Large-scale analysis of the Vologda sample (Part 1)
The Vologda (also known as HGDP) sample of Russians was collected near the town of Konosha, located on the border between modern Arkhangelsk and Vologda regions. It is the oldest of all samples used in peer-reviewed studies, and also the largest sample of Russians from a single region. It includes 24 samples that are not outliers. An important note: only those samples that are in David Reich's dataset were counted.
The objectives of the study are to shed light on the genetic portrait of the population of the Russian North and to demonstrate the tools that are currently essential for the genetic analyses of our project.
Toolkit - QPadm, PCA (plinkPCA).
QPadm
A tool from the ADMIXTOOLS package, designed to estimate ancestry proportions (admixture) in a target population from different sources. This tool is not intended to determine the source of origin; the analysis is performed on a pre-prepared set of populations.
In this section, we will only touch on the Early and Late Bronze Ages, as we believe these periods raise the most questions for readers.
Early Bronze Age / Basic breakdown
Two scenarios were calculated on the main outsource (the set of right populations necessary for modeling in QPadm). One of them considers the option without additional admixture of Eastern hunter-gatherers beyond that present in the Proto-Indo-European component, while the other considers the option with such admixture.
The sample has elevated indicators of steppe origin (Russia_Afanasievo), surpassing most samples from southern Russia in this regard. The Asian admixture places the sample between central and Arkhangelsk Russians, with a noticeable shift toward the latter.
It was found that, in addition to the Baltic Bronze Age component typical of Baltic-Slavic populations, the sample also has an Iranian admixture, which, based on the totality of calculations, can be most accurately estimated at 12% or 1/8.
Regarding the sources of admixture: the Vologda population was formed on the basis of two main gene flows - Slavic and Finno-Ugric. Most of the Baltic Bronze Age ancestry was obtained directly from Slavic medieval settlers, while the Iranian ancestry was almost entirely obtained from the Finno-Ugrians.
PCA
On the resulting raft, we can clearly see a continuous transition within the East Slavic populations from northern Ukrainians to Russians in the Krasnoborsk district of the Arkhangelsk region. Due to its size, the Vologda population allows us to assess the variability of our research subject in detail. The southern point of the cloud is located on the border with the Yaroslavl population, which is located slightly south of the Vologda cloud and is close to Kursk by one individual, while the northern point is much further north than the Krasnoborsk cloud, but there is a clear continuum between the extreme points. The individuals are evenly distributed, without extreme deviations, as is the case in the Kursk or Yaroslavl samples.
