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At least 937 records · Page 52Linked to original sources
PubMed2002

Assessment of population genetic structure in common wild rice Oryza rufipogon Griff. using microsatellite and allozyme markers.

The genetic structure of five natural populations of common wild rice Oryza rufipogon Griff. from China, was investigated with 21 microsatellite loci and compared to estimates of genetic diversity and genetic differentiation detected by 22 allozyme loci. Microsatellite loci, as expected, have much higher levels of genetic diversity (mean values of A = 3.1, P = 73.3%, Ho = 0.358 and He = 0.345) than allozyme loci (mean values of A = 1.2, P = 12.7%, Ho = 0.020 and He = 0.030). Genetic differentiation detected by microsatellite loci ( FST = 0.468, mean I = 0.472) was higher than that for allozyme loci ( FST =0.388, mean I = 0.976). However, microsatellite markers showed less deviation from Hardy-Weinberg expectation (Wright's inbreeding coefficient FIS = -0.069) than do allozymes ( FIS = 0.337). These results suggest that microsatellite markers are powerful high-resolution tools for the accurate assessment of important parameters in population biology and conservation genetics of O. rufipogon, and offer advantages over allozyme markers.

Edible Grain↗
PubMed2005

Population genetic structure and tolerance to dioxin-like compounds of a migratory marine fish (Menidia menidia) at polychlorinated biphenyl-contaminated and reference sites.

The present study was conducted to evaluate evidence of genetic adaptation to local contaminants in populations of the migratory marine fish Menidia menidia residing seasonally in reference sites or an industrial harbor contaminated with dioxin-like compounds (DLCs). For this purpose, we compared DLC sensitivity and genetic patterns of populations sampled from sites both inside and outside New Bedford Harbor (NBH; MA, USA), a U.S. Environmental Protection Agency Superfund site with extreme polychlorinated biphenyl (PCB) contamination. Offspring of M. menidia collected from NBH were significantly less sensitive regarding embryonic exposure to the dioxin-like PCB congener 3,3',4,4',5-pentachlorobiphenyl (PCB 126) than offspring of M. menidia from a reference site. Analysis of 10 polymorphic enzymatic loci indicated little genetic differentiation among populations in the study area. However, genotype frequencies of juveniles from both NBH and an adjacent site in Massachusetts exhibited significant deviations from Hardy-Weinberg equilibrium expectations at one locus, phosphoglucomutase (PGM*). Genetic analysis of survivors of embryonic laboratory exposure to PCB 126 indicated that genotypes at PGM* were related to survivorship. Although a relationship was identified between DLC tolerance and PGM* genotype, regional mixing of M. menidia populations during migration and absence of multigeneration exposure at contaminated sites may limit localized adaptation.

Adaptation, Physiological↗
PubMed1996

[Population genetics of short tandem repeat locus HUMTH01].

The distributions of genotypes and allele frequencies for the short tandem repeat locus HUMTH01 in Chinese and German populations were studied by amplified fragment length polymorphism analysis. The PCR amplification products with different primers were compared by coelectrophoresis and the population data from different laboratories were evaluated. Based on the allele frequencies of HUMTH01, the genetic distances among 25 populations were computed and a phylogenetic tree was constructed accordingly. Some new implications for population genetics were obtained from this phylogenetic tree.

Chromosome Mapping↗
PubMed1976

The population genetics of parthenogenetic strains of Drosophila mercatorium. II The capacity for parthenogenesis in a natural, bisexual population.

Drosophila mercatorum is a bisexual species, but certain strains are capable of parthenogenetic reproduction in the laboratory. We investigated the parthenogenetic capacity of the virgin daughters of females captured from a natural, bisexual population in Hawaii. An isozyme survey indicated the natural population is polymorphic at about 50% of its loci, and its individuals heterozygous at 18% of their loci. The predominant mode of parthogenesis in D. mercatorum causes homozygosity for all loci in a single generation. Despite this radical change in genetic state, 23% of the virgin female lines produced adult parthenogenetic progeny, and 16% produced parthenogenetic progeny themselves capable of parthenogenetic reproduction. The parthenogenetic rats as measured by the number of parthenogenetic progeny themselves capable of parthenogenesis divided by the number of eggs laid is arougn 10(-5) for the virgin female lines. We argue that one of the major reasons for this low rate is that very few of the impaternate zygotes have a genotype that can survive and reproduce under the genetic conditions imposed by parthenogenetic reproduction. This intense selective bottleneck can be passed in a single generation if enough unfertilized eggs are laid, and once passed is accompanied by a large (perhaps a thousandfold) increase in the rate of parthenogenesis and by modifications in many phenotypic traits such as morphology and behavior.

Animals↗
PubMed1999

[The study of the distribution of Chinese surnames and the diversity of genetic population structure in the Song dynasty].

Surname in China, as a cultural genetic factor, is a very huge and remarkable human population study resource. The transmission feature of surname has been proved to be similar to that of the genetic markers on Y chromosome of males. It, therefore, has been applied in the population genetic studies since 1965's. In the present study, we have analyzed a group of Chinese surname data of the Song dynasty (AD. 960-1179). The distribution of the present surname data is corresponded with the Karlin-McGregor's neutral allele model. The surname abundance alpha and the migration rate parameter v in the Song dynasty in 16 provincial regions reflected degrees of migration and admixture at that time. Surname phylogenetic dendrogram analysis demonstrated that the Han Chinese had been segregated into North and South two parts in Song dynasty of 1000 years ago. Wuyi and Nanling Mountains divided Northern and Southern Han populations into the two major parts of Han Chinese. The results also showed that the surname distribution of Song dynasty 1000 years ago was quite similar to the present model. The 100 high frequency surnames in Song dynasty were well corresponded with the current surname distribution. This phenomenon suggests that Chinese surnames have been steadily transmitted from ancient to the present. The present study improved that the Chinese surname is a very important genetic resource for the studies of structure of the Chinese populations, migration, and affinities among different populations.

China↗
PubMedDate not supplied

[Population genetics of the 10 short tandem repeat (STR) loci in the population of Podlasie (Northeastern Poland)].

A population study on 10 STR loci: D3S1358, VWA, D16S539, D2S1338, D8S1179, D21S11, D18S51, D19S433, TH01 and FGA was performed on 620 unrelated individuals born in Podlasie (NE Poland). The DNA was amplified by multiplex PCR using a commercially available multiplex AmpFISTR SGM Plus kit. Capillary electrophoresis with fluorescent detection was carried out using the ABI 310 Genetic Analyzer. The expected performance of the analysed loci for personal identification and paternity testing was estimated. All loci met the Hardy-Weinberg assumption. No significant differences between the studied population and other Polish data were found. The combined values of the Matching Probability and of the Power of Exclusion are 4.18 x 10(-13) and 0.99997, respectively.

Adult↗
PubMed1998

Population genetics of hyperphenylalaninaemia resulting from phenylalanine hydroxylase deficiency in Portugal.

In order to elucidate the molecular basis of phenylketonuria (PKU) in Portugal, a detailed study of the Portuguese mutant phenylalanine hydroxylase (PAH) genes was performed. A total of 222 mutant alleles from 111 PKU families were analysed for 26 mutations and restriction fragment length polymorphismlvariable number tandem repeat (RFLP/VNTR) haplotypes. It was possible to characterise 55% of the mutant alleles, in which 14 different mutations (R261Q, V388M, IVS10nt-11, I65T, P281L, R252W, R158Q, L348V, Y414C, L311P, Y198fsdel22bp, R408W, R270K, and R261X) and three polymorphisms (Q232Q, V245V, and L385L) were identified. A total of 14 different haplotypes were observed, with a high prevalence of haplotype 1 among mutant and normal alleles. The results reported in this study show considerable genetic heterogeneity in the Portuguese PKU population, as has also been described for other southern European populations.

DNA Mutational Analysis↗
PubMed2000

[Population genetics of Chinese surnames. II. Inheritance stability of surnames and regional consanguinity of population].

This paper analyzes and compares the distributional curves and isonymy of surnames and the consanguinity of regional population in the Song and Ming dynasties and the 2 present. The distribution of surnames in the three periods reveals two significant phenomena: (1) The historical inheritance of Chinese surnames is continuous and stable. This explains why the consanguineous culture relics represented by surnames and the evolution of life substances especially Y chromosome has basically the same pattern. (2) Two types of surnames, common and rare, can be identified in China. The 100 common surnames, less than 5% of the total number of Chinese surnames, are connected with more than 85% of the population, while the rare surnames, more than 95% of the total number of surnames, are related to only about 15% of the population. The distribution of common surnames acts as the major factor reflecting the genetic composition in different regions, and it determines the historical population migration and the degree of consanguinity between regional populations. The rare surnames are of regional characteristic and relative isolation. As a result, it is possible that the study of Chinese surnames and of the distribution pattern of population with the same surname serves as an important approaches to Chinese paternal genetics and Y chromosome evolution. This may provide valuable clue for the study of population highly subject to genetic diseases.

Biological Evolution↗
PubMed2004

Comparison of population genetic structures of common wild rice (Oryza rufipogon Griff.), as revealed by analyses of quantitative traits, allozymes, and RFLPs.

We investigated genetic diversity among and within natural populations of Asian common wild rice, Oryza rufipogon, from three different classes of data: quantitative traits, allozymes, and restriction fragment length polymorphisms (RFLPs). The seven populations examined showed polymorphism to varying degrees. The amount of intrapopulation variability appeared to be influenced not only by breeding system but also by the evolutionary history of each population. Interpopulation differentiation was clear, but different classes of data elucidated different patterns. Quantitative traits revealed ecotype differentiation into perennial and annual types of population, whereas allozyme and RFLP analyses revealed geographical differentiation among populations. These results suggest that the diversity patterns shown by quantitative trait analysis reflect mainly the occurrence of adaptive differentiation in response to habitat conditions and that those shown by allozyme and RFLP analyses reflect mainly the effect of isolation by distance. Population differentiation parameters (F(ST)) were highly variable among loci in allozymes as well as in RFLPs.

Alleles↗
PubMed2003

Population genetic structure of earthworms (Lumbricus rubellus) in soils contaminated by heavy metals.

The genetic structure of earthworm (Lumbricus rubellus) populations from plots (N = 3) contaminated by sewage sludge (containing Cd, Cu, Pb, Zn) and reference plots (N = 3) was compared. Earthworms (N = 30-40 per plot) were collected during May 2000 and electrophoretic analyses were used to assess genetic variation at three polymorphic loci (GPI, LAP, PGM). Allele and genotype frequencies for GPI and PGM differed significantly between sludge and reference populations. Sludge populations were characterized by a reduced frequency of the most common genotype and allele at these loci, and the presence of alleles not found in the reference population. Allele and genotype frequencies did not differ significantly among individual plots within the sludge or the reference population. These results suggest that certain alleles and genotypes may be more sensitive to the effects of heavy metals. Multi-locus heterozygosity was significantly higher in the sludge population compared to the reference population; the proportion of individuals heterozygous at two or more loci was more than 15% higher in the sludge population. Results demonstrate that measures of population genetic structure in earthworms may represent useful biological indicators for the assessment of impacted terrestrial habitats.

Alleles↗
PubMed2005

Is variation in susceptibility to Phytophthora ramorum correlated with population genetic structure in coast live oak (Quercus agrifolia)?

California coastal woodlands are suffering severe disease and mortality as a result of infection from Phytophthora ramorum. Quercus agrifolia is one of the major woodland species at risk. This study investigated within- and among-population variation in host susceptibility to inoculation with P. ramorum and compared this with population genetic structure using molecular markers. Susceptibility was assessed using a branch-cutting inoculation test. Trees were selected from seven natural populations in California. Amplified fragment length polymorphism molecular markers were analysed for all trees used in the trials. Lesion sizes varied quantitatively among individuals within populations, with up to an eightfold difference. There was little support for population differences in susceptibility. Molecular structure also showed a strong within-population, and weaker among-population, pattern of variation. Our data suggest that susceptibility of Q. agrifolia to P. ramorum is variable and is under the control of several gene loci. This variation exists within populations, so that less susceptible local genotypes may provide the gene pool for regeneration of woodlands where mortality is high.

California↗
PubMed2000

RAPD variation and population genetic structure in Prunus mahaleb (Rosaceae), an animal-dispersed tree.

We examined the patterns of random amplified polymorphic DNA (RAPD) variation among seven Prunus mahaleb (Rosaceae) populations extending over approximately 100 km2 to examine local differentiation in relation to spatial isolation due to both geographical distance and differences in elevation. No less than 51. 4% of the RAPD loci were polymorphic, but very few were fixed and among-population variation accounted for 16.46% of variation in RAPD patterns. Mean gene diversity was 0.1441, with mean Nei's genetic diversity for individual populations ranging between 0.089 and 0.149. Mean GST value across loci was 0.1935 (range, 0.0162-0.4685), giving an average estimate for Nm of 1.191. These results suggest extensive gene flow among populations, but higher GST and lower Nm values relative to other outcrossing, woody species with endozoochorous dispersal, also suggest a process of isolation by distance. The combined effect of both geographical and elevation distances and nonoverlapping flowering and fruiting phenophases on the GST matrix was partially significant, revealing only marginal isolation of the P. mahaleb populations. The matrix correlation between estimated Nm values among populations and the geographical + elevation distance matrices (r = -0.4623, P = 0.07), suggests a marginal trend for more isolated populations to exchange less immigrants. Long-distance seed dispersal by efficient medium-sized frugivorous birds and mammals is most likely associated to the high levels of within-population genetic diversity. However, vicariance factors and demographic bottlenecks (high postdispersal seed and seedling mortality) explain comparatively high levels of local differentiation.

Animals↗
PubMed2001

A population genetics study of single nucleotide polymorphisms in the interleukin 4 receptor alpha (IL4RA) gene.

Interleukin 4 (IL4) plays a critical role in T helper 2 (Th2) immune responses. Here we report a population genetics study of variation in the gene encoding the alpha-chain of the IL4 receptor (IL4RA) in three ethnic groups: African Americans, European Americans and East Asians. A 2941-bp region spanning exon 12 of IL4RA gene was sequenced in 12 individuals from each group. A total of 24 single nucleotide polymorphisms (SNPs) were identified in the combined sample. The genetic variation of the coding region of exon 12 is two to three times higher than in other reported genes. A significant departure from the expectation of evolutionary neutrality was observed, suggesting that natural selection may have influenced the evolution of this gene. We propose a model in which past selection by pathogens contributed to the increasing prevalence of atopic disorders in Western societies.

Black or African American↗
PubMed1996

PhenoDB: an integrated client/server database for linkage and population genetics.

In this paper we describe PhenoDB, an Internet-accessible client/server database application for population and linkage genetics. PhenoDB stores genetic marker data on pedigrees and populations. A database for population and linkage genetics requires two core functions: data management tasks, such as interactive validation during data entry and editing, and data analysis tasks, such as generating summary population statistics and performing linkage analyses. In PhenoDB we attempt to make these tasks as easy as possible. The client/server architecture allows efficient management and manipulation of large datasets via an easy-to-use graphical interface. PhenoDB data (73 populations, 34 pedigrees, approximately 4200 individuals, and close to 80,000 typings) are stored in a generic format that can be readily exported to (or imported from) the file formats required by various existing analysis programs such as LIPED and Lathrop and Lalouel's Multipoint Linkage. PhenoDB allows performance of complex ad-hoc queries and can generate reports for use in project management. Finally, PhenoDB can produce statistical summaries such as allele frequencies, phenotype frequencies, and Chi-square tests of Hardy-Weinberg ratios of population/pedigree data.

Alleles↗
PubMed1999

Population genetics--making sense out of sequence.

The complete human genome nucleotide sequence and technologies for assessing sequence variation on a genome-scale will prompt comprehensive studies of comparative genomic diversity in human populations across the globe. These studies, besides rejuvenating population genetics and our interest in how genetic variation is created and maintained, will provide the intellectual basis for understanding the genetic basis for complex diseases and traits.

Base Sequence↗
PubMed1983

Population genetic analyses of insulin dependent diabetes mellitus using HLA allele frequencies.

In order to try to detect heterogeneity within insulin dependent diabetes mellitus (IDDM) and to distinguish a mode of inheritance of IDDM, population genetic analyses were performed using HLA allele frequencies. HLA-A and -B typing performed on 231 IDDM individuals and 268 controls from the southeastern U.S. showed significant increases with IDDM in A2, B8, B15 and B18, and significant decreases in Aw23, B7, B14 and B17. The combination of HLA-B8/B15 showed a greatly increased risk (RR = 25.5). Between the 120 IDDM individuals and 123 controls HLA-DR typed, HLA-DR3 and -DR4 were significantly increased among the IDDM group and DR2 and DR7 were decreased. The risk for DR3/4 was 29.2. It appeared that the B15 association was secondary to the DR4, but the B8/DR3 association showed no difference. Using the method of Curie-Cohen, no significant increases in risk were found for the B8/B15 or DR3/DR4 heterozygotes when compared to the respective homozygotes. Using the method of Thomson and Bodmer, the dominant mode of inheritance was excluded for DR4 only. There was a significant increase in B15 and DR4 in those with onset before age 20. No significant differences were found among the DR phenotypes with respect to season.

Age Factors↗