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PubMed2006

HLA class II disease associations in southern Africa.

Southern Africa harbors several population groups representing a diversity of gene pool origins. This provides a unique opportunity to study genetic disease predisposition in these populations against a common environmental background. Human leukocyte antigen (HLA) association studies of these populations could improve knowledge on inter-population variation and HLA-related disease susceptibility. The aim of this paper is to review HLA class II disease associations reported for southern African population groups, compare them with findings in other populations and identify those unique to southern Africa. A number of HLA class II disease associations appear to be unique to southern African populations. These include DRB1*14011 association with insulin-dependent diabetes mellitus susceptibility in the Xhosa and DRB1*10 and DQB1*0302 with rheumatoid arthritis susceptibility in the South African (SA) Indian and SA Coloreds, respectively. A noteworthy similarity in class II disease association was observed among southern African Caucasoid and their European parental populations. Unique HLA class II disease associations observed in southern Africa are consistent with the notion that unique environmental and natural selective factors have resulted in certain ethnic-specific HLA class II disease associations, while common HLA class II disease associations found across different populations support the notion that common diseases are caused by common, ancient alleles present in indigenous African populations.

Africa, Southern↗

PubMed1999

Allelic variation at (TAA)n microsatellite loci in a world collection of chickpea (Cicer arietinum L.) germplasm.

A set of 12 randomly selected (TAA)n microsatellite loci of the cultivated chickpea (Cicer arietinum L.) were screened in a worldwide sample comprising 72 landraces, four improved cultivars and two wild species of the primary gene pool (C. reticulatum and C. echinosperum) to determine the level and pattern of polymorphism in these populations. A single fragment was amplified from all the accessions with each of 12 sequence-tagged microsatellite site markers, except for one locus where no fragment was obtained from either of the two wild species. There was a high degree of intraspecific polymorphism at these microsatellite loci, although isozymes, conventional RFLPs and RAPDs show very little or no polymorphism. Overall, the repeat number at a locus (excluding null alleles) ranged from 7 to 42. The average number of alleles per locus was 14.1 and the average genetic diversity was 0.86. Based on the estimates obtained, 11 out of the 12 frequency distributions of alleles at the loci tested can be considered to be non-normal. A significant positive correlation between the average number of repeats (size of the locus) and the amount of variation was observed, indicating that replication slippage may be the molecular mechanism involved in generation of variability at the loci. A comparison between the infinite allele and stepwise mutation models revealed that for 11 out of the 12 loci the number of alleles observed fell in between the values predicted by the two models. Phylogenetic analysis of microsatellite polymorphism in C. arietinum showed no relationship between accession and geographic origin, which is compatible with the recent expansion of this crop throughout the world.

Alleles↗

PubMed2006

Y-chromosomal STR haplotype analysis reveals surname-associated strata in the East-German population.

In human populations, the correct historical interpretation of a genetic structure is often hampered by an almost inherent inability to differentiate between ancient and more recent influences upon extant gene pools. One method to trace recent population movements is the analysis of surnames, which, at least in Central Europe, can be thought of as traits 'linked' to the Y chromosome. Illegitimacy, extramarital birth and changes of surnames may have substantially obscured this linkage. In order to assess the actual extent of correlation between surnames and Y-chromosomal haplotypes in Central Europe, we typed Y-chromosomal short tandem repeat markers in 419 German males from Halle. These individuals were subdivided into three groups according to the origin of their respective surname, namely German (G), Slavic (S) or 'Mixed' (M). The distribution of the haplotypes was compared by Analysis of Molecular Variance. While the M group was indistinguishable from group G (PhiST=-0.0008, P>0.5), a highly significant difference (PhiST=0.0277, P<0.001) was observed between the S group and the combined G+M group. This surprisingly strong differentiation is comparable to that of European populations of much larger geographic and linguistic difference. In view of the major migration from Slavic countries into Germany in the 19th century, it appears likely that the observed concurrence of Slavic surnames and Y chromosomes is of a recent rather than an early origin. Our results suggest that surnames may provide a simple means to stratify, and thereby to render more efficient, Y-chromosomal analyses of Central Europeans that target more ancient events.

Chromosomes, Human, Y↗

PubMed1996

Genetic diversity among selected ethnic subpopulations of Australia: evidence from three highly polymorphic DNA loci.

Immigration has been the principal source of population growth in Australia since European settlement began in 1788. As a result, the Australian gene pool has been constantly evolving, particularly over the last 50 years, during which peoples from many European and Asian countries have arrived in large numbers. Three highly polymorphic DNA loci (D1S80, HLA-DQA1, and human THO1) are used to assess the level of diversity among six immigrant subpopulations that compose significant elements in present-day Australia, namely, Asians, Italians, Greeks, Slavs, Middle Easterners, and a "general white" sample. Asian migrants are the most distinctive of the groups at all three loci, possessing the highest frequencies of alleles HLA-DQA1*3 and D1S80*27, *28, and *30, and an exceptionally high frequency of THO1*9. The European-derived groups cluster together separately from Asians, but Greeks are characterized by their frequencies of HLA-DQA1*2 and *4 and THO1*8. Middle Easterners lie on the fringe of the European cluster. When the results of the present study are combined with worldwide data for each of the three DNA markers, these hypervariable loci, especially D1S80 and THO1, are able to differentiate the major groups of humans. The level of population differentiation revealed by RST values for the three DNA markers is similar to or even less than the values recorded for the less polymorphic classical genetic markers. Therefore these three DNA markers are highly suitable for both forensic purposes and the investigation of population relationships.

Adult↗

PubMed2004

The genetic basis of adaptive population differentiation: a quantitative trait locus analysis of fitness traits in two wild barley populations from contrasting habitats.

We used a quantitative trait locus (QTL) approach to study the genetic basis of population differentiation in wild barley, Hordeum spontaneum. Several ecotypes are recognized in this model species, and population genetic studies and reciprocal transplant experiments have indicated the role of local adaptation in shaping population differences. We derived a mapping population from a cross between a coastal Mediterranean population and a steppe inland population from Israel and assessed F3 progeny fitness in the natural growing environments of the two parental populations. Dilution of the local gene pool, estimated as the proportion of native alleles at 96 marker loci in the recombinant lines, negatively affected fitness traits at both sites. QTLs for fitness traits tended to differ in the magnitude but not in the direction of their effects across sites, with beneficial alleles generally conferring a greater fitness advantage at their native site. Several QTLs showed fitness effects at one site only, but no opposite selection on individual QTLs was observed across the sites. In a common-garden experiment, we explored the hypothesis that the two populations have adapted to divergent nutrient availabilities. In the different nutrient environments of this experiment, but not under field conditions, fitness of the F3 progeny lines increased with the number of heterozygous marker loci. Comparison of QTL-effects that underlie genotype x nutrient interaction in the common-garden experiment and genotype x site interaction in the field suggested that population differentiation at the field sites may have been driven by divergent nutrient availabilities to a limited extent. Also in this experiment no QTLs were observed with opposite fitness effects in contrasting environments. Our data are consistent with the view that adaptive differentiation can be based on selection on multiple traits changing gradually along ecological gradients. This can occur without QTLs showing opposite fitness effects in the different environments, that is, in the absence of genetic trade-offs in performance between environments.

Adaptation, Biological↗

PubMed2005

Allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released from 1845 to 2004.

Analysis of genetic diversity changes in existing gene pools of cultivated crops is important for understanding the impact of plant breeding on crop genetic diversity and developing effective indicators for genetic diversity of cultivated plants. The objective of this study was to assess genetic diversity changes in 75 Canadian hard red wheat (Triticum aestivum L.) cultivars released from 1845 to 2004 using 31 simple sequence repeats (SSRs) markers. A total of 267 SSR alleles were detected, and their allelic frequencies ranged from 0.01 to 0.97, with an average of 0.14. Significant allelic reduction was observed at only four SSR loci for the cultivars released from 1970 onwards. However, 51 alleles (about 19%) present in pre-1910 cultivars were undetected in cultivars released after 1990 and were spread over 27 SSR loci. The proportion of SSR variation accounted for by six breeding periods was 12.5%, by four ancestral families, 16.5%, and by eight breeding programs, 8.4%. The average genetic diversity measured by three different band-sharing methods did not change significantly among cultivars released from different breeding periods, breeding programs, and ancestral families. However, genetic shift was obvious in the cultivars released over the six breeding periods, reflecting well the various breeding efforts over years. These results clearly show the allelic reduction and genetic shift in the Canadian hard red spring wheat germplasm released over time. Consequently, more effort needs to be made to broaden the wheat breeding base and conserve wheat germplasm.

Analysis of Variance↗

PubMed1995

Rising primary malignant brain tumor mortality in the elderly. A manifestation of differential survival.

BACKGROUND: Increasing primary malignant brain tumor mortality among the elderly in developed countries over the past three decades has been attributed to improved diagnostic techniques and increased environmental carcinogens. OBJECTIVE: To demonstrate that rising primary malignant brain tumor mortality among the elderly can be accounted for by differential survival. DATA SOURCE: Published United States mortality data from the National Center for Health Statistics, 1962 to 1989. MEASURES: Age-specific primary malignant brain tumor mortality rates were determined for the age groups of more than 60 years old and compared with the population size of these age groups. RESULTS: Increasing primary malignant brain tumor mortality rates among the oldest age groups in the United States from 1962 to 1989 were directly proportional to the increasing population size of these age groups. CONCLUSIONS: Comparisons between age-specific mortality rates are generally considered valid since they are inherently age- and sex-matched. Moreover, age-specific mortality rates should not be related to population size. Rather than implying improved diagnosis or enhanced carcinogenesis, these results suggest that differential survival and its effect on the surviving gene pool in an aging population is an alternative explanation for the observed increase in primary malignant brain tumor mortality among the elderly.

Aged↗

PubMed1996

Genetic admixture in the late pleistocene.

The replacement hypothesis of modern human origins holds that the original population of modern humans expanded throughout the world, replacing existing archaic populations as it went. If this expanding population interbred with the peoples it replaced, then some archaic mitochondria might have been introduced into the early modern gene pool. Such mitochondria would be recognizable today because they should differ from other modern mitochondria at several times the number of sites that we are used to seeing in pairwise comparisons. In this paper we ask what can be inferred from the absence of these "divergent" mitochondria from modern samples. We show that if the effective number of females in our species has been large for the past 40,000 years, then the level of admixture must have been low. For example, if this effective number exceeded 1.6 million, then we can reject the hypothesis that more more than 2/1,000 of the mitochondria in the early modern population derived from admixture with archaic peoples. We argue elsewhere that regional continuity would be detectable in the fossil record only if the rate of admixture exceeded 76%. Here, we show that this level of admixture would require the effective female size of the human population to have been less than 1,777 for the past 40,000 years.

Animals↗

PubMed1997

Dental size and shape in the Roman imperial age: two examples from the area of Rome.

Different socioeconomic strata of Roman imperial age are represented by two large dental samples recovered from archaeological excavations near Rome, Italy. Teeth are investigated for crown dimensions and morphological variants. One sample, comprising 1,465 permanent teeth, represents the rural town of Lucus Feroniae (LFR) and is mainly composed of slaves and war veterans. The other, comprising 734 teeth from the Isola Sacra necropolis at Portus Romae (NIS), represents the "middle class" segment of an urban population. Both series show small dental dimensions and fit at the lower end of the trend toward dental reduction in Europe from the Upper Paleolithic to the historical times. The urban sample is less variable metrically and less sexually dimorphic than the rural one. The analysis of discrete crown traits shows absence of rare phenotypic variants in both series. The urban sample is also less variable in this last respect, suggesting that the gene pool of this particular "stratum" of the NIS population was more homogeneous than that of LFR. The occurrence of enamel hypoplasia indicates that metabolic stress during growth and development was similar in LFR and NIS. The overall set of available data is evaluated in the light of the history of the two Roman sites and the composition of each population.

Adult↗

PubMed1998

Human adaptation to high altitude: regional and life-cycle perspectives.

Studies of the ways in which persons respond to the adaptive challenges of life at high altitude have occupied an important place in anthropology. There are three major regions of the world where high-altitude studies have recently been performed: the Himalayas of Asia, the Andes of South America, and the Rocky Mountains of North America. Of these, the Himalayan region is larger, more geographically remote, and likely to have been occupied by humans for a longer period of time and to have been subject to less admixture or constriction of its gene pool. Recent studies of the physiological responses to hypoxia across the life cycle in these groups reveal several differences in adaptive success. Compared with acclimatized newcomers, lifelong residents of the Andes and/or Himalayas have less intrauterine growth retardation, better neonatal oxygenation, and more complete neonatal cardiopulmonary transition, enlarged lung volumes, decreased alveolar-arterial oxygen diffusion gradients, and higher maximal exercise capacity. In addition, Tibetans demonstrate a more sustained increase in cerebral blood flow during exercise, lower hemoglobin concentration, and less susceptibility to chronic mountain sickness (CMS) than acclimatized newcomers. Compared to Andean or Rocky Mountain high-altitude residents, Tibetans demonstrate less intrauterine growth retardation, greater reliance on redistribution of blood flow than elevated arterial oxygen content to increase uteroplacental oxygen delivery during pregnancy, higher levels of resting ventilation and hypoxic ventilatory responsiveness, less hypoxic pulmonary vasoconstriction, lower hemoglobin concentration, and less susceptibility to CMS. Several of the distinctions demonstrated by Tibetans parallel the differences between natives and newcomers, suggesting that the degree of protection or adaptive benefit relative to newcomers is enhanced for the Tibetans. We thus conclude that Tibetans have several physiological distinctions that confer adaptive benefit consistent with their probable greater generational length of high-altitude residence. Future progress is anticipated in achieving a more integrated view of high-altitude adaptation, incorporating a sophisticated understanding of the ways in which levels of biological organization are articulated and a recognition of the specific genetic variants contributing to differences among high-altitude groups.

Adaptation, Physiological↗

PubMed1999

Mitochondrial DNA variation in Koryaks and Itel'men: population replacement in the Okhotsk Sea-Bering Sea region during the Neolithic.

In this study, we analyzed the mitochondrial DNA (mtDNA) variation in 202 individuals representing one Itel'men and three Koryak populations from different parts of the Kamchatka peninsula. All mtDNAs were subjected to high resolution restriction (RFLP) analysis and control region (CR) sequencing, and the resulting data were combined with those available for other Siberian and east Asian populations and subjected to statistical and phylogenetic analysis. Together, the Koryaks and Itel'men were found to have mtDNAs belonging to three (A, C, and D) of the four major haplotype groups (haplogroups) observed in Siberian and Native American populations (A-D). In addition, they exhibited mtDNAs belonging to haplogroups G, Y, and Z, which were formerly called "Other" mtDNAs. While Kamchatka harbored the highest frequencies of haplogroup G mtDNAs, which were widely distributed in eastern Siberian and adjacent east Asian populations, the distribution of haplogroup Y was restricted within a relatively small area and pointed to the lower Amur River-Sakhalin Island region as its place of origin. In contrast, the pattern of distribution and the origin of haplogroup Z mtDNAs remained unclear. Furthermore, phylogenetic and statistical analyses showed that Koryaks and Itel'men had stronger genetic affinities with eastern Siberian/east Asian populations than to those of the north Pacific Rim. These results were consistent with colonization events associated with the relatively recent immigration to Kamchatka of new tribes from the Siberian mainland region, although remnants of ancient Beringian populations were still evident in the Koryak and Itel'men gene pools.

Alaska↗

PubMed1999

Genetic evidence for larger African population size during recent human evolution.

Genetic evidence suggests that the long-term average effective size of sub-Saharan Africa is larger than other geographic regions. A method is described that allows estimation of relative long-term regional population sizes. This method is applied to 60 microsatellite DNA loci from a sample of 72 sub-Saharan Africans, 63 East Asians, and 120 Europeans. Average heterozygosity is significantly higher in the sub-Saharan African sample. Expected heterozygosity was computed for each region and locus using a population genetic model based on the null hypothesis of equal long-term population sizes. Average residual heterozygosity is significantly higher in the sub-Saharan African sample, indicating that African population size was larger than other regions during recent human evolution. The best fit of the model is with relative population weights of 0.73 for sub-Saharan Africa, 0.09 for East Asia, and 0.18 for Europe. These results are similar to those obtained using craniometric variation for these three geographic regions. These results, combined with inferences from other genetic studies, support a major role of Africa in the origin of modern humans. It is less clear, however, whether complete African replacement is the most appropriate model. An alternative is an African origin with non-African gene flow. While Africa is an important region in recent human evolution, it is not clear whether the gene pool of our species is completely out of Africa or predominately out of Africa.

Africa↗

PubMedDate not supplied

Multi-stage sampling in genetic epidemiology.

When data are expensive to collect, it can be cost-efficient to sample in two or more stages. In the first stage a simple random sample is drawn and then stratified according to some easily measured attribute. In each subsequent stage a random subset of previously selected units is sampled for more detailed observation, with a unit's sampling probability determined by its attributes as observed in the previous stages. These designs are useful in many medical studies; here we use them in genetic epidemiology. Two genetic studies illustrate the strengths and limitations of the approach. The first study evaluates nuclear and mitochondrial DNA in U.S. blacks. The goal is to estimate the relative contributions of white male genes and white female genes to the gene pool of African-Americans. This example shows that the Horvitz-Thompson estimators proposed for multi-stage designs can be inefficient, particularly when used with unnecessary stratification. The second example is a multi-stage study of familial prostate cancer. The goal is to gather pedigrees, blood samples and archived tissue for segregation and linkage analysis of familial prostate cancer data by first obtaining crude family data from prostate cancer cases and cancer-free controls. This second example shows the gains in efficiency from multi-stage sampling when the individual likelihood or quasilikelihood scores vary substantially across strata.

Black or African American↗

PubMed2001

Brief communication: paleoanthropology and the population genetics of ancient genes.

The Mezmaiskaya cave mtDNA is similar in many ways to the Feldhofer cave Neandertal sequence and the more recently obtained Vindija cave sequence. If we accept the contention that the Mezmaiskaya cave specimen is a Neandertal infant, its mtDNA provides no new information about the fate of the European Neandertals. However, there is reason to believe that the Mezmaiskaya cave infant is not a Neandertal, and this places its importance in another light, because it delimits the possible hypotheses of Neandertal and recent human genetic relationships. One possibility is a that the pattern found in ancient mtDNA results from the replacement of an isolated gene pool (Neandertals) by one of its contemporaries (modern humans). A second possibility is natural selection expressed as the substitution of an advantageous mtDNA variant within a single large species, including both Neandertals and modern humans. The geologic, archaeological, and dating evidence shows the Mezmaiskaya cave infant to be a burial from a level even more recent than the Upper Paleolithic preserved at the site, and its anatomy does not contradict the assessment that the Mezmaiskaya cave infant is not a Neandertal. Therefore, the second pattern can be favored over the first.

Animals↗

PubMed1993

Sustainable agriculture: an explanation of a concept.

Close relationships between agriculture and many areas of human activity determine countless interlinkages with global issues of natural environment protection, human population increase, food supply, industry and world trade. This broad context promotes different perceptions of sustainable agriculture by different interest groups. Profitable diversification away from overproduction of basic commodities and satisfaction of environmental pressure groups are major preoccupations in developed countries. Elsewhere the main concerns is to maintain a trend of increasing production: food security with a future dimension. Achieving this depends essentially on protecting the agricultural resource base. Inputs and input substitution are important co-related issues but the core of sustainability is the avoidance of any attrition of the potential for future production; this demands that we guard soil, water sources, grazing lands and gene pools against loss and degradation. Though superficially biophysical or technical in nature, most problems of resource degradation and eroding potential are rooted in economic, social and political issues; few such problems will be solved unless the primacy of these issues is recognized and addressed. Sustainable agriculture will likely remain elusive until governments and other agencies accept it as arising only as the outcome of a synthesis of strategies on population, employment, economic planning, technical research and national investment.

Agriculture↗

PubMed2026

Genetic Diversity Analysis of Red Fox Populations (Vulpes vulpes L., 1758) in Natural and Anthropogenic Isolation.

This study presents a comparative analysis of the genetic structure and diversity of three red fox (Vulpes vulpes L.) populations representing different microevolutionary scenarios: panmixia (free-ranging Belarusian foxes), geographic isolation (free-ranging Scottish foxes), and anthropogenic selection (farm-bred foxes). Using a validated set of STR markers, multivariate statistical analysis was conducted to assess the genetic structure and the degree of genetic erosion across the studied groups. The wild red fox population in Belarus has been shown to maintain a state close to panmixia (PHWE = 0.090), characterized by a high effective population size (Ne = 694) and high allelic diversity. The island population from Scotland exhibits moderate gene pool depletion (Ne = 75.9) and a pronounced heterozygote deficiency (FIS = 0.18). Critical genetic erosion, which was characterized by a minimal effective population size (Ne = 60.2) and allelic fixation, was detected in the farm-bred group. The genetic distance between farm-bred and wild foxes (FST = 0.279; p = 0.001) reflects both the phylogeographic divergence between the Nearctic ancestors of farmed lineages and Palearctic wild populations, and the consequences of prolonged anthropogenic isolation, genetic drift, and selective breeding. These data indicate that artificial isolation and the impacts of genetic drift and targeted selection lead to a substantial depletion of the species' adaptive potential.

Animals↗

PubMedDate not supplied

Maximum likelihood estimates of admixture in Northeastern Mexico using 13 short tandem repeat loci.

Tetrameric short tandem repeat (STR) polymorphisms are widely used in population genetics, molecular evolution, gene mapping and linkage analysis, paternity tests, forensic analysis, and medical applications. This article provides allelic distributions of the STR loci D3S1358, vWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317, D7S820, CSF1PO, TPOX, TH01, and D16S539 in 143 Mestizos from Northeastern Mexico, estimates of contributions of genes of European (Spanish), American Indian and African origin in the gene pool of this admixed Mestizo population (using 10 of these loci); and a comparison of the genetic admixture of this population with the previously reported two polymorphic molecular markers, D1S80 and HLA-DQA1 (n = 103). Genotype distributions were in agreement with Hardy-Weinberg expectations (HWE) for almost all 13 STR markers. Maximum likelihood estimates of admixture components yield a trihybrid model with Spanish, Amerindian, and African ancestry with the admixture proportions: 54.99% +/- 3.44, 39.99% +/- 2.57, and 5.02% +/- 2.82, respectively. These estimates were not significantly different from those obtained using D1S80 and HLA-DQA1 loci (59.99% +/- 5.94, 36.99% +/- 5.04, and 3.02% +/- 2.76). In conclusion, Mestizos of Northeastern Mexico showed a similar ancestral contribution independent of the markers used for evolutionary purposes. Further validation of this database supports the use of the 13 STR loci along with D1S80 and HLA-DQA1 as a battery of efficient DNA forensic markers in Northeastern Mestizo populations of Mexico.

Genetic Markers↗

PubMedDate not supplied

Intergenerational correlation of effective family size in early Québec (Canada).

The use of a comprehensive demographic database of the early French Canadian population (1608-1800) reveals an almost null impact of parents' fertility on children's fertility (r approximately 0.01-0.05), which contradicts the commonly held view that family size has a tendency to run in families. However, in this population, there is a clear transmission from one generation to the next of the effective family size within a given geographical area (EFS, defined as the number of children that settle per settled individual). Three types of correlations between EFS of parents and children are presented in order to account for the impact of socio-demographic differentials. Individuals who belong to a large sibship and who settled in a given subdivision tend to encourage the settlement of a high number of their own children in the same subdivision (r approximately 0.1-0.3). An additional correlation was introduced to see if geographically-based differentials of EFS can account for the differential of founders' regional genetic contribution. The analysis shows that EFS correlation has a definite impact on the concentration of a population's gene pool (it increases it by approximately 20%-45%), and partly accounts for the differences between subdivisions in this regard.

Family Characteristics↗