Linkage Disequilibrium in Natural Populations of Trypanosoma cruzi (Flagellate), the Agent of Chagas’ Disease1

ABSTRACT. We have studied linkage disequilibrium in natural populations of Trypanosoma cruzi, the agent of Chagas’ disease, by analyzing (i) a set of 524 stocks from the whole geographical range of the parasite, characterized at four gene loci coding for enzymes; (ii) a subsample of 121 stocks characterized at 12 enzyme loci; and (iii) a subset of 386 stocks from six locations in Bolivia, characterized by four enzyme loci. Our results show that the linkage disequilibrium reaches the maximum possible value, given the observed allelic frequencies, for almost all the locus pairs. This result is most consistent with the hypothesis that genetic recombination is absent or very rare in T. cruzi natural populations. Partition of the linkage disequilibrium variance for the six Bolivian populations shows that both inter- and intrapopulation components are substantial and that the relationships among the components are D_IS² < D_ST², and D'_IS² < D'_ST². These inequalities are interpreted as the result of an interplay between genetic drift, rare or absent mating, and clonal selection in generating linkage disequilibrium in T. cruzi populations.     

Use of morphological traits and microsatellite markers to characterize the Tunisian cultivated and wild figs (Ficus carica L.)

We used 8 morphological traits and 17 simple sequence repeats loci to characterize 71 cultivated and wild Tunisian fig trees (Ficus carica L.). Significant morphological differences were inferred from leaf traits. The statistical analysis showed two major fig groups that indicated a common morphological basis. A total of 74 SSR alleles was revealed, defining 63 unique multilocus genotypes indicating a substantial genetic diversity. Based on multilocus SSR genotypes an identification key was established using MFC30, MFC3, MFC11 and MFC19 loci to identify figs. Analysis of variance components of linkage disequilibrium shown that among 136 pairs of loci, 32 present a significant gametic disequilibrium. The parameter D′²_IS (0.1284) was greater than D′²_ST (0.0079), a pointer of close to zero variance in total simple, and consequently the more pronounced independence of the 17 SSR loci. The majority of Ohta's variance components of linkage disequilibrium followed a pattern caused by genetic drift or a non-systematic disequilibrium profiles and natural selection occurs only for LMFC24-MFC8 pair loci in cultivated figs. Our results suggest that the morphological and SSR markers are suitable to characterize figs and should be recommended in conservation management strategy.     

Genetic Variation and Differentiation among Populations of Chum Salmon Oncorhynchus ketaWalbaum from Southern Russian Far East

Allozyme variation of populations of chum salmon Oncorhynchus ketafrom southern Russian Far East was examined. Of 55 loci screened, 31 were polymorphic. Within-population variation accounted for most of the allele diversity; F _STaveraged over loci was 0.052. Linkage disequilibrium was found in less than 5% of locus pairs in the chum population examined. Analysis of within- and among-population variance components of linkage disequilibrium using D-statistics (Ohta, 1982) showed that most genetic variation was distributed among populations.     

Genome-wide population structure and evolutionary history of the Frizarta dairy sheep

In the present study, we used genomic data, generated with a medium density single nucleotide polymorphisms (SNP) array, to acquire more information on the population structure and evolutionary history of the synthetic Frizarta dairy sheep. First, two typical measures of linkage disequilibrium (LD) were estimated at various physical distances that were then used to make inferences on the effective population size at key past time points. Population structure was also assessed by both multidimensional scaling analysis and k-means clustering on the distance matrix obtained from the animals’ genomic relationships. The Wright’s fixation F_ST index was also employed to assess herds’ genetic homogeneity and to indirectly estimate past migration rates. The Wright’s fixation F_IS index and genomic inbreeding coefficients based on the genomic relationship matrix as well as on runs of homozygosity were also estimated. The Frizarta breed displays relatively low LD levels with r² and |Dʹ| equal to 0.18 and 0.50, respectively, at an average inter-marker distance of 31 kb. Linkage disequilibrium decayed rapidly by distance and persisted over just a few thousand base pairs. Rate of LD decay (β) varied widely among the 26 autosomes with larger values estimated for shorter chromosomes (e.g. β=0.057, for OAR6) and smaller values for longer ones (e.g. β=0.022, for OAR2). The inferred effective population size at the beginning of the breed’s formation was as high as 549, was then reduced to 463 in 1981 (end of the breed’s formation) and further declined to 187, one generation ago. Multidimensional scaling analysis and k-means clustering suggested a genetically homogenous population, F_ST estimates indicated relatively low genetic differentiation between herds, whereas a heat map of the animals’ genomic kinship relationships revealed a stratified population, at a herd level. Estimates of genomic inbreeding coefficients suggested that most recent parental relatedness may have been a major determinant of the current effective population size. A denser than the 50k SNP panel may be more beneficial when performing genome wide association studies in the breed.     

The Direction of Linkage Disequilibrium

The previous paper (Langley, Tobari and Kojima 1974) reports that the directional linkage disequilibria, D_ω = P_ABP_ab-P_AbP_aB, tend to be negative for data between allozymes and linked to inversions. A and B stand for the two alleles with the greatest frequency in the population. In this paper we show that linkage disequilibrium in this direction is produced at equilibrium when double homozygotes have fitnesses that are a constant fraction of the product of the two component single homozygote fitnesses, a pattern that is frequently observed in experimental data.     

Linkage Disequilibrium between Allozymes in Natural Populations of Lodgepole Pine

Pairwise linkage disequilibrium values (D) were estimated for 14 allozyme loci in two natural populations of lodgepole pine (Pinus contorta ssp. latifolia). Maternal multilocus genotypes were inferred from samples of (haploid) megagametophytic seed-endosperms. Coupling/repulsion double heterozygotes were distinguished for closely linked pairs of loci. Assays of seven of the loci in seed embryos allowed estimates of D for these loci in the outcross pollen pool (estimates of outcrossing rates indicate no significant departures from random mating in either population). No disequilibrium was observed between unlinked loci in either maternal genotypes or outcross pollen. However, significant disequilibrium was observed within and between gametes for some allelic combinations of four tightly linked loci; the assumption of random association of gamete types within individuals is thus invalid for some loci in lodgepole pine. Possible causes of the observed D were examined using the noncentrality parameter of the general noncentral chi square distribution. We concluded, from estimates of population size, linkage and measurements of population substructure, that neither drift nor population subdivision was responsible for the significant values of D which were observed and that epistatic selection was the most likely cause of the disequilibrium observed.     

Linkage disequilibrium between two genetic loci of the major histocompatibility complex in rats

The major histocompatibility complex (MHC) in natural populations of rats is composed of genetic phenotypes that are similar, if not identical, to those seen in inbred laboratory strains. Examination of individual wild rats from a single location in the city of Pittsburgh, Pennsylvania, resulted in the identification of seven different RT1.A histocompatibility serotypes and three RT1.B mixed lymphocytes responses. In this population of animals there is a significant association (p < 0.005) between four RT1.A and RT1.B phenotypic pairs: RT1.A⁸B¹, RTl.A^kBⁿ, RTl.A^dB^a and RT1.A¹B^a. The observed values for linkage disequilibrium (0.211,0.076,0.070 and 0.085, respectively) are very high and are close to the maximum expected, given the individual allelic frequencies. Although the animals included in this study were obtained from one location, agreement with Hardy-Weinberg equilibrium is demonstrated for other loci in the same population. The demonstration of equilibrium suggests that significant inbreeding is not affecting this population of rats. Not enough is known about the allelic frequencies in surrounding rat populations to determine how important the effect of migration is on these disequilibrium values. The large linkage disequilibria may indicate that, in the rat, environmental selective forces are operating to ensure the nonrandom association of separate components of the MHC.     

Empirical Distributions of F ST from Large-Scale Human Polymorphism Data

Studies of the apportionment of human genetic variation have long established that most human variation is within population groups and that the additional variation between population groups is small but greatest when comparing different continental populations. These studies often used Wright’s F _ST that apportions the standardized variance in allele frequencies within and between population groups. Because local adaptations increase population differentiation, high-F _ST may be found at closely linked loci under selection and used to identify genes undergoing directional or heterotic selection. We re-examined these processes using HapMap data. We analyzed 3 million SNPs on 602 samples from eight worldwide populations and a consensus subset of 1 million SNPs found in all populations. We identified four major features of the data: First, a hierarchically F _ST analysis showed that only a paucity (12%) of the total genetic variation is distributed between continental populations and even a lesser genetic variation (1%) is found between intra-continental populations. Second, the global F _ST distribution closely follows an exponential distribution. Third, although the overall F _ST distribution is similarly shaped (inverse J), F _ST distributions varies markedly by allele frequency when divided into non-overlapping groups by allele frequency range. Because the mean allele frequency is a crude indicator of allele age, these distributions mark the time-dependent change in genetic differentiation. Finally, the change in mean-F _ST of these groups is linear in allele frequency. These results suggest that investigating the extremes of the F _ST distribution for each allele frequency group is more efficient for detecting selection. Consequently, we demonstrate that such extreme SNPs are more clustered along the chromosomes than expected from linkage disequilibrium for each allele frequency group. These genomic regions are therefore likely candidates for natural selection.     

Electron transfer in reaction centers of Rhodopseudomonas sphaeroides. I. Determination of the charge recombination pathway of D+QAQ−B and free energy and kinetic relations between Q−AQB and QAQ−B

The electron-transfer reactions and thermodynamic equilibria involving the quinone acceptor complex in bacterial reaction centers from R. sphaeroides were investigated. The reactions are described by the scheme: We found that the charge recombination pathway of D⁺Q_AQ^?_B proceeds via the intermediate state D⁺Q^?_AQ_B, the direct pathway contributing less than approx. 5% to the observed recombination rate. The method used to obtain this result was based on a comparison of the kinetics predicted for the indirect pathway (given by the product k_AD-times the fraction of reaction centers in the Q^?_AQ_B state) with the observed recombination rate, k^obs_{D⁺ →D}. The kinetic measurements were used to obtain the pH dependence (6.1 ? pH ? 11.7) of the free energy difference between the states Q^?_AQ_B and Q_AQ^?_B. At low pH (less than 9) Q_AQ^?_B is stabilized relative to Q^?_AQ_B by 67 meV, whereas at high pH Q^?_AQ_B is energetically favored. Both Q^?_A and Q^?_B associate with a proton, with pK values of 9.8 and 11.3, respectively. The stronger interaction of the proton with Q^?_B provides the driving force for the forward electron transfer.     

Allozyme variation of the endangered endemic plant Myricaria laxiflora: Implications for conservation

Myricaria laxiflora, a riparian plant that naturally occurs in the riverbanks of the Yangtze River Valley, has become extinct across its entire geographical distribution range in the wild due to the construction of the Three Gorges Dam. The allozyme variation of M. laxiflora populations was investigated in the present study. Mean number of alleles per locus (A) was 2.35, and the observed heterozygosity (H_o) and expected heterozygosity (H_e) were 0.35 and 0.30, respectively. Six populations showed significant excesses of heterozygotes based on the examination of a multilocus fixation index (F_IS). The population genetic divergence of M. laxiflora is high (G_ST = 0.144 and ?_B = 0.131) and the analysis of molecular variance analysis shows that 19.71% of the total genetic variation is caused by the difference between populations. Based on the obtained genetic information, six management units have been identified, all of which are expected to enhance the effective management of the remaining and transplanted individuals of this endangered species in the future.     

A Model of Functional Epistasis and Linkage Disequilibrium in Populations with Overlapping Generations

A model of functional epistasis is proposed in which it is assumed that coupling and repulsion genotypes differ in metabolic efficiency and thus in development time and net fecundity. The implications of this model are investigated for iteroparous populations with fluctuating rates of increase. It is found that the fluctuations in rate of increase can lead to large fluctuations in gamete frequency and D, the coefficient of linkage disequilibrium, but that D will almost always have a value of zero at some point during the populations' demographic cycle. Some of the model populations would be expected to be in a state of linkage disequilibrium only fleetingly: others would exhibit D-cycles interpretable as random fluctuation. Implications of the model for interpretations of existing data on linkage disequilibrium among enzyme loci in Drosophila are discussed.     

Efficacy of pyramiding elite alleles for dynamic development of plant height in common wheat

Plant height is an important botanical feature closely related to yield. Two populations consisting of 118 and 262 accessions respectively were used to identify elite alleles for plant height and to validate their allelic effects. Plant height was measured from the early booting to the flowering stages. Simple sequence repeat markers for candidate quantitative trait locus (QTL) regions with large effects identified in a doubled haploid (DH) population (Hanxuan 10 × Lumai 14) were selected for further verification by association analysis. Nine loci significantly (P < 0.001) associated with plant height were detected 13 times in the population with 118 accessions. Three loci (Xgwm11-1B, Xwmc349-4B and Xcfd23-4D) were identified in three, two and two periods of plant height growth, respectively. Markers Xbarc168-2D, Xgwm249-2D, Xwmc349-4B, Xcfd23-4D and Xgwm410-5A located at or near additive QTL regions in the DH population proved to coincide with known Rht loci. The results showed a consistency between linkage analysis and association mapping, and also confirmed the value of fine mapping of QTL through combined linkage and association analyses. For final plant height, the alleles Xgwm11-1B ₂₀₈ , Xwmc349-4B ₁₀₃ and Xcfd23-4D ₂₀₂ exhibited negative effects, i.e. reducing plant height; Xwmc349-4B ₁₀₁ and Xcfd23-4D ₂₀₅ showed significant positive effects. A second larger population (262 accessions) was used to validate the effects of these large-effect alleles and the efficacy of pyramiding in eight environments (year × site × water regime combinations). Strong correlations between final plant height and numbers of large-effect alleles indicated that the alleles contributed additively to plant height. The additive effects showed that pyramiding elite alleles for target traits has significant potential for wheat breeding.     

Effect of Mating Structure on Variation in Linkage Disequilibrium

Measurement of linkage disequilibrium involves two sampling processes. First, there is the sampling of gametes in the population to form successive generations, and this generates disequilibrium dependent on the effective population size (N_e) and the mating structure. Second, there is sampling of a finite number (n) of individuals to estimate the population disequilibrium.——Two-locus descent measures are used to describe the mating system and are transformed to disequilibrium moments at the final sampling. Approximate eigenvectors for the transition matrix of descent measures are used to obtain formulae for the variance of the observed disequilibria as a function of N_e, mating structure, n, and linkage or recombination parameter.——The variance of disequilibrium is the same for monoecious populations with or without random selfing and for dioecious populations with random pairing for each progeny. With monogamy, the variance is slightly higher, the proportional difference being greater for unlinked loci.     

Strong population genetic structure and its implications for the conservation and management of the endangered Itasenpara bitterling

To infer the population genetic structure and genetic diversity of Itasenpara bitterling (Acheilognathus longipinnis), a cyprinid species endemic to Japan and distributed in only three specific regions, we investigated mitochondrial DNA variation. The distribution of the haplotypes among the three regions showed distinct geographic structure, and no common haplotypes were observed among regions. Analysis of molecular variance revealed a significant proportion of the genetic variance was partitioned among regions (93.1 %, P < 0.001), and pairwise estimates of D_A and Φ_ST between regions also revealed strong population structure. Given the strong genetic structure and low genetic diversity within regions, we strongly suggest that each region should be treated as a separate unit in any conservation program and any inter-regional translocations should be avoided.     

Patterns of Genetic Diversity in Platanthera bifolia (Orchidaceae) with Respect to Life History Traits and Recent Range Expansion

For evolutionary and ecological analyses, genetic diversity at different scales needs to be studied in terms of biological properties, habitat, population size and population history. We surveyed Platanthera bifolia populations from six regions in northeastern Poland to determine the impact of the mating system and population history on genetic diversity. Based on variation at allozyme markers, genetic variation was relatively moderate (P?=?22.3%, A?=?1.48, H _O?=?0.083, F _IS?=??0.015) and similar to other Platanthera species. These parameters varied between populations (P?=?13.3%–26.6%, A?=?1.26–1.66, H _O?=?0.055–0.111, F _IS?=??0.262–0.147). The genetic diversity patterns were shaped by different proportions of facilitated selfing and/or outcrossing, resulting in positive and negative F _IS values, respectively. No relationship between inbreeding coefficient and population size, however, and no impact of apomixis on the level of genetic diversity of P. bifolia were found. The relatively low level of genetic differentiation among the investigated regions (F _CT?=?0.002, P?>?0.05) and among populations (F _ST?=?0.048, P?<?0.001), and the lack of a significant relationship between genetic and geographical distance, are discussed in the context of possible scenaria of postglacial expansion.     

Endogenous Expression of Adenosine A<Subscript>1</Subscript>, A<Subscript>2 </Subscript>and A<Subscript>3</Subscript> Receptors in Rat C6 Glioma Cells

Inhibitory and stimulatory adenosine receptors have been identified and characterized in both membranes and intact rat C6 glioma cells. In membranes, saturation experiment performed with [³H]DPCPX, selective A₁R antagonist, revealed a single binding site with a K _D = 9.4 ± 1.4 nM and B _max = 62.7 ± 8.6 fmol/mg protein. Binding of [³H]DPCPX in intact cell revealed a K _D = 17.7 ± 1.3 nM and B _max = 567.1 ± 26.5 fmol/mg protein. On the other hand, [³H]ZM241385 binding experiments revealed a single binding site population of receptors with K _D = 16.5 ± 1.3 nM and B _max = 358.9 ± 52.4 fmol/mg protein in intact cells, and K _D = 4.7 ± 0.6 nM and B _max = 74.3 ± 7.9 fmol/mg protein in plasma membranes, suggesting the presence of A_2A receptor in C6 cells. A₁, A_2A, A_2B and A₃ adenosine receptors were detected by Western-blotting and immunocytochemistry, and their mRNAs quantified by real time PCR assays. Giα and Gsα proteins were also detected by Western-blotting and RT-PCR assays. Furthermore, selective A₁R agonists inhibited forskolin- and GTP-stimulated adenylyl cyclase activity and CGS 21680 and NECA stimulated this enzymatic activity in C6 cells. These results suggest that C6 glioma cells endogenously express A₁ and A₂ receptors functionally coupled to adenylyl cyclase inhibition and stimulation, respectively, and suggest these cells as a model to study the role of adenosine receptors in tumoral cells.     

Uniform selection as a primary force reducing population genetic differentiation of cavitation resistance across a species range

Background

Cavitation resistance to water stress-induced embolism determines plant survival during drought. This adaptive trait has been described as highly variable in a wide range of tree species, but little is known about the extent of genetic and phenotypic variability within species. This information is essential to our understanding of the evolutionary forces that have shaped this trait, and for evaluation of its inclusion in breeding programs.

Methodology

We assessed cavitation resistance (P ₅₀), growth and carbon isotope composition in six Pinus pinaster populations in a provenance and progeny trial. We estimated the heritability of cavitation resistance and compared the distribution of neutral markers (F _ST) and quantitative genetic differentiation (Q _ST), for retrospective identification of the evolutionary forces acting on these traits.

Results/Discussion

In contrast to growth and carbon isotope composition, no population differentiation was found for cavitation resistance. Heritability was higher than for the other traits, with a low additive genetic variance (h² _ns = 0.43±0.18, CV_A = 4.4%). Q _ST was significantly lower than F _ST, indicating uniform selection for P ₅₀, rather than genetic drift. Putative mechanisms underlying Q_STST are discussed.     

The dependence of reaction center and antenna triplets on the redox state of Photosystem I

The formation of chlorophyll triplet states during illumination of Photosystem I reaction center samples depends upon the redox state of P-700, X and ferredoxin Centers A and B. When the reaction centers are in the states P-700⁺A₁XFd_BFd^?_A and P-700 A₁XFd^?_BFd^?_A prior to illumination, we observe electron paramagnetic resonance (EPR) spectra from a triplet species which has zero-field splitting parameters (|D| and |E|) larger than those of either the chlorophyll a or chlorophyll b monomer triplet, and a polarization which results from population of the triplet spin sublevels by an intersystem crossing mechanism. We interpret this triplet as arising from photoexcited chlorophyll antenna species associated with reaction centers in the states P-700⁺Fd^?_A and P-700⁺X^?, respectively, which undergo de-excitation via intersystem crossing. When the reaction centers are in the states P-700A₁XFd^?_BFd^?_A and P-700A₁X^?Fd^?_BFd^?_A prior to illumination, we observe a triplet EPR signal with a polarization which results from population of the triplet spin sublevels by radical pair recombination, and which has a |D| value similar to that of chlorophyll a monomer. We interpret this triplet (the radical pair-polarized triplet) as arising from ³P-700 which has been populated by the process $\text{P-700}{}^{\mathrm{+}}\text{A}{}^{\mathrm{?}}{}_1\text{→}{}^3\text{P-700}\text{A}{}_1$. We observe both the radical pair-polarized triplet and the chlorophyll antenna triplet when the reaction centers are in the state P-700 A₁XFd^?_BFd^?_A, presumably because the processes P-700⁺A^?₁X → P-700⁺A₁X^? and $\text{P-700}{}^{\mathrm{+}}\text{A}{}^{\mathrm{?}}{}_1\text{X}\text{→}{}^3\text{P-700}\text{A}{}_1\text{X}$ have similar rate constants when Centers A and B are reduced, i.e., the forward electron transfer time from A^?₁ to X is apparently much slower in the redox state P-700 A₁XFd^?_BFd^?_A than it is in state P-700 A₁XFd_BFd_A. The amplitude of the radical pair-polarized triplet EPR signal does not decrease in the presence of a 13.5-G-wide EPR signal centered at g 2.0 which was recorded in the dark prior to triplet measurements in samples previously frozen under intense illumination. This g 2.0 signal, which has been attributed to phototrapped A^?₁ (Heathcote, P., Timofeev, K.N. and Evans, M.C.W. (1979) FEBS Lett. 101, 105–109), corresponds to as many as 12 spins per P-700 and can be photogenerated during freezing without causing any apparent attenuation of the radical pair-polarized triplet amplitude. We conclude that species other than A^?₁ contribute to the g 2.0 signal.     

Detecting Wahlund effects together with amplification problems: Cryptic species,null alleles and short allele dominance in Glossina pallidipes populations from Tanzania

Population genetics is a convenient tool to study the population biology of non‐model and hard to sample species. This is particularly true for parasites and vectors. Heterozygote deficits and/or linkage disequilibrium often occur in such studies and detecting the origin of those (Wahlund effect, reproductive system or amplification problems) is uneasy. We used new tools (correlation between the number of times a locus is found in significant linkage disequilibrium and its genetic diversity, correlations between Wright's F_IS and F_ST, F_IS and number of missing data, F_IT and allele size and standard errors comparisons) for the first time on a real data set of tsetse flies, a vector of dangerous diseases to humans and domestic animals in sub‐Saharan Africa. With these new tools, and cleaning data from null allele, temporal heterogeneity and short allele dominance effects, we unveiled the coexistence of two highly divergent cryptic clades in the same sites. These results are in line with other studies suggesting that the biodiversity of many taxa still largely remain undescribed, in particular pathogenic agents and their vectors. Our results also advocate that including individuals from different cohorts tends to bias subdivision measures and that keeping loci with short allele dominance and/or too frequent missing data seriously jeopardize parameter's estimations. Finally, separated analyses of the two clades suggest very small tsetse densities and relatively large dispersal.     

Depsipeptides from Metarhizium anisopliae

From the culture medium of a strain of Metarhizium anisopliae, 14 depsipeptides have been isolated. Five of them were identified as known destruxins A, B, C, D and desmethyldestruxin B. The structures of the new compounds, named destruxins E, A₁, A₂, B₁, B₂, C₂, D₁, D₂ and E₁,were established mainly from the mass spectral analysis of their corresponding open-chain derivatives.