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⚡️🔩Felsenstein's Monster🔩⚡️

@josephwb.bsky.social

2.5K followers 450 following 3.1K posts

Comp. evol. biol., fake ornithologist, LFHCfs, Luddite, CSH I get down methodically Without regard to my soul tinyurl.com/G00gleSch0lar HHGG bot: @whalepetunias.bsky.social pfp: Chickens exposed to natural beard hair on a mannequin hdr: socks & sandals

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⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · Dec 28

I made this over the break. Why would I do such a thing? Am I some sort of #phylogenetics dork? Well... yes, but that's not why. To fully explain I'll have to do one of those sewing-strings-wrapped-around-a-spool dealies. 1/ 🧪

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⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · 15h

Yeah, that is not great :(

⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · 15h

The only instance where I think "recent citations are better" necessarily holds is for software papers. Newer versions (which may have methods not previously available) frequently include additional (often junior) authors that do not get credit when you cite the 2003 paper.

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Carl Zimmer @carlzimmer.com · 16h

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

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

Ramos & Pick analyzed the distribution and classification of Pax genes and established the painted lady butterfly (Vanessa cardui) as a model to study Pax gene expression and function.

🔗 doi.org/10.1093/molbev/msaf220

#evobio #molbio #pax

Arthropod Pax Gene Evolution: A Role for Vanessa Cardui Twin of Eyeless in Eye Development

Abstract. Pax genes encode transcription factors involved in diverse processes. First identified in Drosophila, they have been found throughout the animal

doi.org

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RES Publications @respublications.bsky.social · 20h

New #OpenAccess research in #RESSystematicEnt

A new #phylogeny of #Anastrepha (#Diptera: #Tephritidae) based on nuclear loci obtained by #phylogenomic methods
doi.org/10.1111/syen.70003

#Phylogenetics
@gkergoat.bsky.social @wiley.com

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Mostly Harmless @whalepetunias.bsky.social · 20h

Arthur Dent sat and quivered. He had no idea what he was in for, but he knew that he hadn't liked any thing that had happened so far and didn't think things were likely to change.

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Per Alström @peralstrom.bsky.social · 3d

I was honoured to be invited to give a talk on AviList, the new unified global checklist of birds, at the Delta Birding Festival 2+ weeks ago, and the organizers just sent me a link to a YouTube video of my talk: www.youtube.com/watch?v=QO5x... #birds #ornithology #taxonomy

AviList: a unified global bird checklist - Per Alström

YouTube video by Delta Birding Festival

www.youtube.com

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⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · 1d

This was just a prelim paper.

⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · 1d

Just 4?!?

Somewhere on that desk _there is_ printed out the entire mitochondrial genome of Gallus gallus :P

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Timothée Poisot @ctrlalttim.com · 1d

Very sincerely, we don't do the "lay piles of paper on the ground" type of research enough anymore. This was peak research.

⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · 1d

Researchin'

A hirsute and bewiskered dork sits at a messy desk overflowing with various books, notes, and tea. Arranged on the floor in organized (and labelled) piles are papers on various topics.

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Paul F. Tompkins @pftompkins.bsky.social · 1d

FanTASTIC news let’s get this done

The Verge @theverge.com · May 26

Nick Clegg says asking artists for use permission would ‘kill’ the AI industry

Paul McCartne, Elton John and others signed an open letter.

buff.ly

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Ksepka Lab @ksepkalab.bsky.social · 1d

Proud to share a new piece in Scientific American co-authored with the brilliant @lnwilson.bsky.social , edited by @katewong.bsky.social, and featuring this spectacular depiction of the endless daylight of the Cretaceous summer in Alaska by Chase Stone!

www.scientificamerican.com/article/how-...

Bird Migration Is One of Nature’s Greatest Spectacles. Paleontologists Just Found Clues to Its Origin

Tiny fossils hint at when birds began making their mind-blowing journey to the Arctic to breed

www.scientificamerican.com

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BOU @bou.org.uk · 2d

The origins and functions of bowers in the Bowerbirds: a review and synthesis | doi.org/10.1080/0158... | Emu | #ornithology 🪶

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⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · 1d

It was an 80+ y.o. museum building, so drafts were a definite concern!

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Gail Simone @gailsimone.bsky.social · 1d

This gives me anxiety!

⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · 1d

Researchin'

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⚡️🔩Felsenstein's Monster🔩⚡️ @josephwb.bsky.social · 1d

Researchin'

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Chris MacQuarrie @cmacquar.bsky.social · 3d

Entomologists conference: American PI: Canadian PI; European PI

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Adam Kucharski @adamjkucharski.bsky.social · 1d

Want to build an interactive dashboard so others can explore epidemic scenarios? For COVID, @ngdavies.bsky.social spearheaded a great drag-and-drop approach, which made use of the JavaScript-based nature of RShiny... 1/

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Alberta Claw @albertonykus.bsky.social · 2d

New possible Miocene bowerbird from New Zealand, Aeviperditus gracilis: www.tandfonline.com/doi/full/10.... Congratulations, @lizzysteell.bsky.social! 🪶🧪

Fossilized foot bone of an extinct songbird, shown in multiple views.

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Lars Brudvig @lars-brudvig.bsky.social · 2d

Apply to become the next MSU EEB Presidential Postdoctoral Fellow!

These are two year positions with research stipend, working with 2+ MSU EEB faculty. Applications due 10 November 2025. More here:

eeb.msu.edu/initiatives/...

Postdoctoral Fellowship - Ecology, Evolution, and Behavior

eeb.msu.edu

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Matthew Hahn @3rdreviewer.bsky.social · 2d

New preprint led by grad student, Yu Mo! We introduce new software to calculate evolutionary rates of quantitative characters in the presence of discordance

1/

www.biorxiv.org/content/10.1...

Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees

Quantitative traits provide insights into how phenotypes evolve across species. However, standard comparative methods often assume a single species tree and overlook the discordant gene tree histories...

www.biorxiv.org

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Julia Evans @b0rk.jvns.ca · 2d

redirects

wizardzines.com/comics/termi...

(from "The Secret Rules of the Terminal", out now! wizardzines.com/zines/termin...)

redirect to a file:

cmd > file.txt terminal emulator into program, program out to file.txt, error out to terminal emulator
append to a file:

cmd >> file.txt terminal emulator into program, program out to file.txt (append mode), error out to terminal emulator
send a file to stdin:

cmd < file.txt file.txt into program, program out and err to terminal emulator
redirect stderr to a file:

cmd 2 > file.txt terminal emulator into program, program out to nowhere, err out to file.txt
redirect stdout AND stderr:

cmd > file.txt 2>&1 terminal emulator into program, out and err to file.txt
pipe stdout:

cmd1 | cmd2 terminal emulator into program 1, 1 out to program 2 via pipe, 2 out to command line, program 2 out 1 and 2 to terminal emulator
pipe stdout AND stderr:

cmd1 2>&1 | cmd2 terminal emulator into program 1, 1 and 2 out to program 2 via pipe, program 2 out 1 and 2 to terminal emulator
three gotchas

cmd file.txt > file.txt will delete the contents of file.txt some people use set -o noclobber (in bash/zsh) to avoid this

but I just have “never read from redirect to the same file” seared into my memory.

sudo echo blah > /root/file.txt doesn’t write to /root/file.txt as root. Instead, do:

echo blah | sudo tee /root/file.txt or sudo sh -c 'echo blah > /root/file.txt'

cmd 2>&1 > file.txt doesn’t write both stdout and stderr to file.txt. Instead, do: cmd > file.txt 2>&1

cat vs <

I almost always prefer to do:

cat file.txt | cmd

instead of

cmd < file.txt

it works fine & it feels better to me

using cat can be slower if if’s a GIANT file though
&> and &|

some shells support &> and &| to redirect/pipe both stdout and stderr

(also some shells use |& instead of &|)

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Rosa Fernández @rosafernandez.bsky.social · 2d

How did animals repeatedly conquer land? 🌊➡️⛰️ We analysed ~1,000 gene repertoires (24M genes!) from all animal phyla to uncover how this happened. Work led by @gemmaeling.bsky.social & Klara Eleftheriadi, both first coauthors of this titanic effort!
www.biorxiv.org/content/10.1...

Independent genomic trajectories shape adaptation to life on land across animal lineages

How animals repeatedly adapted to life on land is a central question in evolutionary biology. While terrestrialisation occurred independently across animal phyla, it remains unclear whether shared gen...

www.biorxiv.org

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Andrés Cuervo @amcuervo.bsky.social · 2d

onlinelibrary.wiley.com/doi/10.1002/...
anyone else wondering about Hypopyrrhus?
#ornithology #evosky

Feeding Ecology, Evolutionary Allometry, and Convergence in the Lower Jaw of New World Blackbirds and Allied Passerine Birds (Emberizoidea)

We quantify the mandibular shape of icterids and other emberizoids using three-dimensional geometric morphometrics and its relationship with diet, gaping, and evolutionary allometry through phylogene....

onlinelibrary.wiley.com

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Andrés Cuervo @amcuervo.bsky.social · 2d

The Link Between Range Size, Niche Specialisation and Diversification in One of the Most Successful Avian Radiations, the New World Flycatchers (Tyrannoidea).
Journal of Biogeography e70057. #ornithology #evosky
onlinelibrary.wiley.com/doi/10.1111/...

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