#ggtree by @yulab.bsky.social is fantastic for visualizing #phylo data in @rconsortium.bsky.social as it’s mounted on the @posit.co tidyverse. These are some phylopic.org homework plots from the #sistematicaunam class at @ib_unam real purdy ain’t ‘em?

Newick-formatted timetrees of the α-proteobacteria (Wang & Luo 2021) and bTOL (Wang & Luo 2025) are made available separately, such that no need to download the entire online datasets in case you r interested in only the timetree files. sishuowang2022.wordpress.com/resources/ #phylo #molecularclock

how to do +ASC (Ascertainment bias correction) manually under JC69 This blog article will show you how to calculate the phylogenetic logL under a subs. model given +ASC in a (semi-)manual way. So, what is +ASC? As shown at it refers to An ascertainment bias correc…

what is +ASC (ascertainment bias correction) and how to do it manually under JC69 #phylo sishuowang2022.wordpress.com/2026/01/03/h...

very glad to host the visit of
@bqminh.bsky.social to my dept at #cuhk, fantastic talk on recent #iqtree development and its appl. on viral #phylo ; also a great experience to interact with people from #hku haogao_gu and to enjoy the nice view of sai kung from the mountain ma on shan 馬鞍山.

#phylo #phylogenetics

The evolutionary genomics of life-history adaptations in pinnipeds - Yorkshire Environmental Sciences • Doctoral Training Network Project summary Pinnipeds (seals, sea lions, fur seals and walrus) are keystone marine predators, and sentinels for marine ecosystem health. Advances in genomic technology open up the possibility to u...

New PhD studentship opportunity in my lab & with collaborators from the Pinniped Genomes Consortium. Come help us unravel the genomics of seal physiological super powers! Closing date 7th January 2026 🧪🦭🧬🌍🦑🐳 #marine #mammals
#consgen #popgen #phylo #molevol #evolution
yes-dtn.ac.uk/research/the...

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

A paper in Nature Ecology & Evolution presents a time-calibrated phylogeny of Fungi. This timescale suggests an older age of crown Fungi, as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems. #phylo 🧪

A timetree of Fungi dated with fossils and horizontal gene transfers - Nature Ecology & Evolution Combining fossil-based and molecular calibrations with data on horizontal gene transfer events, the authors develop a time-calibrated phylogeny of Fungi. This timescale, which integrates analytic uncertainties, suggests an older age of crown Fungi (1,401–896 million years ago), as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems (1,253–797 Ma).

A paper in Nature Ecology & Evolution presents a time-calibrated phylogeny of Fungi. This timescale suggests an older age of crown Fungi, as well as a minimum age for ancient interactions involving fungi and the algal ancestors of embryophytes in terrestrial ecosystems. #phylo 🧪

Forgot to link in #phylo #phylogenetics #EvoBio

New Ways to Root Phylogenomic trees: the Smart, the symbiotic, the violent To root a phylogenomic tree is very important to study the evolutionary relationship between species. However, typically the substitution models (say GTR, LG, etc.) people use are time-reversible m…

some thoughts on new methods to root a phylogenomic tree: the smart, the symbiotic, the violent

sishuowang2022.wordpress.com/2025/06/19/n...

#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social

How does PAML read a rooted tree? IQ-Tree is the software i use most often to build phylogenetic trees. Sometimes I also need to deal with the output of PAML. However, PAML-MCMCtree could read rooted tree in a different order from …

How does PAML read a rooted tree? sishuowang2022.wordpress.com/2025/04/25/h... #phylo #PAML #iqtree

Dating the Bacterial Tree of Life Based on Ancient Symbiosis Abstract. Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial f

final version of our study "Dating the Bacterial Tree of Life Based on Ancient Symbiosis" doi.org/10.1093/sysb... particularly thx to haiwei luo for his guidance during my postdoc!

see sishuowang2022.wordpress.com/2025/03/01/a... for a brief summary and comparison w/ others #phylo #molecular_clock

Slide with animation of rejection sampling and MCEB2025 My first time to attend MCEB (Mathematical & Computational Evolutionary Biology) in Granada in May 12-16. I presented “new methods in dating deep-time bacterial evolution using ancient sy…

An animation of rejection sampling and MCEB2025 sishuowang2022.wordpress.com/2025/06/04/s... #phylo #phylogenetics #mceb2025 #mceb

ead more in the full paper: [https://doi.org/10.1038/s41586-025-08709-5] #Eukaryotes #TreeOfLife #Phylogenetics #Evolution #LECA #Excavates #OriginOfLife #phylo

A brief summary of our recent work on dating the bacterial tree of life Using Ancient Symbiosis Obtaining a timescale for bacterial evolution is crucial to understand early life evolution but is difficult owing to the scarcity of bacterial fossils. Also, the mixture substitution models like C…

a summary and some further discussions on our recent pape on dating the bToL using ancient symbiosis sishuowang2022.wordpress.com/2025/03/01/a... #phylo #phylogenetics #symbiosis #molecular_clock

[Ad] Computational Genomics Workshop In Science Park, Hong Kong SAR Organized by Sun Yat-Sen Univ Institute of Adv Studies Hong Kong, there will be a nice workshop on computational genomics held in Science Park, Tai Po District, Hong Kong SAR, China, on March 3-6 2…

4-day comp genomics workshop in Hong Kong on mar 3-6 by @zihengyang.bsky.social, xiyun jiao,
@sabifo4.bsky.social, Tomáš Flouri, Yuttapong Thawornwattana. Free registration full but can still apply (see the following link on how to) sishuowang2022.wordpress.com/2025/02/23/a...
#phylo #phylogenetics

A simple example of a phylogenetic tree

Let's see if Bluesky has some magic ...

Is there a way to plot a dated phylogeny with a log-scale time axis? If possible, using R

🧪 #EvolSky #ecoevo @phylogeny.bsky.social #phylo #rstats #plantscience botany

GitHub - evolbeginner/bs_inBV: A tool to help generate the file in.BV when using "complex" substitution models for MCMCtree. Particularly, the hessian is approximated by a bootstrap approach. A tool to help generate the file in.BV when using "complex" substitution models for MCMCtree. Particularly, the hessian is approximated by a bootstrap approach. - evolbeginner/bs_inBV

mcmctree's approx lik dating by approx hessian by bootstrapping: github.com/evolbeginner...
we show profile mixture subs models mostly impact the estimate of the root's age, and branch-specific rate, in deep #phylo; also thx @sabifo4.bsky.social @emoody.bsky.social for testing & improving the script

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

getphylo: rapid and automatic generation of multi-locus phylogenetic trees - BMC Bioinformatics Background The increasing amount of genomic data calls for tools that can create genome-scale phylogenies quickly and efficiently. Existing tools rely on large reference databases or require lengthy d...

📢 Check out this new tool from @thombooth.bsky.social, @wemakemolecules.bsky.social and @tilmweber.bsky.social!

Build phylogenies of BGCs to primates! 🙊

All you need are Gbk files of your chosen sequences. It's super fast and in my regular rotation of bioinformatic tools

#phylo #secmet #micro

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

Exciting opportunity to explore Bayesian #phylo at QMUL

🚨New #phylo paper alert!🚨 🌲+🔥= speciation? This one has been a bit of a journey, but thanks to lead author Dan Turck's expertise on #conifers it has turned out as quite the treasure-trove of conifer evolution! (reading-access link on my website)

What do you think about the future of neo-Darwinism? I feel that more strong voices are turning against it."
#philosophy #philmind #philsky #evolsky #evobio #evolbiol #phylo #popgen #ecoevo #evodevo #molevol #paleobio #systematics

Phylogenetic and Comparative Methods Peeps in this Starter Pack! #science #phylogeny #phylo #biology

use Feeds to track #phylogenetics posts:
bsky.app/profile/sish... #phylo #phylogenetics

The evolutionary genomics of life-history adaptations in pinnipeds - Yorkshire Environmental Sciences • Doctoral Training Network Project summary Pinnipeds (seals, sea lions, fur seals and walrus) are keystone marine predators, and sentinels for marine ecosystem health. Advances in genomics technologies are opening up the possib...

New PhD studentship opportunity in my lab & with collaborators from the Pinniped Genomes Consortium. Come help us unravel the genomics of seal physiological super powers! Closing date 6th January 2025 🧪🦭🧬🌍🦑🐳 #marine #mammals
#consgen #popgen #phylo #molevol #evolution
yes-dtn.ac.uk/research/the...

Reposting for new arrivals. Hope #consgen and #phylo folk find this tool helpful if you're into mitochondrial genomes... 🧪🌍🧬

🧪 #evolution #phylo #PaleoSky #paleontology
*Still learning bluesky and feeds*

Hello! I'm Saismit, a Cornell EEB PhD student exploring rapid eco-evolutionary feedbacks through theory. Excited to connect with fellow researchers!
🌍🧪 🦠 #WomenInSTEM #evosky, #evolution, #evobio, #phylo, #popgen, #ecoevo #molevol, #popgen #complexity #PhDSky #pydata #rstats