iiinova — where your digital self keeps evolving

Reposted by Rui Borges

Casey Dunn @caseywdunn.bsky.social · 25/08/2026

My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.

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Rui Borges @ruiborges23.bsky.social · 19/08/2026

4/4 The main takeaway: for highly diverse organisms, accounting for recurrent mutations can be important for making reliable inferences about their evolutionary dynamics. Very grateful to my coauthor Joseph Hughes, the editors and everyone who contributed to this work!

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Rui Borges @ruiborges23.bsky.social · 19/08/2026

3/4 We compare a model that allows recurrent mutations with one that assumes only boundary mutations. Interestingly, we find that tree topologies are mostly unaffected, but branch lengths and estimates of mutation bias and selection can be distorted when recurrent mutations are ignored.

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Rui Borges @ruiborges23.bsky.social · 19/08/2026

2/4 A key assumption in many molecular evolution models is that mutations are somehow rare. This assumption can be problematic for highly diverse organisms, such as bacteria and viruses, where mutations occur recurrently.

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Rui Borges @ruiborges23.bsky.social · 31/08/2025

If only I wee a candle in the dark.

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Rui Borges @ruiborges23.bsky.social · 22/08/2025

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

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Rui Borges @ruiborges23.bsky.social · 20/08/2025

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

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Rui Borges @ruiborges23.bsky.social · 07/08/2025

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

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Rui Borges @ruiborges23.bsky.social · 08/07/2025

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!

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Rui Borges @ruiborges23.bsky.social · 08/07/2025

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.

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Rui Borges @ruiborges23.bsky.social · 08/07/2025

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

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Reposted by Rui Borges

Sandra Oliveira @sandra-oliveira.bsky.social · 20/05/2025

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!

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Reposted by Rui Borges

Aylwyn Scally @aylwyn-scally.bsky.social · 14/05/2025

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

varsity.co.uk

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

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Reposted by Rui Borges

jydutheil.bsky.social @jydutheil.bsky.social · 02/02/2025

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)

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Reposted by Rui Borges

Chris Sutherland @chrissuthy.bsky.social · 29/01/2025

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!

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Rui Borges @ruiborges23.bsky.social · 27/01/2025

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).

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Rui Borges @ruiborges23.bsky.social · 27/01/2025

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.

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Rui Borges @ruiborges23.bsky.social · 27/01/2025

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.

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Rui Borges @ruiborges23.bsky.social · 27/01/2025

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.

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Rui Borges @ruiborges23.bsky.social · 27/01/2025

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.

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Rui Borges @ruiborges23.bsky.social · 27/01/2025

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).

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Rui Borges @ruiborges23.bsky.social · 27/01/2025

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.

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Rui Borges @ruiborges23.bsky.social · 10/01/2025

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

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Reposted by Rui Borges

Genome Biology and Evolution @genomebiolevol.bsky.social · 26/10/2023

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

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Rui Borges @ruiborges23.bsky.social · 05/12/2024

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:

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Reposted by Rui Borges

Lara Radović @larad1010.bsky.social · 20/11/2024

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 😊

pnas.org

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...

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Reposted by Rui Borges

Davide De Biasio @davidedebiasio.bsky.social · 22/11/2024

Scientists, when do we start lobbying for #Bluesky to implement native LaTeX support? #science #physics #mathematics 🧪⚛️

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Reposted by Rui Borges

Bert van der Veen @vdveenb.bsky.social · 10/11/2024

go.bsky.app/NiaWN5i I'm happy to receive suggestions for this.

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Reposted by Rui Borges

Michael Landis @landismj.bsky.social · 19/11/2024

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

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

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.

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

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.

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

7/9 That said, I still think we’re more likely in an epistemic bubble. This is why I believe questioning the lack of contradictory perspectives in our feeds is a good sign - it shows we’re aware of how it might inflate our epistemic self-confidence.

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

6/9 Now, is Bluesky an echo chamber? It might seem so: it’s a community of like-minded individuals sharing ideas. Plus, we curate our feeds by choosing who and what to follow, which introduces biases based on our interests and views.

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

5/9 Why did this change? I argue this is characteristic of an echo chamber: echo chambers systematically isolate their members from outside epistemic sources.

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

4/9 Yet, over the last few months, my feed shifted - it became anything but scientific. Surprisingly, it didn’t look very different from the feeds of colleagues with very different scientific focuses.

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

3/9 So, is X an echo chamber? Speaking from my experience: when I joined Twitter, I chose to exclusively follow scientists and avoided following any politicians from any side. My goal was to create a purely scientific feed.

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

2/9 Nguyen contrasts epistemic bubbles and echo chambers: an epistemic bubble is a social epistemic structure where relevant voices are left out (perhaps accidentally). In contrast, an echo chamber is a social epistemic structure where other relevant voices are actively excluded and discredited.

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Rui Borges @ruiborges23.bsky.social · 18/11/2024

1/9 I’ve seen many posts here asking whether Bluesky is an echo chamber. I don’t think so, and I’d argue that the very fact we’re questioning it is already an indication that it’s not. I’d like to bring up Nguyen’s paper on the differences between epistemic bubbles and echo chambers:

cambridge.org

ECHO CHAMBERS AND EPISTEMIC BUBBLES | Episteme | Cambridge Core

ECHO CHAMBERS AND EPISTEMIC BUBBLES - Volume 17 Issue 2

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Reposted by Rui Borges

Michael Landis @landismj.bsky.social · 17/11/2024

I'm building a Starter Pack of Early Career Evolutionary Biologists. It's hard to gather usernames using the search tool. Please add your name to this thread if you want to be added!

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Rui Borges @ruiborges23.bsky.social · 16/11/2024

In my free time, I love solving math competition problems that don’t require extensive prior knowledge. They're mostly based on intuition and are super fun to tackle! Here's one from the Portuguese Mathematical Olympiad -- can you guess the answer? #maths #mathproblems

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Rui Borges @ruiborges23.bsky.social · 13/11/2024

Looking forward to hearing about others' projects and insights — especially anyone working at the intersection of #stats, #maths and #biology!

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Rui Borges @ruiborges23.bsky.social · 13/11/2024

Hi Bluesky! New here and excited to connect with others, especially fellow scientists! I'm a lecturer in Statistics at the University of St Andrews and my research involves merging mathematical models with statistical methods to tackle evolutionary questions.

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