Abstract
Joint phylogenetic analysis of ancient DNA (aDNA) with modern phylogenies is hampered by low sequence coverage and post-mortem deamination, often resulting in overconservative or incorrect assignment. We provide a new efficient likelihood-based workflow, pathPhynder, that takes advantage of all the polymorphic sites in the target sequence. This effectively evaluates the number of ancestral and derived alleles present on each branch and reports the most likely placement of an ancient sample in the phylogeny and a haplogroup assignment, together with alternatives and supporting evidence. To illustrate the application of pathPhynder, we show improved Y chromosome assignments for published aDNA sequences, using a newly compiled Y variation data set (120,908 markers from 2,014 samples) that significantly enhances Y haplogroup assignment for low coverage samples. We apply the method to all published male aDNA samples from Africa, giving new insights into ancient migrations and the relationships between ancient and modern populations. The same software can be used to place samples with large amounts of missing data into other large non-recombining phylogenies such as the mitochondrial tree.
Highlights
The development of high-throughput sequencing methods and their application to archaeological remains has dramatically changed our understanding of deep human history
To evaluate the advantages of using this additional variation, we selected 52 ancient DNA (aDNA) samples which had been assigned in the literature using catalogued variants in the International Society of Genetic Genealogy (ISOGG) database to upstream branches of the phylogeny, such as BT-M91 or CT-M168, or were unassigned, and reanalyzed them with pathPhynder
In order to demonstrate the usefulness of our method for real data, we examine ancient and present-day Y-chromosome diversity in Africa by placing all ancient male samples from the African continent published at the time of this study (n=63) (Fregel et al, 2018; Lipson et al, 2020; Llorente et al, 2015; Prendergast et al, 2019; Schlebusch et al, 2017; Schuenemann et al, 2017; Skoglund et al, 2017; Van de Loosdrecht et al, 2018; Wang et al, 2020), and additional samples from the Levant (n=15) (Lazaridis et al, 2016) into the Y-chromosome tree using pathPhynder (Supplementary Table 1)
Summary
The development of high-throughput sequencing methods and their application to archaeological remains has dramatically changed our understanding of deep human history. While there are methods which use likelihoods for the placement of sequences into a preestimated phylogenetic tree, such as pplacer (Matsen et al, 2010) and RAxML’s Evolutionary Placement algorithm (Berger et al, 2011), these do not take the degraded nature of ancient DNA into account and can provide erroneous assignments. Such likelihood methods do not provide explicit output regarding which or how many SNPs were used for the placement, which is relevant for evaluating the reliability of the results and where on the placement branch the ancient sample diverged. They are computationally expensive when applied to the thousands of samples currently available for analysis (Hallast et al, 2020; Poznik et al, 2016)
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