Although microsatellites are a very efficient tool for many population genetics applications, they may occasionally produce “null” alleles, which, when present in high proportion, may affect estimates of key parameters such as inbreeding and relatedness coefficients or measures of genetic differentiation. In order to account for the presence of null alleles, it is first necessary to estimate their frequency within studied populations. However, the commonly used null allele frequency estimators are not of general applicability because they can produce upwardly biased estimates when a population under study experiences some inbreeding. In such a case, 2 formerly described approaches, population inbreeding model and individual inbreeding model, can be applied for simultaneous estimation of null allele frequencies and of the inbreeding coefficient. In this study, we demonstrate the properties and utility of these 2 methods and show that they outperform the commonly used approaches in the estimation of null allele frequencies based on genotypic data. The methods are applied to empirical data from a natural population of European beech (Fagus sylvatica L.), and results are briefly discussed. The methods presented in this paper are implemented in the Windows-based user-friendly INEST computer program (available free of charge at http://genetyka.ukw.edu.pl/INEst10_setup.exe).

Estimating seed and pollen gene flow in plants on the basis of samples of naturally regenerated seedlings can provide much needed information about “realized gene flow,” but seems to be one of the greatest challenges in plant population biology. Traditional parentage methods, because of their inability to discriminate between male and female parentage of seedlings, unless supported by uniparentally inherited markers, are not capable of precisely describing seed and pollen aspects of gene flow realized in seedlings. Here, we describe a maximum-likelihood method for modeling female and male parentage in a local plant population on the basis of genotypic data from naturally established seedlings and when the location and genotypes of all potential parents within the population are known. The method models female and male reproductive success of individuals as a function of factors likely to influence reproductive success (e.g., distance of seed dispersal, distance between mates, and relative fecundity–i.e., female and male selection gradients). The method is designed to account for levels of seed and pollen gene flow into the local population from unsampled adults; therefore, it is well suited to isolated, but also wide-spread natural populations, where extensive seed and pollen dispersal complicates traditional parentage analyses. Computer simulations were performed to evaluate the utility and robustness of the model and estimation procedure and to assess how the exclusion power of genetic markers (isozymes or microsatellites) affects the accuracy of the parameter estimation. In addition, the method was applied to genotypic data collected in Scots pine (isozymes) and oak (microsatellites) populations to obtain preliminary estimates of long-distance seed and pollen gene flow and the patterns of local seed and pollen dispersal in these species.

Polyploids, organisms that have multiple sets of chromosomes, are common in certain plant and animal taxa. However, there are only a few reports of intraspecific ploidy variation within the genus Quercus. The aim of the study was to investigate the suspected ploidy level of two oaks that have unusual microsatellite banding patterns. Polyploidy was investigated by using microsatellite analysis, stomata length measurements and nuclear DNA content estimation by flow cytometry. Each putative triploid tree has patterns of microsatellite variation unexpected for diploid genomes, with up to three alleles at some loci, significantly longer stomata and 1.5 times more DNA per nucleus compared with diploids. To our knowledge, this report contains the first evidence for triploidy in Q. petraea and confirmation of this phenomenon in Q. robur. Regardless of the positive or negative aspects of the presence of triploid oaks in forest stands, it is of value to be able to screen for them. This study demonstrates that nuclear microsatellites and estimation of DNA content by flow cytometry can readily be used for this purpose.