Fine-Scale Genetic Structure in the United Arab Emirates Reflects Endogamous and Consanguineous Culture,Population History,and Geography

The indigenous population of the United Arab Emirates (UAE) has a unique demographic and cultural history. Its tradition of endogamy and consanguinity is expected to produce genetic homogeneity and partitioning of gene pools while population movements and intercontinental trade are likely to have contributed to genetic diversity. Emiratis and neighboring populations of the Middle East have been underrepresented in the population genetics literature with few studies covering the broader genetic history of the Arabian Peninsula. Here, we genotyped 1,198 individuals from the seven Emirates using 1.7 million markers and by employing haplotype-based algorithms and admixture analyses, we reveal the fine-scale genetic structure of the Emirati population. Shared ancestry and gene flow with neighboring populations display their unique geographic position while increased intra- versus inter-Emirati kinship and sharing of uniparental haplogroups, reflect the endogamous and consanguineous cultural traditions of the Emirates and their tribes.     

Pedigree analysis of the Turkish Arab horse population: structure,inbreeding and genetic variability

The aim of this study was to evaluate genetic variability in the Turkish Arab horse population using pedigree information. This study is the first detailed pedigree analysis of the breed in Turkey. Pedigree data were collected from the National Studbook. The pedigree data for 23 668 horses, born between 1904 and 2014, were used in the analysis. From this data set, a reference population (RP) of 14 838 animals symbolising the last generation was defined. Demographic parameters, the inbreeding level (F), the average relatedness (AR), the effective population size (N_e), the effective number of founders (f_e), the effective number of ancestors (f_a) and the number of founder genome equivalents (f_g) were calculated for the population. The average generation interval for the RP was 12.2±4.6 years, whereas the calculated pedigree completeness levels were 98.2%, 96.6% and 95.0% for the first, second and third known generations. The mean equivalent generations (t), the average complete generations and the mean maximum generations for the RP were 7.8, 5.4 and 12.2, respectively, whereas the meanFand AR were 4.6% and 9.5% for the RP. The rate of inbred animals was 94.2% for the RP, whereas the number of founders, the number of ancestors and thef_e,f_aandf_gwere 342, 223, 40, 22 and 9.6 for the RP. The large differences observed betweenf_e, and the number of founders demonstrates that genetic diversity decreased between the founder and the RP. Contribution of the 14 most influential founder to the RP was 50.0%, whereas just eight ancestral horses can account for 50% of the genetic variability.N_eestimated via an individual increase in inbreeding per generation (${\overline{N}}_{\text{e}}$), and paired increase in coancestry$\left(\text{}{\overline{N}}_{eC}\right)$, were 74.4±3.9 and 73.5±0.58, respectively. The inbreeding increases with the pedigree knowledge. In addition, the decrease in inbreeding in last years is more noticeable.     

Gc subtypes in some population groups from Israel. Comparison between world population groups and between Jews and non-Jews of the same areas

Results of Gc subtyping on 1,222 Israelis, Arabs and Jews, are summarized and their gene frequencies are analyzed in comparison with available data on Gc subtypes in non-Jews. A discriminant and a cluster analysis demonstrated that in their Gc subtype frequencies European and non-European Jews resemble the populations of the areas where they lived before immigrating to Israel. A possible explanation for this resemblance, which is seen in some and not seen in other genetic markers in Jews, is suggested here to be connected with the function of Gc as a vitamin D-binding protein.     

State mutability and ethnic civil society: the Palestinian Arab minority in Israel

This article identifies the phenomenon of ethnic civil society activism as mobilization that seeks to empower an ethnic community and challenges the institutional order. The case of the Palestinian Arab minority in Israel is discussed and is used to reveal the conditions under which disaffected minorities pursue the path of ethnic civil society. The study finds that an analytical framework that stresses the mutability of state structures and changes in broader state-society relations provides a better explanation than existing theories of ethnic conflict. State-society characteristics conducive to this type of mobilization are a well-institutionalized state that can prevent deviation from the state's foundational rules and a counterbalanced dispersion of authority that limits regime capacity to control society.     

Allelic frequencies and statistical data obtained from 12 codis STR loci in an admixed population of the Brazilian Amazon

The allelic frequencies of 12 short tandem repeat loci were obtained from a sample of 307 unrelated individuals living in Macapá, a city in the northern Amazon region, Brazil. These loci are the most commonly used in forensics and paternity testing. Based on the allele frequency obtained for the population of Macapá, we estimated an interethnic admixture for the three parental groups (European, Native American and African) of, respectively, 46%, 35% and 19%. Comparing these allele frequencies with those of other Brazilian populations and of the Iberian Peninsula population, no significant distances were observed. The interpopulation genetic distances (F(ST) coefficients) to the present database ranged from F(ST) = 0.0016 between Macapá and Belém to F(ST) = 0.0036 between Macapá and the Iberian Peninsula.     

Dating the Lower to Middle Paleolithic transition in the Levant: A view from Misliya Cave,Mount Carmel,Israel

The transition from the Lower to the Middle Paleolithic in the Levant is a crucial event in human evolution, since it may involve the arrival of a new human population. In the current study, we present thermoluminescence (TL) dates obtained from 32 burnt flints retrieved from the late Lower Paleolithic (Acheulo-Yabrudian) and Early Middle Paleolithic (Mousterian) layers of Misliya Cave, Mount Carmel, Israel. Early Middle Paleolithic industries rich in Levallois and laminar products were assigned mean ages ranging from ∼250 to ∼160 ka (thousands of years ago), suggesting a production of this industry during MIS 7 and the early part of MIS 6. The mean ages obtained for the samples associated with the Acheulo-Yabrudian (strengthened by an isochron analysis) indicate a production of this cultural complex ∼250 ka ago, at the end of MIS 8. According to the Misliya TL dates, the transition from the Lower to the Middle Paleolithic in the site took place at the limit MIS 8/7 or during the early part of MIS 7. The dates, together with the pronounced differences in lithic technology strongly suggest the arrival of a new population during this period.     

Revision of the Widow-spider genus Latrodectus (Araneae:Theridiidae) in Israel

The six species of Widow-spiders ( Latrodectus ) found in Israel are revised. Three of them are reported for the first time from this region. The Mediterranean L.tredecimguttatus is maintained as a distinct species differing from the American L.mactans , while evidence on the occurrence in Israel of a distinct population, close to the American L.hesperus is provided. Five sympatric species of Latrodectus are found in the more arid zones of Israel and one allopatric population of the cosmotropical L.geometricus occurs in the Mediterranean Coastal Plain. A conspectus on the systematics alongside distribution and ecological records of each species is given. The biological and morphological distinctive characters separating the species are then assessed in an extended discussion. Illustrations and a key to the species are provided.     

Spiders of the genus Lachesana and a new storenoid genus from Israel (Araneae: Zodariidae)

Zodariid spiders of two genera in Israel are revised. The genus Lachesana is represented by two species. Only one male of these was ever depicted while the females of both and their hitherto unknown retreats were never described. Pax gen. nov. has been erected to accommodate five species, some of which have formerly been placed in Slorena, Selamia or Habronestes . Diagnostic characters of the West Mediterranean Selamia and the Australian Habronestes are newly illustrated. No drawings of Pax libani and P. islamita were ever published; the male of the latter is described here for the first time. Pax palmonii sp. nov. and P. engediensis sp. nov. are described and affinities of all taxa are discussed. Illustrations, records of distribution and keys to the species are provided.     

Group-specific component (Gc): subtypes in the Finnish population. Description of a new allele and an apparent mother-child incompatibility

The group-specific component (Gc) subtypes were determined in 575 adult Finns by immunoblotting after isoelectric focusing in agarose gel. The gene frequencies were Gc1S = 0.661, Gc1F = 0.139 and Gc2 = 0.200. This material included one rare allele, a more acidically focusing Gc 2 (named Gc 2A18). The phenotypes of 200 mother-child pairs studied were in accordance with the three-allelic mode of inheritance. An apparent mother-child incompatibility observed during routine paternity testing is reported.     

Pilot study for the characterization of pharmacogenetically relevant CYP2D6, CYP2C19 and ABCB1 gene polymorphisms in the Hungarian population

Polymorphisms of CYP450 metabolizer enzymes and transport proteins play crucial roles in the inter‐individual variability of drug efficiency. The aim of our study was to predict the frequency of functional variants of CYP2D6, CYP2C19 and ABCB1 genes in the Hungarian population. One hundred twelve unrelated healthy subjects donated DNA sample in the study. ABCB1 C3435T and G2677T/A single‐nucleotide polymorphisms (SNPs) were determined by LightCycler polymerase chain reaction. Because only limited amount of data is available on the rare allelic variants of CYP2D6 in the European populations, our study applied an expanded set of CYP2D6 and CYP2C19 alleles by using AmpliChip test. Our results show that the CYP2D6 phenotypes were 1.9% ultra‐rapid metabolizer, 6.5% intermediate metabolizer (IM), 8.3% poor metabolizer (PM) and 83.3% extensive metabolizer (EM), and the CYP2C19 phenotypes were 1.8% PM, 31.2% IM and 67% EM. The prevalence of the commonly observed CYP2D6 and CYP2C19 alleles in our study corresponds with that of other European populations. Nevertheless, our study confirms that extending the CYP2D6 allele set with loss‐of‐function variants such as CYP2D6*7, *9, *41 is worth considering. Frequency of the wild type ABCB1 3435C was 42.8% whereas the prevelance of 2677 G was 50.4%. Although frequency data of G2677T/A SNP in the European area are limited, some discrepancies with other studies were found. Copyright © 2011 John Wiley & Sons, Ltd.     

A phylogeographical study of the Turnip mosaic virus population in East Asia reveals an 'emergent' lineage in Japan

The genetic structure of populations of Turnip mosaic virus (TuMV) in East Asia was assessed by making host range and gene sequence comparisons of 118 isolates utilizing a population genetic approach. Most, but not all, isolates collected from Brassica plants in China infected only Brassica plants, whereas those from Japan infected both Brassica and Raphanus (BR) plants. Analyses of the positions of recombination sites in five regions of the genomes (one third of the full sequence) of the many recombinant isolates were fully congruent with the results of phylogenetic analysis, and at least one recombination type pattern was shared between Chinese and Japanese populations. One lineage of nonrecombinant isolates from the basal-BR lineage was found in 2000 in Kyushu, Japan but none in China, and have since been found over the whole island. The sudden expansion of this basal-BR population was strongly supported by calculations showing the deviations from the neutral equilibrium model for the individual geographical lineages with overall lack of nucleotide diversity, and by analysis of mismatch distribution. Our study shows that the recent Chinese and Japanese TuMV isolates are part of the same population but are discrete lineages.     

Garra tibanica ghorensis subsp.nov. (Pisces: Cyprinidae), an African element in the cyprinid fauna of the Levant

Garra tibanica ghorensis subsp. nov. is described from the southern Dead Sea Valley. In the Levant it represents the only cyprinid fish with African affinities known to date. It is suggested that G. t. ghorensis reached the area of its present distribution from the south and is not to be regarded as a relict of an earlier migration of the species to Africa via the Levant.Results of the travels of R. Kinzelbach to the countries of the Middle East, No. 18.Results of the travels of R. Kinzelbach to the countries of the Middle East, No. 18.     

Patchy population structure in a short-distance migrant: evidence from genetic and demographic data

Species often occur in subdivided populations as a consequence of spatial heterogeneity of the habitat. To describe the spatial organization of subpopulations, existing theory proposes three main population models: patchy population, metapopulation and isolated populations. These models differ in their predicted levels of connectivity among subpopulations, and in the risk that a subpopulation will go extinct. However, spatially discrete subpopulations are commonly considered to be organized as metapopulations, even though explicit tests of metapopulation assumptions are rare. Here, we test predictions of the three models on the basis of demographic and genetic data, a combined approach so far surprisingly little used in mobile organisms. From 2002 to 2005, we studied nine subpopulations of the wetland-restricted reed bunting ( Emberiza schoeniclus ) in the southeastern part of the Canton Zurich (Switzerland), from which local declines of this species have been reported. Here, wetlands are as small as 2.7 ha and separated through intensively used agricultural landscapes. Demographic data consisted of dispersal of colour-banded individuals among subpopulations, immigration rates and extinction-/recolonization dynamics. Genetic data were based on the distribution of genetic variability and gene flow among subpopulations derived from the analysis of nine microsatellite loci. Both demographic and genetic data revealed that the patchy population model best described the spatial organization of reed bunting subpopulations. High levels of dispersal among subpopulations, high immigration into the patchy population, and genetic admixture suggested little risk of extinction of both subpopulations and the entire patchy population. This study exemplifies the idea that spatially discrete subpopulations may be organized in ways other than a metapopulation, and hence has implications for the conservation of subpopulations and species.     

Islands within an island: Repeated adaptive divergence in a single population

Physical barriers to gene flow were once viewed as prerequisites for adaptive evolutionary divergence. However, a growing body of theoretical and empirical work suggests that divergence can proceed within a single population. Here we document genetic structure and spatially replicated patterns of phenotypic divergence within a bird species endemic to 250 km² Santa Cruz Island, California, USA. Island scrub‐jays (Aphelocoma insularis) in three separate stands of pine habitat had longer, shallower bills than jays in oak habitat, a pattern that mirrors adaptive differences between allopatric populations of the species’ mainland congener. Variation in both bill measurements was heritable, and island scrub‐jays mated nonrandomly with respect to bill morphology. The population was not panmictic; instead, we found a continuous pattern of isolation by distance across the east–west axis of the island, as well as a subtle genetic discontinuity across the boundary between the largest pine stand and adjacent oak habitat. The ecological factors that appear to have facilitated adaptive differentiation at such a fine scale—environmental heterogeneity and localized dispersal—are ubiquitous in nature. These findings support recent arguments that microgeographic patterns of adaptive divergence may be more common than currently appreciated, even in mobile taxonomic groups like birds.     

Bayesian phylogenetic analysis of Semitic languages identifies an Early Bronze Age origin of Semitic in the Near East

The evolution of languages provides a unique opportunity to study human population history. The origin of Semitic and the nature of dispersals by Semitic-speaking populations are of great importance to our understanding of the ancient history of the Middle East and Horn of Africa. Semitic populations are associated with the oldest written languages and urban civilizations in the region, which gave rise to some of the world''s first major religious and literary traditions. In this study, we employ Bayesian computational phylogenetic techniques recently developed in evolutionary biology to analyse Semitic lexical data by modelling language evolution and explicitly testing alternative hypotheses of Semitic history. We implement a relaxed linguistic clock to date language divergences and use epigraphic evidence for the sampling dates of extinct Semitic languages to calibrate the rate of language evolution. Our statistical tests of alternative Semitic histories support an initial divergence of Akkadian from ancestral Semitic over competing hypotheses (e.g. an African origin of Semitic). We estimate an Early Bronze Age origin for Semitic approximately 5750 years ago in the Levant, and further propose that contemporary Ethiosemitic languages of Africa reflect a single introduction of early Ethiosemitic from southern Arabia approximately 2800 years ago.     

The White-breasted Kingfisher,Halcyon smyrnensis,in Turkey: On the occurrence of an endangered species

Abstract

The size of the Turkish population of the White-breasted Kingfisher is estimated to be about 100–150 pairs of which approx. 75% are concentrated in five localities. This makes the species vulnerable. A distribution map is given.