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PubMed2000

Population structure in admixed populations: effect of admixture dynamics on the pattern of linkage disequilibrium.

Gene flow between genetically distinct populations creates linkage disequilibrium (admixture linkage disequilibrium [ALD]) among all loci (linked and unlinked) that have different allele frequencies in the founding populations. We have explored the distribution of ALD by using computer simulation of two extreme models of admixture: the hybrid-isolation (HI) model, in which admixture occurs in a single generation, and the continuous-gene-flow (CGF) model, in which admixture occurs at a steady rate in every generation. Linkage disequilibrium patterns in African American population samples from Jackson, MS, and from coastal South Carolina resemble patterns observed in the simulated CGF populations, in two respects. First, significant association between two loci (FY and AT3) separated by 22 cM was detected in both samples. The retention of ALD over relatively large (>10 cM) chromosomal segments is characteristic of a CGF pattern of admixture but not of an HI pattern. Second, significant associations were also detected between many pairs of unlinked loci, as observed in the CGF simulation results but not in the simulated HI populations. Such a high rate of association between unlinked markers in these populations could result in false-positive linkage signals in an admixture-mapping study. However, we demonstrate that by conditioning on parental admixture, we can distinguish between true linkage and association resulting from shared ancestry. Therefore, populations with a CGF history of admixture not only are appropriate for admixture mapping but also have greater power for detection of linkage disequilibrium over large chromosomal regions than do populations that have experienced a pattern of admixture more similar to the HI model, if methods are employed that detect and adjust for disequilibrium caused by continuous admixture.

Africa↗
PubMed2005

Genetic variation and population structure in remnant populations of black rhinoceros, Diceros bicornis, in Africa.

Black rhinoceros (Diceros bicornis) are one of the most endangered mammal species in Africa, with a population decline of more than 96% by the end of the last century. Habitat destruction and encroachment has resulted in fragmentation of the remaining populations. To assist in conservation management, baseline information is provided here on relative genetic diversity and population differentiation among the four remaining recognized subspecies. Using microsatellite data from nine loci and 121 black rhinoceros individuals, and comparing the results with those of other African species affected in similar ways, Diceros bicornis michaeli retained the most genetic diversity (heterozygosity 0.675) compared with Diceros bicornis minor (0.459) and Diceros bicornis bicornis (0.505), suggesting that the duration of the known bottlenecks in these populations has only had a limited impact on diversity. Comparable and moderate degrees of population differentiation were found between D. b. minor, D. b. bicornis and D. b. michaeli. Results from the single sample available of the most endangered subspecies, Diceros bicornis longipes, showed the least diversity of all individuals examined. This information should assist conservation management decisions, especially those affecting population viability assessments and selection of individuals for translocations, and will also facilitate subspecies identification for ex situ individuals of uncertain origin.

Africa, Eastern↗
PubMed1978

Population structure in Kanoya population, Japan.

The mean inbreeding coefficients found for Minami-cho (366 couples) and Shinsei-cho (511 couples) were 0.00307 and 0.00191, respectively. The mean inbreeding coefficient decreased and the mean marital distance increased as the year of marriage becomes more recent. The mean distances and their standard deviations between birthplaces of mates, father-offspring, mother-offspring, and sibs are 69.05 +/- 229.64, 73.09 +/- 246.66, 49.81 +/- 158.43, and 39.53 +/- 159.51 km, respectively, at Minami-cho. These values are 188.45 +/- 387.05, 187.79 +/- 562.59, 148.26 +/- 326.35, and 73.93 +/- 225.92 km, respectively, at Shinsei-cho. The dimensionality of migration is closest to one dimension.

Consanguinity↗
PubMed2002

Effective population size and population subdivision in demographically structured populations.

A fast-timescale approximation is applied to the coalescent process in a single population, which is demographically structured by sex and/or age. This provides a general expression for the probability that a pair of alleles sampled from the population coalesce in the previous time interval. The effective population size is defined as the reciprocal of twice the product of generation time and the coalescence probability. Biologically explicit formulas for effective population size with discrete generations and separate sexes are derived for a variety of different modes of inheritance. The method is also applied to a nuclear gene in a population of partially self-fertilizing hermaphrodites. The effects of population subdivision on a demographically structured population are analyzed, using a matrix of net rates of movement of genes between different local populations. This involves weighting the migration probabilities of individuals of a given age/sex class by the contribution of this class to the leading left eigenvector of the matrix describing the movements of genes between age/sex classes. The effects of sex-specific migration and nonrandom distributions of offspring number on levels of genetic variability and among-population differentiation are described for different modes of inheritance in an island model. Data on DNA sequence variability in human and plant populations are discussed in the light of the results.

Animals↗
PubMed2002

Pseudomonas aeruginosa displays an epidemic population structure.

Bacteria can have population structures ranging from the fully sexual to the highly clonal. Despite numerous studies, the population structure of Pseudomonas aeruginosa is still somewhat contentious. We used a polyphasic approach in order to shed new light on this issue. A data set consisting of three outer membrane (lipo)protein gene sequences (oprI, oprL and oprD), a DNA-based fingerprint (amplified fragment length polymorphism), serotype and pyoverdine type of 73 P. aeruginosa clinical and environmental isolates, collected across the world, was analysed using biological data analysis software. We observed a clear mosaicism in the results, non-congruence between results of different typing methods and a microscale mosaic structure in the oprD gene. Hence, in this network, we also observed some clonal complexes characterized by an almost identical data set. The most recent clones exhibited serotypes O1, 6, 11 and 12. No obvious correlation was observed between these dominant clones and habitat or, with the exception of some recent clones, geographical origin. Our results are consistent with, and even clarify, some seemingly contradictory results in earlier epidemiological studies. Therefore, we suggest an epidemic population structure for P. aeruginosa, comparable with that of Neisseria meningitidis, a superficially clonal structure with frequent recombinations, in which occasionally highly successful epidemic clones arise.

Alleles↗
PubMed2005

Effects of population structure on genetic association studies.

Population-based case-control association is a promising approach for unravelling the genetic basis of complex diseases. One potential problem of this approach is the presence of population structure in the samples. Using the Collaborative Study on the Genetics of Alcoholism (COGA) single-nucleotide polymorphism (SNP) datasets, we addressed three questions: How can the degree of population structure be quantified, and how does the population structure affect association studies? How accurate and efficient is the genomic control method in correcting for population structure? The amount of population structure in the COGA SNP data was found to inflate the p-value in association tests. Genomic control was found to be effective only when the appropriate number of markers was used in the control group in order to correctly calibrate the test. The approach presented in this paper could be used to select the appropriate number of markers for use in the genomic control method of correcting population structure.

Databases, Genetic↗
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↗
PubMed2006

Population structure and gene flow among wild populations of the black muntjac (Muntiacus crinifrons) based on mitochondrial DNA control region sequences.

The black muntjac (Muntiacus crinifrons) is a rare species endemic to China and its current distribution is confined to partial mountain ranges in eastern China. To assess the population structure and gene flow among the extant populations, we sequenced a portion of the mitochondrial control region (424 bp) for 47 samples collected from its current three large populations (Huangshan, Tiammushan and Suichang). A total of 18 unique haplotypes were defined based on 22 polymorphic sites. Of these haplotypes, 15 ones were population-specific and only one haplotype was shared among the three populations. Significant genetic differentiation was detected between Suichang and Huangshan populations (ø(ST)=0.1677, P<0.001) or between Suichang and Tianmushan populations (ø(ST)=0.2002, P<0.001), indicating that the Suichang population may be spatially structured from other two populations along matriline. The Mantel test revealed that this significant differentiation was not driven by geographic distance (P=0.14), implying that genetic divergence of Suichang population might result from recent human disturbances. Phylogenetic analyses suggested the mitochondrial control region haplotypes were split into two well divergent clades (Clade I and Clade II). Interestingly, the two distinct haplotype clades were found to coexist in Suichang area. The nested clade analysis revealed a significant phylogeographic structure among the black muntjac populations (total cladogram: chi2=18.68; P<0.001), which was inferred to result from past fragmentation followed by range expansion. The population expansion was supported by the analysis of mismatch distribution and the tests of neutrality. Therefore, we suggest that the coexistence of distinct haplotypes in Suichang population was induced by historical population expansion after fragmentation and that the current genetic differentiation should be attributed to the reduction of female-mediated gene flow due to recent habitat fragmentation and subsequent loss.

Animals↗
PubMed1999

Population structure of North American beluga whales (Delphinapterus leucas) based on nuclear DNA microsatellite variation and contrasted with the population structure revealed by mitochondrial DNA variation

Beluga whales (Delphinapterus leucas) in North American waters migrate seasonally between wintering areas in broken pack ice and summering locations in estuaries and other open water areas in the Arctic and sub-Arctic. Results from our previous investigation of beluga whale mitochondrial DNA (mtDNA) revealed genetic heterogeneity among beluga from different summering locations that was interpreted as representing a high degree of summering site philopatry. However, mtDNA is maternally inherited and does not reflect mating that may occur among beluga from different summering locations in wintering areas or during annual migrations. To test the possibility that breeding occurs among beluga from different summering locations, genetic variability at five nuclear DNA (nDNA) microsatellite loci was examined in the same animals tested in the mtDNA study. Beluga samples (n = 640) were collected between 1984 and 1994 from 24 sites across North America, mostly during the summer. Whales from the various sites were categorized into eight summering locations as identified by mtDNA analysis, as well as four hypothesized wintering areas: Bering Sea, Hudson Strait (Hudson Strait, Labrador Sea, southwest Davis Strait), Baffin Bay (North Water, east Davis Strait), and St Lawrence River. Microsatellite allele frequencies indicated genetic homogeneity among animals from summering sites believed to winter together but differentiation among whales from some of the wintering areas. In particular, beluga from western North America (Bering Sea) were clearly distinguished from beluga from eastern North America (Hudson Strait, Baffin Bay, and St Lawrence River). Based upon the combined data set, the population of North American beluga whales was divided into two evolutionarily significant units. However, the population may be further subdivided into management units to reflect distinct groups of beluga at summering locations.

Journal Article↗
PubMed2026

treestructure: an R package to detect population structure in phylogenetic trees.

MOTIVATION: How population structure can shape genetic diversity is a longstanding problem in population genetics. While the use of geographic locations, when available, can help answer some of these questions, it is still difficult to determine population structure when such metadata are not available or when the potential population structure is not easily observed. Here, we present an updated version of treestructure, an R package that implements a statistical test based on coalescent theory to detect unobserved population structure in a time-scaled phylogenetic tree. AVAILABILITY: treestructure is available at CRAN at https://cloud.r-project.org/web/packages/treestructure/ and at https://emvolz-phylodynamics.github.io/treestructure/.

Phylogeny↗
PubMed1985

[A model of structural transition based on the molecular-type population structure theorem].

The author presents a model of structural transition based on a theorem of molecular-type population structure. "Household or family has been sometimes called [a] demographic molecule, when compared with the unit of ordinary population, i.e., a person, which in turn [is called a] demographic atom. Molecular population structure is defined by the author as the age structure of the population composed of people included in certain [sorts] of molecules. The molecular age structure is basically represented by matrices whose elements...are the numbers of people aged i whose other member person in the same molecule, for example mother, is aged j." (summary in ENG)

Age Distribution↗
PubMed1998

Analysis of population structure in autotetraploid species.

Population structure parameters commonly used for diploid species are reexamined for the particular case of tetrasomic inheritance (autotetraploid species). Recurrence equations that describe the evolution of identity probabilities for neutral genes in an "island model" of population structure are derived assuming tetrasomic inheritance. The expected equilibrium value of FST is computed. In contrast to diploids, the correlation of genes between individuals within populations with respect to genes between populations (FST) may vary among loci due to the particular segregation patterns expected under tetrasomic inheritance and is consequently inappropriate for estimating demographic parameters in such populations. We thus define a new parameter (rho) and derive its relationship with Nm. This relationship is shown to be independent from both the selfing rate and the proportion of double reduction. Finally, the statistical procedure required to evaluate these parameters using data on gene frequencies distribution among autotetraploid populations is developed.

Chromosome Segregation↗
PubMed2001

The population structure of Neisseria meningitidis serogroup A fits the predictions for clonality.

The population structure of Neisseria meningitidis is supposedly epidemic according to. The model predicts that linkage disequilibrium in N. meningitidis populations is only temporary and arises due to the outgrowth of highly successful clonal genotypes from an essentially sexual population. These clones should disappear after a few years because of frequent recombination. In contrast, multilocus enzyme electrophoresis (MLEE) data had previously been interpreted as showing that serogroup A meningococci are truly clonal and possess only limited genetic variability (Wang et al., 1992). The two interpretations are contradictory. In order to elucidate the true population structure of serogroup A meningococci, we analyzed data for a representative group of 84 serogroup A isolates obtained by MLEE, random amplified polymorphic DNA (RAPD) and multilocus sequence typing (MLST). Analysis of linkage disequilibrium and bootstrap analyses of cluster analysis showed a strongly structured population with highly significant linkage disequilibrium. This was not due to the overrepresentation of certain genotypes, in contrast to the expectations for an epidemic population. The analyses identify two main clades, within each of which linkage disequilibrium was also highly significant, thus, excluding a cryptic speciation model. These observations support a population structure based on clonal evolution, in which clones are much more stable than expected for epidemic clonality. We propose that serogroup A meningococci may possess a different population structure from other serogroups of Neisseria meningitidis.

Clone Cells↗
PubMed1996

Population structure and genetic differentiation among 16 tribal populations of central India.

Genetic polymorphisms for six blood groups, three red cell enzymes, three serum proteins, and hemoglobin were examined in sixteen central Indian tribal populations. Nine of the tribes belonged to Orissa, five to Madhya Pradesh, and two to Maharashtra. Eleven tribes spoke the Dravidian language, three Indo-Ayran, and two the language of the Austro-Asiatic families. The population structure of these tribal populations was analyzed at the inter- and intrastate and linguistic levels, using data for 13 genetic systems (38 alleles or haplotypes). Nine of the 13 loci showed significant heterogeneity in the 16 tribes, and the pattern of heterogeneity was also discernible in the different states and in the Dravidian-speaking tribes. As expected, the extent of genetic differentiation or gene diversity was the highest so far reported from central India. The mean FIS and HS for each locus in the different state, linguistic, and total tribal groups were consistently higher than the FST and GST values, respectively, showing that the genetic structure of each tribe is highly influenced by inbreeding. In a genetic affinity analysis by genetic distance the Indo-Aryan and Austro-Asiatic language groups showed little affinity with each other, although there was some tendency toward geographic affinity. The present analysis indicates that, in addition to genetic drift, gene flow, and selection, the genetic structure of the populations of central India is also highly influenced by sociocultural adaptation and inbreeding.

Ethnicity↗
PubMed2003

Genetic population structure of the white sifaka (Propithecus verreauxi verreauxi) at Beza Mahafaly Special Reserve, southwest Madagascar (1992-2001).

Gene flow within and between social groups is contingent on behaviourally mediated patterns of mating and dispersal. To understand how these patterns affect the genetic structure of primate populations, long-term data are required. In this study, we analyse 10 years of demographic and genetic data from a wild lemur population (Propithecus verreauxi verreauxi) at Beza Mahafaly Special Reserve, southwest Madagascar. Our goal is to specify how patterns of mating and dispersal determine kinship and genetic diversity among animals in the population. Specifically, we use microsatellite, parentage, and census data to obtain estimates of genetic subdivision (FST), within group homozygosity (FIS), and relatedness (r) within and among social groups in the population. We analyse different classes of individuals (i.e. adults, offspring, males, females) separately in order to discern which classes most strongly influence aspects of population structure. Microsatellite data reveal that, across years, offspring are consistently more heterozygous than expected within social groups (FIS mean = -0.068) while adults show both positive and negative deviations from expected genotypic frequencies within groups (FIS mean = 0.003). Offspring cohorts are more genetically subdivided than adults (FST mean = 0.108 vs. 0.052) and adult females are more genetically subdivided than adult males (FST mean = 0.098 vs. 0.046). As the proportion of females in social groups increases, the proportion of offspring sired by resident males decreases. Offspring are characterized by a heterozygote excess as resident males (vs. nonresident males) sire the majority of offspring within groups. We link these genetic data to patterns of female philopatry, male dispersal, exogamy, and offspring sex-ratio. Overall, these data reveal how mating and dispersal tactics influence the genetic population structure in this species.

Animals↗
PubMed2006

A non-parametric approach to population structure inference using multilocus genotypes.

Inference of population structure from genetic markers is helpful in diverse situations, such as association and evolutionary studies. In this paper, we describe a two-stage strategy in inferring population structure using multilocus genotype data. In the first stage, we use dimension reduction methods such as singular value decomposition to reduce the dimension of the data, and in the second stage, we use clustering methods on the reduced data to identify population structure. The strategy has the ability to identify population structure and assign each individual to its corresponding subpopulation. The strategy does not depend on any population genetics assumptions (such as Hardy-Weinberg equilibrium and linkage equilibrium between loci within populations) and can be used with any genotype data. When applied to real and simulated data, the strategy is found to have similar or better performance compared with STRUCTURE, the most popular method in current use. Therefore, the proposed strategy provides a useful alternative to analyse population data.

Cluster Analysis↗
PubMed2005

Conservation implications of complex population structure: lessons from the loggerhead turtle (Caretta caretta).

Complex population structure can result from either sex-biased gene flow or population overlap during migrations. Loggerhead turtles (Caretta caretta) have both traits, providing an instructive case history for wildlife management. Based on surveys of maternally inherited mtDNA, pelagic post-hatchlings show no population structure across the northern Atlantic (phi(ST) < 0.001, P = 0.919), subadults in coastal habitat show low structure among locations (phi(ST) = 0.01, P < 0.005), and nesting colonies along the southeastern coast of the United States have strong structure (phi(ST) = 0.42, P < 0.001). Thus the level of population structure increases through progressive life history stages. In contrast, a survey of biparentally inherited microsatellite DNA shows no significant population structure: R(ST) < 0.001; F(ST) = 0.002 (P > 0.05) across the same nesting colonies. These results indicate that loggerhead females home faithfully to their natal nesting colony, but males provide an avenue of gene flow between regional nesting colonies, probably via opportunistic mating in migratory corridors. As a result, all breeding populations in the southeastern United States have similar levels of microsatellite diversity (H(E) = 0.70-0.89), whereas mtDNA haplotype diversity varies dramatically (h = 0.00-0.66). Under a conventional interpretation of the nuclear DNA data, the entire southeastern United States would be regarded as a single management unit, yet the mtDNA data indicate multiple isolated populations. This complex population structure mandates a different management strategy at each life stage. Perturbations to pelagic juveniles will have a diffuse impact on Atlantic nesting colonies, mortality of subadults will have a more focused impact on nearby breeding populations, and disturbances to adults will have pinpoint impact on corresponding breeding populations. These findings demonstrate that surveys of multiple life stages are desirable to resolve management units in migratory marine species.

Analysis of Variance↗