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Jiansi Gao @jsigao.bsky.social · 17/06/2025

We also discuss potential ways for optimizing phylodynamic analysis settings and developing more efficient algorithms for traversing the tree space. If interested, please check our preprint out! n/n (More tree space animations of each dataset we analyzed are available at tinyurl.com/ssstreeanim.)

tinyurl.com

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Jiansi Gao @jsigao.bsky.social · 17/06/2025

Nonetheless, some global parameters governed by general tree shape are rather robust to the sampling problems. E.g., the demographic trajectories are barely distinguishable among the chains, meaning that relatively short chains would be sufficient if such parameter is of primary interest. 6/

Impact of the tree sampling problems tends to be negligible on some global parameters (e.g., the effective population size through time).

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Jiansi Gao @jsigao.bsky.social · 17/06/2025

Tree space ruggedness and consequent sampling problems can strongly distort biological conclusions. E.g., our analyses of an HIV dataset reveal distinct early spread history of HIV among the chains. 5/ (The number of dispersal events between two focal geographic areas; each panel shows a chain.)

Distinct peaks in tree space can lead to different biological conclusions.

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Jiansi Gao @jsigao.bsky.social · 17/06/2025

Our new MCMC diagnostics reveal that the sampling problems typically stem from a small part of the tree. E.g., in a LASV dataset, removing just two of the 551 sequences reshapes the tree space and effectively resolves the sampling problems. 4/ (Tree space samplers before and after the removal.)

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Jiansi Gao @jsigao.bsky.social · 17/06/2025

We are interested in understanding phylodynamic tree landscape and its biological impacts. Here we show that the tree landscape is usually highly rugged, leading to widespread sampling problems. 3/ (MCMC progress in MDS tree space; each panel shows a dataset and each dot represents a tree.)

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Jiansi Gao @jsigao.bsky.social · 17/06/2025

Unlike typical phylogenetic settings where the tree topology is our focus and the best tree is strongly supported by the informative genomic data, phylodynamic inference uses viral sequences with limited genetic diversity and frequently treats the topology as a nuisance. 2/

Conceptual illustration of a rugged tree landscape and the consequent sampling problems.

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Jiansi Gao @jsigao.bsky.social · 17/06/2025

Excited to share my new preprint developed with @matsen.bsky.social, in collaboration with Marius Brusselmans, Luiz Carvalho, @msuchard.bsky.social, and @guybaele.bsky.social, on the biological causes and impacts of tree space ruggedness in phylodynamic inference. 1/ www.biorxiv.org/content/10.1...

biorxiv.org

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