New tskit-related papers

A trio of high-impact papers

In May and August 2023 the following papers, which make extensive use of tskit projects, were published:

A weakly structured stem for human origins in Africa – Nature

Figure 3b: demographic plot of a weak stem with multiple mergers

A paper by @apragsdale and colleagues, who contribute to msprime software development, uses msprime simulations (among other techniques) to argue for a complex history of structured subpopulations in deep human history.

On the genes, genealogies, and geographies of Quebec – Science

Figure 1b: Visualizing the ancestry of French Canadians across regions (x axis) over time

This paper uses the recently implemented feature in msprime to simulate genetic transmission through a known pedigree. In this case, a human pedigree based on 4 million Canadian genealogical records was used. Results highlight the multiple impacts of geography on human migration, and a freely available simulated whole-genome dataset of almost 1.5 million individuals is provided.

Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies – Nature Genetics

Figure 2a: Accuracy and sparsity of the LDGM precision matrix

This paper shows how common statistical genetic algorithms, for example used in GWAS studies, can be both sped up and made more accurate by leveraging genetic genealogies inferred from real data by tsinfer.