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PubMed1983

Population genetical investigations on Indian tribals. Preliminary report.

Data on the distribution of genetic markers in Indian tribal populations as well as in Southwest and Southeast Asiatic populations have been recorded in order to study comparatively the extent of genetic similarity and dissimilarity, respectively, 1. within the various regional tribal groups, and 2. among tribals and the populations from Southwest and Southeast Asia. The--preliminary--results of these comparisons are discussed considering the racial history of the Indian subcontinent.

Asia↗
PubMed2005

Patterns of hybridization and population genetic structure in the terrestrial orchids Liparis kumokiri and Liparis makinoana (Orchidaceae) in sympatric populations.

We investigated the potential for gene flow and genetic assimilation via hybridization between common and rare species of the terrestrial orchid genus Liparis, focusing specifically on sympatric and allopatric populations of the common Liparis kumokiri and the rare Liparis makinoana. We utilized analyses of genetic diversity, morphology, and the spatial distributions of individuals and genotypes to quantify the dynamics of interspecific gene flow at within- and among-population scales. High levels of allozyme genetic diversity (HE) were found in populations of the rare L. makinoana (0.317), whereas the common L. kumokiri (N = 1744 from 14 populations) revealed a complete lack of variation. This contrast may reflect different breeding systems and associated rates of genetic drift (L. makinoana is self-incompatible, whereas L. kumokiri is self-compatible). At the two known sympatric sites, individuals were found that recombined parental phenotypes, possessing floral characteristics of L. kumokiri and vegetative characteristics of L. makinoana. These putative hybrids were the only individuals found segregating alleles diagnostic of both parental species. Analysis of these individuals indicated that hybrid genotypes were skewed towards L. kumokiri and later generation recombinants of L. kumokiri at both sympatric sites. Furthermore, Ripley's bivariate L(r) statistics revealed that at one site these hybrids are strongly spatially clustered with L. kumokiri. Nonetheless, the relatively low frequency of hybrids, absence of ongoing hybridization (no F1s or first generation backcrossess), and strong genetic differentiation between morphologically 'pure' parental populations at sympatric sites (FST = 0.708-0.816) indicates that hybridization was not an important bridge for gene flow. The results from these two species suggest that natural hybridization has not played an important role in the diversification of Liparis, but instead support the view that genetic drift and limited gene flow are primarily responsible for speciation in Liparis. Based on genetic data and current status of the species, implications of the research for conservation are considered to provide guidelines for appropriate conservation and management strategies.

Conservation of Natural Resources↗
PubMed1995

A population genetic test of selection at the molecular level.

The role of natural selection in molecular evolution has been inferred primarily by rejection of null hypotheses based on neutral theory, rather than by acceptance of specific predictions based on selection. In this report, a population genetic test of a specific prediction for selection on DNA polymorphism is presented. Pyrethroid insecticide use constitutes an experiment for which form of selection and molecular target (voltage-gated sodium channels) are both known. As predicted, differential pyrethroid selection on tobacco budworm populations generated significant geographic heterogeneity in sodium channel marker allele frequencies, compared with arbitrary loci.

Alleles↗
PubMed2002

The paradoxical population genetics of Plasmodium falciparum.

Among the leading causes of death in African children is cerebral malaria caused by the parasitic protozoan Plasmodium falciparum. Endemic forms of this disease are thought to have originated in central Africa 5000-10000 years ago, coincident with the innovation of slash-and-burn agriculture and the diversification of the Anopheles gambiae complex of mosquito vectors. Population genetic studies of P. falciparum have yielded conflicting results. Some evidence suggests that today's population includes multiple ancient lineages pre-dating human speciation. Other evidence suggests that today's population derives from only one, or a small number, of these ancient lineages. Resolution of this issue is important for the evaluation of the long-term efficacy of drug and immunological control strategies.

Animals↗
PubMed2003

Molecular population genetics of inducible antibacterial peptide genes in Drosophila melanogaster.

Insects respond to septic infection in part by producing a suite of antimicrobial peptides that may be subject to host-pathogen coevolutionary dynamics. In order to infer population genetic forces acting on Drosophila antibacterial peptide genes, we examine global properties of polymorphism and divergence in the Drosophila melanogaster defensin, drosocin, metchnikowin, attacin C, diptericin A, and cecropin A, B, and C genes. As a functional class, antibacterial peptides exhibit low levels of interspecific amino acid divergence. There are multiple amino acid polymorphisms segregating within D. melanogaster, however, a high proportion of which change the charge or polarity of the variable residue. These polymorphisms are particularly prevalent in processed signal and propeptide domains. We find that models of coevolutionary "arms races" and selectively maintained hypervariability do not adequately describe the population dynamics of mature antibacterial peptides in D. melanogaster, but that a highly significant excess of high-frequency derived polymorphisms coupled with substantial intralocus linkage disequilibrium suggests that positive selection may act on antibacterial peptide genes. Some attributes of the data may be consistent with a simple demographic model of population founding followed by expansion, but departures from the equilibrium null tend to be more pronounced in the peptide genes than at other loci around the genome.

Amino Acid Sequence↗
PubMed1979

Equilibrium stability of a diffusion process in population genetics.

De Finetti introduced a model of a continuously reproducing population with phenotypic assortative mating for a pair of dominant-recessive autosomal genes. In this paper it is rigorously proved that this model admits of stable equilibria which lie above the Hardy--Weinberg parabola in the de Finetti diagram.

Genetics, Population↗
PubMed2001

Population genetic structure of the cleistogamous plant species Viola pubescens Aiton (Violaceae), as indicated by allozyme and ISSR molecular markers.

Few studies of genetic variation have focused on species that reproduce through both showy, chasmogamous (CH) flowers and self-pollinated, cleistogamous (CL) flowers. Using two different techniques, genetic variation was measured in six populations of Viola pubescens Aiton, a yellow-flowered violet found in the temperate forests of eastern North America. Results from eight allozyme loci showed that there was considerable genetic variation in the species, and population structuring was indicated by the presence of unique alleles and a theta (F(ST)) value of 0.29. High genetic variation was also found using ISSR (inter-simple sequence repeat) markers, and population structuring was again evident with unique bands. Viola pubescens appears to have a true mixed-mating system in which selfing through CL and CH flowers contributes to population differentiation, and outcrossing through CH flowers increases genetic variation and gene flow among populations. Overall, allozyme and ISSR techniques yielded similar results, indicating that ISSR markers show potential for use in population genetic studies.

Alleles↗
PubMed1990

Granular corneal dystrophy Groenouw type I. 115 Danish patients. An epidemiological and genetic population study.

An epidemiological and genetic study in Denmark of granular corneal dystrophy Groenouw type I is described. Ninety-one living patients were found. The disease is inherited as an autosomal dominant trait with a 100% penetrance of the gene. The 91 cases could be traced back to 6 different mutations. The mutation rate was estimated to be about 0.3/1,000,000; the possible sources of error of this estimate are discussed. The age distribution of the patients is shown to be similar to that of the Danish population in general.

Adolescent↗
PubMed1991

Analysis of population genetic structure by DNA fingerprinting.

DNA fingerprint similarity is now being used widely to make inferences about the genetic structure of natural and domesticated populations, often with little regard to the limitations of such data. This paper provides an overview of the statistical theory of DNA fingerprint analysis with special focus on applications to natural populations for which little if anything is known about the detailed genetics of the DNA profiles. Approaches to estimating individual and population homozygosity, effective population size, population subdivision, and relatedness are reviewed, and issues concerning the biases and sampling properties of the statistics are discussed.

DNA Fingerprinting↗
PubMed2000

Expression of porcine transcription factors and genes related to fatty acid metabolism in different tissues and genetic populations.

Several transcription factors are involved in regulating lipid metabolism in various tissues of animals. Adipocyte determination and differentiation-dependent factor 1 (ADD1), peroxisome proliferator activated receptor alpha (PPAR alpha), and peroxisome proliferator activated receptor gamma (PPAR gamma) regulate both lipogenesis and fatty acid oxidation. We determined the tissue distribution and genetic difference in mRNA concentrations of these transcription factors in two genetic populations of pigs (Newsham XL-sired Newsham Landrace x Large White Duroc and Duroc-sired US Yorkshire x Duroc-Landrace). We also determined the tissue distribution and genetic difference in the mRNA concentration of fatty acid synthase (FAS) and acyl-CoA oxidase (ACO). Our data showed that ADD1 was highly expressed in adipose tissue and liver and that mRNA concentrations of ADD1 were similar between the two genotypes. The PPAR alpha mRNA concentration was high in adipose tissue and was similar between the two genotypes. In both populations, PPAR gamma mRNA was detected only in adipose tissue. There was no difference between the two genotypes in PPAR gamma mRNA concentration. The ACO mRNA was expressed in adipose tissue, skeletal muscle, and liver with no difference between genotypes. The FAS mRNA concentration in adipose tissue was seven times higher than that in the liver. There was no detectable FAS mRNA in skeletal muscle. These data support the concept that pig adipose tissue has considerable capability for fatty acid oxidation and synthesis. The uniqueness of expression patterns for FAS and ADD1 mRNA further indicates that adipose tissue is significantly involved in fatty acid and triacylglycerol synthesis in pigs.

Acyl-CoA Oxidase↗
PubMed1990

Social mechanisms in the population genetics of Tay-Sachs and other lethal autosomal recessive diseases: a computer simulation model.

A computer simulation model was developed to study the effects of various feudal social customs on the incidence of lethal autosomal recessive genes. Populations of 500 individuals were created in which each person was characterized by sibship, genotype, and sex. The numbered sibships were sorted into numerical order. Each individual then sought a mate from 6 or 12 sibships on either side of his or her own sibship. The resulting couples were sorted in order of the husband's sibship number, after which the couples produced children in accordance with the prevailing birth rate. This ordering of sibships made the probability of a gene remaining in one locality higher than the probability of it drifting to distant localities. A lethal autosomal recessive gene was introduced into populations at a starting carrier rate of 10%. This fell after 20 generations to 2.54 +/- 0.17% (SEM) which was significantly less than the 5.00% carrier rate predicted by a deterministic model in which random mating occurred in an infinite population. The excessive loss of the lethal gene was caused by the high incidence of consanguineous marriages and by the occurrence of random inequalities in the distribution of the gene. The avoidance of sib marriages raised the final carrier frequency (3.28 +/- 0.19%) as did reproductive compensation (4.33 +/- 0.26%). The combination of the incest taboo and reproductive compensation raised the final carrier rate to 5.05 +/- 0.28%. It is concluded that the social factors which may have operated over a period of many centuries in the past have had a significant effect on the population genetics of lethal autosomal recessive genes.

Computer Simulation↗
PubMed2005

Population genetics of Neisseria gonorrhoeae in a high-prevalence community using a hypervariable outer membrane porB and 13 slowly evolving housekeeping genes.

Baltimore, Md., is an urban community with a high prevalence of Neisseria gonorrhoeae. Due to partially protective immune responses, introduction of new strains from other host populations, and exposure of N. gonorrhoeae to antibiotics, the phenotypic and genotypic characteristics of the circulating strains can fluctuate over time. Understanding the overall genetic diversity and population structure of N. gonorrhoeae is essential for informing public health interventions to eliminate this pathogen. We studied gonococci population genetics in Baltimore by analyzing a hypervariable and strongly selected outer membrane porB gene and 13 slowly evolving and presumably neutral housekeeping genes (abcZ, adk, aroE, fumC, gdh, glnA, gnd, pdhC, pgm, pilA, ppk, pyrD, and serC) in 204 isolates collected in 1991, 1996, and 2001 from male and female patients of two public sexually transmitted diseases clinics. Genetic diversity (), recombination (C), growth (g), population structure, and adaptive selection under codon-substitution and amino acid property models were estimated and compared between these two gene classes. Estimates of the F(ST) fixation index and the chi(2) test of sequence absolute frequencies revealed significant temporal substructuring for both gene types. Baltimore's N. gonorrhoeae populations have increased since 1991 as indicated by consistent positive values of g. Female patients showed similar or lower levels of and C than male patients. Within the MLST housekeeping genes, levels of and C ranged from 0.001-0.013 and 0.000-0.018, respectively. Overall recombination seems to be the dominant force driving evolution in these populations. All loci showed amino acid sites and physicochemical properties under adaptive (or positive-destabilizing) selection, rejecting the generally assumed hypothesis of stabilizing selection for these MLST genes. Within the porB gene, protein I B showed higher and C values than protein I A. Directional positive selection possibly mediated by the immune system operates to a significant extent in the protein I sequences, as indicated by the distribution of the positively selected sites in the surface-exposed loops. Thirteen amino acid physicochemical properties seem to drive protein evolution of the PI porins in N. gonorrhoeae.

Amino Acid Sequence↗
PubMed1996

Population genetic study of three VNTR loci (D2S44, D7S22, and D12S11) in five ethnically defined populations of the Indian subcontinent.

Using RFLP (restriction fragment length polymorphism) analysis, we have characterized the genotypic variation of three VNTR (variable number of tandem repeat) loci (D2S44, D7S22, and D12S11) with probes YNH24, g3, and MS43a, respectively, for 288 individuals from 5 genetically well-defined ethnic groups (Brahmins, Maratha, Gujarati Patel, Sinhalese, and Moors) of the Indian subcontinent. The distributions of VNTR alleles at the binned level were examined among the five populations, and the genetic affinities obtained using the VNTR data were compared with serogenetic data on 22 blood group and protein loci previously reported from our laboratory. For classical genetic markers the Sinhalese show slight affinity with the populations of western India. However, the genetic affinity results considerably parallel the results for VNTR loci and 25 combined VNTR/blood group/protein loci, suggesting that the Sinhalese show the least affinity with the populations of western India. These results confirm the findings of a recent study of genetic relationships of the populations of Sri Lanka based on admixture analysis. The concerns regarding whether or not the pattern of genetic variation of VNTR loci at the bin level can be studied using classical population principles are addressed.

Ethnicity↗
PubMed1991

Population genetics of four hypervariable loci.

Populations of white Caucasians, Afro-Caribbeans and Asians residing within the UK have been analysed at 4 different hypervariable loci. A computerised system was used to store and to analyse the data. Simulation experiments were carried out in order to determine whether there was any evidence for population stratification, which would lead to non-independence of allelic distributions.

Alleles↗
PubMed1999

Microgeographic population genetic structure in the northern water snake, Nerodia sipedon sipedon detected using microsatellite DNA loci.

We describe the isolation and genetic characterization of eight microsatellite DNA loci from the northern water snake, Nerodia sipedon sipedon and use these loci to analyse levels of genetic differentiation between local (< 2 km apart) populations of these snakes in Ontario. These loci are variable, with expected heterozygosities ranging from 0.28 to 0.91, and can correctly exclude nonsires in parentage analyses with a high probability (0.998). Population analyses reveal significant deviation from expected heterozygosity levels for one population, probably a result of a null allele(s) at a single locus and small but significant levels of genetic differentiation among all three populations. This demonstrates that microgeographic genetic structure exists in this species, possibly due to limited dispersal.

Alleles↗
PubMed2005

Population genetics of CAPN10 and GPR35: implications for the evolution of type 2 diabetes variants.

A positional cloning study of type 2 diabetes in Mexican Americans identified a region, termed "NIDDM1," on chromosome 2q37 with significant linkage evidence. Haplotype combinations at the calpain-10 gene (CAPN10) within this region were shown to increase diabetes risk in several populations. On the basis of the thrifty genotype hypothesis, variants that increase susceptibility to type 2 diabetes under modern lifestyle conditions provided a survival advantage in past environments by increasing the efficiency of energy use and storage. Here, our goal is to make inferences about the evolutionary forces shaping variation in genes in the NIDDM1 region and to investigate the population genetics models that may underlie the thrifty genotype hypothesis. To this end, we surveyed sequence variation in CAPN10 and in an adjacent gene, G-protein-coupled receptor 35 (GPR35), in four population samples from different ethnic groups. These data revealed two distinct deviations from the standard neutral model in CAPN10, whereas GPR35 variation was largely consistent with neutrality. CAPN10 showed a significant deficit of variation in the haplotype class defined by the derived allele at SNP44, a polymorphism that is significantly associated with diabetes in meta-analysis studies. This suggests that this haplotype class was quickly driven to high frequency by positive natural selection. Interestingly, the derived allele at SNP44 is protective against diabetes. CAPN10 also showed a local excess of polymorphism and linkage disequilibrium decay in intron 13. Simulations show that this pattern may be explained by long-standing balancing selection that maintains multiple selected alleles. Alternatively, it is possible that the local mutation and recombination rates changed since the divergence of human and chimpanzee; this scenario does not require the action of natural selection on intron 13 variation.

Calpain↗
PubMed1999

Cleistogamy in Scutellaria indica (Labiatae): effective mating system and population genetic structure.

Scutellaria indica is a perennial herb with both chasmogamous (CH) and cleistogamous (CL) flowers on the same plant in some populations, and only CL flowers in other populations. Actual seed production by CH and CL flowers was investigated in populations of S. indica. The average seed set of CL flowers was 19 times higher than CH flowers, indicating much greater fertilization success. The CL seeds were also significantly heavier than the CH seeds. However, the resource cost of producing a CH flower was much higher than that of producing a CL flower. The CH flower was approximately seven times larger, and its pollen/ovule ratio was approximately five times higher than flowers. The level and pattern of genetic diversity at both allozyme and random amplified polymorphic DNA (RAPD) levels were consistent with a predominantly selfing system in the species. The average amount of within-population genetic variation was extremely low (A = 1.025, P = 2.36%, HO = 0.001 and HE = 0.008 based on allozyme data, and P = 8.94% and HE = 0.03 based on RAPD data). At the species level, the estimates of total gene diversity (HT) were 0. 101 based on allozyme data and 0.139 based on RAPD data. A very high level of genetic differentiation occurred between populations (allozyme GST = 0.92 and RAPD GST = 0.81). Genetic drift coupled with predominant cleistogamous selfing apparently played the major role in determining the population genetic structure in S. indica. Although the features associated with CH and CL flower and seed production seem to be sufficient for the evolution of complete cleistogamy in S. indica, random fixation of alternative alleles for dimorphic or complete cleistogamy in small populations could maintain the multiple strategy of chasmogamous and cleistogamous reproduction in the species.

DNA Primers↗