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At least 613 records · Page 34Linked to original sources
PubMed2000

The linkage disequilibrium between chloroplast DNA and mitochondrial DNA haplotypes in Beta vulgaris ssp. maritima (L.): the usefulness of both genomes for population genetic studies.

The structure and evolution of the plant mitochondrial genome may allow recurrent appearance of the same mitochondrial variants in different populations. Whether the same mitochondrial variant is distributed by migration or appears recurrently by mutation (creating homoplasy) in different populations is an important question with regard to the use of these markers for population genetic analyses. The genetic association observed between chloroplasts and mitochondria (i.e. two maternally inherited cytoplasmic genomes) may indicate whether or not homoplasy occurs in the mitochondrial genome. Four-hundred and fourteen individuals sampled in wild populations of beets from France and Spain were screened for their mitochondrial and chloroplast polymorphisms. Mitochondrial DNA (mtDNA) polymorphism was investigated with restriction fragment length polymorphism (RFLP) and chloroplast DNA (cpDNA) polymorphism was investigated with polymerase chain reaction PCR-RFLP, using universal primers for the amplification. Twenty and 13 variants for mtDNA and cpDNA were observed, respectively. Most exhibited a widespread geographical distribution. As a very strong linkage disequilibrium was estimated between mtDNA and cpDNA haplotypes, a high rate of recurrent mutation was excluded for the mitochondrial genome of beets. Identical mitochondrial variants found in populations of different regions probably occurred as a result of migration. We concluded from this study that mtDNA is a tool as valuable as cpDNA when a maternal marker is needed for population genetics analyses in beet on a large regional scale.

Chenopodiaceae↗
PubMed1999

DNA fingerprinting data and the analysis of population genetic structure by comparing band-sharing patterns.

Genetic isolation among populations can be effectively investigated by multilocus DNA fingerprinting. If populations have diverged, it is expected that the mean proportion of bands shared by individuals from the same population, Bw, exceeds the corresponding mean, Bb, calculated from pairs of individuals from distinct populations. A problem arises in deciding whether any difference between Bw and Bb is statistically significant. In fact, any two band-sharing data (bij), contributing to Bw or Bb, are not independent if they share a common individual (like bij and bjl). This prevents a correct application of parametric tests, such as the Student's t-test. Recently, a modification of this test has been proposed that should avoid the independence problem. Using a large number of samples of fingerprints, simulated from an appropriate 'genetic' model, under a wide range of conditions, we compared the performances of the Student's t-test, the modified t-test and five new permutation tests, where individuals, rather than bij values, are permuted. We found that: (i) the Student's t-test can be very permissive, rejecting too often the null hypothesis when true, but is correct or conservative in certain cases; (ii) the modified t-test is extremely conservative when the null hypothesis is true and very inefficient otherwise; (iii) all five permutation tests are strictly correct, provided that individuals are ordered randomly on gels; and (iv) in this case, the permutation tests are equally efficient, and are not inferior to the Student's t-test when the latter is approximately correct and provides a fair benchmark.

DNA Fingerprinting↗
PubMed2006

Population genetics of the bovine/cattle lungworm (Dictyocaulus viviparus) based on mtDNA and AFLP marker techniques.

Mitochondrial DNA (mtDNA) sequence data and amplified fragment length polymorphism (AFLP) patterns were compared for the lungworm Dictyocaulus viviparus, a nematode parasite of cattle. Eight individual D. viviparus samples from each of 8 herds in Sweden and 1 laboratory isolate were analysed, with the aim of describing the diversity and genetic structure in populations using different genetic markers on exactly the same DNA samples. There was qualitative agreement between the whole-genome AFLP data and the mtDNA sequence data, both indicating relatively strong genetic differentiation among the Swedish farms. However, the AFLP data detected much more genetic variation than did the mtDNA data, even after allowing for the different inheritance patterns of the markers, and indicated that there was much less differentiation among the populations. The mtDNA data therefore seemed to be more informative about the most recent history of the parasite populations, as the general patterns were less obscured by detailed inter-relationships among individual worms. The 4 mtDNA genes sequenced (1542 bp) showed consistent patterns, although there was more genetic variation in the protein-coding genes than in the structural RNA genes. Furthermore, there appeared to be at least 3 distinct genetic groups of D. viviparus infecting Swedish cattle, 1 of which was predominant and showed considerable differentiation between farms, but not necessarily within farms. Second, the 2 smaller genetic groups occurred on farms where the predominant group also occurred, suggesting that these farms have had multiple introductions of D. viviparus.

Animals↗
PubMed2007

Argentine population genetic structure: large variance in Amerindian contribution.

Argentine population genetic structure was examined using a set of 78 ancestry informative markers (AIMs) to assess the contributions of European, Amerindian, and African ancestry in 94 individuals members of this population. Using the Bayesian clustering algorithm STRUCTURE, the mean European contribution was 78%, the Amerindian contribution was 19.4%, and the African contribution was 2.5%. Similar results were found using weighted least mean square method: European, 80.2%; Amerindian, 18.1%; and African, 1.7%. Consistent with previous studies the current results showed very few individuals (four of 94) with greater than 10% African admixture. Notably, when individual admixture was examined, the Amerindian and European admixture showed a very large variance and individual Amerindian contribution ranged from 1.5 to 84.5% in the 94 individual Argentine subjects. These results indicate that admixture must be considered when clinical epidemiology or case control genetic analyses are studied in this population. Moreover, the current study provides a set of informative SNPs that can be used to ascertain or control for this potentially hidden stratification. In addition, the large variance in admixture proportions in individual Argentine subjects shown by this study suggests that this population is appropriate for future admixture mapping studies.

Asian People↗
PubMed2004

[Population-genetic structure of beaver (Castor fiber L., 1758) communities and estimation of effective reproductive size Ne of an elementary population].

The absence of panmixia at all hierarchical levels of the European beaver communities down to individual families implies a complex organization of the population-genetic structures of the species, in particular, a large intergroup component of gene diversity in the populations. Testing this assumption by analysis of 39 allozyme loci in the communities of reintroduced beaver from the Vyatka river basin (Kirov oblast) has shown that only the beaver colonies exhibit high intergroup gene diversity (Gst = 0.32) whereas this parameter is much lower when estimated among beaver groups from individual Vyatka River tributaries and among localities of one of the tributaries (0.07 and 0.11, respectively). The data suggesting genetic heterogeneity among individual settles within colonies have been obtained. The factors affecting the structure of the beaver communities of the lower hierarchical ranks are considered: the common origin, founder effect, selection, gene drift, assortative mating, and social and behavior features of the species. The conclusion is drawn that the founder effect could be the primary factor of population differentiation only at the time of their formation. The heterogeneity among colonies and among settles is maintained largely by isolation of colonies from one another. The strong interspecific competition for food resources, which is behaviorally implemented in the species at the level of minimal structural units (individual settles) creates a profound and unique population-genetic subdivision of the species. These results substantiate the suggestion that an elementary population (micropopulation) of European beaver is a colony, i.e., a set of related settles of different types. Based on ecological and genetic parameters, the effective reproductive size Ne of the minimum beaver population was estimated to be equal to three animals. This extremely low value of effective reproductive population size largely explains the high tolerance of European beaver to inbreeding and striking viability of the species, which from the early 19th century has been for more than hundred years on the brink of survival in the condition which would made any other mammalian species vanish from the Earth.

Animals↗
PubMed2003

Allozyme variation and population genetic structure of Betula alnoides from Guangxi, China.

Allozyme variation and population genetic structure of Betula alnoides Buch Ham. ex D. Don in 11 natural populations from Guangxi Zhuang Autonomous Region, China, were investigated by starch gel electrophoresis. Variation at 15 loci from 10 enzyme systems was analyzed. Allozyme analysis revealed a high level of genetic variation in this species, with percentage of polymorphic loci (P(p)), the average number of alleles per locus (A(p)), and the expected heterozygosity (H(ep)) being 55.2%, 2.0, and 0.204, respectively, which exceeds the average level among out-crossing wind-pollinated woody species at the population level. At the species level, P(s), A(s), and H(es) were 60.0%, 2.67, and 0.206, respectively. The observed heterozygosity (H(op)) was higher than H(ep), indicating the existence of natural selection against homozygotes. The negative fixation index (F = -0.216) implied a significant excess of heterozygosity at the population level Among-population differentiation (F(ST)) accounted for 4.0% of the total variation. No significant correlation was detected between the genetic distance and geographic distance among populations. Extensive gene flow was inferred, based on the allozyme data (N(m) = 6.000 from F(ST), N(m) = 5.605 from the "private allele" method). The results demonstrated that the fragmentation status of B. alnoides had no remarkable effects on the population genetic structure of this species. Some populations are recommended for both in situ genetic conservation and germplasm collection for breeding programs.

Betula↗
PubMed1995

Population genetic study among the Orange Asli (Semai Senoi) of Malaysia: Malayan aborigines.

A population genetic study was undertaken to provide gene frequency data on the additional blood genetic markers in the Semai and to estimate the genetic relations between the Semai and their neighboring and linguistically related populations by genetic distance and principal components analyses. Altogether 10 polymorphic and 7 monomorphic blood genetic markers (plasma proteins and red cell enzymes) were studied in a group of 349 Senoi Semai from 11 aboriginal settlements (villages) in the Pahang State of western Malaysia. Both the red cell glucose-6-phosphate dehydrogenase (G6PD) and 6-phosphogluconate dehydrogenase (PGD) loci reveal the presence of polymorphic frequencies of a nondeficient slow allele at the G6PD locus and a fast allele at the PGD locus. The Semai are characterized by high prevalences of ahaptoglobinemia and G6PD deficiency, high frequencies of HP*1, HB*E, RH*R1, ACP*C, GLO1*1, PGM1*2+, and GC*1F and corresponding low frequencies of ABO*A, HbCoSp, HB*B0, TF*D, CHI, and GC*2. Genetic distance analyses by both cluster and principal components models were performed between the Semai and 14 other populations (Malay; Javanese; Khmer; Veddah; Tamils of Malaysia, Sri Lanka, and India; Sinhalese; Oraon; Toda and Irula of India; Chinese; Japanese; Koreans) on the basis of 30 alleles at 7 polymorphic loci. A more detailed analysis using 53 alleles at 13 polymorphic loci with 10 populations was carried out. Both analyses give genetic evidence of a close relationship between the Semai and the Khmer of Cambodia. Furthermore, the Semai are more closely related to the Javanese than to their close neighbors--the Malay, Chinese, and Tamil Indians. There is no evidence for close genetic relationship between the Semai and the Veddah or other Indian tribes. The evidence fits well with the linguistic relationship of the Semai with the Mon-Khmer branch of the Austro-Asiatic language family.

Adolescent↗
PubMed1992

The population genetics of alleles affecting enzyme activity.

It is possible to predict the population genetics of allozymes by assuming that fitness is proportional to flux through a biochemical pathway. The model presented here extends previous work by incorporating two additional features of biological realism. Firstly, that more than one biochemical route may exist between any two metabolites. The major routes have been identified as the classical biochemical pathways but in the event of a mutation blocking a major route, minor routes become significant. These minor routes are named "bypass fluxes" and have profound effects on the population genetics of allozymes. Secondly, recent work has suggested that a metabolic cost is associated with enzyme synthesis; this will constitute an additional selective pressure on alleles which affect the amount of enzyme synthesized. The model generates a fitness curve which predicts the fitness associated with any level of enzyme activity. It can utilize data on null or near-null, structural or regulatory, mutations in the presence or absence of bypass fluxes. When data from natural populations of Drosophila are investigated, it is concluded that selection pressures acting on enzyme variants may be much higher than previously thought.

Animals↗
PubMed2005

Population genetic analysis identifies source-sink dynamics for two sympatric garter snake species (Thamnophis elegans and Thamnophis sirtalis).

Population genetic structure can be shaped by multiple ecological and evolutionary factors, but the genetic consequences of these factors for multiple species inhabiting the same environment remain unexplored. We used microsatellite markers to examine the population structures of two coexisting species of garter snake, Thamnophis elegans and Thamnophis sirtalis, to determine if shared landscape and biology imposed similar population genetic structures. These snakes inhabit a series of ponds, lakes and flooded meadows in northern California and tend to converge on prey type wherever they coexist. Both garter snakes had comparable effective population sizes and bidirectional migration rates (estimated using a maximum-likelihood method based on the coalescent) with low but significant levels of genetic differentiation (F(ST) = 0.024 for T. elegans and 0.035 for T. sirtalis). Asymmetrical gene flow revealed large source populations for both species as well as potential sinks, suggesting frequent extinction-recolonization and metapopulation dynamics. In addition, we found a significant correlation between their genetic structures based on both pairwise F(ST)s for shared populations (P = 0.009) and for bidirectional migration rates (P = 0.024). Possible ecological and evolutionary factors influencing similarities and differences in genetic structure for the two species are discussed. Genetic measures of effective population size and migration rates obtained in this study are also compared with estimates obtained from mark-recapture data.

Animal Migration↗
PubMedDate not supplied

Isolation and characterization of nine microsatellite loci from the Hawaiian grouper Epinephelus quernus (Serranidae) for population genetic analyses.

The availability of variable genetic markers for groupers (Serranidae) has generally been limited to mitochondrial DNA. For studies of population genetic structure, more loci are usually required; particularly useful are those that are nuclear in origin such as microsatellites. Here, we isolated and characterized 9 microsatellite loci from the endemic Hawaiian grouper Epinephelus quernus using a biotin-labeled oligonucleotide-streptavidin-coated magnetic bead approach. Of the 20 repeat-containing fragments isolated, 15 had sufficient flanking region in which to design primers. Among these, 9 produced consistent polymerase chain reaction product, and 6 were highly variable. These 6 loci were all composed of dinucleotide repeats, with the number of alleles ranging from 6 to 18, and heterozygosities from 33.3% to 91.7%. The high levels of variability observed should make these markers useful for population genetic studies of E. quernus, and potentially other epinephelines.

Animals↗
PubMed1986

[Genetic and ecological study of aboriginal populations of northeastern Siberia. I. Gm-haplotypes and their frequency in 10 chukchi populations. Genetic structure of reindeer chukchi].

G1m (z, a, x, f) and G3m (g, b0, b1, b3, b5, s, t) allotypes were tested in 1079 Chukchi inhabitants of interior Chukotka and adjacent Kamchatka. Genetic variation at this particular locus is provided by the presence of three haplotypes, namely, za;g, zax;g and za;bO35st, revealed with mean frequencies of 0.748, 0.089 and 0.154, respectively. Traces of Caucasian Gm (f;bO135) haplotype were observed in 9 of 10 populations studied. Judging from its frequency in the whole group (0.009), European admixture in Reindeer Chukchi did not exceed 1.3%. Analysis of covariance and variance matrices containing gene frequencies for 11 polymorphic loci revealed the aspects of genetic structure. Simultaneously, the action of systematic versus nonsystematic pressure was also evaluated and interpreted in the light of historical and ecological events.

Asian People↗
PubMed2003

Population genetics in Israel in the 1950s. The unconscious internalization of ideology.

This essay describes the effects of Zionist ideology on research into human population genetics carried out in Israel during the 1950s and early 1960s. I argue that the internalization of the dominant Zionist narrative is reflected in the articles that were written by Israeli geneticists and physicians during these years. My claim is based on a comparison of articles about human population genetics written and published by Israeli scientists between 1951 and 1963 with similar articles written by non-Israelis. The comparison reveals that during this period the Israeli human geneticists and physicians emphasized the sociological and historical aspects of their research and used their work, among other things, as a vehicle for establishing a national identity and confirming the Zionist narrative.

Emigration and Immigration↗
PubMed1993

[The use of the 5'PstEJ6.6 probe containing a Ha-ras oncogene promoter in population genetics research by DNA fingerprinting].

The Mendelian inheritance of population genetic markers according to their zygosity has been established in a population investigation carried out in Kazakhstan and the northwestern region of Russia, using the 5'PstEJ6.6 DNA probe genetic variability both for persons of different nationality in a population and between two distant populations has been observed. Said procedure has proved more acceptable than the M13 phage DNA test for mass screening examinations because it involves genome analysis on the basis of DNA markers common to each population.

Adult↗
PubMed2002

Homoplasy and mutation model at microsatellite loci and their consequences for population genetics analysis.

Homoplasy has recently attracted the attention of population geneticists, as a consequence of the popularity of highly variable stepwise mutating markers such as microsatellites. Microsatellite alleles generally refer to DNA fragments of different size (electromorphs). Electromorphs are identical in state (i.e. have identical size), but are not necessarily identical by descent due to convergent mutation(s). Homoplasy occurring at microsatellites is thus referred to as size homoplasy. Using new analytical developments and computer simulations, we first evaluate the effect of the mutation rate, the mutation model, the effective population size and the time of divergence between populations on size homoplasy at the within and between population levels. We then review the few experimental studies that used various molecular techniques to detect size homoplasious events at some microsatellite loci. The relationship between this molecularly accessible size homoplasy size and the actual amount of size homoplasy is not trivial, the former being considerably influenced by the molecular structure of microsatellite core sequences. In a third section, we show that homoplasy at microsatellite electromorphs does not represent a significant problem for many types of population genetics analyses realized by molecular ecologists, the large amount of variability at microsatellite loci often compensating for their homoplasious evolution. The situations where size homoplasy may be more problematic involve high mutation rates and large population sizes together with strong allele size constraints.

Biological Evolution↗
PubMed1994

Molecular evolution and population genetics of Greater Caribbean green turtles (Chelonia mydas) as inferred from mitochondrial DNA control region sequences.

The molecular evolution and population genetics of migratory green turtles (Chelonia mydas) in the Greater Caribbean were examined with mitochondrial DNA (mtDNA) control region I sequences. A total of 488 base positions (bp) per individual were aligned for 44 individuals from four nesting populations in Florida, Costa Rica, Aves Island (Venezuela), and Surinam. Twelve sequence polymorphisms were detected, representing ten transitions, one transversion, and one 10-bp repeat. Sequence analyses of within- and between-population diversity revealed a deep divergence between western and eastern Caribbean nesting colonies and an inverse relationship between reproductive female population size and mtDNA diversity. In small populations, genetic admixture was important to maintaining high diversity, whereas larger populations appear to have experienced historical bottlenecks or resulted from founder effects. Mitochondrial DNA sequences of the control region offer an order of magnitude greater resolution than restriction site data for addressing questions about mtDNA variation, both within and between populations of green turtles.

Animals↗
PubMed2003

Population genetic screening programmes: principles, techniques, practices, and policies.

This paper examines the professional and scientific views on the principles, techniques, practices, and policies that impact on the population genetic screening programmes in Europe. This paper focuses on the issues surrounding potential screening programmes, which require further discussion before their introduction. It aims to increase, among the health-care professions and health policy-makers, awareness of the potential screening programmes as an issue of increasing concern to public health. The methods comprised primarily the review of the existing professional guidelines, regulatory frameworks and other documents related to population genetic screening programmes in Europe. Then, the questions that need debate, in regard to different types of genetic screening before and after birth, were examined. Screening for conditions such as cystic fibrosis, Duchenne muscular dystrophy, familial hypercholesterolemia, fragile X syndrome, hemochromatosis, and cancer susceptibility was discussed. Special issues related to genetic screening were also examined, such as informed consent, family aspects, commercialization, the players on the scene and monitoring genetic screening programmes. Afterwards, these questions were debated by 51 experts from 15 European countries during an international workshop organized by the European Society of Human Genetics Public and Professional Policy Committee in Amsterdam, The Netherlands, 19-20, November, 1999. Arguments for and against starting screening programmes have been put forward. It has been questioned whether genetic screening differs from other types of screening and testing in terms of ethical issues. The general impression on the future of genetic screening is that one wants to 'proceed with caution', with more active impetus from the side of patients' organizations and more reluctance from the policy-makers. The latter try to obviate the potential problems about the abortion and eugenics issues that might be perceived as a greater problem than it is in reality. However, it seems important to maintain a balance between a 'professional duty of care' and 'personal autonomy'.

Ethics↗