Rob Denton
@rddenton.bsky.social
Bio Professor | scientist (genomics, evolution, conservation), educator, perpetual student | he/him | posts don't represent employer
Reposted by Rob Denton
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 Rob Denton
Science People: We at NSF are still recovering/catching up/getting our lives together. But the agency posted these FAQs about post-shutdown resumption of operations which might answer a lot of Qs for you: www.nsf.gov/resumption-o...
Resumption of Operations at NSF
Information for NSF staff and the research community regarding the agency's resumption of operations after a lapse in appropriations.
www.nsf.gov
November 18, 2025 at 6:08 PM
Science People: We at NSF are still recovering/catching up/getting our lives together. But the agency posted these FAQs about post-shutdown resumption of operations which might answer a lot of Qs for you: www.nsf.gov/resumption-o...
Lori is, without a doubt, one of the best people.
📖Cover Stories📖
📙Dr Lori Neuman-Lee shares the story behind the cover of Volume 29, Issue 11 of Functional Ecology, published in 2015!
🐍Lori discusses the challenges of snapping snakes in the field (and in the third trimester!) and her research journey since then
buff.ly/IycDaiM
🧪🌍
📙Dr Lori Neuman-Lee shares the story behind the cover of Volume 29, Issue 11 of Functional Ecology, published in 2015!
🐍Lori discusses the challenges of snapping snakes in the field (and in the third trimester!) and her research journey since then
buff.ly/IycDaiM
🧪🌍
Cover Stories: Dr. Lori Neuman-Lee
Dr. Lori Neuman-Lee, professor at Arkansas State University, discusses the story behind the cover for Volume 29, Issue 11 of Functional Ecology, published all the way back in 2015. Lori is a compar…
buff.ly
November 14, 2025 at 4:00 PM
Lori is, without a doubt, one of the best people.
Reposted by Rob Denton
"Fishman", proposal for a journal cover.
Commissioned by MY Dennis' lab @mydennis.bsky.social for a study focused on identifying human-specific gene duplications and their role in brain evolution using genomics and zebrafish as model. @dcsoto.bsky.social
#art #digitalart #sciart #fish
Commissioned by MY Dennis' lab @mydennis.bsky.social for a study focused on identifying human-specific gene duplications and their role in brain evolution using genomics and zebrafish as model. @dcsoto.bsky.social
#art #digitalart #sciart #fish
September 25, 2025 at 9:33 AM
"Fishman", proposal for a journal cover.
Commissioned by MY Dennis' lab @mydennis.bsky.social for a study focused on identifying human-specific gene duplications and their role in brain evolution using genomics and zebrafish as model. @dcsoto.bsky.social
#art #digitalart #sciart #fish
Commissioned by MY Dennis' lab @mydennis.bsky.social for a study focused on identifying human-specific gene duplications and their role in brain evolution using genomics and zebrafish as model. @dcsoto.bsky.social
#art #digitalart #sciart #fish
Your lab isn't a home until you've hung up your prized Tiktaalik. My Live, Laugh, Love wall decals gotta be in a box somewhere.
November 7, 2025 at 4:39 PM
Your lab isn't a home until you've hung up your prized Tiktaalik. My Live, Laugh, Love wall decals gotta be in a box somewhere.
Reposted by Rob Denton
I am so proud & happy to see our Potamo genome assembly finally out there in the world! The process ended up being way more challenging than expected, but for some really cool reasons. ❤️🐌🧬
TLDR: Surprise! A VERY recent WGD.
academic.oup.com/gbe/article/...
Photo: C. Böck, ILIM, Mondsee, Austria)
TLDR: Surprise! A VERY recent WGD.
academic.oup.com/gbe/article/...
Photo: C. Böck, ILIM, Mondsee, Austria)
November 5, 2025 at 4:50 PM
I am so proud & happy to see our Potamo genome assembly finally out there in the world! The process ended up being way more challenging than expected, but for some really cool reasons. ❤️🐌🧬
TLDR: Surprise! A VERY recent WGD.
academic.oup.com/gbe/article/...
Photo: C. Böck, ILIM, Mondsee, Austria)
TLDR: Surprise! A VERY recent WGD.
academic.oup.com/gbe/article/...
Photo: C. Böck, ILIM, Mondsee, Austria)
Now in Evolution: academic.oup.com/evolut/artic...
This paper started when @3rdreviewer.bsky.social, Mike, and I had a lunch at which there was a lot of, "What do you mean when you say X?" Fun to spend time thinking about when terms get too muddy, and great work by Drew to pull it all together!
This paper started when @3rdreviewer.bsky.social, Mike, and I had a lunch at which there was a lot of, "What do you mean when you say X?" Fun to spend time thinking about when terms get too muddy, and great work by Drew to pull it all together!
November 4, 2025 at 6:06 PM
Now in Evolution: academic.oup.com/evolut/artic...
This paper started when @3rdreviewer.bsky.social, Mike, and I had a lunch at which there was a lot of, "What do you mean when you say X?" Fun to spend time thinking about when terms get too muddy, and great work by Drew to pull it all together!
This paper started when @3rdreviewer.bsky.social, Mike, and I had a lunch at which there was a lot of, "What do you mean when you say X?" Fun to spend time thinking about when terms get too muddy, and great work by Drew to pull it all together!
Reposted by Rob Denton
Check out the recent publication in Annual Reviews of Ecology, Evolution, and Systematics where the authors explore genomic species delimitation in depth. You'll see a number of #sciart figures I created to help explain some of the concepts!
www.annualreviews.org/content/jour...
www.annualreviews.org/content/jour...
October 29, 2025 at 1:00 PM
Check out the recent publication in Annual Reviews of Ecology, Evolution, and Systematics where the authors explore genomic species delimitation in depth. You'll see a number of #sciart figures I created to help explain some of the concepts!
www.annualreviews.org/content/jour...
www.annualreviews.org/content/jour...
Reposted by Rob Denton
The CAMBIUM NSF NRT is recruiting PhD students @uarizona.bsky.social! Fellowships for interdisciplinary training in biodiversity big data to adapt to & mitigate climate change impacts. Great fit for evolutionary genomics, bioinformatics, plant adaptation, ecology & more. cambium.arizona.edu 🧬🌐🌎
October 24, 2025 at 5:19 AM
The CAMBIUM NSF NRT is recruiting PhD students @uarizona.bsky.social! Fellowships for interdisciplinary training in biodiversity big data to adapt to & mitigate climate change impacts. Great fit for evolutionary genomics, bioinformatics, plant adaptation, ecology & more. cambium.arizona.edu 🧬🌐🌎
Reposted by Rob Denton
Genomics help: From this FastQC report for our low coverage whole genome sequences, what is the polyA adapter that is showing up? Can I trim them out like I did the TruSeq adapters? I've not seen these show up before.
October 28, 2025 at 7:34 PM
Genomics help: From this FastQC report for our low coverage whole genome sequences, what is the polyA adapter that is showing up? Can I trim them out like I did the TruSeq adapters? I've not seen these show up before.
John K. Samson wrote the two best songs about academia, one about someone who I choose to believe achieved their goals ("Postdoc Blues") and one about someone who probably didn't ("When I Write My Masters Thesis")
October 28, 2025 at 3:59 PM
John K. Samson wrote the two best songs about academia, one about someone who I choose to believe achieved their goals ("Postdoc Blues") and one about someone who probably didn't ("When I Write My Masters Thesis")
Genome assembly fresh of the supercomputer, total size = 29,892,519,935 base pairs 🦎🧬
October 27, 2025 at 7:01 PM
Genome assembly fresh of the supercomputer, total size = 29,892,519,935 base pairs 🦎🧬
Reposted by Rob Denton
In response to anti-DEI legislation in the states, universities have started to hire more white male faculty.
This increase starts before bills are signed into law.
Universities appear to be anticipating anti-DEI legislation and preemptively hiring more white men.
This increase starts before bills are signed into law.
Universities appear to be anticipating anti-DEI legislation and preemptively hiring more white men.
October 22, 2025 at 3:26 PM
In response to anti-DEI legislation in the states, universities have started to hire more white male faculty.
This increase starts before bills are signed into law.
Universities appear to be anticipating anti-DEI legislation and preemptively hiring more white men.
This increase starts before bills are signed into law.
Universities appear to be anticipating anti-DEI legislation and preemptively hiring more white men.
Reposted by Rob Denton
The #PolyploidyWebinar series is back for another season! 🧬 Join us for talks at 9AM Pacific on the second Thursday of each month. Are you working on something exciting in polyploidy? We'd love to have you speak! Sign up for open dates at the link below. Looking forward to the great research ahead!
Polyploidy Webinar Speaker Signup 25-26
docs.google.com
October 17, 2025 at 2:37 AM
The #PolyploidyWebinar series is back for another season! 🧬 Join us for talks at 9AM Pacific on the second Thursday of each month. Are you working on something exciting in polyploidy? We'd love to have you speak! Sign up for open dates at the link below. Looking forward to the great research ahead!
Reposted by Rob Denton
OUT TODAY: SimHumanity, a SLiM 5 model of the human genome, replete with demography, autosomes, X/Y & mtDNA.
A shared starting point for reproducible evolutionary simulations.
Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer.
🔗 www.pivotscipub.com/hpgg/5/4/0006
A shared starting point for reproducible evolutionary simulations.
Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer.
🔗 www.pivotscipub.com/hpgg/5/4/0006
October 16, 2025 at 12:10 PM
OUT TODAY: SimHumanity, a SLiM 5 model of the human genome, replete with demography, autosomes, X/Y & mtDNA.
A shared starting point for reproducible evolutionary simulations.
Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer.
🔗 www.pivotscipub.com/hpgg/5/4/0006
A shared starting point for reproducible evolutionary simulations.
Huge thanks to coauthors Ben Haller, @mufernando.bsky.social & Philipp Messer.
🔗 www.pivotscipub.com/hpgg/5/4/0006
Reposted by Rob Denton
We will be writing more of these. If you’re a scientist and your science has been disrupted, we want to hear from you: www.nytimes.com/2025/10/08/c...
Has Your Scientific Work Been Cut? We Want to Hear.
www.nytimes.com
October 9, 2025 at 2:50 PM
We will be writing more of these. If you’re a scientist and your science has been disrupted, we want to hear from you: www.nytimes.com/2025/10/08/c...
Reposted by Rob Denton
Wait what's happening with CIPRES?!
www.phylo.org
www.phylo.org
CIPRES
www.phylo.org
October 8, 2025 at 11:45 PM
Wait what's happening with CIPRES?!
www.phylo.org
www.phylo.org
Reposted by Rob Denton
Now published in Cell! We found that ~15% of SNPs from divergent refs did not liftover as SNPs in the gray fox ref—half mapped to monomorphic sites, half failed to map. Co-authored with Matthew Genchev, @elliecat.bsky.social, and @jazlynmooney.bsky.social
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
September 22, 2025 at 5:41 PM
Now published in Cell! We found that ~15% of SNPs from divergent refs did not liftover as SNPs in the gray fox ref—half mapped to monomorphic sites, half failed to map. Co-authored with Matthew Genchev, @elliecat.bsky.social, and @jazlynmooney.bsky.social
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Rob Denton
Jane Goodall challenged what it meant to be a scientist.
In this news story we look at three ways she changed science.
A loss for science, a loss for the community, a loss for everyone
🧪 #academicSky
www.nature.com/articles/d41...
In this news story we look at three ways she changed science.
A loss for science, a loss for the community, a loss for everyone
🧪 #academicSky
www.nature.com/articles/d41...
Jane Goodall’s legacy: three ways she changed science
The primatologist challenged what it meant to be a scientist.
www.nature.com
October 2, 2025 at 2:59 PM
Jane Goodall challenged what it meant to be a scientist.
In this news story we look at three ways she changed science.
A loss for science, a loss for the community, a loss for everyone
🧪 #academicSky
www.nature.com/articles/d41...
In this news story we look at three ways she changed science.
A loss for science, a loss for the community, a loss for everyone
🧪 #academicSky
www.nature.com/articles/d41...
Reposted by Rob Denton
Staff members at the NIH seem to have done the impossible: spend the agency's $48 billion budget.
“Everyone has been rallying together to clean up the mess, but it’s a mess that did not need to be made,” an NIH program officer told me.
www.nature.com/articles/d41...
“Everyone has been rallying together to clean up the mess, but it’s a mess that did not need to be made,” an NIH program officer told me.
www.nature.com/articles/d41...
NIH races to spend its 2025 grant money — but fewer projects win funding
Despite political obstacles, officials are on track to disburse all of the research funds allocated to US biomedical behemoth.
www.nature.com
September 30, 2025 at 3:32 PM
Staff members at the NIH seem to have done the impossible: spend the agency's $48 billion budget.
“Everyone has been rallying together to clean up the mess, but it’s a mess that did not need to be made,” an NIH program officer told me.
www.nature.com/articles/d41...
“Everyone has been rallying together to clean up the mess, but it’s a mess that did not need to be made,” an NIH program officer told me.
www.nature.com/articles/d41...
Went to a little workshop on universal design yesterday, and someone shared this document that has been super helpful to A) get new ideas and B) map things I already do universal design intentions.
www.researchgate.net/publication/...
www.researchgate.net/publication/...
(PDF) Universal Design: Places to Start
PDF | Beginning with a series of possible ways to introduce an essay on Universal Design for Learning, this contribution instead resolves to offer a... | Find, read and cite all the research you need ...
www.researchgate.net
September 24, 2025 at 1:45 PM
Went to a little workshop on universal design yesterday, and someone shared this document that has been super helpful to A) get new ideas and B) map things I already do universal design intentions.
www.researchgate.net/publication/...
www.researchgate.net/publication/...
Reposted by Rob Denton
Happy to share that our paper on the #evolution and #genomics of the most common #color polymorphism in #frogs is now out in @pnas.org! My favorite frogs even made the cover of this week’s issue! 🎉🐸🎉
Read the paper here: www.pnas.org/doi/10.1073/...
Read the paper here: www.pnas.org/doi/10.1073/...
September 17, 2025 at 10:42 AM
Happy to share that our paper on the #evolution and #genomics of the most common #color polymorphism in #frogs is now out in @pnas.org! My favorite frogs even made the cover of this week’s issue! 🎉🐸🎉
Read the paper here: www.pnas.org/doi/10.1073/...
Read the paper here: www.pnas.org/doi/10.1073/...
I've been a biology student/professional for like 20 years. I still regularly see things like this that blow me away. What a life.
The buff-tip moth (Phalera bucephala) has mastered a very particular kind of camouflage.
When they close their wings up, they resemble a broken twig.
Native to large parts of Europe, there's regional pattern variation that reflects the local tree species. This one best resembles birch twigs?
When they close their wings up, they resemble a broken twig.
Native to large parts of Europe, there's regional pattern variation that reflects the local tree species. This one best resembles birch twigs?
September 17, 2025 at 2:44 PM
I've been a biology student/professional for like 20 years. I still regularly see things like this that blow me away. What a life.
Reposted by Rob Denton
SquidSim is the coolest package - it let's you build complex hierarchical data structures and then simulate data from the world you create. The best tool for doing proper power analyses and testing how well your models can uncover the 'truth'. I've been recommending it to everyone!
Interested in simulating the kind of data that you might commonly find in evolutionary and ecological studies?
Then we have the R package for you - squidSim!!
Check our new preprint:
ecoevorxiv.org/repository/v...
Then we have the R package for you - squidSim!!
Check our new preprint:
ecoevorxiv.org/repository/v...
squidSim: a flexible R package for structured and reproducible simulations in Ecology and Evolutionary Biology
ecoevorxiv.org
September 15, 2025 at 5:08 PM
SquidSim is the coolest package - it let's you build complex hierarchical data structures and then simulate data from the world you create. The best tool for doing proper power analyses and testing how well your models can uncover the 'truth'. I've been recommending it to everyone!