Kyle T David

Jane Goodall, ethologist and conservationist, has died. She was 91

Discovery of additional ancient genome duplications in yeasts Whole genome duplication (WGD) has had profound macroevolutionary impacts on diverse lineages, preceding adaptive radiations in vertebrates, teleost fish, and angiosperms. In contrast to the many know...

We often talk about THE whole genome duplication in yeasts, but we find new evidence of additional whole genome duplications in other yeast species!

Check out this preprint led by @kylethedavid.bsky.social www.biorxiv.org/content/10.1...

Opinion | America First? Not When It Comes to Your Health.

New York Times story with profiles of researchers whose grants were terminated.

[Gift Link]

www.nytimes.com/2025/08/24/o...

Trump’s Cuts May Spell the End for America’s Only Antarctic Research Ship

An excellent article in the NYTimes about the impending demise of the last U.S. Antarctic research vessel, the N.B. Palmer, featuring US and overseas colleagues (including @polarrobs.bsky.social). Gift link:

www.nytimes.com/2025/08/22/c...

the old vs. new cracker barrel logo is contrasted with the old vs. new vanderbilt logo, which I also hate

I said what I said

Population structure in a fungal human pathogen is potentially linked to pathogenicity Nature Communications - Genetic diversity between clinical and environmental fungal isolates of Aspergillus flavus is poorly studied. Here, the authors analysed genomic data from a global set of...

Thrilled to share that the final chapter of my PhD with @rokaslab.bsky.social is now out in @natcomms.nature.com 🎉
Read it to find out how population structure impacts pathogenicity in Aspergillus flavus, a fungus that infects humans 🧪
rdcu.be/eAToj

a peek under the hood

This weekend me and @evolutionvu.bsky.social collaborated with some local girl scouts to run an advanced evolution simulator, saw some cool convergence as well as a plesiomorphy that hung around way longer than I thought it would

a close up of a man 's face with a slight smirk on his face Alt: Patrick Bateman "oooh" reaction gif

When the final sentence of the abstract begins with "Taken together,"

Snow White and the Seven Dwarfs: a fairytale for endocrinologists ‘Snow White and the Seven Dwarfs’, a fairytale that is widely known across the Western world, was originally written by the Brothers Grimm, and published in 1812 as ‘Snow White’. Though each dwarf was...

the study in question for those interested
pmc.ncbi.nlm.nih.gov/articles/PMC...

Google's infamously terrible AI Overview feature cites the NIH to list the names of the seven dwarfs

oh okay

The biology textbook John T. Scopes taught from, displaying a (woefully outdated) figure of animal diversity and relationships

over 500,000 animal species, can you imagine!?

Myself posing with my PI Antonis Rokas and a model chimpanzee

Myself posing with the statue of Clarence Darrow, defendant of John Scopes in the "monkey trial"

Had a great time celebrating the centennial of the Scopes trial with a trip to Dayton, hallowed ground for an evolutionary biologist! Thanks to @evolutionvu.bsky.social for organizing!

Plant grafting is so cool it makes me jealous. Like what do you mean you can just mash two species together

Kyle David @kylethedavid.bsky.social discusses two new genome 🧬 duplications 🧬🧬 in the yeast subphylum

With three WGD clades, we can ask what are the causes and consequences of WGD in yeast

@evolutionvu.bsky.social @rokaslab.bsky.social

#Evol2025 #Evol24

Tag yourself im Dibbler

Neuropeptides specify and reprogram division of labor in the leafcutter ant Atta cephalotes We identify specific neuropeptides mediating worker division of labor in the leafcutting ant A. cephalotes, finding two neuropeptides associated with characteristic behaviors of leafcutting and of bro...

visual abstract from:
www.cell.com/cell/abstrac...

Visual abstract from "Neuropeptides specify and reprogram division of labor in the leafcutter ant Atta cephalotes": a cartoon depiction of several leafcutter ant castes, whose behaviors the paper demonstrates can be manipulated

Nice argument. Unfortunately, I've already depicted you as the fungal cultivating minima caste and me as the neuroparsin-A upregulated soldier major caste

“Shrimps is bugs” is a funny meme, but there’s some truth in the reverse version, “Bugs is shrimps” 🐛🦐 Since insects are literally a group of terrestrial crustacean. And among all the insects, bristletails are probably the most shrimp-like in my opinion!

ty!

do you have a good citation for this?

Thanks! probably spent as much (or more) time moving parallelograms around as I did on the actual paper

If any of that sounds cool to you please check out the paper (and let me know if you need a copy!), and for those of you going to #Evol2025 I’ll be talking about this (and other cool stuff) at the Genomics and Macroevolution section on Tuesday!

So not only are convergent traits mostly the result of the same gene families, some of these families are contributing to multiple traits as well!

We also found a few gene families that were associated with as many as 23% of all traits. We believe these ‘keystone’ families play important roles across the evolution of diverse metabolic traits.

With help from @jgschraiber.bsky.social we found that gains and losses of both traits and genes closely mirrored one another in at least one family (such as Raffinose and SUC) for 81% of tested traits, indicating parallel evolution across deep time may be more common than previously believed

To address this question I used a dataset of 56 metabolic traits and genomes from 993 species of yeasts (special thanks to @lablabella.bsky.social & @marie-clairehar.bsky.social!). Each trait has independently evolved dozens to hundreds of times, providing unprecedented statistical power

Homologous Convergence (left): Different species (represented by images of various animal eyes) have independently evolved complex eyes, but all are regulated by a shared ancestral gene, PAX, indicating a common genetic origin despite differences in eye structure. Nonhomologous Convergence (right): Multiple fish species have independently evolved antifreeze proteins (AFPI) to survive in icy waters. Each species uses a different gene family to produce similar proteins, illustrating convergence through distinct genetic pathways without a shared ancestral gene for this trait.

When novel phenotypes occur independently on the tree of life (convergence) they can be the result of the same (homologous) or unique (nonhomologous) genomic elements. But how common is parallelism across deep timescales? Are stories like eyes or antifreeze proteins more common?

How many paths lead to evolutionary innovation? How versatile are genomic toolkits? Excited to announce my new @pnas.org paper addressing these questions in collaboration with @rokaslab.bsky.social, @hittingerlab.bsky.social, and the Pennell lab!

www.pnas.org/doi/10.1073/...

NIH funding supporting the HMMER and Infernal software projects has been terminated. NIH states that our work, as well as all other federally funded research at Harvard, is of no benefit to the US.