The possibility of investigation of the genetic structure of the temperate actinophage phi C31 of Streptomyces coelicolor A3(2).
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Bacteriophages↗
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Genetic structure of Salmonella revealed by fragment analysis.
Recently, the genus Salmonella has been studied by multilocus enzyme electrophoresis (MLEE) and three collections of strains defined by this method, SARA, SARB and SARC, have been assembled to represent the genetic diversity of Salmonella choleraesuis (commonly known as Salmonella enterica) subspecies I and of the genus as a whole. The novel technique fluorescent amplified-fragment length polymorphism (FAFLP) analysis was applied to these collections to determine the genetic diversity of Salmonella. FAFLP broadly confirmed the MLEE findings but added precision to them, successfully distinguishing between the subspecies of S. enterica. It revealed the clonal nature of some serotypes of S. enterica subspecies I and the diversity of others. The enteric Salmonella Paratyphi B strains clustered separately from those associated with gastroenteritis. FAFLP is a powerful, highly flexible, whole-genome method that can be used to provide an unweighted view of genetic variation within Salmonella.
Animals↗
Geographical and altitudinal population genetic structure of two dung fly species with contrasting mobility and temperature preference.
Local adaptation of populations requires some degree of spatio-temporal isolation. Previous studies of the two dung fly species Scathophaga stercoraria and Sepsis cynipsea have revealed low levels of geographic and altitudinal genetic differentiation in quantitative life history and morphological traits, but instead high degrees of phenotypic plasticity. These patterns suggest that gene flow is extensive despite considerable geographic barriers and large spatio-temporal variation in selection on body size and related traits. In this study we addressed this hypothesis by investigating genetic differentiation of dung fly populations throughout Switzerland based on the same 10 electrophoretic loci in each species. Overall, we found no significant geographic differentiation of populations for either species. This is inconsistent with the higher rates of gene flow expected due to better flying capacity of the larger S. stercoraria. However, heterozygote deficiencies within populations indicated structuring on a finer scale, seen for several loci in S. cynipsea, and for the locus PGM (Phosphoglucomutase) in S. stercoraria. Additionally, S. cynipsea showed a tendency towards a greater gene diversity at higher altitudes, mediated primarily by the locus MDH (malate dehydrogenase), at which a second allele was only present in populations above 1000 m. This may be caused by increased environmental stress at higher altitudes in this warm-adapted species. MDH might thus be a candidate locus subject to thermal selection in this species, but this remains to be corroborated by direct evidence. In S. stercoraria, no altitudinal variation was found.
Altitude↗
Fine-scale genetic structure of grape phylloxera from the roots and leaves of Vitis.
Patterns of variation at microsatellite loci suggest that root populations of the pest grape phylloxera (Daktulosphaira vitifoliae) are largely parthenogenetic in Australian vineyards. To investigate reproduction in leaf galling phylloxera and the association between these individuals and phylloxera on roots, we examined in detail genetic variation in phylloxera from a vineyard block. Some genotypes found on leaf galls within this block were not present on roots, whereas others spanned both zones. There was no evidence that genotypes on roots were the product of sexual reproduction in leaf galls. mtDNA variation was not associated with the location of the phylloxera clones. The spatial distribution of genotypes within a root population was further investigated by intensively sampling phylloxera from another vineyard block. Join-count spatial autocorrelation statistics were used to explore fine-scale spatial structure. Clones were nonrandomly distributed within the block and there was evidence that the distribution of clones followed rows. These findings suggest firstly that there is limited dispersal of root and leaf feeding phylloxera, and secondly that factors, other than vine host, are likely to be important and contribute to clonal structure within populations.
Animals↗
The AH-receptor: genetics, structure and function.
The AH-receptor is a ligand-activated transcription factor that regulates a number of biological responses to planar aromatic hydrocarbons. Interest in this receptor is related to its role in the toxic action of a variety of environmental chemicals, the simplicity and elegance of the murine genetics that led to its characterization and the distinctive mechanism by which this receptor activates gene expression. Recent cloning experiments have demonstrated that the AH-receptor is structurally related to the Per, ARNT and Sim proteins. Members of this newly described gene family are characterized by two N-terminal domains, the most characteristic of which is a motif referred to as a PAS domain. In the AH-receptor, this domain harbours sequences involved in the formation of a hydrophobic pocket that bind receptor agonists. Adjacent to the PAS domain in the AH-receptor, ARNT and Sim proteins is a basic/helix-loop-helix (bHLH) domain that appears to mediate heterodimerization and sequence specific DNA binding properties. The observation that the bHLH domain is present in the AH-receptor and the ARNT protein, a factor required for proper AH-receptor function, suggests that these proteins are heterodimeric partners that activate gene expression in a manner similar to Myc/Max and MyoD/E2A. The objectives of this review are to describe recent experimental results in this field and to use this information to develop a molecular model of AH-receptor mediated signal transduction.
Animals↗
Temporal variation in genetic structure of a colonising species: Aedes albopictus in the United States.
The medically important mosquito, Aedes albopictus, has recently become established in several locations within the United States. A three-year survey of temporal variation in allele frequencies at ten enzymatic loci in 17 populations was undertaken to determine the extent and direction of change since the colonization event. Significant, but non-directional, changes were detected in allele frequencies at most of the loci in all populations. Some alleles detected at low frequencies in earlier samples were not found in subsequent samples. Variance of allele frequencies remained unchanged. In at least two locations, there was an increase in mean heterozygosity, perhaps because of gene flow. There was no significant change in the levels of genetic variation within and among populations. The results from this study indicate that the breeding structure of Ae. albopictus in the U.S. did not differ substantially from that in a native habitat, either soon after colonisation or after several generations in the new habitat. We suggest that a large founder population, gene flow and a rapid population expansion could explain the present breeding structure of Ae. albopictus.
Aedes↗
Genetic structure of wild rice Oryza glumaepatula populations in three Brazilian biomes using microsatellite markers.
The existence of Oryza glumaepatula is threatened by devastation and, thus, the implementation of conservation strategies is extremely relevant. This study aimed to characterize the genetic variability and estimate population parameters of 30 O. glumaepatula populations from three Brazilian biomes using 10 microsatellite markers. The levels of allelic variability for the SSR loci presented a mean of 10.3 alleles per locus and a value of 0.10 for the average allelic frequency value. The expected total heterozygosity (H(e)) ranged from 0.63 to 0.86. For the 30 populations tested, the mean observed (H(o)) and expected heterozygosities (H(e)) were 0.03 and 0.11 within population, respectively, indicating an excess of homozygotes resulting from the preferentially self-pollinating reproduction habit. The estimated fixation index ( (IS) ) was 0.79 that differed significantly from zero, indicating high inbreeding within each O. glumaepatula population. The total inbreeding of the species ((IT) ) was 0.98 and the genetic diversity indexes among populations, (ST) and (ST), were 0.85 and 0.90, respectively, indicating high genetic variability among them. Thus, especially for populations located in regions threatened with devastation, it is urgent that in situ preservation conditions should be created or that collections be made for ex situ preservation to prevent loss of the species genetic variability.
Alleles↗
Multiple hybrid origins, genetic diversity and population genetic structure of two endemic Sorbus taxa on the Isle of Arran, Scotland.
Understanding the processes that have given rise to polyploid hybrid taxa is central to our understanding of plant evolution. In this study, we use an array of genetic markers in a population analysis to elucidate the hybrid origins of the Arran whitebeams Sorbus arranensis and S. pseudofennica, two woody plant taxa endemic to the Isle of Arran, Scotland. It has been proposed that S. arranensis was derived by hybridization between S. aucuparia and S. rupicola, and that subsequent hybridization between S. arranensis and S. aucuparia gave rise to S. pseudofennica. Analyses of species-specific isozyme, nuclear intron and chloroplast DNA markers confirm the proposed origin of S. arranensis, and indicate that S. aucuparia was the female parent in the hybridization. Analysis of microsatellite markers suggests that there have been at least three origins of S. arranensis on Arran. Microsatellite markers also support the proposed hypothesis for the origin of S. pseudofennica, and indicate at least five hybrid origins of this taxon. In total, three multilocus genotypes of S. arranensis and eight of S. pseudofennica were detected on Arran and multilocus genotypic diversity levels Hg were 0.09 and 0.63, respectively. Genetic differentiation (thetaST) values based on multilocus genotypes are substantial (0.344 and 0.470 for S. arranensis and S. pseudofennica, respectively) implying limited seed flow among populations. These results indicate that the endemic Sorbus taxa on Arran are the products of multiple and ongoing evolutionary events. This information must be incorporated into management policies for their future conservation.
Conservation of Natural Resources↗
The genetic structure of recombinant inbred mice: high-resolution consensus maps for complex trait analysis.
BACKGROUND: Recombinant inbred (RI) strains of mice are an important resource used to map and analyze complex traits. They have proved particularly effective in multidisciplinary genetic studies. Widespread use of RI strains has been hampered by their modest numbers and by the difficulty of combining results derived from different RI sets. RESULTS: We have increased the density of typed microsatellite markers two- to five-fold in each of several major RI sets that share C57BL/6 as a parental strain (AXB, BXA, BXD, BXH and CXB). A common set of 490 markers was genotyped in just over 100 RI strains. Genotypes of around 1,100 additional microsatellites in one or more RI sets were generated, collected and checked for errors. Consensus RI maps that integrate genotypes of approximately 1,600 microsatellite loci were assembled. The genomes of individual strains typically incorporate 45-55 recombination breakpoints. The collected RI set - termed the BXN set - contains approximately 5,000 breakpoints. The distribution of recombinations approximates a Poisson distribution and distances between breakpoints average about 0.5 centimorgans (cM). Locations of most breakpoints have been defined with a precision of < 2 cM. Genotypes deviate from Hardy-Weinberg equilibrium in only a small number of intervals. CONCLUSIONS: Consensus maps derived from RI strains conform almost exactly to theoretical expectation and are close to the length predicted by the Haldane-Waddington equation (x3.6 for a 2-3 cM interval between markers). Non-syntenic associations between different chromosomes introduce predictable distortions in quantitative trait locus (QTL) datasets that can be partly corrected using two-locus correlation matrices.
Alleles↗
The genetic structure of the incompatibility factors of Schizophyllum commune: comparative studies of primary mutations in the B factor.
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Alleles↗
[Genetic structure of the populations (contribution to a study of the Belgian population)].
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ABO Blood-Group System↗
Is the genetic structure of human personality universal? A cross-cultural twin study from North America, Europe, and Asia.
This study examined whether universality of the 5-factor model (FFM) of personality operationalized by the Revised NEO Personality Inventory is due to genetic influences that are invariant across diverse nations. Factor analyses were conducted on matrices of phenotypic, genetic, and environmental correlations estimated in a sample of 1,209 monozygotic and 701 dizygotic twin pairs from Canada, Germany, and Japan. Five genetic and environmental factors were extracted for each sample. High congruence coefficients were observed when phenotypic, genetic, and environmental factors were compared in each sample as well as when each factor was compared across samples. These results suggest that the FFM has a solid biological basis and may represent a common heritage of the human species.
Canada↗
Genetic structure and population history of Ireland: a comparison of blood group and anthropometric analyses.
Population structure and history may be studied on a local or a regional level. This paper examines the regional population structure of the Republic of Ireland and Northern Ireland with respect to population history and demographic processes. Blood-group and anthropometric data obtained from the literature are analysed. The blood-group data consist of ABO and Rhesus gene frequencies for 32 counties and the Aran Islands. Anthropometric data consist of summary statistics for 15 variables collected from 19 regions. The degree and pattern of population differentiation is assessed using new methods of population-structure analysis. Both blood group and anthropometric analyses show a west-east division of populations corresponding to the known history of inhabitation of Ireland, where successive waves of immigrants pushed earlier populations further west. In both analyses there were two deviations to this basic pattern: the Aran Islands and the midlands. In both cases, alternative historical explanations are examined. The genetic relationship of the Aran Islands to the rest of Ireland and England appears to be due to English admixture following the garrisoning of soldiers several centuries ago. The genetic position of the midlands is more complex, but suggests the effects of early Viking inhabitation. These findings are related to studies of the local, rather than regional, population structure of Ireland.
Anthropometry↗
The genetic structure of human populations studied through short insertion-deletion polymorphisms.
In a landmark study Rosenberg et al. (2002) analyzed human genome diversity with 377 microsatellites in the HGDP-CEPH Genome Diversity Panel and reported that the populations were structured into five geographical regions: America, Sub-Saharan Africa, East Asia, Oceania and a cluster composed of Europe, the Middle East and Central Asia. They also observed that the within-population component accounted for 93-95%, and that the among-regions portion was only 3.6%, of the total genetic variance. We have also studied the HGDP-CEPH Diversity Panel (1,064 individuals from 52 populations) with a set of 40 biallelic slow-evolving short insertion-deletion polymorphisms (indels). We confirmed the partition of worldwide diversity into five genetic clusters that correspond to major geographic regions. Using the indels we have also disclosed an among-regions component of genetic variance considerably larger (12.1%) than had been estimated using microsatellites. Our study demonstrates that a set of 40 well-chosen biallelic markers is sufficient for the characterization of human population structure at the global level.
DNA Transposable Elements↗
Is the genetic structure of Gran Chaco populations unique? Interregional perspectives on native South American mitochondrial DNA variation.
This study reevaluates the hypothesis in Demarchi et al. (2001 Am. J. Phys. Anthropol. 115:199-203) that Gran Chaco peoples demonstrate a unique pattern of genetic diversity due to a distinct regional population history. Specifically, they found populations in the central part of the Gran Chaco, or Central Chaco, to have higher within- and lower between-population mitochondrial DNA (mtDNA) haplogroup frequency variation compared to populations in other South American regions. To test this hypothesis of regional uniqueness, we applied analytical and simulation methods to mtDNA first hypervariable (HVI) region sequence data from a broad set of comparative South and Central American population samples. Contrary to the results of Demarchi et al. (2001 Am. J. Phys. Anthropol. 115:199-203), we found that the Gran Chaco's regional within-population diversity is about average among regions, and populations are highly differentiated from each other. When we limited the scale of analysis to the Central Chaco, a more localized subregion of the Gran Chaco, our results fell more in line with the original findings of Demarchi et al. (2001 Am. J. Phys. Anthropol. 115:199-203). Still, we conclude that neither the Gran Chaco regional pattern, nor the Central Chaco subregional pattern, is unique within South America. Nonetheless, the Central Chaco pattern accords well with the area's history, including pre-European contact lifeways and the documented historical use of the area as an interregional crossroads. However, we cannot exclude post-European contact disruption of traditional mating networks as an equally plausible explanation for the observed diversity pattern. Finally, these results additionally inform broader models of South American genetic diversity. While other researchers proposed an east-west continental division in patterns of genetic variation (e.g., Fuselli et al. 2003 Mol. Biol. Evol. 20:1682-1691), we found that in the geographically intermediate Central Chaco, a strict east-west divide in genetic variation breaks down. We suggest that future genetic characterizations of the continent, and subsequent interpretations of evolutionary history, involve a broad regional sampling of South American populations.
Argentina↗
Genetic structure of Atriplex halimus populations in the Mediterranean Basin.
BACKGROUND AND AIMS: The saltbush Atriplex halimus is a chenopodiaceous plant well adapted to dry saline habitats and widely distributed in the Mediterranean Basin. A study was carried out to analyse the genetic diversity of A. halimus at the level of the Mediterranean Basin. METHODS: To assess the intra- and interpopulational variation of A. halimus a total of 51 populations and six plants per populations was analysed with the RAPD-PCR technique. For the study of the phylogeny of the populations, 21 samples of A. halimus and seven samples of other species of Atriplex were analysed by the sequencing of the ITS (internal transcribed spacer) region of the ribosomal DNA. KEY RESULTS: The AMOVA analysis of the RAPD results showed that populations were divided into two discrete genetic groups, as the variation among groups accounted for 54.36 % of the total variance of the collection. At the same time, the intrapopulational diversity was high, as 301 out of 306 plants analysed constituted an individual RAPD haplotype. The sequencing of the ITS region also showed a significant separation of the two genetic groups, with a genetic distance of 0.023 nucleotide substitutions per site. Using A. breweri, A. canescens, A. glauca and A. prostrata as outgroups in the phylogenetic analysis, A. breweri and A. canescens are the species closest to A. halimus from this group, while A. prostrata is the most distant. CONCLUSIONS: The present work indicates that two genetic groups of A. halimus can be distinguished after analysing the genetic diversity of 51 populations from ten countries in the Mediterranean Basin.
Analysis of Variance↗
Genetic structure of Himalayan snowcock (Tetraogallus himalayensis) populations in China.
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Animals↗