Josef Uyeda
@pseudacris.bsky.social
Reposted by Josef Uyeda
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
PhyloWeaver – Interactive phylogenetic tree editor
Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.
yawak.jp
November 18, 2025 at 1:59 AM
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
Reposted by Josef Uyeda
How the fuck does Larry Summers still have a job
November 17, 2025 at 3:35 AM
How the fuck does Larry Summers still have a job
Reposted by Josef Uyeda
I have a new essay coming out next week so stay tuned! since one of the ppl I critique in it is a hardcore "gamete truther", I figured I'd re-up this – discusses both the actual biology & the bonkers anti-trans talking point that's grown out of it (no paywall): juliaserano.medium.com/why-are-gend...
Why Are “Gender Critical” Activists So Fond of Gametes?
plus my new video “Trans People and Biological Sex: What the Science Says”
juliaserano.medium.com
November 16, 2025 at 4:37 PM
I have a new essay coming out next week so stay tuned! since one of the ppl I critique in it is a hardcore "gamete truther", I figured I'd re-up this – discusses both the actual biology & the bonkers anti-trans talking point that's grown out of it (no paywall): juliaserano.medium.com/why-are-gend...
Reposted by Josef Uyeda
The Linscott Lab at NMSU is looking for new graduate students interested in ecophysiology, systematics, and trait evolution (often in molluscs)!
Please reach out to contact me and see more at my lab website (linscottlab.com) and here: shorturl.at/DvUZa.
Please reach out to contact me and see more at my lab website (linscottlab.com) and here: shorturl.at/DvUZa.
November 17, 2025 at 5:09 PM
The Linscott Lab at NMSU is looking for new graduate students interested in ecophysiology, systematics, and trait evolution (often in molluscs)!
Please reach out to contact me and see more at my lab website (linscottlab.com) and here: shorturl.at/DvUZa.
Please reach out to contact me and see more at my lab website (linscottlab.com) and here: shorturl.at/DvUZa.
Very excited to see this come to fruition @jackstack.bsky.social !
I would like to make sure I thank my committee @evovert.bsky.social @pseudacris.bsky.social Michelle Stocker and Sterling Nesbitt for their encouragement and support to take on such an enormous project in my PhD. Wasila Dahdul was also extremely generous in helping make this project a reality.
Very excited to share my exploration of the phylogenetics of early ray-finned fishes, out today in the Anatomical Record! Really busy day but I’ll have more info shortly.
anatomypubs.onlinelibrary.wiley.com/doi/10.1002/...
anatomypubs.onlinelibrary.wiley.com/doi/10.1002/...
November 17, 2025 at 3:28 PM
Very excited to see this come to fruition @jackstack.bsky.social !
There is a affordability crisis, but if you suffer from it you are obviously too dumb and blinded by selfishness to solve it. Only if you benefit from class imbalance can you be deemed mature enough for access to power. The sneering derision Bezos and his ilk hold for the rest of America.
You guys realize that taxing people to pay for services isn't socialism, right? This is just how governments work.
November 17, 2025 at 3:11 PM
There is a affordability crisis, but if you suffer from it you are obviously too dumb and blinded by selfishness to solve it. Only if you benefit from class imbalance can you be deemed mature enough for access to power. The sneering derision Bezos and his ilk hold for the rest of America.
Reposted by Josef Uyeda
Very excited to share my exploration of the phylogenetics of early ray-finned fishes, out today in the Anatomical Record! Really busy day but I’ll have more info shortly.
anatomypubs.onlinelibrary.wiley.com/doi/10.1002/...
anatomypubs.onlinelibrary.wiley.com/doi/10.1002/...
An ontological morphological phylogenetic framework for living and extinct ray‐finned fishes (Actinopterygii)
The ray-finned fishes include one out of every two species of living vertebrates on Earth and have an abundant fossil record stretching 380 million years into the past. The division of systematic kno...
anatomypubs.onlinelibrary.wiley.com
November 17, 2025 at 12:52 PM
Very excited to share my exploration of the phylogenetics of early ray-finned fishes, out today in the Anatomical Record! Really busy day but I’ll have more info shortly.
anatomypubs.onlinelibrary.wiley.com/doi/10.1002/...
anatomypubs.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Josef Uyeda
Former UVA president Jim Ryan, who resigned over the summer due to pressure from the Trump Administration, just shared this 12-page letter with the Faculty Senate, detailing his experience with the Board of Visitors and DOJ.
It's a surreal--and troubling--read.
drive.google.com/file/d/1Is6x...
It's a surreal--and troubling--read.
drive.google.com/file/d/1Is6x...
November 14, 2025 at 2:15 PM
Former UVA president Jim Ryan, who resigned over the summer due to pressure from the Trump Administration, just shared this 12-page letter with the Faculty Senate, detailing his experience with the Board of Visitors and DOJ.
It's a surreal--and troubling--read.
drive.google.com/file/d/1Is6x...
It's a surreal--and troubling--read.
drive.google.com/file/d/1Is6x...
Reposted by Josef Uyeda
Big news - I’ll be starting an #insect #systematics lab at University of Nebraska-Lincoln this coming academic year! I’m looking to #recruit #PhDstudents to work in #wasp systematics, especially gall systems, to begin Fall 2026. Please help me spread the word — more details on the flyer below!
November 12, 2025 at 12:55 PM
Big news - I’ll be starting an #insect #systematics lab at University of Nebraska-Lincoln this coming academic year! I’m looking to #recruit #PhDstudents to work in #wasp systematics, especially gall systems, to begin Fall 2026. Please help me spread the word — more details on the flyer below!
Reposted by Josef Uyeda
The Dobzhansky Prize recognizes the accomplishments and future promise of an outstanding early-career evolutionary biologist. The awardee will present the Dobzhansky Prize plenary at #Evol2026. Apply by December 1! shorturl.at/p70wY
November 3, 2025 at 2:29 AM
The Dobzhansky Prize recognizes the accomplishments and future promise of an outstanding early-career evolutionary biologist. The awardee will present the Dobzhansky Prize plenary at #Evol2026. Apply by December 1! shorturl.at/p70wY
Reposted by Josef Uyeda
The scoop: To get to Mesquite's adventure game, type "ZoL" into the log window. You will find yourself in an open field with a mailbox. 📬 (If that does nothing, then you'll need to turn on "Use Log Window for Command" under File>Defaults>.)
Has anyone taken up the challenge of finding the adventure game in Mesquite? 🔍
Mesquite now has a built-in adventure game, which you may be able to find if you say the correct magic word. You can also build your own versions of the game.
🤔
🤔
October 28, 2025 at 4:23 PM
The scoop: To get to Mesquite's adventure game, type "ZoL" into the log window. You will find yourself in an open field with a mailbox. 📬 (If that does nothing, then you'll need to turn on "Use Log Window for Command" under File>Defaults>.)
Reposted by Josef Uyeda
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
Applied Biostatistics
ybrandvain.github.io
October 24, 2025 at 2:47 PM
Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...
More on rate-scaling in phenotypic evolution, pointing toward biological explanations, from Brune Kinneberg & Voje. Lots of debate about this pattern, but comes down to how we define "noise" vs. "biology" as represented in models. Important philosophical discussion.
academic.oup.com/evolut/advan...
academic.oup.com/evolut/advan...
Rate-time scaling in phenotypic evolution: Limitations of current models in capturing temporal dynamics
Abstract. Evolutionary rates correlate negatively with time, which makes it complicated to compare rates across lineages that have diversified on different
academic.oup.com
October 13, 2025 at 2:06 PM
More on rate-scaling in phenotypic evolution, pointing toward biological explanations, from Brune Kinneberg & Voje. Lots of debate about this pattern, but comes down to how we define "noise" vs. "biology" as represented in models. Important philosophical discussion.
academic.oup.com/evolut/advan...
academic.oup.com/evolut/advan...
Reposted by Josef Uyeda
I have been trying to get this published as an op-ed, but I am going to post it here since I think it is timely in light of the "consent" extortion events.
Deafening Quiet from the Scientific Establishment
jeremymberg.github.io/jeremyberg.g...
1/14
Deafening Quiet from the Scientific Establishment
jeremymberg.github.io/jeremyberg.g...
1/14
jeremymberg.github.io
October 6, 2025 at 11:28 PM
I have been trying to get this published as an op-ed, but I am going to post it here since I think it is timely in light of the "consent" extortion events.
Deafening Quiet from the Scientific Establishment
jeremymberg.github.io/jeremyberg.g...
1/14
Deafening Quiet from the Scientific Establishment
jeremymberg.github.io/jeremyberg.g...
1/14
The pattern on the back of this Nepenthes pitcher plant takes me back to playing MS-DOS games in the 90s.
October 3, 2025 at 1:23 AM
The pattern on the back of this Nepenthes pitcher plant takes me back to playing MS-DOS games in the 90s.
Master's degree position at Towson University with Daniel Caetano on macroevolutionary and phylogenetic comparative methods! Daniel is an awesome human and a great mentor, share with your students!
caetanods.weebly.com/join-the-lab...
caetanods.weebly.com/join-the-lab...
Join the lab
The Caetano lab at Towson University (Maryland, USA) is seeking a Master's degree student to start in Fall 2026. A Research Assistant (RA) position is available to the student during part (or all) of....
caetanods.weebly.com
October 2, 2025 at 8:50 PM
Master's degree position at Towson University with Daniel Caetano on macroevolutionary and phylogenetic comparative methods! Daniel is an awesome human and a great mentor, share with your students!
caetanods.weebly.com/join-the-lab...
caetanods.weebly.com/join-the-lab...
Reposted by Josef Uyeda
I wrote this piece about 7th anniversary of Jamal Khashoggi's murder.
On the costs of speaking the truth in today's world.
And how Jamal's memory still stalks Saudi Arabia--- and the Washington Post.
open.substack.com/pub/karenatt...
On the costs of speaking the truth in today's world.
And how Jamal's memory still stalks Saudi Arabia--- and the Washington Post.
open.substack.com/pub/karenatt...
Jamal Khashoggi, the Washington Post, and the Cost of Speaking Out
As Saudi Arabia hosts comedians and courts gamers, the silenced voice of Jamal Khashoggi still echoes.
open.substack.com
October 2, 2025 at 6:35 PM
I wrote this piece about 7th anniversary of Jamal Khashoggi's murder.
On the costs of speaking the truth in today's world.
And how Jamal's memory still stalks Saudi Arabia--- and the Washington Post.
open.substack.com/pub/karenatt...
On the costs of speaking the truth in today's world.
And how Jamal's memory still stalks Saudi Arabia--- and the Washington Post.
open.substack.com/pub/karenatt...
Reposted by Josef Uyeda
Reposted by Josef Uyeda
DHS is proposing a rule that would end "duration of status" for J, F and other visa holders. This would decimate the international graduate student and postdoc population, which are a crucial part of the United States biomedical workforce. There's still time for you to comment on the proposed rule.
Establishing a Fixed Time Period of Admission and an Extension of Stay Procedure for Nonimmigrant Academic Students, Exchange Visitors, and Representatives of Foreign Information Media
Unlike most nonimmigrant classifications, which are admitted for a fixed time period, aliens in the F (academic student), J (exchange visitor), and most I (representatives of foreign information media...
www.federalregister.gov
September 28, 2025 at 7:35 PM
DHS is proposing a rule that would end "duration of status" for J, F and other visa holders. This would decimate the international graduate student and postdoc population, which are a crucial part of the United States biomedical workforce. There's still time for you to comment on the proposed rule.
Reposted by Josef Uyeda
Ever wondered how to incorporate fossils as tips in a phylogenetic tree?
Our new paper provides a comprehensive guide!
#EarlyFossilFriday
#FossilFriday
#TipDating
#Phylogeny
#EvolutionaryBiology
Our new paper provides a comprehensive guide!
#EarlyFossilFriday
#FossilFriday
#TipDating
#Phylogeny
#EvolutionaryBiology
I am extremely happy to see that our review on fossil tip-dating is out in early view in Systematic Biology! A huge thanks to all the authors of this massive project (@heckeberg.bsky.social, @basantakhakurel.bsky.social, Gustavo Darlim, and @hoehna.bsky.social)! academic.oup.com/sysbio/advan...
September 25, 2025 at 1:21 PM
Ever wondered how to incorporate fossils as tips in a phylogenetic tree?
Our new paper provides a comprehensive guide!
#EarlyFossilFriday
#FossilFriday
#TipDating
#Phylogeny
#EvolutionaryBiology
Our new paper provides a comprehensive guide!
#EarlyFossilFriday
#FossilFriday
#TipDating
#Phylogeny
#EvolutionaryBiology
Mitch Hedberg:
"An escalator can never break: it can only become stairs. You should never see an 'Escalator Temporarily Out Of Order' sign, just 'Escalator Temporarily Stairs. Sorry for the convenience.'"
RIP
"An escalator can never break: it can only become stairs. You should never see an 'Escalator Temporarily Out Of Order' sign, just 'Escalator Temporarily Stairs. Sorry for the convenience.'"
RIP
Turns out, you can walk on the escalator. Who knew.
September 23, 2025 at 8:51 PM
Mitch Hedberg:
"An escalator can never break: it can only become stairs. You should never see an 'Escalator Temporarily Out Of Order' sign, just 'Escalator Temporarily Stairs. Sorry for the convenience.'"
RIP
"An escalator can never break: it can only become stairs. You should never see an 'Escalator Temporarily Out Of Order' sign, just 'Escalator Temporarily Stairs. Sorry for the convenience.'"
RIP
This thread says scientists on blue sky stoke political flames, rather than build science communities, as evidenced by viral posts being political. The problem w/social media is the optimization target--but we evaluate the success of domain-specific science discourse by virality metrics? Huh?!?
💡2/ I was inspired to write this by an analysis by my colleague @lassehjorthmadsen.bsky.social . It shows that among 200 highly influential scientists on Bluesky worldwide, the posts with the most reposts and likes are overwhelmingly about US politics:
lassehjorthmadsen.github.io/blueskyanaly...
lassehjorthmadsen.github.io/blueskyanaly...
Scientists on Bluesky - What are they posting?
lassehjorthmadsen.github.io
September 22, 2025 at 8:51 PM
This thread says scientists on blue sky stoke political flames, rather than build science communities, as evidenced by viral posts being political. The problem w/social media is the optimization target--but we evaluate the success of domain-specific science discourse by virality metrics? Huh?!?
Reposted by Josef Uyeda
The rampant violations of academic freedom and intrusions on extramural speech are escalating rapidly. Faculty members have the right to speak or write as citizens, free from institutional censorship or discipline. Expression of opinion as a citizen does not constitute grounds for dismissal.
Clemson fires two more faculty members over Charlie Kirk comments
Clemson leaders had come under increased pressure from people online as well as South Carolina Republican politicians to take action.
www.wcnc.com
September 16, 2025 at 6:07 PM
The rampant violations of academic freedom and intrusions on extramural speech are escalating rapidly. Faculty members have the right to speak or write as citizens, free from institutional censorship or discipline. Expression of opinion as a citizen does not constitute grounds for dismissal.
Reposted by Josef Uyeda
We write to remind leaders of colleges & universities of their fundamental duty to protect academic freedom & the absolute necessity to ensure that the freedom to discuss topics of public import without constraint is not curtailed under political pressure.
2/4
2/4
September 15, 2025 at 2:53 PM
We write to remind leaders of colleges & universities of their fundamental duty to protect academic freedom & the absolute necessity to ensure that the freedom to discuss topics of public import without constraint is not curtailed under political pressure.
2/4
2/4