Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Genetic Structures”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

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

At least 1,495 records · Page 83Linked to original sources

High levels of genetic differentiation of Oryza officinalis Wall. ex Watt. from China.

In order to determine the population genetic structure of wild rice (Oryza officinalis Wall. ex Watt.), an endangered tropical and subtropical species, allozyme diversity encoded by 24 loci was analyzed electrophoretically in 145 individuals of eight natural populations from Hainan, Guangxi, and Yunnan provinces, China. A fairly high genetic differentiation (F(ST) = 0.882 and mean I = 0.786) was found among the studied populations. Our results suggest that restricted gene flow may play a significant role in shaping such a population genetic structure. In addition, high genetic differentiation among populations within a geographically limited region may stem from a reduced population size and consequent genetic drift.

China↗

Population structure and inbreeding in a rare and declining bumblebee, Bombus muscorum (Hymenoptera: Apidae).

Owing to habitat loss populations of many organisms have declined and become fragmented. Vertebrate conservation strategies routinely consider genetic factors, but their importance in invertebrate populations is poorly understood. Bumblebees are important pollinators, and many species have undergone dramatic declines. As monoandrous social hymenopterans they may be particularly susceptible to inbreeding due to low effective population sizes. We study fragmented populations of a bumblebee species, on a model island system, and on mainland Great Britain where it is rare and declining. We use microsatellites to study: population genetic structuring and gene flow; the relationships between genetic diversity, population size and isolation; and frequencies of (sterile) diploid males - an indicator of inbreeding. We find significant genetic structuring (theta = 0.12) and isolation by distance. Populations > 10 km apart are all significantly differentiated, both on oceanic islands and on the mainland. Genetic diversity is reduced relative to closely related common species, and isolated populations exhibit further reductions. Of 16 populations, 10 show recent bottlenecking, and 3 show diploid male production. These results suggest that surviving populations of this rare insect suffer from inbreeding as a result of geographical isolation. Implications for the conservation of social hymenopterans are discussed.

Animals↗

[Genetic relationships between Ewenki minority in Inner Mongolia and other 14 groups].

OBJECTIVE: To study the STR genetic structure of an Ewenki Ethnic minority Group of Inner Mongolia, and analyze the genetic relationship among Ewenki and other 14 groups. METHODS: Genetic distribution for 9 STR loci (D3S1358, vWA, FGA, TH01, TPOX, CSF1PO, D5S818, D13S317, and D7S820) were determined based on gene scan marked by fluorescence. Principle component analysis was performed using SPSS. RESULTS: Sixty-four alleles and 158 genotypes were observed in 90 unrelated Ewenki individuals. The corresponding gene frequency and genotype frequency was 0.0056 to 0.4722 and 0.0111 to 0.3, respectively. The expected and observed genotype frequency of the 9 STR loci were in accordance with the Hardy-Weinberg equilibrium (P>0.05). The principle component analysis showed that Ewenki clustered with groups of Mongolian and Tujue language branch. CONCLUSION: Nine of the STR genetic structure of an Ewenki Ethnic minority Group of Inner Mongolia were obtained. Those ethnic groups in subfamilies of Altaic language family clustered as their geographical location and those with close genetic relationships use similar language.

Alleles↗

Short-term impact of 1997/1998 ENSO-induced disturbance on abundance and genetic variation in a tropical butterfly.

In order to assess the short-term impact of habitat loss after disturbance, we studied Arhopala epimuta (Lepidoptera: Lycaenidae) populations in 5 landscapes in Borneo that were differentially affected by the 1997/1998 El Niño Southern Oscillation-induced drought and fire. Sampling was conducted before (1997) and after (1998 and 2000) disturbance. This study combined demographic and genetic data inferred from the analysis of 5 microsatellite loci and mitochondrial DNA (mtDNA) control region sequences. Over all 5 landscapes, a total of 313 A. epimuta were sampled over the 3-year survey. Butterfly abundance varied greatly both spatially and temporally (within disturbed landscapes). After the disturbance, a 4-fold population expansion was observed in a small unburned isolate, whereas population extinction was observed in one of the severely burned areas. The analysis of mtDNA sequences in a subsample of 106 A. epimuta revealed no significant spatial or temporal genetic structure. The analysis of 5 microsatellite loci revealed high frequencies of null alleles. Genetic evidence of recent change in population size was found in all 3 unburned landscapes using microsatellites. Congruent to mtDNA, microsatellites failed to detect significant genetic structure according to sampling year or landscapes. Our results suggest that, for mobile species within recently fragmented habitat, habitat loss after disturbance may lead to local population extinction but may augment genetic diversity in remnant local populations because of increased gene flow.

Animals↗

Population structure inhibits evolutionary diversification under competition for resources.

A model is presented that explores how population structure affects the evolutionary outcome of ecological competition for resources. The model assumes that competition for resources occurs within groups of a finite number of individuals (interaction groups), and that limited dispersal of individuals between groups (according to Wright's island model of population structure) results in genetic structuring of the population. It is found that both finite-sized interaction groups and limited dispersal can have substantial effects on the evolution of resource exploitation strategies as compared to models with a single, infinitely large, well-mixed interaction group. Both effects, in general, tend to select for less aggressive competitive strategies. Moreover, both effects also tend to reduce the likelihood of the evolutionary diversification of resource exploitation strategies that often occurs in models of resource competition with infinite populations. The results are discussed in the context of theories of the evolutionary diversification of resource exploitation strategies and speciation.

Biological Evolution↗

The response of amino acid frequencies to directional mutation pressure in mitochondrial genome sequences is related to the physical properties of the amino acids and to the structure of the genetic code.

The frequencies of A, C, G, and T in mitochondrial DNA vary among species due to unequal rates of mutation between the bases. The frequencies of bases at fourfold degenerate sites respond directly to mutation pressure. At first and second positions, selection reduces the degree of frequency variation. Using a simple evolutionary model, we show that first position sites are less constrained by selection than second position sites and, therefore, that the frequencies of bases at first position are more responsive to mutation pressure than those at second position. We define a measure of distance between amino acids that is dependent on eight measured physical properties and a similarity measure that is the inverse of this distance. Columns 1, 2, 3, and 4 of the genetic code correspond to codons with U, C, A, and G in their second position, respectively. The similarity of amino acids in the four columns decreases systematically from column 1 to column 2 to column 3 to column 4. We then show that the responsiveness of first position bases to mutation pressure is dependent on the second position base and follows the same decreasing trend through the four columns. Again, this shows the correlation between physical properties and responsiveness. We determine a proximity measure for each amino acid, which is the average similarity between an amino acid and all others that are accessible via single point mutations in the mitochondrial genetic code structure. We also define a responsiveness for each amino acid, which measures how rapidly an amino acid frequency changes as a result of mutation pressure acting on the base frequencies. We show that there is a strong correlation between responsiveness and proximity, and that both these quantities are also correlated with the mutability of amino acids estimated from the mtREV substitution rate matrix. We also consider the variation of base frequencies between strands and between genes on a strand. These trends are consistent with the patterns expected from analysis of the variation among genomes.

Amino Acids↗

Genetic and structural characterization of H-2-controlled allelic forms of murine C4.

The patterns of expression of several types of genetic variation in murine C4 were investigated. Dominance was assessed for S-region-determined differences in molecular weight of the C4 alpha-chain from Sw7 strains relative to all other strains examined and in C4 hemolytic titers. Codominant expression in F1 hybrids was shown for both of the above variations. Comparison of tryptic peptide profiles of radiolabeled C4 beta-chains encoded by different S regions revealed differences in their primary structures. The demonstration of codominant expression for the variant C4 traits examined and the evidence from tryptic peptide maps for haplotype differences in C4 primary structure strongly support the hypothesis that polymorphism of murine C4 is controlled by structural genes which are located in the S region.

Alleles↗

[Genetic-demographic structure and prevalence of congenital malformations in rural regions of the Kursk district].

Investigation of the the genetics, demography, and epidemiology of congenital malformations (CMs) in Kursk oblast revealed statistically significant correlations between population parameters and the incidence of CM in the rural rations of the oblast. The general prevalence of CM and that of the separate CM forms ("guard" CM, multiple CM, hemangioma, congenital heart disease, congenital myelocele, talipes valgus, congenital femoral luxation, polydactyly, cryptorchism) increased with an increase in the average marital age of men and women of the reproductive part of the population and with an increase in the level of the populations homozygosity (an increase in the local consanguinity and ethnic marriage assortativeness, a decrease in the populations's migration activity, an increase in the proportion of genotypes homozygous for recessive genes, etc).

Congenital Abnormalities↗

Mitochondrial DNA sequence polymorphisms of five ethnic populations from northern China.

To study the mitochondrial DNA (mtDNA) polymorphisms in a total of 232 individuals from five ethnic populations (Daur, n=45; Ewenki, n=47; Korean, n=48; Mongolian, n=48; Oroqen, n=44) in northern China, we analyzed the control region sequences and typed for a number of characteristic mutations in coding regions (especially the region 14576-16047), by direct sequencing or restriction-fragment-length-polymorphism (RFLP) analysis. With the exception of 14 individuals belonging to the European-specific haplogroups R2, H, J, and T, the mtDNAs considered could be assigned into the East Asian-specific haplogroups described recently. The polymorphisms in cytochrome b sequence were found to be very informative for defining or supporting the haplogroups status of East Asian mtDNAs in addition to the reported regions 10171-10659 and 14055-14590 in our previous study. The haplogroup distribution frequencies varied in the five ethnic populations, but in general they all harbored a large amount of north-prevalent haplogroups, such as D, G, C, and Z, and thus were in agreement with their ethnohistory of northern origin. The two populations (Ewenki and Oroqen) with small population census also show concordant features in their matrilineal genetic structures, with lower genetic diversities observed.

Asian People↗

Molecular biology of transposable elements.

Transposable elements play an essential part in the epidemic spread of antibiotic resistances among bacterial populations. Their ubiquity and their role in the molecular evolution of genomes and organisms has captured the interest of molecular biologists, who investigate the genetic structure and novel mechanisms of recombination underlying transposition. This article, after introducing the general structure of mobile genetic elements and basic mechanistic concepts of transposition in bacteria, uses the well-studied Tn3 family as paradigm for gene organization, gene function and gene regulation. Finally, new applications of transposons in genetic engineering will be described.

DNA Transposable Elements↗

Seasonal changes in the rhizosphere microbial communities associated with field-grown genetically modified canola (Brassica napus).

The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified plants were temporary and did not persist into the next field season.

Bacteria↗

Patterns of allozyme variation in diploid and tetraploid Centaurea jacea at different spatial scales.

The extent and spatial patterns of genetic variation at allozyme markers were investigated within and between diploid and autotetraploid knapweeds (Centaurea jacea L. sensu lato, Asteraceae) at contrasted geographic scales: (1) among populations sampled from a diploid-tetraploid contact zone in the northeastern part of the Belgian Ardennes, and (2) within mixed populations from that zone where diploids and tetraploids coexist. Our data were also compared with a published dataset by Sommer (1990) describing allozyme variation in separate diploid and tetraploid knapweeds populations collected throughout Europe. Genetic diversity was higher in tetraploids. In the Belgian Ardennes and within the mixed populations, both cytotypes had similar levels of spatial genetic structure, they were genetically differentiated, and their distributions of allele frequencies were not spatially correlated. In contrast, at the European scale, diploids and tetraploids did not show differentiated gene pools and presented a strong correlation between their patterns of spatial genetic variation. Numerical simulations showed that the striking difference in patterns observed at small and large geographic scales could be accounted for by a combination of (1) isolation by distance within cytotypes; and (2) partial reproductive barriers between cytotypes and/or recurrent formation of tetraploids. We suggest that this may explain the difficulty of the taxonomic treatment of knapweeds and of polyploid complexes in general.

Asteraceae↗

Random amplified polymorphic DNA analysis of Anopheles nuneztovari (Diptera: Culicidae) from Western and northeastern Colombia.

Random amplified polymorphic DNA (RAPD) markers were used to analyze 119 DNA samples of three Colombian Anopheles nuneztovari populations to study genetic variation and structure. Genetic diversity, estimated from heterozygosity, averaged 0.34. Genetic flow was greater between the two populations located in Western Colombia (F ST: 0.035; Nm: 6.8) but lower between these two and the northeastern population (F ST: 0.08; Nm: 2.8). According to molecular variance analysis, the genetic distance between populations was significant (phi ST 0.1131, P < 0.001). The variation among individuals within populations (phi ST 0.8869, P < 0.001)was also significant, suggesting a greater degree of population subdivision, not considered in this study. Both the parameters evaluated and the genetic flow suggest that Colombian An. nuneztovari populations are co-specific.

Animals↗

Parasite genotypes identify source populations of migratory fish more accurately than fish genotypes.

DNA-based assignment of individuals to their population of origin has many applications such as mixed-stock analysis, identifying individuals from protected populations, and elucidating migration patterns. However, low genetic differentiation among populations will cause misassignments. Thus, an alternative means of determining an individual's population of origin is needed in cases where there is little or no neutral differentiation among source populations. Here, we test the hypothesis that parasite genotypes can be used to identify the origins of hosts more accurately than host genotypes. Using microsatellite markers from steelhead trout and their trematode parasites, we show that the odds of correct assignment are four times greater with the parasite's genotypes than with the host's genotypes. Our analyses show that this result is simply explained by the greater genetic structure among populations of the trematode parasite. Recent studies on the comparative genetic structure of other host and parasite species suggest that our results are not unusual or unique to the host-parasite system we studied. Thus, our work indicates that parasites will be useful for a wide range of applied and basic research that requires the assignment of individuals to source populations.

Animal Migration↗

Study of the populations of the Balearic Islands (Spain) using mtDNA RFLPs.

The Balearic archipelago (Spain) is composed of three major islands, Majorca, Minorca, and Ibiza. Majorca is the largest and most populous island. Minorca is the second largest in area and third in population, and Ibiza is the smallest of the three and has the second largest population. Ibiza also shows differences from the other two islands in its landscape, vegetation, and especially origins of the founding settlements. The three islands also have been settled by people of different cultures. We have carried out a genetic analysis at the level of mtDNA RFLPs in these populations and found that the three populations are genetically structured, with differences in the RFLP haplotype frequencies reflecting the different population substrata of the three islands. In this structure Ibiza is genetically more different from Majorca and Minorca. In addition, we found a new haplotype in Minorca, named haplotype 150, which seems to originate from haplotype 56.

DNA, Mitochondrial↗

A formal test of linguistic and genetic coevolution in native Central and South America.

This paper investigates a mechanism of linguistic and genetic coevolution in Native Central and South America. This mechanism proposes that a process of population fissions, expansions into new territories, and isolation of ancestral and descendant groups will produce congruent language and gene trees. To evaluate this population fissions mechanism, we collected published mtDNA sequences for 1,381 individuals from 17 Native Central and South American populations. We then tested the hypothesis that three well-known language classifications also represented the genetic structure of these populations. We rejected the hypothesis for each language classification. Our tests revealed linguistic and genetic correspondence in several shallow branches common to each classification, but no linguistic and genetic correspondence in the deeper branches contained in two of the language classifications. We discuss the possible causes for the lack of congruence between linguistic and genetic structure in the region, and describe alternative mechanisms of linguistic and genetic correspondence and their predictions.

Cluster Analysis↗

Molecular genetic approaches to the study of primate behavior, social organization, and reproduction.

In the past several decades, the development of novel molecular techniques and the advent of noninvasive DNA sampling, coupled with the ease and speed with which molecular analyses can now be performed, have made it possible for primatologists to directly examine the fitness effects of individual behavior and to explore how variation in behavior and social systems influences primate population genetic structure. This review describes the theoretical connections between individual behavior and primate social systems on the one hand and population genetic structure on the other, discusses the kinds of molecular markers typically employed in genetic studies of primates, and summarizes what primatologists have learned from molecular studies over the past few decades about dispersal patterns, mating systems, reproductive strategies, and the influence of kinship on social behavior. Several important conclusions can be drawn from this overview. First, genetic data confirm that, in many species, male dominance rank and fitness are positively related, at least over the short term, though this relationship need not simply be a reflection of male-male contest competition over mates. More importantly, genetic research reveals the significance of female choice in determining male reproductive success, and documents the efficacy of alternative mating tactics among males. Second, genetic data suggest that the presumed importance of kinship in structuring primate social relationships needs to be evaluated further, at least for some taxa such as chimpanzees in which demographic factors may be more important than relatedness. I conclude this paper by offering several suggestions of additional ways in which molecular techniques might be employed in behavioral and ecological studies of primates (e.g., for conducting "molecular censuses" of unhabituated populations, for studying disease and host-parasite interactions, or for tracking seed fate in studies of seed dispersal) and by providing a brief introduction to the burgeoning field of nonhuman primate behavioral genetics.

Animals↗

Amino acid contribution to the genetic code structure: end-atom chemical rules of doublet composition.

Up-to-date knowledge is not yet enough to prove or reject completely one of the leading alternative hypotheses considering external or internal origin of the genetic code organization (term "internal" means a peculiarity of amino acids and nucleotides which can propose some logical basis for explanation why definite codons are assigned to particular and not to other amino acids; term "external" in this context implies tRNAs and aminoacyl-tRNA synthetases which provide accuracy of translation but are not presented in the code table in the evident from). New data in favour of the internal approach have been proposed. A close correlation exists between chemical nature of single, the most remote from C alpha, end atoms of amino acid side chains and types of bases in appropriate codon doublets. There are two main rules reflecting this correspondence: (1) all O- or N-ended amino acids (i.e. with O, OO, N, NN, ON, OC and NC end patterns) possess the A-containing codon doublets; (2) all solely C-ended (excluding Ala) and S-ended amino acids (i.e. residues with C, CC and S ends) have the U-containing codon doublets. The discovered asymmetry is characterized by the following high reliable differences of A and U distribution among 21 patterns of individual doublets belonging to 18 amino acids (Pro and Gly are discarded): (a) proportion of A plus U bases corresponding to the two rules, 22/26 is much more than proportion of such bases in violating cases, 4/26; (b) A and U are dominant bases over each of other base types in the doublets of O/N- and C/S-ending amino acids, respectively; (c) the numbers of doublets bearing (18) and not bearing (3) dominant A or U bases are also significantly different. The concept of indicative amino acid end atoms (O/N and non-O/non-N) and doublet A/U bases has been proposed and discussed as so far unknown regulative system of submolecular level of heredity which, additionally to possible key role in the process of the genetic code arising, provides now control of its universality, stability and fidelity.

Amino Acids↗