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PubMed2006

A general population-genetic model for the production by population structure of spurious genotype-phenotype associations in discrete, admixed or spatially distributed populations.

In linkage disequilibrium mapping of genetic variants causally associated with phenotypes, spurious associations can potentially be generated by any of a variety of types of population structure. However, mathematical theory of the production of spurious associations has largely been restricted to population structure models that involve the sampling of individuals from a collection of discrete subpopulations. Here, we introduce a general model of spurious association in structured populations, appropriate whether the population structure involves discrete groups, admixture among such groups, or continuous variation across space. Under the assumptions of the model, we find that a single common principle--applicable to both the discrete and admixed settings as well as to spatial populations--gives a necessary and sufficient condition for the occurrence of spurious associations. Using a mathematical connection between the discrete and admixed cases, we show that in admixed populations, spurious associations are less severe than in corresponding mixtures of discrete subpopulations, especially when the variance of admixture across individuals is small. This observation, together with the results of simulations that examine the relative influences of various model parameters, has important implications for the design and analysis of genetic association studies in structured populations.

Computer Simulation↗

PubMed2000

The interface between epidemiology and population genetics.

Modern biology increasingly integrates disparate disciplines. Here, Steve Paterson and Mark Viney examine the interface between epidemiology and population genetics. They argue that infection and inheritance can be considered as analogous processes, and that epidemiology and population genetics share many common features. They consider the potential for existing population genetic theory to dissect epidemiological patterns in field studies and they consider other relationships between genetics and epidemiology that provide a research challenge for the future.

Alleles↗

PubMed2006

Mitochondrial genomes of parasitic arthropods: implications for studies of population genetics and evolution.

Over 39000 species of arthropods parasitize humans, domestic animals and wildlife. Despite their medical, veterinary and economic importance, most aspects of the population genetics and evolution of the vast majority of parasitic arthropods are poorly understood. Mitochondrial genomes are a rich source of markers for studies of population genetics and evolution. These markers include (1) nucleotide sequences of each of the 37 mitochondrial genes and non-coding regions; (2) concatenated nucleotide sequences of 2 or more genes; and (3) genomic features, such as gene duplications, gene rearrangements, and changes in gene content and secondary structures of RNAs. To date, the mitochondrial genomes of over 700 species of multi-cellular animals have been sequenced entirely, however, only 24 of these species are parasitic arthropods. Of the mitochondrial genome markers, only the nucleotide sequences of 4 mitochondrial genes, cox1, cob, rrnS and rrnL, have been well explored in population genetic and evolutionary studies of parasitic arthropods whereas the sequences of the other 33 genes, and various genomic features have not. We review current knowledge of the mitochondrial genomes of parasitic arthropods, summarize applications of mitochondrial genes and genomic features in population genetic and evolutionary studies, and highlight prospects for future research.

Animals↗

PubMed1999

Population genetics of the yellow fever mosquito in Trinidad: comparisons of amplified fragment length polymorphism (AFLP) and restriction fragment length polymorphism (RFLP) markers.

Recent development of DNA markers provides powerful tools for population genetic analyses. Amplified fragment length polymorphism (AFLP) markers result from a polymerase chain reaction (PCR)-based DNA fingerprinting technique that can detect multiple restriction fragments in a single polyacrylamide gel, and thus are potentially useful for population genetic studies. Because AFLP markers have to be analysed as dominant loci in order to estimate population genetic diversity and genetic structure parameters, one must assume that dominant (amplified) alleles are identical in state, recessive (unamplified) alleles are identical in state, AFLP fragments segregate according to Mendelian expectations and that the genotypes of an AFLP locus are in Hardy-Weinberg equilibrium (HWE). The HWE assumption is untestable for natural populations using dominant markers. Restriction fragment length polymorphism (RFLP) markers segregate as codominant alleles, and can therefore be used to test the HWE assumption that is critical for analysing AFLP data. This study examined whether the dominant AFLP markers could provide accurate estimates of genetic variability for the Aedes aegypti mosquito populations of Trinidad, West Indies, by comparing genetic structure parameters using AFLP and RFLP markers. For AFLP markers, we tested a total of five primer combinations and scored 137 putative loci. For RFLP, we examined a total of eight mapped markers that provide a broad coverage of mosquito genome. The estimated average heterozygosity with AFLP markers was similar among the populations (0.39), and the observed average heterozygosity with RFLP markers varied from 0.44 to 0.58. The average FST (standardized among-population genetic variance) estimates were 0.033 for AFLP and 0.063 for RFLP markers. The genotypes at several RFLP loci were not in HWE, suggesting that the assumption critical for analysing AFLP data was invalid for some loci of the mosquito populations in Trinidad. Therefore, the results suggest that, compared with dominant molecular markers, codominant DNA markers provide better estimates of population genetic variability, and offer more statistical power for detecting population genetic structure.

Aedes↗

PubMed2005

Population genetic structure of annual and perennial populations of Zostera marina L. along the Pacific coast of Baja California and the Gulf of California.

The Baja California peninsula represents a biogeographical boundary contributing to regional differentiation among populations of marine animals. We investigated the genetic characteristics of perennial and annual populations of the marine angiosperm, Zostera marina, along the Pacific coast of Baja California and in the Gulf of California, respectively. Populations of Z. marina from five coastal lagoons along the Pacific coast and four sites in the Gulf of California were studied using nine microsatellite loci. Analyses of variance revealed significant interregional differentiation, but no subregional differentiation. Significant spatial differentiation, assessed using theta(ST) values, was observed among all populations within the two regions. Z. marina populations along the Pacific coast are separated by more than 220 km and had the greatest theta(ST) (0.13-0.28) values, suggesting restricted gene flow. In contrast, lower but still significant genetic differentiation was observed among populations within the Gulf of California (theta(ST) = 0.04-0.18), even though populations are separated by more than 250 km. This suggests higher levels of gene flow among Gulf of California populations relative to Pacific coast populations. Direction of gene flow was predominantly southward among Pacific coast populations, whereas no dominant polarity in the Gulf of California populations was observed. The test for isolation by distance (IBD) showed a significant correlation between genetic and geographical distances in Gulf of California populations, but not in Pacific coast populations, perhaps because of shifts in currents during El Niño Southern Oscillation (ENSO) events along the Pacific coast.

Analysis of Variance↗

PubMed1992

An optimizing principle of natural selection in evolutionary population genetics.

This paper brings together two themes in evolutionary population genetics theory. The first concerns Fisher's Fundamental Theorem of Natural Selection: a recent interpretation of this theorem claims that it is an exact result, relating to the so-called "partial" increase in mean fitness. The second theme concerns the desire to find an optimality principle in genetic evolution. Such a principle is found here: of all gene frequency changes which lead to the same partial increase in mean fitness as the natural selection gene frequency changes, the natural selection values minimize a generalized distance measure between parent and daughter generation gene frequency values.

Alleles↗

PubMed2004

The effect of the last glacial age on speciation and population genetic structure of the endangered Ethiopian wolf (Canis simensis).

During the last glacial age, Afro-alpine habitats were widespread across the highlands of Ethiopia. A wolf-like canid ancestor is thought to have colonized this expanding habitat and given rise to a new species that was remarkably well adapted to the high altitude environment: the Ethiopian wolf Canis simensis. Here, we address the timing of genetic divergence and examine population genetic history and structure by investigating the distribution of mitochondrial DNA (mtDNA) sequence variation. The pattern of mtDNA variation and geographical distribution indicate an initial population expansion, probably immediately after divergence from the wolf-like ancestor, around 100,000 years ago. The partition of mtDNA haplotypes that followed was most likely the result of habitat reduction and fragmentation at the onset of deglaciation approximately 15,000 years ago. Phylogenetic and geographical associations suggest that the most likely genetic partitioning corresponds to three mountain areas, Arsi/Bale, Wollo/Shoa and Simien/Mt. Guna. Although there is a degree of clustering of haplotypes from both sides of the Rift Valley, the lack of reciprocal monophyly does not support the taxonomic classification of two subspecies. This study highlights the importance of populations north of the Rift Valley for the maintenance of genetic variability within the species and has consequent implications for conservation.

Analysis of Variance↗

PubMed2003

Rhizobium etli and Rhizobium gallicum nodulate common bean (Phaseolus vulgaris) in a traditionally managed milpa plot in Mexico: population genetics and biogeographic implications.

The stability of the genetic structure of rhizobial populations nodulating Phaseolus vulgaris cultivated in a traditionally managed milpa plot in Mexico was studied over three consecutive years. The set of molecular markers analyzed (including partial rrs, glnII, nifH, and nodB sequences), along with host range experiments, placed the isolates examined in Rhizobium etli bv. phaseoli and Rhizobium gallicum bv. gallicum. Cluster analysis of multilocus enzyme electrophoresis and plasmid profile data separated the two species and identified numerically dominant clones within each of them. Population genetic analyses showed that there was high genetic differentiation between the two species and that there was low intrapopulation differentiation of the species over the 3 years. The results of linkage disequilibrium analyses are consistent with an epidemic genetic structure for both species, with frequent genetic exchange taking place within conspecific populations but not between the R. etli and R. gallicum populations. A subsample of isolates was selected and used for 16S ribosomal DNA PCR-restriction fragment length polymorphism analysis, nifH copy number determination, and host range experiments. Plasmid profiles and nifH hybridization patterns also revealed the occurrence of lateral plasmid transfer among distinct multilocus genotypes within species but not between species. Both species were recovered from nodules of the same plants, indicating that mechanisms other than host, spatial, or temporal isolation may account for the genetic barrier between the species. The biogeographic implications of finding an R. gallicum bv. gallicum population nodulating common bean in America are discussed.

Agriculture↗

PubMed2004

Spatial and population genetic structure of microsatellites in white pine.

We evaluated the population genetic structure of seven microsatellite loci for old growth and second growth populations of eastern white pine (Pinus strobus). From each population, located within Hartwick Pines State Park, Grayling, Michigan, USA, 120-122 contiguous trees were sampled for genetic analysis. Within each population, genetic diversity was high and inbreeding low. When comparing these populations, there is a significant, but small (less than 1%), genetic divergence between populations. Spatial distance between populations or timber harvest at the second growth site were reasonable explanations for the observed minor differences in allele frequencies between populations. Spatial autocorrelation analysis suggested that, for the old growth population, weak positive structuring at 15 m fits the isolation by distance model for a neighbourhood size of about 100 individuals. In comparison, genotypes were randomly distributed in the second growth population. Thus, logging may have decreased spatial structuring at the second growth site, suggesting that management practices may be used to alter natural spatial patterns. In addition, the amount of autocorrelation in the old growth population appears to be lower for some of the microsatellites, suggesting higher numbers of rare alleles and that higher mutation rates may have directly affected spatial statistics by reducing structure.

Forestry↗

PubMed1998

The effects of mating probability on the population genetics of nematodes.

We review how constraints on the mating probability of female worms by segregation within individual host guts form a critical element in the parasite population structure of nematodes. We consider the effects of these constraints on the population genetics of nematodes under various assumptions regarding worm competition as reflected in the relationship between the abundance of a certain genotype within the gut and the probability of reproductive success. The consequences for the emergence of resistance to drugs and immunotherapy and implications for host-parasite coevolution are discussed. We also review evidence for genetic heterogeneity in parasite populations as a necessary prerequisite for the applicability of mating probability models designed to assess the population genetics of nematodes.

Animals↗

PubMed2006

Ecological factors influence population genetic structure of European grey wolves.

Although the mechanisms controlling gene flow among populations are particularly important for evolutionary processes, they are still poorly understood, especially in the case of large carnivoran mammals with extensive continuous distributions. We studied the question of factors affecting population genetic structure in the grey wolf, Canis lupus, one of the most mobile terrestrial carnivores. We analysed variability in mitochondrial DNA and 14 microsatellite loci for a sample of 643 individuals from 59 localities representing most of the continuous wolf range in Eastern Europe. We tested an array of geographical, historical and ecological factors to check whether they may explain genetic differentiation among local wolf populations. We showed that wolf populations in Eastern Europe displayed nonrandom spatial genetic structure in the absence of obvious physical barriers to movement. Neither topographic barriers nor past fragmentation could explain spatial genetic structure. However, we found that the genetic differentiation among local populations was correlated with climate, habitat types, and wolf diet composition. This result shows that ecological processes may strongly influence the amount of gene flow among populations. We suggest natal-habitat-biased dispersal as an underlying mechanism linking population ecology with population genetic structure.

Animals↗

PubMed1980

Population genetic basis of the evolutionary change.

Short introduction is given to population genetic treatment of the evolutionary change. The evolutionary change in the population is based upon the appearance (by mutation or immigration) of new genetic information. The proportion of this new information may increase or decrease by selection and/or random processes. The aid of population genetics is to formulate models in order to understand the essence of the evolutionary change. Some simple deterministic and stochastic single-locus models are quoted from elementary population genetic theory.

Biological Evolution↗

PubMed2005

Development of microsatellite markers for Japanese scallop (Mizuhopecten yessoensis) and their application to a population genetic study.

The Japanese scallop (Mizuhopecten yessoensis) is one of the main fishery products in Japan, but with the expansion of culture operations of the Japanese scallop, various problems have been encountered including high mortality, poor growth, poor seed production, and so on. Moreover, there is concern that many years of cultivation may have affected the genetic structure of the scallop population. To approach these problems and concerns, we developed microsatellite markers as a molecular tool for population genetic studies. By using 4 microsatellite markers as well as a mitochondrial marker, we investigated the genetic structure of samples from the islands of Hokkaido (14 populations) and Honshu (Tohoku, 3 populations) in Japan, and south Primorye (4 populations) in Russia. All the populations sampled had high genetic diversity (average expected heterozygosity, 0.7011 to 0.7622; haplotype diversity, 0.6090 to 0.8848), and almost all showed a tendency of homozygote excess, which was significant in 2 populations. Hierarchical analysis of molecular variance tests based on the microsatellite and mitochondrial markers indicated that the 3 geographic regions were genetically divergent from one another, with little evidence of divergence within regions. Homogeneity in allele frequency distributions between natural and cultured scallops and allele frequency stability over a period of 2 decades indicated that the culturing operations have probably not had a substantial effect on the genetic structure of the populations.

Animals↗

PubMed2006

Temporal trends in gonococcal population genetics in a high prevalence urban community.

Molecular evolutionary studies can provide insights into the spread of infectious diseases and inform infection control measures. We performed a population genetic analysis of gonococcal isolates obtained over a 15-year interval in Baltimore, MD, where gonorrhea is highly prevalent. Categorical analysis of genetic differentiation revealed temporal structuring of the gonococcal population. The use of a new method to determine the historical demography of Neisseria gonorrhoeae from sequence data showed a strong correlation with trends in the number of reported cases of N. gonorrhoeae. The historical trends may also reflect the influence of social and demographic factors and the impact of antimicrobial resistance on the molecular epidemiology of gonorrhea in Baltimore over the past 2 decades. The strong correlation between the population genetic inferences over the last 20 years and the demographic data collected over the same time period demonstrates the utility of these approaches for the accurate inference of complex population dynamics using multilocus sequence data. The real time application of population genetic analysis can provide sentinel data on gonococcal prevalence, antibiotic resistance patterns and changing epidemiology of gonococcal infections.

Adult↗

PubMedDate not supplied

Population genetics of Lithuanians.

The primary objective of this article was to overview the present-day knowledge on genetic features of the Lithuanian population. Genetic differentiation within the Lithuanian population and the relationship between Lithuanians and other European populations was analysed by means of blood groups, serum protein polymorphisms and DNA markers including mtDNA. The results of the research have shown small differences between present-day Lithuanian ethnolinguistic groups, which probably go back to the prehistoric Baltic tribal structure. The Baltic peoples show a mixture of eastern and western genetic traits, e.g. a high frequency of the blood group B combined with a very high frequency of the Rh-negative blood group. Studies of the Baltic 'tribal gene' LWb indicate the presence of a considerable Baltic admixture in the neighbouring Finno-Ugric and Slavic populations.

Ethnicity↗

PubMed2000

The evolution of RNA viruses: A population genetics view.

RNA viruses are excellent experimental models for studying evolution under the theoretical framework of population genetics. For a proper justification of this thesis we have introduced some properties of RNA viruses that are relevant for studying evolution. On the other hand, population genetics is a reductionistic theory of evolution. It does not consider or make simplistic assumptions on the transformation laws within and between genotypic and phenotypic spaces. However, such laws are minimized in the case of RNA viruses because the phenotypic space maps onto the genotypic space in a much more linear way than on higher DNA-based organisms. Under experimental conditions, we have tested the role of deleterious and beneficial mutations in the degree of adaptation of vesicular stomatitis virus (VSV), a nonsegmented virus of negative strand. We also have studied how effective population size, initial genetic variability in populations, and environmental heterogeneity shapes the impact of mutations in the evolution of vesicular stomatitis virus. Finally, in an integrative attempt, we discuss pros and cons of the quasispecies theory compared with classic population genetics models for haploid organisms to explain the evolution of RNA viruses.

Biological Evolution↗

PubMed2001

Mississippians in motion? A population genetic analysis of interregional gene flow in West-Central Illinois.

Population genetic and biological distance studies of Late Woodland and Mississippian populations from west-central Illinois have provided insight into a number of prehistoric demographic processes at the regional level. However, a formal analysis of diachronic interregional gene flow has not been attempted within a population genetics framework. In this study, cranial measurements of 489 individuals from 13 skeletal samples across the central and lower Illinois valleys are analyzed to address two central issues. First, the potential impact of Cahokia's decline and associated demographic events on the population structure of west-central Illinois Mississippians is examined. Second, the Mississippian and Late Woodland interregional migration patterns are compared to determine if geographic and/or cultural boundaries affected local population structure. Following Relethford and Blangero ([1990] Hum Biol 62:5-25), R matrix methods are utilized to calculate observed and expected phenotypic variances, minimum genetic distances, and F(ST) values in order to detect patterns of differential external gene flow over time. The results indicate that Late Woodland peoples had a larger sphere of biological interaction than Mississippians. In the Mississippian period, culturally imposed barriers paralleled geographic boundaries between regions such that the geographic distribution of biological variation closely adheres to a classic isolation-by-distance model. Further, intraregional population movement was a more significant contributor to Mississippian population structure than interregional gene flow, even during periods of sociopolitical strife. Small-scale intraregional shuffling is consistent with other recent studies of prehistoric Mississippian biocultural and geographic landscapes in the southeast United States.

Adolescent↗

PubMed2004

Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex.

Accessory gland proteins are a major component of Drosophila seminal fluid. These proteins have a variety of functions and may be subject to sexual selection and/or antagonistic evolution between the sexes. Most population genetic data from these proteins are from D. melanogaster and D. simulans. Here, we extend the population genetic analysis of Acp genes to the other simulans complex species, D. mauritiana and D. sechellia. We sequenced population samples of seven Acp's from D. mauritiana, D. sechellia, and D. simulans. We investigated the population genetics of these genes on individual simulans complex lineages and compared Acp polymorphism and divergence to polymorphism and divergence from a set of non-Acp loci in the same species. Polymorphism and divergence data from the simulans complex revealed little evidence for adaptive protein evolution at individual loci. However, we observed a dramatically inflated index of dispersion for amino acid substitutions in the simulans complex at Acp genes, but not at non-Acp genes. This pattern of episodic bursts of protein evolution in Acp's provides the strongest evidence to date that the population genetic mechanisms driving Acp divergence are different from the mechanisms driving evolution at most Drosophila genes.

Animals↗