Y-SNP analysis versus Y-Haplogroup Predictor in the Slovak population

Petrejčíková, Eva; Čarnogurská, Jana; Hronská, Danica; Bernasovská, Jarmila; Boroňová, Iveta; Gabriková, Dana; Bôžiková, Alexandra; Mačeková, Soňa

doi:10.1127/0003-5548/2014/0368

Cited by 21 publications

(14 citation statements)

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“…4). Athey's algorithm is reported to be relatively efficient for prediction of haplogroups as compared to the other available tools 21 and it has been shown that the use of 17 or more Y-STRs is efficient for the prediction of haplogroups 22,23 . However, caution must be exercised while drawing interpretations based on the haplogroups derived from this algorithm.…”

Section: Discussionmentioning

confidence: 99%

The genetic affinities of Gujjar and Ladakhi populations of India

Singh

Sarkar

Kumar

et al. 2020

Sci Rep

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The Union Territories of Jammu and Kashmir (J&K) and Ladakh in North India owing to their unique geographic location offer a wide variety of landscape from plains to high altitudes and is a congruence of many languages and cultural practices. Here, we present the genetic diversity studies of Gujjars from Jammu region of J&K and Ladakhi population based on a battery of autosomal single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), Y-chromosomal STRs and the control region of the mitochondrial genome. These two populations were observed to be genetically distant to each other as well as to other populations from India. Interestingly, Y-STR analyses showed a closer affinity of Gujjars to other nomadic populations of Pashtuns from Baghlans and Kunduz provinces of Afghanistan and Pashtuns and Sindhis of Pakistan. Gujjars exhibited lesser genetic diversity as compared to Ladakhi population. M30f and M9 were the most abundant mitochondrial haplogroups observed among Gujjars and Ladakhis, respectively. A lower matrilineal to patrilineal diversity was observed for both these populations. The current study presents the first comprehensive analysis of Gujjars and Ladakhis and reveals their unique genetic affiliations with other populations of the world. The Indian subcontinent, which represents about one-sixth of the world population, is a unique conglomerate of multiple cultures, languages and genetic diversity. Together with sub-Himalayan countries and the present day Pakistan, Bangladesh and Sri Lanka, the Indian subcontinent is one of the oldest geographical regions inhabited by modern humans and is a witness to ancient human migratory histories 1. The two northernmost Union Territories of India viz., Jammu and Kashmir (J&K) and Ladakh, owing to their geographical location, are believed to have served as a corridor for ancient human migrations between main land of Indian subcontinent and NorthEast Asia, Eurasia or Africa 2,3. The populations of J&K and Ladakh offer a unique platform for looking into the past anthropological and demographic events which may have shaped the extant human population diversity. However, there is scant information about these populations in phylogenetic studies reported in the literature 4-6. In this study we have attempted to understand the genetic relationship of Gujjars (GJ) from Jammu region of J&K and Ladakhis (LL) with other populations of Indian subcontinent. Gujjars inhabit the northwestern region of the Indian subcontinent spanning across the regions of J&K, Himachal Pradesh (HP), Rajasthan (RJ), Haryana and Gujarat in India, and in the neighboring countries of Pakistan and Afghanistan. In the Union Territory of J&K, Gujjars constitute the third-largest population group and follow a nomadic/semi-nomadic lifestyle and are dependent on rearing of cattle, goats and sheep 7. Few research groups had previously reported on the genetic diversity studies among Gujjars 8-11 , however, considering the unique geographical distribution of Gujjars and their under-representation...

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Section: Discussionmentioning

confidence: 99%

The genetic affinities of Gujjar and Ladakhi populations of India

Singh

Sarkar

Kumar

et al. 2020

Sci Rep

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“…Another predictor tool[16], was also used for confirmation purposes. These two haplogroup prediction tools have been found to have a validity of 99% and 97%, respectively, in assigning major haplogroups and subclades[17]. Haplotypes that were assigned a haplogroup with a probability <90%, underwent specific Y-SNP genotyping to confirm the haplogroup.…”

Section: Methodsmentioning

confidence: 99%

“…Our approach for determining haplogroup distributions comprised the following steps: (i) extracting the raw haplogroup data (absolute numbers) from each study; (ii) standardizing the nomenclature for each haplogroup [International Society of Genetic Genealogy (2016)]; (iii) merging data from different studies and summing the absolute frequency of each haplogroup for each population/sub-population; and (iv) calculating relative frequencies (%) of each haplogroup for each population/sub-population, using the merged data. Due to the fact that a key study containing Turkish and Kurdish samples from Central Anatolia[29] did not provide specific subclades for haplogroup E1b1b, a validated haplogroup prediction tool was used for determining those[16,17]. Y-haplogroup frequencies for Cypriots and for all other relevant populations can be found in S6 Table and S7 Table, respectively.…”

Section: Methodsmentioning

confidence: 99%

Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots

et al. 2017

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Genetics can provide invaluable information on the ancestry of the current inhabitants of Cyprus. A Y-chromosome analysis was performed to (i) determine paternal ancestry among the Greek Cypriot (GCy) community in the context of the Central and Eastern Mediterranean and the Near East; and (ii) identify genetic similarities and differences between Greek Cypriots (GCy) and Turkish Cypriots (TCy). Our haplotype-based analysis has revealed that GCy and TCy patrilineages derive primarily from a single gene pool and show very close genetic affinity (low genetic differentiation) to Calabrian Italian and Lebanese patrilineages. In terms of more recent (past millennium) ancestry, as indicated by Y-haplotype sharing, GCy and TCy share much more haplotypes between them than with any surrounding population (7–8% of total haplotypes shared), while TCy also share around 3% of haplotypes with mainland Turks, and to a lesser extent with North Africans. In terms of Y-haplogroup frequencies, again GCy and TCy show very similar distributions, with the predominant haplogroups in both being J2a-M410, E-M78, and G2-P287. Overall, GCy also have a similar Y-haplogroup distribution to non-Turkic Anatolian and Southwest Caucasian populations, as well as Cretan Greeks. TCy show a slight shift towards Turkish populations, due to the presence of Eastern Eurasian (some of which of possible Ottoman origin) Y-haplogroups. Overall, the Y-chromosome analysis performed, using both Y-STR haplotype and binary Y-haplogroup data puts Cypriot in the middle of a genetic continuum stretching from the Levant to Southeast Europe and reveals that despite some differences in haplotype sharing and haplogroup structure, Greek Cypriots and Turkish Cypriots share primarily a common pre-Ottoman paternal ancestry.

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“…The other populations that were also covered in the same article demonstrate only minor differences in few percentages which typing. Petrejčíková et al (2014) used 3 different predictors for the research based on 12 STRs and obtained 98.80%, 97.59% and 98.19% accuracy for Whit Athey´s haplogroup predictor, Jim Cul-len´s haplogroup predictor and Vadim Urasin´s haplogroup predictor, respectively. Furthermore, Dogan et al (2016) used 4 haplogroup predictors for analysing the B&H population and obtained a 99% average accuracy while the current study obtained a 91% average accuracy for all populations.…”

Section: Discussionmentioning

confidence: 99%

“…Y chromosomal haplogroups can be assigned from Y-STR haplotypes using haplogroup predictors, which are very useful for analysing previous published Y-STR datasets (Dogan et al 2016;Dogan et al 2017;Heraclides et al 2017;Gurkan et al 2017) as well as validation purposes of haplogroup assignments based on Y SNP data (Petrejčíková et al 2014 andEmmerova et al 2017). The four haplogroup predictors that are in focus in this study are: Whit Athey haplogroup predictor (Athey 2006), Nevgen haplogroup predictor (Ćetković -Gentula and Nevski 2015), Vadim Urasin's…”

Section: Introductionmentioning

confidence: 99%

A glance of genetic relations in the Balkan populations utilizing network analysis based on in silico assigned Y-DNA haplogroups

Šehović¹,

Zieger²,

Spahić³

et al. 2018

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The aim of this study is to provide an insight into Balkan populations' genetic relations utilizing in silico analysis of Y-STR haplotypes and performing haplogroup predictions together with network analysis of the same haplotypes for visualization of the relations between chosen haplotypes and Balkan populations in general. The population dataset used in this study was obtained using 23, 17, 12, 9 and 7 Y-STR loci for 13 populations. The 13 populations include: Bosnia and Herzegovina (B&H), . The overall dataset contains a total of 2179 samples with 1878 different haplotypes. I2a was detected as the major haplogroup in four out of thirteen analysed Balkan populations. The four populations (B&H, Croatia, Montenegro and Serbia) which had I2a as the most prevalent haplogroup were all from the former Yugoslavian republic. The remaining two major populations from former Yugoslavia, Macedonia and Slovenia, had E1b1b and R1a haplogroups as the most prevalent, respectively. The populations with E1b1b haplogroup as the most prevalent one are Macedonian, Romanian, as well as Albanian populations from Kosovo and Albania. The I2a haplogroup cluster is more compact when compared to E1b1b and R1b haplogroup clusters, indicating a larger degree of homogeneity within the haplotypes that belong to the I2a haplogroup. Our study demonstrates that a combination of haplogroup prediction and network analysis represents an effective approach to utilize publicly available Y-STR datasets for population genetics.

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Y-SNP analysis versus Y-Haplogroup Predictor in the Slovak population

Cited by 21 publications

References 0 publications

The genetic affinities of Gujjar and Ladakhi populations of India

The genetic affinities of Gujjar and Ladakhi populations of India

Y-chromosomal analysis of Greek Cypriots reveals a primarily common pre-Ottoman paternal ancestry with Turkish Cypriots

A glance of genetic relations in the Balkan populations utilizing network analysis based on in silico assigned Y-DNA haplogroups

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