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Population genetic analysis among five Indian population groups using six microsatellite markers.

Genetic variation at six tetranucleotide microsatellites (HUMTHO1, HUMVWA, F13A01, D3S1359, D12S66, and D12S67) has heen determined in five endogamous ethnic population groups of India belonging to two major linguistic families. The populations analyzed were Konkanastha Brahmins and Marathas (Maharashtra state) from the Indo-Aryan linguistic family and Nairs, Ezhavas, and Muslims (Kerala state) from the Dravidian family. All six loci show high gene diversity, ranging from 0.63 +/- 0.04 to 0.84 +/- 0.02. The average GST value observed was 1.7%, indicating that the differences between the populations account for less than 2% of the diversity, while the genetic variation is high within the five population groups studied (>98%). The phylogenetic tree fails to show any clear cluster. The absence of any cluster along with low average GST is suggestive of substantial genetic similarity among the studied populations, in spite of clear geographical, linguistic, and cultural barriers. This similarity indicates either a greater gene flow between these groups or, alternatively, may reflect a recent evolution for them, considering that the Indian caste system evolved only about 3000 years ago.

Alleles↗

A population genetic analysis of chloroplast DNA in wild populations of Prunus avium L. in Europe.

A population genetic study of chloroplast DNA was carried out in 23 wild populations of Prunus avium sampled from several European deciduous forests. An analysis of approx. 9% of the chloroplast genome detected mostly insertion-deletion mutations and one point mutation. In all, 16 haplotypes were detected. Six haplotypes were shared by two or more populations and 10 were unique. One haplotype was present in 21 of the 23 populations and 161 of 211 individuals, which probably indicates its ancient origin. The level of population subdivision, using unordered and ordered alleles, was low, GSTC=0.29 and NSTC=0.33, respectively. The difference between GSTC and NSTC is nonsignificant, indicating an absence of correlation between haplotype phylogeny and geographical distribution. The absence of phylogeographic structure in wild cherry may be attributed to long distance gene flow among populations by birds, animals and anthropogenic activities. The minimum-length spanning tree depicting the phylogenetic relationships between the haplotypes indicates the possible existence of two lineages represented by the haplotypes H3 and H4. The information about homogeneity or heterogeneity of populations in terms of haplotype constitution and detection of rare haplotypes in some populations will be useful for formulation of conservation and management strategies of wild cherry.

DNA Restriction Enzymes↗

Ionizing radiation and genetic risks. I. Epidemiological, population genetic, biochemical and molecular aspects of Mendelian diseases.

This paper reviews the currently available information on naturally occurring Mendelian diseases in man; it is aimed at providing a background and framework for discussion of experimental data on radiation-induced mutations (papers II and III) and for the estimation of the risk of Mendelian disease in human populations exposed to ionizing radiation (paper IV). Current consensus estimates indicate that a total of about 125 per 10(4) livebirths are directly affected by one or another naturally occurring Mendelian disease (autosomal dominants, 95/10(4); X-linked ones, 5/10(4); and autosomal recessives, 25/10(4). These estimates are conservative and take into account conditions which are very rare and for which prevalence estimates are unavailable. Most, although not all, of the recognized "common" dominants have onset in adult ages while most sex-linked and autosomal recessives have onset at birth or in childhood. Autosomal dominant and X-linked diseases (i.e., the responsible mutant alleles) presumed to be maintained in the population due to a balance between mutation and selection are the ones which may be expected to increase in frequency as a result of radiation exposures. Viewed from this standpoint, the above assumption seems safe only for a small proportion of such diseases; for the remainder, there is no easy way to discriminate between different mechanisms that may be responsible or to rigorously exclude some in favor of some others. Mutations in genes that code for enzymic proteins are more often recessive in contrast to those that code for non-enzymic proteins, which are more often dominant. At the molecular level, with recessives, a wide variety of changes is possible and these include specific types of point mutations, small and large intragenic deletions, multilocus deletions and rearrangements. In the case of dominants, however, the kinds of recoverable point mutations and deletion-type changes are less extensive because of functional constraints. The mutational potential of genes varies, depending on the gene, its size, sequence content and arrangement, location and its normal functions, and can be grouped into three groups: those in which only point mutations have been found to occur, those in which only deletions or other gross changes have been recovered and those in which both kinds of changes are known. Molecular data are available for about 75 Mendelian conditions and these suggest that in approximately 50% of them, the changes categorized to date are point mutations and in the remainder, intragenic deletions or other gross changes; there does not seem to be any fundamental difference between dominants and recessives with respect to the underlying molecular defect.(ABSTRACT TRUNCATED AT 400 WORDS)

Animals↗

The STR loci HumTPO and HumLPL: population genetic data in eight populations.

The two STR systems HumTPO and HumLPL were investigated in eight human populations (Moroccans, Ovambos, Papuans, Australian aborigines, Germans, Turks, Japanese and Chinese). After electrophoresis, seven and eight alleles were identified in the HumTPO and HumLPL systems, respectively. In each population, no deviations from Hardy-Weinberg equilibrium were observed, but considerable differences in phenotype frequencies of each system were found between major ethnic groups.

Ethnicity↗

Population genetic comparisons among eight populations using allele frequency and sequence data from three microsatellite loci.

Eight different population samples (Moroccans, Ovambos, Papuans, Australian aborigines, Germans, Turks, Japanese and Chinese) were studied using the tetranucleotide short tandem repeat systems HumTHO1 (THO1), Hum VWFA31 (VWA) and HumACTBP2 (ACTBP2). Ten alleles were differentiated in THO1, 11 alleles in VWA and 28 alleles in ACTBP2. THO1 showed 1 bp deletions in the repeat region, VWA sequence and structure variations of the 4-bp repeat motif and ACTBP2 sequence, structure and length variations in the repeat array and deletions/insertions (1-6 bp) in the flanking regions. A phylogenetic tree was constructed (UPGMA method) leading to branches which grouped Germans and Turks, Japanese and Chinese, and Papuans and Australian aborigines.

Asian People↗

DnaSP version 2.0: a novel software package for extensive molecular population genetics analysis.

MOTIVATION: Several methods in molecular population genetics have recently been described to estimate the amount and pattern of the DNA polymorphism in natural populations, and also to test the neutral theory of molecular evolution. These methods are essential for understanding the molecular evolutionary process. However, a comprehensive computer program for the analysis is not currently available. RESULTS: Here we present DnaSP (DNA Sequence Polymorphism) version 2.0, a software package for Windows that performs extensive population genetics analyses on DNA sequence data. DnaSP estimates several measures of DNA sequence variation within and between populations, linkage disequilibrium, recombination, gene flow and gene conversion (a new algorithm to detect gene conversion tracts has been included). DnaSP can also carry out several tests of neutrality: those of Fu and Li; Hudson, Kreitman and Aguadé; and Tajima. The results of the analyses are displayed in tabular and graphic form. AVAILABILITY: For academic uses, DnaSP is available via anonymous ftp: ftp.ebi.ac.uk in the directory/pub/software/dos.

Algorithms↗

Hitchhiking mapping--functional genomics from the population genetics perspective.

Several statistical tests based on population genetic theory are used to identify genes that have recently acquired a beneficial mutation. Here, I describe the extension of these tests to a multilocus approach for a genome-wide survey for genes that have been under recent positive selection. As this strategy could potentially identify genes with weak phenotypic effects, it will be very useful in population genetic approaches aimed at understanding adaptation processes in natural populations. Furthermore, this 'hitchhiking mapping' could also help in the functional characterization of genomes.

Animals↗

Molecular population genetic analysis of emerged bacterial pathogens: selected insights.

Research in bacterial population genetics has increased in the last 10 years. Population genetic theory and tools and related strategies have been used to investigate bacterial pathogens that have contributed to recent episodes of temporal variation in disease frequency and severity. A common theme demonstrated by these analyses is that distinct bacterial clones are responsible for disease outbreaks and increases in infection frequency. Many of these clones are characterized by unique combinations of virulence genes or alleles of virulence genes. Because substantial interclonal variance exists in relative virulence, molecular population genetic studies have led to the concept that the unit of bacterial pathogenicity is the clone or cell line. Continued new insights into host parasite interactions at the molecular level will be achieved by combining clonal analysis of bacterial pathogens with large-scale comparative sequencing of virulence genes.

Bacteria↗

PCR-based assays of mendelian polymorphisms from anonymous single-copy nuclear DNA: techniques and applications for population genetics.

This paper outlines a PCR-based approach for population genetics that offers several advantages over conventional Southern blotting methods for revealing restriction-fragment-length polymorphisms (RFLPs) in nuclear DNA. Primers are constructed from clones isolated from a nuclear DNA library, and these primers subsequently are employed in in vitro syntheses of homologous regions. Amplified products are then screened directly for RFLPs by using gel-staining procedures. Population applications for this PCR-based approach, including potential strengths and weaknesses, are exemplified by two RFLP data sets generated to estimate (a) male-mediated gene flow in the green turtle (Chelonia mydas) and (b) geographic population genetic structure in the American oyster (Crassostrea virginica). Restriction assays of amplified products from 14 or 15 independent primer pairs in each species revealed polymorphisms at several loci that proved highly informative in the population genetic analyses. In general, the Mendelian polymorphisms produced by this PCR-based approach will provide useful genetic markers for population studies, particularly in situations where simpler and less expensive allozyme methods have failed, for whatever reason, to provide adequate information.

Animals↗

The population genetics of Trypanosoma brucei and the origin of human infectivity.

The African trypanosome, Trypanosoma brucei, is a zoonotic parasite transmitted by tsetse flies. Two of the three subspecies, T. brucei gambiense and T.b. rhodesiense, cause sleeping sickness in humans whereas the third subspecies, T.b. brucei, is not infective to humans. We propose that the key to understanding genetic relationships within this species is the analysis of gene flow to determine the importance of genetic exchange within populations and the relatedness of populations. T.brucei parasites undergo genetic exchange when present in infections of mixed genotypes in tsetse flies in the laboratory, although this is not an obligatory process. Infections of mixed genotype are surprisingly common in field isolates from tsetse flies such that there is opportunity for genetic exchange to occur. Population genetic analyses, taking into account geographical and host species of origin, show that genetic exchange occurs sufficiently frequently in the field to be an important determinant of genetic diversity, except where particular clones have acquired the ability to infect humans. Thus, T. brucei populations have an 'epidemic' genetic structure, but the better-characterized human-infective populations have a 'clonal' structure. Remarkably, the ability to infect humans appears to have arisen on multiple occasions in different geographical locations in sub-Saharan Africa. Our data indicate that the classical subspecies terminology for T. brucei is genetically inappropriate. It is an implicit assumption in most infectious disease biology that when a zoonotic pathogen acquires the capability to infect humans, it does so once and then spreads through the human population from that single-source event. For at least one major pathogen in tropical medicine, T. brucei, this assumption is invalid.

Africa↗

"Bioethics in action" and human population genetics research.

Recent disputes about human population genetics research have been provoked by the field's political vulnerability (the historic imbalance of power between the geneticists and the people they study) and conceptual vulnerability (the mismatch between scientific and popular understandings of the genetic basis of collective identity). The small, isolated groups often studied by this science are now mobilizing themselves as political subjects, pressing sovereignty claims, and demanding control over the direction and interpretation of research. Negotiations between the geneticists and the people asked to donate DNA have resulted not only in explicit bioethics protocols but also in diffuse anxiety over the incommensurability between expert and non-expert views about genetic evidence for identity claims. This article compares two disputes over genetics research: the Human Genome Diversity Project and the use of genetics to prove identity claims among the Melungeons of Tennessee. The case studies illustrate "bioethics in action": how particular controversies and interests drive the production of bioethics discourses and techniques (such as informed consent protocols). They also illustrate some limits on the usual apparatus of bioethics in overcoming this science's multiple vulnerabilities.

Bioethics↗

Integration of genotoxic and population genetic endpoints in biomonitoring and risk assessment.

Genetic ecotoxicology is a multifaceted discipline that examines the effects of xenobiotic compounds on the structure and function of DNA. This paper discusses the role of genetic ecotoxicology in environmental biomonitoring and risk assessment. Genetic ecotoxicology may include somatic effects (e.g., DNA damage) or population genetic effects (changes in genetic diversity or gene frequencies). Traditionally, genetic ecotoxicology studies have focused on either one of these sub-disciplines, but integration of these two approaches would be advantageous for three reasons. First, at the population level, concordant responses between changes in population genetic structure and elevated levels of DNA damage may provide evidence that the population genetic changes are influenced by exposure to genotoxic chemicals. Second, if the frequencies of alleles or other genetic markers differ between genotoxicant-contaminated and reference populations, associations between relative amount of DNA damage and genotype may provide evidence that these changes are due to genotoxicant-induced selection. Third, genetic analysis of gene flow may provide insight into patterns of dispersal that could obscure differences between contaminated and reference populations. In order to demonstrate the application of these ideas, three lines of research are summarized herein. The first is a series of studies that focus on radionuclide-contaminated populations of mosquitofish (Gambusia). This research identified RAPD markers that may be indicative of genetic adaptation to radionuclide stress. Relative amounts of DNA damage among genotypes presented evidence that these markers may be indicators of relative radioresistance. The second study examined DNA damage and population genetic structure in radionuclide-contaminated kangaroo rat (Dipodomys) populations. It was found that between-population differences in genetic diversity paralleled those for DNA damage and relative levels of contamination. Also, population genetic analysis indicated that there was dispersal between contaminated and reference populations, and that between-population differences in the amount of DNA damage could not be detected until this dispersal was taken into account. In the third study, populations of redbreast sunfish (Lepomis auritris) from streams contaminated with complex mixtures of industrial chemicals were examined. It was found that the genetic distances between populations within the contaminated stream corresponded with the relative magnitude of molecular and community-level effects. It was concluded that genetic ecotoxicology could make significant contributions to the fields of environmental biomonitoring and ecological risk assessment, and that integration of genotoxicology and population genetic studies would be a definite advantage toward this end.

Animals↗

Recent trends in population genetics: more data! More math! Simple models?

Recent developments in population genetics are reviewed and placed in a historical context. Current and future challenges, both in computational methodology and in analytical theory, are to develop models and techniques to extract the most information possible from multilocus DNA datasets. As an example of the theoretical issues, five limiting forms of the island model of population subdivision with migration are presented in a unified framework. These approximations illustrate the interplay between migration and drift in structuring gene genealogies, and some of them make connections between the fairly complicated island-model genealogical process and the much simpler, unstructured neutral coalescent process which underlies most inferential techniques in population genetics.

Computational Biology↗

Population genetic studies: is there an emerging legal obligation to share benefits?

It appears that large-scale population genetic studies are the necessary next step in genomics research. Such studies promise to provide correlative data to permit researchers to understand the etiology of a vast array of complex human diseases. Simultaneously, such studies are increasingly seen as yet another mechanism for the developed world to benefit at the expense of the developing world. In fact, a recent World Health Organization Report suggests that "without explicit attention at the international level, the initial technological fruits of genomics are likely to consist primarily of therapeutic and diagnostic applications for conditions affecting large populations in rich countries." (World Health Organization, Genomics and World Health, 2002). In developed and developing countries alike, there are concerns that the pharmaceutical industry stands to gain at the expense of the population(s) from which population genetic data are derived. In light of the current interest concerning ongoing population genetic studies and an increasing interest by many countries, Canada included, in embarking on large-scale population genetic research, it is appropriate to consider the concept of benefit-sharing as a potential mechanism to assuage these concerns. It is the author's position that by virtue of common law equitable principles and developing norms in international law, including the Human Genome Organization Statement on Benefit-Sharing, that there are principled legal and ethical reasons to compel the sharing of benefits that accrue from the commercialization of the resulting data. Using the United Nations Convention on Biological Diversity and the Bonn Guidelines as a model, I suggest that appropriate benefit-sharing mechanisms have been considered in the context of non-human biological materials and that these same mechanisms may be applicable in the context of international and intra-national population genetic studies.

Access to Information↗