iiinova — where your digital self keeps evolving

Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

10. Thanks a lot to co-authors Théo Gaboriau and Nicolas Salamin, all how gave feedbacks, anonymous reviewers, and editors at Evolution Letters.

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

9. Take-home: when claiming neutral drift, use a phylogram as backbone. When modeling selective regimes, use a chronogram. Paper: doi.org/10.1093/evle... Code: github.com/ThibaultLatrille/ChronoPhylogram

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

8. When generation time varies (the biologically realistic case), π cleanly separates the regimes. Neutral → phylogram preferred. Selection → chronogram preferred. Constant generation time → π≈0.5 for all regimes, as expected.

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

7. Validated using Wright-Fisher simulations on a mammalian-like phylogeny: 3 regimes (neutral / moving optimum / discrete optima), with variable generation time, mutation rate, and Ne, mimicking real mammalian diversity.

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

6. We formalized this with a Bayesian switch variable π: π=0 fits BM on the chronogram, π=1 on the phylogram (both rescaled to equal length). Posterior mean of π from MCMC gives continuous support for one tree over the other.

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

5. A phylogram naturally absorbs variation in generation time. Neutral trait → better BM fit on a phylogram. Trait tracking a moving optimum → better fit on a chronogram. This gives us a way to distinguish them.

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

4. Neutral divergence scales with generations, not absolute time. Mice accumulate far more neutral changes per year than elephants. Chronograms ignore this. Phylograms, where branch lengths = neutral substitutions, don't.

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

3. A trait tracking a randomly moving optimum (i.e. under selection) also generates a BM-like pattern. BM fit alone cannot distinguish neutral drift from selection on a moving target. The key lies in the branch lengths.

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

2. Standard practice: fit BM (neutral drift), OU (stabilizing selection), or shifted OU (directional) to trait data on a chronogram. Best fit → inferred process. Simple in principle. But there's a fundamental ambiguity.

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Thibault Latrille @phylogenetrips.bsky.social · 24/04/2026

1. Chronograms are everywhere in comparative biology. When modeling traits like body size or brain mass across species, branches are almost universally expressed in units of time. This seems natural, but is it always appropriate?

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Reposted by Thibault Latrille

Nicolas Clairis @nclairis.bsky.social · 09/03/2026

Based on our WhereToPublish database, we were curious to see if the APCs depend on the publisher type and with relatively no surprise at all, the journals that are for-profit are way above: For-profit journals = 2635 +/- 37€ (mean +/- sem) Non-profit & University Press journals = 1996 +/- 63€ 1/4

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Reposted by Thibault Latrille

Nicolas Clairis @nclairis.bsky.social · 10/02/2026

Dear all, I'm happy to present you a side project done with @diegoharta.bsky.social @phylogenetrips.bsky.social & Lucas Baudouin regarding the publication landscape in Biology: wheretopublish.github.io 1/4

wheretopublish.github.io

Where to Publish?

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

Call for abstracts for the symposium on "Microevolutionary processes and Macroevolutionary patterns" (S36) at ESEB 2025 (@eseb2025.bsky.social), taking place from 17-22 August in Barcelona, Spain. With @lhliow.bsky.social and Jonathan Rolland as invited speakers.

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

Many thanks to the anonymous reviewers, and many more all co-authors Julien Joseph, Diego Hartasánchez and Nicolas Salamin.

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

8/8 Using exomes of 96 mammals with polymorphism data for 28 populations from 6 genera, we show that non-adaptive mutations constitute an important fraction of beneficial mutations (P[B₀|B]).

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

7/8 We then estimated the proportion of beneficial mutations that are not adaptive innovations among all beneficial mutations at the population scale.

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

6/8 We first estimated selective effects of mutations inside mammalian protein coding sequences, under a model assuming no adaptation at the phylogenetic scale.

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

5/8 Despite leaving similar signatures when looking only at populations, adaptive mutations promote phenotypic diversification (C) while non-adaptive mutations reduce diversity between species and stabilize existing systems (D).

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

4/8 Even though the existence of these beneficial yet non adaptive mutations is predicted by the nearly neutral theory (B), they have been largely overlooked, and positive selection has been often interpreted as adaptation to changing environments (A).

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

3/8 These mutations are then subsequently reverted by beneficial mutations, generating a balance at which genomes are constantly both “damaged” and “repaired” simultaneously at different loci.

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

2/8 Our study is based on the premise that slightly deleterious mutations scattered across the genome are reaching fixation due to genetic drift.

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

1/8 In this work based on genome-wide studies across mammalian species and populations, we estimated the proportion of beneficial mutations in protein coding sequences that are restoring pre-existing functions.

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Thibault Latrille @phylogenetrips.bsky.social · 14/03/2025

As my first bsky post (about time), I’m happy to share our genomic work published in PLOS Genetics (@plos.org) 🧬🐒🐀 Beneficial yet non-adaptive mutations doi.org/10.1371/jour...

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Reposted by Thibault Latrille

Masahito Tsuboi @masahitotsuboi.bsky.social · 03/12/2024

Now our special issue on the relationship between microevolution and macroevolution is online @jevbio.bsky.social! We hope that it marks the beginning of a new era of exciting discoveries. link to the issue: ow.ly/LHol50UjJql link to the editorial: doi.org/10.1093/jeb/...

ow.ly

Volume 37 Issue 12 | Journal of Evolutionary Biology | Oxford Academic

Journal of Evolutionary Biology

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