Broad maternal geographic origin of domestic sheep in Anatolia and the Zagros

We investigated the controversial origin of domestic sheep (Ovis aries) using large samples of contemporary and ancient domestic individuals and their closest wild relatives: the Asiatic mouflon (Ovis gmelini), the urial (Ovis vignei) and the argali (Ovis ammon). A phylogeny based on mitochondrial DNA, including 213 new cytochrome-b sequences of wild Ovism confirmed that O. gmelini is the maternal ancestor of sheep and precluded mtDNA contributions from O. vignei (and O. gmelini × O. vignei hybrids) to domestic lineages. We also produced 54 new control region sequences showing shared haplogroups (A, B, C and E) between domestic sheep and wild O. gmelini which localized the domestication center in eastern Anatolia and central Zagros, excluding regions further east where exclusively wild haplogroups were found. This overlaps with the geographic distribution of O. gmelini gmelini, further suggesting that the maternal origin of domestic sheep derives from this subspecies. Additionally, we produced 57 new CR sequences of Neolithic sheep remains from a large area covering Anatolia to Europe, showing the early presence of at least three mitochondrial haplogroups (A, B and D) in Western colonization routes. This confirmed that sheep domestication was a large-scale process that captured diverse maternal lineages (haplogroups).

Honey Bee Diversity Is Swayed by Migratory Beekeeping and Trade Despite Conservation Practices: Genetic Evidence for the Impact of Anthropogenic Factors on Population Structure

The intense admixture of honey bee (Apis melliferaL.) populations at a global scale is mostly attributed to the widespread migratory beekeeping practices and replacement of queens and colonies with non-native races or hybrids of different subspecies. These practices are also common in Anatolia and Thrace, but their influence on the genetic make-up of the five native subspecies of honey bees has not been explored. Here, we present an analysis of 30 microsatellite markers from honey bees from six different regions in Anatolia and Thrace (N= 250 samples), with the aim of comparing the impact of: (1) migratory beekeeping, (2) queen and colony trade, and (3) conservation efforts on the genetic structure of native populations. Populations exposed to migratory beekeeping showed less allegiance than stationary ones. We found genetic evidence for migratory colonies, acting as a hybrid zone mobile in space and time, becoming vectors of otherwise local gene combinations. The effect of honey bee trade leaves very high introgression levels in native honey bees. Despite their narrow geographic range, introgression occurs mainly with the highly commercial Caucasian bees. We also measured the direction and magnitude of gene flow associated with bee trade. A comparison between regions that are open and those closed to migratory beekeeping allowed the evaluation of conservation sites as centers with limited gene flow and demonstrated the importance of establishing such isolated regions. Despite evidence of gene flow, our findings confirm high levels of geographically structured genetic diversity in four subspecies of honey bees in Turkey and emphasize the need to develop policies to maintain this diversity. Our overall results are of interest to the wider scientific community studying anthropogenic effects on the population diversity of honey bees and other insects. Our findings on the effects of migratory beekeeping, replacement of queens and colonies have implications for the conservation of honey bees, other pollinators, and invertebrates, in general, and are informative for policy-makers and other stakeholders in Europe and beyond.

Metatranscriptomic analyses of honey bee colonies

Honey bees face numerous biotic threats from viruses to bacteria, fungi, protists, and mites. Here we describe a thorough analysis of microbes harbored by worker honey bees collected from field colonies in geographically distinct regions of Turkey. Turkey is one of the World's most important centers of apiculture, harboring five subspecies of Apis mellifera L., approximately 20% of the honey bee subspecies in the world. We use deep ILLUMINA-based RNA sequencing to capture RNA species for the honey bee and a sampling of all non-endogenous species carried by bees. After trimming and mapping these reads to the honey bee genome, approximately 10% of the sequences (9–10 million reads per library) remained. These were then mapped to a curated set of public sequences containing ca. Sixty megabase-pairs of sequence representing known microbial species associated with honey bees. Levels of key honey bee pathogens were confirmed using quantitative PCR screens. We contrast microbial matches across different sites in Turkey, showing new country recordings of Lake Sinai virus, two Spiroplasma bacterium species, symbionts Candidatus Schmidhempelia bombi, Frischella perrara, Snodgrassella alvi, Gilliamella apicola, Lactobacillus spp.), neogregarines, and a trypanosome species. By using metagenomic analysis, this study also reveals deep molecular evidence for the presence of bacterial pathogens (Melissococcus plutonius, Paenibacillus larvae), Varroa destructor-1 virus, Sacbrood virus, and fungi. Despite this effort we did not detect KBV, SBPV, Tobacco ringspot virus, VdMLV (Varroa Macula like virus), Acarapis spp., Tropilaeleps spp. and Apocephalus (phorid fly). We discuss possible impacts of management practices and honey bee subspecies on microbial retinues. The described workflow and curated microbial database will be generally useful for microbial surveys of healthy and declining honey bees.

Measuring individual locomotor rhythms in honey bees, paper wasps and other similar-sized insects

Circadian rhythms in social insects are highly plastic and are modulated by multiple factors. In addition, complex behaviors such as sun-compass orientation and time learning are clearly regulated by the circadian system in these organisms. Despite these unique features of social insect clocks, the mechanisms as well as the functional and evolutionary relevance of these traits remain largely unknown. Here we show a modification of the Drosophila activity monitoring (DAM) system that allowed us to measure locomotor rhythms of the honey bee, Apis mellifera (three variants; gAHB, carnica and caucasica), and two paper wasps (Polistes crinitus and Mischocyttarus phthisicus). A side-by-side comparison of the endogenous period under constant darkness (free-running period) led us to the realization that these social insects exhibit significant deviations from the Earth's 24 h rotational period as well as a large degree of inter-individual variation compared with Drosophila. Experiments at different temperatures, using honey bees as a model, revealed that testing the endogenous rhythm at 35°C, which is the hive's core temperature, results in average periods closer to 24 h compared with 25°C (23.8 h at 35°C versus 22.7 h at 25°C). This finding suggests that the degree of tuning of circadian temperature compensation varies among different organisms. We expect that the commercial availability, cost-effectiveness and integrated nature of this monitoring system will facilitate the growth of the circadian field in these social insects and catalyze our understanding of the mechanisms as well as the functional and evolutionary relevance of circadian rhythms.

Morphometric analysis of oppiid mites (Acari, Oribatida) collected from Turkey

In order to assess the relationship between the oppiid mite species (Acari, Oribatida) collected from Turkey, traditional and geometric morphometric methods were used. We have taken photographs of 128 specimens belonging to 11 species from six subfamilies of Oppiidae. These photographs were digitized and 17 interval measurements were taken for traditional morphometric analysis, and 20 landmarks were recognized on the ventral surface of each specimen for geometric morphometric analysis. The effectiveness to separate taxa was compared between the two morphometric analyses. In both dendrograms Oppia nitens formed a single cluster, Oxyoppia ilicaensis was singled out from the remaining nine species, which were clustered together. Two species, Lauroppia fallax and Rhinoppia obsoleta, clustered together implying a very close relationship.

Proboscis conditioning experiments with honeybees, Apis mellifera caucasica, with butyric acid and DEET mixture as conditioned and unconditioned stimuli

Three experiments are described investigating whether olfactory repellents DEET and butyric acid can support the classical conditioning of proboscis extension in the honeybee, Apis mellifera caucasica (Hymenoptera: Apidae). In the first experiment DEET and butyric acid readily led to standard acquisition and extinction effects, which are comparable to the use of cinnamon as a conditioned stimulus. These results demonstrate that the odor of DEET or butyric acid is not intrinsically repellent to honey bees. In a second experiment, with DEET and butyric acid mixed with sucrose as an unconditioned stimulus, proboscis conditioning was not established. After several trials, few animals responded to the unconditioned stimulus. These results demonstrate that these chemicals are gustatory repellents when in direct contact. In the last experiment a conditioned suppression paradigm was used. Exposing animals to butyric acid or DEET when the proboscis was extended by direct sucrose stimulation or by learning revealed that retraction of the proboscis was similar to another novel odor, lavender, and in all cases greatest when the animal was not permitted to feed. These results again demonstrate that DEET or butyric acid are not olfactory repellents, and in addition, conditioned suppression is influenced by feeding state of the bee.

Map position of phosphoglucomutase (Pgm) locus on autosome IV of house fly (Diptera: Muscidae)

We determined the map position of phosphoglucomutase (Pgm) locus on autosome IV of housefly, Musca domestica L. (Diptera: Muscidae), by using three and five point linkage test crosses. Test strains had visible mutant markers (car, bwb, cyw, and aabys). We analyzed 1738 offspring in total from two groups of single-pair matings by electrophoresis. Here, we report the linkage of Pgm locus to autosome IV loci curly wing (cyw) and yellow eyes (ye) with recombination frequency of 16.9 and 1.1%, respectively. We combined the distances calculated from this study and the previously published data. An updated linkage map of the M. domestica L. Autosome IV was drawn based on combined data in terms of real map units obtained from the mapping function.

Genetic aspects of human male infertility: the frequency of chromosomal abnormalities and Y chromosome microdeletions in severe male factor infertility

OBJECTIVE

The main purpose of this study is to detect the frequency and type of both chromosomal abnormalities and Y chromosome microdeletions in patients with severe male factor infertility and fertile control subjects. The association between the genetic abnormality and clinical parameters was also evaluated.

METHODS

This study was carried out in 208 infertile and 20 fertile men. Results of 208 patients, 119 had non-obstructive azoospermia and 89 had severe oligoasthenoteratozoospermia (OAT). Seventeen out of 119 (14.3%) azoospermic patients and two out of 89 (2.2%) patients with OAT had Y chromosome microdeletions. In total, 19 cases with deletions were detected in 208 infertile men, with a frequency of 9.1%. The AZFc locus, mainly DAZ gene cluster was the most frequently deleted region. Five other cases with azoospermia (4.2%) and two cases with OAT (2.2%) had a chromosomal abnormality, with a total number of seven (3.4%). Including Y chromosome deletions and structural chromosome abnormalities, the rate of genetic abnormalities was 12.5% (26/208) in our patients. On the other hand, 20 men with proven fertility and fathers of five cases with microdeletions were genetically normal. Y chromosome deletions and chromosomal abnormalities were associated with various histological alterations in testis. Sertoli cell-only (SCO) syndrome and maturation arrest predominated in these cases, whereas hypospermatogenesis occurred more frequently in genetically normal patients.

CONCLUSION

Various chromosomal abnormalities and deletions of Y chromosome can cause spermatogenic breakdown resulting in chromosomally derived infertility. All these findings strongly support the recommendation of genetic screening of infertile patients.

Genetic relationships among perennial and annual Cicer species growing in Turkey assessed by AFLP fingerprinting

AFLP markers were used to assess genetic relationships among Cicer species with distribution in Turkey. Genetic distances were computed among 47 Cicer accessions representing four perennial and six annual species including chickpea, using 306 positions on AFLP gels. AFLP-based grouping of species revealed two clusters, one of which includes three perennial species, Cicer montbretii, Cicer isauricum and Cicer anatolicum, while the other cluster consists of two subclusters, one including one perennial, Cicer incisum, along with three annuals from the second crossability group ( Cicer pinnatifidum, Cicer judaicum and Cicer bijugum) and the other one comprising three annuals from the first crossability group ( Cicer echinospermum, Cicer reticulatum and Cicer arietinum). Consistent with previous relationship studies in the same accession set using allozyme and RAPD markers, in AFLP-based relationships, C. incisum was the closest perennial to nearly all annuals, and C. reticulatum was the closest wild species to C. arietinum. Cluster analysis revealed the grouping of all accessions into their distinct species-clusters except for C. reticulatum accessions, ILWC247, ILWC242 and TR54961; the former was found to be closer to the C. arietinum accessions while the latter two clustered with the C. echinospermum group. Small genetic distance values were detected among C. reticulatum accessions (0.282) and between C. reticulatum and C. arietinum (0.301) indicating a close genetic similarity between these two species. Overall, the AFLP-based genetic relationships among accessions and species were congruous with our previous study of genetic relationships using allozymes. The computed level of AFLP variation and its distribution into within and between Cicer species paralleled the previous report based on RAPD analyses. AFLP analysis also confirmed the presence of the closest wild relatives and previous projections of the origin of chickpea in southern Turkey. Results presented in this report indicate that AFLP analysis is an efficient and reliable marker technology in determination of genetic variation and relationships in the genus Cicer. Obviously, the use of AFLP fingerprinting in constructing a detailed genetic map of chickpea and cloning, and characterizing economically important traits would be promising as well.

Analysis of genetic relationships among perennial and annual Cicer species growing in Turkey using RAPD markers

Random amplified polymorphic DNA (RAPD) fragments were used to assess genetic relationships among Cicer spp. growing in Turkey. Seven 10-mer primers selected from a 50 random oligonucleotide primer set, depending on their ability to amplify genomic DNA in all species, were used to detect RAPD variation in 43 wild and cultivated accessions representing ten species. These primers yielded 95 reproducible amplification products, 92 of which were polymorphic. Pairwise genetic distances of accessions estimated according to Nei and Li (1979) were used to produce a dendrogram using UPGMA. The dendrogram contained two main clusters, one of which comprised accessions of the four perennial species ( Cicer montbretii, Cicer isauricum, Cicer anatolicum and Cicer incisum) together with the accessions of the three annual species ( Cicer pinnatifidum, Cicer judaicum and Cicer bijugum), and the other cluster included the remaining three annual species ( Cicer echinospermum, Cicer reticulatum and Cicer arietinum). Analysis of RAPD variation showed that C. incisum is the most similar perennial species to annuals, and C. reticulatum is the closest annual species to chickpea. These results generally agree with our allozyme study which was carried out using same Cicer collection and previous studies of relationships among annual species. The results also show that RAPD markers can be used to distinguish Cicer species and to survey genetic variation and relationships among taxonomic units in this genus.

Polymorphism of M factors in populations of the housefly, Musca domestica L., in Turkey

M factors, which determine maleness in Musca domestica, were found on the second, third, fourth and fifth linkage groups in housefly populations of Turkey. As in European populations, the male-determining factor was more frequently located on linkage group III (MIII). Some males homozygous or double heterozygous for M factors were identified. Deviations from a 1:1 sex ratio in favour of males, as well as mosaics for somatic marker mutations and sexual mosaics (gynandromorphs), were also observed. The results reveal an extensive polymorphism in the sex-determining system.

Polymorphism of precore region of hepatitis B virus DNA among patients with chronic HBV infection in Turkey

The prevalence of mutations in the precore and core promoter regions of hepatitis B virus DNA and the association with the hepatitis B e antigen-negative phenotype vary in different geographical areas. It is rather high especially in the Far East and Mediterranean countries. The mutations occurring in the precore and the minimal essential region of the core promoter of HBV-DNA were analyzed in the sera of 81 patients (HBeAg-positive, 47 patients; HBeAg-negative, 34 patients) with chronic hepatitis B virus infection by direct sequencing of amplified polymerase chain reaction products. All patients had thymine at nucleotide 1858. Seven of 47 HBeAg-positive patients (15%) and 29 of 34 HBeAg-negative patients (85%) had precore stop codon mutations (G to A change at nucleotide 1896). No nucleotide change was found in the minimal essential region of HBV core promoter in any patient studied. In conclusion, the hepatitis B e antigen-negative phenotype in Turkish patients with chronic hepatitis B is associated with mutations in the precore but not in the minimal essential region of the core promoter. These results representing a part of the eastern Mediterranean support the studies conducted for the other populations of the region.

Geographic variation analysis of the ABO and RH systems in Turkey

In this study, we report the results of a geographical variation analysis on the gene frequencies of ABO and RH systems in 67 provinces of Turkey. The gene frequencies of A, O and RH(-), were subjected to spatial autocorrelation analysis and significant spatial autocorrelation coefficients were observed for each gene in the first distance class. The average I-correlogram for the three genes displayed a clinal pattern. The results also suggested a marked decrease in genetic similarity in relation to geographic distance.

Control of insecticide resistance in laboratory populations of house fly (Diptera: Muscidae) by introduction of susceptibility genes

We investigated the effects of immigration of individuals carrying susceptibility alleles on the level of resistance in populations of the house fly, Musca domestica L., selected for malathion resistance. Two types of males, WHO/IN males (homozygous for susceptibility genes) and A14-WHO males (heterozygous for the second chromosome) were released into the resistant populations in 1:9, 1:1, and 9:1 ratios of immigrant/resident males. In both experiments, we observed that increasing the ratio of immigrant to resident males from 1:9 to 9:1 caused an associated increase in mortality caused by malathion applications. Release of A14-WHO males was more effective in stopping the evolution of resistance in resistant populations than was release of WHO/IN males. Fitness parameters of resistant and susceptible strains were also compared. The WHO/IN strain had low viability and fecundity. R and A14-WHO males were longer-lived compared with WHO/IN males, although they did not differ in mating success.

A rare-male advantage in the housefly induced by wing clipping and some general considerations for Drosophila

Multiple-choice crosses among five geographic strains of the housefly, Musca domestica L., were carried out in equal (10:10) and low-frequency (4:16) ratios. Initially, a low-frequency-male mating advantage was apparent, but further analyses related this minority advantage to a reduction of male mating success during marking by wing clipping. When there are fluctuating differences in the level of sexual vigor between competing male types over replicate trials of a cross, a mating advantage will accrue to the minority type. Even if males from the two competing strains are equally vigorous, such fluctuating differences will occur during sampling of flies. Harming the flies during marking will serve to enhance this effect and make significant departures toward greater mating success of rare males highly likely. This statistical bias in favor of minority males was substantiated in simulations of the KENCE-BRYANT model of mating success and compared with our results of a minority advantage in the housefly and with published results of a minority advantage in Drosophila. Our evidence, though circumstantial, that an advantage to minority males could have been induced by such an experimental bias suggests that a re-examination of existing data, as well as new experimentation, is necessary to discern whether or not a real rare-male advantage exists.

The survival of mutants at very low frequencies in tribolium populations

Forty population cages, each with 499 adult T. castaneum of the wild-type UPF strain, received a bb female newly mated with UPF males. Half of the immigrants had a Chicago Black genetic background, the other half a UPF background. These conditions simulate, respectively, the fate of a rare, genetically differing immigrant or the fate of a mutation in populations of considerable size. Adults were censused for 11 discrete generations. The semi-dominant autosomal black gene survived in 26 out of 40 cultures by the end of the experiment, demonstrating its selective advantage at these very low frequencies. The gene increased from an initial frequency of 0.002 to 0.055 (at generation 11) in at least one replicate. Although frequency-dependent fitness has been shown for black at higher frequencies, no such dependence could be demonstrated at the low frequencies of this study. The cultures simulating mutations (immigrants with native backgrounds) had a higher average gene frequency, different distribution of gene frequencies across replicates, and a lower extinction rate of black than did the cultures with alien background immigrants. The observations only partially fitted expectation based on a branching process model. The data show a tendency for the persistence of a few heterozygotes in cultures and for a deficiency of cultures that lost the mutant or those with many heterozygotes. The increase in frequency of black cannot be attributed to increased reproductive success of heterozygotes. The advantage of heterozygotes appears due to delayed developmental period as a result of tactile stimulation and probable differential cannibalism among pupae.