Multilocus Linkage Disequilibrium Research Articles

Extensive microsatellite diversity in the human malaria parasite Plasmodium vivax

The population structure of Plasmodium vivax remains elusive. The markers of choice for large-scale population genetic studies of eukaryotes, short tandem repeats known as microsatellites, have been recently reported to be less polymorphic in P. vivax. Here we investigate the microsatellite diversity and geographic structure in P. vivax, at both local and global levels, using 14 new markers consisting of tri- or tetranucleotide repeats. The local-level analysis, which involved 50 field isolates from Sri Lanka, revealed unexpectedly high diversity (average virtual heterozygosity [HE], 0.807) and significant multilocus linkage disequilibrium in this region of low malaria endemicity. Multiple-clone infections occurred in 60% of isolates sampled in 2005. The global-level analysis of field isolates or monkey-adapted strains identified 150 unique haplotypes among 164 parasites from four continents. Individual P. vivax isolates could not be unambiguously assigned to geographic populations. For example, we found relatively low divergence among parasites from Central America, Africa, Southeast Asia and Oceania, but substantial differentiation between parasites from the same continent (South Asia and Southeast Asia) or even from the same country (Brazil). Parasite relapses, which may extend the duration of P. vivax carriage in humans, are suggested to facilitate the spread of strains across continents, breaking down any pre-existing geographic structure.

Population Genetic Variation and Structure of the Invasive Weed Mikania micrantha in Southern China: Consequences of Rapid Range Expansion

Invasive plants such as Mikania micrantha provide valuable opportunities for studying population genetic consequences of rapid range expansion. Twenty-eight populations of M. micrantha throughout its introduced range in southern China were examined by using intersimple sequence repeat markers. Population genetic parameters were estimated by Bayesian approaches as well as conventional methods. Bottleneck signature, multilocus linkage disequilibrium, character compatibility, and cluster analyses were conducted to assay the factors that may act to shape population variability. High levels of genetic variation and differentiation were detected in the introduced populations of M. micrantha. All populations experienced severe bottlenecks. Most of them demonstrated significant linkage disequilibrium and matrix compatibility. Populations were mainly clustered into 2 groups, and those from different regions intermingled in the unweighted pair group method with arithmetic mean (UPGMA) dendrogram. No geographical signature was found in the pattern of population genetic variation. This research indicates that during M. micrantha invasion, multiple introductions mitigated the loss of genetic variation associated with bottlenecks. Nonetheless, bottlenecks enhanced the population differentiation. Human-mediated long-distance dispersal events of seeds or propagules explain the lack of geographic structure in genetic variation. Although asexual reproduction is the predominant mating mode in M. micrantha, it has little effect on the population genetic composition.

Multilocus sequence typing (MLST) reveals high genetic diversity and clonal population structure of the toxic cyanobacterium Microcystis aeruginosa

Microcystis aeruginosa is one of the most prevalent bloom-forming cyanobacteria and has been the cause of increasing public health concern due to the production of hepatotoxins (microcystins). To investigate the genetic diversity, clonality and evolutionary genetic background with regard to the toxicity of M. aeruginosa, a multilocus sequence typing (MLST) scheme was developed, based on seven selected housekeeping loci (ftsZ, glnA, gltX, gyrB, pgi, recA and tpi). Analysis of a collection of 164 isolates from Japan and other countries identified 79 unique sequence types (STs), revealing a high level of genetic diversity (H=0.951). Although recombination between loci was indicated to be substantial by Shimodaira-Hasegawa (SH) tests, multilocus linkage disequilibrium analyses indicated that recombination between strains probably occurs at some frequency but not to the extent at which alleles are associated randomly, suggesting that the population structure of M. aeruginosa is clonal. Analysis of subsets of strains also indicated that the clonal population structure is maintained even in a local population. Phylogenetic analysis based on the concatenated sequences of seven MLST loci demonstrated that microcystin-producing genotypes are not monophyletic, providing further evidence for the gain and loss of toxicity during the intraspecific diversification of M. aeruginosa. However, toxic strains are genetically distinct from non-toxic strains in MLST allelic profiles, and it was also shown that non-toxic strains harbouring toxin genes fall into a single monophyletic clade, except for one case. These results suggest that the toxicity of M. aeruginosa is relatively stable in the short term, and therefore can be unequivocally characterized by MLST. The MLST scheme established here will be of great help for future detailed population genetic studies of M. aeruginosa.

Population Genetic Structure of Septoria passerinii in Northern Great Plains Barley

ABSTRACT The genetic structure of Septoria passerinii from nine field populations was examined at several scales (within lesions, among lesions in a leaf, among leaves in a field, and among fields in North Dakota and western Minnesota) by using amplified fragment length polymorphism (AFLP) markers. A total of 390 isolates were sampled from seven barley fields located in North Dakota and two barley fields located nearby in western Minnesota in 2003 and 2004. Based on 57 polymorphic AFLP markers, AFLP DNA fingerprints identified 176 different genotypes among 390 (non-clone-corrected) isolates in nine different fields. In two intensively sampled sites, ND16 (Williston, ND) and ND17 (Langdon, ND), only one to four different genotypes were found within a lesion. A higher level of genetic and genotypic diversity was found within a leaf in which six to nine different genotypes were found from lesions on a leaf. The genetic diversity within a leaf was similar to the genetic diversity within a field. The average genetic diversity (H) within a field across all AFLP loci was approximately 0.3, except at site ND12 (Carrington, ND) where it was 0.16. Genotypic diversity was high in all populations, and with the exception of ND15 (Rothsay, MN), very low multilocus linkage disequilibrium values ( r(d)) were found in all populations. The population differentiation, G(ST), was relatively high (G(ST) = 0.238) among the nine populations due to the high G(ST) in ND12, ND14 (Twin Valley, MN), and ND15. Population differentiation without those three populations was 0.09. A lack of correlation between geographical distance and genetic distance was found, suggesting the potential for a high level of gene flow between different geographical regions. The population genetic structure described in this study for S. passerinii in North Dakota and western Minnesota is consistent with that of a sexually reproducing fungus.

Molecular biodiversity in the moss Leptodon smithii (Neckeraceae) in relation to habitat disturbance and fragmentation

Bryophytes seem particularly suitable to investigate genetic diversity in relation to habitat disturbance due to their large employment as bioindicators and to the recent application of molecular markers to moss population studies. Genetic variation and structure were analysed in seven urban, extraurban and remote populations of Leptodon smithii, an epiphytic moss of Quercus ilex, a phanerogamic species of Mediterranean climax vegetation. A total of 210 individual shoots were DNA extracted and amplified with internal simple sequence repeat (ISSR) primers, and 54 haplotypes were identified. An uneven distribution of haplotype number and frequencies was observed among sites, with a higher number of haplotypes and more homogeneous haplotype frequencies in the extraurban/remote populations. Molecular diversity indices were overall higher in the extraurban sites than in the urban ones. Multilocus linkage disequilibrium values were in line with the occurrence of sexual/asexual reproduction in the seven populations. The isolation-by-distance model was not supported by Mantel test among sites; however, within-population fixation index (F(ST)) highlighted a clear relation between genetic and physic distances among trees, suggesting a limited dispersal range for L. smithii's spores. The genetic structure was mainly affected by population size, wood structure and extent, and genetic drift consequent to habitat fragmentation and human-induced disturbance.

European Mathematical Genetics Meeting, Heidelberg, Germany, 12th–13th April 2007

European Mathematical Genetics Meeting, Heidelberg, Germany, 12^th–13^th April 2007

Prediction of multi-locus inbreeding coefficients and relation to linkage disequilibrium in random mating populations

An algorithm to predict the level of identity by descent simultaneously at multiple loci is presented, which can in principle be extended to any number of loci. The model assumes a random mating population, with random association of haplotypes. The relationship is shown between coefficients of multi-locus identity or non-identity by descent and moments of multi-locus linkage disequilibrium. Thus, these moments can be computed from the multilocus identity or, using algorithms derived previously to predict the disequilibria moments, vice-versa. The results can be applied to predict multi-locus identity in, for example, gene mapping.

Population Structure and Transmission Dynamics ofPlasmodium vivaxin Rural Amazonia

Understanding the genetic structure of malaria parasites is essential to predict how fast some phenotypes of interest originate and spread in populations. In the present study, we used highly polymorphic microsatellite markers to analyze 74 Plasmodium vivax isolates, which we collected in cross-sectional and longitudinal surveys performed in an area of low malaria endemicity in Brazilian Amazonia, and to explore the transmission dynamics of genetically diverse haplotypes or strains. P. vivax populations are more diverse and more frequently comprise multiple-clone infections than do sympatric Plasmodium falciparum isolates, but these features paradoxically coexist with high levels of inbreeding, leading to significant multilocus linkage disequilibrium. Moreover, the high rates of microsatellite haplotype replacement that we found during 15 months of follow-up most likely do not result from strong diversifying selection. We conclude that the small-area genetic diversity in P. vivax populations under low-level transmission is not severely constrained by the low rates of effective meiotic recombination, with clear public health implications.

Genetic structure of the widespread and common Mediterranean bryophyte Pleurochaete squarrosa (Brid.) Lindb. (Pottiaceae) — evidence from nuclear and plastidic DNA sequence variation and allozymes

The Mediterranean Basin as one the world's most biologically diverse regions provides an interesting area for the study of plant evolution and spatial structure in plant populations. The dioecious moss Pleurochaete squarrosa is a widespread and common bryophyte in the Mediterranean Basin. Thirty populations were sampled for a study on molecular diversity and genetic structure, covering most major islands and mainland populations from Europe and Africa. A significant decline in nuclear and chloroplast sequence and allozyme variation within populations from west to east was observed. While DNA sequence data showed patterns of isolation by distance, allozyme markers did not. Instead, their considerable interpopulation genetic differentiation appeared to be unrelated to geographic distance. Similar high values for coefficients of gene diversity (G(ST)) in all data sets provided evidence of geographic isolation and limited gene flow among populations (i) within islands, (ii) within mainland areas, and (iii) between islands and mainland. Notably, populations in continental Spain are strongly genetically isolated from all other investigated areas. Surprisingly, there was no difference in gene diversity and G(ST) between islands and mainland areas. Thus, we conclude that large Mediterranean islands may function as 'mainland' for bryophytes. This hypothesis and its implication for conservation biology of cryptogamic plants warrant further investigation. While sexually reproducing populations were found all over the Mediterranean Basin, high levels of multilocus linkage disequilibrium provide evidence of mainly vegetative propagation even in populations where sexual reproduction was observed.

Quantifying the amount of missing information in genetic association studies

Many genetic analyses are done with incomplete information; for example, unknown phase in haplotype-based association studies. Measures of the amount of available information can be used for efficient planning of studies and/or analyses. In particular, the linkage disequilibrium (LD) between two sets of markers can be interpreted as the amount of information one set of markers contains for testing allele frequency differences in the second set, and measuring LD can be viewed as quantifying information in a missing data problem. We introduce a framework for measuring the association between two sets of variables; for example, genotype data for two distinct groups of markers, or haplotype and genotype data for a given set of polymorphisms. The goal is to quantify how much information is in one data set, e.g. genotype data for a set of SNPs, for estimating parameters that are functions of frequencies in the second data set, e.g. haplotype frequencies, relative to the ideal case of actually observing the complete data, e.g. haplotypes. In the case of genotype data on two mutually exclusive sets of markers, the measure determines the amount of multi-locus LD, and is equal to the classical measure r(2), if the sets consist each of one bi-allelic marker. In general, the measures are interpreted as the asymptotic ratio of sample sizes necessary to achieve the same power in case-control testing. The focus of this paper is on case-control allele/haplotype tests, but the framework can be extended easily to other settings like regressing quantitative traits on allele/haplotype counts, or tests on genotypes or diplotypes. We highlight applications of the approach, including tools for navigating the HapMap database [The International HapMap Consortium, 2003], and genotyping strategies for positional cloning studies.

A sliding‐window weighted linkage disequilibrium test

Multilocus linkage disequilibrium (LD) tests that consider inter-marker (LD) are more powerful than single-locus tests when disease etiology is contributed simultaneously by several linked and correlated loci. However, inclusion of redundant non-informative markers may result in reduced testing power and/or inflated false-positive rate, therefore selection of proper marker sets is important in such tests. We introduce a unified LD test based on a convenient marker-selection procedure (sliding window) combined with an adjustment approach (marker weighting) to dilute the impact of nuisance markers on tests. The proposed procedure includes several conventional p-value combination methods as its special cases. Simulation studies were performed to evaluate the impact of inclusion of nuisance markers and performance of the procedure. The results showed that testing power was often inversely proportional to the quantity of nuisance markers. Among a class of p-value combination methods, the product p-value method had the highest testing power. P-value truncation somewhat reduced the testing power but controlled the false-positive rate well. Compared with conventional unweighted approaches, the weighted strategy alleviated the false-positive rate and/or increased testing power when nuisance markers were included. Analyses of two authentic data sets for psoriasis and Alzheimer's disease using our proposed method confirmed previous findings.

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

Improvements in technology have made it possible to conduct genome-wide association mapping at costs within reach of academic investigators, and experiments are currently being conducted with a variety of high-throughput platforms. To provide an appropriate context for interpreting results of such studies, we summarize here results of an investigation of one of the first of these technologies to be publicly available, the Affymetrix GeneChip Human Mapping 100K set of single nucleotide polymorphisms (SNPs). In a systematic analysis of the pattern and distribution of SNPs in the Mapping 100K set, we find that SNPs in this set are undersampled from coding regions (both nonsynonymous and synonymous) and oversampled from regions outside genes, relative to SNPs in the overall HapMap database. In addition, we utilize a novel multilocus linkage disequilibrium (LD) coefficient based on information content (analogous to the information content scores commonly used for linkage mapping) that is equivalent to the familiar measure r 2 in the special case of two loci. Using this approach, we are able to summarize for any subset of markers, such as the Affymetrix Mapping 100K set, the information available for association mapping in that subset, relative to the information available in the full set of markers included in the HapMap, and highlight circumstances in which this multilocus measure of LD provides substantial additional insight about the haplotype structure in a region over pairwise measures of LD.

Multilocus linkage disequilibrium mapping of epistatic quantitative trait loci that regulate HIV dynamics: a simulation approach

The time-dependent change of HIV particle load, i.e. HIV dynamics, is likely to be controlled by a multitude of quantitative trait loci (QTL) that interact with each other as well as with various developmental and environmental factors in a coordinated manner. In this article, we have derived a new statistical model for mapping the epistatic QTL responsible for HIV dynamics in a natural human population. This model, constructed on the integrated theme of functional mapping and linkage disequilibrium (LD) mapping, can make use of information from multiple markers genotyped from the human genome. It allows for the test and estimation of genetic actions and interactions involved in the control of HIV progression and provides a general platform to identify the detailed genetic architecture of resistance or susceptibility of humans to HIV on a dynamic scale. We have generalized this model to accommodate various complicated clincal designs for AIDS studies. Simulation studies with different scenarios are performed to examine the statistical behaviour of the model. The genetic and statistical extensions of this mapping model to HIV/AIDS genomic research are discussed.

Multilocus linkage disequilibrium mapping by the decay of haplotype sharing with samples of related individuals

We consider the problem of multilocus linkage disequilibrium (LD) mapping of a trait-associated variant from case-control samples in which some individuals may be related. Our method, which we call DHS-R, is an extension of the decay of haplotype sharing (DHS) method of McPeek and Strahs and Strahs and McPeek. The DHS-R method shares the main features of the DHS method: (1) it allows construction of a confidence interval for the location of a trait-associated variant; (2) it allows for missing observations and unphased genotype data, with the uncertainty in the haplotypes taken into account in the analysis; and (3) it allows for heterogeneity, mutation, recombination, and background LD. The main advances of the DHS-R are (1) the ability to include individuals of arbitrary known relationship (including inbreeding) in the case and control samples; (2) an extension to allow partially-phased haplotypes derived from case-parent trio genotype data; and (3) an extension to allow for genotyping error in the model. Our method, which uses a hidden Markov model for likelihood calculation and maximization, has the advantage of being computationally feasible even in a large, complex pedigree. Simulations based on a 13-generation, 1,623-member Hutterite pedigree demonstrate accurate coverage of the confidence intervals for location of the variant. We apply the method to fine-mapping of a susceptibility locus for bronchial hyperresponsiveness (BHR) in the Hutterites. The results confirm the importance of taking into account the relatedness of individuals in LD mapping.

Fragmented Population Structure ofPlasmodium falciparumin a Region of Declining Endemicity

The population genetic structure of Plasmodium falciparum differs between endemic regions, but the characteristics of a population recently fragmented by effective malaria control have been unknown. Genotypic analysis of 10 microsatellite loci widely separated in the parasite genome was conducted on 288 P. falciparum isolates from 8 foci in Malaysian Borneo, a region in which malaria incidence has been progressively reduced. Within all P. falciparum foci, moderate levels of allelic diversity were found, but levels of multilocus linkage disequilibrium were extremely variable. The population with the highest proportion of mixed-clone infections also had the highest allelic diversity and nonsignificant linkage disequilibrium. In contrast, several populations showed evidence of clonal expansion, and one offshore island population had exceptionally high levels of linkage disequilibrium. Genetic differentiation between many populations was very high and strongly associated with the geographical distance between them. High levels of differentiation and contrasting population structure among P. falciparum populations in Malaysian Borneo indicate that they are genetically independent. This supports the feasibility of individually eradicating the remaining P. falciparum foci.

Multilocus LD measure and tagging SNP selection with generalized mutual information

Linkage disequilibrium (LD) plays a central role in fine mapping of disease genes and, more recently, in characterizing haplotype blocks. Classical LD measures, such as D' and r(2), are frequently used to quantify relationship between two loci. A pairwise "distance" matrix among a set of loci can be constructed using such a measure, and based upon which a number of haplotype block detection and tagging single nucleotide polymorphism (SNP) selection algorithms have been devised. Although successful in many applications, the pairwise nature of these measures does not provide a direct characterization of joint linkage disequilibrium among multiple loci. Consequently, applications based on them may lead to loss of important information. In this report, we propose a multilocus LD measure based on generalized mutual information, which is also known as relative entropy or Kullback-Leibler distance. In essence, this measure seeks to quantify the distance between the observed haplotype distribution and the expected distribution assuming linkage equilibrium. We can show that this measure is approximately equal to r(2) in the special case with two loci. Based on this multilocus LD measure and an entropy measure that characterizes haplotype diversity, we propose a class of stepwise tagging SNP selection algorithms. This represents a unified approach for SNP selection in that it takes into account both the haplotype diversity and linkage disequilibrium objectives. Applications to both simulated and real data demonstrate the utility of the proposed methods for handling a large number of SNPs. The results indicate that multilocus LD patterns can be captured well, and informative and nonredundant SNPs can be selected effectively from a large set of loci.

Effect of Two- and Three-Locus Linkage Disequilibrium on the Power to Detect Marker/Phenotype Associations

There has been much recent interest in describing the patterns of linkage disequilibrium (LD) along a chromosome. Most empirical studies that have examined this issue have concentrated on LD between collections of pairs of markers and have not considered the joint effect of a group of markers beyond these pairwise connections. Here, we examine many different patterns of LD defined by both pairwise and joint multilocus LD terms. The LD patterns we considered were chosen in part by examining those seen in real data. We examine how changes in these patterns affect the power to detect association when performing single-marker and haplotype-based case-control tests, including a novel haplotype test based on contrasting LD between affected and unaffected individuals. Through our studies we find that differences in power between single-marker tests and haplotype-based tests in general do not appear to be large. Where moderate to high levels of multilocus LD exist, haplotype tests tend to be more powerful. Single-marker tests tend to prevail when pairwise LD is high. For moderate pairwise values and weak multilocus LD, either testing strategy may come out ahead, although it is also quite likely that neither has much power.

Genetic structure of Plasmodium falciparum populations in the Brazilian Amazon region.

After a major increase in incidence between the 1970s and the 1990s, the Brazilian Amazon region now accounts for the most cases of Plasmodium falciparum malaria in the Americas. Polymorphism of 10 microsatellite loci in the P. falciparum genome was studied in 196 isolates obtained from 5 populations in the region. There was significant multilocus linkage disequilibrium, particularly within populations with lower proportions of mixed-genotype infections. However, most multilocus genotypes in different isolates were distinct, and there was no evidence of any recent epidemic expansion of particular clones. Genetic divergence between populations was very substantial but did not fit a simple model of isolation by distance. Thus, different foci of P. falciparum in Brazil are quite independent, with distinct population structures and minimal gene flow, a finding that has implications for strategies to control infection and to contain the spread of drug resistance at a regional level.

A survey of current Bayesian gene mapping method

Recently, there has been much interest in the use of Bayesian statistical methods for performing genetic analyses. Many of the computational difficulties previously associated with Bayesian analysis, such as multidimensional integration, can now be easily overcome using modern high-speed computers and Markov chain Monte Carlo (MCMC) methods. Much of this new technology has been used to perform gene mapping, especially through the use of multi-locus linkage disequilibrium techniques. This review attempts to summarise some of the currently available methods and the software available to implement these methods.

Renin-angiotensin system gene polymorphisms and atrial fibrillation.

The activated local atrial renin-angiotensin system (RAS) has been reported to play an important role in the pathogenesis of atrial fibrillation (AF). We hypothesized that RAS genes might be among the susceptibility genes of nonfamilial structural AF and conducted a genetic case-control study to demonstrate this. A total of 250 patients with documented nonfamilial structural AF and 250 controls were selected. The controls were matched to cases on a 1-to-1 basis with regard to age, gender, presence of left ventricular dysfunction, and presence of significant valvular heart disease. The ACE gene insertion/deletion polymorphism, the T174M, M235T, G-6A, A-20C, G-152A, and G-217A polymorphisms of the angiotensinogen gene, and the A1166C polymorphism of the angiotensin II type I receptor gene were genotyped. In multilocus haplotype analysis, the angiotensinogen gene haplotype profile was significantly different between cases and controls (chi2=62.5, P=0.0002). In single-locus analysis, M235T, G-6A, and G-217A were significantly associated with AF. Frequencies of the M235, G-6, and G-217 alleles were significantly higher in cases than in controls (P=0.000, 0.005, and 0.002, respectively). The odds ratios for AF were 2.5 (95% CI 1.7 to 3.3) with M235/M235 plus M235/T235 genotype, 3.3 (95% CI 1.3 to 10.0) with G-6/G-6 genotype, and 2.0 (95% CI 1.3 to 2.5) with G-217/G-217 genotype. Furthermore, significant gene-gene interactions were detected by the multifactor-dimensionality reduction method and multilocus linkage disequilibrium tests. This study demonstrates the association of RAS gene polymorphisms with nonfamilial structural AF and may provide the rationale for clinical trials to investigate the use of ACE inhibitor or angiotensin II antagonist in the treatment of structural AF.