Y-Chromosome Diversity in Modern Bulgarians: New Clues about Their Ancestry

To better define the structure and origin of the Bulgarian paternal gene pool, we have examined the Y-chromosome variation in 808 Bulgarian males. The analysis was performed by high-resolution genotyping of biallelic markers and by analyzing the STR variation within the most informative haplogroups. We found that the Y-chromosome gene pool in modern Bulgarians is primarily represented by Western Eurasian haplogroups with , 40% belonging to haplogroups E-V13 and I-M423, and 20% to R-M17. Haplogroups common in the Middle East (J and G) and in South Western Asia (R-L23*) occur at frequencies of 19% and 5%, respectively. Haplogroups C, N and Q, distinctive for Altaic and Central Asian Turkic-speaking populations, occur at the negligible frequency of only 1.5%. Principal Component analyses group Bulgarians with European populations, apart from Central Asian Turkic-speaking groups and South Western Asia populations. Within the country, the genetic variation is structured in Western, Central and Eastern Bulgaria indicating that the Balkan Mountains have been permeable to human movements. The lineage analysis provided the following interesting results: (i) R-L23* is present in Eastern Bulgaria since the post glacial period; (ii) haplogroup E-V13 has a Mesolithic age in Bulgaria from where it expanded after the arrival of farming; (iii) haplogroup J-M241 probably reflects the Neolithic westward expansion of farmers from the earliest sites along the Black Sea. On the whole, in light of the most recent historical studies, which indicate a substantial proto-Bulgarian input to the contemporary Bulgarian people, our data suggest that a common paternal ancestry between the proto-Bulgarians and the Altaic and Central Asian Turkic-speaking populations either did not exist or was negligible

Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge

<p>Abstract</p> <p>Background</p> <p>Mitochondrial DNA is an ideal source of information to conduct evolutionary and phylogenetic studies due to its extraordinary properties and abundance. Many insights can be gained from these, including but not limited to screening genetic variation to identify potentially deleterious mutations. However, such advances require efficient solutions to very difficult computational problems, a need that is hampered by the very plenty of data that confers strength to the analysis.</p> <p>Results</p> <p>We develop a systematic, automated methodology to overcome these difficulties, building from readily available, public sequence databases to high-quality alignments and phylogenetic trees. Within each stage in an autonomous workflow, outputs are carefully evaluated and outlier detection rules defined to integrate expert knowledge and automated curation, hence avoiding the manual bottleneck found in past approaches to the problem. Using these techniques, we have performed exhaustive updates to the human mitochondrial phylogeny, illustrating the power and computational scalability of our approach, and we have conducted some initial analyses on the resulting phylogenies.</p> <p>Conclusions</p> <p>The problem at hand demands careful definition of inputs and adequate algorithmic treatment for its solutions to be realistic and useful. It is possible to define formal rules to address the former requirement by refining inputs directly and through their combination as outputs, and the latter are also of help to ascertain the performance of chosen algorithms. Rules can exploit known or inferred properties of datasets to simplify inputs through partitioning, therefore cutting computational costs and affording work on rapidly growing, otherwise intractable datasets. Although expert guidance may be necessary to assist the learning process, low-risk results can be fully automated and have proved themselves convenient and valuable.</p

A Reflective Model for First Class Dependencies

We propose a reflective model to express and to automatically manage dependencies between objects. This model describes reflective facilities which enable the changing of language semantics. Although the importance of inter-object dependencies is well accepted, there is only limited objectoriented language support for their specification and implementation. In response to this lack of expressiveness of object models, the flo language integrates dependency management into the object oriented paradigm. Dependencies are described as first class objects and flo automatically maintains the consistency of the dependency graph. In this paper, we first show how a user can declare dependencies and how the system maintains the consistency of the graph of expressed dependencies. In a second part, we focus on the implementation of this management by controlling the messages sent to linked objects. In order to make dependency management orthogonal to other application concerns, we propose an abstr..

Y-chromosomal haplogroups in Bulgarians

In order to reconstruct Bulgarian paternal genetic history, we have analyzed the Y chromosome diversity across the country. This initial effort was performed through genotyping of 13 biallelic markers in a sample of 127 Bulgarian males. These markers define the main Y chromosome haplogroups and some of their subclades. We have determined five predominant haplogroups, which probably reflect three different steps in the colonization of the Balkan Peninsula. The obtained pattern of the Bulgarian Y chromosome diversity was compared to that of populations previously analyzed at the same phylogenetic resolution. Based on this comparison and on historical data, we have estimated definitely greater Indo-European (IE) than Central Asian (Altaic, AL) contribution to the modern Bulgarian gene pool