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The aim of the present study was to define the mtDNA variability of Polish population and to visualize the genetic relations between Poles. For the first time, the study of Polish population was conducted on such a large of individuals representing administrative units of both levels of local administration in Poland voivodeships and counties. Additionally, clustering was used as a method of population subdivision. Haplogroups were classified and their geographical distribution was visualized using surface interpolation maps.
Furthermore, the level of differentiation within the Polish population was quite low but the existing genetic differences could be explained well with geographic distances.
This may lead to a conclusion that Poles can be considered as genetically homogenous but with slight differences, highlighted at the regional level. Some patterns of variability were observed and could be explained by the history of demographic processes in Poland such as resettlements and migrations of women or relatively weaker urbanisation and higher rural population retention of some regions. It is used especially in population genetics and molecular evolution studies and allows to understand the question of human migration and settlement from different regions of a country or the whole world [ 12 ].
Maternally inherited mitochondrial DNA haplogroups indicate the mother line ancestry and have been identified in geographically isolated populations throughout the globe [ 3 ]; indicating the human migration and ancestry [ 4 ]. Haplogroups from Africa L0, L1, L2, L3 are found to be the oldest and those which have evolved to European, Asian and Native American ones with geographic migrations and climate adaptations [ 5 ].
Several sources indicate the haplogroup H as the most frequent in Europe [ 8 ]. Clustering, as an additional method of grouping of individuals, has also never been used in relation to the Polish population. National population biobanks and sample repositories store human biological material for the use mostly in genetic research to connect the lifestyle and medical history with genetic traits.
Genetic and molecular information associated with the data about the sample donor can also be used in population studies [ 12 ]. Furthermore, high-density SNP microarrays, a successful tool to analyse large amounts of genetic data, were used in many population studies to analyse the structure and ancestry of global [ 13 ], European [ 141516 ] and individual country populations [ 1718 ]. The aim of the present study was to determine mtDNA variability of the Polish population, including geographical and historical context.
For this purpose, obtained haplotypes of individuals were classified into major haplogroups and subhaplogroups, and their distribution for units of the first voivodeship and second county level of local government and administration in Poland was analysed. For the first time, the study of the Polish population was conducted on such a large of individuals. The experimental group included samples taken from individuals representing administrative units of both levels of local administration in Poland: all 16 voivodeships Fig.
S1 and the majority of counties out of total —this includes counties and city counties. Written information about the place of birth and current residence was obtained from each subject.
All procedures were performed in accordance with the Declaration of Helsinki ethical principles for medical research involving human subjects. The full set of can be obtained at the European Genotype Archive [ 21 ] www.
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The map showing location of counties with the voivodeships Athe clusters B and population samples C used in the following study. K-means clustering method applied to spatial coordinates was used to merge individual counties in larger geographic groups clusters on the basis of the nearest mean.
Each cluster Fig. Clustering was performed with Scikit-learn package [ 23 ] in Python ver. The list of clusters containing the information about the cluster to which each county was ased as well as the name of the corresponding geographic region, is gathered in Supplementary Table S1.
Qualitative analysis was performed to identify outliers and artefacts on the microarray. Samples were excluded if call rate was below 0.
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Visual inspection was conducted to investigate the heteroplasmy, which was detected only in a few cases. S 2 according to recommendations for the description of sequence variants [ 25 ]. Haplogroup frequencies were calculated for every voivodeship and county by counting. To visualize the relationships between every voivodeship and every cluster, multidimensional scaling MDS analysis was constructed to plot the pairwise genetic distances F ST with cmd scale function in R ver.
As expected, haplogroup H was the most frequent in the Polish population Among mtDNA subhaplogroups, H1 Haplogroups: L 0. The haplogroup and subhaplogroup frequencies are presented in Table 1 and Table S3. J, T, HV, K. However, they were represented by as the largest and the smallest sample ; and 72, respectively.
Therefore, interpolation analysis was performed for the frequencies of eight main haplogroups to show their distribution across Poland.
Illustration of the frequencies of haplogroups on the map of Poland using interpolation method allowed us to underline the differences between regions. Different pattern of distribution of eight main haplogroups was observed for every voivodeship. However, observed differences were on a relatively low level Figs 3 and 4. To define differentiation among Polish population in terms of the similarities and differences between voivodeships, paired F ST analysis were performed. All F ST estimates were positive but low and ranged from 0. S2 and Table S S2 and Tab. Additionally, paired F ST analysis was also performed for clusters.
In this case, F ST estimates were positive, quite low and ranged between 0 and 0. S3 and Table S S3 and Tab. Detailed information about F ST values calculated for all voivodeships and clusters are gathered in Tables S14 and S15 in Supplementary materials and are presented on Figure S2 and S3respectively. Another MDS plot was constructed to visualize the relationships between generated clusters Fig. Analysis of molecular variance based on the mtDNA sequences reveals that most of the variation occurs within populations when voivodeships were taken into Only a small proportion of total variance was attributed to variation among groups also in the case of voivodeships 0.
Analysis of molecular variance computed for cluster populations also reveals that most of the variation occurs within populations Only a small proportion of total variance was attributed to variation among clusters 0.
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The highest variance among groups was observed when the population was divided into 2 groups cluster no. With the ncreasing of groups we could observe downward sloping trend with fluctuations, so we could identify local maxima 2, 4, 7, 11, 15, 18, 21, 23, 25, 29 and 31 groups.
When dividing into groups corresponding to local maxima, the following clusters were separate: no. When dividing into the maximum of 33 groups, the variance among groups was equal to 0.
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In the current study, an attempt to completely describe mtDNA variability and genetic connections for Polish population was made, based on a large group of individuals and including administrative unit clustering as an additional method of population dividing for increased geographical relevance. Analysing the frequencies of haplogroups, H was found to be the one most often occurring in the Polish population.
It is consistent with the findings of Grzybowski et al. An interesting analysis of haplogroup and subhaplogroup distribution was done by Malyarchuk et al. The cited study of Polish population showed Similarly, in the case of U, J, T, K and W haplogroups, frequencies obtained in the current study were practically the same compared to Malyarchuk et al.
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The only difference was observed in the case of HV haplogroup. Malyarchuk et al. The of individuals can be an explanation, as in the case of rare haplogroups, the size of studied samples has a great importance. Our findings are also consistent with other studies of European population [ 833 ] as well as individual countries such as: Spain [ 3435 ], Portugal [ 36 ] with Azores [ 37 ], islands of North Atlantic [ 38 ], Sardinia [ 39 ] and Russia [ 12 ], where haplogroup H was also indicated as the most frequent.
Most of the voivodeships in Poland reveal divergent patterns of major haplogroup frequencies, which differ from the values for Poland in general. In the case of haplogroup H, our compared at the level of appropriate administrative units, i. Relating to the studies about Ashkenazi maternal lineages [ 40 ] and mitochondrial markers of Jewish ancestry [ 41 ] and analysing proposed motifs to define four major Ashkenazi founder clusters K1a1b1a, K1a9, K2a2a and NH1b1we could not present their occurrence within the Polish population because of the lack of polymorphic sites on the microarray used.
Only one site from the proposed motif was present Grzybowski et al. Interestingly, the frequency of L haplogroup, one of the rarest in Europe, observed in the current study and the study of Mielnik-Sikorska et al. L1b is the most common African clade in Europe; [ 42 ] in the studies of Mielnik-Sikorska et al.
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In the current study, L0a1a was found in 2 individuals from Tatra county. In the current study, we focused on the genetic relationships and regional connections, omitting a detailed subhaplogroup analysis. However, the frequencies were calculated and H1 As mentioned above, the Polish population was the subject of the genetic research, but only in comparison to broader groups of Slavs or Europeans.
However, MDS analysis did not show this region as ificantly divergent. Nevertheless, MDS analysis did not show Podlaskie as a divergent voivodeship. It could be another reason for difficulties in the comparison of .
Furthermore, Malyarchuk et al. On the other hand, their MDS plot showed Poles as separate from the rest of the studied populations. It is worth adding that in this case, Polish population was represented only by individuals from Kuyavian-Pomeranian region. In our study, Kuyavian-Pomerania was analysed as a separate voivodeship but also as two separate clusters cluster no.
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However, F ST values were still very low and cannot prove genetic separation, which is confirmed by the MDS plot, where Kuyavian-Pomeranian was grouped together with the rest of voivodeships. At the level of clusters, the situation is different.
F ST values ranged between 0. MDS plot clearly illustrated the separation of this region from the rest of Poland. Interestingly, Eastern Kuyavia cluster no.