Marina Faerman

The Y Chromosome Pool of Jews as Part of the Genetic Landscape of the Middle East

A sample of 526 Y chromosomes representing six Middle Eastern populations (Ashkenazi, Sephardic, and Kurdish Jews from Israel; Muslim Kurds; Muslim Arabs from Israel and the Palestinian Authority Area; and Bedouin from the Negev) was analyzed for 13 binary polymorphisms and six microsatellite loci. The investigation of the genetic relationship among three Jewish communities revealed that Kurdish and Sephardic Jews were indistinguishable from one another, whereas both differed slightly, yet significantly, from Ashkenazi Jews. The differences among Ashkenazim may be a result of low-level gene flow from European populations and/or genetic drift during isolation. Admixture between Kurdish Jews and their former Muslim host population in Kurdistan appeared to be negligible. In comparison with data available from other relevant populations in the region, Jews were found to be more closely related to groups in the north of the Fertile Crescent (Kurds, Turks, and Armenians) than to their Arab neighbors. The two haplogroups Eu 9 and Eu 10 constitute a major part of the Y chromosome pool in the analyzed sample. Our data suggest that Eu 9 originated in the northern part, and Eu 10 in the southern part of the Fertile Crescent. Genetic dating yielded estimates of the expansion of both haplogroups that cover the Neolithic period in the region. Palestinian Arabs and Bedouin differed from the other Middle Eastern populations studied here, mainly in specific high-frequency Eu 10 haplotypes not found in the non-Arab groups. These chromosomes might have been introduced through migrations from the Arabian Peninsula during the last two millennia. The present study contributes to the elucidation of the complex demographic history that shaped the present-day genetic landscape in the region.

Sex identification of archaeological human remains based on amplification of the X and Y amelogenin alleles

Sex identification of archaeological human remains is essential for the exploration of gender differences in past populations. Traditional morphometric analyses fail to identify the gender of incomplete skeletal remains and that of immature individuals. In the present work, we have established a sensitive and reliable method, based on amplification of the single-copy amelogenin-encoding gene (AMG). The Y allele carries a small deletion in the first intron, facilitating the design of distinct X- and Y-specific polymerase chain reactions. Amplification with three primers, two of which are allele-specific, allows unambiguous identification of both X and Y chromosome signals in a single reaction, providing an internal control. For added confidence, the reaction may be performed in separate tubes for each allele. Using this method, the sex was determined from the skeletal remains of 18 individuals, including young children, out of 22 examined from periods ranging from 200 to around 8000 years ago. The state of skeletal preservation ranged from poor to good. Cortical and cranial bones, as well as teeth, were found to provide sufficiently preserved DNA. The success of retrieval of amplifiable DNA was not related either to the period or to the burial site. On the other hand, the method of DNA purification was critical. In our hands, direct DNA purification by Chelex from minute samples of bone/tooth powder gave the best results. This study demonstrates the applicability of the method for gender determination in skeletal remains from different periods.

High-resolution Y chromosome haplotypes of Israeli and Palestinian Arabs reveal geographic substructure and substantial overlap with haplotypes of Jews

High-resolution Y chromosome haplotype analysis was performed in 143 paternally unrelated Israeli and Palestinian Moslem Arabs (I&P Arabs) by screening for 11 binary polymorphisms and six microsatellite loci. Two frequent haplotypes were found among the 83 detected: the modal haplotype of the I&P Arabs (∼14%) was spread throughout the region, while its one-step microsatellite neighbor, the modal haplotype of the Galilee sample (∼8%), was mainly restricted to the north. Geographic substructuring within the Arabs was observed in the highlands of Samaria and Judea. Y chromosome variation in the I&P Arabs was compared to that of Ashkenazi and Sephardic Jews, and to that of North Welsh individuals. At the haplogroup level, defined by the binary polymorphisms only, the Y chromosome distribution in Arabs and Jews was similar but not identical. At the haplotype level, determined by both binary and microsatellite markers, a more detailed pattern was observed. Single-step microsatellite networks of Arab and Jewish haplotypes revealed a common pool for a large portion of Y chromosomes, suggesting a relatively recent common ancestry. The two modal haplotypes in the I&P Arabs were closely related to the most frequent haplotype of Jews (the Cohen modal haplotype). However, the I&P Arab clade that includes the two Arab modal haplotypes (and makes up 32% of Arab chromosomes) is found at only very low frequency among Jews, reflecting divergence and/or admixture from other populations.

Y chromosome evidence for a founder effect in Ashkenazi Jews

Recent genetic studies, based on Y chromosome polymorphic markers, showed that Ashkenazi Jews are more closely related to other Jewish and Middle Eastern groups than to their host populations in Europe. However, Ashkenazim have an elevated frequency of R-M17, the dominant Y chromosome haplogroup in Eastern Europeans, suggesting possible gene flow. In the present study of 495 Y chromosomes of Ashkenazim, 57 (11.5%) were found to belong to R-M17. Detailed analyses of haplotype structure, diversity and geographic distribution suggest a founder effect for this haplogroup, introduced at an early stage into the evolving Ashkenazi community in Europe. R-M17 chromosomes in Ashkenazim may represent vestiges of the mysterious Khazars.

Oral Microbes in Health and Disease

Oral bacteria were the first bacteria reported over 300 years ago, yet oral microbiology is still a developing field. Recent advances in molecular biology greatly improve our understanding of the oral microbiota. Oral bacteria form multispecies biofilms on oral surfaces in order to resist salivary wash and mechanical cleaning. These multispecies environments dictate oral health or disease. More than 700 oral bacterial species have been identified so far. Current technology enables for the first time the definition of the microbial composition associated with oral health and disease. Understanding the changes occurring in the microbial composition during transition from oral health to disease should lead to novel approaches to prevent and to treat oral disease.

Mitochondrial DNA Analysis in a 5300-year-old Specimen from Israel

We attempted DNA extraction from 14 bone and dental specimens found at Wadi Maqoch site, which is located in the Jordan Valley and dated to the Chalcolithic period. DNA was isolated from tiny amounts of bone and tooth powder following a slightly modified silica extraction protocol. Stringent precautions were undertaken to prevent possible contamination of the samples. Each DNA sample was subjected to a number of PCR reactions. Sex identification was performed using primers and conditions described by Sullivan and colleagues, but failed to provide positive results. Hypervariable segment I (HS-I) of the mitochondrial DNA control region was amplified in three overlapping PCR reactions. One of the DNA samples yielded amplification products of 153 bp, 232 bp and 271 bp that together comprised almost the complete HS-I. Automated sequencing revealed the following changes as compared to the Cambridge Reference Sequence: G to C at position 16,129, C to T at position 16,223. In addition, equal peaks of C and T were...

Women in Distress: Victims of the Iron Age Destruction at Tell eṣ-Ṣâfi/Gath

The widespread signs of destruction and fire seen at Tell eṣ-Ṣâfi/Gath in the upper and lower parts of the city (Namdar et al. 2011; Zukerman and Maeir 2012) include the charred skeletal remains of three women found in Area D, Stratum D3, and five individuals found in Area A, Stratum A3. All appear to have been victims of the same event, namely, the destruction of the city at the end of the ninth century B.C.E. by Hazael of Aram (Maeir 2012). We provide here a detailed description of these remains and the circumstances surrounding their deaths using standards published in Bass 1995 to determine their age and sex, and the Munsell color chart (Ellingham et al. 2015) to estimate the extent and pattern of burning on the bodies.

DNA analysis of a 30,000-year-old Urocitellus glacialis from northeastern Siberia reveals phylogenetic relationships between ancient and present-day arctic ground squirrels

In contrast to the abundant fossil record of arctic ground squirrels, Urocitellus parryii, from eastern Beringia, only a limited number of fossils is known from its western part. In 1946, unnamed GULAG prisoners discovered a nest with three mummified carcasses of arctic ground squirrels in the permafrost sediments of the El’ga river, Yakutia, Russia, that were later attributed to a new species, Citellus (Urocitellus) glacialis Vinogr. To verify this assignment and to explore phylogenetic relationships between ancient and present-day arctic ground squirrels, we performed 14C dating and ancient DNA analyses of one of the El’ga mummies and four contemporaneous fossils from Duvanny Yar, northeastern Yakutia. Phylogenetic reconstructions, based on complete cytochrome b gene sequences of five Late Pleistocene arctic ground squirrels and those of modern U. parryii from 21 locations across western Beringia, provided no support for earlier proposals that ancient arctic ground squirrels from Siberia constitute a distinct species. In fact, we observed genetic continuity of the glacialis mitochondrial DNA lineage in modern U. parryii of the Kamchatka peninsula. When viewed in a broader geographic perspective, our findings provide new insights into the genetic history of U. parryii in Late Pleistocene Beringia.