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Reposted by Sandra Álvarez

ERR_Moody @emoody.bsky.social · Aug 12

Very happy to announce our new paper on the evolution of metabolism is out now! royalsocietypublishing.org/doi/10.1098/...

With @tweethinking.bsky.social @sabifo4.bsky.social @ssolo.bsky.social Davide Pisani, Tim Lenton and @phil-donoghue.bsky.social

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The emergence of metabolisms through Earth history and implications for biospheric evolution | Philosophical Transactions of the Royal Society B: Biological Sciences

We investigate the evolution of microbial metabolisms from the last universal common ancestor to the extant biota through comparative phylogenomics, reconciling the evolution of the genes that underpi...

royalsocietypublishing.org

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Sandra Álvarez @sabifo4.bsky.social · Jun 6

More than grateful to the CoME25 organisers for inviting me one more year, it is always so much fun!! Ευχαριστώ πάρα πολύ και τα λέμε σύντομα! 💙

Ziheng Yang Lab @zihengyang.bsky.social · Jun 6

What a busy (but sunny) May in Crete!🔆 Ziheng & @sabifo4.bsky.social enjoyed teaching and meeting the participants at the Computational Molecular Evolution course! Ziheng then joined the satellite workshop on Biodiversity Genomics 🌍🧬 Thanks to everyone who made these fantastic meetings possible!!

Instructors and participants at the 2025 Computational Molecular Evolution course in Crete (group picture).

Sandy teaching Bayesian node-dating analyses for timetree inference at the Computational Molecular Evolution course.

Attendees joining the 2025 Satellite Workshop "Biodiversity Genomics: sample types, data, and tools to assess past, present and future biodiversity" in Crete (group picture)

Ziheng's talk at the satellite workshop "Biodiversity Genomics: sample types, data, and tools to assess past, present and future biodiversity". Talk title: "Inference of between-species gene flow using genomic data"

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Ziheng Yang Lab @zihengyang.bsky.social · May 2

Congratulations Dr Jiayi Ji!! 🥳Thanks to examiners @hernanaburbano.bsky.social and Simon Martin, now time to enjoy the long weekend! 🎉

Post viva celebrations with Dr Jiayi Yi. Left to right: Hernán Burbano, Jiayi Ji, Simon Martins, and Ziheng Yang.

Post viva celebrations with Dr Jiayi Yi. Jiayi holding one of his PhD presents: a PhD mug and a cute chipmunk plush.

Post viva celebrations with Dr Jiayi Yi. Jiayi showing his new chipmunk plush.

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Sandra Álvarez @sabifo4.bsky.social · May 1

Had so much fun at the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop! 💫 Hope that everyone who attended this event enjoyed the two-day journey on theory, methods, and applications of Bayesian Phylogenetics and... Hopefully see you all again soon in future events! 💻🧬

Systematics Association @systassn.bsky.social · Apr 30

And that's a wrap on the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop!

Thank you to all the attendees, instructors (@anaserrasilva.bsky.social, @sabifo4.bsky.social, Tomas Flouri and Yuttapong Thawornwattana) and to our wonderful TA @lauramulvey.bsky.social!

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Philip Donoghue @phil-donoghue.bsky.social · Apr 4

Really pleased to be part of this project which shows that aerobic bacteria arose in the Archaean, long before the GOE - after which aerobes proliferated through HGT. Fun @bristolpalaeo.bsky.social collab including @tweethinking.bsky.social @sabifo4.bsky.social @emoody.bsky.social Davide Pisani

ssolo.bsky.social @ssolo.bsky.social · Apr 4

Dating Bacteria is hard due to the lack of maxima. Assuming aerobes likely postdated the GOE gave us better resolved ages, but also surprised us, but not Dr Dayhoff, showing O2 use predated its atmospheric rise by 900 Mys and helped oxygenic photosynthesis to evolve. www.science.org/doi/10.1126/...

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Sandra Álvarez @sabifo4.bsky.social · Mar 26

The Physalia Phylogenomics course is back this December! Join us for a computational journey on phylogeny and timetree inference with genomic datasets 🧬 💻

More information about the course and how you can register on the post below ⬇️

Physalia-courses@Online @physaliacourses.bsky.social · Mar 25

Registrations are now open for the #Phylogenomics course with this amazing team of instructors Paschalia, Tomas, @sabifo4.bsky.social and @zihengyang.bsky.social

www.physalia-courses.org/courses-work...

Phylogenomics

1-5 December 2025

www.physalia-courses.org

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Sandra Álvarez @sabifo4.bsky.social · Mar 14

The clock is ticking 🕔! Pre-registration will close today March 14th (17:00h GMT+0), do not miss your chance to join us at the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop! 💻🧬

Sandra Álvarez @sabifo4.bsky.social · Feb 28

The deadline to apply for student travel bursaries to attend the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop 💻🧬 is approaching: March 3rd! Pre-registration will be open until March 14th.

Do not miss the deadlines, submit your application before it is too late!
sruk.org.uk/ceru-events/...

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Sandra Álvarez @sabifo4.bsky.social · Mar 6

Thanks to all organisers that have made the Workshop of Computational Genomics possible and all the participants that have joined us both in person and online -- we have had such a great time in Hong Kong! 🌹 Hope to see you all again in future meetings 🤗 Next stop: 🚗 Shenzhen!

Ziheng Yang Lab @zihengyang.bsky.social · Mar 6

Our Workshop on Genomics at Sun Yat-sen University Institute of Advanced Studies Hong Kong has come to an end! We are grateful to all organisers and very pleased to have meet such fantastic and hard-working participants! 下次见, 谢谢 🌹(1/2)

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Sandra Álvarez @sabifo4.bsky.social · Feb 28

Applications for student travel bursaries will only be considered if you are part of at least one of the Societies funding the event: The Systematics Association or the Society of Spanish Researchers in the UK. More details on their websites:
sruk.org.uk/ceru-events/...
systass.org/workshop-bay...

Sandra Álvarez @sabifo4.bsky.social · Feb 28

The deadline to apply for student travel bursaries to attend the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop 💻🧬 is approaching: March 3rd! Pre-registration will be open until March 14th.

Do not miss the deadlines, submit your application before it is too late!
sruk.org.uk/ceru-events/...

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Systematics Association @systassn.bsky.social · Feb 27

Looking for funds for a small systematics-focused project?

You have until 23:59 GMT+0 MONDAY, MARCH 10TH to apply to the LinneSys scheme!

You can apply for up to 1500GBP, you just need to be a member of @systassn.bsky.social or @linneansociety.bsky.social!

Details here: systass.org/linnesys/

LinneSys: Systematics Research Fund

LinneSys: Systematics Research Fund The Councils of The Linnean Society of London and The Systematics Association jointly administer this fund for the benefit of systematics research. The Fund has …

systass.org

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Sandra Álvarez @sabifo4.bsky.social · Feb 18

This activity co-organised with @systassn.bsky.social is the one with which @pablomurod.bsky.social , @martapina.bsky.social, and I are launching the SRUK/CERU Evolution committee! We are looking for volunteers to join us, check our site and get in touch if interested! 🍏🧬
sruk.org.uk/initiatives/...

Evolution Committee - SRUK/CERU

Future Events To launch the SRUK/CERU Evolution Committee, we have partnered with the Systematics Association to co-organise a workshop on Bayesian phylogenetics! This two day event will be run by exp...

sruk.org.uk

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Sandra Álvarez @sabifo4.bsky.social · Feb 18

Introduction to Bayesian inference; practical sessions focused on the usage of MCMCtree, BPP, and PhyloBayes; discussion sessions... Does this sound like something you would like to delve into over a two-day workshop? 💻🧬 Then pre-register your interest to join before March 14th! More details below 🔽

Systematics Association @systassn.bsky.social · Feb 18

We are organising an in-person Bayesian Phylogenetics Workshop, in partnership with SRUK/CERU.

When: April 29-30, 2025

Where: University College London

There are limited places, so please pre-register by March 14th!!!

Find more details here: systass.org/workshop-bay...

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Philip Donoghue @phil-donoghue.bsky.social · Feb 13

Our latest: a Richard Boyle (Exeter) production, using simulations to show how differential selection of biogeochemical cycles can lead to planetary homeostasis, with some empirical data from @emoody.bsky.social and @sabifo4.bsky.social @bristolpalaeo.bsky.social

Persistence selection between simulated biogeochemical cycle variants for their distinct effects on the Earth system | PNAS

The average long-term impact of Darwinian evolution on Earth’s habitability remains extremely uncertain. Recent attempts to reconcile this uncertai...

www.pnas.org

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Sandra Álvarez @sabifo4.bsky.social · Jan 27

When you supervise students, you have the opportunity to witness how they learn and grow both at an academic and personal level. Thank you, Morena, it was wonderful seeing you progress and lead this project, congratulations!! 🎉 These are the moments that make you love academia 💙 (2/2)

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Sandra Álvarez @sabifo4.bsky.social · Jan 27

Would you like to learn more about the evolutionary history of sea spiders? You may want to read our latest study led by Morena @morena99.bsky.social, who has nicely summarised the key findings of our research in the quoted thread below 🔽 (1/2)

morena99.bsky.social @morena99.bsky.social · Jan 27

Sea spiders (Pycnogonida) are an ancient Class of chelicerates with a fascinating evolutionary tale. A new study we just published on the EJLS uncovers their evolutionary history! 🧵 #Evolution #TheLinneanSociety #SeaSpiders #Arthropoda

academic.oup.com/evolinnean/a...

A timescale for the evolutionary history of sea spiders (Arthropoda: Pycnogonida)

Abstract. Sea spiders (Arthropoda: Pycnogonida) are an ancient lineage of chelicerates represented by a single living order, Pantopoda, and a patchy fossil

academic.oup.com

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Sishuo Wang @sishuowang.bsky.social · Jan 24

Our study (haiwei luo & i) on dating bacterial tree of life by new methods integrating host-microbe symbiosis, complex subs models & extended sequential dating, is online Syst Biol. @systbiol.bsky.social shorturl.at/Ywoud #phylo

sky.social

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Joseph Williamson @josephwilliamson.bsky.social · Jan 9

🚨New paper 🚨We argue that abrupt biodiversity losses can be driven by populations sharing similar tolerances to warming 🦋🌎🥵. Out now in @royalsocietypublishing.org. Summary thread below 🧵
royalsocietypublishing.org/doi/epdf/10....

screenshot of the article in Philosophical Transactions of the Royal Society B titled 'Clustered warming tolerances and the nonlinear risks of biodiversity loss on a warming planet'

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Sandra Álvarez @sabifo4.bsky.social · Dec 9

Such a great PhD opportunity with fantastic advisors!! 💫🎓TREES will soon be open for applications but, in the meantime, they have announced the closing date on their website: January 20th 2025 at 5pm (UK time). More info about the project in the post below ⬇️

Ziheng Yang Lab @zihengyang.bsky.social · Dec 9

Thinking of starting a PhD on Bayesian phylogenetics next October 2025 in London? 🎓
You may want to check the TREES project led by the dos Reis Lab on integrating morphology and genomes for timetree inference! 🦴🧬💻Project supervisors: @mariodosreis.bsky.social & Ziheng Yang. More info in link 🔽

Mario dos Reis @mariodosreis.bsky.social · Dec 6

We have a project on Bayesian phylogenetics: www.trees-dla.ac.uk/projects/int... with @zihengyang.bsky.social

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Reposted by Sandra Álvarez

Society for the Study of Evolution @sse-evolution.bsky.social · Nov 29

Applications are due February 19 for the R. C. Lewontin Early Awards, which provide up to $2500 in research funds for 1st year master’s and 1st or 2nd year PhD students. Read the full requirements, instructions, and evaluation criteria here: https://buff.ly/3YZlUHf

Text: Society for the Study of Evolution, Graduate Research Excellence Grants, 2025 R. C. Lewontin Early Award, Deadline: February 19, 5:00 PM Eastern.

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Sandra Álvarez @sabifo4.bsky.social · Dec 6

What a wonderful and friendly group of participants, had lots of fun! 💫

If you have joined Paschalia, Tomas, @zihengyang.bsky.social , @mariodosreis.bsky.social & I this week, we hope that you have liked the course and learnt more about phylogenomics analyses! Now, time to enjoy the weekend! 🙌

Physalia-courses@Online @physaliacourses.bsky.social · Dec 5

Here’s the amazing Phylogenomics Group 2024 📸

Thank you to our incredible instructors for sharing their knowledge and making complex topics approachable and engaging! 🙌

And a big shoutout to all participants—Thanks for joining us this week🎉 @sabifo4.bsky.social @zihengyang.bsky.social

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Physalia-courses@Online @physaliacourses.bsky.social · Dec 6

Wrapping up an incredible 5-day course on #Phylogenomics with a fascinating lecture on Molecular-Clock dating of species divergence by @mariodosreis.bsky.social, followed by a hands-on session with @sabifo4.bsky.social 🧬🕰️
Huge thanks to all participants for an inspiring [email protected]

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Natalie Cooper @nhcooper123.bsky.social · Nov 28

For anyone looking for PhDs in the UK starting October 2025 in ecology, evolution, environment etc. The new Doctoral Landscape Awards (DLAs) recently got announced so lots of people will be adverting PhDs with January deadlines. Check out findaphd.com to search for ones that interest you!

PhD Programmes, Research Projects & Studentships in the UK & Europe

FindAPhD is a comprehensive guide to PhD studentships and postgraduate research degrees

findaphd.com

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Physalia-courses@Online @physaliacourses.bsky.social · Dec 4

✨ Day 2 highlight! ✨ Tomas Flouri and @sabifo4.bsky.social delivered masterful lectures and an exceptional hands-on session on Bayesian inference in Phylogenomics. 🎓💡 Their expertise truly shone through!
Excited for the insights Day 3 will bring—stay tuned! 🚀

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Sandra Álvarez @sabifo4.bsky.social · Nov 29

An interactive PAML Wiki is now available! Please read the thread published by Ziheng Yang Lab to learn more about the PAML discussion group & the PAML GitHub repo. Hope you enjoy the Wiki as much as I enjoyed working on it 💫
P.S: The Wiki is still a work in progress, there is still more to come! 😄

Ziheng Yang Lab @zihengyang.bsky.social · Nov 29

If you have ever wondered whether the PAML documentation could be more interactive... We have good news for you! The PAML GitHub repository has been updated and a fresh PAML Wiki is now available for you to navigate the PAML documentation! 📄💻 (1/n)

github.com/abacus-gene/...

HOME

PAML is a program package for model fitting and phylogenetic tree reconstruction using DNA and protein sequence data. Please report only **technical issues** on this repository (e.g., compiling, pr...

github.com

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