Stellarator equilibria and the problem of position control

Interpolation frequency maps (% of the population) of broadly distributed H sub-clades (H2, H4, H5 and H6). Map templates were taken from Natural Earth free map repository ( http://www.naturalearthdata.com/ ). (PDF 2058 kb

Construction of a YAC contig covering human chromosome 6p22

A contig covering human chromosome 6p22 that consists of 134 YAC clones aligned based on the presence/absence of 52 DNA markers is presented. This contig overlaps with the 6p23 contig at its telomeric end and with the 6p21.3 contig at its centromeric end. The order of loci within the contig resolves the relative positions of several genetically mapped markers. Among the additional markers used here, there are eight novel PCR assays. The 12 known genes and anonymous ESTs located within the contig establish a first step toward a transcriptional map of this region. The instability of YAC clones observed during this work is also discussed. (C) 1996 Academic Press, Inc

Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data

We estimate parameters of a general isolation-with-migration model using resequence data from mitochondrial DNA (mtDNA), the Y chromosome, and two loci on the X chromosome in samples of 25-50 individuals from each of 10 human populations. Application of a coalescent-based Markov chain Monte Carlo technique allows simultaneous inference of divergence times, rates of gene flow, as well as changes in effective population size. Results from comparisons between sub-Saharan African and Eurasian populations estimate that 1500 individuals founded the ancestral Eurasian population similar to 40 thousand years ago (KYA). Furthermore, these small Eurasian founding populations appear to have grown much more dramatically than either African or Oceanian populations. Analyses of sub-Saharan African populations provide little evidence for a history, of population bottlenecks and suggest that die), began diverging from one another upward of 50 KYA. We surmise that ancestral African populations had already been geographically structured prior to the founding of ancestral Eurasian populations. African populations are shown to experience low levels of mitochondrial DNA gene flow, but high levels of Y chromosome gene flow. In particular, Y chromosome gene flow appears to be asymmetric, i.e., from the Bantu-speaking population into other African populations. Conversely, mitochondrial gene flow is more extensive between non-African populations, but appears to be absent between European and Asian Populations

CYP1A1 Variability In Human Populations

The human cytochrome P4501A1 (CYP1A1) enzyme plays an important role in the metabolism of xenobiotics and endogenous substrates. Because polymorphisms within the CYP1A1 gene have been shown to be associated with various cancer risks and with the predicting clinical efficacy of some chemotherapies in different populations, most studies focus on their clinical significance. We, however, were interested in evaluating whether the polymorphisms could be used to distinguish human populations. Four single nucleotide CYP1A1 polymorphisms (rs4646903/ g.75011641; rs1048943/g.75012985; g.75012235; and rs1799814/ g.75012987) were analysed via PCR-RFLP assay in 1,195 individuals of various human groups from all over the world. In order to gain a more complete view of the genetic variability of the CYP1A1 gene, different statistical analyses were performed upon the populations of the present study and upon the limited data gleaned from previously studied populations. The allele and haplotype frequencies vary among populations: the rs4646903 (C) and rs1048943 (G) have been found to be nearly always linked and were found at the highest frequencies in Native Americans, while the variant associated to the position g.75012235 was only detected in certain African populations. Our work clearly indicates that the CYP1A1 polymorphisms differ among populations and that the prediction of genotypes constitutes an important aspect of precision medicine since some variants were associated with certain cancers and rs1048943 show strong association with optimized chemotherapy. Moreover, the CYP1A1 gene plays an important role in the metabolism of xenobiotics and it is likely that its frequencies could be strongly influenced by environmental factors

Trophic niches of four sympatric rainforest anurans from southern Nigeria: does resource partitioning play a role in structuring the community ?

Le partage des ressources est un mécanisme qui peut réduire l'intensité de la compétition interspécifique dans un cortège d'espèces syntopiques, morphologiquement et éco-éthologiquement semblables. La documentation du partage des ressources, entre quatre espèces d'Anoures sympatriques, a été recherchée par l'examen du régime alimentaire (par dissection stomacale) de spécimens obtenus auprès de fournisseurs de viande de brousse dans le sud-est du Nigéria. Pour l'ensemble des quatres espèces, nous avons trouvé au total 32 différents types de proies. Ptychadena oxyrhynchus en a consommé 28, contre 17 pour P. aequiplicata, 15 pour Bufo maculatus et 10 seulement pour Hoplobatrachus occipitalis. Pour les courbes cumulatives de diversité des trois premières espèces un plateau a été atteint, montrant que la composition des régimes pouvait être considérée comme correctement établie. Les proies communes, consommées par les quatre espèces d'Anoures, étaient des Formicoidea, des Coléoptères adultes, des Aranéides, des Isopodes, des Oligochètes et des Pulmonés. Les proies communes, consommées par trois des quatre amphibiens, étaient des Dermaptères, des Hémiptères, des Odonates adultes et des Orthoptères. Les largeurs de tête variaient significativement entre les espèces d'Anoures ; toutefois, les deux espèces de Ptychadena ne montraient pas de différence significative entre elles sur ce point Pour trois espèces, la largeur de tête était significativement corrélée au volume de proies dans l'estomac. Le partage des ressources (en termes de types de proies) a été trouvé particulièrement net entre deux espèces de Ptychadena étroitement apparentées. La divergence entre Ptychadena oxyrhynchus et P. aequiplicata apparut telle que des analyses multivariées ont placé chacune d'elles, du point de vue alimentaire, plus près de Hoplobatrachus occipitalis ou de Bufo maculatus que de son congénère. Une divergence si forte semblerait jouer un rôle majeur dans le maintien de la structure de ce peuplement mixte d'Anoures.Resource partitioning is a mechanism that can reduce the intensity of inter-specifie competition between morphologically and eco-ethologically similar, syntopic species . Evidence for resource partitioning, between four syntopic anuran species, was investigated by examining the diet (through stomach dissection) of frogs bought from bush meat traders in southeastern Nigeria . Considering the four species together, a total of 32 different prey types were found. Ptychadena oxyrhynchus consumed 28 of them, while P. aequiplicata consumed 17 , Bufo maculatus 15 and Hoplobatrachus occipitalis only 10. For the first three species, the cumulative-diversity curves indicated that a plateau phase was reached, i .e . that the prey composition could be considered reliably assessed. Common prey items, which were consumed by all four anuran species, were : Formicoidea, Coleoptera adults, Araneidae, Jsopoda, Oligochaeta, and Pulmonata. Common prey items, which were consumed by three of the four amphibians, were : Dermaptera, Hemiptera, Odonata adults, and Orthoptera. Head width varied significantly between species, but there was no statistical difference between the two Ptychadena species. Head width was significantly correlated with prey volume in the stomach in each of three species. Resource partitioning (in terms of prey types) was found to be particularly strong between two closely related species of Ptychadena. The divergence bewteen Ptychadena oxyrhynchus and P. aequiplicata was such that multivariate analyses placed each one of them closer in feeding ecology to either Hoplobatrachus occipitalis or Bufo maculatus, than to their congener. Such strong divergence is hypothesized to play a major role in maintaining the structure of this mixed anuran community

Population stratification may bias analysis of PGC-1α as a modifier of age at Huntington disease motor onset

Huntington’s disease (HD) is an inherited neurodegenerative disorder characterized by motor, cognitive and behavioral disturbances, caused by the expansion of a CAG trinucleotide repeat in the HD gene. The CAG allele size is the major determinant of age at onset (AO) of motor symptoms, although the remaining variance in AO is highly heritable. The rs7665116 SNP in PPARGC1A, encoding the mitochondrial regulator PGC-1α, has been reported to be a significant modifier of AO in three European HD cohorts, perhaps due to affected cases from Italy. We attempted to replicate these findings in a large collection of (1,727) HD patient DNA samples of European origin. In the entire cohort, rs7665116 showed a significant effect in the dominant model (p value = 0.008) and the additive model (p value = 0.009). However, when examined by origin, cases of Southern European origin had an increased rs7665116 minor allele frequency (MAF), consistent with this being an ancestry-tagging SNP. The Southern European cases, despite similar mean CAG allele size, had a significantly older mean AO (p < 0.001), suggesting population-dependent phenotype stratification. When the generalized estimating equations models were adjusted for ancestry, the effect of the rs7665116 genotype on AO decreased dramatically. Our results do not support rs7665116 as a modifier of AO of motor symptoms, as we found evidence for a dramatic effect of phenotypic (AO) and genotypic (MAF) stratification among European cohorts that was not considered in previously reported association studies. A significantly older AO in Southern Europe may reflect population differences in genetic or environmental factors that warrant further investigation

The Y-Chromosome Tree Bursts into Leaf: 13,000 High-Confidence SNPs Covering the Majority of Known Clades

Many studies of human populations have used the male-specific region of the Y chromosome (MSY) as a marker, but MSY sequence variants have traditionally been subject to ascertainment bias. Also, dating of haplogroups has relied on Y-specific short tandem repeats (STRs), involving problems of mutation rate choice, and possible long-term mutation saturation. Next-generation sequencing can ascertain single nucleotide polymorphisms (SNPs) in an unbiased way, leading to phylogenies in which branch-lengths are proportional to time, and allowing the times-to-most-recent-common-ancestor (TMRCAs) of nodes to be estimated directly. Here we describe the sequencing of 3.7 Mb of MSY in each of 448 human males at a mean coverage of 51x, yielding 13,261 high-confidence SNPs, 65.9% of which are previously unreported. The resulting phylogeny covers the majority of the known clades, provides date estimates of nodes, and constitutes a robust evolutionary framework for analyzing the history of other classes of mutation. Different clades within the tree show subtle but significant differences in branch lengths to the root. We also apply a set of 23 Y-STRs to the same samples, allowing SNP- and STR-based diversity and TMRCA estimates to be systematically compared. Ongoing purifying selection is suggested by our analysis of the phylogenetic distribution of nonsynonymous variants in 15 MSY single-copy genes

Haplotype differences for copy number variants in the 22q11.23 region among human populations: a pigmentation-based model for selective pressure.

Two gene clusters are tightly linked in a narrow region of chromosome 22q11.23: the macrophage migration inhibitory factor (MIF) gene family and the glutathione S-transferase theta class. Within 120 kb in this region, two 30-kb deletions reach high frequencies in human populations. This gives rise to four haplotypic arrangements, which modulate the number of genes in both families. The variable patterns of linkage disequilibrium (LD) between these copy number variants (CNVs) in diverse human populations remain poorly understood. We analyzed 2469 individuals belonging to 27 human populations with different ethnic origins. Then we correlated the genetic variability of 22q11.23 CNVs with environmental variables. We confirmed an increasing strength of LD from Africa to Asia and to Europe. Further, we highlighted strongly significant correlations between the frequency of one of the haplotypes and pigmentation-related variables: skin color (R2=0.675, P<0.001), distance from the equator (R2=0.454, P<0.001), UVA radiation (R2=0.439, P<0.001), and UVB radiation (R2=0.313, P=0.002). The fact that all MIF-related genes are retained on this haplotype and the evidences gleaned from experimental systems seem to agree with the role of MIF-related genes in melanogenesis. As such, we propose a model that explains the geographic and ethnic distribution of 22q11.23 CNVs among human populations, assuming that MIF-related gene dosage could be associated with adaptation to low UV radiatio