READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics-Reference-Cited by-同舟云学术

READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics

Published:2024-08-12 Issue:1 Volume:25 Page:
ISSN:1474-760X
Container-title:Genome Biology
language:en
Short-container-title:Genome Biol

Author:

Alaçamlı Erkin,Naidoo Thijessen,Güler Merve N.,Sağlıcan Ekin,Aktürk Şevval,Mapelli Igor,Vural Kıvılcım Başak,Somel Mehmet,Malmström Helena,Günther Torsten^ORCID

Abstract

AbstractThe advent of genome-wide ancient DNA analysis has revolutionized our understanding of prehistoric societies. However, studying biological relatedness in these groups requires tailored approaches due to the challenges of analyzing ancient DNA. READv2, an optimized Python3 implementation of the most widely used tool for this purpose, addresses these challenges while surpassing its predecessor in speed and accuracy. For sufficient amounts of data, it can classify up to third-degree relatedness and differentiate between the two types of first-degree relatedness, full siblings and parent-offspring. READv2 enables user-friendly, efficient, and nuanced analysis of biological relatedness, facilitating a deeper understanding of past social structures.

Funder

Riksbankens Jubileumsfond

HORIZON EUROPE European Research Council

Uppsala University

Publisher

Springer Science and Business Media LLC

Link

https://link.springer.com/content/pdf/10.1186/s13059-024-03350-3.pdf

Reference66 articles.

1. Racimo F, Sikora M, Vander Linden M, Schroeder H, Lalueza-Fox C. Beyond broad strokes: sociocultural insights from the study of ancient genomes. Nat Rev Genet. 2020;21:355–66. https://doi.org/10.1038/s41576-020-0218-z.

2. Orlando L, Allaby R, Skoglund P, Der Sarkissian C, Stockhammer PW, Ávila-Arcos MC, et al. Ancient DNA analysis. Nat Rev Methods Primers. 2021;1:1–26. https://doi.org/10.1038/s43586-020-00011-0.

3. Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, et al. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science. 2017;358:659–62.

4. Amorim CEG, Vai S, Posth C, Modi A, Koncz I, Hakenbeck S, et al. Understanding 6th-century barbarian social organization and migration through paleogenomics. Nat Commun. 2018;9:3547. https://doi.org/10.1038/s41467-018-06024-4.

5. O’Sullivan N, Posth C, Coia V, Schuenemann VJ, Price TD, Wahl J, et al. Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard. Science Advances. 2018;4:eaao1262. https://doi.org/10.1126/sciadv.aao1262.