 56% and 40%, respectively. Neither warming nor drought changed the leaf N concentrations in the N-fixing species D. pentaphyllum, although warming increased stem N concentration by 9%. In G. alypum, the increase of stem N concentrations contributed to the observed increase of N accumulation in stem biomass in drought treatments with respect to control plots (8 kg N ha⁻¹). Neither warming nor drought changed NUE in the period 1999–2005. Warming increased soil organic C relative to drought. The effects of warming and drought on C and N concentrations, on N accumulation and on leaf/stem N distribution were not the result of dilution or concentration effects produced by changes in biomass accumulation. Other factors such as the changes in soil N availability, photosynthetic capacity, and plant internal C and N remobilization must be involved. These changes which differed depending on the species and the plant tissue show that the climate change projected for the coming decades will have significant effects on the C and N cycle and stoichiometry, with probable implications for ecosystem structure and function, such as changes in plant–herbivore relationships, decomposition rates or community species composition.     

Comparison of clonal diversity in mountain and Piedmont populations of Trillium cuneatum (Melanthiaceae-Trilliaceae), a forest understory species

The balance between clonal and sexual reproduction can vary widely among plant populations, and the extent of clonality may be influenced by the combined effects of historical land use and variation in environmental conditions. We investigated patterns of clonal spread in five Trillium cuneatum populations, two in the Appalachian Mountains characterized by mesic, cooler conditions, and three at lower elevations experiencing warmer, drier conditions and greater disturbance. Using a new measure of the genet effective number and innovative orthogonal contrast methods, we quantified genet structure, contrasting clonal growth in the mountains with that in the Piedmont. Asexual propagation was more common in the Piedmont, where 25% of the sampled ramets were clonally derived, but was much less frequent in the mountains (7% clonal replicates). Hierarchical partitioning of variation in genet diversity showed that the majority (75.8%) of the variation resulted from more vegetative replication in the Piedmont. Most of the remaining variation (21.6%) was attributable to differences between urban and rural Piedmont populations, and a small, statistically nonsignificant fraction of the variation (2.6%) was due to interpopulation differences within the mountains. Higher frequency of cloning may enhance both genetic and demographic population viability in fragmented Piedmont habitats.     

Directionality in protein fold prediction

Background  

Ever since the ground-breaking work of Anfinsen et al. in which a denatured protein was found to refold to its native state, it has been frequently stated by the protein fold prediction community that all the information required for protein folding lies in the amino acid sequence. Recent in vitro experiments and in silico computational studies, however, have shown that cotranslation may affect the folding pathway of some proteins, especially those of ancient folds. In this paper aspects of cotranslational folding have been incorporated into a protein structure prediction algorithm by adapting the Rosetta program to fold proteins as the nascent chain elongates. This makes it possible to conduct a pairwise comparison of folding accuracy, by comparing folds created sequentially from each end of the protein.     

Gene flow and fine-scale genetic structure in a wind-pollinated tree species, Quercus lobata (Fagaceaee)

California Valley oak (Quercus lobata), one of the state's most distinctive oak species, has experienced serious demographic attrition since the 19th century, due to human activities. Recent estimates of pollen dispersal suggest a small reproductive neighborhood. Whether small neighborhood size is a recent phenomenon, a consequence of reduced gene flow caused by demographic changes, or whether it has been historically restricted, remains unclear. To examine this question, we have characterized the spatial genetic structure of N = 191 Q. lobata individuals, spread over an area of 230 ha, using eight microsatellite loci. The observed autocorrelogram suggests an historical standard deviation of gene flow distance of about 350 m per generation, higher than contemporary pollen dispersal estimates. To determine whether our estimates were affected by strong prevailing winds from the west-northwest, we developed and utilized a novel anisotropic autocorrelation analysis. We detected no more than a hint of anisotropy, and we concluded that adult spatial structure is indicative of strong historical signature of "isolation by distance." This historical estimate provides a useful reference value against which to gauge the future gene flow consequences of ongoing anthropogenic disturbance.     

THE FITNESS CONSEQUENCES OF MULTIPLE-LOCUS HETEROZYGOSITY: THE RELATIONSHIP BETWEEN HETEROZYGOSITY AND GROWTH RATE IN PITCH PINE (PINUS RIGIDA MILL.)

Positive correlations between measures of “fitness” and the number of electrophoretic loci for which an individual is heterozygous have been observed in many species. Two major hypotheses have been proposed to explain this phenomenon: inbreeding depression and overdominance. Until recently, there has been no way to distinguish between these hypotheses. The overdominance model devised by Smouse (1986) is used here in a reanalysis of Ledig et al.‘s (1983) study of heterozygosity and growth rate in eight populations of pitch pine and is contrasted with an inbreeding-depression analysis. Ledig et al. (1983) regressed mean growth rate per heterozygosity class on the number of heterozygous loci, a method of analysis which, although it points to general trends in the data, does not differentiate between hypotheses. The correlations they obtained in four populations were significant only because regressing on the means eliminates most of the sum of squares for error and does not weight the unequally sized heterozygosity classes. Reanalysis of Ledig et al.‘s data using individuals, not means, showed no significant correlations between heterozygosity and fitness. A major assumption of Smouse's overdominance model is that genetic polymorphism is in part a reflection of selection for heterozygotes at genetic equlibrium. The homozygote for the most frequent allele at a locus should be more fit than a homozygote for a less frequent allele, with the heterozygote superior to both homozygotes. Smouse's model predicts a negative, linear relationship between fitness and “adaptive distance,” a variable that for a heterozygote is zero and for homozygotes is equal to the inverse of the frequency of the corresponding allele. The adaptive-distance model accounted for between 15% and 50% of the variation in growth rate within eight P. rigida population samples by accounting for genotypic differences at eight polymorphic loci. This is over twice as much of the variation in growth rate accounted for by Ledig et al.'s (1983) analysis using individuals. Significant correlations were found between adaptive distance and growth rate in four of the eight populations, but in only two of the populations were more of the partial coefficients negative than positive, as would be predicted by the overdominance hypothesis. The remaining two populations in which correlations were significant did not lend themselves to such clear-cut interpretation, as the majority of the partial coefficients were positive. Positive partial coefficients indicate that the growth rate of the heterozygote is inferior to that of at least one of the homozygotes. The adaptive-distance analysis provides evidence that specific genotypes do play a role in determining growth rate in pitch pine. The correlation between growth rate and adaptive distance increased significantly with the age of the population, possibly reflecting competition subsequent to crown closure.     

Two-generation analysis of pollen flow across a landscape. II. Relation between phi(ft), pollen dispersal and interfemale distance

We study the behavior of Phi(ft), a recently introduced estimator of instantaneous pollen flow, which is basically the intraclass correlation of inferred pollen cloud genetic frequencies among a sample of females drawn from a single population. Using standard theories of identity by descent and spatial processes, we show that Phi(ft) depends on the average distance of pollen dispersal (delta) and on the average distance between sampled mothers (x(1)). Provided that mothers are sampled far enough apart (x(1) > 5delta), Phi(ft) becomes independent of x(1) and is then inversely proportional to the square of delta. Provided that this condition is fulfilled, delta is directly estimable from Phi(ft). Even when x(1) < 5delta, estimation can easily be achieved via numerical evaluation. We show that the relation between Phi(ft) and delta is only modestly affected by the shape of the distribution function, a result of importance, since this shape is generally unknown. We also study the impact of adult density within the population on Phi(ft), showing that to achieve the correct inference of delta from Phi(ft) it must be taken into account, but that it has no effect on the distance at which mothers must be sampled.     

Measuring the genetic structure of the pollen pool as the probability of paternal identity

Contemporary pollen flow in forest plant species is measured by the probability of paternal identity (PPI) for two randomly sampled offspring, drawn from a single female, and contrasting that with PPI for two random offspring, drawn from different females. Two different estimation strategies have emerged: (a) an indirect approach, using the 'genetic structure' of the pollen received by different mothers and (b) a direct approach, based on parentage analysis. The indirect strategy is somewhat limited by the assumptions, but is widely useful. The direct approach is most appropriate where a large majority of the true fathers can be identified exactly, which is sometimes possible with high-resolution SSR markers. Using the parentage approach, we develop estimates of PPI, showing that the obvious estimates are severely biased, and providing an unbiased alternative. We then illustrate the methods with SSR data from a 36-tree isolated population of Pinus sylvestris from the Meseta region of Spain, for which categorical paternity assignment was available for over 95% of offspring. For all the females combined, we estimate that PPI=0.0425, indicating uneven male reproductive contributions. Different (but overlapping) arrays of males pollinate different females, and for the average female, PPI=0.317, indicating substantial 'pollen structure' for the population. We also relate the direct measures of PPI to those available from indirect approaches, and show that they are generally comparable.     

THE IMPACT OF ELECTROPHORETIC GENOTYPE ON LIFE HISTORY TRAITS IN PINUS TAEDA

Reports of positive associations between allozymic heterozygosity and measures of fitness are routine, but it has not been possible to distinguish between the two preeminent explanations of the phenomenon, dominance and overdominance. We tested several of the assumptions of these hypotheses in our study of the relationship between electrophoretic genotype and three life history traits in loblolly pines (Pinus taeda L.). Traits examined included the survival and growth of selfed and outcrossed progeny of 45 maternal trees, and maternal fecundity, measured as the number of surviving progeny per mother tree. Inbreeding depression was severe; the relative fitness of the selfed progeny was only 8% that of the outcrossed progeny. We found a heterozygote fecundity advantage, which should have resulted in an excess of rare alleles in the progeny. Instead, there was evidence of severe survival selection against rare alleles in both heterozygous and homozygous forms. The deficit of rare alleles averaged 69 and 50% in the selfed and outcrossed progeny, respectively. The one allele in the sample that we should have suspected of being maintained by overdominance (a PGI2 mid-frequency allele) appeared to be overdominant for outcrossed height growth and probably for fecundity as well. Multiple-locus genotype explained very little of the variation in growth, however, and rather than seeing evidence for overdominance as a force in maintaining most of the observed polymorphism, we were left to explain, in the face of the severe survival selection, why the rare alleles were present at all. Projection of the stand into the future through computer simulation showed how balancing selection acting on differential growth, fecundity, and mortality among genotypes could, over the life of the stand, account for the maintenance of the rare alleles in the population.