The ARG: * Captured key biological signals * Encoded genomic data more efficiently than conventional formats * Resulted in the highest predictive ability when combining both subspecies (though not by much) - ThreadSky

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gregorgorjanc.bsky.social • 37 days ago

The ARG:

* Captured key biological signals
* Encoded genomic data more efficiently than conventional formats
* Resulted in the highest predictive ability when combining both subspecies (though not by much)

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gregorgorjanc.bsky.social•37 days ago

Taken together, the results demonstrated the potential of ARGs for the quantitative genetic analysis of diverse populations.

gregorgorjanc.bsky.social•37 days ago

This builds upon the work of tskit community - there is an advanced manuscript in the pipeline on how to build relationship/relatedness matrix from tree sequence encoding of an ARG!

gregorgorjanc.bsky.social•37 days ago

After building the ARG, we demonstrated it captures biological signals using genealogical nearest neighbors (GNN) - it clearly distinguished indica and japonica rice subspecies and effectively represented population structure.

gregorgorjanc.bsky.social•37 days ago

Local trees from two genomic regions showed distinct patterns: (A) revealed deep separation between indica and japonica, linked to the DST gene associated with panicle length in japonica. The (B) region segregated in both subspecies and was linked to panicle traits in both.

gregorgorjanc.bsky.social•37 days ago

The ARG encoded genomic data more efficiently than the standard VCF: the tree sequence file for all chromosomes was 62 MB, compared to 228 MB for the VCF—nearly four times smaller!

gregorgorjanc.bsky.social•37 days ago

The age distributions for (A) nodes (ancestors), (B) mutations, and (C) SNP sites (i.e., first mutation at each site) were heavily right-skewed towards the present (as expected).

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