The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes

The Allen Ancient DNA Resource (AADR) seeks to provide a publicly available, uniformly curated dataset that is maximally useful for scientists carrying out analyses of population history and natural selection. The dataset consists of thousands of ancient and present-day individuals genotyped at up to 1.23 million positions in the genome (in hg19 coordinates). The genotypes in the AADR are not a perfect match to those from the associated published papers. To make it easier to co-analyze datasets, we have started from bam or fastq files; trimmed the ends of sequences to reduce errors due to ancient DNA damage in a way that is largely uniform across datasets and may be slightly different from that used in the individual publications; and determined genotypes anew by sampling a random sequence to cover each position. Researchers who wish to use this compilation should provide two citations. The first should be to the Dataverse page and the specific version of AADR they use as the basis of their analyses (e.g. version 6.1, the March 6 2023 release, as in the example below). The second should be to the manuscript describing AADR. (1) \"Swapan Mallick and David Reich (2023) \"The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes\", https://doi.org/10.7910/DVN/FFIDCW”, Harvard Dataverse, XX data release [April 5, 2023].\" (2) \"Swapan Mallick, Adam Micco, Matthew Mah, Harald Ringbauer, Iosif Lazaridis, Iñigo Olalde, Nick Patterson and David Reich (2023) \"The Allen Ancient DNA Resource (AADR): A curated compendium of ancient human genomes.\" bioRxiv XXX.\" Citing the AADR is not a substitute for citing the original papers that produced the component data, which must be specifically referenced in each publication that uses data from them. We aim to update and enhance this resource every couple of months to make the releases maximally useful to the community. We rely on feedback from the user community to improve the AADR, so please write jointly to Swapan Mallick ([e-mail]) and David Reich ([e-mail]) if you identify errors or other issues. The first version of AADR was made publicly on February 22 2019 via the Reich laboratory website at Harvard Medical School, which hosted a total of six primary releases. All releases are now copied to Dataverse which has the virtue of including a permanent digital object identifier (doi) that can be cited in a straightforward way, and data access not tied to the website of a Principal Investigator. Below is a translation from the versions on the Reich laboratory website to the Dataverse versions. V54.1.p1 (Dataverse 8.0) March 6 2023 V54.1 (Dataverse 7.0) Nov 16 2022 V52.2 (Dataverse 6.0) Aug 22 2022 V50.0.p1 (Dataverse 5.0) Aug 1 2022 V50.0 (Dataverse 4.0) Oct 10 2021 V44.3 (Dataverse 3.0) Jan 20 2021 V42.4 (Dataverse 2.0) Mar 25 2020 V37.2 (Dataverse 1.0) Feb 22 2019 We thank the John Templeton Foundation, a grant from the National Institutes of Health, the Howard Hughes Medical Institute, and the Allen Discovery Center program, a Paul G. Allen Frontiers Group advised program of the Paul G. Allen Family Foundation, for providing the resources needed to create and update this dataset.