ArticleScientific reports2021
TKGWV2: an ancient DNA relatedness pipeline for ultra-low coverage whole genome shotgun data.
Article in Scientific reports, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Fault-tolerant pedigree reconstruction from pairwise kinship relations.Bioinformatics (Oxford, England) · 2026Article
- Multiple Genetic Shifts at the Crossroads of the Eastern Steppe and Loess Plateau Over 4,000 Years.Nature communications · 2026Article
- On the Edge of Empire: Paleogenomic Insights into Roman Dacia.bioRxiv : the preprint server for biology · 2026Article
- Evaluating the performance of ancient DNA genetic relatedness estimation methods using high-fidelity pedigree simulations.Genome biology · 2026Article
- Individual identification and kinship testing from hair shaft nuclear DNA: leveraging short amplicon strategy and bioinformatics models.International journal of legal medicine · 2026Article
- Article
- The genomic history of East Asian Middle Neolithic millet- and rice-agricultural populations.Cell genomics · 2025Article
- clusIBD: Robust Detection of Identity-by-descent Segments Using Unphased Genetic Data from Poor-quality Samples.Genomics, proteomics & bioinformatics · 2025Article
- Genomic diversity and structure of prehistoric alpine individuals from the Tyrolean Iceman's territory.Nature communications · 2025Article
- Ancient genomes shed light on the genetic history of the Iron Age to historical central Xinjiang, northwest China.BMC biology · 2025Article
- The cranium from the Octagon in Ephesos.Scientific reports · 2025Article
- The genomic portrait of the Picene culture provides new insights into the Italic Iron Age and the legacy of the Roman Empire in Central Italy.Genome biology · 2024Article
- READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics.Genome biology · 2024Article
- Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France.Proceedings. Biological sciences · 2024Article
- Geographic origin, ancestry, and death circumstances at the Cornaux/Les Sauges Iron Age bridge, Switzerland.Scientific reports · 2024Article
- Article
- Ancestry and kinship in a Late Antiquity-Early Middle Ages cemetery in the Eastern Italian Alps.iScience · 2023Article
- Genome-wide analysis of a collective grave from Mentesh Tepe provides insight into the population structure of early neolithic population in the South Caucasus.Communications biology · 2023Article
- Inferring biological kinship in ancient datasets: comparing the response of ancient DNA-specific software packages to low coverage data.BMC genomics · 2023Article
- Neolithic genomic data from southern France showcase intensified interactions with hunter-gatherer communities.iScience · 2022Article
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Estimation of genetically related individuals is playing an increasingly important role in the ancient DNA field. In recent years, the numbers of sequenced individuals from single sites have been increasing, reflecting a growing interest in understanding the familial and social organisation of ancient populations. Although a few different methods have been specifically developed for ancient DNA, namely to tackle issues such as low-coverage homozygous data, they require a 0.1-1× minimum average genomic coverage per analysed pair of individuals. Here we present an updated version of a method that enables estimates of 1st and 2nd-degrees of relatedness with as little as 0.026× average coverage, or around 18,000 SNPs from 1.3 million aligned reads per sample with average length of 62 bp-four times less data than 0.1× coverage at similar read lengths. By using simulated data to estimate false positive error rates, we further show that a threshold even as low as 0.012×, or around 4000 SNPs from 600,000 reads, will always show 1st-degree relationships as related. Lastly, by applying this method to published data, we are able to identify previously undocumented relationships using individuals that had been excluded from prior kinship analysis due to their very low coverage. This methodological improvement has the potential to enable relatedness estimation on ancient whole genome shotgun data during routine low-coverage screening, and therefore improve project management when decisions need to be made on which individuals are to be further sequenced.
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