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PubMed2005

Conservation genetics and population history of the threatened European mink Mustela lutreola, with an emphasis on the west European population.

In species of great conservation concern, special attention must be paid to their phylogeography, in particular the origin of animals for captive breeding and reintroduction. The endangered European mink lives now in at least three well-separated populations in northeast, southeast and west Europe. Our aim is to assess the genetic structure of these populations to identify 'distinct population segments' (DPS) and advise captive breeding programmes. First, the mtDNA control region was completely sequenced in 176 minks and 10 polecats. The analysis revealed that the western population is characterized by a single mtDNA haplotype that is closely related to those in eastern regions but nevertheless, not found there to date. The northeast European animals are much more variable (pi = 0.012, h = 0.939), with the southeast samples intermediate (pi = 0.0012, h = 0.469). Second, 155 European mink were genotyped using six microsatellites. The latter display the same trends of genetic diversity among regions as mtDNA [gene diversity and allelic richness highest in northeast Europe (H(E) = 0.539, R(S) = 3.76), lowest in west Europe (H(E) = 0.379, R(S) = 2.12)], and provide evidences that the southeast and possibly the west populations have undergone a recent bottleneck. Our results indicate that the western population derives from a few animals which recently colonized this region, possibly after a human introduction. Microsatellite data also reveal that isolation by distance occurs in the western population, causing some inbreeding because related individuals mate. As genetic data indicate that the three populations have not undergone independent evolutionary histories for long (no phylogeographical structure), they should not be considered as distinct DPS. In conclusion, the captive breeding programme should use animals from different parts of the species' present distribution area.

Animals↗

PubMed2006

Decoupled mitochondrial and chloroplast DNA population structure reveals Holocene collapse and population isolation in a threatened Mexican-endemic conifer.

Chihuahua spruce (Picea chihuahuana Martínez) is a montane subtropical conifer endemic to the Sierra Madre Occidental in northwestern México. Range-wide variation was investigated using maternally inherited mitochondrial (mtDNA) and paternally inherited chloroplast (cpDNA) DNA markers. Among the 16 mtDNA regions analysed, only two mitotypes were detected, while the study of six cpDNA microsatellite markers revealed eight different chlorotypes. The average cpDNA diversity (H = 0.415) was low but much higher than that for mtDNA (H = 0). The distribution of mitotypes revealed two clear nonoverlapping areas (G(ST) = N(ST) = 1), one including northern populations and the second one including the southern and central stands, suggesting that these two regions may represent different ancestral populations. The cpDNA markers showed lower population differentiation (G(ST) = 0.362; R(ST) = 0.230), implying that the two ancestral populations continued to exchange pollen after their initial geographic separation. A lack of a phylogeographic structure was revealed by different spatial analyses of cpDNA (G(ST) > R(ST); and samova), and reduced cpDNA gene flow was noted among populations (Nm = 0.873). Some stands deviated significantly from the mutation-drift equilibrium, suggesting recent bottlenecks. Altogether, these various trends are consistent with the hypothesis of a population collapse during the Holocene warming and suggest that most of the modern P. chihuahuana populations are now effectively isolated with their genetic diversity essentially modelled by genetic drift. The conservation efforts should focus on most southern populations and on the northern and central stands exhibiting high levels of genetic diversity. Additional mtDNA sequence analysis confirmed that P. martinezii (Patterson) is not conspecific with P. chihuahuana, and thus deserves separate conservation efforts.

Base Sequence↗

PubMed2006

The effect of population structure on the adaptive radiation of microbial populations evolving in spatially structured environments.

Spatial structure is thought to be an important factor influencing the emergence and maintenance of genetic diversity. Previous studies have demonstrated that environmental heterogeneity, provided by spatial structure, leads to adaptive radiation of populations. In the present study, we investigate not only the impact of environmental heterogeneity on adaptive radiation, but also of population fragmentation and niche construction. Replicate populations founded by a single genotype of Escherichia coli were allowed to evolve for 900 generations by serial transfer in either a homogeneous environment, or a spatially structured environment that was either kept intact or destroyed with each daily transfer. Only populations evolving in the structured environment with intact population structure diversified: clones are significantly divergent in sugar catabolism, and show frequency-dependent fitness interactions indicative of stable coexistence. These findings demonstrate an important role for population fragmentation, a consequence of population structure in spatially structured environments, on the diversification of populations.

Adaptation, Physiological↗

PubMed2006

Molecular population genetics and phenotypic diversification of two populations of the thermophilic cyanobacterium Mastigocladus laminosus.

We investigated the distributions of genetic and phenotypic variation for two Yellowstone National Park populations of the heterocyst-forming cyanobacterium Mastigocladus (Fischerella) laminosus that exhibit dramatic phenotypic differences as a result of environmental differences in nitrogen availability. One population develops heterocysts and fixes nitrogen in situ in response to a deficiency of combined nitrogen in its environment, whereas the other population does neither due to the availability of a preferred nitrogen source. Slowly evolving molecular markers, including the 16S rRNA gene and the downstream internal transcribed spacer, are identical among all laboratory isolates from both populations but belie considerable genetic and phenotypic diversity. The total nucleotide diversity at six nitrogen metabolism loci was roughly three times greater than that observed for the human global population. The two populations are genetically differentiated, although variation in performance on different nitrogen sources among genotypes could not be explained by local adaptation to available nitrogen in the respective environments. Population genetic models suggest that local adaptation is mutation limited but also that the populations are expected to continue to diverge due to low migratory gene flow.

Cyanobacteria↗

PubMed2001

Population genomics: genome-wide sampling of insect populations.

Modern population genetics underwent a major paradigm shift during the last decade of the 20th century with the discovery that thousands of genes of known function and position in a genome can be analyzed simultaneously in a single individual. The impact of this technology on insect population genetics is potentially profound. Sampling distributions of genetic statistics can now be derived from many individual loci or among many segregating sites within a gene. Inferences regarding random mating, gene flow, effective population sizes, disequilibrium, and relatedness among populations can now be based on patterns of variation at many loci. More importantly, genome-wide sampling enables population geneticists to distinguish effects that act on the whole genome from those that act on individual loci or nucleotides. We introduce the term "population genomics" to describe the process of simultaneous sampling of numerous variable loci within a genome and the inference of locus-specific effects from the sample distributions. The four critical assumptions implicit in the population genomics approach are explained in detail. Studies adopting this paradigm are reviewed, and the steps necessary to complete a population genomics study are outlined.

Animals↗

PubMed2007

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

BACKGROUND: Copy number variants (CNVs) account for a significant proportion of normal phenotypic variation and may have an important role in human pathological variation. The alpha-defensin cluster on human chromosome 8p23.1 is one of the better-characterized CNVs, in which high copy number variability affecting the DEFA1 and DEFA3 genes has been reported. Moreover, the DEFA3 gene has been found to be absent in a significant proportion of control population subjects. CNVs involving immune genes, such as alpha-defensins, are possibly contributing to innate immunity differences observed between individuals and influence predisposition and susceptibility to disease. RESULTS: We have tested the DEFA3 absence in 697 samples from different human populations. The proportion of subjects lacking DEFA3 has been found to vary from 10% to 37%, depending on the population tested, suggesting differences in innate immune function between populations. Absence of DEFA3 was correlated with the region's haplotype block structure. African samples showed a higher intra-populational variability together with the highest proportion of subjects without DEFA3 (37%). Association analysis of DEFA3 absence with 136 SNPs from a 100-kb region identified a conserved haplotype in the Caucasian population, extending for the whole region. CONCLUSION: Complexity and variability are essential genomic features of the alpha-defensin cluster at the 8p23.1 region. The identification of population differences in subjects lacking the DEFA3 gene may be suggestive of population-specific selective pressures with potential impact on human health.

Asian People↗

PubMed1991

'Unique' alleles in admixed populations: a strategy for determining 'hereditary' population differences of disease frequencies.

The genetic contribution of a parental population in an admixed population can be estimated from the frequencies of unique alleles that exist only in that parental population. In this work we show that although the estimated admixture component from a single such unique allele may be quite unstable, when multiple numbers of unique alleles are recognized, they together allow precise estimation of admixture components in an admixed population. We develop a statistical theory of linear regression incorporating estimation errors of frequencies of unique alleles in the parental and admixed populations. In addition, we show that the distribution of unique alleles detected in individuals can be used to measure the admixture component of an admixed individual. Applications of these theories to data on unique African alleles in an American black population show that such estimates are quite reliable. The distribution of unique alleles detected from the multiple-locus genotype of an admixed individual allows an opportunity to extend the studies on the "hereditary" basis of disease risk variation across populations to individuals from a single homogeneous admixed population.

Africa↗

PubMed2002

Density-dependent growth as a key mechanism in the regulation of fish populations: evidence from among-population comparisons.

It is generally assumed that fish populations are regulated primarily in the juvenile (pre-recruit) phase of the life cycle, although density dependence in growth and reproductive parameters within the recruited phase has been widely reported. Here we present evidence to suggest that density-dependent growth in the recruited phase is a key process in the regulation of many fish populations. We analyse 16 fish populations with long-term records of size-at-age and biomass data, and detect significant density-dependent growth in nine. Among-population comparisons show a close, inverse relationship between the estimated decline in asymptotic length per unit biomass density, and the long-term average biomass density of populations. A simple population model demonstrates that regulation by density-dependent growth alone is sufficient to generate the observed relationship. Density-dependent growth should be accounted for in fisheries' assessments, and the empirical relationship established here can provide indicative estimates of the density-dependent growth parameter where population-specific data are lacking.

Aging↗

PubMed1993

[Comparison of the population of the Krasnodar region with other Russian populations regarding genetic and demographic parameters].

The estimates of some genetical and demographical parameters important for populational structure of the population of West part of Krasnodar province are presented. The differences in forming of population structure of districts was revealed. In general, the decrescent type of reproduction, active family planning (average family value is 2.10 +/- 0.07 when average pregnancy quantity is 6.31 +/- 0.32), significant migration activity approached rural populations of Krasnodar district to those of urban type. The migration processes was the main factor of structure population forming. When effort of natural selection was studied the decrease of index Crow was discovered in comparison with rural Russian populations Kirov and Kostroma regions. Population of Krasnodar district approaches to pan-mixture one by genetic and demographic parameters. It can be considered as a gene sample from all regions when Russian live.

Age Distribution↗

PubMed2004

Acetylation phenotype status in a Bangladeshi population and its comparison with that of other Asian population data.

The objective of the present study was to determine the acetylator status of the Bangladeshi population and to compare the findings with the acetylator status of other Asian populations. The acetylator phenotype was determined in 517 unrelated healthy Bangladeshi subjects. The phenotyping procedure was done according to Price Evans' method using the NAT2 specific probe drug--sulphadimidine. The Bangladeshi population showed a bimodal distribution of fast and slow acetylators. Of a total of 517 healthy Bangladeshi, 79.5% (n=411) were fast acetylators and the rest 20.5% (n=106) were slow acetylators. The high frequency of the fast acetylators in the population of Bangladesh was comparable to other populations in East Asia. When this acetylator status was compared with other Asian data, the Asian population showed a positive correlation between the acetylator status and the geographical longitude (r=0.919; t=7.37; p>0.001; d.f.=10). The regression line of the scatter diagram showed that the frequency of acetylating capacity increasingly occurred in the populations towards eastern Asia (regression coefficient=0.54; constant=52.36). This line was termed as the Asian fast acetylator longitude (AFAL). Thus the AFAL was able to predict the acetylator status of the Asian population by the east-west geographical longitude. The AFAL could be a useful prognosticator in the disposition for the effective and safe use of numerous drugs and xenobiotic compounds in humans.

Acetylation↗

PubMed1998

Characterization of a population of cells in the bone marrow that phenotypically mimics hematopoietic stem cells: resting stem cells or mystery population?

We have identified a population of cells in murine bone marrow that has many of the phenotypic characteristics attributed to resting hematopoietic stem cells but does not reconstitute irradiated mice. These cells express high levels of Sca-1, H-2K and CD38 and low levels of Thy-1.1, but do not express CD34 nor any of the lineage markers including CD3, CD4, CD5, CD8 NK1.1, I-A, B220, Ig(MGA), CD40, kappa, Mac-1, Gr-1 or Ter119. In addition, this population can be found at normal frequency in nu/nu as well as rag-1-/- mice. These cells incorporate only low levels of Rh123, are resistant to the cytotoxic effects of 5-fluorouracil and, consistent with their resting phenotype, less than 2% of these cells are in the S/G2/M phases of the cell cycle. The only phenotypic characteristic that distinguishes these cells from the lineage- Sca-1+, Thy-1.1low long-term reconstituting hematopoietic stem cell population is their lack of c-kit expression. Here we have explored the possibility that these cells represent a truly resting population of hematopoietic stem cells. We found that the lineage-, Sca-1+, c-kit- cells do not respond to hematopoietic growth factors in vitro, either alone or in combination with stromal layers. Furthermore, these cells do not form in vivo spleen colonies nor do they have the ability to reconstitute irradiated mice. Thus, this population may represent either a population of resting stem cells for which we lack the appropriate activating stimulus, or simply represent a "mystery population" that phenotypically mimics most of the physical properties of resting stem cells. Given the close phenotypic similarity of the c-kit- mystery population cells to the c-kit+ long-term reconstituting stem cells, investigators must be rigorous to exclude their effects from other stem cell assays.

ADP-ribosyl Cyclase↗

PubMed1994

Population genetic characteristics of the D1S80 locus in seven human populations.

We have analyzed the allele frequency distribution at the highly polymorphic variable number of tandem repeat (VNTR) locus D1S80 (pMCT118) in seven ethnic populations (namely, New Guinea Highlanders of Papua New Guinea, Dogrib Indians of Canada, Pehuenche Indians of Chile, American and Western Samoans, Kacharis of Northeast India, and German Caucasians) using the polymerase chain reaction (PCR) technique. In the pooled sample of 443 unrelated individuals 20 segregating alleles were detected. A trimodal pattern of allelic distribution is present in the majority of populations and is indicative of the evolutionary antiquity of the polymorphism at this locus. In spite of the observed high degree of polymorphism (expected heterozygosity 56%-86%), with a single exception--the marginally significant P value (0.04) of the exact test in American Samoans--the genotype distributions in all populations conform to their respective Hardy-Weinberg expectations. Summary statistics indicate that, in general, the allele frequency distribution at this locus may be approximated by the infinite allele model. The data also demonstrate that alleles that are shared by all populations have the highest average frequency within populations. Furthermore, the kinship bioassay analysis demonstrates that the extensive variation observed at the D1S80 locus is at the interindividual within population level, which dwarfs any interpopulation allele frequency variation, consistent with the population dynamics of hypervariable polymorphisms. These characteristics of the D1S80 locus make it a very useful marker for population genetic research, genetic linkage studies, forensic identification of individuals, and for determination of biological relatedness of individuals.

Alleles↗

PubMed2006

A multilevel approach to predict toxicity in copepod populations: assessment of growth, genetics, and population structure.

One of the goals of environmental risk assessment (ERA) is to understand effects of toxicant exposure on individual organisms and populations. We hypothesized that toxicant exposure can reduce genetic diversity and alter genotype composition, which may ultimately lead to a reduction in the average fitness of the exposed population. To test this hypothesis, we exposed a copepod, Nitocra psammophila, to a toxic reference compound and assayed resulting alterations in genetic structure, i.e. expected heterozygosity and percent polymorphic loci, as well as other population- and fitness-related measures, i.e. population abundance, demographic structure and juvenile growth. The copepods were exposed to 0.11-1.1 microg of the pentabromo-substituted diphenyl ether (BDE-47) mg(-1) freeze-dried algae for 24 days (i.e. >1 generation). There was no significant decline in total population abundance. However, there were significant alterations in population structure, manifested as diminished proportion of nauplii and increased proportion of copepodites. In addition, individual RNA content in copepodites decreased significantly in exposed individuals, indicating declined growth. Finally, in the exposed populations, heterozygosity was lower and genotype composition was altered compared to the controls. These results therefore confirm the hypothesized reduction in overall genetic variability resulting from toxicant exposure. Multilevel approaches, such as the one used in the present study, may help unravel subtle effects on the population level, thus increasing the predictive capacity of future ERA.

Animals↗

PubMed2006

Population history, biogeography, and taxonomy of orangutans (Genus: Pongo) based on a population genetic meta-analysis of multiple loci.

This paper examines orangutan population history and evolution through a meta-analysis of seven loci collected from both Sumatran and Bornean orangutans. Within orangutans, most loci show that the Sumatran population is about twice as diverse as the Bornean population. Orangutans are more diverse than African apes and humans. Sumatran and Bornean populations show significant genetic differentiation from one another and their history does not differ significantly from an 'island model' (population splitting without gene flow). Two different methods support a divergence of Bornean and Sumatran orangutans at 2.7-5 million years ago. This suggests that Pleistocene events, such as the cyclical exposure of the Sunda shelf and the Toba volcanic eruption, did not have a major impact on the divergence of Bornean and Sumatran orangutans. Pairwise mismatch analyses, however, suggest that Bornean orangutans have undergone a recent population expansion (beginning 39,000-64,000 years ago), while Sumatran orangutan populations were stable. Pleistocene events may have contributed to these aspects of orangutan population history. These conclusions are applied to the debate on orangutan taxonomy.

Animals↗

PubMed2001

Variability levels, population size and structure of American and European Drosophila montana populations.

The level and patterns of nucleotide diversity have been characterized for two X-linked loci, fused (fu; a region of 2362 bp) and suppressor of sable (su(s); a region of 413 bp), in one European and one American D. montana population. Sequence variation at these loci shows that the two populations are divergent, although they may not be completely isolated. Data on the level of silent site variability at su(s) (1.1% and 0.5% for the European and American populations, respectively) suggest that the effective population sizes of the two populations may be similar. At the fused locus, one European sequence was highly divergent and may have resulted from gene conversion, and was excluded from the analysis. With this sequence removed, the level of silent site variability was significantly lower in the European population (0.28%) than in the American population (2.3%), which suggests a selective sweep at or near fu in the former population.

Animals↗

PubMed2001

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↗

PubMed2001

Genetic variation and population structure in Scandinavian wolverine (Gulo gulo) populations.

Wolverine (Gulo gulo) numbers in Scandinavia were significantly reduced during the early part of the century as a result of predator removal programmes and hunting. Protective legislation in both Sweden and Norway in the 1960s and 1970s has now resulted in increased wolverine densities in Scandinavia. We report here the development of 15 polymorphic microsatellite markers in wolverine and their use to examine the population sub-structure and genetic variability in free-ranging Scandinavian wolverine populations as well as in a sample of individuals collected before 1970. Significant subdivision between extant populations was discovered, in particular for the small and isolated population of southern Norway, which represents a recent recolonization. Overall genetic variability was found to be lower than previously reported for other mustelids, with only two to five alleles per locus and observed heterozygosities (H(O)) ranging from 0.269 to 0.376 across the examined populations, being lowest in southern Norway. Analysis of the mitochondrial DNA control region revealed no variation throughout the surveyed populations. As the historical sample did not show higher levels of genetic variability, our results are consistent with a reduction in the genetic variation in Scandinavian wolverines that pre-dates the demographic bottleneck observed during the last century. The observed subdivision between populations calls for management caution when issuing harvest quotas, especially for the geographically isolated south Norwegian population.

Animals↗

PubMed2003

Development of a food frequency questionnaire (FFQ) for an elderly population based on a population survey.

Older people have different eating patterns than their younger counterparts, although in most nutritional studies of older populations, food frequency questionnaires (FFQ) that were developed and validated for the general adult population are used. In this paper, we present the advantages of developing an FFQ for an older population based on a population survey. A random sample of the Negev's (Southern Israel) Jewish population > or = 35 y old was recruited and interviewed for their dietary intake using 24-h recalls. Foods eaten were aggregated into conceptually similar groups and entered into stepwise regression models to predict variation in nutrient intake. We interviewed 796 people age 35-64 y and 377 people > or = 65 y old for the study. Significantly more items were required to reach 80% between-person variability for zinc, magnesium, vitamin E and protein for the elderly compared with the younger age group. Portion sizes of most items consumed by the elderly were smaller compared with the Israeli Ministry of Health portion sizes booklet and the younger age group's intake estimates. The nutrient values assigned for each line based on a weighted mean of the intake of the elderly were different from those using the most frequently used item. The above findings highlight some of the advantages of developing an FFQ for an older population based on a population survey. Further studies are required to compare the validity of existing tools adapted for the elderly to those developed on the basis of population surveys.

Adult↗