Decreased Rate of Evolution in Y Chromosome STR Loci of Increased Size of the Repeat Unit

Polymorphic Y chromosome short tandem repeats (STRs) have been widely used in population genetic and evolutionary studies. Compared to di-, tri-, and tetranucleotide repeats, STRs with longer repeat units occur more rarely and are far less commonly used.In order to study the evolutionary dynamics of STRs according to repeat unit size, we analysed variation at 24 Y chromosome repeat loci: 1 tri-, 14 tetra-, 7 penta-, and 2 hexanucleotide loci. According to our results, penta- and hexanucleotide repeats have approximately two times lower repeat variance and diversity than tri- and tetranucleotide repeats, indicating that their mutation rate is about half of that of tri- and tetranucleotide repeats. Thus, STR markers with longer repeat units are more robust in distinguishing Y chromosome haplogroups and, in some cases, phylogenetic splits within established haplogroups.Our findings suggest that Y chromosome STRs of increased repeat unit size have a lower rate of evolution, which has significant relevance in population genetic and evolutionary studies

Y-STR Haplotypic Polymorphisms for the Hakka Population in West China and Its Phylogenic Comparison with Other Chinese Populations

The Hakkas, undergone a series of great migrations, are usually identified with people who speak the Hakka language or share at least same Hakka ancestry. As the largest Hakka dialect island in West China, the Dongshan region was closely linked with the great migration wave of Hakka. However, the paternal genetic profiles of Dongshan Hakka have never been revealed. In the present study, 41 Y-chromosomal short tandem repeat (Y-STR) loci included in the SureID® PathFinder Plus Kit were analyzed in 353 unrelated male individuals (171 Hakka and 182 Han) of Sichuan Province, China. By analyzing 166 different haplotypes among Dongshan Hakkas and 176 different haplotypes among Sichuan Han males, haplotype diversity (HD) of the Hakka population was calculated as 0.9997 with a discrimination capacity (DC) of 0.9708. HD and DC were 0.9996 and 0.9670 for the Sichuan Han population, respectively. Most of the Y-STR loci were highly informative in both populations except DYS645. The genetic relationships were evaluated by comparing the Hakka population with 11 other groups that are relevant to the migration routes of Hakkas. The results of the MDS plot and phylogenetic tree indicate that the Dongshan Hakka population was closely related to Han nationalities from Anhui, Jiangxi, and Fujian Provinces

Predicting haplogroups using a versatile machine learning program (PredYMaLe) on a new mutationally balanced 32 Y-STR multiplex (CombYplex): Unlocking the full potential of the human STR mutation rate spectrum to estimate forensic parameters

We developed a new mutationally well-balanced 32 Y-STR multiplex (CombYplex) together with a machine learning (ML) program PredYMaLe to assess the impact of STR mutability on haplogourp prediction, while respecting forensic community criteria (high DC/HD). We designed CombYplex around two sub-panels M1 and M2 characterized by average and high-mutation STR panels. Using these two sub-panels, we tested how our program PredYmale reacts to mutability when considering basal branches and, moving down, terminal branches. We tested first the discrimination capacity of CombYplex on 996 human samples using various forensic and statistical parameters and showed that its resolution is sufficient to separate haplogroup classes. In parallel, PredYMaLe was designed and used to test whether a ML approach can predict haplogroup classes from Y-STR profiles. Applied to our kit, SVM and Random Forest classifiers perform very well (average 97 %), better than Neural Network (average 91 %) and Bayesian methods (< 90 %)

Towards Genetic Identification with Male-specific Mutations

The identification and application of new genetic variants for differentiation patrilineally related male relatives using Y chromosomal short tandem repeats (Y-STRs)

The imprint of the Slave Trade in an African American population: mitochondrial DNA, Y chromosome and HTLV-1 analysis in the Noir Marron of French Guiana

<p>Abstract</p> <p>Background</p> <p>Retracing the genetic histories of the descendant populations of the Slave Trade (16^th-19^thcenturies) is particularly challenging due to the diversity of African ethnic groups involved and the different hybridisation processes with Europeans and Amerindians, which have blurred their original genetic inheritances. The Noir Marron in French Guiana are the direct descendants of maroons who escaped from Dutch plantations in the current day Surinam. They represent an original ethnic group with a highly blended culture. Uniparental markers (mtDNA and NRY) coupled with HTLV-1 sequences (<it>env </it>and LTR) were studied to establish the genetic relationships linking them to African American and African populations.</p> <p>Results</p> <p>All genetic systems presented a high conservation of the African gene pool (African ancestry: mtDNA = 99.3%; NRY = 97.6%; HTLV-1 e<it>nv </it>= 20/23; HTLV-1 LTR = 6/8). Neither founder effect nor genetic drift was detected and the genetic diversity is within a range commonly observed in Africa. Higher genetic similarities were observed with the populations inhabiting the Bight of Benin (from Ivory Coast to Benin). Other ancestries were identified but they presented an interesting sex-bias. Whilst male origins spread throughout the north of the bight (from Benin to Senegal), female origins were spread throughout the south (from the Ivory Coast to Angola).</p> <p>Conclusions</p> <p>The Noir Marron are unique in having conserved their African genetic ancestry, despite major cultural exchanges with Amerindians and Europeans through inhabiting the same region for four centuries. Their maroon identity and the important number of slaves deported in this region have maintained the original African diversity. All these characteristics permit to identify a major origin located in the former region of the Gold Coast and the Bight of Benin; regions highly impacted by slavery, from which goes a sex-biased longitudinal gradient of ancestry.</p

III. Béla király csontjainak tanúsága – Az Árpád-ház eredete

The role of applications based on machine learning is continuously growing in the industry, health sector/bioinformatics and scientific research. American researchers published a bit more than 10 years ago the first machine learning algorithms, which were able to safely predict Y-SNP based haplogroups from Y-STR data. The goal of the present study was to predict with machine learning algorithms the SNP-based subgroup of three ancient DNA samples (King Béla III and two Khazar samples) belonging to Y-DNA Haplogroup R1a, in order to predict their geographic origin and mutual genetic relatedness more accurately. This is the first study applying machine learning algorithms for researching Hungarian prehistory. Based on the Y-STR haplotype of King Béla III, we estimated with the machine learning algorithm in the first step that he belonged to the R1a-Z93 subgroup that is most common among Indo-Iranic and Turkic speaking peoples. The second step predicted that King Béla III belonged to the Z2123 subgroup of R1a-Z93. The Phylogenetic analysis showed King Béla III most likely belonged to the relatively rare YP451+ YP449- subgroup of Z2123, which practically only appears in the North Caucasus, especially among Karachays and Balkars. Based on our results, we could hypothetically conclude that the Árpád Dynasty has common origin with one ethnic component of the Karachay people. In our study we proved that it is possible to increase the accuracy of Y-DNA haplogroup prediction of historical aDNA samples with mathematical methods using contemporary Y-STR haplotypes. With the help of this method, larger historical aDNA studies could save a lot of research funds and DNA carrying out tailored deep SNP-testing of samples instead of using general SNaPshots