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PubMed2006

Population genetics study of isoniazid resistance mutations and evolution of multidrug-resistant Mycobacterium tuberculosis.

The molecular basis for isoniazid resistance in Mycobacterium tuberculosis is complex. Putative isoniazid resistance mutations have been identified in katG, ahpC, inhA, kasA, and ndh. However, small sample sizes and related potential biases in sample selection have precluded the development of statistically valid and significant population genetic analyses of clinical isoniazid resistance. We present the first large-scale analysis of 240 alleles previously associated with isoniazid resistance in a diverse set of 608 isoniazid-susceptible and 403 isoniazid-resistant clinical M. tuberculosis isolates. We detected 12 mutant alleles in isoniazid-susceptible isolates, suggesting that these alleles are not involved in isoniazid resistance. However, mutations in katG, ahpC, and inhA were strongly associated with isoniazid resistance, while kasA mutations were associated with isoniazid susceptibility. Remarkably, the distribution of isoniazid resistance-associated mutations was different in isoniazid-monoresistant isolates from that in multidrug-resistant isolates, with significantly fewer isoniazid resistance mutations in the isoniazid-monoresistant group. Mutations in katG315 were significantly more common in the multidrug-resistant isolates. Conversely, mutations in the inhA promoter were significantly more common in isoniazid-monoresistant isolates. We tested for interactions among mutations and resistance to different drugs. Mutations in katG, ahpC, and inhA were associated with rifampin resistance, but only katG315 mutations were associated with ethambutol resistance. There was also a significant inverse association between katG315 mutations and mutations in ahpC or inhA and between mutations in kasA and mutations in ahpC. Our results suggest that isoniazid resistance and the evolution of multidrug-resistant strains are complex dynamic processes that may be influenced by interactions between genes and drug-resistant phenotypes.

Alleles↗
PubMed2006

Merozoite surface protein-3alpha is a reliable marker for population genetic analysis of Plasmodium vivax.

BACKGROUND: The knowledge on population structure of the parasite isolates has contributed greatly to understanding the dynamics of the disease transmission for designing and evaluating malaria vaccines as well as for drug applications. msp-1 and msp-3alpha genes have been used as a genetic marker in population studies of Plasmodium vivax isolates. In this study, msp-3alpha was compared and assessed with msp-1 marker in order to find whether msp-3alpha is a reliable genetic marker for P. vivax population studies. METHODS: This comparative study was designed and carried out as the first assessment of diversity in Pvmsp-3alpha gene by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) in the 50 northern and 94 southern P. vivax isolates from Iran, which had been analysed before for msp-1 gene. RESULTS: Three allele size as, Type A (1.8 kb), Type B (1.5 kb) and Type C (1.2 kb) have been detected among both northern and southern isolates based on PCR results. Type C (70%) and Type A (68.7%) were the predominant fragments among northern and southern parasites, respectively. 99 distinct Pvmsp-3alpha fragments defined by the size were detected in the 94 southern samples by PCR analysis. However, no mixed genotype infections have been detected among northern isolates. Based on restriction pattern from digestion with Hha I and Alu I 12 and 49 distinct allelic variants have been detected among 50 northern and 94 southern isolates. However, based on msp-1 gene, 30 distinct variants identified in all 146-sequenced Iranian P. vivax isolate. CONCLUSION: The results suggested that PCR-RFLP on msp-3alpha gene is an adequate, applicable and easily used technique for molecular epidemiology studies of P. vivax isolates without the need for further sequencing analysis.

Alleles↗
PubMed2002

The population genetics of sporophytic self-incompatibility in Senecio squalidus L. (Asteraceae) I: S allele diversity in a natural population.

Twenty-six individuals of the sporophytic self-incompatible (SSI) weed, Senecio squalidus were crossed in a full diallel to determine the number and frequency of S alleles in an Oxford population. Incompatibility phenotypes were determined by fruit-set results and the mating patterns observed fitted a SSI model that allowed us to identify six S alleles. Standard population S allele number estimators were modified to deal with S allele data from a species with SSI. These modified estimators predicted a total number of approximately six S alleles for the entire Oxford population of S. squalidus. This estimate of S allele number is low compared to other estimates of S allele diversity in species with SSI. Low S allele diversity in S. squalidus is expected to have arisen as a consequence of a disturbed population history since its introduction and subsequent colonisation of the British Isles. Other features of the SSI system in S. squalidus were also investigated: (a) the strength of self-incompatibility response; (b) the nature of S allele dominance interactions; and (c) the relative frequencies of S phenotypes. These are discussed in view of the low S allele diversity estimates and the known population history of S. squalidus.

Crosses, Genetic↗
PubMed1999

Mitochondrial DNA polymorphism, sex ratio distorters and population genetics in the isopod Armadillidium vulgare.

Two maternally inherited sex ratio distorters (SRD) impose female-biased sex ratios on the wood louse Armadillidium vulgare by feminizing putative males. These SRD are (i) an intracytoplasmic bacterium of the genus Wolbachia, and (ii) another non-Mendelian element of unknown nature: the f element. Mitochondrial DNA variation was investigated in A. vulgare field populations to trace the evolution of host-SRD relationships and to investigate the effect of SRD on host cytoplasmic polymorphism. The Wolbachia endosymbionts showed no polymorphism in their ITS2 sequence and were associated with two closely related mitochondrial types. This situation probably reflects a single infection event followed by a slight differentiation of mitochondria. There was no association between the f element and a given mitochondrial type, which may confirm the fact that this element can be partially paternally transmitted. The spreading of a maternally inherited SRD in a population should reduce the mitochondrial diversity by a hitchhiking process. In A. vulgare, however, a within-population mtDNA polymorphism was often found, because of the deficient spread of Wolbachia and the partial paternal inheritance of the f element. The analysis of molecular variance indicated that A. vulgare populations are genetically structured, but without isolation by distance.

Animals↗
PubMed2006

Focusing on comparative ape population genetics in the post-genomic age.

The initial human and chimpanzee genome sequences have been published, and additional primate genomes, including those of gorilla and orang-utan, are in progress. With these new resources, we can now address what makes our species unique, by focusing on the underlying genetic differences associated with phenotypes. Comparative primate population genomics, including studies of structural changes, mobile elements, gene expression and functional analyses, will shed light on how natural selection and population demography are involved in the processes that lead to differences among great apes. Historically, this research has focused on the human perspective; however, we will learn much about ourselves with a focus on genomic diversity in hominoids as a group.

Animals↗
PubMed1975

Population genetics of euphydryas butterflies. I Genetic variation and the neutrality hypothesis.

Twenty-one populations of the checkerspot butterfly, Euphydryas editha, and ten populations of Euphydryas chalcedona were sampled for genetic variation at eight polymorphic enzyme loci. Both species possessed loci that were highly variable from population to population and loci that were virtually identical across all populations sampled. Our data indicate that the neutrality hypothesis is untenable for the loci studied, and therefore selection is indicated as the major factor responsible for producing these patterns. Thorough ecological work allowed gene flow to be ruled out (in almost all instances) as a factor maintaining similar gene frequencies across populations. The Lewontin-Krakauer test indicated magnitudes of heterogeneity among standardized variances of gene frequencies inconsistent with the neutrality hypothesis. The question of whether or not to correct this statistic for sample size is discussed. Observed equitability of gene frequencies of multiple allelic loci was found to be greater than that predicted under the neutrality hypothesis. Genetic differentiation persisting through two generations was found between the one pair of populations known to exchange significant numbers of individuals per generation. Two matrices of genetic distance between populations, based on the eight loci sampled, were found to be significantly correlated with a matrix of environmental distance, based on measures of fourteen environmental parameters. Correlations between gene frequencies and environmental parameters, results of multiple regression analysis, and results of principle component analysis showed strong patterns of association and of "explained" variation. The correlation analyses suggest which factors might be further investigated as proximate selective agents.

Animals↗
PubMed1980

[Population genetics and etho-historical considerations of the uniqueness of the Prasun Kafirs and the Kalash (central Hindu Kush) with regard to the ABO blood group system].

An attempt has been made to interpret the quite rare distribution pattern of ABO blood group genes (p > 0.5000, q < 0.1000 and r < 0.5000) among the Prasun Kafirs and the Kalsh of the central Hindu Kush from the point of view of population genetics and ethnohistory. If we consider the different age groups of the Prasun sample it will be observed that there is a marked increase in the frequency of blood group gene A and a corresponding decrease in blood group gene O as we proceed from older to younger age groups. These changes cna be readily explained on the basis of a prenatal selection through mother-child incompatibility. Because of the relatively small starting value of r < 0.5 a selection takes place against O, resulting in an increase of the blood group gene A. The differences in the gene frequencies among the various age groups are so large that apart from mother-child incompatibility other selective factors may have been involved, as for example the smallpox epidemics in the 1930's and in the beginning of the 1940's. Moreover, significant differences in blood group distribution were secured between the upper and lower valley samples which do not accord with the close marital relationships and the relatively long history of the settlement. It must be assumed therefore that particularly the greater frequency of the blood group gene B in the lower portion of the valley is to be attributed to marital relationships with other Kafir tribes or other ethnic groups (Pathans) which have become more frequent since the islamization at the end of the last century. In the case of the Kalash an age and regional differentiation is only possible to a limited extent. Nevertheless it must be assumed that the extremely high A frequency and the lower O and B frequencies are caused by the same genetic and ethnohistorical factors as it is the case with the Prasun Kafirs.

ABO Blood-Group System↗
PubMed2001

The impact of habitat fragmentation and social structure on the population genetics of roe deer (Capreolus capreolus L.) in Central Europe.

Nine out of 57 bovine and caprine microsatellites investigated have proved polymorphic in roe deer populations from Central Europe. The polymorphism of four to nine microsatellites (with two to 16 alleles each) has been screened in 492 roe deer from 27 sample locations in Germany, the Netherlands and France, and 10 allozyme loci have been investigated in 118 roe deer from Germany. These studies have revealed a genetically homogeneous population, but with a local scatter of allele frequencies. The mean genetic distance among sample pairs, and the overall fixation index for the 27 population samples were D=0.1638 and GST=0.0972 for four microsatellite loci, and D=0.0598 and GST=0.1459 for 10 allozyme loci. No isolation-by-distance was observed. Roe deer from isolated habitats could be distinguished by various measures of genetic variability. The expected heterozygosity and the allelic diversity were higher in male than in female roe deer, but mean genetic distances and fixation indices were higher in females. The fixation indices of pairs of adjacent samples, and the genetic distance among these samples correlated highly significantly with the density of human settlement, measured by the percentage of land surface covered by roads and villages. The utility of allozymes and microsatellites for population genetic studies in cervids are compared.

Alleles↗
PubMed2004

Molecular population genetics of redundant floral-regulatory genes in Arabidopsis thaliana.

Functional redundancy between duplicated genes is predicted to be transitory, as one gene either loses its function or gains a new function, or both genes accrue degenerative, yet complimentary mutations. Yet there are many examples where functional redundancy has been maintained between gene duplicates. To determine whether selection is acting on functionally redundant gene duplicates, we performed molecular evolution and population genetic analyses between two pairs of functionally redundant MADS-box genes from the model plant Arabidopsis thaliana: SEPALLATA1 (SEP1) and SEPALLATA2 (SEP2), involved in floral organ identity, and SHATTERPROOF1 (SHP1) and SHATTERPROOF2 (SHP2), involved in seed shattering. We found evidence for purifying selection acting to constrain functional divergence between paralogous genes. The protein evolution of both pairs of duplicate genes is functionally constrained, as evidenced by Ka/Ks ratios of 0.16 between paralogs. This functional constraint is stronger in the highly conserved DNA-binding and protein-binding MIK region than in the C-terminal region. We also assayed the evolutionary forces acting between orthologs of the SEP and SHP genes in A. thaliana and the closely related species, Arabidopsis lyrata. Heterogeneity analyses of the polymorphism-to-divergence ratio indicate selective sweeps have occurred within the transcriptional unit of SHP1 and the promoter of SHP2 in the A. thaliana lineage. Similar analyses identified a significant reduction in polymorphism within the SEP1 locus, spanning the 3' region of intron 1 to exon 3, that may represent an intragenic sweep within the SEP1 locus. We discuss whether the evolutionary forces acting on SEP1 and SEP2 versus SHP1 and SHP2 vary according to their position in the floral developmental pathway, as found with other floral-regulatory genes.

Arabidopsis↗
PubMed1990

[Genetic analysis of the structure of predisposition to diabetes mellitus. IV. Population-genetics study of two types of diabetes mellitus with onset at age 20-40].

It was found that age-specific morbidity risks of type I diabetes mellitus (DM I) increased from the age of 0-4 yrs (0.012-0.013%) to the age of 10-14 yrs (0.04-0.045%) and then slightly decreased to 0.02-0.03%, remaining at this level up to 40 yrs. The "cumulative" morbidity risk of DM I (population risk of development of DM I for each born individual, irrespective of family history) was found to be 0.2% for the age from 0-4 to 40 yrs. Assuming the age-specific morbidity risks of DM I after the age of 40 yrs to be the same as that at 40 yrs (0.02-0.03%), the "cumulative" morbidity risk for this type of DM from birth to 75 yrs old was estimated to be 0.36-0.44%. First incidences of DM II in the population were only observed in 20 yrs olds. The morbidity risk level for DM II at the age 20-24 yrs was found to be lower than that for DM I at this age. The risk was about the same level both for DM I and for DM II at the age 25-34 yrs, the morbidity risk levels for DM II after 35 yrs exceeding that for DM I. The "cumulative" risk of DM II by the age of 40 yrs was 0.1% for men and 0.15% for women. Analysis of familial data revealed statistically significant increase in recurrent morbidity risk in relatives only for the types of DM presented in probands.(ABSTRACT TRUNCATED AT 250 WORDS)

Adult↗
PubMed2000

Population genetics of rhizobia: construction and analysis of an "Infection and Release" model.

A mathematical model is created to assess the inputs of sym gene transfer of in planta multiplication and of interstrain competition into dynamics of the rhizobia populations. Their microevolution is presented as a series of the "infection and release" cycles; each cycle includes transfer of sym genes from virulent initial symbionts to avirulent local bacteria yielding the virulent novel symbionts; competition between initial symbionts and novel symbionts for the host nodulation; multiplication of initial symbionts and novel symbionts in planta and their release into soil; competition between the released novel symbionts and resident local bacteria for ex planta survival. A recurrent equation is created to determine the number of novel symbionts at each cycle of evolution of the closed bacteria-plant system. Its analysis demonstrates that under certain, really allowable values of the introduced parameters two major effects may occur: (a) rapid multiplication of novel symbionts arisen from sym gene transfer; and (b) increase of frequency of rare local bacteria genotypes after acquisition of virulence. Multiplication of very rare strains (p<10(-19)) in the plant-associated bacteria population is possible at certain parameters of the system. Variation of the sizes of bacteria populations and of the parameters for interstrain competition may influence the evolutionary rate of the bacteria population. The "infection and release" model represents a selective mechanism which may be responsible for a high taxonomic diversity of rhizobia and for a panmictic structure of their populations.

Genetics, Population↗
PubMed2003

The population genetics of multistage carcinogenesis.

Despite the many successes of cancer research, we lack the framework necessary to predict the ratio of familial (inherited) to sporadic (non-inherited) cancers. An evolutionary model of multistage carcinogenesis provides this framework by demonstrating that the number of tumour suppressor loci (TSLs) preventing cancer in a given tissue is expected to depend upon the tissue's vulnerability to pre-reproductive somatic mutation. Since this vulnerability increases with tissue size, single gene control of human cancer may be restricted to retinoblastoma, a cancer of the tiny embryonic retina. The model is used to estimate the frequency of mutant alleles causing inherited cancers, based on the population genetics of the mutation-selection balance between new mutations arising and selection that eliminates them. For each specific cancer, this balance is determined by the effectiveness with which pre-reproductive cancer is suppressed in the non-mutant genotype characteristic of that population. Effectiveness depends on an interaction between the number of TSLs suppressing the cancer and factors determining the tissue-wide somatic mutation rate, such as tissue size and number of pre-reproductive cell divisions. The model predicts that the commonest pre-reproductive cancers will have the lowest proportion of familial cases, and that cancers associated with the most TSLs will have the highest post-reproductive incidence but no elevated pre-reproductive risk (a pattern seen in human epithelial cancers).

Age of Onset↗
PubMedDate not supplied

Population genetic structure and colonization sequence of Drosophila subobscura in the Canaries and Madeira Atlantic Islands as inferred by autosomal, sex-linked and mtDNA traits.

The genetic structure in Atlantic Islands and continental populations of Drosophila subobscura has been studied using autosomal and sex-linked allozymes and mitochondrial DNA (mtDNA) haplotypes. From the data it is deduced that whereas the Canary islands have long been isolated, the neighboring island of Madeira has been subjected to continuous migration from the mainland. In addition, sex-linked allozymes and mtDNA data show a large divergence between the geologically younger western islands of the Canarian Archipelago and the older central ones, finding strong founder effects in the former. Divergence rates of sex-linked and mitochondrial genes relative to autosomic loci several times higher than expected under neutrality have been explained by differential migration between sexes. The Canarian Archipelago colonization fits in well with a stepping-stone model of a directional east-west migration that parallels the geological origin of these Islands.

Animals↗
PubMed1986

Mitochondrial DNA differentiation in North Atlantic eels: Population genetic consequences of an unusual life history pattern.

A survey of restriction site polymorphism in the mitochondrial DNA (mtDNA) of the American eel Anguilla rostrata showed no genetic divergence among samples from a 4000-km stretch of North America coastline. Lack of geographic differentiation in mtDNA over such a large area contrasts sharply with results for terrestrial and freshwater vertebrates and is most likely attributable to the extraordinary life history of these catadromous fishes, which involves perhaps a single spawning population in the western tropical mid-Atlantic Ocean and subsequent widespread dispersal of larvae by ocean currents. However, samples of the European eel (nominally Anguilla anguilla) are highly distinct from A. rostrata in mtDNA genotype (distinguishable by 11 of 14 restriction endonucleases), contradicting some previous suggestions that the two forms belong to the same panmictic population. Results of this study emphasize the importance of life history in shaping population genetic structure.

Journal Article↗
PubMed2006

Multiple gene genealogical analyses reveal both common and distinct population genetic patterns among replicons in the nitrogen-fixing bacterium Sinorhizobium meliloti.

Sinorhizobium meliloti is a Gram-negative alpha-proteobacterium that can form symbiotic relationships with alfalfa and fix atmospheric nitrogen. The complete genome of a laboratory strain, Rm1021, was published in 2001, and the genome of this strain is arranged in three replicons: a chromosome of 3.65 million base pairs (Mb), and two megaplasmids, pSymA (1.35 Mb) and pSymB (1.68 Mb). However, the potential difference in genetic variation among the three replicons in natural strains remains poorly understood. In this study, a total of 16 gene fragments were sequenced, four from pSymA and six each from the chromosome and pSymB, for 49 natural S. meliloti strains. The analyses identified significant differences in divergence among genes, with the mean Hasegawa-Kishino-Yano-1985 (HKY85) distance ranging from 0.00157 to 0.04109 between pairs of strains. Overall, genes on pSymA showed the highest mean HKY85 distance, followed by those on pSymB and the chromosome. Although evidence for recombination was found, the authors' population genetic analyses revealed overall significant linkage disequilibria among genes within both pSymA and the chromosome. However, genes on pSymB were in overall linkage equilibrium, consistent with frequent recombination among genes on this replicon. Furthermore, the genealogical comparisons among the three replicons identified significant incongruence, indicating reassortment among the three replicons in natural populations. The results suggest both shared and distinct patterns of molecular evolution among the three replicons in the genomes of natural strains of S. meliloti.

Genes, Bacterial↗
PubMed2004

Susceptibility to lung tuberculosis--a population-genetic study.

The aim of this study was to compare the genetic structure of lung tuberculosis (LTB) patients (Pts) to healthy controls i.e. to evaluate dependency of LTB occurrence and course of the disease in regard to subject's genetic constitution. The study group consisted of 100 LTB Pts, while the same number of healthy non-sibling individuals served as controls. The groups were analyzed with respect to homozygous recessive characteristics (HRC) that served as genetic markers, which were studied in each subject. Twenty-three HRCs were chosen according to HRC-test rules. The results show significant difference in average HRC number between two samples, a decreased number in Pts group, total cumulative chi2 difference (p<0.001) and frequency distribution (p = 0.0027). We conclude that the analyzed groups make two different samples in regard to their population-genetic structure. It means that they may give a different response to similar environmental agents. A significantly decreased HRC number in the Pts group may be a manifestation of their decreased degree of homozygosity and indicate a dominant factor inluence in predisposition to LTB. It is possible that individuals with such genetic and physiological constitution are more liable to infection/disease caused by M. tuberculosis. Deviation from optimal degree of homozygosity appoints to possibility of altered genetic-physiological organism homeostasis and its altered reaction norm that leads to illness. Particular phenotype distribution analysis of significantly decreased frequency of HRC and characteristic expression (eye and hair colour) suggest that there is a possibility of related gene alleles association with genetic basis for susceptibility to TB in humans.

Gene Frequency↗
PubMed2004

Population genetics of the roan antelope (Hippotragus equinus) with suggestions for conservation.

The roan antelope (Hippotragus equinus) is the second largest African antelope, distributed throughout the continent in sub-Saharan savannah habitat. Mitochondrial DNA (mtDNA) control region sequencing (401 bp, n = 137) and microsatellite genotyping (eight loci, n = 137) were used to quantify the genetic variability within and among 18 populations of this species. The within-population diversity was low to moderate with an average mtDNA nucleotide diversity of 1.9% and average expected heterozygosity with the microsatellites of 46%, but significant differences were found among populations with both the mtDNA and microsatellite data. Different levels of genetic resolution were found using the two marker sets, but both lent strong support for the separation of West African populations (samples from Benin, Senegal and Ghana) from the remainder of the populations studied across the African continent. Mismatch distribution analyses revealed possible past refugia for roan in the west and east of Africa. The West African populations could be recognized together as an evolutionarily significant unit (ESU), referable to the subspecies H. e. koba. Samples from the rest of the continent constituted a geographically more diverse assemblage with genetic associations not strictly corresponding to the other recognized subspecies.

Africa↗