Rui Borges

If only I wee a candle in the dark.

Glad to share my work on phylogenetic inference for wee, tiny organisms (or highly diverse): the infered topologies seem largely unaffected by unaccounted recurrent mutations, but branch lengths, and mutation-selection usage biases, are significantly impacted.
#eseb #eseb2025

@janekay27.bsky.social presenting her work on merging time scales of evolution to infer adaptive evolution. Great talk! #eseb #fwf

This might sound naive, but I once genuinely believed that the European Union stood firmly for freedom, the rule of law, and human rights.

The students absolutely nailed it, and I was genuinely surprised by how financially literate they were in interpreting the simulation results. People often forget how mathematics can be a tremendous help in making better, more informed decisions in everyday life!

In our session today, we wrapped up the activity by simulating the Gambler’s Ruin in R, using a popular scratchcard game as the example. The game costs £5 per card and has a win probability of roughly 1 in 3.3. One of the photos shows one of these simulations.

I love engaging in outreach activities with math-enthusiastic students, and I always take the opportunity to introduce them to stochastic processes. One process I particularly enjoy teaching is the Gambler’s Ruin.

@uniofstandrews.bsky.social
#standrews #smmb #statistics #maths

Happy to share a PhD opportunity in my new lab at the University of Zurich! Application deadline: June 30. Do not hesitate to contact me for any questions!

Lectures are optional so give us the recordings Katie Nicholson argues that faculties must make some changes if they expect students to attend lectures regularly

Are university lectures on the way out? It seems to me we have to rethink what their purpose is, if any. Because an increasing number of students seem to place relatively little value on them, at least as a real-time experience.

www.varsity.co.uk/comment/29679

New study from the Lab! Jinyang Liang assesses the possibility of inferring ancestral alleles (aka allele polarization) without outgroup sequence, using the ancestral recombination graph (ARG) alone. Here are some of our findings. (1/5)

Now accepting applicants for 25-26 intake of our #StatisticalEcology MSc: bit.ly/3ooHNyc. A unique opportunity to develop skills at the interface of #statistics and #ecology (some partial scholarships available too). Please help me share!

8/8 This study emphasizes the importance of considering recurrent mutations in highly diverse species for accurate population genetics inference.

(Abstract also available in European Portuguese).

7/8 To illustrate how mutation models can influence the quantification of forces other than drift, we further present a case study showing that the BM model exaggerates the intensity of selective constraints acting on the three codon positions of the bacterium Pseudomonas fluorescens.

GitHub - mrborges23/mutation_models: This repository provides a tutorial along with R scripts for utilizing Bayesian estimators of the effective population size with a boundary mutation and recurrent ... This repository provides a tutorial along with R scripts for utilizing Bayesian estimators of the effective population size with a boundary mutation and recurrent mutation model. - mrborges23/mutat...

6/8 We address these biases by proposing a Bayesian estimator for population size that accounts for recurrent mutations. You can find them here: github.com/mrborges23/m...

5/8 Our analyses further reveal that the BM model tends to overestimate the effective population size, particularly in bacteria, where estimated population sizes can be more than five times larger than those expected by the recurrent mutation model.

4/8 By examining mutation rates and effective population sizes across the Tree of Life, we demonstrate that the BM model remains valid for most species but significantly deviates in bacteria.

3/8 However, one can alternatively assume a recurrent mutation model (RM), which additionally considers mutations contributing to shifts in allele frequency.
In this study, we compare these two models.

2/8 A common assumption is that mutations are infrequent, so when a new mutation arises, the previous one has either become fixed or lost. This assumption implies that mutations occur exclusively at fixed sites and is referred to as the boundary mutation model (BM).

1/8 Mutations are fundamental for evolution, and their mathematical modelling in population genetics heavily relies on our perception of their frequency and the timescale over which they occur.

The rarity of mutations and the inflation of bacterial effective population sizes Mutations are fundamental for evolution, and their mathematical modelling in population genetics heavily relies on our perception of their frequency and the timescale over which they occur. A comm...

Glad to see this out today in MEE!
The rarity of mutations and the inflation of bacterial effective population sizes
besjournals.onlinelibrary.wiley.com/doi/10.1111/...

#popgen #populationgenetics #evolution #bacteriagenomics #bacteria #microsky #statsstandrews @uniofstandrews.bsky.social

Glad to present my work on the implications of different mutation models in #popgen and #phylo inference at #PopGroup58 in Sheffield (even tried my hand at cèilidh dancing). Kudos to the organizers for this excellent meeting! #statsstandrews

Genome Biology and Evolution is excited to now be on Bluesky. Please help us by recommending accounts and feeds for us to follow!

Super proud of @janekay27.bsky.social for receiving an OEAW grant to continue their PhD work on codon evolution for another two years 🥳 It was a pity I couldn't be there in person for the award ceremony, but @bio-diogo.bsky.social did a fantastic job stepping in and capturing some great photos:

The global spread of Oriental Horses in the past 1,500 years through the lens of the Y chromosome | PNAS Since their domestication, horses have accompanied mankind, and humans have constantly shaped horses according to their needs through stallion-cent...

Update on our latest research featured in PNAS! 🐴 ✨ We used Y chromosome to explain the legacy of Oriental horses, embedded in a 1,500-year-old Crown lineage 👑 spread across continents and centuries! 🌍
Check it out 😊

A problem for a stormy, rainy day: #maths #mathproblems #OPM

Scientists, when do we start lobbying for #Bluesky to implement native LaTeX support?

#science #physics #mathematics

🧪⚛️

go.bsky.app/NiaWN5i

I'm happy to receive suggestions for this.

Here's a starter pack for early career researchers in evolutionary biology. I prioritized the most-junior folks, and this list quickly filled up with undergrads, grad students, and postdocs. Might do another list later, but I'm tired. Have fun everyone! 🐒 #evobio

go.bsky.app/MzND7nX

9/9 The real challenge is how scientists can foster trust in the scientific community. This is a big problem in itself, but it pales in comparison to what politicians face: rebuilding trust in democratic institutions as a whole. I am totally clueless here though.

8/9 Should scientists help people escape echo chambers? Echo chambers actively undermine trust in anything outside their own beliefs. This means they’re are designed to reject any evidence that challenges their views. So, the issue isn’t about providing evidence - it’s about building trust.