Sebastian Duchene (@sebduchene)

In analyses of ancient HBV, we argue that prior sensitivity is more important than tests of temporal signal. We provide some guidelines for assessing the reliability of estimates derived form the molecular clock. (3/3)

09.07.2025 13:00 👍 0 🔁 0 💬 0 📌 0

We describe the relationship between two fundamental concepts in molecular evolution, the phylodynamic threshold and measurably evolving populations, and the role of tests of temporal signal. (2/3)

09.07.2025 13:00 👍 0 🔁 0 💬 0 📌 0

The phylodynamic threshold of measurably evolving populations The molecular clock is a fundamental tool for understanding the time and pace of evolution, requiring calibration information alongside molecular data. Sampling times are often used for calibration since some organisms accumulate enough mutations over the course of their sampling period. This practice ties two key concepts: measurably evolving populations and the phylodynamic threshold. Current dogma suggests that populations meeting these criteria are suitable for molecular clock calibration via sampling times. However, the definitions and implications of these concepts remain unclear. Using Hepatitis B virus-like simulations and analyses of empirical data, this study shows that determining whether a population is measurably evolving or has reached the phylodynamic threshold does not only depend on the data, but also on model assumptions and sampling strategies. In Bayesian applications, a lack of temporal signal due to a narrow sampling window results in a prior that is overly informative relative to the data, such that a prior that is potentially misleading typically requires a wider sampling window than one that is reasonable. In our analyses we demonstrate that assessing prior sensitivity is more important than the outcome of tests of temporal signal. Our results offer guidelines to improve molecular clock inferences and highlight limitations in molecular sequence sampling procedures. ### Competing Interest Statement The authors have declared no competing interest. Agence Nationale de la Recherche, https://ror.org/00rbzpz17, ANR-16-CONV-0005

I thought I’d share a recent article in collaboration with Ariane Weber and Sanni Översti ( @mpi) , and Julia Kende (
@pasteur.fr).

www.biorxiv.org/content/10.1...

Summary in replies (1/3)

09.07.2025 13:00 👍 1 🔁 0 💬 2 📌 0

In analyses of ancient HBV, we argue that prior sensitivity is more important than tests of temporal signal. We provide some guidelines for assessing the reliability of estimates derived form the molecular clock. (3/3)

09.07.2025 12:55 👍 0 🔁 0 💬 0 📌 0

We describe the relationship between two fundamental concepts in molecular evolution, the phylodynamic threshold and measurably evolving populations, and the role of tests of temporal signal. (2/3)

09.07.2025 12:55 👍 0 🔁 0 💬 0 📌 0

The Next Pandemic? A Scenario. It began with a chimpanzee-trekking tour of a remote forest in Uganda and ended with the outbreak of a deadly new disease. And all because of health cuts and the disruption of a wild animal habitat.

If you have not yet, it is so worth reading (and re-reading) this post by medical historian @honigsbaum.bsky.social because it is so hauntingly realistic and well researched it makes your nails curl.

The Next Pandemic? A Scenario. open.substack.com/pub/markhoni...

23.06.2025 14:21 👍 9 🔁 6 💬 1 📌 0

Postdoctoral positions in epidemic mathematical/statistical modelling - Research Job description We are recruiting postdocs to contribute to research projects in the Mathematical Modelling of Infectious Diseases Unit, at Institut Pasteur in Paris. The candidates will be expected t...

New postdoc positions with a number of exciting epidemic modelling projects opening in our Unit at @pasteur.fr in beautiful Paris. Deadline for applications: 26th June.
research.pasteur.fr/en/job/postd...

05.06.2025 05:22 👍 55 🔁 66 💬 0 📌 3

I'm super proud to share this piece of work, led by @nrascovan.bsky.social, @avanzich.bsky.social and @marialopopolo.bsky.social. See details in Maria's post here:

30.05.2025 07:26 👍 6 🔁 2 💬 0 📌 0

You might be wondering why we haven't updated outbreak.info for months.

Well, the reason is that GISAID cut our access in January - as they did others. Without telling us.

After a ♾️ back and forth, that is now permanent.

More on that soon - and why GISAID should not be trusted with critical data.

28.05.2025 23:02 👍 263 🔁 124 💬 3 📌 10

For simple estimands, treating everything as Gaussian works unreasonably well! But lots to learn from less simple estimands. @avehtari.bsky.social has a nice case study examining this (part of our forthcoming book on workflow) users.aalto.fi/~ave/casestu...

28.05.2025 18:24 👍 69 🔁 8 💬 2 📌 0

The recency and geographical origins of the bat viruses ancestral to SARS-CoV and SARS-CoV-2 Recombination-aware evolutionary analyses of the entire genomes of SARS-CoV-1-like and SARS-CoV-2-like viruses indicate that SARS-CoV-1 and SARS-CoV-2 descend from bat coronaviruses that circulated as...

Sooo happy to finally have this one published!! (3 years in the making… 👀) A comprehensive investigation into the recency and geographical origins of both SARS-CoVs that spilled to humans in the past few decades, now in @cp-cell.bsky.social www.cell.com/cell/fulltex...

10.05.2025 16:46 👍 148 🔁 61 💬 2 📌 4

Sebastian Duchene

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