PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “GENETICS, POPULATION”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 253 records · Page 14Linked to original sources
PubMed2003

Population genetics of threatened wild plants in Japan.

Approximately one-fourth of Japan's native plant species are threatened with extinction. To conserve these species, it is critical to evaluate genetic diversity at species-level and population-level. Some factors, including population size and geographic distribution, are known to influence the population genetic diversity of wild plant species. This article briefly reviews the population genetic studies that have been conducted on wild threatened plants in Japan. A large population size or wide geographic distribution does not always lead to large genetic diversity, suggesting that historical factors such as speciation processes and population expansion often play more important roles in determining genetic diversity than the number of remnant individuals. The mating system of a species also affects genetic diversity; predominantly selfing species tend to have smaller genetic diversity than outcrossing congeners. Another issue of concern in the conservation genetics of wild plants in Japan is the genetic diversity of insular endemics, because Japan consists of many islands, and the insular flora contains many endemic and threatened species. Previous studies on endemic plants on the Bonin and the Ryukyu Islands are reviewed. Compared to the cases of the Bonin Islands or other oceanic islands, there is much larger genetic diversity in plants endemic to the Ryukyu Islands. This difference is probably the result of the differences in the geological history of these islands.

Conservation of Natural Resources↗
PubMed2006

Mycobacterium tuberculosis complex genetic diversity: mining the fourth international spoligotyping database (SpolDB4) for classification, population genetics and epidemiology.

BACKGROUND: The Direct Repeat locus of the Mycobacterium tuberculosis complex (MTC) is a member of the CRISPR (Clustered regularly interspaced short palindromic repeats) sequences family. Spoligotyping is the widely used PCR-based reverse-hybridization blotting technique that assays the genetic diversity of this locus and is useful both for clinical laboratory, molecular epidemiology, evolutionary and population genetics. It is easy, robust, cheap, and produces highly diverse portable numerical results, as the result of the combination of (1) Unique Events Polymorphism (UEP) (2) Insertion-Sequence-mediated genetic recombination. Genetic convergence, although rare, was also previously demonstrated. Three previous international spoligotype databases had partly revealed the global and local geographical structures of MTC bacilli populations, however, there was a need for the release of a new, more representative and extended, international spoligotyping database. RESULTS: The fourth international spoligotyping database, SpolDB4, describes 1939 shared-types (STs) representative of a total of 39,295 strains from 122 countries, which are tentatively classified into 62 clades/lineages using a mixed expert-based and bioinformatical approach. The SpolDB4 update adds 26 new potentially phylogeographically-specific MTC genotype families. It provides a clearer picture of the current MTC genomes diversity as well as on the relationships between the genetic attributes investigated (spoligotypes) and the infra-species classification and evolutionary history of the species. Indeed, an independent Naïve-Bayes mixture-model analysis has validated main of the previous supervised SpolDB3 classification results, confirming the usefulness of both supervised and unsupervised models as an approach to understand MTC population structure. Updated results on the epidemiological status of spoligotypes, as well as genetic prevalence maps on six main lineages are also shown. Our results suggests the existence of fine geographical genetic clines within MTC populations, that could mirror the passed and present Homo sapiens sapiens demographical and mycobacterial co-evolutionary history whose structure could be further reconstructed and modelled, thereby providing a large-scale conceptual framework of the global TB Epidemiologic Network. CONCLUSION: Our results broaden the knowledge of the global phylogeography of the MTC complex. SpolDB4 should be a very useful tool to better define the identity of a given MTC clinical isolate, and to better analyze the links between its current spreading and previous evolutionary history. The building and mining of extended MTC polymorphic genetic databases is in progress.

Computational Biology↗
PubMed1990

Formal and population genetics of F13A and FUCA1 polymorphisms in northern Portugal.

Subunit A of coagulation factor XIII (F13A) and alpha-L-fucosidase (FUCA1) polymorphisms were studied in unrelated healthy blood donors from northern Portugal. The gene frequencies found were: F13A*2 = 0.241 and FUCA1*2 = 0.308. Segregation analysis in mother/child pairs and nuclear families confirmed the previously described modes of inheritance for F13A and FUCA1, and no evidence for silent genes was found.

Factor XIII↗
PubMed1994

Population genetic characteristics of the D1S80 locus in seven human populations.

We have analyzed the allele frequency distribution at the highly polymorphic variable number of tandem repeat (VNTR) locus D1S80 (pMCT118) in seven ethnic populations (namely, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, American and Western Samoans, Kacharis of Northeast India, and German Caucasians) using the polymerase chain reaction (PCR) technique. In the pooled sample of 443 unrelated individuals 20 segregating alleles were detected. A trimodal pattern of allelic distribution is present in the majority of populations and is indicative of the evolutionary antiquity of the polymorphism at this locus. In spite of the observed high degree of polymorphism (expected heterozygosity 56%-86%), with a single exception--the marginally significant P value (0.04) of the exact test in American Samoans--the genotype distributions in all populations conform to their respective Hardy-Weinberg expectations. Summary statistics indicate that, in general, the allele frequency distribution at this locus may be approximated by the infinite allele model. The data also demonstrate that alleles that are shared by all populations have the highest average frequency within populations. Furthermore, the kinship bioassay analysis demonstrates that the extensive variation observed at the D1S80 locus is at the interindividual within population level, which dwarfs any interpopulation allele frequency variation, consistent with the population dynamics of hypervariable polymorphisms. These characteristics of the D1S80 locus make it a very useful marker for population genetic research, genetic linkage studies, forensic identification of individuals, and for determination of biological relatedness of individuals.

Alleles↗
PubMed2004

Exploring population genetic structure in three species of Lesser Antillean bats.

We explore population genetic structure in phyllostomid bats (Ardops nichollsi, Brachyphylla cavernarum and Artibeus jamaicensis) from the northern Lesser Antilles by investigating the degree to which island populations are genetically differentiated. Our hypothesis, that the island populations are genetically distinct because of a combination of founding events, limited migration and genetic drift exacerbated by catastrophe-induced fluctuations in population size, is derived from a priori hypotheses erected in the literature. The first prediction of this hypothesis, that within each species island populations are monophyletic, was tested using a parametric bootstrap approach. Island monophyly could not be rejected in Ardops nichollsi (P = 0.718), but could be rejected in B. cavernarum (P < 0.001) and Artibeus jamaicensis (P < 0.001). A second prediction, that molecular variance is partitioned among islands, was tested using an amova and was rejected in each species [Ardops nichollsi (P = 0.697); B. cavernarum (P = 0.598); Artibeus jamaicensis (P = 0.763)]. In B. cavernarum and Artibeus jamaicensis, the admixture in mitochondrial haplotypes from islands separated by > 100 km of ocean can be explained either by interisland migration or by incomplete lineage sorting of ancestral polymorphism in the source population. As an a posteriori test of lineage sorting, we used simulations of gene trees within a population tree to suggest that lineage sorting is an unlikely explanation for the observed pattern of nonmonophyly in Artibeus jamaicensis (PW < 0.01; PSE = 0.04), but cannot be rejected in B. cavernarum (PW = 0.81; PSE = 0.79). A conservative interpretation of the molecular data is that island populations of Artibeus jamaicensis, although isolated geographically, are not isolated genetically.

Analysis of Variance↗
PubMed2006

Characterisation of Teladorsagia circumcincta microsatellites and their development as population genetic markers.

There is a need to develop tools to study the genetics of parasitic nematodes. This is particularly urgent for those species in which anthelmintic resistance is common such as the sheep parasite Teladorsagia (Ostertagia) circumcincta. The lack of information on the population genetics of such parasites severely limits our ability to study the genetic basis of anthelmintic resistance. This paper presents the results of three approaches used to isolate microsatellite markers from T. circumcincta and the development of a panel of markers suitable for population genetic analysis. Hybridisation screening of small insert genomic libraries and interspecies PCR amplification of Haemonchus contortus microsatellites were used to identify CA/GT microsatellites. Many of these loci were associated with a 146bp tandem repeat, named TecRep, that is related to a repetitive element previously identified in other trichostrongylid nematode genomes but apparently absent from other nematode groups. A large proportion of the loci isolated were problematic for use as population genetic markers, predominantly due to a high frequency of null alleles or the association with the TecRep repeat. Bioinformatic screening of a T. circumcincta EST database identified both di- and tri-nucleotide microsatellite repeats and a greater proportion of these turned out to be more robust markers than those derived from genomic sequence. A panel of seven markers has been selected and characterised which are sufficiently robust and polymorphic to be valuable population genetic markers for this parasite.

Animals↗
PubMed2000

[Impacts of stochastic migration of seed and pollen on differentiation of plant population genetic structure].

The island model was extended to plant population with incorporation of the effects of stochastic migration of seed and pollen grain. Exact mean and variance of gene frequencies were formulated for each of three genomes with different modes of inheritance (bi-parental, paternal and maternal). Theoretical results indicate that stochastic migration in both seed and pollen may increase the variance of gene frequencies among populations, depending upon how large the variations of migration rate and/or migrant gene frequency are. Fluctuation in migration rate or in migrant gene frequencies of seed and pollen grain is also an important factor influencing population genetic structure, perhaps as important as the absolute value of migration rate. One important result is that the combined effect induced by the fluctuation of both migration rate and migrant gene frequency of seed and pollen can greatly intensify differentiation of population genetic structure. Application of these theoretical results in practical work was discussed in detail.

Demography↗