Aykut Kence

The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals

The emergence of farming during the Neolithic transition, including the domestication of livestock, was a critical point in the evolution of human kind. The goat (Capra hircus) was one of the first domesticated ungulates. In this study, we compared the genetic diversity of domestic goats to that of the modern representatives of their wild ancestor, the bezoar, by analyzing 473 samples collected over the whole distribution range of the latter species. This partly confirms and significantly clarifies the goat domestication scenario already proposed by archaeological evidence. All of the mitochondrial DNA haplogroups found in current domestic goats have also been found in the bezoar. The geographic distribution of these haplogroups in the wild ancestor allowed the localization of the main domestication centers. We found no haplotype that could have been domesticated in the eastern half of the Iranian Plateau, nor further to the east. A signature of population expansion in bezoars of the C haplogroup suggests an early domestication center on the Central Iranian Plateau (Yazd and Kerman Provinces) and in the Southern Zagros (Fars Province), possibly corresponding to the management of wild flocks. However, the contribution of this center to the current domestic goat population is rather low (1.4%). We also found a second domestication center covering a large area in Eastern Anatolia, and possibly in Northern and Central Zagros. This last domestication center is the likely origin of almost all domestic goats today. This finding is consistent with archaeological data identifying Eastern Anatolia as an important domestication center.

Managed honey bee colony losses in Canada, China, Europe, Israel and Turkey, for the winters of 2008–9 and 2009–10

Summary In 2008 the COLOSS network was formed by honey bee experts from Europe and the USA. The primary objectives set by this scientific network were to explain and to prevent large scale losses of honey bee (Apis mellifera) colonies. In June 2008 COLOSS obtained four years support from the European Union from COST and was designated as COST Action FA0803—COLOSS (Prevention of honey bee Colony Losses). To enable the comparison of loss data between participating countries, a standardized COLOSS questionnaire was developed. Using this questionnaire information on honey bee losses has been collected over two years. Survey data presented in this study were gathered in 2009 from 12 countries and in 2010 from 24 countries. Mean honey bee losses in Europe varied widely, between 7–22% over the 2008–9 winter and between 7–30% over the 2009–10 winter. An important finding is that for all countries which participated in 2008–9, winter losses in 2009–10 were found to be substantially higher. In 2009–10, winter losses in South East Europe were at such a low level that the factors causing the losses in other parts of Europe were absent, or at a level which did not affect colony survival. The five provinces of China, which were included in 2009–10, showed very low mean (4%) A. mellifera winter losses. In six Canadian provinces, mean winter losses in 2010 varied between 16–25%, losses in Nova Scotia (40%) being exceptionally high. In most countries and in both monitoring years, hobbyist beekeepers (1–50 colonies) experienced higher losses than practitioners with intermediate beekeeping operations (51–500 colonies). This relationship between scale of beekeeping and extent of losses effect was also observed in 2009–10, but was less pronounced. In Belgium, Italy, the Netherlands and Poland, 2008–9 mean winter losses for beekeepers who reported ‘disappeared’ colonies were significantly higher compared to mean winter losses of beekeepers who did not report ‘disappeared’ colonies. Mean 2008–9 winter losses for those beekeepers in the Netherlands who reported symptoms similar to “Colony Collapse Disorder” (CCD), namely: 1. no dead bees in or surrounding the hive while; 2. capped brood was present, were significantly higher than mean winter losses for those beekeepers who reported ‘disappeared’ colonies without the presence of capped brood in the empty hives. In the winter of 2009–10 in the majority of participating countries, beekeepers who reported ‘disappeared’ colonies experienced higher winter losses compared with beekeepers, who experienced winter losses but did not report ‘disappeared’ colonies.

A Comparative Genetic Analysis of the Subterranean Termite Genus Reticulitermes (Isoptera: Rhinotermitidae)

Abstract DNA sequencing analysis of the mitochondrial DNA cytochrome oxidase II (COII) region was used to examine genetic variation in the termite genus Reticulitermes Holmgren. We examined 21 species and subspecies from three continents. Sequencing of a 677-bp region of a 780-bp amplicon from 41 individuals and from 17 sequences obtained from GenBank revealed 221 polymorphic sites within the genus. Tajima-Nei distances from species ranged from 0.9 to 12.7%, and parsimony and maximum likelihood analysis revealed several clades within the genus. Reticulitermes flavipes (Kollar) formed a distinct clade along with R. santonensis De Feytaud. European R. lucifugus (Rossi) formed a distinct clade with R. banyulensis (Béziers). Turkish R. lucifugus was distinct relative to European R. lucifugus, and along with R. clypeatus Lash from Israel formed a sister group with R. balkanensis Clément from Greece. This study provides support for the separation of Turkish R. lucifugus from European members of the species. This mitochondrial DNA marker was also able to identify several Reticulitermes specimens from Oklahoma, Texas, Missouri, and South Korea to R. flavipes, R. hageni Banks, R. virginicus (Banks), and R. speratus Shimizu.

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

Abstract.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.

A review of methods for discrimination of honey bee populations as applied to European beekeeping

Summary Here, scientists from 19 European countries, most of them collaborating in Working Group 4: “Diversity and Vitality” of COST Action FA 0803 “Prevention of honey bee COlony LOSSes” (COLOSS), review the methodology applied in each country for discriminating between honey bee populations. Morphometric analyses (classical and geometric) and different molecular markers have been applied. Even if the approach has been similar, however, different methodologies regarding measurements, landmarks or molecular markers may have been used, as well as different statistical procedures. There is therefore the necessity to establish common methods in all countries in order to have results that can be directly compared. This is one of the goals of WG4 of the COLOSS project.

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.

Mitochondrial DNA variation in honey bee (Apis mellifera L.) populations from Turkey

Summary We have studied mitochondrial (mt) DNA variation in 334 honey bee colonies from 7 different geographic regions of Turkey. We have evaluated Dra I restriction profiles of the CO-I CO-II intergenic region, Hinf-I and Taq-I restriction profiles of the CO-I gene and EcoR-I restriction profiles of the whole mtDNA. We obtained three different mtDNA patterns by EcoR-I digestion. The pattern typical for A. m. carnica/A. m. ligustica predominated throughout Turkey (327 colonies, 97.9%). We observed the pattern common in African subspecies only in Hatay province (6 colonies, 1.8%) and a previously unreported pattern in one colony from Balıkesir province (0.3%). Dra-I restriction analysis of the CO-I CO-II intergenic region yielded seven haplotypes. Haplotype 1 (TrDra-1) was the most common one found in Turkey, whereas haplotype 2 (TrDra-2) was widely distributed in Eastern Anatolia. Based on mitochondrial ND2 sequences taken from two samples collected in each region, bees from Hatay clustered with A. m. lamarckii and A. m. meda (morphological A and O lineages), while bees from central Anatolia clustered within the C morphological lineage group.

Polymorphism of Precore Region of Hepatitis B Virus DNA among Patients with Chronic HBV Infection in Turkey

SummaryThe 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.

Genetic structure of honeybee, Apis mellifera L. (Hymenoptera :Apidae) populations of Turkey inferred from microsatellite analysis

Summary We analyzed the genetic structure of II honeybee (Apis mellifera L) populations from Turkey and one from Cyprus using 9 microsatellite marker loci. Heterozygosity levels, mean number of alleles per population, number of diagnostic alleles, and pairwise FST values were computed for the populations studied. Heterozygosity levels were found to range between 0.54 and 0.68. We detected high levels of genetic divergence among the populations based on pairwise FST values; 50 of 66 pairwise FST values were significant. The presence of a large number of rare alleles and highly differentiated populations of honeybees are consistent with Anatolias role as a genetic center for Middle Eastern honeybees. We suggest that certain precautions should be taken to limit introduction of foreign subspecies to preserve native genetic resources.

Numerical taxonomic study on Turkish Lathyrus (Leguminoseae)

This study examines whether a satisfactory classification of Turkish Lathyrus species can be obtained from phenetic clustering based on external vegetative and floral morphological characters of herbarium specimens. Forty morphological characters for each species of the genus Lathyrus L. were scored and the data subjected to numerical taxonomic analyses. The results of this study suggest that there are basically nine sections ( Orobus, Lathyrostylis, Aphaca, Nissolia, Orobon, Gorgonia, Clymenum, Cicercula and Lathyrus ) which can be grouped under two subgenera, namely subgenus Lathyrus and subgenus Orobus , as far as the material belonging to 54 of the 58 species cited in Flora of Turkey allows. Sect. Gorgonia Dogan is described.