ArticleAmerican journal of human genetics2019
Inference of Population Structure from Time-Series Genotype Data.
Article in American journal of human genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Pangolin museum genomics reveal the dynamic genetic consequences and extinction risk of the critically endangered Chinese pangolin.Molecular biology and evolution · 2026Article
- Temporal shifts in polygenic traits track major epidemics in Western Eurasia.bioRxiv : the preprint server for biology · 2026Article
- Exploring the genomic population structure and history of Austroasiatic speakers in Mainland Southeast Asia.Communications biology · 2026Article
- Lessons learned: Recommendations for reproducible paleogenomic data analyses.American journal of human genetics · 2025Review
- Ancient Genomics Reveals the Origin, Dispersal, and Human Management of East Asian Domestic Pigs.Molecular biology and evolution · 2025Article
- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.PLoS genetics · 2025Article
- A novel expectation-maximization approach to infer general diploid selection from time-series genetic data.bioRxiv : the preprint server for biology · 2025Article
- Estimating effective population size trajectories from time-series identity-by-descent segments.Genetics · 2025Article
- 9,000 years of genetic continuity in southernmost Africa demonstrated at Oakhurst rockshelter.Nature ecology & evolution · 2024Article
- Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria.Cell genomics · 2024Article
- Genome-wide variation in the Angolan Namib Desert reveals unique pre-Bantu ancestry.Science advances · 2023Article
- The genomic diversity of Taiwanese Austronesian groups: Implications for the "Into- and Out-of-Taiwan" models.PNAS nexus · 2023Article
- Resurrection genomics provides molecular and phenotypic evidence of rapid adaptation to salinization in a keystone aquatic species.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Lineage and role in integrative taxonomy of a heterotrophic orchid complex.Molecular ecology · 2022Article
- Ancient genomes from the last three millennia support multiple human dispersals into Wallacea.Nature ecology & evolution · 2022Article
- The genomic history of the Middle East.Cell · 2021Article
- Factor analysis of ancient population genomic samples.Nature communications · 2020Article
- Learning the properties of adaptive regions with functional data analysis.PLoS genetics · 2020Article
- A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years.American journal of human genetics · 2020Article
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2 authors.
Funding
Abstract
Sequencing ancient DNA can offer direct probing of population history. Yet, such data are commonly analyzed with standard tools that assume DNA samples are all contemporary. We present DyStruct, a model and inference algorithm for inferring shared ancestry from temporally sampled genotype data. DyStruct explicitly incorporates temporal dynamics by modeling individuals as mixtures of unobserved populations whose allele frequencies drift over time. We develop an efficient inference algorithm for our model using stochastic variational inference. On simulated data, we show that DyStruct outperforms the current state of the art when individuals are sampled over time. Using a dataset of 296 modern and 80 ancient samples, we demonstrate DyStruct is able to capture a well-supported admixture event of steppe ancestry into modern Europe. We further apply DyStruct to a genome-wide dataset of 2,067 modern and 262 ancient samples used to study the origin of farming in the Near East. We show that DyStruct provides new insight into population history when compared with alternate approaches, within feasible run time.
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