Multilocus Systems in Evolution

Scalable bias-corrected linkage disequilibrium estimation under genotype uncertainty

Linkage disequilibrium (LD) estimates are often calculated genome-wide for use in many tasks, such as SNP pruning and LD decay estimation. However, in the presence of genotype uncertainty, naive approaches to calculating LD have extreme attenuation biases, incorrectly suggesting that SNPs are less dependent than in reality. These biases are particularly strong in polyploid organisms, which often exhibit greater levels of genotype uncertainty than diploids. A principled approach using maximum likelihood estimation with genotype likelihoods can reduce this bias, but is prohibitively slow for genome-wide applications. Here, we present scalable moment-based adjustments to LD estimates based on the marginal posterior distributions of the genotypes. We demonstrate, on both simulated and real data, that these moment-based estimators are as accurate as maximum likelihood estimators, but are almost as fast as naive approaches based only on posterior mean genotypes. This opens up bias-corrected LD estimation to genome-wide applications. In addition, we provide standard errors for these moment-based estimators. All methods discussed in this manuscript are implemented in the ldsep package, available on the Comprehensive R Archive Network ( https://cran.r-project.org/package=ldsep ).

Pairwise linkage disequilibrium estimation for polyploids

Many tasks in statistical genetics involve pairwise estimation of linkage disequilibrium (LD). The study of LD in diploids is mature. However, in polyploids, the field lacks a comprehensive characterization of LD. Polyploids also exhibit greater levels of genotype uncertainty than diploids, yet no methods currently exist to estimate LD in polyploids in the presence of such genotype uncertainty. Furthermore, most LD estimation methods do not quantify the level of uncertainty in their LD estimates. Our study contains three major contributions. (i) We characterize haplotypic and composite measures of LD in polyploids. These composite measures of LD turn out to be functions of common statistical measures of association. (ii) We derive procedures to estimate haplotypic and composite LD in polyploids in the presence of genotype uncertainty. We do this by estimating LD directly from genotype likelihoods, which may be obtained from many genotyping platforms. (iii) We derive standard errors of all LD estimators that we discuss. We validate our methods on both real and simulated data. Our methods are implemented in the R package ldsep, available on the Comprehensive R Archive Network https://cran.r-project.org/package=ldsep.

ASSOCIATIONS BETWEEN MITOCHONDRIAL AND NUCLEAR GENOTYPES IN CUTTHROAT TROUT HYBRID SWARMS

We examined mtDNA and nuclear allozyme genotypes in hybrid populations formed from interbreeding of westslope cutthroat trout (Oncorhynchus clarki lewisi) and Yellowstone cutthroat trout (O. c. bouvieri). These subspecies show substantial genetic divergence (Nei's D = 0.30; mtDNA P = 0.02). Diagnostic alleles at multiple nuclear loci and two distinct mtDNA haplotypes segregate in the hybrids. Nuclear and mtDNA genotypes are largely randomly associated, although there is slight disequilibrium in both nuclear and cytonuclear measures in some samples. Consistent positive gametic disequilibria for three pairs of nuclear loci confirm one previously reported linkage, and indicate two more. Allele frequencies provide no evidence for selection on individual chromosome segments. However, westslope mtDNA haplotype frequencies exceed westslope nuclear allele frequencies in all samples. This may be explained by differences in the frequency of occurrence of reciprocal F₁ matings, by viability, fertility, or sex ratio differences in the progeny of reciprocal matings, or by weak selection on mtDNA haplotypes.

The molecular epidemiology of parasite infections: tools and applications

Molecular epidemiology, broadly defined, is the application of molecular genetic techniques to the dynamics of disease in a population. In this review, we briefly describe molecular and analytical tools available for molecular epidemiological studies and then provide an overview of how they can be applied to better understand parasitic disease. A range of new molecular tools have been developed in recent years, allowing for the direct examination of parasites from clinical or environmental samples, and providing access to relatively cheap, rapid, high throughput molecular assays. At the same time, new analytical approaches, in particular those derived from coalescent theory, have been developed to provide more robust estimates of evolutionary processes and demographic parameters from multilocus, genotypic data. To date, the primary application of molecular epidemiology has been to provide specific and sensitive identification of parasites and to resolve taxonomic issues, particularly at the species level and below. Population genetic studies have also been used to determine the extent of genetic diversity among populations of parasites and the degree to which this diversity is associated with different host cycles or epidemiologically important phenotypes. Many of these studies have also shed new light on transmission cycles of parasites, particularly the extent to which zoonotic transmission occurs, and on the prevalence and importance of mixed infections with different parasite species or intraspecific variants (polyparasitism). A major challenge, and one which is now being addressed by an increasing number of studies, is to find and utilize genetic markers for complex traits of epidemiological significance, such as drug resistance, zoonotic potential and virulence.

On the uses and applications of the most commonly used measures of linkage disequilibrium from the comparative analysis of their statistical properties

BACKGROUND/OBJECTIVE

The analysis of linkage disequilibrium is relevant for the exploration of the structure and evolution of genomes and for the gene mapping of quantitative characters and human diseases. The strength of linkage disequilibrium between diallelic loci is commonly measured by the coefficients D' and r. Recent studies suggest that r is more useful than D' as a general measure of the strength of disequilibrium because it provides much more precise (lower sampling variance) and accurate (lower bias) estimates of disequilibrium. We compared for the first time the statistical properties of D' and r taking into account their differences in range.

METHODS

The sampling properties of D' and r were evaluated by simulation under a variety of realistic population conditions and varying sample sizes using standardised statistics that allow for comparisons of the precision, accuracy and efficiency of estimates with different ranges.

RESULTS

Simulations revealed that estimates of r do not tend to be significantly more precise, accurate or efficient than those of D' when compared by means of standardised statistics.

CONCLUSION

The supposed advantage of r over D' based on direct comparisons of their sampling distributions is more apparent than real. The obtained results are useful to assess the uses and applications of these widely used disequilibrium measures.

Structure of genetic diversity in the two major gene pools of common bean (Phaseolus vulgaris L., Fabaceae)

Domesticated materials with well-known wild relatives provide an experimental system to reveal how human selection during cultivation affects genetic composition and adaptation to novel environments. In this paper, our goal was to elucidate how two geographically distinct domestication events modified the structure and level of genetic diversity in common bean. Specifically, we analyzed the genome-wide genetic composition at 26, mostly unlinked microsatellite loci in 349 accessions of wild and domesticated common bean from the Andean and Mesoamerican gene pools. Using a model-based approach, implemented in the software STRUCTURE, we identified nine wild or domesticated populations in common bean, including four of Andean and four of Mesoamerican origins. The ninth population was the putative wild ancestor of the species, which was classified as a Mesoamerican population. A neighbor-joining analysis and a principal coordinate analysis confirmed genetic relationships among accessions and populations observed with the STRUCTURE analysis. Geographic and genetic distances in wild populations were congruent with the exception of a few putative hybrids identified in this study, suggesting a predominant effect of isolation by distance. Domesticated common bean populations possessed lower genetic diversity, higher F(ST), and generally higher linkage disequilibrium (LD) than wild populations in both gene pools; their geographic distributions were less correlated with genetic distance, probably reflecting seed-based gene flow after domestication. The LD was reduced when analyzed in separate Andean and Mesoamerican germplasm samples. The Andean domesticated race Nueva Granada had the highest F(ST) value and widest geographic distribution compared to other domesticated races, suggesting a very recent origin or a selection event, presumably associated with a determinate growth habit, which predominates in this race.

Testing for homogeneity of gametic disequilibrium across strata

Background

Assessing the non-random associations of alleles at different loci, or gametic disequilibrium, can provide clues about aspects of population histories and mating behavior and can be useful in locating disease genes. For gametic data which are available from several strata with different allele probabilities, it is necessary to verify that the strata are homogeneous in terms of gametic disequilibrium.

Results

Using the likelihood score theory generalized to nuisance parameters we derive a score test for homogeneity of gametic disequilibrium across several independent populations. Simulation results demonstrate that the empirical type I error rates of our score homogeneity test perform satisfactorily in the sense that they are close to the pre-chosen 0.05 nominal level. The associated power and sample size formulae are derived. We illustrate our test with a data set from a study of the cystic fibrosis transmembrane conductance regulator gene.

Conclusion

We propose a large-sample homogeneity test on gametic disequilibrium across several independent populations based on the likelihood score theory generalized to nuisance parameters. Our simulation results show that our test is more reliable than the traditional test based on the Fisher's test of homogeneity among correlation coefficients.

Genetic regulation of colony social organization in fire ants: an integrative overview

Expression of colony social organization in fire ants appears to be under the control of a single Mendelian factor of large effect. Variation in colony queen number in Solenopsis invicta and its relatives is associated with allelic variation at the gene Gp-9, but not with variation at other unlinked genes; workers regulate queen identity and number on the basis of Gp-9 genotypic compatibility. Nongenetic factors, such as prior social experience, queen reproductive status, and local environment, have negligible effects on queen numbers which illustrates the nearly complete penetrance of Gp-9. As predicted, queen number can be manipulated experimentally by altering worker Gp-9 genotype frequencies. The Gp-9 allele lineage associated with polygyny in South American fire ants has been retained across multiple speciation events, which may signal the action of balancing selection to maintain social polymorphism in these species. Moreover, positive selection is implicated in driving the molecular evolution of Gp-9 in association with the origin of polygyny. The identity of the product of Gp-9 as an odorant-binding protein suggests plausible scenarios for its direct involvement in the regulation of queen number via a role in chemical communication. While these and other lines of evidence show that Gp-9 represents a legitimate candidate gene of major effect, studies aimed at determining (i) the biochemical pathways in which GP-9 functions; (ii) the phenotypic effects of molecular variation at Gp-9 and other pathway genes; and (iii) the potential involvement of genes in linkage disequilibrium with Gp-9 are needed to elucidate the genetic architecture underlying social organization in fire ants. Information that reveals the links between molecular variation, individual phenotype, and colony-level behaviors, combined with behavioral models that incorporate details of the chemical communication involved in regulating queen number, will yield a novel integrated view of the evolutionary changes underlying a key social adaptation.

A study of wing morphology and fluctuating asymmetry in interspecific hybrids between Drosophila buzzatii and D. koepferae

In this work we investigate the effect of interspecific hybridization on wing morphology using geometric morphometrics in the cactophilic sibling species D. buzzatii and D. koepferae. Wing morphology in F1 hybrids exhibited an important degree of phenotypic plasticity and differs significantly from both parental species. However, the pattern of morphological variation between hybrids and the parental strains varied between wing size and wing shape, across rearing media, sexes, and crosses, suggesting a complex genetic architecture underlying divergence in wing morphology. Even though there was significant fluctuating asymmetry for both, wing size and shape in F1 hybrids and both parental species, there was no evidence of an increased degree of fluctuating asymmetry in hybrids as compared to parental species. These results are interpreted in terms of developmental stability as a function of a balance between levels of heterozygosity and the disruption of coadaptation as an indirect consequence of genomic divergence.

Quantitative genetics of functional characters inDrosophila melanogaster populations subjected to laboratory selection

What are the genetics of phenotypes other than fitness, in outbred populations? To answer this question, the quantitative-genetic basis of divergence was characterized for outbred Drosophila melanogaster populations that had previously undergone selection to enhance characters related to fitness. Line-cross analysis using first-generation and second-generation hybrids from reciprocal crosses was conducted for two types of cross, each replicated fivefold. One type of cross was between representatives of the ancestral population, a set of five populations maintained for several hundred generations on a two-week discrete-generation life cycle and a set of five populations adapted to starvation stress. The other type of cross was between the same set of ancestral-representative populations and another set of five populations selected for accelerated development from egg to egg. Developmental time from egg to eclosion, starvation resistance, dry body weight and fecundity at day 14 from egg were fit to regression models estimating single-locus additive and dominant effects, maternal and paternal effects, and digenic additive and dominance epistatic effects. Additive genetic variation explained most of the differences between populations, with additive maternal and cytoplasmic effects also commonly found. Both within-locus and between-locus dominance effects were inferred in some cases, as well as one instance of additive epistasis. Some of these effects may have been caused by linkage disequilibrium. We conclude with a brief discussion concerning the relationship of the genetics of population differentiation to adaptation.

GENETIC ARCHITECTURE OF A SELECTION RESPONSE IN ARABIDOPSIS THALIANA

Quantitative trait locus (QTL) mapping has become an established and effective method for studying the genetic architecture of complex traits. In this report, we use a QTL mapping approach in combination with data from a large selection experiment in Arabidopsis thaliana to explore a response to selection of experimental populations with differentiated genetic backgrounds. Experimental populations with genetic backgrounds derived from ecotypes Landsberg and Niederzenz were exposed to multiple generations of fertility and viability selection. This selection resulted in phenotypic shifts in a number of life-history and fitness-related characters including early development time, flowering time, dry biomass, longevity, and fruit production. Quantitative trait loci were mapped for these traits and their positions were compared to previously characterized allele frequency changes in the experimental populations (Ungerer et al. 2003). Quantitative trait locus positions largely colocalized with genomic regions under strong and consistent selection in populations with differentiated genetic backgrounds, suggesting that alleles for these traits were selected similarly in differentiated genetic backgrounds. However, one QTL region exhibited a more variable response; being positively selected on one genetic background but apparently neutral in another. This study demonstrates how QTL mapping approaches can be combined with map-based population genetic data to study how selection acts on standing genetic variation in populations.

Seasonal cycles of allozyme-by-chromosomal-inversion gametic disequilibrium in Drosophila subobscura

Allozyme loci are frequently found non randomly associated to the chromosomal inversions in which they are included in Drosophila. Two opposite views compete to explain strong allozyme-by-inversion gametic disequilibria: they result from natural selection or, conversely, merely represent remnants of associations accidentally established at the origin of inversions. Empirical efforts aimed at deciding between adaptive and historical scenarios have focused on the spatial distribution of disequilibria. Yet, the evolutionary significance of these associations remains uncertain. I report here the results of a time-series analysis of the seasonal variation of alleles at six allozyme loci (Acph, Lap, Pept-1, Ao, Mpi, and Xdh) in connection with the O chromosomal polymorphisms of D. subobscura. The findings were: (1) in the segment I of the O chromosome, Lap and Pept-1 allozymes changed seasonally in a cyclical fashion within the ST gene arrangement, but they changed erratically within the 3 + 4 gene configuration; (2) the frequencies of Lap1.11 and Pept-1(0.40) within ST dropped to their lowest values in early and late summer, respectively, when the seasonal level of the ST arrangement is lowest. Furthermore, Lap1.11 and Pept-1(0.40) covary with ST only within these seasons, yet in a fashion inconsistent with these alleles having a major influence on the dynamics of the inversion; (3) seasonal cycling of alleles within inversions were not detected at Acph, Ao, Mpi, and Xdh, yet these loci are nearly monomorphic at the study population, and/or their sampled series were shorter than those for Lap and Pept-1; and (4) simply monitoring allozyme frequencies separately for each inversion proved to be superior, for evidencing the seasonal cycles of the disequilibria, to the use of the D' coefficient of association. Observed seasonal cycles of allozymes within inversions likely reflect natural selection.

Genotypic diversity and gene flow in brooding and spawning corals along the Great Barrier Reef, Australia

Marine organisms exhibit great variation in reproductive modes, larval types, and other life-history traits that may have major evolutionary consequences. We measured local and regional patterns of genetic variation in corals along Australia's Great Barrier Reef to determine the relative contributions of sexual and asexual reproduction to recruitment and to infer levels of gene flow both locally (among adjacent sites, < 5 km apart) and regionally (among reefs separated by 500-1,200 km). We selected five common brooding species (Acropora cuneata, A. palifera, Pocillopora damicornis, Seriatopora hystrix, and Stylophora pistillata) and four broadcast spawners (Acropora hyacinthus, A. cytherea, A. millepora, and A. valida), which encompassed a wide range of larval types and potential dispersal capabilities. We found substantial genotypic diversity at local scales in six of the nine species (four brooders, two spawners). For these six, each local population displayed approximately the levels of multilocus genotypic diversity (Go) expected for outcrossed sexual reproduction (mean values of Go:Ge ranged from 0.85 to 1.02), although consistent single-locus heterozygous deficits indicate that inbreeding occurs at the scale of whole reefs. The remaining three species, the brooder S. hystrix and the spawners A. valida and A. millepora displayed significantly less multilocus genotypic diversity (Go) than was expected for outcrossed sexual reproduction (Ge) within each of several sites. Acropora valida and A. millepora showed evidence of extensive localized asexual replication: (1) a small number of multilocus (clonal) genotypes were numerically dominant within some sites (Go:Ge values were as low as 0.17 and 0.20): (2) single-locus genotype frequencies were characterized by both excesses and deficits of heterozygotes (cf. Hardy-Weinberg expectations), and (3) significant linkage disequilibria occurred. For the brooding S. hystrix Go:Ge values were also low within each of four sites (x = 0.48). However, this result most likely reflects the highly restricted dispersal of gametes or larvae, because levels of genetic variation among sites within reefs were extremely high (FSR = 0.28). For all species, we detected considerable genetic subdivision among sites within each reef (high FSR-values), and we infer that larval dispersal is surprisingly limited (i.e., Nem among sites ranging from 0.6 to 3.3 migrants per generation), even in species that have relatively long planktonic durations. Nevertheless, our estimates of allelic variation among reefs (FRT) also imply that for all four broadcast spawning species and three of the brooders, larval dispersal is sufficient to maintain moderate to high levels of gene flow along the entire Great Barrier Reef (i.e., Nem among reefs ranged from 5 to 31). In contrast, widespread populations of S. hystrix and S. pistilata (the two remaining brooders) are relatively weakly connected (Nem among reefs was 1.4 and 2.5, respectively). We conclude that most recruitment by corals is very local, particularly in brooders, but that enough propagules are widely dispersed to ensure that both broadcast spawning and brooding species form vast effectively panmictic populations on the Great Barrier Reef.

Genetic analysis of the population structure of socially organized oystercatchers (Haematopus ostralegus) using microsatellites

On the island of Schiermonnikoog (The Netherlands), the breeding population of oystercatchers can be divided into two groups: 'residents' and 'leapfrogs', based on their distinct social characteristics and limited probabilities of status change between breeding seasons. In order to investigate whether this social organization has caused local genetic differentiation, leapfrogs and residents were compared at eight polymorphic microsatellite loci. No significant genetic subdivision between residents and leapfrogs was observed (theta = 0.0000; 95% confidence interval (CI), -0.0027-0.0033), indicating that the oystercatcher population on the island of Schiermonnikoog has to be considered as one panmictic unit. Investigation of three additional locations in the northern part of The Netherlands did not reveal significant genetic population subdivision either (theta = -0.0005; 95% CI, -0.0045-0.0037), despite the fact that adult osytercatchers show extreme fidelity to their breeding localities. These results indicate panmixis and considerable levels of gene flow within the northern part of The Netherlands. Thus, the results from genetical analyses do not seem to be in agreement with observational data on the dispersal behaviour of breeding individuals. It is argued that the lack of population structure, locally on Schiermonnikoog as well as across larger geographical distances, is to be attributed to high levels of gene flow through dispersal of juvenile birds.

Limited polymorphism at major histocompatibility complex (MHC) loci in the Swedish moose A. alces

The Swedish moose was analysed for genetic variability at major histocompatibility complex (MHC) class I and class II DQA, DQB and DRB loci using restriction fragment length polymorphism (RFLP) and single strand conformation polymorphism (SSCP) techniques. Both methods revealed limited amounts of polymorphism. Since the SSCP analysis concerned an expressed DRB gene it can be concluded that the level of functional MHC class II polymorphism, at least at the DRB locus, is low in Swedish moose. DNA fingerprinting was used to determine if the unusual pattern of low MHC variability could be explained by a low degree of genome-wide genetic diversity. Hybridizations with two minisatellite probes gave similarity indices somewhat higher than the average for other natural population, but the data suggest that the low MHC variability cannot be explained by a recent population bottleneck. However, since minisatellite sequences evolve more rapidly than MHC sequences, the low levels of MHC diversity may be attributed to a bottleneck of more ancient origin. The selection pressure for MHC variability in moose may also be reduced and we discuss the possibility that its solitary life style may reduce lateral transmission of pathogens in the population.

Finding genetic markers for complex phenotypic traits in parasites

The identification, mapping and eventual cloning of genes which determine or influence important epidemiological traits in parasites can have great benefits for the control of parasitic disease. In this review, strategies are outlined for identifying genetic markers for complex, quantitative traits. A genetic marker is a variable DNA sequence which co-occurs with a variable quantitative trait. Candidate markers are chosen because they are thought to directly influence the trait whereas random markers are expected to be linked to another DNA sequence which influences the trait. Association studies compare the value of a quantitative trait between different marker genotype classes in a population, without regard to family structure. Linkage studies compare the value of a quantitative trait between marker genotype classes within families or within a population (usually derived from a cross between inbred lines) which is segregating for both marker and quantitative trait loci. The most commonly used analytical methods for determining the significance of association or linkage between marker and quantitative trait loci, and for estimating parameters such as recombination rate and quantitative gene action, are least-squares and maximum likelihood. Both methods may be used to test either single markers or the interval between flanking markers, and both suffer from the need to minimize type I and type II error rates with multiple tests.

Restriction fragment length polymorphism of bovine lysozyme genes

Genetic polymorphism of bovine lysozyme (LYZ) genes was investigated by analysing restriction fragment length polymorphism (RFLP). The analysis revealed three RFLP loci designated LYZ1, LYZ2 and LYZ2. Each system included two or three allelic variants. Evidence for close genetic linkage of the three loci was found. There was also a significant linkage disequilibrium among the three loci in a sample of about 200 breeding bulls from one breed. No statistically significant association was found between LYZ RFLPs and breeding values of bulls for disease or milk production traits.