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PubMed2001

Historical bottlenecks decrease genetic diversity in natural populations of Dryopteris cristata.

The reconstruction of recent historical population sizes allowed us to investigate the influence of random evolutionary processes on present-day genetic diversity in populations of Dryopteris cristata. This long-lived, allotetraploid fern is rare and endangered in the study area at the southwestern border of its European distribution. Random amplified polymorphic DNA (RAPD) diversity of 280 individuals from 14 populations of D. cristata was extraordinarily low, suggesting an ancient bottleneck in the species' history. Analysis of molecular variance (AMOVA) of 25 different RAPD multiband phenotypes revealed significant genetic variation among three geographical regions (15%) and among populations within regions (34%); 51% of total variance was attributed to variation within populations. High population differentiation indicated limited gene flow among populations, and genetic divergence was not correlated with geographical distance. There was no relationship between genetic variation within population, estimated as molecular variance, and present-day population size. Populations with recent historical bottlenecks of fewer than 25 individuals showed a substantial and significant reduction in genetic variation, compared with populations without bottlenecks. Comparatively high levels of genetic variation were still maintained in small remnants (60-110 individuals) of formerly large populations. Average deviations of frequencies of widespread polymorphic markers within populations from their frequencies in the whole dataset were significantly higher in small or recently bottlenecked populations than in constantly large populations, thus providing evidence for random sampling effects during genetic bottlenecks and drift in small populations. The present investigation demonstrates the importance of population history for understanding present-day genetic diversity within natural populations, as well as for conservation biology.

DNA, Plant↗

PubMed2001

Population genetic analysis of the genes APOE, APOB(3'VNTR) and ACE in some black and Amerindian communities from Colombia.

A population genetic study was carried out with the APOE, APOB and ACE loci in 17 Colombian human populations. Ten of them were Amerindian communities coming from the northeastern part of Colombia, Pacific region, Eastern Plains and Amazonia. Six were black populations from Providence Island, Caribbean and Pacific coasts. Finally, the Mestizo population of Bogota was studied as well. The APOE and ACE loci were in Hardy-Weinberg equilibrium, whereas the APOB locus was not studied in all populations. The genetic heterogeneity was substantially greater among the Amerindian populations (G(ST) = 0.059) than in the Afrocolombian populations (G(ST) = 0.009). Also the gene flow population pair estimates were so much higher among the Afrocolombian populations (Nm = 49.08 +/- 43.07) than among Amerindian populations (Nm = 9.66 +/- 18.04). Different phylogenetic and multivariant analyses showed that the Amerindian populations analyzed were clustered in three different arrays: one constituted by the Colombian northeastern and Pacific populations, the second one by the two Amazon populations (Coreguaje and Nukak) and the last one by the Yuco (the unique Caribbe-speaking population among those studied). The latter population was highly divergent from a genetic point of view from the remainder Amerindian populations studied. By using the Mantel test, the existence of a positive and significant correlation between the genetic and geographical distances found among Amerindian populations was demonstrated. This fact was not observed among the Afrocolombian populations. Nevertheless, an isolation-by-distance Slatkin analysis test did not show a significant clear structure of this special pattern among the Indian tribes studied.

Alleles↗

PubMed2004

Genetic determination of tolerance to lethal and sublethal copper concentrations in field populations of Daphnia longispina.

In order to study the effects of environmental pollution on the genetic diversity of natural populations, two field populations of the cladoceran Daphnia longispina were sampled: one in a reference site (uncontaminated) and the other in a site historically stressed with acid mine drainage (AMD). Five hypotheses were formulated: (1) the stressed population presents a higher tolerance to lethal levels of copper than the reference population, (2) differences in tolerance to lethal levels, observed between the two populations, are due to the loss of sensitive lineages, (3) differences in tolerance to lethal levels of copper between the two populations are due to the appearance of new genotypes, (4) the acquisition of tolerance to lethal levels of copper involved changes in life-history patterns and fitness costs under optimal conditions, and (5) historical contamination by AMD resulted in tolerance differences to sublethal levels between populations, within categories similarly tolerant to lethality, specifically, lineages with similar tolerance to lethal levels from both populations show differences in tolerance to sublethal levels, the stressed population being more tolerant to sublethal levels of contamination than the reference population. Over 125 acclimated cloned lineages, from each population, were exposed to different copper concentrations for 24 hours. At the end of each assay, mortality and feeding inhibition were monitored. Life-cycle traits under optimal conditions were also monitored (time to first brood, number of neonates per brood, inter-brood time, body length, and ingested algae). At lethal levels of copper, significant differences were found in the frequency of sensitive lineages between the two populations. The stressed population did not include the most sensitive lineages, though the most tolerant ones were also present in the reference population. Thus, the hypothesis of presence of new genotypes in the stressed population resulting in an overall increase tolerance of the population at lethal levels was rejected. Changes in life-history patterns were detected, though they were not fully consistent with predictions of life-history theory. Furthermore, these changes in life-history patterns did not involve fitness costs. The fifth hypothesis was rejected since, at sublethal levels of copper, no significant differences were found between the feeding inhibitions of similarly lethal tolerant lineages of the two populations, with only one exception. Therefore, the present study further confirmed the genetic erosion hypothesis and gave further support to the incorporation of genetic diversity measurements into risk assessments.

Animals↗

PubMed2000

Human population expansion and microsatellite variation.

Polymorphisms at di-, tri-, and tetranucleotide microsatellite loci have been analyzed in 14 worldwide populations. A statistical index of population expansion, denoted S(k), is introduced to detect historical changes in population size using the variation at the microsatellites. The index takes the value 0 at equilibrium with constant population size and is positive or negative according to whether the population is expanding or contracting, respectively. The use of S(k) requires estimation of properties of the mutation distribution for which we use both family data of Dib et al. for dinucleotide loci and our population data on tri- and tetranucleotide loci. Statistical estimates of the expansion index, as well as their confidence intervals from bootstrap resampling, are provided. In addition, a dynamical analysis of S(k) is presented under various assumptions on population growth or decline. The studied populations are classified as having high, intermediate, or low values of S(k) and genetic variation, and we use these to interpret the data in terms of possible population dynamics. Observed values of S(k) for samples of di-, tri-, and tetranucleotide data are compatible with population expansion earlier than 60,000 years ago in Africa, Asia, and Europe if the initial population size before the expansion was on the order of 500. Larger initial population sizes force the lower bound for the time since expansion to be much earlier. We find it unlikely that bottlenecks occurred in Central African, East Asian, or European populations, and the estimated expansion times are rather similar for all of these populations. This analysis presented here suggests that modern human populations departed from Africa long before they began to expand in size. Subsequently, the major groups (the African, East Asian, and European groups) started to grow at approximately same time. Populations of South America and Oceania show almost no growth. The Mbuti population from Zaire appears to have experienced a bottleneck during its expansion.

Animals↗

PubMed1986

Density-dependent migration and human population structure in historical Massachusetts.

Studies of population structure often focus on the effects of population size and migration rates on genetic variation. Few studies, however, have investigated the relationship between these two factors. The purpose of this paper is to determine the extent to which migration (and gene flow) is density-dependent (that is, affected by population size) for populations in historical Massachusetts. Data from 4,859 marriage records were analyzed from four populations in north-central Massachusetts during the time period 1741 to 1849. These data were placed into 29 samples defined in terms of population and time cohort. Within each cohort the overall exogamy rate was computed along with three estimates of gene flow based on marital migration: local migration (k), long-distance migration (m), and effective migration rate (me). Three samples show unusually low rates that reflect the history of settlement. Regression analyses were used with the remaining samples, and they show nonlinear density-dependent migration that is unrelated to temporal trends. Migration is highest in samples with small population sizes (less than 800) and large population sizes (greater than 1,600). Migration is lowest in medium-sized populations. Two processes are suggested to explain this curvilinear relationship of migration and population size. In small populations, the lack of suitable potential mates and/or availability of settled land leads to an increase in migration into the population. As population size increases, this migration decreases. After populations reach a certain size, migration increases again, most likely reflecting the economic pull of larger populations. These patterns could act to enhance, or counter, genetic drift, depending on the direction of density dependence.

Female↗

PubMed1991

Origins of H-2 polymorphism in the house mouse. II. Characterization of a model population and evidence for heterozygous advantage.

Comparison of the rate of synonymous and nonsynonymous nucleotide substitutions suggests that certain regions of the functional H-2 genes, which are part of the mouse major histocompatibility complex (Mhc), are under strong positive selection pressure. Thus far, however, little evidence has been provided for the existence of such pressure in natural mouse populations. We have, therefore, initiated experiments designed to test the hypothesis of positive selection acting on H-2 loci. The experiments are being carried out on two natural mouse populations in Jerusalem, Israel. One population occupies a space of about 100 m2 in a chicken coop, the other lives in a nearby field in which "mouse stations" providing food and shelter have been set up. Extensive typing of these two populations revealed the presence of only four H-2 haplotypes. Mice in the two populations breed continually all year around, yet population size varies seasonally, with population maxima in winter and minima in summer. The population in the chicken coop contains a relatively stable nucleus which may be organized in demes with an excess of females over males and limited territorial mobility. The rest of the mice stay in the population for a short time only and then either die or emigrate. The field population is smaller and more loosely organized than the chicken-coop population, with demes probably forming only during population maxima. For the rest of the time breeding in this population is probably panmictic. At a population minimum in the summer of 1984, H-2 homozygotes happened to predominate over heterozygotes. This situation, however, lasted for a short time only and thereafter there was a continuous, statistically highly significant increase in the proportion of H-2 heterozygotes of one or two types. The increase occurred in both populations but was more apparent in the chicken-coop population. This observation provides the first experimental evidence that heterozygous advantage might be one of the mechanisms maintaining high H-2 polymorphism in natural populations of the house mouse.

Animals↗

PubMed2006

Genetic structure of Przewalski's rock partridge (Alectoris magna) populations in the Longzhong Loess Plateau, China.

In this paper, we have analyzed the nuclear DNA of Alectoris magna samples, collected from the Longzhong Loess Plateau. We used allelic variation at eight microsatellite markers to describe the genetic structure of A. magna populations. The primary goal of this study was to examine the population genetic structure and determine the extent of population differentiation among populations of A. magna. The average value of H(E) (0.455) was smaller than H(O) (0.477), and there was a heterozygote deficit at the MCW135 locus in the Lanzhou population and the Beidao population. The AB063167 locus in each population (except that of Jingyuan) was not in equilibrium (P < 0.05). The Lixian edge population had a lower proportion of genetic diversity than the central geographic populations; the Haiyuan and Jingyuan populations had higher genetic diversity than the central geographic populations. Analysis of population structure revealed clear differentiation among the eight populations of A. magna, suggesting strong isolation of these populations and correspondingly low levels of migration or gene flow. The A. magna populations of Longzhong Loess Plateau are separated into eastern and western populations by a clustering chart. Genetic data indeed suggest that patterns of speciation and population diversification of A. magna in the Longzhong Plateau have been affected by the stability of the climate, natural selection, and human intervention.

Alleles↗

PubMed2005

Population structure within lineages of Wheat streak mosaic virus derived from a common founding event exhibits stochastic variation inconsistent with the deterministic quasi-species model.

Structure of Wheat streak mosaic virus (WSMV) populations derived from a common founding event and subjected to serial passage at high multiplicity of infection (MOI) was evaluated. The founding population was generated by limiting dilution inoculation. Lineages of known pedigree were sampled at passage 9 (two populations) and at passage 15, with (three populations) or without mixing (four populations) of lineages at passage 10. Polymorphism within each population was assessed by sequencing 17-21 clones containing a 1371 nt region (WSMV-Sidney 81 nts 8001-9371) encompassing the entire coat protein cistron and flanking regions. Mutation frequency averaged approximately 5.0 x 10(-4)/nt across all populations and ranged from 2.4 to 11.6 x 10(-4)/nt within populations, but did not consistently increase or decrease with the number of passages removed from the founding population. Shared substitutions (19 nonsynonymous, 10 synonymous, and 3 noncoding) occurred at 32 sites among 44 haplotypes. Only four substitutions became fixed (frequency = 100%) within a population and nearly one third (10/32) never achieved a frequency of 10% or greater in any sampled population. Shared substitutions were randomly distributed with respect to genome position, with transitions outnumbering transversions 5.4:1 and a clear bias for A to G and U to C substitutions. Haplotype composition of each population was unique with complexity of each population varying unpredictably, in that the number and frequency of haplotypes within a lineage were not correlated with number of passages removed from the founding population or whether the population was derived from a single or mixed lineage. The simplest explanation is that plant virus lineages, even those propagated at high MOI, are subject to frequent, narrow genetic bottlenecks during systemic movement that result in low effective population size and stochastic changes in population structure upon serial passage.

Base Sequence↗

PubMedDate not supplied

Antiquity, geographic contiguity and genetic affinity among Tibeto-Burman populations of India: a microsatellite study.

BACKGROUND: The Tibeto-Burman (TB) populations are one of the four major linguistic population groups of India. They are considered belonging to different stocks and show wide variation in culture and language; however, their genetic relationship, antiquity and migration history among the regional populations has been little investigated. Molecular genetic studies are expected to clearly show the antiquity and genetic diversity of these populations. AIM: This paper seeks to understand the extent and magnitude of genetic affinities and diversities among 14 TB populations (12 Indian and two global groups), investigate the findings based on classical genetic markers and verify the historical accounts of their migration and genetic history based on 12 microsatellite markers. SUBJECTS AND METHODS: The allele frequency data for 12 STR loci of 13 Asian (Tibeto-Burman) populations were obtained from the literature and the Adi Pasi data was obtained by microsatellite typing of their blood samples. The 12 loci studied are D5S818, FGA, D8S1179, D21S11, D7S820, CSF1PO, D3S1358, THO1, D13S317, vWa, TPOX, D18S51. Three different distance measures, two phylogenetic trees and PCA plot have been employed to understand the genetic relationship of the studied populations. RESULTS: Average heterozygosity values range from 68 to 79% and the average G(ST) value is 4.7%. The dendrogram, based on the D(A) distance, shows the clustering of populations based on their diversities and geographical contiguity; the Mizoram and Arunachal Pradesh populations especially cluster together, populations from Sikkim form a separate subcluster and Manipur populations along with the Garo of West Bengal separate out from the other clusters. The Harpending and Ward regression model shows isolated populations positioned below the regression line and others, who experience external gene flow, placed above the line. The results support folklore migration accounts of their possible antiquity with the Tibetan and southern Chinese populations. CONCLUSIONS: Overall, geographic contiguity, punctuated by isolating barriers, is a major influencing factor of genetic affinity among the TB population; contiguous populations within a region show greater genetic relationship than with distant TB populations over a wide geographical area. The results of the microsatellite study also support the history of diverse routes of migration of these populations.

DNA Fingerprinting↗

PubMed2003

Population size and identity influence the reaction norm of the rare, endemic plant Cochlearia bavarica across a gradient of environmental stress.

Habitat degradation and loss can result in population decline and genetic erosion, limiting the ability of organisms to cope with environmental change, whether this is through evolutionary genetic response (requiring genetic variation) or through phenotypic plasticity (i.e., the ability of a given genotype to express a variable phenotype across environments). Here we address the question whether plants from small populations are less plastic or more susceptible to environmental stress than plants from large populations. We collected seed families from small (<100) versus large natural populations (>1,000 flowering plants) of the rare, endemic plant Cochlearia bavarica (Brassicaceae). We exposed the seedlings to a range of environments, created by manipulating water supply and light intensity in a 2 x 2 factorial design in the greenhouse. We monitored plant growth and survival for 300 days. Significant effects of offspring environment on offspring characters demonstrated that there is phenotypic plasticity in the responses to environmental stress in this species. Significant effects of population size group, but mainly of population identity within the population size groups, and of maternal plant identity within populations indicated variation due to genetic (plus potentially maternal) variation for offspring traits. The environment x maternal plant identity interaction was rarely significant, providing little evidence for genetically- (plus potentially maternally-) based variation in plasticity within populations. However, significant environment x population-size-group and environment x population-identity interactions suggested that populations differed in the amount of plasticity, the mean amount being smaller in small populations than in large populations. Whereas on day 210 the differences between small and large populations were largest in the environment in which plants grew biggest (i.e., under benign conditions), on day 270 the difference was largest in stressful environments. These results show that population size and population identity can affect growth and survival differently across environmental stress gradients. Moreover, these effects can themselves be modified by time-dependent variation in the interaction between plants and their environment.

Biological Evolution↗

PubMed2003

[Assessment of population differentiation using DNA fingerprinting and modified Wright's Fst-statistics].

Using our results and literature data on multilocus DNA fingerprinting, we propose a method of obtaining unbiased estimates of the between--population genetic similarity index and a measure of population subdivision based on modified Wright's FST-statistics. On the basis of multiple comparison T2 Hotelling's test and Holmes' procedure, the FST-statistics was applied to assess differentiation of four (Pacific and Atlantic) subpopulations of humpback whale Megaptera novaeangliae, six populations of California island gray fox Urocyon littoralis, and geographically isolated Ob' and Yakutia populations of Siberian white crane Crus leucogeranus. It was shown that the regional humpback whale subpopulations do not constitute a single panmictic unit (P < 10(-4)). The subdivision index of the Pacific and Atlantic populations expressed in terms of FST-statistics varied from 0.101 to 0.157. The differentiation estimates for the island fox populations, which ranged from 0.2109 to 0.4027, indicate that subdivision of these populations is a function of the distance between the islands, island size, and population size. In particular, the smallest and the greatest differences were found respectively between the populations of the geographically closest northern islands (FST = 0.2157, FST = 0.2109) and between those of the most distant northern and southern islands (FST = 0.4027, FST = 0.3869). Subdivision of the island populations with minimum areas and low population number was intermediate (FST = 0.3789). Mean values of heterozygosity, within-population genetic similarity index, and the number of coinciding fragments for two random individuals of Siberian white crane from the Ob' and Yakutia population were not statistically significantly different (P > or = 0.852, (P > or = 0.491, (P > or = 0.325). However, pairwise comparisons of mean FST values indicated that the differentiation estimates for samples from these populations fall within the limits of population subdivision (P = 0.01). The subdivision estimate (0.108-0.133) of various groups of Siberian white cranes is comparable to interregional subdivision of humpback whale. Based on the results of this study, we recommend the approach based on modified Wright's FST-statistics for studying genetic population structure aimed at detecting population subdivision.

Animals↗

PubMed2005

Resistance to metal contamination by historically-stressed populations of Ceriodaphnia pulchella: environmental influence versus genetic determination.

Field populations of daphnids historically-stressed by metal contamination may show increased resistance to those contaminants. This study was undertaken aiming to confirm/infirm three main hypotheses: (1) field populations living in historically-impacted environments are more tolerant to metal stress than populations from reference sites; (2) resistance differences are genetically-determined, i.e., differences persist after controlling for environmental and maternal effects, by acclimating cloned lineages to similar conditions; and (3) resistance to stress in field populations living in historically-impacted environments is due to the disappearance of sensitive individuals rather than the appearance of highly resistant ones, i.e., the shift in the central tendency of resistance is linked to a decrease in the range of population resistance and not to an increased upper limit of the population resistance. Three populations of the cladoceran Ceriodaphnia pulchella Sars in Southern Portugal were sampled; one of which has been historically-stressed by acid mine drainage (AMD) from an abandoned cupric-pyrite mine and two from reference sites within the same watershed. To assess if resistance differences were genetically-determined, the three populations were acclimated for at least five generations under the same controlled conditions. Assays with AMD contaminated water samples were performed with both non-acclimated and acclimated individuals from all studied populations. Reproduction results in sub-lethal assays revealed significant differences between the reference and stressed populations. Significant differences in resistance to lethal levels of toxicity were observed for both non-acclimated and acclimated populations, individuals from population I being more resistant than those from reference populations. The existence of genetically-determined sensitivity differences was attested by the presence of significant differences in resistance to lethal levels of toxicity in acclimated individuals from reference and stressed populations. Results from cumulative mortality assays revealed that sensitive individuals were most probably present in the original population, but no conclusion could be draw about the presence of extreme resistant individuals in the historically-stressed population. Finally, it was shown that responses among populations converged from high to low levels of contamination.

Adaptation, Physiological↗

PubMed2006

Asthma hospitalizations among American Indian and Alaska Native people and for the general US population.

STUDY OBJECTIVES: Asthma is one of the most common chronic diseases in the United States. High rates of asthma hospitalization have been reported for some ethnic minorities; however, asthma hospitalization rates for American Indian/Alaska Native (AI/AN) populations of all ages have not been studied. In this study, we examined and compared hospitalization rates for AI/AN populations and the general population in the United States. DESIGN: Hospital discharge records with a first-listed diagnosis of asthma were evaluated for AI/AN populations and the US general population of all ages from 1988 to 2002. RESULTS: The asthma hospitalization rate for AI/AN populations decreased from 17.8/10,000 per year in 1988 to 1990 to 12.9/10,000 per year in 2000 to 2002. The overall age-adjusted rate for 2000 to 2002 was slightly lower than that for the general US population (12.9/10,000 and 16.4/10,000, respectively). However, AI/AN populations living in the Southwest region (17.6/10,000) had the highest asthma hospitalization rate among the Indian Health Service regions and the rate from 2000 to 2002 was similar to that for the general US population. The 2000 to 2002 asthma hospitalization rate for AI/AN populations < 1 year of age (infants) was higher than that in US infants, and the rates for AI/AN age groups > or = 1 year were similar to or lower than those for the general US population. CONCLUSIONS: While asthma was rarely reported among AI/AN populations before 1975, the average annual age-adjusted asthma hospitalization rate was only slightly lower for AI/AN populations than that for the US general population from 2000 to 2002. Furthermore, the asthma hospitalization rates for AI/AN populations living in the Southwest and East regions were similar to the rate for the general US population. Efforts to further increase asthma awareness and symptom recognition among AI/AN populations should be implemented to help to reduce asthma hospitalizations.

Adolescent↗

PubMed2000

RAPD variation among and within small and large populations of the rare clonal plant Ranunculus reptans (Ranunculaceae).

In the pre-alpine region of Europe numbers and sizes of populations of the clonal lake shore plant Ranunculus reptans have declined because of the regulation of lake water levels. We investigated genetic variation among and within 17 populations of different size (cover 1-10 000 m) in R. reptans with RAPD (random amplified polymorphic DNA) profiles. We sampled 127 rosettes in 14 populations at Lake Constance and three populations at or near Lake Como. There was significant genetic variation between plants from the two lake regions (5.9%, analysis of molecular variance [AMOVA], P < 0.001), among populations within lake regions (20.4%, P < 0.001), and within populations (73.7%, P < 0.001). Under the assumptions of Wright's island model the variation among populations corresponds to a gene flow of N(e)m = 0.70. Within the 14 Lake Constance populations we detected significant genetic variation among subpopulations separated by only a few metres (4.0% of the within-population variation; P < 0.05). Molecular variance was 24% smaller in small populations covering <100 m area than in larger ones (P < 0.03), indicating that samples from large populations were genetically more variable than samples representing comparable areas of smaller populations. We conclude that gene flow among populations is very limited and that genetic drift has caused reduced genetic variability of smaller populations. Conservation of genetic variability in R. reptans requires persistence of large and also of small populations (because of population differentiation), and it could be enhanced by increasing the size of small populations (to counter genetic drift).

Journal Article↗

PubMed2003

Genetic differences in interleukin-1 betapolymorphisms among four Asian populations: an analysis of the Asian paradox between H. pylori infection and gastric cancer incidence.

The prevalence of Helicobacter pylori infection is high among Asian populations, but the incidences of gastric cancer differ greatly among northern and southern Asian populations. Here, we studied histopathological findings in stomach tissue using an updated Sydney System and the frequencies of interleukin (IL)-1betapolymorphisms, thought to be associated with an increased risk of gastric cancer, in four Asian populations. Endoscopic-guided biopsies from three regions of the stomach and the -511 T-to-C polymorphism in the IL-1betagene were examined in 228 Japanese, 116 Chinese, 159 Thai and 83 Vietnamese patients with gastric diseases. H. pylori colonization, inflammation and activity were more severe in the Japanese and Thai populations than in the Chinese and Vietnamese populations and these scores were more antrum-predominant in the Thai and Vietnamese populations than in the Japanese and Chinese populations, with the most severe degree of atrophy and intestinal metaplasia occurring in the angulus region of the Japanese population. The IL-1betapolymorphisms did not differ among the four populations overall, but in cases with severe mucosal atrophy (pepsinogen I/II ratio <3.0), the CC polymorphism was dominant in the Japanese population and the TT+TC polymorphism was dominant in the Chinese population; no difference in C and T allele frequencies was found in the Thai and Vietnamese populations. In conclusion, the incidence of gastric cancer is extremely low, but the prevalence of H. pylori infection is high in the Thai population (Asian paradox). In the Thai population, the scores for corpus gastritis and intestinal metaplasia, which are associated with a high risk of gastric cancer, were low in comparison with the Japanese population. IL-1betapolymorphisms were correlated with mucosal atrophy in the Japanese and Chinese populations, but not in the Thai and Vietnamese populations.

Adolescent↗

PubMed2005

Twelve short tandem repeat loci Y chromosome haplotypes: genetic analysis on populations residing in North America.

A total of 2443 male individuals, previously typed for the 13 CODIS STR loci, distributed across the five North American population groups African American, Asian, Caucasian, Hispanic, and Native American were typed for the Y-STR loci DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438 and DYS439 using the PowerPlex Y System. All population samples were highly polymorphic for the 12 Y-STR loci with the marker DYS385a/b being the most polymorphic across all sample populations. The Native American population groups demonstrated the lowest genetic diversity, most notably at the DYS393 and DYS437 loci. Almost all of the 12-locus haplotypes observed in the sample populations were represented only once in the database. Haplotype diversities were greater than 99.6% for the African Americans, Caucasians, Hispanics, and Asians. The Native Americans had the lowest haplotype diversities (Apaches, 97.0%; Navajo, 98.1%). Population substructure effects were greater for Y-haplotypes, compared with that for the autosomal loci. For the apportionment of variance for the 12 Y-STRs, the within sample population variation was the largest component (>98% for each major population group and approximately 97% in Native Americans), and the variance component contributed by the major population groups was less than the individual component, but much greater than among sample populations within a major group (11.79% versus 1.02% for African Americans/Caucasians/Hispanics and 15.35% versus 1.25% for all five major populations). When each major population is analyzed individually, the R(ST) values were low but showed significant among group heterogeneity. In 692 confirmed father-son pairs, 14 mutation events were observed with the average rate of 1.57x10(-3)/locus/generation (a 95% confidence bound of 0.83x10(-3) to 2.69x10(-3)). Since the Y-STR loci reside on the non-recombining region of the Y chromosome, the counting method is one approach suggested for conveying an estimate of the rarity of the Y-haplotype. Because the Y-STR loci are not all in disequilibrium to the same extent, the counting method is a very conservative approach. The data also support that autosomal STR frequencies can be multiplied by the upper bound frequency estimate of a Y-haplotype in the individual population group or those pooled into major population groups (i.e., Caucasian, African American, Hispanic, and Asian). These analyses support use of the haplotype population data for estimating Y-STR profile frequencies for populations residing in North America.

Canada↗

PubMed2001

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↗

PubMed2005

High genetic diversity in French invasive populations of common ragweed, Ambrosia artemisiifolia, as a result of multiple sources of introduction.

Ambrosia artemisiifolia is an aggressive North American annual weed, found particularly in sunflower and corn fields. Besides its economic impact on crop yield, it represents a major health problem because of its strongly allergenic pollen. Ragweed was imported inadvertently to Europe in the 18th century and has become invasive in several countries, notably in the Rhône Valley of France. It has recently expanded in both the Provence-Alpes-Côte-d'Azur and Bourgogne regions. As first steps towards understanding the causes and mechanisms of ragweed invasion, genetic variability of French and North American populations was analysed using microsatellites. Overall genetic variability was similar in North America and in the Rhône-Alpes region, but within-population levels of genetic variability were surprisingly lower in native than in invasive French populations. French populations also exhibited lower among-population differentiation. A significant pattern of isolation by distance was detected among North American populations but not among French populations. Assignment tests and distribution of rare alleles did not point to a single origin for all French populations, nor for all individuals within populations and private alleles from different North American populations were found in the same French populations. Indeed, within all French populations, individual plants were roughly equally assigned to the different North American populations. Altogether, these results suggest that the French invasive populations include plants from a mixture of sources. Reduced diversity in populations distant from the original area of introduction indicated that ragweed range expansion probably occurred through sequential bottlenecks from the original populations, and not from subsequent new introductions.

Ambrosia↗