Different waves and directions of Neolithic migrations in the Armenian Highland

Background: The peopling of Europe and the nature of the Neolithic agricultural migration as a primary issue in the modern human colonization of the globe is still widely debated. At present, much uncertainty is associated with the reconstruction of the routes of migration for the first farmers from the Near East. In this context, hospitable climatic conditions and the key geographic position of the Armenian Highland suggest that it may have served as a conduit for several waves of expansion of the first agriculturalists from the Near East to Europe and the North Caucasus. Results: Here, we assess Y-chromosomal distribution in six geographically distinct populations of Armenians that roughly represent the extent of historical Armenia. Using the general haplogroup structure and the specific lineages representing putative genetic markers of the Neolithic Revolution, haplogroups R1b1a2, J2, and G, we identify distinct patterns of genetic affinity between the populations of the Armenian Highland and the neighboring ones north and west from this area. Conclusions: Based on the results obtained, we suggest a new insight on the different routes and waves of Neolithic expansion of the first farmers through the Armenian Highland. We detected at least two principle migratory directions: (1) westward alongside the coastline of the Mediterranean Sea and (2) northward to the North Caucasus. Electronic supplementary material The online version of this article (doi:10.1186/s13323-014-0015-6) contains supplementary material, which is available to authorized users

Elevated systemic antibodies towards commensal gut microbiota in autoinflammatory condition

Article No. e3172Non peer reviewedPublisher PD

Origin and spread of human mitochondrial DNA haplogroup U7

Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region

Defining the causes of sporadic Parkinson's disease in the global Parkinson's genetics program (GP2)

The Global Parkinson’s Genetics Program (GP2) will genotype over 150,000 participants from around the world, and integrate genetic and clinical data for use in large-scale analyses to dramatically expand our understanding of the genetic architecture of PD. This report details the workflow for cohort integration into the complex arm of GP2, and together with our outline of the monogenic hub in a companion paper, provides a generalizable blueprint for establishing large scale collaborative research consortia

Multi-ancestry genome-wide association meta-analysis of Parkinson?s disease

Although over 90 independent risk variants have been identified for Parkinson’s disease using genome-wide association studies, most studies have been performed in just one population at a time. Here we performed a large-scale multi-ancestry meta-analysis of Parkinson’s disease with 49,049 cases, 18,785 proxy cases and 2,458,063 controls including individuals of European, East Asian, Latin American and African ancestry. In a meta-analysis, we identified 78 independent genome-wide significant loci, including 12 potentially novel loci (MTF2, PIK3CA, ADD1, SYBU, IRS2, USP8, PIGL, FASN, MYLK2, USP25, EP300 and PPP6R2) and fine-mapped 6 putative causal variants at 6 known PD loci. By combining our results with publicly available eQTL data, we identified 25 putative risk genes in these novel loci whose expression is associated with PD risk. This work lays the groundwork for future efforts aimed at identifying PD loci in non-European populations

Paternal Lineage Analysis Supports an Armenian Rather Than a Central Asian Genetic Origin of the Hamshenis

The Hamshenis are an isolated geographic group of Armenians with a strong ethnic identity who, until the early decades of the twentieth century, inhabited the Pontus area on the southern coast of the Black Sea. Scholars hold alternative views on their origin, proposing Eastern Armenia, Western Armenia, and Central Asia, respectively, as their most likely homeland. To ascertain whether genetic data from the nonrecombining portion of the Y chromosome are supportive of any of these suggestions, we screened 82 Armenian males of Hamsheni descent for 12 biallelic and 6 microsatellite Y-chromosomal markers. These data were compared with the corresponding data set from the representative populations of the three candidate regions. Genetic difference between the Hamshenis and other groups is significant and backs up the hypothesis of the Armenian origin of the Hamshenis, indicating central historical Armenia as a homeland of the ancestral population. This inference is further strengthened by the results of admixture analysis, which does not support the Central-Asian hypothesis of the Hamshenis’ origin. Genetic diversity values and patterns of genetic distances suggest a high degree of genetic isolation of the Hamshenis consistent with their retention of a distinct and ancient dialect of the Armenian language

Predominant role of host genetics in controlling the composition of gut microbiota

Background: The human gastrointestinal tract is inhabited by a very diverse symbiotic microbiota, the composition of which depends on host genetics and the environment. Several studies suggested that the host genetics may influence the composition of gut microbiota but no genes involved in host control were proposed. We investigated the effects of the wild type and mutated alleles of the gene, which encodes the protein called pyrin, one of the regulators of innate immunity, on the composition of gut commensal bacteria. Mutations in MEFV lead to the autoinflammatory disorder, familial Mediterranean fever (FMF, MIM249100), which is characterized by recurrent self-resolving attacks of fever and polyserositis, with no clinical signs of disease in remission. Methodology/Principal Findings: A total of 19 FMF patients and eight healthy individuals were genotyped for mutations in the MEFV gene and gut bacterial diversity was assessed by sequencing 16S rRNA gene libraries and FISH analysis. These analyses demonstrated significant changes in bacterial community structure in FMF characterized by depletion of total numbers of bacteria, loss of diversity, and major shifts in bacterial populations within the Bacteroidetes, Firmicutes and Proteobacteria phyla in attack. In remission with no clinical signs of disease, bacterial diversity values were comparable with control but still, the bacterial composition was substantially deviant from the norm. Discriminant function analyses of gut bacterial diversity revealed highly specific, well-separated and distinct grouping, which depended on the allele carrier statu

Mean numbers of predominant bacteria in fecal samples of FMF patients in both stages of the disease and healthy controls detected by FISH.

<p>Mean count±SD.</p>*<p>Counts 10⁸ cells per gram of fecal specimen.</p>**<p>The percentage relative to the total number of cells determined by Eub338.</p>†<p>p<0.05 as compared to healthy controls.</p>††<p>p<0.01 as compared to healthy controls.</p

Collector's curves of the observed and estimated phylotype richness of 16S libraries.

<p>Collector's curves of the observed (shown in dark blue) and estimated (Chao1 (light blue) and ACE (red)) phylotype richness calculated for healthy subjects (A), FMF remission (B), and FMF attack (C) with the phylogenetic depth defined at 99% level.</p