Genome-Wide Linkage-Disequilibrium Profiles from Single Individuals

Although the analysis of linkage disequilibrium (LD) plays a central role in many areas of population genetics, the sampling variance of LD is known to be very large with high sensitivity to numbers of nucleotide sites and individuals sampled. Here we show that a genome-wide analysis of the distribution of heterozygous sites within a single diploid genome can yield highly informative patterns of LD as a function of physical distance. The proposed statistic, the correlation of zygosity, is closely related to the conventional population-level measure of LD, but is agnostic with respect to allele frequencies and hence likely less prone to outlier artifacts. Application of the method to several vertebrate species leads to the conclusion that >80% of recombination events are typically resolved by gene-conversion-like processes unaccompanied by crossovers, with the average lengths of conversion patches being on the order of one to several kilobases in length. Thus, contrary to common assumptions, the recombination rate between sites does not scale linearly with distance, often even up to distances of 100 kb. In addition, the amount of LD between sites separated by <200 bp is uniformly much greater than can be explained by the conventional neutral model, possibly because of the nonindependent origin of mutations within this spatial scale. These results raise questions about the application of conventional population-genetic interpretations to LD on short spatial scales and also about the use of spatial patterns of LD to infer demographic histories.     

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.     

Reticulated and epidemic population genetic structure of Rhizobium etli biovar phaseoli in a traditionally managed locality in Mexico

We conducted a multilocus enzyme electrophoresis (MLEE) study to assess the genetic structure of the nitrogen-fixing bacteria Rhizobium etli bv. phaseoli . We analysed the genetic variation at 10 enzyme-encoding chromosomal loci of 482 isolates from root nodules of Phaseolus vulgaris and P. coccineus bean plants. The isolates were obtained from six traditionally managed agricultural plots in two localities in the State of Puebla, in Central Mexico. The total mean genetic diversity ( H _E) for the six plots was 0.531. Among the 482 isolates collected, 126 distinctive multilocus genotypes (electrophoretic types [Ets]) were obtained, and approximately half of the isolates are represented by five widespread ETs. A significant degree of genetic differentiation among the six plots ( G _ST = 0.072) and between the two localities ( G _ST = 0.022) was detected. The main part of the observed variability (70%) was found among the isolates within the plants. The cluster analysis revealed two deeply diverging lineages, separated at a genetic distance of 0.7. When a multilocus linkage disequilibrium analysis was performed at different hierarchical levels, we found significant linkage disequilibrium, but when the analysis was performed for the genotypes within the two diverging lineages, we found evidence of recombination. We propose for R. etli bv. phaseoli a reticulated and epidemic genetic structure, in which few genotypes increase in frequency to produce numerically dominant clones, and genetic exchange occurs mainly among genotypes within each lineage.     

Genome-Wide Estimation of Linkage Disequilibrium from Population-Level High-Throughput Sequencing Data

Rapidly improving sequencing technologies provide unprecedented opportunities for analyzing genome-wide patterns of polymorphisms. In particular, they have great potential for linkage-disequilibrium analyses on both global and local genetic scales, which will substantially improve our ability to derive evolutionary inferences. However, there are some difficulties with analyzing high-throughput sequencing data, including high error rates associated with base reads and complications from the random sampling of sequenced chromosomes in diploid organisms. To overcome these difficulties, we developed a maximum-likelihood estimator of linkage disequilibrium for use with error-prone sampling data. Computer simulations indicate that the estimator is nearly unbiased with a sampling variance at high coverage asymptotically approaching the value expected when all relevant information is accurately estimated. The estimator does not require phasing of haplotypes and enables the estimation of linkage disequilibrium even when all individual reads cover just single polymorphic sites.     

Analysis of genetic structure in soil populations of Rhizobium leguminosarum recovered from the USA and the UK

Although many studies have shown that animal-associated bacterial species exhibit linkage disequilibrium at chromosomal loci, recent studies indicate that both animal-associated and soil-borne bacterial species can display a nonclonal genetic structure in which alleles at chromosomal loci are in linkage equilibrium. To examine the situation in soil-borne species further, we compared genetic structure in two soil populations of Rhizobium leguminosarum bv. trifolii and two populations of R. leguminosarum bv. viciae from two sites in Oregon, with genetic structure in R. leguminosarum bv. viciae populations recovered from peas grown at a site in Washington, USA, and at a site in Norfolk, UK. A total of 234 chromosomal types (ET) were identified among 682 strains analysed for allelic variation at 13 enzyme-encoding chromosomal loci by multilocus enzyme electrophoresis (MLEE). Chi-square tests for heterogeneity of allele frequencies showed that the populations were not genetically uniform. A comparison of the genetic diversity within combined and individual populations confirmed that the Washington population was the primary cause of genetic differentiation between the populations. Each individual population exhibited linkage disequilibrium, with the magnitude of the disequilibrium being greatest in the Washington population and least in the UK population of R. leguminosarum bv. viciae. Linkage disequilibrium in the UK population was created between two clusters of 9 and 23 ETs, which, individually, were in linkage equilibrium. Strong linkage disequilibrium between the two major clusters of 8 and 12 ETs in the Washington population was caused by the low genetic diversity of the ETs within each cluster relative to the inter-cluster genetic distance. Because neither the magnitude of genetic diversity nor of linkage disequilibrium increased as hierarchical combinations of the six local populations were analysed, we conclude that the populations have not been isolated from each other for sufficient time, nor have they been exposed to enough selective pressure to develop unique multilocus genetic structure.     

The population genomics of hepatitis B virus

Hepatitis B virus (HBV) infection is considered as the fifth leading cause of death due to infectious diseases and has a worldwide prevalence. The particular geographical distribution of the eight previously defined genotypes of HBV suggests that the viral population is highly structured. The presence of such population structure is likely to affect the geographical distribution of polymorphisms involved in disease progression. In this study, we determined the structure of the HBV population using a clustering approach based on the observed allele frequencies at the polymorphic loci. We used all full-genome sequences publicly available and obtained a significant clustering of the HBV population into four main clusters, strongly associated with the current classification into genotypes. One of these main clusters could itself be split into three well-supported subclusters, highlighting the hierarchical nature of the population differentiation between HBV strains. The extremely clear-cut subdivision of the HBV population further indicates that recombination in HBV is not as extensive as previously assumed.     

Migration, isolation and hybridization in island crop populations: the case of Madagascar rice

Understanding how crop species spread and are introduced to new areas provides insights into the nature of species range expansions. The domesticated species Oryza sativa or Asian rice is one of the key domesticated crop species in the world. The island of Madagascar off the coast of East Africa was one of the last major Old World areas of introduction of rice after the domestication of this crop species and before extensive historical global trade in this crop. Asian rice was introduced in Madagascar from India, the Malay Peninsula and Indonesia approximately 800-1400 years ago. Studies of domestication traits characteristic of the two independently domesticated Asian rice subspecies, indica and tropical japonica, suggest two major waves of migrations into Madagascar. A population genetic analysis of rice in Madagascar using sequence data from 53 gene fragments provided insights into the dynamics of island founder events during the expansion of a crop species' geographic range and introduction to novel agro-ecological environments. We observed a significant decrease in genetic diversity in rice from Madagascar when compared to those in Asia, likely the result of a bottleneck on the island. We also found a high frequency of a unique indica type in Madagascar that shows clear population differentiation from most of the sampled Asian landraces, as well as differential exchange of alleles between Asia and Madagascar populations of the tropical japonica subspecies. Finally, despite partial reproductive isolation between japonica and indica, there was evidence of indica/japonica recombination resulting from their hybridization on the island.     

Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus

Aflatoxins are toxic and carcinogenic polyketides produced by several Aspergillus species that are known to contaminate agricultural commodities, posing a serious threat to animal and human health. Aflatoxin (AF) biosynthesis is almost fully characterized and involves the coordinated expression of approximately 25 genes clustered in a 70-kb DNA region. Aspergillus parasiticus is an economically important and common agent of AF contamination. Naturally occurring nonaflatoxigenic strains of A. parasiticus are rarely found and generally produce O-methylsterigmatocystin (OMST), the immediate precursor of AF. To elucidate the evolutionary forces acting to retain AF and OMST pathway extrolites (chemotypes), we sequenced 21 intergenic regions spanning the entire cluster in 24 A. parasiticus isolates chosen to represent the genetic diversity within a single Georgia field population. Linkage disequilibrium analyses revealed five distinct recombination blocks in the A. parasiticus cluster. Phylogenetic network analyses showed a history of recombination between chemotype-specific haplotypes, as well as evidence of contemporary recombination. We performed coalescent simulations of variation in recombination blocks and found an approximately twofold deeper coalescence for cluster genealogies compared to noncluster genealogies, our internal standard of neutral evolution. Significantly deeper cluster genealogies are indicative of balancing selection in the AF cluster of A. parasiticus and are further corroborated by the existence of trans-species polymorphisms and common haplotypes in the cluster for several closely related species. Estimates of Ka/Ks for representative cluster genes provide evidence of selection for OMST and AF chemotypes, and indicate a possible role of chemotypes in ecological adaptation and speciation.     

Genome-wide variation in the human and fruitfly: a comparison

Average levels of nucleotide diversity are ten-fold lower in humans than in the fruitfly, Drosophila melanogaster. Despite this difference, apparently as a result of a lower population size, patterns of genomic diversity are strikingly similar in being correlated with local rates of recombination, and influenced by similar interactions between positive natural selection and recombination. Both species also show lower levels of variation on average in non-African compared to African populations, reflecting a similar evolutionary history and perhaps both natural selection and founder effects in new environments.     

An extensive candidate gene approach to speciation: diversity,divergence and linkage disequilibrium in candidate pigmentation genes across the European crow hybrid zone

Colouration patterns have an important role in adaptation and speciation. The European crow system, in which all-black carrion crows and grey-coated hooded crows meet in a narrow hybrid zone, is a prominent example. The marked phenotypic difference is maintained by assortative mating in the absence of neutral genetic divergence, suggesting the presence of few pigmentation genes of major effect. We made use of the rich phenotypic and genetic resources in mammals and identified a comprehensive panel of 95 candidate pigmentation genes for birds. Based on functional annotation, we chose a subset of the most promising 37 candidates, for which we developed a marker system that demonstrably works across the avian phylogeny. In total, we sequenced 107 amplicons (∼3 loci per gene, totalling 60 kb) in population samples of crows (n=23 for each taxon). Tajima''s D, Fu''s F_S, DHEW and HKA (Hudson–Kreitman–Aguade) statistics revealed several amplicons that deviated from neutrality; however, none of these showed significantly elevated differentiation between the two taxa. Hence, colour divergence in this system may be mediated by uncharacterized pigmentation genes or regulatory regions outside genes. Alternatively, the observed high population recombination rate (4N_er∼0.03), with overall linkage disequilibrium dropping rapidly within the order of few 100 bp, may compromise the power to detect causal loci with nearby markers. Our results add to the debate as to the utility of candidate gene approaches in relation to genomic features and the genetic architecture of the phenotypic trait in question.     

Protein electrophoresis as a management tool: Detection of hybridization between banteng (Bos javanicus d'Alton) and domestic cattle

The ability of protein electrophoresis to detect hybridization was evaluated by a detailed examination of 30 banteng-domestic cattle hybrids. These hybrids were run as unknowns in a sample of 53 individuals that included both banteng and domestic cattle. Twenty-six of the 30 hybrid animals could be unambiguously identified as such, while the remaining hybrids were indistinguishable from domestic cattle. Theoretical analysis showed that the sensitivity of the protein assays at the individual level increased slowly with the number of available markers. The probability of detecting limited amounts of hybrid influence (5–10%) in an individual was less than 70% for any biologically realistic number of protein markers. Hybridization was much easier to detect at the population level, where the sensitivity of an electrophoretic assay increased rapidly with increased sample size. The combined results of the protein electrophoresis and the theoretical analysis suggest that there is an 94.8% probability that there are essentially no genes from domestic cattle in the North American banteng herd at the present time. Zoos interested in obtaining new animals should examine the source population as well as the individuals in question whenever it is feasible. An electrophoretic survey would also provide useful information when a species survival plan is organized.     

Bayesian inference of fine-scale recombination rates using population genomic data

Recently, several statistical methods for estimating fine-scale recombination rates using population samples have been developed. However, currently available methods that can be applied to large-scale data are limited to approximated likelihoods. Here, we developed a full-likelihood Markov chain Monte Carlo method for estimating recombination rate under a Bayesian framework. Genealogies underlying a sampling of chromosomes are effectively modelled by using marginal individual single nucleotide polymorphism genealogies related through an ancestral recombination graph. The method is compared with two existing composite-likelihood methods using simulated data.Simulation studies show that our method performs well for different simulation scenarios. The method is applied to two human population genetic variation datasets that have been studied by sperm typing. Our results are consistent with the estimates from sperm crossover analysis.