mtDNA of Slovaks

From the paper:

Recent mtDNA variability study in Czechs, the neighbors of Slovaks, has shown that they are genetically similar with adjacent European populations, but characterized by a small frequency of East Eurasian (2.8%) and Roma-specific (2.8%) mtDNA lineages (Malyarchuk et al. 2006b). Therefore, the aim of the present study was to characterize the mtDNA variation in Slovaks from western and eastern areas of Slovakia, based on variation of the HVS I and HVS II sequences, followed by a hierarchical survey of mtDNA haplogroup-specific restriction fragments length polymorphism (RFLP) markers.

In the above passage they are referring to this paper. More on the haplogroup M in Slovaks:

However, in contrast to the previously studied Czech population from western Bohemia (Malyarchuk et al. 2006b), samples from Slovakia do not display any East Eurasian mtDNAs. One of the Slovak M-haplotype belongs to subhaplogroup M1b and is identical to M1b1a-haplotypes revealed in Italians and Bedouins from southern Israel (Olivieri et al. 2006) as well as in Saudi Arabs (Abu-Amero et al. 2007). A second M-lineage detected in Slovaks is defined by variants at positions 16129–16223-16230–16233-16304–16344. This lineage is identical to those revealed previously in gene pools of the Bulgarian Roma at frequency of 3.6% (Gresham et al. 2001). Based on the presence of the 16129 variant, Gresham et al. (2001) suggested that this lineage belongs to Indian-specific haplogroup M5. Nevertheless, to determine its exact phylogenetic status we completely sequenced our Slovak sample (Slv227) and compared it with Indian M-haplotypes published by Sun et al. (2006) (Fig. 1). As a result, we have found that our sample belongs to haplogroup M35 due to mutations at positions 199 and 12561. Moreover, it shared transition at 15928 with the South Indian sample T17 (from Andhra Pradesh) that allowed us to define a new Indian/Roma branch called as M35b.

And on a Roma-related J1* lineage:

Previously, we have found that the Polish Roma population is characterized by high incidence (18.8%) of haplogroup J1* lineage, defined by HVS I motif 16069–16126-16145–16222-16235–16261-16271 (Malyarchuk et al. 2006a). This and a similar haplotype, lacking only the 16271 transition, are very rare in European Roma populations, being found only in the Spanish, Bulgarian and Hungarian Roma (Gresham et al. 2001; Egyed et al. 2007). Among Europeans, such haplotypes have been revealed only in French (0.5%; Dubut et al. 2004), Hungarian (0.5%; Egyed et al. 2007) and Czech (about 3%; Vanecek et al. 2004; Malyarchuk et al. 2006b) populations. In the present study, we have found that 2.9% of individuals from eastern Slovakia are characterized by exactly the same J1*-haplotype.

On differences within Slovakia:

The MDS analysis performed on the basis of pairwise F_ST values revealed that Slovak populations do not cluster together. Western Slovaks are located together with the Czechs and Austrians (in accordance with their geographic proximity), whereas eastern Slovaks are placed close to Slovenians (Fig. 3).

Ann Hum Genet (OnlineEarly Articles). doi:10.1111/j.1469-1809.2007.00410.x

Mitochondrial DNA Variability in Slovaks, with Application to the Roma Origin
Annals of Human Genetics

A. Malyarchuk, M. A. Perkova, M. V. Derenko, T. Vanecek, J. Lazur, P. Gomolcak

To gain insight into the mitochondrial gene pool diversity of European populations, we studied mitochondrial DNA (mtDNA) variability in 207 subjects from western and eastern areas of Slovakia. Sequencing of two hypervariable segments, HVS I and HVS II, in combination with screening of coding region haplogroup-specific RFLP-markers, revealed that the majority of Slovak mtDNAs belong to the common West Eurasian mitochondrial haplogroups (HV, J, T, U, N1, W, and X). However, a few sub-Saharan African (L2a) mtDNAs were detected in a population from eastern part of Slovakia. In addition, about 3% of mtDNAs from eastern Slovakia encompass Roma-specific lineages. By means of complete mtDNA sequencing we demonstrate here that the Roma-specific M-lineages observed in gene pools of different Slavonic populations (Slovaks, Poles and Russians), belong to Indian-specific haplogroups M5a1 and M35. Moreover, we show that haplogroup J lineages found in gene pools of the Roma and some Slavonic populations (Czechs and Slovaks) belong to new subhaplogroup J1a, which is defined by coding region mutation at position 8460.

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