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PubMed1995

[Analysis of maintenance of redundant genetic structures in the yeast Saccharomyces cerevisiae: effect of mutations cdc28-srm and srm1].

The effects of nuclear gene mutations cdc28-srm and srm1 on the maintenance of various recombinant facultative genetic structures (FGSs) in Saccharomyces cerevisiae were studied. These structures are ARS1 TRP1 mini-coils, noncentromeric circular plasmids containing various ARS elements, and extended linear yeast artificial chromosomes (YAC). These mutations led to an increase in the mitotic stability of some of the FGS tested and the disturbed maintenance of the others. Mutation srm1 imposed a stabilizing effect on the maintenance of various recombinant FGSs with ARS chromosomal elements. Mutation cdc28-srm destabilized the maintenance of only those recombinant FGS that shared full or detectable homology with sequences of the nuclear genome of the yeast cell.

Chromosomes, Artificial, Yeast↗
PubMed1989

Anthropometric variation and the genetic structure of the Jirels of Nepal.

Anthropometric measurements (head length, head breadth, bizygomatic diameter, minimum frontal diameter, head circumference, and stature) for 526 adult Jirels are utilized to establish the pattern of phenotypic relationships between seven villages in eastern Nepal. An analytical framework is provided that justifies the interpretation of biological distances as minimum genetic distances. Using this approach, estimates of the minimum pairwise genetic distances between villages and the minimum FST for the population are derived from the purely phenotypic data. The FST obtained in this way is consistent with results obtained from other data available for this population, confirming the utility of phenetic analysis of quantitative traits for elucidating genetic structure.

Anthropometry↗
PubMed2006

HLA-C molecular characterization of a Lebanese population and genetic structure of 39 populations from Europe to India-Pakistan.

Lebanon is located at a continental crossroad between Europe, Africa, and Asia. This region has been the center of wide-scale movements of populations as well as the theater of genetic and cultural trade off among neighboring populations. In this study, HLA-C alleles were characterized by a PCR-SSOP (sequence-specific oligonucleotide probes) hybridization protocol in a sample of 97 Lebanese. A total of 23 alleles were identified with four predominant, Cw*0401, Cw*0602, Cw*0701/06, and Cw*1203, accounting for almost 60% of HLA-C allele frequencies. We included the Lebanese data into a broad analysis of the HLA-C genetic structure of a large set of populations located in Europe, the Middle East, and the Indian subcontinent. Our results indicate that Lebanese exhibit an intermediate genetic profile among the populations from the Middle East, which constitute a rather homogeneous genetic group. In Europe, a high correlation coefficient is found between genetic and geographic distances. In this continent, we also identified a significant genetic frontier following a north-east to south-west axis. This frontier cuts through the Alps and the Pyrenees, thus separating the north-western European populations from those located in the eastern and Mediterranean areas. Finally, the populations from India - Pakistan are very heterogeneous, particularly the Dravidians. Their differentiation has probably been caused by rapid genetic drift under complex influences of cultural, linguistic, and/or religious barriers. Overall, the results show that the HLA-C genetic patterns of these three geographic regions, i.e., the Middle East, Europe, and India-Pakistan, have been shaped by very different genetic histories.

Alleles↗
PubMed2004

Genetic structure of four socio-culturally diversified caste populations of southwest India and their affinity with related Indian and global groups.

BACKGROUND: A large number of microsatellites have been extensively used to comprehend the genetic diversity of different global groups. This paper entails polymorphism at 15 STR in four predominant and endogamous populations representing Karnataka, located on the southwest coast of India. The populations residing in this region are believed to have received gene flow from south Indian populations and world migrants, hence, we carried out a detailed study on populations inhabiting this region to understand their genetic structure, diversity related to geography and linguistic affiliation and relatedness to other Indian and global migrant populations. RESULTS: Various statistical analyses were performed on the microsatellite data to accomplish the objectives of the paper. The heretozygosity was moderately high and similar across the loci, with low average GST value. Iyengar and Lyngayat were placed above the regression line in the R-matrix analysis as opposed to the Gowda and Muslim. AMOVA indicated that majority of variation was confined to individuals within a population, with geographic grouping demonstrating lesser genetic differentiation as compared to linguistic clustering. DA distances show the genetic affinity among the southern populations, with Iyengar, Lyngayat and Vanniyar displaying some affinity with northern Brahmins and global migrant groups from East Asia and Europe. CONCLUSION: The microsatellite study divulges a common ancestry for the four diverse populations of Karnataka, with the overall genetic differentiation among them being largely confined to intra-population variation. The practice of consanguineous marriages might have attributed to the relatively lower gene flow displayed by Gowda and Muslim as compared to Iyengar and Lyngayat. The various statistical analyses strongly suggest that the studied populations could not be differentiated on the basis of caste or spatial location, although, linguistic affinity was reflected among the southern populations, distinguishing them from the northern groups. Our study also indicates a heterogeneous origin for Lyngayat and Iyengar owing to their genetic proximity with southern populations and northern Brahmins. The high-ranking communities, in particular, Iyengar, Lyngayat, Vanniyar and northern Brahmins might have experienced genetic admixture from East Asian and European ethnic groups.

Alleles↗
PubMed2005

Analysis of the genetic structure of nontypeable pneumococcal strains isolated from conjunctiva.

More than 50% of the nontypeable (NT) pneumococcal strains received in our laboratory for reference purposes are isolated in sporadic cases of conjunctivitis. To determine the genetic structure of the population of these NT conjunctival strains, we analyzed 75 pneumococci (40 NT and 35 typeable) isolated from conjunctivas and 30 (15 NT and 15 typeable) isolated from other sources. The NT and typeable conjunctival strains grouped in separate clusters, whereas NT and typeable pneumococci isolated from other sources were similarly distributed. NT conjunctival strains belonged to two well-differentiated clonal lineages. The first, represented by three newly described sequence types, featured fully antibiotic susceptible strains and appeared to be characteristic of conjunctival tissue; the second, represented by the previously described ST344, had a pattern of multiresistance to penicillin, tetracycline, and erythromycin and shared a genetic background with some NT strains isolated from other sources.

Bacterial Typing Techniques↗
PubMed2001

Genetic structure of spatial and verbal working memory.

Working memory (WM) encompasses both short-term memory (storage) and executive functions that play an essential role in all forms of cognition. In this study, the genetic structure of storage and executive functions engaged in both a spatial and verbal WM span task is investigated using a twin sample. The sample consists of 143 monozygotic (MZ) and 93 dizygotic (DZ) Japanese twin pairs, ages 16 to 29 years. In 155 (87 MZ, 62 DZ) of these pairs, cognitive ability scores from the Kyodai Japanese IQ test are also obtained. The phenotypic relationship between WM and cognitive ability is confirmed (r = 0.26-0.44). Individual differences in WM storage and executive functions are found to be significantly influenced by genes, with heritability estimates all moderately high (43%-49%), and estimates for cognitive ability comparable to previous studies (65%). A large part of the genetic variance in storage and executive functions in both spatial and verbal modalities is due to a common genetic factor that accounts for 11% to 43% of the variance. In the reduced sample, this common genetic factor accounts for 64% and 26% of the variance in spatial and verbal cognitive ability, respectively. Additional genetic variance in WM (7%-30%) is due to modality specific factors (spatial and verbal) and a storage specific factor that may be particularly important for the verbal modality. None of the variance in cognitive ability is accounted for by the modality and storage genetic factors, suggesting these may be specific to WM.

Adult↗
PubMed2000

Complex social organization reflects genetic structure and relatedness in the cooperatively breeding bell miner, Manorina melanophrys.

The cooperatively breeding bell miner, Manorina melanophrys, differs from most other cooperative breeding species in the complexity of its social system, where discrete social organization occurs on at least three levels. Microsatellite markers were used to investigate the degree of genetic structure underlying the social organization of M. melanophrys by comparing colonies, coteries and nest contingents. The genetic data confirmed behavioural observations of M. melanophrys living in male kin-based groups between which females disperse short distances to breed. Estimates of FST revealed restricted gene flow between eight colonies located within 30 km that was significantly associated with geographical distance when the two most distant colonies were included. Within a high density colony significant differences were found between coteries; analysis of the degree of relatedness between coterie members showed that this is due to related individuals associating preferentially with each other. Similarly, the contingent of individuals attending a nest were generally close relatives of the young they were aiding, supporting models invoking kin selection as the selective agency mediating helping.

Animals↗
PubMed2003

A survey of the Anopheles funestus (Diptera: Culicidae) group of mosquitoes from 10 sites in Kenya with special emphasis on population genetic structure based on chromosomal inversion karyotypes.

We sampled Anopheles funestus Giles mosquitoes from 10 sites in Kenya to determine (1) the different members of this group present at these sites and (2) the population genetic structure of these species based on chromosomal inversion karyotypes with particular reference to the role of the Eastern arm of the Great Rift Valley and geographical distance as barriers to gene flow. Four members of this species group, namely An. funestus s.s., An. parensis, An. leesoni, and An. rivulorum, were found. An. funestus was found almost exclusively inside human dwellings while An. rivulorum was found almost exclusively outdoors. An. parensis was found both indoors and outdoors in comparable proportions. Earlier attempts to collect this group of mosquitoes from two of the sites yielded no mosquitoes, suggesting that numbers of mosquitoes change during the year, sometime reaching zero or very near zero. Significant levels of differentiation were observed among some An. funestus s.s. populations studied. Results suggest that the Rift Valley acts as a barrier to gene flow for An. funestus, but that levels of differentiation are not associated with the geographical distance between populations. The results are discussed in the light of the fact that inversions may have some adaptive significance to differences in environmental conditions.

Animals↗
PubMed2002

Clonal reproduction and population genetic structure of grape phylloxera, Daktulosphaira vitifoliae, in Australia.

The grape phylloxera, Daktulosphaira vitifoliae, is a viticultural pest that in the past has devastated vineyards worldwide, yet little is known about this insect's biology. The genetic structure of Australian populations of grape phylloxera and its mode of reproduction were studied following the development of four polymorphic microsatellite loci. Insects were collected from 28 vineyards, with a total of 361 insects included in the study. The majority of vineyards were infested by functionally parthenogenetic lineages of grape phylloxera that inhabit the root system and there was little support for the traditionally described holocyclic life cycle for this species. Clonal diversity was limited in all of the vineyard regions, with the exception of the Rutherglen region. A multiple founder scenario or occasional sex may contribute to diversity within the Rutherglen region. Leaf galling populations comprised classes distinct from the common genotypic classes identified on the roots, suggesting limited exchange between these groups. Implications for the management of D. vitifoliae are discussed.

Animals↗
PubMed1999

Genetic structure of Aedes albifasciatus (Diptera: Culicidae) populations in central Argentina determined by random amplified polymorphic DNA-polymerase chain reaction markers.

The floodwater mosquito, Aedes albifasciatus (Macquart), is the main vector of western equine encephalomyelitis virus in Argentina. Previous studies on the genetic structure of this species using allozymes showed low levels of polymorphism, absence of subpopulations at distinct habitats, and moderate differentiation among localities separated up to 500 km. To examine gene flow using other genetic methods, we analyzed random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) polymorphism in 28 presumptive loci of Ae. albifasciatus from 6 populations in central Argentina. Allele frequencies were estimated assuming that RAPD products segregate as dominants and that genotype frequencies at those loci are in Hardy-Weinberg equilibrium. Expected heterozygosity ranged between 0.19 and 0.31, approximately 3 times the value obtained on the basis of the 16 allozymic loci studied previously. Four of the populations formed a single panmictic unit. Allele frequencies in populations occupying different phytogeographic regions gave significant FST values at 5 loci. Effective migration rates among populations estimated from FST ranged from 2.3 to 9.0. The results support the existence of a north-south cline.

Aedes↗
PubMed1984

Physical and genetic structure of the glpK-cpxA interval of the Escherichia coli K-12 chromosome.

Mutations at the cpxA locus of Escherichia coli K-12 affect cellular processes that are not otherwise related. We have now determined the physical and genetic structure of the E. coli chromosome in the region of cpxA (87.5 min). Our results indicate that cpxA is a single gene. Previous studies showed cpxA to be linked to tpiA. We therefore isolated two tpiA+ recombinant plasmids, pRA200 and pRA300, from EcoRI and BamHI digests of F'133, respectively. By genetic complementation or enzyme overproduction, the 9.5 kb EcoRI fragment in pRA200 was shown to include glpK, tpiA and cdh. The 13.6 kb BamHI fragment of pRA300 lacks glpK, but includes tpiA, pfkA and cpxA. Neither fragment complemented a deletion of the rha operon. These data indicate the chromosomal gene order: 87 min-rha-cpxA-pfkA-cdh-tpiA-glpK-88 min. The EcoRI and BamHI fragments overlap in an interval corresponding to about 8.2 kb of DNA. The total region of the E. coli K12 chromosome covered by the two fragments is about 15 kb. A terminal 2 kb EcoRI-BamHI fragment from pRA300 complemented the chromosomal cpxA2[Ts] allele with respect to isoleucine and valine synthesis, RNA bacteriophage sensitivity and surface exclusion in Hfr strains, and envelope protein composition. Complementation occurred when the fragment was subcloned in pBR325 but not when it was subcloned in pBR322, suggesting that the 2 kb fragment lacks expression sequences that are supplied by cat (chloramphenicol acetyltransferase gene) expression sequences of pBR325. The cpxA locus on the E. coli chromosome was established with respect to two chromosomal Tn10 insertions by a combination of genetic and physical analyses. The locus established by those analyses was consistent with the location of the 2 kb EcoRI-BamHI fragment in the physical map of the region. Physical analyses of (rha-pfkA) and (rha-tpiA) deletion strains showed that they lack cpxA and surrounding genes. Since these strains were viable, cpxA is not essential under all growth conditions.

Bacterial Proteins↗
PubMed2005

Genetic structure of Flores island (Azores, Portugal) in the 19th century and in the present day: evidence from surname analysis.

The island of Flores is the most westerly of the Azores archipelago (Portugal). Despite its marked geographic isolation and reduced population size, biodemographic and genetic studies conducted so far do not support the idea that its population constitutes a genetic isolate. In this study we conducted a surname analysis of the Flores population for two time periods: the second half of the 19th century and the present day. Our main purposes were (1) to biodemographically and genetically characterize the island, taking into account the strong reduction in population observed from the middle of the 19th century to the present day; and (2) to analyze the influence that the effective population size and geographic distance have on the genetic structure of populations. For both periods analyzed, all indicators of diversity revealed a high level of surname diversity. Our results are in accordance with the diversity estimates obtained from both monoparental genetic markers located in the Y chromosome and frequencies of mtDNA haplogroups. Contrary to what could be expected, considering the strong reduction of population in the last 150 years, we observed that diversity was maintained and that microdifferentiation decreased. Both observations support a higher openness of parishes as a consequence of the increase in communication routes. From the first to the second period analyzed, a change in surname composition is evident, although the more frequent surnames in Flores are almost the same for both periods and some of them are reported to be surnames present in the first settlers of Flores. This result testifies to the impact of founders on the present-day gene pool of Flores island and allows us to infer that the genetic characterization of the present-day population of Flores could provide reliable information about the history of the peopling of the Azores.

Azores↗
PubMed1996

[Genetic structure of the Pinzgauer breed in the Carpathian region].

Phenotypic and genotypic characteristics of groups of Pinzgauer cattle bred at lowland, highland, and alpine farms in the Carpathian Mountains were studied. A high variation of the cattle with respect to blood groups was revealed. It was found that the genetic structure of the highland group of Pinzagauer cattle was somewhat similar to that of Brown Carpathian cattle with respect to biochemical genetic systems, mainly transferrin and amylase-I loci. It is thought that the similarity found may be accounted for by close ecological and geographical breeding conditions of the groups of cattle studied.

Altitude↗
PubMedDate not supplied

Genetic structure of the Azores: marriage and inbreeding in Flores.

Flores is one of the smallest and most westerly islands of the Atlantic archipelago of the Azores. This preliminary account of the population's demography and genetic structure uses dispensations to contract consanguineous marriages taken from the Roman Catholic marriage registers in order to estimate mean inbreeding rates in the population over the period 1860-1980. Comparisons are made with inbreeding rates on the Portuguese mainland and elsewhere in Western Europe, and reasons suggested to explain the rather high rates of inbreeding encountered on Flores.

Azores↗
PubMed2000

Genetic structure through surnames in Campobasso Province, Italy.

The population of Campobasso Province shows a level of inbreeding that is distinct from most Italian rural populations, regardless of their geographic location (Fr=0.0040; Fn=0.0102; Ft=0.0142). The genetic structure of the Italian-Greek communities of Lecce and Reggio Calabria Provinces does not appear to be affected by ethnicity. The level of inbreeding in Italian-Greeks of Reggio Calabria Province is similar to other Italians of Campobasso Province (Fr=0.0041; Fn=0.0127; Ft=0.0168). The Italian-Greeks of Lecce Province show random mating, and their inbreeding is in fact very low (Fr=0.0038; Fn=0.0024; Ft=0.0062).

Consanguinity↗
PubMed1991

The genetic structure of admixed populations.

A method for simultaneously estimating the admixture proportions of a hybrid population and Wright's fixation index, FST, for that hybrid is presented. It is shown that the variance of admixture estimates can be partitioned into two components: (1) due to sample size, and (2) due to evolutionary variance (i.e., genetic drift). A chi-square test used to detect heterogeneity of admixture estimates from different alleles, or loci, can now be corrected for both sources of random errors. Hence, its value for the detection of natural selection from heterogeneous admixture estimates is improved. The estimation and testing procedures described above are independent of the dynamics of the admixture process. However, when the admixture dynamics can be specified, FST can be predicted from genetic principles. Two admixture models are considered here, gene flow and intermixture. These models are of value because they lead to very different predictions regarding the accumulation of genes from the parental populations and the accumulation of variance due to genetic drift. When there is not evidence for natural selection, and it is appropriate to apply these models to data, the variance effective size (Ne) of the hybrid population can be estimated. Applications are made to three human populations: two of these are Afro-American populations and one is a Yanomamö Indian village. Natural selection could not be detected using the chi-square test in any of these populations. However, estimates of effective population sizes do lead to a richer description of the genetic structure of these populations.

Black People↗
PubMed2004

Isozyme polymorphism and genetic structure of the population of Sorbus torminalis (L.) Crantz from the Bytyń Forest (Poland).

Dormant buds collected from 35 wild service trees (Sorbus torminalis) in the Bytyń Forest were tested with horizontal gel electrophoresis to assess the genetic structure of the population. Among 16 investigated isozyme loci, seven loci (ADH-A, 6PGD-A, GDH-B, ME-A, SOD-A, PGM-A, PGM-B) proved to be polymorphic, whereas the other nine loci (SDH-A, SDH-B, DIA-C, DIA-D, FLE-A, FLE-B, GOT-B, IDH-A, IDH-B) were monomorphic. The number of alleles per polymorphic locus ranged from two to three, with a mean of 2.29. The average observed and expected heterozygosities were 0.2665 and 0.3462, respectively. The combined FIS value over all polymorphic loci was 0.2179, which reflects a substantial deficit of heterozygotes. Two polymorphic loci (SOD-A, PGM-A) were identified in S. torminalis for the first time.

Gene Frequency↗