Recombination and linkage disequilibrium among mitochondrial genes in structured populations of the gynodioecious plant Silene vulgaris

The impact of intergenic recombination on the population genetics of plant mitochondrial genomes is unknown. In an effort to study this in the gynodioecious plant Silene vulgaris three-locus PCR/RFLP genotypes (based on the mitochondrial genes atpA, cox1, and cob) were determined for 239 individuals collected from 20 North American populations. Seventeen three-locus PCR/RFLP genotypes were found. Recombination was indicated by observation of each of the four two-locus genotypes possible when the two most common alleles are considered for each of two loci. Based on these common alleles the absolute values of standardized linkage disequilibrium |D'| between pairs of loci range from 0.17 to 0.78. This indicates modest disequilibrium, rather than the maximum value expected in the absence of recombination |D'=1|, or the linkage equilibrium expected if recombination is pervasive (D'=0). Values of D' did not depend on which pair of loci contributed alleles to the analysis. The direction of D' obtained for the common atpA and cox1 alleles was comparable in sign and magnitude to that obtained by examining similar information obtained in a prior study of European samples. All three loci indicated a high degree of population structure (average FST=0.63), which would limit the within-population genetic diversity required for intergenic recombination to create novel genotypes, if most mating is local. Thus, population structure acts as a constraint on the approach to linkage equilibrium.     

Measuring the extent of linkage disequilibrium in commercial pig populations

To evaluate the extent of linkage disequilibrium in domestic pigs, we genotyped 33 and 44 unrelated individuals from two commercial populations for 29 and five microsatellite markers located on chromosomes 15 and 2 respectively. A high proportion of marker pairs up to 40 cM apart exhibited significant linkage disequilibrium in both populations. Pair-wise r(2) values averaged between 0.15 and 0.50 (depending on chromosome and population) for markers <1 cM apart and declined to values of 0.05 for more distant syntenic markers. Our results suggest that both populations underwent a bottleneck approximately 20 generations ago, which reduced the effective population size from thousands to <200 animals.     

Impact of polymorphic transposable elements on linkage disequilibrium along chromosomes

Recombination and selection drive the extent of linkage disequilibrium (LD) among loci and therefore affect the reshuffling of adaptive genetic variation. However, it is poorly known to what extent the enrichment of transposable elements (TEs) in recombinationally‐inert regions reflects their inefficient removal by purifying selection and whether the presence of polymorphic TEs can modify the local recombination rate. In this study, we investigate how TEs and recombination interact at fine scale along chromosomes and possibly support linked selection in natural populations. Whole‐genome sequencing data of 304 individuals from nearby alpine populations of Arabis alpina were used to show that the density of polymorphic TEs is specifically correlated with local LD along chromosomes. Consistent with TEs modifying recombination, the characterization of 28 such LD blocks of up to 5.5 Mb in length revealed strong evidence of selective sweeps at a few loci through either site frequency spectrum or haplotype structure. A majority of these blocks were enriched in genes related to ecologically relevant functions such as responses to cold, salt stress or photoperiodism. In particular, the S‐locus (i.e., supergene responsible for strict outcrossing) was identified in a LD block with high levels of polymorphic TEs and evidence of selection. Another such LD block was enriched in cold‐responding genes and presented evidence of adaptive loci related to photoperiodism and flowering being increasingly linked by polymorphic TEs. These results are consistent with the hypothesis that TEs modify recombination landscapes and thus interact with selection in driving blocks of linked adaptive loci in natural populations.     

Genome-wide linkage disequilibrium in two Japanese beef cattle breeds

There is little knowledge about the degree of linkage disequilibrium (LD) in beef cattle. This study aims to perform a genome-wide search for LD in Japanese Black and Japanese Brown beef cattle and to compare the level of LD between these two breeds. Parameter D' (the LD coefficient) was used as a measure of LD, and LD was tested for significance of allelic associations between syntenic and between non-syntenic marker pairs. Effects of breed, chromosome, genetic map distance and their interactions with D' were tested based on least squares analyses. Both breeds showed high levels of LD, which ranged over several tens of cM and declined as the marker distance increased for syntenic marker pairs. A rapid decline of the D' value was observed between markers that were spaced 5 and 20 cM apart. LD was significant in most cases for marker pairs <40 cM apart but was not significant between non-syntenic loci. The pattern of LD found in these two breeds was similar to that previously published for dairy cattle. The D' value between breeds was not significantly different (P > 0.05), but the interaction between breed and chromosome was highly significant (P < 0.001). Genetic selection seems to have caused the heterogeneity of the D' values among chromosomes within breed. These results indicate that LD mapping is a useful tool for fine-mapping quantitative trait loci of economically important traits in Japanese beef cattle.     

Chromosome-wide linkage disequilibrium caused by an inversion polymorphism in the white-throated sparrow (Zonotrichia albicollis)

Chromosomal inversions have been of long-standing interest to geneticists because they are capable of suppressing recombination and facilitating the formation of adaptive gene complexes. An exceptional inversion polymorphism (ZAL2^m) in the white-throated sparrow (Zonotrichia albicollis) is linked to variation in plumage, social behavior and mate choice, and is maintained in the population by negative assortative mating. The ZAL2^m polymorphism is a complex inversion spanning >100 Mb and has been proposed to be a strong suppressor of recombination, as well as a potential model for studying neo-sex chromosome evolution. To quantify and evaluate these features of the ZAL2^m polymorphism, we generated sequence from 8 ZAL2^m and 16 ZAL2 chromosomes at 58 loci inside and 4 loci outside the inversion. Inside the inversion we found that recombination was completely suppressed between ZAL2 and ZAL2^m, resulting in uniformly high levels of genetic differentiation (F_ST=0.94), the formation of two distinct haplotype groups representing the alternate chromosome arrangements and extensive linkage disequilibrium spanning ∼104 Mb within the inversion, whereas gene flow was not suppressed outside the inversion. Finally, although ZAL2^m homozygotes are exceedingly rare in the population, occurring at a frequency of <1%, we detected evidence of historical recombination between ZAL2^m chromosomes inside the inversion, refuting its potential status as a non-recombining autosome.     

Patterns of polymorphism and gene flow of gender-associated mitochondrial DNA lineages in European mussel populations

Mussels of the genus Mytilus have two types of mitochondrial DNA (mtDNA). The M type is transmitted paternally and the F type is transmitted maternally. RFLP analysis is used to assess phylogenetic relationships and nucleotide diversity and divergence for both mtDNA genomes in European populations of M. edulis and Atlantic and Mediterranean forms of M. galloprovincialis. Ten restriction endonucleases were used to assay variation in regions of the ND2 and COIII genes for a total of 77 individuals. F and M genomes show a concordant phylogenetic split into two major divergent clades, one specific to Mediterranean M. galloprovincialis and the other containing haplotypes from the three taxa. For both genomes, the geographical distribution of mtDNA variation suggests: (i) extensive levels of mtDNA introgression; (ii) asymmetric mtDNA gene flow from Atlantic to Mediterranean populations; and (iii) recurrent historical hybridization events. Significantly higher mtDNA diversity and divergence are observed for the M than F genome in all three Mytilus taxa, although the evolutionary forces responsible for these differences cannot be resolved. The extensive mtDNA gene flow between European Mytilus taxa conflicts with the restricted mtDNA introgression observed in American mussels , implying geographical variation in the nature of nuclear/mtDNA interactions regulating biparental inheritance.     

Properties of 2-locus genealogies and linkage disequilibrium in temporally structured samples

Archeogenetics has been revolutionary, revealing insights into demographic history and recent positive selection. However, most studies to date have ignored the nonrandom association of genetic variants at different loci (i.e. linkage disequilibrium). This may be in part because basic properties of linkage disequilibrium in samples from different times are still not well understood. Here, we derive several results for summary statistics of haplotypic variation under a model with time-stratified sampling: (1) The correlation between the number of pairwise differences observed between time-staggered samples (πΔt) in models with and without strict population continuity; (2) The product of the linkage disequilibrium coefficient, D, between ancient and modern samples, which is a measure of haplotypic similarity between modern and ancient samples; and (3) The expected switch rate in the Li and Stephens haplotype copying model. The latter has implications for genotype imputation and phasing in ancient samples with modern reference panels. Overall, these results provide a characterization of how haplotype patterns are affected by sample age, recombination rates, and population sizes. We expect these results will help guide the interpretation and analysis of haplotype data from ancient and modern samples.     

An evaluation of the methods to estimate effective population size from measures of linkage disequilibrium

In 1971, John Sved derived an approximate relationship between linkage disequilibrium (LD) and effective population size for an ideal finite population. This seminal work was extended by Sved and Feldman (Theor Pop Biol 4, 129, 1973) and Weir and Hill (Genetics 95, 477, 1980) who derived additional equations with the same purpose. These equations yield useful estimates of effective population size, as they require a single sample in time. As these estimates of effective population size are now commonly used on a variety of genomic data, from arrays of single nucleotide polymorphisms to whole genome data, some authors have investigated their bias through simulation studies and proposed corrections for different mating systems. However, the cause of the bias remains elusive. Here, we show the problems of using LD as a statistical measure and, analogously, the problems in estimating effective population size from such measure. For that purpose, we compare three commonly used approaches with a transition probability‐based method that we develop here. It provides an exact computation of LD. We show here that the bias in the estimates of LD and effective population size are partly due to low‐frequency markers, tightly linked markers or to a small total number of crossovers per generation. These biases, however, do not decrease when increasing sample size or using unlinked markers. Our results show the issues of such measures of effective population based on LD and suggest which of the method here studied should be used in empirical studies as well as the optimal distance between markers for such estimates.     

Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability

Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D′) between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005–0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species'' newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system.     

癌症相关的DNA甲基化连锁区域

DNA甲基化是重要的表观遗传标记之一,在转录调控中起直接作用。DNA甲基化的异常与癌症的发生发展密切相关。高通量测序使得在单碱基分辨率下检测全基因组的DNA甲基化水平成为可能。本文基于临近CpGs位点甲基化水平的相关性挖掘DNA甲基化连锁区域。结果发现DNA甲基化连锁区域的甲基化水平和模式在癌症中存在异常,而且显著富集到分化/发育相关的生物学功能。DNA甲基化连锁区域的挖掘有助于对具有生物学功能的表观遗传标记的进一步理解,有助于对癌症诊断的表观遗传标记的挖掘。     

Combined linkage disequilibrium and linkage mapping: Bayesian multilocus approach

Quantitative trait loci (QTL) affecting the phenotype of interest can be detected using linkage analysis (LA), linkage disequilibrium (LD) mapping or a combination of both (LDLA). The LA approach uses information from recombination events within the observed pedigree and LD mapping from the historical recombinations within the unobserved pedigree. We propose the Bayesian variable selection approach for combined LDLA analysis for single-nucleotide polymorphism (SNP) data. The novel approach uses both sources of information simultaneously as is commonly done in plant and animal genetics, but it makes fewer assumptions about population demography than previous LDLA methods. This differs from approaches in human genetics, where LDLA methods use LA information conditional on LD information or the other way round. We argue that the multilocus LDLA model is more powerful for the detection of phenotype–genotype associations than single-locus LDLA analysis. To illustrate the performance of the Bayesian multilocus LDLA method, we analyzed simulation replicates based on real SNP genotype data from small three-generational CEPH families and compared the results with commonly used quantitative transmission disequilibrium test (QTDT). This paper is intended to be conceptual in the sense that it is not meant to be a practical method for analyzing high-density SNP data, which is more common. Our aim was to test whether this approach can function in principle.     

Linkage disequilibrium for different scales and applications

Assessing the patterns of linkage disequilibrium (LD) has become an important issue in both evolutionary biology and medical genetics since the rapid accumulation of densely spaced DNA sequence variation data in several organisms. LD deals with the correlation of genetic variation at two or more loci or sites in the genome within a given population. There are a variety of LD measures which range from traditional pairwise LD measures such as D' or r2 to entropy-based multi-locus measures or haplotype-specific approaches. Understanding the evolutionary forces (in particular recombination) that generate the observed variation of LD patterns across genomic regions is addressed by model-based LD analysis. Marker type and its allelic composition also influence the observed LD pattern, microsatellites having a greater power to detect LD in population isolates than SNPs. This review aims to explain basic LD measures and their application properties.     

Physical linkage and mate preference generate linkage disequilibrium for behavioral isolation in two parapatric crickets

Behavioral isolation is a potent barrier to gene flow and a source of striking diversity in the animal kingdom. However, it remains unclear if the linkage disequilibrium (LD) between sex‐specific traits required for behavioral isolation results mostly from physical linkage between signal and preference loci or from directional mate preferences. Here, we test this in the field crickets Gryllus rubens and G. texensis. These closely related species diverged with gene flow and have strongly differentiated songs and preference functions for the mate calling song rhythm. We map quantitative trait loci for signal and preference traits (pQTL) as well as for gene expression associated with these traits (eQTL). We find strong, positive genetic covariance between song traits and between song and preference. Our results show that this is in part explained by incomplete physical linkage: although both linked pQTL and eQTL couple male and female traits, major effect loci for different traits were never on the same chromosome. We suggest that the finely tuned, highly divergent preference functions are likely an additional source of LD between male and female traits in this system. Furthermore, pleiotropy of gene expression presents an underappreciated mechanism to link sexually dimorphic phenotypes.     

A program to test linkage disequilibrium between loci in autotetraploid species

No software currently implements a test of linkage disequilibrium in autotetraploid species. We propose a program, LD4X that performs a Fisher's exact test between pairs of alleles at two loci. All combinations of alleles from two loci are treated in turn. If two alleles of a pair of loci have a nonrandom distribution, the markers are considered as linked. The program was tested on a set of microsatellite markers in synthetic alfalfa populations.     

Insights from linked single nucleotide polymorphisms: what we can learn from linkage disequilibrium

New methods for analyzing sequence polymorphism data have uncovered some striking patterns of linkage disequilibrium in both humans and fruitflies. These methods have revealed examples where the observed amount of linkage disequilibrium is either much more or much less than expected, and have led to advances in our understanding of the forces that affect naturally occurring genetic variation. With the recent explosion of sequence polymorphism data, the prospects for further progress from these methods are quite promising.     

Mitonuclear linkage disequilibrium in human populations

There is extensive evidence from model systems that disrupting associations between co-adapted mitochondrial and nuclear genotypes can lead to deleterious and even lethal consequences. While it is tempting to extrapolate from these observations and make inferences about the human-health effects of altering mitonuclear associations, the importance of such associations may vary greatly among species, depending on population genetics, demographic history and other factors. Remarkably, despite the extensive study of human population genetics, the statistical associations between nuclear and mitochondrial alleles remain largely uninvestigated. We analysed published population genomic data to test for signatures of historical selection to maintain mitonuclear associations, particularly those involving nuclear genes that encode mitochondrial-localized proteins (N-mt genes). We found that significant mitonuclear linkage disequilibrium (LD) exists throughout the human genome, but these associations were generally weak, which is consistent with the paucity of population genetic structure in humans. Although mitonuclear LD varied among genomic regions (with especially high levels on the X chromosome), N-mt genes were statistically indistinguishable from background levels, suggesting that selection on mitonuclear epistasis has not preferentially maintained associations involving this set of loci at a species-wide level. We discuss these findings in the context of the ongoing debate over mitochondrial replacement therapy.     

Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data

A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD) information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC) methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.     

Statistical software for gene mapping by admixture linkage disequilibrium

Admixture mapping is a statistical methodology that detects genetic variants in recently admixed populations that are responsible for ethnic differences in disease risk. Three software packages are now available for admixture mapping and we provide a brief overview of the statistical methods and other principal features they implement.     

Population differences in levels of linkage disequilibrium in the wild

Information about the levels of linkage disequilibrium (LD) in wild animal populations is still limited, and this is true particularly with respect to possible interpopulation variation in the levels of LD. We compared the levels and extent of LD at the genome‐wide scale in three Siberian jay (Perisoreus infaustus) populations, two of which (Kuusamo and Ylläs) represented outbred populations within the main distribution area of the species, whereas the third (Suupohja) was a semi‐isolated, partially inbred population at the margin of the species’ distribution area. Although extensive long‐range LD (>20 cM) was observed in all three populations, LD generally decayed to background levels at a distance of 1–5 cM or c. 200–600 kb. The degree and extent of LD differed markedly between populations but aligned closely with both observed levels of within‐population genetic variation and expectations based on population history. The levels of LD were highest in the most inbred population with strong population substructure (Suupohja), compared with the two outbred populations. Furthermore, the decay of LD with increasing distance was slower in Suupohja, compared with the other two populations. By demonstrating that levels of LD can vary greatly over relatively short geographical distances within a species, these results suggest that prospects for association mapping differ from population to population. In this example, the prospects are best in the Suupohja population, given that minimized marker genotyping and a minimum marker spacing of 1–5 cM (c. 200–600 kb) would be sufficient for a whole genome scan for detecting QTL.     

Associative overdominance: Evaluating the effects of inbreeding and linkage disequilibrium

Expressions are obtained for the expected phenotypic values of homozygous and heterozygous genotypes for a neutral marker locus linked to a locus segregating for a recessive deleterious gene. The phenotypic values are functions of the allele frequencies at the marker locus, the inbreeding coefficient and the degree of association of the deleterious gene with the marker alleles. The analysis is extended to more than two alleles at the marker locus. Either linkage disequilibrium or inbreeding alone can produce an apparent superiority of heterozygotes for the marker locus (unless specified otherwise, the terms ‘homozygote’ and ‘heterozygote’ will refer to the marker locus). The effect of linkage disequilibrium on the difference between the heterozygote and homozygote values can be positive (associative overdominance) or negative (associative underdominance), depending on the frequencies of the marker alleles and the degree of their association with the deleterious gene. Inbreeding has always a positive effect. In general, the expected value of a homozygote is a positive function of its allele frequency. When the various homozygous genotypes are combined into one class and the various heterozygous genotypes into another, the phenotypic difference of the two classes is a function of the evenness of the allelic frequency distribution. Inbreeding is a more likely explanation of associative overdominance if the frequency of the deleterious gene is low, but its effect on the character high. Conversely, linkage disequilibrium is more likely if the frequency is high and the effect low. The degrees of association between marker alleles and the deleterious gene can, in principle, be estimated from the observed phenotypic scores and used to calculate expected multi-locus genotype scores. This could provide the basis for statistical tests of the associative overdominance hypothesis as an explanation of observed correlations between multi-locus heterozygosity and phenotypic traits.