Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment (2024)

  • Article
  • Published:
  • Bill Tseng1,
  • Hsiao-Lin Hwa1,
  • Chun-Yen Lin2,
  • Yu-Jen Yu1,
  • Adrian Linacre3 &
  • James Chun-I Lee1

Journal of Human Genetics volume67,pages 487–493 (2022)Cite this article

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  • 3 Citations

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Subjects

  • Genomic analysis
  • Population genetics

Abstract

The application of massively parallel sequencing (MPS) data from whole genomes has allowed very many more Y-SNP loci to be genotyped simultaneously than previously possible. Although this greatly increases the resolution of Y-SNP haplogroups to link common ancestors, it remains a great challenge to provide a phylogenetic tree to clearly display the relationship of varying haplogroups. Y-SNP Haplogroup Hierarchy Finder is a web tool to generate hierarchical haplogroups based on Y-SNP data with the derived allele at the terminal of a haplogroup tree. The input data can include that from whole-genome sequencing. Confidence in assignment using Y-SNP Haplogroup Hierarchy Finder was demonstrated using Y-SNP genotypes of 1233 samples, sourced from the 1000 genomes project phase 3, used to generate the expected haplogroups. The outcome includes 2 reports: a ‘Haplogroup Report’ lists mutation types from the submitted Y-SNPs and their corresponding haplogroups, and a ‘Haplogroup Hierarchy Report’ lists all possible hierarchical haplogroups and ranks the three most supported haplogroups. Each layer of the descending haplogroups from one step to the next is shown and the supporting numbers of Y-SNPs are also included in these reports. All haplogroups that exhibited a clear relationship between the ancestral through to the derived SNPs can be clustered into a hierarchy of haplogroups. The assigned 1233 haplogroups were compared with 2 other software programs designed to assemble haplogroups, which resulted in one where there were many differences and the other one where there was only minor difference. The advantage of this web-based tool is that it provides an easy way to assign Y-SNP haplogroup based on the visualized hierarchical pattern.

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Acknowledgements

We thank the Ministry of Science and Technology of Taiwan by a grant [MOST 107-2320-B-002-045-MY3] and the Taiwan Biobank for advising data analysis.

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Authors and Affiliations

  1. Department of Forensic Medicine, College of Medicine, National Taiwan University, No.1 Jen-Ai Road Section 1, Taipei, 10051, Taiwan

    Bill Tseng,Hsiao-Lin Hwa,Yu-Jen Yu&James Chun-I Lee

  2. Institute of Forensic Medicine, Ministry of Justice, New Taipei City, 23016, Taiwan

    Chun-Yen Lin

  3. College of Science & Engineering, Flinders University, Adelaide, SA, 5001, Australia

    Adrian Linacre

Authors

  1. Bill Tseng

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  2. Hsiao-Lin Hwa

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  3. Chun-Yen Lin

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  5. Adrian Linacre

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  6. James Chun-I Lee

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Contributions

BT conducted the creation of new software. HLH, CYL and YJY carried data analyses. AL and JCL designed the study and drafted the manuscript.

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Correspondence to James Chun-I Lee.

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Supplementary information

10038_2022_1033_MOESM2_ESM.pdf

Y-SNP Haplogroup comparison between results reported by HaploGrouper,Y-LineageTracker and Y-Finder based on 1,233 samples taken from 1000 Genome Project

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Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment (5)

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Tseng, B., Hwa, HL., Lin, CY. et al. Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment. J Hum Genet 67, 487–493 (2022). https://doi.org/10.1038/s10038-022-01033-0

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Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment (2024)

FAQs

What is the most common Y-DNA haplogroup? ›

Y-DNA Clade/Haplogroup R is the most frequent (72%) and I the second most common Y-DNA haplogroup (19%). Y-DNA haplogroups subclades observed in ALSPAC are shown in Figure 1b.

What is the difference between SNP and haplogroup? ›

Haplogroups are defined through mutations (SNPs). Y-DNA haplogroups are defined by the presence of a series of Y-DNA SNP markers. Subclades are defined by a terminal SNP, the SNP furthest down in the Y-chromosome phylogenetic tree.

What does haplogroup tell you? ›

The Haplogroup Report provides haplogroup assignments which allow you to trace your ancestry from your mother through her mother and beyond and, for men, from your father through his father and beyond.

What is the Y-DNA haplogroup analysis? ›

Y-DNA tests

Y-chromosome testing uncovers a person's Y-chromosome haplogroup, the ancient group of people from whom one's patrilineage descends. Because only one's male-line direct ancestors are traced by Y-DNA testing, no females (nor their male ancestors) from whom a male descends are encapsulated in the results.

What is the rarest haplogroup? ›

The rarest haplogroup is U8a, part of haplogroup U. “Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe.”

What are the Y haplogroups of Vikings? ›

Haplogroups reasonably thought to have participated in the Viking and Invader migration are F, G, I1, I2, N, Q, R1a and R1b.

What race is haplogroup A? ›

By definition of haplogroup A as "non-BT", it is almost completely restricted to Africa, though a very small handful of bearers have been reported in Europe and Western Asia.

What haplogroup do Native Americans belong to? ›

On the basis of comprehensive RFLP analysis, it has been inferred that ∼97% of Native American mtDNAs belong to one of four major founding mtDNA lineages, designated haplogroups “A”–“D.” It has been proposed that a fifth mtDNA haplogroup (haplogroup X) represents a minor founding lineage in Native Americans.

Am I related to everyone in my haplogroup? ›

Most of your genetic relatives will actually fall outside of your haplogroup, because your haplogroup only tells you about direct paternal-line or maternal-line ancestors.

What haplogroup is the Y-DNA in the gypsy? ›

The Y chromosome H-M82 and the mtDNA M haplogroups are characterised by limited internal haplotype and sequence diversity, which can easily be explained with the accumulation of mutations within the Gypsy population subsequent to its founding, rather than variation among the founders.

What Y-DNA haplogroups are Italians? ›

The most frequent Y-DNA haplogroups in the group represented by populations from North-Western Italy, including Tuscany and most of the Padana plain, are four R1b-lineages (R-U152*, R-M269*, R-P312* and R-L2*).

What haplogroup is Native American Y-DNA? ›

Most Native American Y chromosomes belong to haplogroup Q and lie within the branch Q-L54, which coalesces at 18.9 (16.7–21.4) kya but also contains Northern Eurasian chromosomes (Figures 2 and S1).

What is the most common Y haplogroup in Europe? ›

Haplogroup R1b1b2 (R-M269) is the commonest European Y-chromosomal lineage, increasing in frequency from east to west, and carried by 110 million European men.

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