Milton Tan

Petunia hybrida has been bred into an incredible diversity of colors and patterns.

Most arise from mutations in the anthocyanin pathway or post-transcriptional gene silencing that turns pigment genes on and off 🧬🎨

Our Galapagos program this summer officially got the green light. Looking forward to it.

A picture in Puerto Ayora from a few years ago. Man, I miss the tropical sun and ocean!

U.S. government has lost more than 10,000 STEM Ph.D.s since Trump took office A Science analysis reveals how many were fired, retired, or quit across 14 agencies

The U.S. government has lost more than 10,000 STEM Ph.D.s since Trump took office.

A Science analysis reveals how many were fired, retired, or quit across 14 agencies. Read more: https://scim.ag/4boPkq8

Society for the Study of Evolution Site description

Applications now open for the Graduate Research Excellence Grants! These provide evolutionary biology research funds for early and advanced Master’s and PhD students. Proposals due May 18.
www.evolutionsociety.org/content/soci...

Evolution of the facial musculature in basal ray-finned fishes - Frontiers in Zoology Background The facial musculature is a remarkable anatomical complex involved in vital activities of fishes, such as food capture and gill ventilation. The evolution of the facial muscles is largely u...

This provides clear paleontological support for a congruent re-interpretation of acipenseriform jaw bone homologies made recently on the basis of comparative studies of facial musculature in living actinopterygians: link.springer.com/article/10.1...

Multicolored image showing a CT model of a fish skull. Different anatomical regions appear as contrasting colors, and individual bones are labeled.

We were struck by how closely the large lateral upper jaw bone—identified as a dermopalatine in living acipenseriforms—resembled the maxilla of early ray-finned fishes. So I borrowed the specimen and zapped it with the new (at the time) CT scanner at Michigan in late 2017. Beautiful scan data.

Photogrammetric model of a fossil paddlefish skull set against a dark blue background. This fossil was collected, along with a sturgeon, inside the body cavity of an Edmontosaurus.

Bizarrely, some of the best Mesozoic acipenseriform fossils are from inside hadrosaur skeletons. They were almost certainly scavenging within the body cavities of dinosaur carcasses and became accidentally entombed, preserving their delicate anatomy. umorf.ummp.lsa.umich.edu/wp/specimen-...

Illustration of sturgeon cranial anatomy from Parker (1882). Images include a sturgeon skull and jaws, a head in sagittal section, and the branchial arches. https://royalsocietypublishing.org/rstl/article/doi/10.1098/rstl.1882.0004/119303/III-On-the-structure-and-development-of-the-skull?guestAccessKey=

Acipenseriform jaws are fiercely weird. Because they are so modified relative to other ray-fins, it is hard to determine the identity of individual bones. Many recent accounts of acipenseriform skeletal anatomy indicate that the maxilla—the major upper jaw bone in other groups—is absent.

Photograph of a fossil fish skull in right lateral view. The bone is dark brown/black against a gray matrix.

Out now in Contributions from me and @gilespalaeo.bsky.social, a deep dive into an early member of the sturgeon and paddlefish lineage. Bear with me, but there’s a long backstory highlighting uncertainty about the anatomy of living species and how well-studied fossils can still yield new insights.

Using Variable Window Sizes for Phylogenomic Analyses of Whole Genome Alignments https://www.biorxiv.org/content/10.64898/2026.03.04.709403v1

New blog post on #ai and #bioinformatics code - and {edgePython} - a port of {edgeR} from #rstats to #python

https://brianrepko.github.io/blog/posts/2026-02-26-edgepython-and-ai/

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

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-...

snputils (snputils.org): A High-Performance Python Library for Genetic Variation and Population Structure www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/AI-sandbox/s...

Comparative Genomics and Phylogenomics of the Mustelinae Lineage (Mustelidae, Carnivora) https://pubmed.ncbi.nlm.nih.gov/41782205/

Very proud of this perspective that came out of some really interesting and difficult conversations with friends and colleagues!

TLDR: how do scientists define sex? why does it matter??
#EcoEvo #Ecology #Evolution 🧪

Graph of award probability of R35 and R01 from NIH factbook as a function of review rank percentile. As is apparent, 2025 is a significant departure, with lower award probabilities at all scores <40 and significant departures from norm, where even being in the top 10% is no longer a nearly certain indicator of success. Data source: https://report.nih.gov/nihdatabook/report/302

The data is in: the NIH goalposts have shifted.

What were once almost certain fundable scores have become coin flips and what used to be likely grants have become aspirational, leading to fewer awards.

Another manifestation of how HHS policies have led to fewer awards and less science.

Largescale sucker.

First largescale sucker of the spring.

Deltaviruses spread through a viral Trojan Horse Hepatitis D-like satellite viruses, known as deltaviruses, have been recently discovered in a wide range of animals. These viruses are thought to expr…

We found a viral Trojan Horse: a virus can hide inside another virus.This one surprised us: deltaviruses don’t just borrow a helper virus. They can travel inside it.
A literal Trojan Horse “virus-in-a-virus” route into cells. 🤯 Kudos to 1st author @viroscope.bsky.social and co-authors !

Here is the "effective payline" for each institute, estimated (by Claude) as the percentile where one can expect 80% probability of funding from a logistic regression fit. The effective payline has gone from a historic ~12% to 6% in 2025.

Toaster oven sized glass chamber with 3-D preserved pterosaur skull inside. Humidity monitor dial appears to be on cusp of the red zone, unfortunately.

Closer look at the skull, which is displayed on its side so the palate is facing us.

This acid-prepped pterosaur skull is displayed in a humidity-controlled case within a case to help maintain the immaculately preserved, paper-thin bones. #FossilFriday

Assembling a fully-dated complete tree of life https://www.biorxiv.org/content/10.64898/2026.03.05.709771v1

Did you know that Evolution Letters now publishes reviews?! Our inaugural one is fantastic! Deep learning is opening new doors for evolutionary genomics, especially for nonmodel organisms with sparse or uncertain genomic data. doi.org/10.1093/evle...

I teach a segment on conservation genetics in my molecular ecology class. My favorite moment is when my students realize that Colossal is just a bunch of conservation grifters. Technically, these guys would make more money by MORE species going extinct.

Largest Silurian fish illuminates the origin of osteichthyan characters https://pubmed.ncbi.nlm.nih.gov/41781738/

RE: https://ecoevo.social/@marcrr/115656029348896562

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.
There is a similar problem with branch-site dN/dS tests, and a solution has […]

The complete mitochondrial genome and phylogenetic analysis of Leptobotia bellacauda (Teleostei: Cypriniformes: Botiidae) https://pubmed.ncbi.nlm.nih.gov/41777733/

a slide introducing GA, when the researchers found the GA mutant, they called them "foolish seedling". Then on the right corner I inserted Kagura from Gintama saying "お前ら　馬鹿ですか”

Successfully inserted anime in my plant bio lecture! 💅 Throwback to the good old time that I transcribed subtitles for many anime for two years at the end of my undergrad, now I'm telling a room of undergrads the plants and anime that I love. I love my job! #ib103 #anime #plantjoy

The bitterest pill about AI cheating for me is that AI'ed assignments take much longer to grade than honest assignments because they turn grading into an investigation.

So when the student spends less time, I spend more. Fun!

V. important perspective piece by @madeline-eppley.bsky.social & @andylee.bsky.social on biological sex and why a lack of scientific consensus should not be used to dictate human rights doi.org/10.1111/ele.... 🧪