The use of posterior probabilities to summarize genotype uncertainty is pervasive across genotype, sequencing and imputation platforms. Prior work in many contexts has shown the utility of incorporating genotype uncertainty (posterior probabilities) in downstream statistical tests. Typical approaches to incorporating genotype uncertainty when testing Hardy-Weinberg equilibrium tend to lack cali...

this study was carried out to investigate the genetic diversity and population structure of 90 specimens of oxynoemacheilus argyrogramma collected from sepidbarg, gamasiab and ghaleji rivers, in the west of iran. analyses using three microsatellite loci indicated that the average number of alleles in the population was 12, which was well above the reported values for freshwater fishes. the expe...

This paper aims to show that certain syntactic differences between arguments and adjuncts can be thought of as a transparent reflection of differences between their contributions to neo-Davidsonian logical forms. Specifically, the crucial underlying distinction will be that between modifying an event variable directly, and modifying an event variable indirectly via a thematic relation. I note a...

Panmixia is a key issue in maintaining genetic diversity, which facilitates evolutionary potential during environmental changes. Additionally, conservation biologists suggest the importance of avoiding small or subdivided populations, which are prone to losing genetic diversity. In this paper, computer simulations were performed to the genetic drift of neutral alleles in random mating populatio...

Amethod of complexity control in multinomial mixture modeling of multiple-marker genotype data, imposing the Hardy-Weinberg equilibrium (HWE) between the genotype values, is studied. This is a very natural restriction and known to hold at population level under modest assumptions. The hypothesis under study is that imposing this restriction will prevent overfitting and lead to a better model. T...

Seven single-nucleotide polymorphism (SNP) sites located in ASAP1 gene have been found associated with tuberculosis (TB) susceptibility by genome-wide association studies in Russia. The case-control study was carried out to test whether these seven SNPs were associated with susceptibility to TB in a Chinese Xinjiang Muslim population. The seven SNPs were genotyped in a case-control design that ...

The chicken growth hormone gene of intron I region from three varieties of Kadaknath breed of poultry was amplified by PCR and a 770 bp product was obtained. The products from each variety (Jet black, Golden and Pencilled) were digested with Msp I (5 U), which recognizes the 5′-C ↓ C G G-3′ sequence. The RFLP pattern revealed restriction fragments of 529, 373, 241 and 156 bp sizes, which indica...

Deviations from Hardy-Weinberg equilibrium (HWE) can indicate inbreeding, population stratification, and even problems in genotyping. In samples of affected individuals, these deviations can also provide evidence for association. Tests of HWE are commonly performed using a simple chi2 goodness-of-fit test. We show that this chi2 test can have inflated type I error rates, even in relatively larg...

We analyze the general (multiallelic) Hardy-Weinberg equilibrium problem from an objective Bayesian testing standpoint. We argue that for small or moderate sample sizes the answer is rather sensitive to the prior chosen, and this suggests to carry out a sensitivity analysis with respect to the prior. This goal is achieved through the identification of a class of priors specifically designed for...