The Galician sympatric ecotypes of Littorina saxatilis have been proposed as a model system for studying parallel ecological speciation. Such a model system makes a clear prediction: candidate loci (for divergent adaptation) should present a higher level of geographical differentiation than noncandidate (neutral) loci. We used 2356 amplified fragment length polymorphisms (AFLPs) and four micros...

Genotypes for melatonin receptor type 1A (MTNR1A) and Calpastatin (CAST) were determined by enzymatic digestion of PCR products and Calpain(CAPN) genotype detected by PCR-SSCP method in Iranian Karakul sheep. Blood samples were collected from 100 purebred Karakul sheep. The extraction of genomic DNA was based on guanidinium thiocyanate- silica gel method. PCR amplicons were digested with restri...

This paper presents a method for identifying image loci that can be used as a basis for object segmentation and image registration. The focus is on 1D and 2D shape loci in 3D images. This method, called marching ridges, uses generalized height ridges, oriented medialness measures and a marching cubes like algorithm to extract optimal scale-orientation cores. This algorithm can can also be used ...

The potential epistasis that may explain a large portion of the phenotypic variation for complex traits has been ignored in many genetic association studies. A Baysian method using a Gibbs sampler was introduced to draw inferences about multilocus genotypic effects based on their marginal posterior distributions by a Gibbs sampler. This method would be applied to studies for interaction effects...

Susceptibility loci identified by GWAS generally account for a limited fraction of heritability. Predictive models based on identified loci also have modest success in risk assessment and therefore are of limited practical use. Many methods have been developed to overcome these limitations by incorporating prior biological knowledge. However, most of the information utilized by these methods is...

The HLA system has been extensively studied from an evolutionary perspective. Although it is clear that selection has acted on the genes in the HLA complex, the nature of this selection has yet to be fully clarified. A study of constrained disequilibrium values is presented that is applicable to HLA and other less polymorphic systems with three or more linked loci, with the purpose of identifyi...

Outlier detection is an integral part of data mining and has attracted much attention recently [BKNS00, JTH01, KNT00]. In this paper, we propose a new method for evaluating outlier-ness, which we call the Local Correlation Integral (LOCI). As with the best previous methods, LOCI is highly effective for detecting outliers and groups of outliers (a.k.a. micro-clusters). In addition, it offers the...

Molecular ecologists seek to genotype hundreds to thousands of loci from hundreds to thousands of individuals at minimal cost per sample. Current methods, such as restriction-site-associated DNA sequencing (RADseq) and sequence capture, are constrained by costs associated with inefficient use of sequencing data and sample preparation. Here, we introduce RADcap, an approach that combines the maj...