The article presents an algorithm and an application to estimate haplotype frequencies from genotype data for unrelated individuals. Presented approach can handle loci with multiple alleles as well as silent (null) alleles. The mathematical model and an expanded Expectation-Maximization algorithm is described. The computer program, called NullHap, available freely at http://staff.elka.pw.edu.pl...

To determine genetic characteristics of the maternal lineage of the Kiso horse based on polymorphisms of the mitochondrial DNA D-loop region, we collected blood samples from 136 Kiso horses, 91% of the entire population, and sequenced 411 bp from 15,437 to 15,847 in the region. First of all, we estimated the demographic history; by searching homology between the obtained and known sequences usi...

Reproductive development of higher plants comprises successive events of organ differentiation and growth which finally lead to the formation of a mature fruit. However, most of the genetic and molecular mechanisms which coordinate such developmental events are yet to be identified and characterized. Arlequin (Alq), a semi-dominant T-DNA tomato mutant showed developmental changes affecting flow...

Background Past climate changes have severely influenced the current distribution of species and their genetic diversity. Phylogeography is the study of the principles and processes governing the geographic distributions of genealogical lineages [1]. South America has the world’s largest area of swamps, floodplains and wetlands in general [2]. Brazil’s major wetlands cover 2% of the country’s h...

In this paper, we propose a multiscale coupling approach to performMonte-Carlo simulations on systems described at the atomic scale and subjected to random phenomena. The method is based on the Arlequin framework, developed to date for deterministic models involving coupling a region of interest described at a particle scale with a coarser model (continuum model). The new method can result in a...

The paper deals with the issue of accuracy for multiscale methods applied to solve stochastic problems. It more precisely focuses on the control of a coupling, performed using the Arlequin framework, between a deterministic continuum model and a stochastic continuum one. Using residual-type estimates and adjoint-based techniques, a strategy for goal-oriented error estimation is presented for th...

Variable microsatellite DNA markers are powerful tools to study parentage and gene flow in fish populations. In this work, we cloned and characterized 60 (GT) repeat microsatellite sequences from the bluegill sunfish (Lepomis macrochirus) genome. We report the frequency distribution, the lengths, and the proportions of the repeat classes for comparison with microsatellites isolated from other t...

We present the mathematical study of a computational approach originally introduced by R. Cottereau in [R. Cottereau, IJNME 2013]. The aims at evaluating effective (a.k.a. homogenized) coefficient medium with some fine-scale structure. It combines, using Arlequin coupling method, original description an and optimizes upon to best fit response equivalent purely homogeneous medium. prove here tha...