Biomedical subjects

K Belkhir

Publications and source records attributed to K Belkhir.

6 recordsLinked to original sources

PubMed2004

Mouse biodiversity in the genomic era.

Comparative genomics has developed by comparison of distantly related genomes, for which the link between the reported evolutionary changes and species development/physiology/ecology is not obvious. It is argued that the mouse (genus Mus) is an optimal model for microevolutionary genomics in vertebrates. This is because the mouse genome sequence, physical and genetic map have been completed, because mouse genetics, morpho-anatomy, pathology, behavior and ecology are well-studied, and because the Mus genus is a diverse, well- documented taxon, allowing comparative studies at the level of individual, population, subspecies, and species. The potential of the interaction between mouse genome and mouse biodiversity is illustrated by recent studies of speciation in the house mouse Mus musculus, and studies about the evolution of isochores, the peculiar pattern of GC-content variation across mammalian genomes.

Animals↗

PubMed2002

Heterozygote deficiencies in small lacustrine populations of brook charr Salvelinus Fontinalis Mitchill (Pisces, Salmonidae): a test of alternative hypotheses.

Empirical studies of natural populations have commonly reported departures from Hardy-Weinberg expected proportions of heterozygote individuals. Recent advances in statistical population genetics now offer the potential to exploit individual multilocus genotypic information to test more rigorously for possible sources of heterozygote deficiencies. In a previous study in lacustrine brook charr (Salvelinus fontinalis), we reported stronger deficits in small than in large lakes. In the present paper, we propose a methodology for empirically testing alternative hypotheses to identify the cause of the deficits observed in three of the smallest lakes (85, 109 and 182 ha) analysed. First, as in several salmonid species, brook charr may exhibit a trophic polymorphism in north temperate lakes. If morphs are genetically divergent, indiscriminate sampling of both forms would result in less heterozygote individuals than expected in a randomly mating population (Wahlund effect). Using an individual-based method aiming at detecting cryptic population structure, we can reject this explanation as the sole source of deficits for all three lakes. Secondly, mating among relatives could also be frequent in small lakes and lead to heterozygote deficiencies. Significantly more fish than expected at random had low individual multilocus heterozygosity in two of the lakes, suggesting that inbred fish may have been present. Thirdly, sampling of genetically related fish would also lead to departures from Hardy-Weinberg proportions. In the same two lakes, the distribution of pairwise relatedness coefficients departed from its random expectation, suggesting that non-random sampling of kin may have occurred.

Animals↗

PubMed2002

Chromosomal and allozyme analysis of a hybrid zone between parapatric Robertsonian races of the house mouse: a case of monobrachial homology.

A detailed chromosomal and allozyme analysis of Robertsonian (Rb) populations of the house mouse in Alsace (France) was performed to evaluate the model of speciation by monobrachial centric fusions. The karyological analysis confirmed the existence of a hybrid zone between two Rb races differentiated by monobrachially homologous Rb fusions. The clinical distribution of Rb fusions showed that almost no overlap occurred between the Rb fusions specific to each race, indicating the presence of an acrocentric peak in the center of the hybrid zone. Thus, only chromosomal heterozygotes carrying one to three trivalents were present, instead of the expected highly unfit interracial hybrids, none of which were observed. The effect of karyotypic differentiation on genic divergence was tested across the hybrid zone by comparing levels of genetic structure for chromosomal and allozyme markers according to the isolation by distance model. Results confirmed the highly significant spatial structure for chromosomes, but revealed none for allozymes, indicating that genic diversity was not structured according to karyotype. These data suggest the absence of a strong chromosomal barrier to gene flow, which does not conform with predictions of the model of speciation by monobrachial centric fusions. In addition, the relatedness of these Rb races to neighboring ones, as well as the nonrandom contribution of several chromosomes to the Rb fusions, was analyzed.

Animals↗

PubMed2001

A Bayesian approach to the identification of panmictic populations and the assignment of individuals.

We present likelihood-based methods for assigning the individuals in a sample to source populations, on the basis of their genotypes at co-dominant marker loci. The source populations are assumed to be at Hardy-Weinberg and linkage equilibrium, but the allelic composition of these source populations and even the number of source populations represented in the sample are treated as uncertain. The parameter of interest is the partition of the set of sampled individuals, induced by the assignment of individuals to source populations. We present a maximum likelihood method, and then a more powerful Bayesian approach for estimating this sample partition. In general, it will not be feasible to evaluate the evidence supporting each possible partition of the sample. Furthermore, when the number of individuals in the sample is large, it may not even be feasible to evaluate the evidence supporting, individually, each of the most plausible partitions because there may be many individuals which are difficult to assign. To overcome these problems, we use low-dimensional marginals (the 'co-assignment probabilities') of the posterior distribution of the sample partition as measures of 'similarity', and then apply a hierarchical clustering algorithm to identify clusters of individuals whose assignment together is well supported by the posterior distribution. A binary tree provides a visual representation of how well the posterior distribution supports each cluster in the hierarchy. These methods are applicable to other problems where the parameter of interest is a partition of a set. Because the co-assignment probabilities are independent of the arbitrary labelling of source populations, we avoid the label-switching problem of previous Bayesian methods.

Algorithms↗

PubMed1991

[New Robertsonian populations of the house mouse (Mus musculus domesticus) from north of the Alps].

New Robertsonian (Rb) populations of the house mouse (Mus musculus domesticus) carrying different combinations of centric fusions are reported in France, Switzerland, and Germany. In Alsace (France), the diploid number varied from 2n = 38 to 34; four fusions were present, with Rb(4.12) homozygous in all populations whereas Rb(5.10), Rb(5.7), or Rb(10.14) were found to be segregating. In Switzerland, only all-acrocentric mice (2n = 40) were present in Bern while Rb(5.7) and Rb(9.16) occurred in Basel. In the Konstanz locality from southern Germany, all the mice were homozygous for nine Rb fusions: Rb(1.18), Rb(2.5), Rb(3.6), Rb(4.12), Rb(7.15), Rb(8.17), Rb(9.14), Rb(10.11), and Rb(13.16). The phylogenetic relationship of these new Rb populations with those already known is discussed.

Animals↗

PubMedDate not supplied

DetSel 1.0: a computer program to detect markers responding to selection.

Estimating population parameters from polymorphism frequency data requires neutral genetic markers. Any departure from neutrality may invalidate the inferences drawn from such analyses. We recently discussed the possibility of identifying markers that show deviation from neutral expectations in pairwise comparisons of diverging populations. We are now releasing a user-friendly software package that implements all the necessary steps to identify the signature of selection among molecular markers in a set of polymorphism data. This software can be downloaded free of charge at http://www.univ-montp2.fr/~genetix/detsel/detsel.html.

Data Interpretation, Statistical↗