Joseph W. Brown

usually if you ask experts why an empire fell they’ll say it’s nuanced and multifaceted, so i think it’s kind of cool that with America future historians will get to just say like “oh they took the idiot train to moronsville”

A phylogenetic classification of diatoms (Bacillariophyta) Diatoms are known for their extraordinary species richness, cornerstone roles in aquatic ecosystems, and immense contributions to the global cycling of carbon, oxygen, and silica. For nearly 2 centur....

Our phylogenetic classification of >400 diatom genera is now published in Journal of Phycology.
onlinelibrary.wiley.com/doi/10.1111/...

The Null Hypothesis is Always Wrong No two populations are identical for any trait. No two communities have the same species composition. No detectable phenotype is ever compl...

The Null Hypothesis is Always Wrong!

New blog post - check it out.

ecoevoevoeco.blogspot.com/2026/03/the-...

Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.

The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...

Figure 1 shows they key result

Two scientists walk through a cluttered old-fashioned science laboratory. The female scientist says “Analogue instruments! Paper records! Chalk boards! I thought you'd agreed to modernise the laboratory?” The male scientist replies “That's what i'm so excited about: we have moved to cloud-based storage for our data!” They step out onto a balcony. She says: “Please tell me you haven't built a library zeppelin” This is exactly what he has done. It floats across the sky and he adds “It's got a fax machine!”

My cartoon for this week’s @newscientist.com

📢 Including fossil tips in your phylogeny can double your continuous trait model fitting accuracy!

Updated preprint out now on @ecoevorxiv.bsky.social.

🔗 doi.org/10.32942/X27...

with @pedrolgodoy.bsky.social @macroecoevoale.bsky.social and @bethanyjallen.bsky.social

I don't think I've ever seen an albino Gray Squirrel before yesterday.

Ohio has many white squirrels, but they're almost all leucistic (still some melanin production, which you can see in their dark eyes). I've got some leucistic squirrels in my backyard park.

But those are some pink eyes!

i love data, me too meme

Update of our preprint on detecting selection on regulatory sequences! We notably added an analysis for human, where the likelihood test per ChIPseq peak lacks power.
www.biorxiv.org/content/10.1...

An unconventional Rubisco small subunit underpins the CO2-concentrating organelle in land plants In many algae, photosynthesis is boosted by biophysical CO2-concentrating mechanisms, which pack the CO2-fixing enzyme Rubisco into liquid-like organelles called pyrenoids. Engineering C3 crops with a...

Our work on #hornwort #pyrenoids is finally out in @science.org! 🎉 We uncovered how hornworts pack their Rubisco into pyrenoids and successfully recreated them in Arabidopsis. A key step toward engineering more efficient photosynthesis in crops @btiscience.bsky.social www.science.org/doi/10.1126/...

Me, bursting into the Colossal Biosciences PR office:

You guys! I've got the beginnings of our new slogan!

A phylogenetic tree of insects is shown annotating the presence or absence of a an antimicrobial peptide gene across winged insects

Various phylogenetic secondary loss events are mapped to a tree of insects to explain the parsimony calculations necessary to explain the diversity of insect Drosomycin antimicrobial peptide genes

Antimicrobial peptides (AMPs) are key defence molecules of the innate immune system of plants and animals. Understanding the evolutionary origins of AMPs can help to explain how immune systems acquire novelty and vary in their defensive capabilities. However, AMPs evolve rapidly, and so the origins of similar AMPs across organisms is often unclear. Furthermore, false negatives due to low search sensitivity are common and can hinder confident annotations about true absences. Due to these difficulties, understanding whether similar AMP genes found in diverse organisms represent ancestral molecules or evolutionary novelties has been challenging. In this report, we present evidence of horizontal gene transfer (HGT) of the antifungal peptide gene Drosomycin across insects. We show that in Diptera, the presence of Drosomycin is restricted to the Melanogaster group and additionally the distant relative Drosophila busckii. We go on to recover Drosomycin genes in cockroaches (Blattodea), mantises (Mantodea), one katydid (Orthoptera), various beetles (Coleoptera), and a recently acquired pseudogenized Drosomycin locus in Liposcelis booklice (Psocodea), but no other insects. Explaining this diversity through shared ancestry requires at least 50 independent loss events, or just seven HGT events. Previous studies have suggested that similar AMPs found across divergent species reflect conservation from a common ancestor, or due to their small size, that they arose via convergent evolution resulting from pathogen-imposed selection. Our findings suggest horizontal gene transfer can be responsible for the presence of some AMP genes found scattered across the tree of life. By presenting a mechanism through which immune systems can acquire novelty, our study also suggests a possible explanation for certain lineage-specific competencies for defence against infectious disease. While loss of AMP genes is common in certain lineages, here we suggest gain of AMPs can occur just as suddenly.

Pleased to finally share this fun collab that began at #Ento23

@cedricaumont.bsky.social presented & I had seen NCBI annotated some cockroach genomes as "contaminated." Turns out NCBI & I were wrong (much more fun).

Horizontal transfer of an #AntimicrobialPeptide across insects
bit.ly/DrsHGT

1/🧵

Dear 🪰folks, for a project I am looking for D. buzzati, D. gaucha, D. recens and Z. sepsoides. Please get in touch if you have them in your lab and willing to share.

@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs).

If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.

A digital CAPTCHA verification window titled "Select all squares with PIPES" against a plain white background. The window contains a 3×3 grid of numbered squares, mixing literal hardware, smoking pipes, and programming syntax.

These captchas just keep getting harder #rstats

This is a profound continental divide. Canadians overwhelmingly view other Canadians, even those unlike them, as being good people. Americans, more than any other country, view their neighbours and fellow citizens as bad people. Anti-Americanism flourishes in the United States

MKado: a toolkit for McDonald-Kreitman tests of natural selection https://www.biorxiv.org/content/10.64898/2026.03.02.709122v1

Cover image of paperback edition of the Tree of Life book by Max Telford.

On world book day might you be tempted to preorder the paperback edition of The Tree of Life?

Out in pb on April 23rd.

www.amazon.co.uk/Tree-Life-So...

Excited to see this analysis based on AVONET & AVOTREX bird trait data.

Do bird radiations tend to avoid regions of trait space already occupied by other lineages? This analysis suggests the answer is yes!

The "Birds The Don't Exist" actually do exist, just in related passerine clades.

Reginald from Beartato (Nedroid) shrugging and saying "GUESS I'VE GOT BRAIN PROBLEMS!"

Does anyone know if Beartato is done or on hiatus? I am missing that insanity in my life :/ @nedroid.com

Birds That Don't Exist: Niche Pre‐Emption as a Constraint on Morphological Evolution in the Passeroidea We use topological data analysis to reveal a persistent morphological gap in a major group of songbirds (superfamily Passeroidea). The gap remained unoccupied for millions of years, even though nearb....

This looks like it might be particularly interesting to folks in #hpbio e.g. interested in niche concepts or some of Lewontin's arguments. "Birds That Don't Exist: Niche Pre-­Emption as a Constraint on Morphological Evolution in the Passeroidea" by Chia et al. onlinelibrary.wiley.com/doi/full/10....

White−crowned Hornbill, Wrinkled Hornbill and Bushy−crested Hornbill for
#BirdsSeeinIn2026
#birds
#Borneo

If you smell toast, you might be having a stroke... a stroke of luck that is. It’s toast time.

Species and gene trees showing expected sequence divergence under ingroup versus ghost lineage introgression models.

From the upcoming #AppsPlantSci special issue "Branching out: Resolving #PlantEvolution through #Phylogenetic Networks"

Introducing ghostbuster: a new tool to detect cryptic ghost lineage introgression in genomic datasets (by Forsythe et al)

bsapubs.onlinelibrary.wiley.com/doi/full/10.... #botany

rix, my package that leverages #Nix to provide reproducible data science environments for #RStats (and #python and #julia) is in the top 10 starred ropensci packages!

that’s pretty cool

On the expansion and evolution of a master’s project Academics often lament that hardly any master’s projects – even the best ones – get published. The student moves on. Other research takes priority. No one has time to do the final analyses. Here I tel...

Academics often lament that hardly any master’s projects get published. The student moves on. Other research takes priority. No one has time to do the final analyses. Here I tell how one master’s project was, through persistent teamwork, finally carried over the finish line: go.nature.com/4aKs7N3

New paper out from @hoehna.bsky.social Lab, led by the brilliant @bjorntko.bsky.social! We applied the Pesto software (Kopperud & Höhna, 2025) to look at lineage-specific shifts in diversification rate on large, densely-sampled phylogenies across the Tree of Life doi.org/10.1093/evle...

Misery, dejection. More misery and more dejection. He needed a project and he gave himself one. He would find where his cave had been.

I tell people that if the government is covering up the existence of aliens, NASA is absolutely not involved, because astrobiologists can't keep a secret to save their lives

I keep telling people I recently had my first “AI-enabled” undergrad interns. It was worse than if they knew nothing. People who know nothing at least ask for help

I let them work for a few months because I was curious to see if some latent desire for help and instruction might kick in, but nope