Disagreement among Genomic Markers Profoundly Influences Phylogenetic Inference in Squamates https://www.biorxiv.org/content/10.64898/2026.01.06.698024v1
08.01.2026 04:32
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Disagreement among Genomic Markers Profoundly Influences Phylogenetic Inference in Squamates https://www.biorxiv.org/content/10.64898/2026.01.06.698024v1
New lab preprint! PhD work of @drsimonegable.bsky.social
- 12 million base pairs of DNA ✅🧬
- hundreds of species of lizards and snakes ✅🦎🐍
- biological, molecular, and artifactual factors confounding phylogenetic inference ✅💻
- most ‼️ for your 🦌➡️ protein-coding genes
www.biorxiv.org/content/10.6...
New in BMC Genomics! Genome size in anurans (frogs and toads) ranges from 0.5Gb to 10.0Gb of DNA. John Neddermeyer and I teamed with Andrew Rubio and @adamstuckert.bsky.social and found one type of retrotransposon active over the last ~30my is the likely culprit: link.springer.com/article/10.1...
I’ve been playing with a
now popular A.I. scientific manuscript review tool and it’s cool but imo it seems built on a “keep adding experiments if you want to get this into Nature” mindset. It reads like that kind of reviewer. I wish there was a society journal reviewer option 🤣
Awesome week meeting with our whole team investigating the genomic basis of phenotypic evolution across all squamates at @princetonupress.bsky.social and @amnh.org with my fellow PIs @marcanthonytollis.bsky.social and Frank Burbrink and all our students and postdocs in this enterprise!
I love how there is a point in every kid's life where in their daily quest for sugar they realize they ain't got time for no Teddy Grahams
Makin moves over here
no I will not be navigating to your electronic calendar to schedule a meeting with you. You can just tell me when you are available 🤣
unless you are like a dean or a provost, then I get it. But another professor? Cmon
New paper out! 🤩 "Shrinking to bird size with dinosaur-level cancer defences: Evolution of cancer suppression over macroevolutionary time" with @kokkonut.bsky.social and @marcanthonytollis.bsky.social. doi.org/10.1371/jour... A short thread:
Check out our awesome review of squamates, covering fossils, phylogenetics, and genomics!
bsky.app/profile/marc...
This suggests that LINE movement in the genome promotes tumor growth, but once SINEs, which depend on LINE enzymatic machinery, get moving, that’s what causes trouble (i.e. malignant cancers)
Interestingly, he found that across mammals LINE activity predicts neoplasia prevalence, but when you add SINEs to the mix, it predicts malignancy
New lab preprint! Vahid Fard looked across mammals and found that species with more recently active LINE and SINE retrotransposons in their genomes also get more cancer, supporting a model where genome instability promotes neoplasia and malignancy
never forget what they stole from you
Yeah I’ll be skipping my usual conference not because it overlaps with the first week of classes (it always does) but rather the Knicks are coming to town that weekend
#PopGen #PopulationGenomics #PopulationGenetics
For a project, we needed a tool that will batch download phylogeographic DNA samples (like mtDNA and nucDNA) for lots of species, which have just been sitting on NCBI since the PCR and Sanger-sequencing era (ca. 2003-2015) and can still be hella useful, so I wrote one. It aligns the sequences, too 👍
We are still doing the negotiated F&A.
Yeah my summer plan was to put in a grant by August but I’m changing course to focus on beefing up the preliminary work, and push it into the fall.
Provided there is an NSF DEB by then.
Has anybody been consulted on the NSF “shakeup”? Should PIs not bother submitting proposals at this point? I mean odds for funding were always low but are we just throwing effort into the wind now?
Sophie came to NAU from Ireland to work on this project one fall, to follow up on on a study we published in 2020 (also in MBE). It couldn't have gone better, and the new paper is a welcome contribution to the cancer evolution literature. oup2-idp.sams-sigma.com/authorize?au...
Sophie Matthews’s lovely paper on gene copy number and cancer prevalence across mammals has been published in Molecular Biology and Evolution @official-smbe.bsky.social, check it out! academic.oup.com/mbe/advance-...
Morale is pretty low among scientists given the new regime. Funding scenarios are up in the air, many MDs and PhDs are unsure of their status. But don’t despair! Put the energy into your students. Teach like a MFer, light the fire, they will be ready when the smoke clears.
Haha Gen X has no complaints, just “whatever”
Fellow parents: amirite, it’s one thing to step on a lego but it’s even more infuriating to step on a cheerio
Here mt Xmas playlist ive been building for more than 10 years. Enjoy! open.spotify.com/playlist/0Qn...
I don’t know why (well, money). Superman (1978) is a perfect movie and still holds up
the only time I want someone to be over-bubbly and friendly in an email is when they have to respond to my dumb question. Please be nice!
It doesn’t get easier. They stay difficult, except are huge, mobile, and extremely talkative (until they become teenagers and stop talking for a little while)
