ArticleMolecular biology and evolution2022
Placing Ancient DNA Sequences into Reference Phylogenies.
Article in Molecular biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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50 citing papers in PubMed.
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- Equal in death: Ancient genomic analysis of children's early Christian burials.Science advances · 2026Article
- Metagenomic peek into a corn mummy.Scientific reports · 2026Article
- Bioarchaeological analysis illustrates the life of a 16th-century Sámi individual from Kitka, Kuusamo, northern Finland.BMC genomics · 2026Article
- Complex peopling history and expansion events inferred from large-scale modern and ancient Y chromosome sequences.Science advances · 2026Article
- Panmap: Scalable phylogeny-guided alignment, genotyping, and placement on pangenomes.bioRxiv : the preprint server for biology · 2026Article
- Analysis of medieval burials from Ibiza reveals genetic and pathogenic diversity during the Islamic period.Nature communications · 2026Article
- Modern and Ancient Genomes Reveal Neolithic Paternal Expansions of Millet and Rice Farmers and Demic Diffusion from China into Mainland Southeast Asia.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Genomes of the Golden Horde elites and their implications for the rulers of the Mongol Empire.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Multiple southward migrations of Neolithic Chinese farmers into Southeast Asia revealed from large-scale Y-chromosome sequences.Science advances · 2026Article
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- Tracing bronze to iron age population dynamics in Northwest Xinjiang using ancient time-series genomic data.Genome biology · 2026Article
- Continuity of eastern Beringian megafauna phylogenetic diversity following deposition of the Late Pleistocene Dawson tephra.Arctic, antarctic, and alpine research · 2026Article
- Whole-genome ancestry of an Old Kingdom Egyptian.Nature · 2025Article
- A New Perspective on the Arrival of the Eastern Mediterranean Genetic Influx in Central Italy Before the Onset of the Roman Empire.Genome biology and evolution · 2025Article
- A New Perspective on the Arrival of the Eastern Mediterranean Genetic Influx in Central Italy Before the Onset of the Roman Empire.Genome biology and evolution · 2025Article
- Medieval genomes from eastern Iberia illuminate the role of Morisco mass deportations in dismantling a long-standing genetic bridge with North Africa.Genome biology · 2025Article
- Sedimentary DNA insights into Holocene Adélie penguin (Pygoscelis adeliae) populations and ecology in the Ross Sea, Antarctica.Nature communications · 2025Article
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4 authors.
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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.
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