AYChr-DB: a Database of Ancient Human Y Haplogroups

Overview

Journal NAR Genom Bioinform

Publisher Oxford University Press

Specialty Biology

Date 2021 Feb 12

PMID 33575627

Citations 5

Authors

Laurence Freeman

Conrad Stephen Brimacombe

Eran Elhaik

Affiliations

Soon will be listed here.

Abstract

Ancient Y-Chromosomal DNA is an invaluable tool for dating and discerning the origins of migration routes and demographic processes that occurred thousands of years ago. Driven by the adoption of high-throughput sequencing and capture enrichment methods in paleogenomics, the number of published ancient genomes has nearly quadrupled within the last three years (2018-2020). Whereas ancient mtDNA haplogroup repositories are available, no similar resource exists for ancient Y-Chromosomal haplogroups. Here, we present aYChr-DB-a comprehensive collection of 1797 ancient Eurasian human Y-Chromosome haplogroups ranging from 44 930 BC to 1945 AD. We include descriptors of age, location, genomic coverage and associated archaeological cultures. We also produced a visualization of ancient Y haplogroup distribution over time. The aYChr-DB database is a valuable resource for population genomic and paleogenomic studies.

Citing Articles

Big Epidemiology: The Birth, Life, Death, and Resurgence of Diseases on a Global Timescale.

Bragazzi N, Lehr T Epidemiologia (Basel). 2024; 5(4):669-691.

PMID: 39584937 PMC: 11586986. DOI: 10.3390/epidemiologia5040047.

The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes.

Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I Sci Data. 2024; 11(1):182.

PMID: 38341426 PMC: 10858950. DOI: 10.1038/s41597-024-03031-7.

Temporal population structure, a genetic dating method for ancient Eurasian genomes from the past 10,000 years.

Behnamian S, Esposito U, Holland G, Alshehab G, Dobre A, Pirooznia M Cell Rep Methods. 2022; 2(8):100270.

PMID: 36046618 PMC: 9421539. DOI: 10.1016/j.crmeth.2022.100270.

On the Forensic Use of Y-Chromosome Polymorphisms.

de Knijff P Genes (Basel). 2022; 13(5).

PMID: 35627283 PMC: 9141910. DOI: 10.3390/genes13050898.

Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe.

Rohrlach A, Papac L, Childebayeva A, Rivollat M, Villalba-Mouco V, Neumann G Sci Rep. 2021; 11(1):15005.

PMID: 34294811 PMC: 8298398. DOI: 10.1038/s41598-021-94491-z.

References

Prohaska A, Racimo F, Schork A, Sikora M, Stern A, Ilardo M . Human Disease Variation in the Light of Population Genomics. Cell. 2019; 177(1):115-131. DOI: 10.1016/j.cell.2019.01.052. View

Lipson M, Cheronet O, Mallick S, Rohland N, Oxenham M, Pietrusewsky M . Ancient genomes document multiple waves of migration in Southeast Asian prehistory. Science. 2018; 361(6397):92-95. PMC: 6476732. DOI: 10.1126/science.aat3188. View

Elhaik E, Tatarinova T, Klyosov A, Graur D . The 'extremely ancient' chromosome that isn't: a forensic bioinformatic investigation of Albert Perry's X-degenerate portion of the Y chromosome. Eur J Hum Genet. 2014; 22(9):1111-6. PMC: 4135414. DOI: 10.1038/ejhg.2013.303. View

Zhao Y, Zhang Y, Li H, Cui Y, Zhu H, Zhou H . Ancient DNA evidence reveals that the Y chromosome haplogroup Q1a1 admixed into the Han Chinese 3,000 years ago. Am J Hum Biol. 2014; 26(6):813-21. DOI: 10.1002/ajhb.22604. View

Esposito U, Das R, Syed S, Pirooznia M, Elhaik E . Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians. Genes (Basel). 2018; 9(12). PMC: 6316245. DOI: 10.3390/genes9120625. View

Morozova I, Flegontov P, Mikheyev A, Bruskin S, Asgharian H, Ponomarenko P . Toward high-resolution population genomics using archaeological samples. DNA Res. 2016; 23(4):295-310. PMC: 4991838. DOI: 10.1093/dnares/dsw029. View

Szecsenyi-Nagy A, Brandt G, Haak W, Keerl V, Jakucs J, Moller-Rieker S . Tracing the genetic origin of Europe's first farmers reveals insights into their social organization. Proc Biol Sci. 2015; 282(1805). PMC: 4389623. DOI: 10.1098/rspb.2015.0339. View

Haak W, Lazaridis I, Patterson N, Rohland N, Mallick S, Llamas B . Massive migration from the steppe was a source for Indo-European languages in Europe. Nature. 2015; 522(7555):207-11. PMC: 5048219. DOI: 10.1038/nature14317. View

Brandt G, Szecsenyi-Nagy A, Roth C, Alt K, Haak W . Human paleogenetics of Europe--the known knowns and the known unknowns. J Hum Evol. 2014; 79:73-92. DOI: 10.1016/j.jhevol.2014.06.017. View

10.

Kivisild T . The study of human Y chromosome variation through ancient DNA. Hum Genet. 2017; 136(5):529-546. PMC: 5418327. DOI: 10.1007/s00439-017-1773-z. View

11.

Ehler E, Novotny J, Juras A, Chylenski M, Moravcik O, Paces J . AmtDB: a database of ancient human mitochondrial genomes. Nucleic Acids Res. 2018; 47(D1):D29-D32. PMC: 6324066. DOI: 10.1093/nar/gky843. View

12.

Haak W, Balanovsky O, Sanchez J, Koshel S, Zaporozhchenko V, Adler C . Ancient DNA from European early neolithic farmers reveals their near eastern affinities. PLoS Biol. 2010; 8(11):e1000536. PMC: 2976717. DOI: 10.1371/journal.pbio.1000536. View

13.

Underhill P, Kivisild T . Use of y chromosome and mitochondrial DNA population structure in tracing human migrations. Annu Rev Genet. 2007; 41:539-64. DOI: 10.1146/annurev.genet.41.110306.130407. View