Gene flow between genetically distinct populations creates linkage disequilibrium (admixture linkage disequilibrium [ALD]) among all loci (linked and unlinked) that have different allele frequencies in the founding populations. We have explored the distribution of ALD by using computer simulation of two extreme models of admixture: the hybrid-isolation (HI) model, in which admixture occurs in a...

Linkage disequilibrium has been a powerful tool in identifying rare disease alleles in human populations. To date, most research has been directed to isolated populations which have undergone a bottleneck followed by rapid exponential expansion. While this strategy works well for rare diseases in which all disease alleles in the population today are clonal copies of some common ancestral allele...

The approximate variance for the standardized measure of gametic linkage disequilibrium has been described. However, this approach assumes knowledge of the phase of double heterozygotes or Hardy-Weinberg equilibrium. Here we give the approximate variance for a composite measure of linkage disequilibrium which depends only on genotype frequencies. We show by simulation that this variance approxi...

RESULTS: All 16 KIR genes known were observed in the Albanian individuals and framework genes (KIR3DL3, KIR3DP1, KIR2DL4, and KIR3DL2) were present in all individuals. The frequencies of other KIR genes were: KIR2DP1 (0.981), KIR2DL1 (1), KIR2DL2 (0.615), KIR2DL3 (0.865), KIR2DL5 (0.414), KIR3DL1 (0.933), KIR2DS1 (0.462), KIR2DS2 (0.606), KIR2DS3 (0.327), KIR2DS4 (0.875), KIR2DS5 (0.298), and K...

The basis of susceptibility to rheumatoid arthritis (RA) is complex, comprising genetic and environmental susceptibility factors. We have reviewed the available approaches to the investigation of the genetic basis of complex diseases and how these are being applied to RA. Affected-sibling-pair methods for nonparametric linkage analysis, linkage-disequilibrium-based approaches, transmission dise...

The fixation of advantageous mutations by natural selection has a profound impact on patterns of linked neutral variation. While it has long been appreciated that such selective sweeps influence the frequency spectrum of nearby polymorphism, it has only recently become clear that they also have dramatic effects on local linkage disequilibrium. By extending previous results on the relationship b...

Models of background variation in genomic regions form the basis of linkage disequilibrium mapping methods. In this work we analyze a background model that groups SNPs into haplotype blocks and represents the dependencies between blocks by a Markov chain. We develop an error measure to compare the performance of this model against the common model that assumes that blocks are independent. By ex...

A model of functional epistasis is proposed in which it is assumed that coupling and repulsion genotypes differ in metabolic efficiency and thus in development time and net fecundity. The implications of this model are investigated for iteroparous populations with fluctuating rates of increase. It is found that the fluctuations in rate of increase can lead to large fluctuations in gamete freque...

Linkage disequilibrium has become important in the context of gene mapping. We argue that to understand the pattern of association between alleles at different loci, and of DNA sequence polymorphism in general, it is useful first to consider the underlying genealogy of the chromosomes. The stochastic process known as the coalescent is a convenient way to model such genealogies, and in this pape...