The genetic diversity and introgression of Juglans regia and Juglans sigillata in Tibet as revealed by SSR markers

We demonstrate that the mean ratio of the number of alleles to the range in allele size, which we term M, calculated from a population sample of microsatellite loci, can be used to detect reductions in population size. Using simulations, we show that, for a general class of mutation models, the value of M decreases when a population is reduced in size. The magnitude of the decrease is positively correlated with the severity and duration of the reduction in size. We also find that the rate of recovery of M following a reduction in size is positively correlated with post-reduction population size, but that recovery occurs in both small and large populations. This indicates that M can distinguish between populations that have been recently reduced in size and those which have been small for a long time. We employ M to develop a statistical test for recent reductions in population size that can detect such changes for more than 100 generations with the post-reduction demographic scenarios we examine. We also compute M for a variety of populations and species using microsatellite data collected from the literature. We find that the value of M consistently predicts the reported demographic history for these populations. This method, and others like it, promises to be an important tool for the conservation and management of populations that are in need of intervention or recovery.

Microsatellite markers are routinely used to investigate the genetic structuring of natural populations. The knowledge of how genetic variation is partitioned among populations may have important implications not only in evolutionary biology and ecology, but also in conservation biology. Hence, reliable estimates of population differentiation are crucial to understand the connectivity among populations and represent important tools to develop conservation strategies. The estimation of differentiation is c from Wright's FST and/or Slatkin's RST, an FST -analogue assuming a stepwise mutation model. Both these statistics have their drawbacks. Furthermore, there is no clear consensus over their relative accuracy. In this review, we first discuss the consequences of different temporal and spatial sampling strategies on differentiation estimation. Then, we move to statistical problems directly associated with the estimation of population structuring itself, with particular emphasis on the effects of high mutation rates and mutation patterns of microsatellite loci. Finally, we discuss the biological interpretation of population structuring estimates.

Currently, there is a demand for software to analyze polymorphism data such as microsatellite DNA and single nucleotide polymorphism with easily accessible interface in many fields of research. In this article, we would like to make an announcement of POPTREE2, a computer program package, that can perform evolutionary analyses of allele frequency data. The original version (POPTREE) was a command-line program that runs on the Command Prompt of Windows and Unix. In POPTREE2 genetic distances (measures of the extent of genetic differentiation between populations) for constructing phylogenetic trees, average heterozygosities (H) (a measure of genetic variation within populations) and G(ST) (a measure of genetic differentiation of subdivided populations) are computed through a simple and intuitive Windows interface. It will facilitate statistical analyses of polymorphism data for researchers in many different fields. POPTREE2 is available at http://www.med.kagawa-u.ac.jp/ approximately genomelb/takezaki/poptree2/index.html.