Persistence of a Wolbachia infection frequency cline in Drosophila melanogaster and the possible role of reproductive dormancy

Field populations of arthropods are often polymorphic for Wolbachia but the factors maintaining intermediate Wolbachia frequencies are generally not understood. In Drosophila melanogaster, Wolbachia frequencies are highly variable across the globe. We document the persistence of a Wolbachia infection frequency cline in D. melanogaster populations from eastern Australia across at least 20 years, with frequencies generally high in the tropics but lower in cool temperate regions. The results are interpreted using a model of frequency dynamics incorporating cytoplasmic incompatibility (CI), imperfect maternal transmission and Wolbachia effects on fitness. Clinal variation is less pronounced in eastern North America which may reflect annual recolonization at higher latitudes. Limited samples from Africa from latitudes matching our tropical and subtropical samples from Australia and North America show comparably high infection frequencies, but some equatorial samples show lower frequencies. Adult dormancy across cold periods may contribute to the Australian Wolbachia cline. Infected flies exposed to cold conditions for an extended period had reduced fecundity and viability, an effect not evident in unexposed controls. These fitness costs may contribute to the relatively low Wolbachia frequencies in Australian temperate areas; whereas different processes, including CI induced by young males, may contribute to higher frequencies in tropical locations.     

The frequency of P1 transduction of the genes of Escherichia coli as a function of chromosomal position: preferential transduction of the origin of replication.

Summary The frequencies with which the generalized transducing phage P1 transduced 26 selected markers on the E. coli. chromosome were measured. The frequencies were found to vary relative to argH ⁺=1 from a maximum of 6.8 near the origin of replication to a minimum of 0.23 for a marker not far from the terminus. The low frequencies obtained for some markers were shown not to result from poor expression under the selective conditions employed. When plotted as a function of marker position on the chromosome the frequencies were found to exhibit a series of peaks and troughs which correspond to those in gene density noted by Bachmann et al. (1976). The possible relationship of these results to the structure of the E. coli chromosome and to the mechanism of generalized transduction are discussed.     

Recombination rates of soybean varieties from different periods of introduction and release

Theory predicts that selection for adaptability during the short term also favors selection for a reduced recombination rate in the population. The objective of this study was to test whether the cyclic short-term selection which has taken place in soybean breeding programs in the USA since the introduction of the crop has measurably reduced recombination frequencies. Thirteen soybean varieties separated into four different release periods (prior to 1940, 1940–1954, 1955–1969, after 1970) were evaluated for their recombination frequencies within three locus pairs. Recombination frequencies among the individual varieties ranged from 7.6 to 24.1 % at thep ₁ r locus pair, from 20.9 to 30.1 % at thelnp ₂ locus pair, and from 28.7 to 41.6% at thedt ₁ l ₁ locus pair. Recombination frequencies were significantly different among varieties within a release period for thep ₁ r andlnp ₂ locus pairs, but recombination frequencies did not differ among release periods for any locus pair. Thus, apparently, plant breeders have developed soybean varieties with improved adaptation without influencing recombination rates.     

Polymorphism of hordein-coding loci in barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) populations of Iran and Central Asian countries

Starch gel electrophoresis was performed to study polymorphism of hordeins encoded by the Hrd A, Hrd B, and Hrd F loci in 366 local old barley accessions from Iran and Central Asian countries, including Turkmenistan, Uzbekistan, Tajikistan (Mountain Badahsan), and Kirgizia. In total, 60 alleles with frequencies of 0.0003–0.2818 were observed for the Hrd A locus, 106 alleles with frequencies of 0.0003–0.1603 were observed for the Hrd B locus, and five alleles with frequencies of 0.0164–0.4131 were observed for the Hrd F locus. The alleles and allele frequencies displayed irregular distributions in barley populations of the above countries. Cluster analysis of the matrix of allele frequencies in populations from known collection sites revealed a cluster structure of local barley populations within each country. Local populations formed five differently sized clusters in Iran, six in Turkmenistan, three in Uzbekistan, and three in Kirgizia. The variation and allele frequency distribution of the hordein-coding loci in Iran and Central Asian countries were assumed to result from the introduction and spreading of barley forms via migrations of husbandmen.     

Reduced parasitism of a leaf-mining moth on trees with high infection frequencies of an endophytic fungus

We investigated relationships between endophytic fungi and a leaf-mining moth, Phyllonorycter sp., along an elevational gradient from 2255 to 2895 m. The fungi and moth larvae inhabit leaves of Quercus gambelii. Fungal frequencies and larval densities varied with elevation. However, larval densities were not associated with the frequencies of infection by endophytic fungi. Survival of larvae was positively associated with the most dominant fungus, Gnomonia cerastis, owing to reduced parasitism of moth larvae on trees with high frequencies of Gnomonia.     

Inference of chromosomal inversion dynamics from Pool‐Seq data in natural and laboratory populations of Drosophila melanogaster

Sequencing of pools of individuals (Pool‐Seq) represents a reliable and cost‐effective approach for estimating genome‐wide SNP and transposable element insertion frequencies. However, Pool‐Seq does not provide direct information on haplotypes so that, for example, obtaining inversion frequencies has not been possible until now. Here, we have developed a new set of diagnostic marker SNPs for seven cosmopolitan inversions in Drosophila melanogaster that can be used to infer inversion frequencies from Pool‐Seq data. We applied our novel marker set to Pool‐Seq data from an experimental evolution study and from North American and Australian latitudinal clines. In the experimental evolution data, we find evidence that positive selection has driven the frequencies of In(3R)C and In(3R)Mo to increase over time. In the clinal data, we confirm the existence of frequency clines for In(2L)t, In(3L)P and In(3R)Payne in both North America and Australia and detect a previously unknown latitudinal cline for In(3R)Mo in North America. The inversion markers developed here provide a versatile and robust tool for characterizing inversion frequencies and their dynamics in Pool‐Seq data from diverse D. melanogaster populations.     

An interpretation of the frequencies of host specific phenotypes of Phytophthora infestans in North Wales

Race surveys of Phytophthora infestans over 4 years in North Wales have shown that races unselected by host resistance are frequent. In most cases frequencies of complex races are those expected from the frequencies of simple race characters if these assort at random. These results suggest that recombination between races may be unrestricted. The significance of unexpected deviations from the predicted frequencies are discussed.     

Geographic pattern of allozyme and inversion polymorphism on chromosome O of Drosophila subobscura and its evolutionary origin

The chromosome O of Drosophila subobscura was studied with respect to genetic variability at three enzyme loci (Odh, Me, and Lap-4) and with respect to inversion polymorphism. Population samples were taken from seven localities along a north-south gradient from Sweden and Scotland to Tunisia.The chromosomal analysis revealed clinal frequency changes for gene arrangements from north to south. With the enzyme loci Odh and Me allele frequencies are similar throughout the distribution range. Both loci are located outside the common inversion complex O₃₊₄. On the other hand, frequency changes parallel to those of the gene arrangements were observed for the alleles of the Lap-locus. Nonrandom associations between Lap-alleles and the superimposed gene arrangements O_ST, O₃₊₄, O₃₊₄₊₈, and O₃₊₄₊₂₃ were found. These gene arrangements differ from each other with respect to allele frequencies at the Lap-locus but for a given gene arrangement the relative frequencies of Lap-alleles remain relatively constant along the north-south gradient. Thus allele frequencies at the Lap-locus can be predicted from inversion frequencies.These observations can be interpreted in such a way that the pattern of allozyme variation within gene arrangements is due to founder effects caused by the unique origin of inversions. The gene blocks in the different inversions seem to represent more or less separated gene pools. In polymorphic populations the coexistence of genetically differentiated inversions presumably gives rise to heterotic interaction.     

Effects of Chemotherapeutics on Bacterial Ecology in the Water of Ponds and the Intestinal Tracts of Cultured Fish,Ayu (Plecoglossus altivelis)

Drug-resistant gram-negative bacilli conferred with R factors were isolated with high frequencies from the intestinal tracts of ayu (Plecoglossus altivelis) cultured in ponds, in which chemotherapeutics had often been used, and with relatively low frequencies from ayu which received no administration of chemotherapeutics. Drug-resistant bacteria were also isolated at low frequencies from the intestinal tracts of wild ayu in rivers, as well as from the water of ayu-culturing ponds and some of them carried R factors. The drug-resistant bacteria carrying R factors were Aeromonas liquefaciens, Citrobacter, Enterobacter cloacae, Escherichia coli, Hafnia and unidentified strains. All the R factors were classified as the Fi^–(F) type, except the two R factors detected in an E. coli strain and in an unidentified strain.     

Polymorphism of hordein-coding loci in cultivated barley (<Emphasis Type="Italic">Hordeum vulgare</Emphasis> L.) in Afghanistan

Polymorphism of hordeins encoded by the Hrd A, Hrd B, and Hrd F loci was analyzed in 84 accessions of local barley (Hordeum vulgare L.) varieties from major agricultural regions of Afghanistan using starch gel electrophoresis. Forty alleles of the Hrd A locus with the frequencies from 0.12 to 32.73%, 62 alleles of the Hrd B locus with the frequencies from 0.12 to 14.29%, and five alleles of the Hrd F locus with the frequencies from 0.59 to 32.15% have been identified. The conclusion about genetic similarity of barley populations from different regions of Afghanistan is made on the basis of cluster analysis of the matrix of allele frequencies in barley populations from 31 localities. The local barley populations form four unequal clusters. The largest cluster I includes populations from 14 localities of Afghanistan. The second largest cluster IV consists of populations from ten localities, and clusters II and III comprise populations from four and three localities, respectively. Each of the four clusters includes populations from different regions of northern and southern Afghanistan. Based on our results, we conclude that the diversity of hordein-coding loci and the distribution of their alleles among different regions of Afghanistan are the consequences of introduction of barley landraces and their distribution over trade routes.     

Effects of hydration on scale factors for ab initio force constants. IV. trans and cis N-methylacetamide

Scaled quantum mechanical force fields have been calculated using the 4-31G basis for trans and cis conformers of both isolated and water-solvated N-methylacetamide (NMA). (1) A single set of scale factors for isolated NMA yields relatively correct predictions of the shifts in vibrational frequencies between the trans and cis conformers. This is also true of a single set of scale factors for trans and cis NMA in water. The total standard deviation between measured and calculated frequencies for trans NMA in both isolated and solvated states is 6 cm^?1. This implies that it should be possible to use a single set of scale factors to accurately predict the vibrational spectra of a peptide in a variety of conformational states. (2) The computationally predicted effect of hydration on force constants for the supermolecule NMA · nH₂O are generally consistent with the experimentally measured effects of hydration on scale factors. These results indicate that supermolecule calculations can be useful in predicting the effects of hydration on spectra. (3) Three types of scale factors are calculated as follows: (a) first from ab initio calculations on an isolated molecule using frequencies measured from isolated molecules; (b) second from calculations on an isolated molecule using frequencies measured from water-solvated or otherwise hydrogen-bonded molecules; (c) and third from supermolecule calculations on a molecule hydrogen-bonded to water, using frequencies measured from water-solvated molecules. (4) The third type of scale factors are similar to the first type, for confidently measured modes, even though some of the force constants are very different. This suggests that one set of scale factors may be transferable to both isolated and hydrogen-bonded molecules, and that the simple representation of hydration used here may be a useful approximation. The second type of scale factors yield accurate frequencies, but they may not be generally transferable.     

Diurnal variability of gene arrangement frequencies in Drosophila subobscura populations from two habitats*

The rich inversion polymorphism of chromosomes of Drosophila subobscura varies in association with environmental changes at spatial and temporal level. Due to random factors this might become less regular and this might be the reason that there is little evidence of altitudinal and seasonal, microgeographic and habitat‐related variability. The variability of gene arrangement frequencies over daytime period was investigated in populations of D. subobscura from two ecologically different habitats. According to gene arrangement frequencies and inversion polymorphism parameters populations fit into the existing patterns of regional polymorphism. Even though populations display daytime variability for the frequencies of arrangements of chromosomes U and J, the nonsignificant differences in other arrangement frequencies, as well as data obtained from genetic distances between samples from different times of day, rule out the existence of subpopulations distinguished from each other by diurnal activity within two habitats. Some particular arrangement frequencies vary according to temperature and humidity and some changes appear for different karyotypic combinations between beech and oak habitat, which suggests different adaptive advantages and selective mechanisms. Cluster analysis of gene arrangement frequencies indicates some importance of A chromosome arrangements for diurnal activity and show in dependence to other ecological data that internally fixed daily activity rhythm might exists in D. subobscura. Analysis of light, temperature and humidity factors in relation to the frequency data obtained indicate a choice of different ecological niche in a temporally structured habitat due to behavioural genetic information.     

Study of the Association between Constitutional Exogenous Obesity and Polymorphism of the Apolipoprotein B Gene

An attempt was made to associate the insertion–deletion (Ins/Del) polymorphism of the apolipoprotein B gene (apoB) with obesity and to identify alleles and genotypes predisposing to this disorder. The apoB Ins/Del allele frequencies observed in the Russian population were similar to those in West European populations and significantly differed from frequencies reported for Asian populations. Patients with obesity did not differ from healthy individuals in allele and genotype frequencies regardless of whether total or sex-stratified samples were compared. Estimation of relative risk for individuals with genotype Ins/Ins did not reveal a significant association between obesity and this genotype. Thus, constitutional exogenous obesity did not prove to be associated with the Ins/Del polymorphism of theapoB gene in the Russian population.     

Worldwide allele frequencies of the human apolipoprotein E gene: Climate,local adaptations,and evolutionary history

The ?4 allele of the apolipoprotein E (APOE) gene is associated with increased cholesterol levels and heart disease. Population allele frequencies of APOE have previously been shown to vary, with ?4 frequencies generally increasing with latitude. We hypothesize that this trend resulted from natural selection protecting against low‐cholesterol levels. In high‐latitude cold environments and low‐latitude hot environments, metabolic rate is elevated, which could require higher cholesterol levels. To explore this hypothesis, we compiled APOE allele frequencies, latitude, temperature, and elevation from populations around the world. ?4 allele frequencies show a curvilinear relationship with absolute latitude, with lowest frequencies found in the mid‐latitudes where temperatures generally require less expenditure on cooling/thermogenesis. Controlling for population structure in a subset of populations did not appreciably change this pattern of association, consistent with selection pressures that vary by latitude shaping ?4 allele frequencies. Temperature records also predict APOE frequency in a curvilinear fashion, with lowest ?4 frequencies at moderate temperatures. The model fit between historical temperatures and ?4 is less than between latitude and ?4, but strengthened after correcting for estimated temperature differences during the Paleolithic. Contrary to our hypothesis, we find that elevation did not improve predictive power, and an integrated measure of the cholesterol effect of multiple APOE alleles was less related to latitude than was ?4 alone. Our results lend mixed support for a link between past temperature and human APOE allele distribution and point to the need to develop better models of past climate in future analyses. Am J Phys Anthropol 143:13–20, 2010. © 2010 Wiley‐Liss, Inc.     

Genetic studies in Paraguay: blood group, red cell, and serum genetic patterns of the Guayaki and Ayore Indians, Mennonite settlers, and seven other Indian tribes of the Paraguayan Chaco

Genetic studies of 540 Paraguayan Indians from nine tribal groups and 51 Mennonites are presented for ABO, MNSs, P₁, Rh, Kell, Lewis, Duffy, Diego; for serum immunoglobulins and haptoglobins, G6PD-deficiency, and thalassemia trait. Group O gene frequencies for all Indian groups were 1.00; for r (cde), 0.00. Tapiete, Lengua, Toba, and Sanapana R_z (CDE) frequencies were among the highest ever reported. N frequencies were high for Ache Kwera (Guayaki), Lengua, Cheroti, Guarayu, Tapiete; N and s low for Ayore. MS frequencies were high for Sanapana, Lengua, Ayore; Ns for Tapiete. Diego was notably absent for Toba, Lengua, Guarayu, Tapiete, Ayore. Homogeneous frequencies for Fy^a (1.000) occurred among Guarayu and Tapiete, and for P₁ among Guayaki. Inv(a) frequencies were low for Cheroti, Chulupi, Guayaki. Hp 1 among Guayaki (Ache Kwera 0.15) is lowest ever reported. G6PD deficiency and abnormal hemoglobins were uniformly absent from all groups. Mennonite results were homogeneous and point toward Dutch origins. Differences among groups studied, and between Paraguayan and other Amerinds emphasize importance of genetic drift and founder principle. Abandonment of their tribes by mixed-blood offspring is partly responsible for apparent genetic purity and homogeneity of groups.     

Sister chromatid exchanges in cultured immature embryos of wheat species and regenerants

Immature embryos of Triticum aestivum (ten cultivars and lines), T. durum, T. dicoccum and T. monococcum were cultured in vitro on MS medium supplemented with 1 or 2 mg/l of 2,4-D and 20 or 30 g/l of sucrose for 3 days and processed to score sister chromatid exchanges (SCEs) per chromosome. Media components affect DNA replication from the start of the culture. The SCE frequencies were dependent on the genotype and were not correlated with the degree of ploidy. They increased after doubling of the concentration of 2,4-D and/or sucrose, except in one cultivar of T. aestivum. The mean numbers were lower than observed in root meristems of T. aestivum (two cultivars) and T. dicoccum. Immature embryos of regenerants of T. aestivum (one cultivar) and T. durum demonstrated variable SCE frequencies, which may have been caused by mutations in the parental cell cultures. In the T. aestivum embryos the lowest frequencies were found in regenerants obtained from explants with the highest frequencies.     

Genomic instability in chidren born after the Chernobyl Nuclear Accident (in vivo and in vitro studies)

Analysis of peripheral blood lymphocytes in children born after the accident at the Chernobyl Nuclear Power Plant in the period from 1987 to 2004 (permanent residents of territories contaminated with radionuclides, n = 92; and children of irradiated fathers-liquidators, n = 88) revealed increased levels of aberrant cells (ACs) and aberrations of the chromosomal type as compared to the control (P < 0.05). In three subgroups of children with different initial AC frequencies (children with high AC frequencies, ≥3%; children with medium AC frequencies, 2%; and children with low AC frequencies, ≤1%), the levels of aberrations of the chromosomal type are increased as compared to the control (P < 0.05). The levels of aberrant cells and chromosome aberrations (CAs) in the subgroup of children with ≥3% frequencies significantly differ from those in the subgroup of children with ≤1% AC frequencies. No dependence of the AC and CA frequencies on the year of birth after the Chernobyl accident was revealed. After fractional and single γ-irradiation (137Cs) of blood in vitro in the 10–30 cGy dose range, the average CA frequencies in the first and second mitoses increased in a similar way depending on the initial AC frequencies in the children and parents. All these results suggest an individual character of genomic instability induced by low radiation doses and its transgenerational phenomenon in the organisms of children.     

Resource partitioning of sonar frequency bands in rhinolophoid bats

Summary In the Constant Frequency portions of the orientation calls of various Rhinolophus and Hipposideros species, the frequency with the strongest amplitude was studied comparatively. (1) In the five European species of the genus Rhinolophus call frequencies are either species-specific (R. ferrumequinum, R. blasii and R. euryale) or they overlap (R. hipposideros and R. mehelyi). The call frequency distributions are approximately 5–9 kHz wide, thus their ranges spead less than ±5% from the mean (Fig. 1). Frequency distributions are considerably narrower within smaller geographic areas. (2) As in other bat groups, call frequencies of the Rhinolophoidea are negatively correlated with body size (Fig. 3). Regression lines for the genera Rhinolophus and Rhinolophus, species from dryer climates have on the average higher call frequencies than species from tropical rain forests. (4) The Krau Game Reserve, a still largely intact rain forest area in Malaysia, harbours at least 12 syntopic Rhinolophus and Hipposiderso species. Their call frequencies lie between 40 and 200 kHz (Fig. 2). Distribution over the available frequency range is significantly more even than could be expected from chance alone. Two different null hypotheses to test for random character distribution were derived from frequency-size-relations and by sampling species assemblages from a species pool (Monte Carlo method); both were rejected. In particular, call frequencies lying close together are avoided (Figs. 4, 5). Conversely, the distribution of size ratios complied with a corresponding null hypothesis. This even distribution may be a consequence of resource partitioning with respect to prey type. Alternatively, the importance of these calls as social signals (e.g. recognition of conspecifics) might have necessitated a communication channel partitioning.     

Genetic structure of Halotydeus destructor and Penthaleus major populations in Victoria (Acari: Penthaleidae)

The redlegged earth mite (Halotydeus destructor) and the blue oat mite (Penthaleus major) are major pests of pastures and crops in southern Australia. Reproductive modes, migration rates and levels of differentiation between populations were investigated using allozyme electrophoresis. Collections were made throughout Victoria and a sample was also obtained from Western Australia. Three enzyme loci were polymorphic in H. destructor (Mdh-1, Mdh-2 and Idh). Genotype frequencies of these loci did not differ between phenotypic males and females, providing no evidence for haplodiploidy. Allele frequencies were in Hardy-Weinberg equilibrium, indicating that H. destructor is diploid and sexual. This was confirmed via crosses between males and females. Allele frequencies differed between Victorian sites, although F statistics indicated little differentiation over all loci. A sample from Western Australia did not differ in allele frequencies from the Victorian sites. Four polymorphic loci were found in P. major (Mdh-1, Mdh-2, Idh and Gpi). Only a few multilocus genotypes occurred in a sample, indicating that P. major is parthenogenic. No male P. major were found in this study. A number of colour morphs were also identified and a genetic association between genital plate colour and clonal type was found in one population of P. major. Two different body colour morphs were associated with different clonal types.     

Behavioral responses of two Malaysian primates (Hylobates lar andPresbytis melalophos) to selective logging: Vocal behavior,territoriality, and nonemigration

The durations of logging operations may be regarded as critical periods in which primates will be required to make rapid adjustments in behavioral patterns. Primates are extremely difficult to observe during logging operations, but their behavioral response may be interpreted from analysis of calling patterns. In Hylobates lar,increased calling frequencies of groups may be indicative of intruder pressure, as may reduced calling frequencies of animals which are avoiding confrontation with conspecifics or avoiding detection by loggers. In Presbytis melalophosthe function of calling is to mediate intergroup avoidance, such that differential calling frequencies would not be expected. Where reduction in calling occurs it is probably directed toward concealment from loggers. Groups do not emigrate from active logging areas and movement outside of established territories occurs only to a very limited extent.