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Silas Tittes

@silastittes.bsky.social
1.6K followers 1.1K following 269 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 · 30/09/2026
Great opportunity! Chris is a rockstar.
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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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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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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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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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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
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
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
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
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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Angel G. Rivera-Colón @arcolon14.bsky.social · 29/04/2026
The barnacles are on the loose! Check out my preprint with @stsmall.bsky.social, @johnwares.bsky.social, Erin Jezuit, and Andy Kern: The genome of the Pacific acorn barnacle provides insights into the evolution of extremely large populations doi.org/10.64898/202... 1/n
doi.org
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Dan Schrider @samurscicop.bsky.social · 28/04/2026
Please circulate: I will have a postdoc opening soon, ideally with a start date sometime this summer or fall. If you're interested in empirical population genetics, computational methods development, and/or evolutionary modeling via simulation, don't hesitate to reach out. For more info on the lab:
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Oded Rechavi @odedrechavi.bsky.social · 27/04/2026
Super awesome paper 👇Coalescence and translation: A language model for population genetics | PNAS www.pnas.org/doi/10.1073/...
pnas.org
Coalescence and translation: A language model for population genetics | PNAS
Probabilistic models such as the sequentially Markovian coalescent have long provided a powerful framework for population genetic inference, enabli...
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Merrilee Proffitt @merrileeiam.bsky.social · 21/04/2026
I'm excited to share that we've made a collection of historic Supreme Court Records and Briefs available via @archive.org I've written a blog post where I go into detail about the importance of this collection. blog.archive.org/2026/04/20/u...
blog.archive.org
U.S. Supreme Court Records and Briefs: The Arguments That Shaped America, Now Freely Available | Internet Archive Blogs
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Mark Hibbins, Great Lakes Swashbuckler @rejectresubmit.bsky.social · 17/04/2026
I'm hiring a postdoc (start date flexible) and a PhD student (for Fall 2027) to work in any area of computational phylogenetics! More info here: mhibbins.github.io I will be attending both PEQG and Evolution in June, so please reach out if you want to chat at these meetings!
mhibbins.github.io
Hibbins Lab
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Jennifer Raff @jenniferraff.bsky.social · 14/04/2026
I am so happy to share this new paper that I wrote with @cegamorim.bsky.social! We hope that it will help encourage dialogue and collaboration between archaeologists and geneticists trying to understand kinship in the past. www.cambridge.org/core/journal... 🧬🧪
cambridge.org
Scrutinizing Kinship and Biological Relatedness Through the Lens of Palaeogenomics | Cambridge Archaeological Journal | Cambridge Core
Scrutinizing Kinship and Biological Relatedness Through the Lens of Palaeogenomics - Volume 36 Issue 2
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Good Trailcams @goodtrailcams.bsky.social · 04/04/2026
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ACLU @aclu.org · 01/04/2026
Our immigrant loved ones were front of mind as we argued for babies born in the U.S. and everyone who loves them.
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Moi Expósito-Alonso (MOILAB) @mexpositoalonso.bsky.social · 26/03/2026
Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens! Read it in Science dx.doi.org/10.1126/scie... @ucberkeleyofficial.bsky.social @hhmi-science.bsky.social
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Silas Tittes @silastittes.bsky.social · 28/03/2026
Alright linguistics nerds, if we survive all this nonsense, and the bots keep improving, how does this change language evolution? More homogeneous or less? My intuition says it reduces pressure to conform, leading to more drifty and rapid changes at local scales. I’m probably very wrong though.
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Princess Vimentin PhD | Cancer Biologist @princess-vimentin.bsky.social · 28/03/2026
🧪This is important. Russel Vought fact check by @jenna-m-norton.bsky.social When a non-scientist says w/ certainty that NIH caused the Covid19 pandemic, it is a red flag & arrogance. His intention is to destroy science & implement Project 2025. Articles of impeachment have been drafted.
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Dr Thomas Clements @taphonomist.bsky.social · 27/03/2026
The beautiful preservstion of trilobite compound eyes will never cease to amaze me. On this little 400ish million year old Phacops you can see all the little lenses - each one a rigid calcite mineral crystal! Together they had excellent 360° vision, perfect for finding lunch on the seafloor.
A grey rock that has a beautiful fossil trilobite. The rock is rough, but the trilobite sections are smooth. One of the main features is a compound eye, made of of many lenses.
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Joshua B. Plotkin @jplotkin.bsky.social · 24/03/2026
How many teachers are enough? Zero? Hirotaka Goto and I analyze the optimal allocation of dedicated teachers in a population. @carlbergstrom.com www.pnas.org/doi/10.1073/...
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John Wares @johnwares.bsky.social · 19/03/2026
I’m happy to share github.com/jpwares/mole... it’s got a long way to go but I felt a need to change my approach a few years ago. It’s clunky AF. I enjoy shaping it and keep useful stuff like your shiny apps there to help folks learn more experientially.
github.com
GitHub - jpwares/molecoltext: molecular ecology - interactive textbook
molecular ecology - interactive textbook. Contribute to jpwares/molecoltext development by creating an account on GitHub.
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John Wares @johnwares.bsky.social · 19/03/2026
Been working off-and-on towards an .Rmd interactive textbook but haven't been able to work on for a while; need a Shiny tool in there that @silastittes.bsky.social wrote, and so I open it to 'cover image' - always struck by beauty of these #barnacles on rusty iron structures on the Florida coast.
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jamelle @jamellebouie.net · 17/03/2026
unbeatable cookbook www.ranchogordo.com/products/fag...
ranchogordo.com
Fagioli: The Bean Cuisine of Italy
This revised and expanded edition of Judith Barrett's seminal book on Italian bean cuisine honors every region of Italy with more than 120 inspiring recipes for modern home cooks. Barrett introduces u...
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Silas Tittes @silastittes.bsky.social · 17/03/2026
Thought I would share this famous analogy from Felsentein’s book I just re-stumbled on. Just in case you’re bug in a box and missed it 😜
Bugs in a box-an analogy
We can make a physical analogy (if a somewhat fanciful one) by considering a box containing hyperactive, indiscriminate, voracious, and insatiable bugs. We put k bugs into the box. They run about without paying any attention to where they are going. Occasionally two bugs collide. When they do, one instantly eats the other.
Being insatiable, it then resumes running as quickly as before. It is obvious what will happen. The number of bugs in the box gradually falls from k to k - 1, to k-2, as the bugs coalesce, until finally only one bug is left.
The analogy is actually fairly precise. The number of pairs of bugs that can collide is k(k - 1) /2. If there are 2N "places" in the box that can be occupied, the probability of a collision will be proportional to k(k - 1)/4N. The size of the population corresponds to the size of the box. A box with twice as many "places" will slow the coalescence process down by a factor of two. So a simpleminded physical analysis of the bugs-in-a-box process will have the Kingman coalescent distribution as the probability distribution of its outcomes.
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Silas Tittes @silastittes.bsky.social · 13/03/2026
The last stages of finishing and submitting papers is folding laundry.
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Silas Tittes @silastittes.bsky.social · 13/03/2026
Angel, Clara (@ramencult.bsky.social), and Andy put together a really nice program for computing the various flavors McDonald-Kreitman tests and related analyses. Give it a spin! www.biorxiv.org/content/10.6...
biorxiv.org
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 03/03/2026
Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!
github.com
GitHub - RILAB/argprep: Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files.
Snakemake pipeline for generating SINGER input files from whole genome alignment .maf files. - RILAB/argprep
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Max Kozlov @maxkozlov.bsky.social · 02/03/2026
It's a pretty funny criticism because 1) the data are sourced from a public database, NIH RePORTER 2) "Deranged activist" Jeremy Berg was an NIH institute director for 7 years and most importantly 3) Thacker admits the story is totally accurate
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Jeremy Berg @jeremymberg.bsky.social · 02/03/2026
Apparently Jason Locasale and Paul Thacker have a problem with using publicly available data from NIH Reporter about the number of new and competitive renewal grants from fiscal year 2026 compared to previous fiscal years because I first posted it. 1/2
A post from Jason Locasale quoting Paul Thacker complaining about a Nature story from Max Kozlov using data from NIH Reporter that I posted on my Bluesky account.
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Carl T. Bergstrom @carlbergstrom.com · 24/02/2026
1. Kevin Gross and I have a new paper out today PLOS Biology. We used economic models based around screening games and the market for unpaid labor to highlight a meltdown cycle threatening peer review.
journals.plos.org
Screening, sorting, and the feedback cycles that imperil peer review
The process of peer review is vital to contemporary science, but is also under enormous strain. This study uses mathematical models to dissect the threats to the long-term viability of peer review, su...
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