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Reposted by Ziheng Yang Lab

Molecular Biology and Evolution @molbioevol.bsky.social · Aug 19

Ji, Kapli, Flouri & @zihengyang.bsky.social assess the impact of genotyping errors in phylogenomic data on Bayesian inference of species trees, suggesting that it is better to sequence a few samples at high depths over many samples at low depths.

🔗 doi.org/10.1093/molbev/msaf184

#evobio #molbio

The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model

Abstract. The multispecies coalescent (MSC) model accounts for genealogical fluctuations across the genome and provides a framework for analyzing genomic d

doi.org

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Society for Molecular Biology and Evolution @official-smbe.bsky.social · Jul 20

In the first Plenary speech of #SMBE2025, Ziheng Yang (@zihengyang.bsky.social) taught us quite a few improbable things on gene flow.

We wish you a delicious breakfast for tomorrow, while mulling over these lessons... 😉

Ziheng Yang, SMBE2025 - Six impossible things to believe before breakfast, about gene flow

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Molecular Biology and Evolution @molbioevol.bsky.social · Jul 1

Using simulations and empirical data, Thawornwattana, Flouri, @wtf-r-species.bsky.social & @zihengyang.bsky.social ‬ et al. evaluate the performance of the MSC-M model for inferring gene flow.

🔗 doi.org/10.1093/molbev/msaf121

#evobio #molbio #geneflow

Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified

Abstract. Thanks to genomic data, interspecific gene flow is increasingly recognized as a major evolutionary force that shapes biodiversity. Two models hav

doi.org

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Society for Molecular Biology and Evolution @official-smbe.bsky.social · Jun 23

The first Keynote speech of #SMBE2025 will be given by SMBE's President Ziheng Yang (@zihengyang.bsky.social).

"Six impossible things to believe before breakfast, about gene flow"

20.07.2025 | 18h00

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

And... Some more pictures from the social activities! There was even time to enjoy the beach during lunch breaks and group singing at an evening karaoke session! 🎤🏖️

Organisers of the 2025 Computational Molecular Evolution course. From left to right: Cilia Antoniou, Alexis Stamatakis, Adam Leaché, and Ziheng Yang

Lunch at a Cretan taverna after the social hike.

CoME25 closed the karaoke session at the hotel where we were staying!

Some of the participants and instructors at the lunch break at the beach.

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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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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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Ziheng Yang Lab @zihengyang.bsky.social · May 1

The 2nd day of the SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop was focused on the Multispecies Coalescent Theory and the usage of BPP, led by our lab members Tomas Flouri and Yuttapong Thawornwattana! 💻🧬

Systematics Association @systassn.bsky.social · Apr 30

Day 2 of our (@systassn.bsky.social and SRUK/CERU) joint Bayesian Phylogenetics Workshop is underway!

We started with an introduction to the Multispecies Coalescent by Yuttapong Thawornwattana.

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Ziheng Yang Lab @zihengyang.bsky.social · Apr 30

The SystAssn-SRUK/CERU Bayesian Phylogenetics Workshop started yesterday! During the 1st day, our lab members Tomas Flouri, @anaserrasilva.bsky.social, and @sabifo4.bsky.social had fun sharing their knowledge on Bayesian statistics, phylogeny inference & timetree inference with the participants💻🧬

Systematics Association @systassn.bsky.social · Apr 29

The first joint @systassn.bsky.social and SRUK/CERU Bayesian Phylogenetics Workshop is underway!

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

And some more pictures! Thanks to lab members @sabifo4.bsky.social , Tomas, and Yuttapong too! (2/2)

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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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Ziheng Yang Lab @zihengyang.bsky.social · Feb 19

Our lab members @sabifo4.bsky.social, @anaserrasilva.bsky.social, Tomas Flouri, and Yuttapong Thawornwattana are teaching a two-day workshop on Bayesian Phylogenetics Workshop 💻🧬 Pre-register your interest to join this event before March 14th, do not miss the deadline! 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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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

Integrating morphology and genomes to infer evolutionary timescales | UCL Trees

Large biological datasets are accumulating at a fast pace, such as genome sequences from the EarthBiogenome project or 3D scan data from museum specimens. These datasets can be integrated to resolve e...

www.trees-dla.ac.uk

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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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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 4

🚨 Exciting Day 3 Ahead! 🚨

Today, we’re honored to have one of the giants of Phylogenomics 🧬✨, @zihengyang.bsky.social, kicking off the day with two lectures on the Multispecies Coalescent Model.
Day3 will continue with an hands-on session led by Paschalia Kapli and Tomas Flouri🚀

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

The Physalia Phylogenomics course has started today! Tomas and Paschalia are leading today's session -- now, they are going through the practical session to apply all the concepts they have taught this morning! 💻

Physalia-courses@Online @physaliacourses.bsky.social · Dec 2

Amazing course with an amazing team of instructors.

The Phylogenomics course has just started :) @sabifo4.bsky.social @zihengyang.bsky.social

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

Last, but not least, thanks to @sabifo4.bsky.social for working on the PAML Wiki and for constantly supporting PAML users! 🙌 💫 Also, thanks to Janet Young and @sishuowang.bsky.social for their contributions to the PAML discussion group, which have been valuable for PAML users!🙌 (5/5)

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

If you experience technical issues when running PAML programs (e.g., programs abort, bugs, etc.), please raise an issue on the PAML GitHub repository. Please post all other questions on the PAML discussion group so that other PAML users can have their say and benefit from the discussion! 🌐 💬(4/n)

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

To post a message on the PAML discussion group, you must be part of the group. When requesting to join, please briefly introduce yourself and explain why you would like to join. This is a safety measure we have recently implemented to avoid bots disturbing the PAML community with SPAM. (3/n)

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

If you have gone through the Wiki and still have questions, please visit our PAML Discussion Group! 💻🌐 You can use the search bar to check whether someone has asked the same question before. If not, please share your question with the PAML community! (2/n)
groups.google.com/g/pamlsoftware

PAML discussion group - Google Groups

groups.google.com

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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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Ziheng Yang Lab @zihengyang.bsky.social · Nov 28

Hello BlueSky!

The Ziheng Yang Lab will be using this social account to post news about the software we develop, upcoming workshops, and general news in evolutionary biology and computational methods 💻🧬🦴

Keep an eye on this site, we will be posting some news soon!

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