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Silas Tittes

@silastittes.bsky.social
1.6K followers 1.1K following 273 posts

staff scientist / population geneticist at university of oregon | computational methods | cephalopod evolution | dad jokes kr-colab.github.io

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Silas Tittes @silastittes.bsky.social · 3h
Final version of Gabby Coffing’s last chapter! Reviewer’s made some good suggestions. Nice paper I’m proud to have played a role on! 🐙 academic.oup.com/mbe/advance-...
academic.oup.com
Diversity and divergence of two sympatric, sibling octopus species
Abstract. Coleoid cephalopods have convergently evolved many traits shared with vertebrates, including camera-type eyes, large brain-to-body size ratios, a
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Silas Tittes @silastittes.bsky.social · 03/10/2026
It’s wild how everything was domesticated 10k years ago. Even though it’s literally not wild anymore.
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Silas Tittes @silastittes.bsky.social · 02/10/2026
Oh right, I always forget the CS set up is quite different than bio. Still sounds on the margins of acceptable, but hopefully adjustments can be made for people acting in good faith.
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Silas Tittes @silastittes.bsky.social · 02/10/2026
2 a month per submitter is pretty reasonable no? Each student you train is putting out more than 24 papers a year?
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Silas Tittes @silastittes.bsky.social · 30/09/2026
Great opportunity! Chris is a rockstar.
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Silas Tittes @silastittes.bsky.social · 21/09/2026
Oh yay @xjorjorbinx.bsky.social is here now!
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Silas Tittes @silastittes.bsky.social · 21/09/2026
I’m excited for Jordan Rodriguez’s paper and software, This Must Be the Place and EcoLocator! She uses global prediction of location and climate of origin to identify loci with signatures of local adaptation. Also applies to Doug Fir data. Feedback welcome! www.biorxiv.org/content/10.6...
biorxiv.org
This must be the place: deep learning local adaptation
Climate change is increasingly disrupting the relationship between locally adapted populations and the environments in which they evolved, creating an urgent need for tools that connect genomic variat...
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Silas Tittes @silastittes.bsky.social · 19/09/2026
Dear airlines, Print numbers in the queue area that match the plane seating. Have people line up on those numbers that match their seats. Groups are window, middle, then aisle. You already have do two columns. If we can find our seats on the plane we can find our number of the lobby floor.
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Silas Tittes @silastittes.bsky.social · 19/09/2026
Andy will be very happy you caught the reference 😂
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Harmit Singh Malik @harmitmalik.bsky.social · 13/09/2026
But if you gain fulfillment from the doing & the teaching, from the achievements of others, including your competitors, from those that came before you, & those that will follow, you are somewhat insulated. Ultimately, this is a good moment to reflect on what brings YOU joy & act accordingly.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 26/08/2026
For folks interested I just posted my keynote on ARGs from #PEQG26 on youtube (with permission). Thanks again to @genetics-gsa.bsky.social and organizers for what was a wonderful conference (except for the 24hrs prior to my talk when I was too nervous to sleep or think straight) youtu.be/ntJOdZd0mwc
youtu.be
PEQG Keynote 2026
YouTube video by Jeffrey Ross-Ibarra
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Silas Tittes @silastittes.bsky.social · 25/08/2026
TL;DR —> TL;DW
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Norm Eisen @normeisen.bsky.social · 24/08/2026
Please don't overreact to Roberts Court decision on the contemplated USPS ballot moves They simply held that the injunction came too early in the process, before there was a final rule👇 Now we HAVE a final rule & we will litigate it. I'm as confident in our arguments here as in any of our cases!
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The New York Times @nytimes.com · 24/08/2026
Breaking News: The Supreme Court has allowed the Trump administration to proceed with plans to restrict mail-in voting. The decision clears, for now, an executive order that would create “citizenship lists” and directs the Postal Service to decide who gets a mail-in ballot. nyti.ms/3Ukqoti
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Silas Tittes @silastittes.bsky.social · 18/08/2026
I think they’ve decided Ossoff is a likely presidential nominee and are testing out smear tactics.
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Graham Coop @gcbias.bsky.social · 12/08/2026
Excited for @gabrielesgarlata.bsky.social’s new preprint on the Genome-Wide Effect of Drift and Selection over a Single Generation 1/n www.biorxiv.org/content/10.6...
biorxiv.org
The Genome-Wide Effect of Drift and Selection over a Single Generation
The relative importance of genetic drift versus selection to evolutionary change has long been debated. This debate has mainly focused over long-time-scales (e.g. hundreds of thousands of generations)...
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Mark Hibbins, Great Lakes Swashbuckler @rejectresubmit.bsky.social · 10/08/2026
I'm recruiting a PhD student to work on an NSF-funded project developing new models of trait evolution for phylogenetic comparative methods! Info about the lab here: mhibbins.github.io Applications to our grad program are due December 1. Please share!
mhibbins.github.io
Hibbins Lab
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Jonathan Pritchard @jkpritch.bsky.social · 09/08/2026
Must-know numbers in human genetics -- As many of you know, I'm writing a free online textbook in human genetics. In this blog post I cover a key skill for genome scientists from that book: how to use mental math to figure out key genome properties. jkpritchard.substack.com/p/on-fermi-p...
jkpritchard.substack.com
On Fermi Problems in Human Genetics
and some very useful numbers about human genomes to get you started!
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Rebekah Rogers @evolscientist.bsky.social · 04/08/2026
Officially recruiting postdocs at GW. If you are interested in genetic novelty, structural variation, or evo genetics please get in touch! We have data sets on mulitple organisms with large population sizes (Drosophila, Megalonaias nervosa) and species in decline (fireflies, mussels, elephants).
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Jeff Groh @jeffgroh.bsky.social · 28/07/2026
Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...
pnas.org
Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS
In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...
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Denny Carter @dennycarter.bsky.social · 30/06/2026
the egg price thing under biden was all fake lol
From mid-2022 to early 2025, the egg producers communicated with each other to coordinate bidding activity on a widely used pricing service, according to a complaint filed in a federal court in Iowa.
The complaint details instances of executives for the companies calling and texting each other in an effort to push prices higher.
Under the settlement, the state DOJ says the three companies must end their price coordination, adopt compliance measures and cooperate with
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Silas Tittes @silastittes.bsky.social · 08/07/2026
I would just like to be clear, I never shot this opening sentence down.
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Thomas Lenormand @thomaslenormand.bsky.social · 29/06/2026
🚨Interested in #evolutionary #genomics and #popgen #theory? My lab just opened a 1+ year #postdoc position to work on sex chromosome dosage compensation. At #CEFE Montpellier 👉 bit.ly/4eMWDIh Informal enquiries welcome to me🙂 or Paul Saunders and Sylvain Glémin at #SMBE2026 Thanks for sharing!
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Peter Andolfatto @pandolfatto.bsky.social · 16/06/2026
1/n Check out our new paper, spearheaded by @fborne.bsky.social, just out in PLoS Genetics doi.org/10.1371/jour....
doi.org
Epistasis among clustered lineage-specific amino acid substitutions in the Drosophila Trio protein
Author summary Proteins fold into three-dimensional structures that are essential for their function. Because these structures depend on interactions among amino acids, the fitness effect of a mutatio...
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Silas Tittes @silastittes.bsky.social · 17/06/2026
^relative ease. Everything is hard 😅
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Silas Tittes @silastittes.bsky.social · 17/06/2026
Just a friendly reminder that SLiM is awesome and lets you do cool things like this with ease. Check out this big collaborative paper (and repo) we wrote to learn more! onlinelibrary.wiley.com/doi/full/10.... github.com/kr-colab/spa...
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David Lowry @davidlowry.bsky.social · 10/06/2026
Looking forward to all of these Crow Early Career Research Award talks at #PEQG26 starting now.
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John Stinchcombe @johnstinchcombe.bsky.social · 07/06/2026
Why are leaves the shape that they are? What controls intraspecific, genetic variation in leaf shape? New from my lab, in collaboration with many others, led by PhD student Amanda Peake: mapping the leaf shape polymorphism in Ipomoea hederacea.
Homozygous recessive entire leaf of Ivyleaf morning gloryHomozygous dominant, lobed leaf of Ivyleaf morning glory
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Zamin Iqbal @zaminiqbal.bsky.social · 25/05/2026
This is awful to hear, describing how Sean Eddy (HMMER, infernal, pfam, rfam) has been defunded. The letter said his work "had been determined to be of absolutely no value to the US taxpayer, and therefore it was being specifically terminated," www.npr.org/2026/05/21/n...
npr.org
Researchers say the Trump administration is finding new ways to punish science
Even with federal grants largely restored, scientists say the Trump administration is still preventing those funds from reaching them. The consequences, they say, are already becoming clear.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 12/05/2026
Love this quote: "We used to make fun of Edgar Anderson by saying that he was finding hybrids under every bush. Then we realized that even the bushes were hybrids." academic.oup.com/jeb/article/...
academic.oup.com
Hybridization and speciation*
Abstract. Hybridization has many and varied impacts on the process of speciation. Hybridization may slow or reverse differentiation by allowing gene flow a
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Silas Tittes @silastittes.bsky.social · 07/05/2026
Widow’s Bay is great so far. Highly recommend if you wanna scratch a silly+spooky itch.
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Nandita Garud @nanditagarud.bsky.social · 06/05/2026
Our paper entitled "The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians" is now out in PNAS! www.pnas.org/doi/abs/10.1.... A really fun and informative collaboration with @mharris.bsky.social, Ziyi Mo and Adam Siepel. (1/n)
pnas.org
The persistence and loss of hard selective sweeps amid admixture in ancient Eurasians | PNAS
The extent to which human adaptations have persisted throughout history despite strong eroding demographic events such as admixture, genetic drift,...
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Silas Tittes @silastittes.bsky.social · 06/05/2026
One*
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Silas Tittes @silastittes.bsky.social · 06/05/2026
Awesome! Feel free to send us your thoughts!
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Silas Tittes @silastittes.bsky.social · 06/05/2026
On big picture take away from this work is that it’s a cool system for studying speciation! Lots of neat unknowns here, including better understanding the mechanisms of isolation.
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Silas Tittes @silastittes.bsky.social · 06/05/2026
Yeah it doesn’t seem like it so far!
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Silas Tittes @silastittes.bsky.social · 06/05/2026
All the cell motility enrichment is interesting. We’re not entirely sure what to make of it. Could be larval or sperm evolution? Unclear.
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Silas Tittes @silastittes.bsky.social · 06/05/2026
reduces* not modifies
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Silas Tittes @silastittes.bsky.social · 06/05/2026
There’s more, including some follow up on sex biased mutation rate, and lots of cool enrichment for eye and brain stuff in sweep regions, so check it out more thoroughly! Gabby and I will be at PEQG, where I’ll present on poster on this work, so come say hi and chat more with us then! 7/7
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Silas Tittes @silastittes.bsky.social · 06/05/2026
We also looked at selection more directly with MK test and sweep inference. Both show the same general trend, small pop species has less evidence for selection. 6/n
 Volcano plots of Neutrality Index and -log10 p value for each species. Each dot showing a MK test. Only *latus has significant genes. Genome wide alpha is 0.06 and 0.24 for *loides and *latus, respectively.Graph of related gene ontology terms colored by enrichment significance for MK test genes in *latus. The most terminal and significant term is “flagellated sperm motility”
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Silas Tittes @silastittes.bsky.social · 06/05/2026
Next we turned to patterns of linked selection, which required estimating recombination rate (relernn). We again see the hallmarks of different population size, with only bimaculatus showing a noisy increase in diversity with recombination, expected when selection modifies neutral variation. 5/n
Recombination rate vs diversity. Very flat for *loides, noisy but for *latus relationship increases and plateaus as has been shown for other species and in theory.
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Silas Tittes @silastittes.bsky.social · 06/05/2026
For further evidence of popsize differences and divergence we fit a n(t) style demography with smc++. Infers split times are more recent (2-4e5 gens). 4/n
Smc++ demographic histories for both species. bimaculoides is consistently lower than bimaculatus.
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Silas Tittes @silastittes.bsky.social · 06/05/2026
We see much higher diversity in bimaculatus, and a goodly bit of divergence (fst is weird because lower diversity in bimaculoides), but DXY suggests ~1e6 gens. Cool cause they look quite similar and were thought to be the same species for a long time. 3/n
Boxplots of nucleotide diversity, Tajima’s D, DXY, and FST across each chromosome for both species. Pi is much higher everywhere for bimaculatus.
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Silas Tittes @silastittes.bsky.social · 06/05/2026
Lots of studies on cephalopods, but not as much popgen, especially wrt selection. We studied sister species, O. bimaculoides and O. bimaculatus. They look similar but have some cool life history differences (egg number, larvae habitat, etc) 2/n
Species range of the sister species. baculatus wraps around sea of Cortez, bimaculoides is further north.
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Silas Tittes @silastittes.bsky.social · 06/05/2026
Our octopus population genetics preprint is up! This is Gabby Coffing’s final PhD chapter, and turned out pretty cool. Here’s a little explainer. 1/n
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Silas Tittes @silastittes.bsky.social · 04/05/2026
Hand drawn graph. X axis is love of peanut butter. Y is probability of finding peanut butter in home. Line curves sharply upward and plateaus and then sharply declines at higher a values of x, but does not drop back to zero.
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Silas Tittes @silastittes.bsky.social · 30/04/2026
His love of the game knows no bounds. His puns embrace rooted forms of the corny spirit.
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Silas Tittes @silastittes.bsky.social · 30/04/2026
Please follow the link below to join my petition to request he makes at least four puns in his acceptance speech.
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Silas Tittes @silastittes.bsky.social · 30/04/2026
So psyched for @jrossibarra.bsky.social! Truly a remarkable scientist and person and couldn’t be more deserving of the recognition. www.ucdavis.edu/news/nationa...
ucdavis.edu
National Academy of Sciences Elects UC Davis Maize Geneticist Jeffrey Ross-Ibarra
The National Academy of Sciences has elected Jeffrey Ross-Ibarra, professor in the Department of Evolution and Ecology at University of California, Davis, as a member. His election was announced April...
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Berna Devezer @devezer.bsky.social · 30/04/2026
📣 The difference between replicable and not replicable is not itself scientifically replicable. 📣 New work with Erkan Buzbas, showing that verdicts such as "X% of results replicated" are based on an inferential machinery that doesn't work. arxiv.org/abs/2604.26268
Screenshot of a paper's title page. Title: "The Difference Between 'Replicable' and 'Not replicable' is not Itself Scientifically Replicable". Authors: Berna Devezer and Erkan O. Buzbas, both at the University of Idaho — Devezer in the Department of Business and the Institute for Modeling Collaboration and Innovation, Buzbas in the Department of Mathematics and Statistical Science. Authors contributed equally. Corresponding author: bdevezer@uidaho.edu.
Abstract: Replication studies estimate the replicability rate of scientific results by aggregating binary verdicts of experiments. Exact replications are rarely attainable, so most replication sequences are non-exact. Experiments differ in ways that matter and do not share a single common data-generating process. We formalize two statistical interpretations of this non-exactness. In a shared latent rate model (benchmark), experiments are exchangeable and depend on a common random replicability rate. In a conditionally independent rates model (operational), each experiment has its own replicability rate drawn independently from a population distribution. Under the shared latent rate model, even small variability among replicability rates induces an irreducible variance floor on the estimated mean replicability rate that cannot be eliminated by adding more replications. Under the conditionally independent rates model, the degree of non-exactness is not identifiable from standard replication data, because one binary verdict per experiment contains no information about between-experiment heterogeneity. Researchers therefore cannot tell which precision regime they are operating in or whether high- and low-replicability sequences can be distinguished in principle. As a result, the usual data structure of one binary verdict per experiment cannot support reliable demarcation between "replicable" and "not replicable" results and systematically understates uncertainty, making high- and low-replicability sequences appear discrim…
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