The harmful effects of close inbreeding have been noticed for many centuries (34, 35, 165). With the rise of Mendelian genetics, it was realized that the main genetic consequence of inbreeding is homozygosis (165, Ch. 2). Two main theories were early proposed to account for inbreeding depression and its converse, heterosis (the increase in vigor observed in an F1 between two inbred lines). These are the overdominance and partial dominance hypotheses, discussed in more detail below. Research into this question has continued up to the present, and this is one of the topics that we discuss. Darwin (35, 36) was the first to point out that the evident adaptations of many plants for ensuring outcrossing could be understood in terms of the selective advantage of avoiding inbreeding depression. We review the evidence that the evolution of breeding systems of animals and plants has been significantly influenced by the occurrence of inbreeding depression. In order to do this, we consider the contemporary genetic theory of inbreeding depression and heterosis, and the experimental data concerning the strength of inbreeding depression. We emphasize data and theory relevant to natural, rather than domesticated, populations as we are chiefly concerned to evaluate the evolutionary significance of inbreeding depression. We do not attempt to give a complete bibliography of this very extensive field but try to concentrate on what seem to be the most significant findings in relation to this aim.

https://www.jstor.org/stable/pdf/2097132.pdf

Inbreeding depression and its evolutionary consequences

Microsatellite null alleles are commonly encountered in population genetics studies, yet little is known about their impact on the estimation of population differentiation. Computer simulations based on the coalescent were used to investigate the evolutionary dynamics of null alleles, their impact on F(ST) and genetic distances, and the efficiency of estimators of null allele frequency. Further, we explored how the existing method for correcting genotype data for null alleles performed in estimating F(ST) and genetic distances, and we compared this method with a new method proposed here (for F(ST) only). Null alleles were likely to be encountered in populations with a large effective size, with an unusually high mutation rate in the flanking regions, and that have diverged from the population from which the cloned allele state was drawn and the primers designed. When populations were significantly differentiated, F(ST) and genetic distances were overestimated in the presence of null alleles. Frequency of null alleles was estimated precisely with the algorithm presented in Dempster et al. (1977). The conventional method for correcting genotype data for null alleles did not provide an accurate estimate of F(ST) and genetic distances. However, the use of the genetic distance of Cavalli-Sforza and Edwards (1967) corrected by the conventional method gave better estimates than those obtained without correction. F(ST) estimation from corrected genotype frequencies performed well when restricted to visible allele sizes. Both the proposed method and the traditional correction method have been implemented in a program that is available free of charge at http://www.montpellier.inra.fr/URLB/. We used 2 published microsatellite data sets based on original and redesigned pairs of primers to empirically confirm our simulation results.

Microsatellite Null Alleles and Estimation of Population Differentiation

The accuracies and efficiencies of three different methods of making phylogenetic trees from gene frequency data were examined by using computer simulation. The methods examined are UPGMA, Farris' (1972) method, and Tateno et al.'s (1982) modified Farris method. In the computer simulation eight species (or populations) were assumed to evolve according to a given model tree, and the evolutionary changes of allele frequencies were followed by using the infinite-allele model. At the end of the simulated evolution five genetic distance measures (Nei's standard and minimum distances, Rogers' distance, Cavalli-Sforza's fλ, and the modified Cavalli-Sforza distance) were computed for all pairs of species, and the distance matrix obtained for each distance measure was used for reconstructing a phylogenetic tree. The phylogenetic tree obtained was then compared with the model tree. The results obtained indicate that in all tree-making methods examined the accuracies of both the topology and branch lengths of a reconstructed tree (rooted tree) are very low when the number of loci used is less than 20 but gradually increase with increasing number of loci. When the expected number of gene substitutions (M) for the shortest branch is 0.1 or more per locus and 30 or more loci are used, the topological error as measured by the distortion index (dT) is not great, but the probability of obtaining the correct topology (P) is less than 0.5 even with 60 loci. When M is as small as 0.004, P is substantially lower. In obtaining a good topology (small dT and high P) UPGMA and the modified Farris method generally show a better performance than the Farris method. The poor performance of the Farris method is observed even when Rogers' distance which obeys the triangle inequality is used. The main reason for this seems to be that the Farris method often gives overestimates of branch lengths. For estimating the expected branch lengths of the true tree UPGMA shows the best performance. For this purpose Nei's standard distance gives a better result than the others because of its linear relationship with the number of gene substitutions. Rogers' or Cavalli-Sforza's distance gives a phylogenetic tree in which the parts near the root are condensed and the other parts are elongated. It is recommended that more than 30 loci, including both polymorphic and monomorphic loci, be used for making phylogentic trees. The conclusions from this study seem to apply also to data on nucleotide differences obtained by the restriction enzyme techniques.

Accuracy of estimated phylogenetic trees from molecular data. II. Gene frequency data.

Interpretation of genetic differentiation values is often problematic because of their dependence on the level of genetic variation. For example, the maximum level of GST is less than the average within population homozygosity so that for highly variable loci, even when no alleles are shared between subpopulations, GST may be low. To remedy this difficulty, a standardized measure of genetic differentiation is introduced here, one which has the same range, 0–1, for all levels of genetic variation. With this measure, the magnitude is the proportion of the maximum differentiation possible for the level of subpopulation homozygosity observed. This is particularly important for situations in which the mutation rate is of the same magnitude or higher than the rate of gene flow. The standardized measure allows comparison between loci with different levels of genetic variation, such as allozymes and microsatellite loci, or mtDNA and Y-chromosome genes, and for genetic differentiation for organisms with d...

A standardized genetic differentiation measure

Genetic assignment methods use genotype likelihoods to draw inference about where individuals were or were not born, potentially allowing direct, real-time estimates of dispersal. We used simulated data sets to test the power and accuracy of Monte Carlo resampling methods in generating statistical thresholds for identifying F0 immigrants in populations with ongoing gene flow, and hence for providing direct, real-time estimates of migration rates. The identification of accurate critical values required that resampling methods preserved the linkage disequilibrium deriving from recent generations of immigrants and reflected the sampling variance present in the data set being analysed. A novel Monte Carlo resampling method taking into account these aspects was proposed and its efficiency was evaluated. Power and error were relatively insensitive to the frequency assumed for missing alleles. Power to identify F0 immigrants was improved by using large sample size (up to about 50 individuals) and by sampling all populations from which migrants may have originated. A combination of plotting genotype likelihoods and calculating mean genotype likelihood ratios (DLR) appeared to be an effective way to predict whether F0 immigrants could be identified for a particular pair of populations using a given set of markers.

Genetic assignment methods for the direct, real-time estimation of migration rate: a simulation-based exploration of accuracy and power

An excess proportion of homozygous carriers of a gene arises on bulking of reproductively isolated subpopulations. This surplus of homozygotes in the mixture, measured relative to the panmictic proportion, is caused by variation of its frequencies in the respective subpopulations. It is shown that the result known as Wahlund's principle can be expressed as a simple function of genic distances among the subpopulations. If used with caution it can be employed to recognize mixtures of seed lots. The effect of bulking can be readily discriminated from that of inbreeding. It may also be distinguished from the effect of assortative mating by analysing such distances at several gene loci. Various effects of selection may disturb inference on whether a given lot is a mixture. Hence application should be confined to the dormant seed. Isozyme loci are most suitable for such checks since complete dominance occurs only rarely. Some advantages peculiar to conifer seed are discussed.

Genetic distance between populations

In a Scots pine seed orchard the genetic structures at an enzyme gene locus active in pine seeds were compared among the parental clones and the allorchard seeds produced over a period of three years. The genotypes of the seeds were identified as ordered pairs consisting of the female and male contribution. The sexual reproductive function monitored at the studied locus differed significantly between the two sexes. This fact proves the necessity of taking sexual asymmetry into account in studies of reproductive selection. This is done by comparing the observed genotypic structures among the offspring with the corresponding multiplicative structure expected under random gametic fusion. Additionally, accounting for partial self-fertilization increased the conformity between the observed and the hypothesized model structures. The differences in female and male gametic contributions to the offspring were used to estimate female and male relative fitness components. Significant deviations between the allelic and/or genotypic structures of orchard clones and their seed, and between seed lots collected in different years, may reduce the efficiency of realizing breeding gains in seed orchards.

Reproductive systems in conifer seed orchards

Forests have become increasingly affected by human influence and forest genetics has gained substantial importance in view of the recently detected genetic implications of environmental changes. Conclusions drawn from genetic structures and their dynamics can help to evaluate the genetic processes and their consequences.

Genetic structures as indicators for adaptation and adaptational potentials

It is argued that the declaration of a collection of biological material as a gene resource must include the following basic specifications: (1) a genetic characterization of the collection, (2) the statement of the objectives to be pursued with the collection, (3) the methods and techniques of conservation, and (4) the methods and techniques for the utilization (regeneration) of the resource. If any of these specifications cannot be made or is incompatible with any other, the collection is either not suitable for declaration as a gene resource, or the specifications need correction. Various standard methods and techniques of conservation and regeneration of gene resources are discussed in relation to the objectives of conservation, and elementary consequences for declaration are drawn. The need for research centered on the field of gene conservation is emphasized, and the significance of legislation in this concern is addressed.

Gene resources and gene conservation in forest trees: General concepts

Analyses of distribution patterns and genetic structures of forest stands can address distinct family structures and provide insights into the association of genetic and phenotypic variation patterns. In this study, point pattern analysis and spatial autocorrelation were used to examine the spatial and genetic structures in two naturally generated beech stands, which differ in age, trunk morphology, and stand management. Significant tree clumping was observed at distances up to 20 m in the young forest stand, whereas dispersion at distances under 10 m was observed in the old stand. The spatial analysis based on Ripley’s k function of the two different groups of trees showed that the non-forked trees match in both stands the spatial pattern of all trees while the forked were randomly distributed. Additionally, according to the bivariate analysis, forked trees in both stands were randomly distributed as related to non-forked tree positions. Finally, Moran’s I values were not very high, though significant genetic autocorrelation was identified at distances up to 20 m in the young stand, suggesting the existence of distinct family structures. However, no significant genetic structuring was observed in the old stand. Our findings suggest that spatial genetic patterns are impacted by stand age, environmental factors and human activities. The spatial distribution of forked trees was not clearly associated to family structures. Random effects and also micro-environmental variation could be additional factors explaining forking of beech individuals.

/pdf/spatial-patterns-and-genetic-structures-within-beech-3muot48ed0.pdf

H. H. Hattemer

Papers

Genetic distance between populations

Reproductive systems in conifer seed orchards

Genetic structures as indicators for adaptation and adaptational potentials

Gene resources and gene conservation in forest trees: General concepts

Spatial patterns and genetic structures within beech populations (Fagus sylvatica L.) of forked and non-forked individuals