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Leyan Wang @leyan-wang.bsky.social · 26/11/2025

Overall, ARG inference tools have demonstrated remarkable robustness to computational phasing errors. While various practical challenges may limit ARG inference quality, we believe that computational phasing inaccuracies should not be a problem of concern. 7/7

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Leyan Wang @leyan-wang.bsky.social · 26/11/2025

Under a selective sweep model, we saw little difference in branch-length-based diversity between ARGs inferred from true and computationally phased haplotypes, demonstrating the practicality of applying ARGs inferred from unphased data in evolutionary analyses. 6/7

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Leyan Wang @leyan-wang.bsky.social · 26/11/2025

Under the CEU bottleneck model, we observed consistently minor effects of phasing errors. The difference between ARG inference methods is much larger than the difference in performance between using true haplotypes and computationally phased haplotypes. 5/7

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Leyan Wang @leyan-wang.bsky.social · 26/11/2025

In constant population size models, we observed only a slight reduction in ARG inference accuracy in terms of estimates of coalescence times or recombination breakpoint counts when using computationally phased haplotypes. The effect also reduced as the sample size increased. 4/7

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Leyan Wang @leyan-wang.bsky.social · 26/11/2025

Here, we show that ARG inference remains robust to phasing errors even at incredibly small sample sizes (8 haplotypes). We simulated ARGs and VCFs under various demographic models, simulated phasing errors, and compared ARGs inferred from true and computationally phased haplotypes. 3/7

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Leyan Wang @leyan-wang.bsky.social · 26/11/2025

ARGs are powerful tools in population genetics. However, ARG inference generally requires phased haplotypes. Phasing quality is limited at small sample sizes, making it difficult in non-model organisms due to the usually limited sample size and a lack of reference panels. 2/7

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Leyan Wang @leyan-wang.bsky.social · 26/11/2025

We are excited to share our recent work on the surprising robustness of Ancestral Recombination Graph (ARG) inference tools to computational phasing errors, now available on BioRxiv: biorxiv.org/content/10.1.... This work is co-advised by @yundeng.bsky.social and Rasmus Nielsen. 1/7