Matthew Williams

This is a great read - it nails a whole bunch of ways in which LLMs simply don’t ‘think’, let alone at a ‘PhD level’.

The genetic history of the Southern Caucasus from the Bronze Age to the Early Middle Ages: 5,000 years of genetic continuity despite high mobility Ancient DNA from the Southern Caucasus reveals remarkable genetic continuity, with some mixing from Anatolia/Iran and the Eurasian Steppe, and shows that even periods of urbanization and increased mob...

Our aDNA time transect centered on modern Georgia is out! 🧬

Genetic continuity over 5000 years, but some Bronze Age gene flow and urban outliers since Antiquity - including some with artificially deformed skulls 💀 linked by IBD segments to Asian nomads.

#aDNA #PopGen

www.cell.com/cell/fulltex...

But perhaps most critically, it’s (imo) irresponsible to attribute this to *science* as a whole; suggesting it’s a monolith when things like the image duplication retractions are pretty limited to a unique corner of science under sleuth spotlights.

Logo for the Genomic History Inference Strategies Tournament.

If you're new to demographic history inference from population genomics, try this webapp I created to illustrate how dadi fits bottleneck models to site frequency spectra: ryangutenkunst-dadi-two-epoch.hf.space . It even outputs files for submitting to the GHIST competition! ghi.st

🧬🏺Calling everyone interested in the intersection of archaeological theory and ancient DNA!

Thrilled to be co-organizing a session for #TRAC2025 with @ezgimou.bsky.social

The virtual conference will be held October 22 - 24 and the call for abstracts is now open. Come join us!

Upcoming Conferences TRAC 2025 The 33rd Theoretical Roman Archaeology ConferenceWe are pleased to announce that TRAC 2025 conference will be held between 22nd and 24th October 2025 in an online format through the Gathe…

TRAC 2025 will be held from 22nd to 24th October 2025 in an online format via the Gather Town platform. Here is the link for further info: www.trac.org.uk/upcoming-con...

🧪 🏺
Excited to co-organize a session with @mootspoints.bsky.social at #TRAC2025!
🧬 Integrating Ancient DNA with Archaeological Theory and Practice
We welcome papers on mobility, migration, & identity in the Roman world and beyond.
📢 Call for abstracts now open! Please spread the word.
#aDNA #science

Postdoctoral Fellow - P Skoglund Lab Salary for this Role: Salary: From £45,500 per annum with benefits, subject to skills and experience. Job Title: Postdoctoral Fellow - P Skoglund Lab Reports to: Pontus Skoglund Closing Date: 20/Aug/2...

New postdoc opening in our lab: crick.wd3.myworkdayjobs.com/External/job... Don't hesitate to send in your details or contact me if interested!

Check out our paper in Evolution Letters!

We used D. melanogaster pigmentation as a focal trait to explore parallelism in phenotypic and genomic responses to environmental change - read more at the link below 👇

Figure showing the experimental overview as a graphic. Remaining alt text taken from the figure caption in the paper: (A) we sampled flies from six wild orchard populations ranging from Homestead, FL, to Lancaster, MA, and established isofemale lines in the laboratory. (B) We returned to a focal orchard in Media, PA, at early- and late-season timepoints and collected flies to capture evolutionary patterns following winter and summer conditions. (C) We then seeded outdoor mesocosms (N = 9) with an outbred population originating from early-season collections in Media, PA, and sampled flies at the end of summer (mid-season) and fall (late-season) to determine if seasonal patterns are recapitulated in experimental populations controlled for migration, drift, and cryptic population structure. (D) Across each wild or experimental context, we sampled flies, established lines in the lab, completed common garden treatment to remove environmental effects, and scored females for abdominal pigmentation. We also conducted pooled DNA sequencing on additional flies sampled from each population to map genomic patterns for candidate pigmentation SNPs.

How predictably does complex trait adaptation proceed over space and time in wild populations?
doi.org/10.1093/evle...

Now in @evolletters.bsky.social by @skylerberardi.bsky.social, @paulrschmidt.bsky.social et al.

📷: Dr. Rush Dhillon

A new perspective on the arrival of the Eastern Mediterranean genetic influx in Central Italy before the onset of the Roman Empire Abstract. Italian genetic history was profoundly shaped by the Romans. While the Iron Age Central Italian gene pool was comparable to that of other coeval

🚨 New paper out in Genome Biology and Evolution!
We present new ancient DNA evidence from Central Italy suggesting that Eastern Mediterranean genetic influence predates the Roman Empire.
@beniamino77.bsky.social @fravasini.bsky.social

🧵👇
🔗 doi.org/10.1093/gbe/...

1/

Archaic ancestry inference in imputed ancient human genomes When modern humans expanded from Africa into Eurasia, they interbred with archaic hominins such as Neanderthals and Denisovans. This groundbreaking discovery, made in part possible through the genomic...

Turns out imputation of introgressed archaic regions in aDNA works really well — sometimes even better than for the rest of the genome. More on this (and other cool results) in our new preprint 👇 #aDNA #ArchaicIntrogression #imputation
doi.org/10.1101/2025...

The 2026 Probabilistic Modeling in Genomics (ProbGen) meeting will be held at UC Berkeley, March 25-28, 2026. We have an amazing list of keynote speakers and session chairs:
probgen2026.github.io

Please help spread the news.

We are a computational lab focusing on developing machine learning algorithms for biological data. Currently we are working on inference tasks related to natural selection and demographic inference, as well as generative models for genomic data from humans, mosquitos, and other species.

The Mathieson Lab at the University of Pennsylvania is hiring a computational postdoc in machine learning and evolutionary biology. Apply with a CV and references: smathi@sas.upenn.edu. More info: https://saramathieson.github.io/lab #postdoc

Come check out my poster this afternoon! On the language we use to talk mobility in ancient DNA studies #SMBE2025

Hence, this highlights the fundamental difference btw genomic and family h2. The former is considering millions of years of mutation while the latter is looking at everything but mutations over a very short period of time.

I can now finally speak out loud my honest thoughts on missing heritability or the genomics/family gap in h2 estimates.
Based on new paper the *issue* is a feature and not a bug.

TLDR: SNP h2 only captures mutational variance and family h2 captures everything but mutation.
1/n

New preprint comparing aDNA preservation and recovery rates during extraction from all three ossicles and the petrous. Congrats @compevohumang.bsky.social!

Join us at the Royal Society in London 14 November for a day on Ancient genomes, human biology and medicine!

Many slots are reserved for talks from submitted abstracts related to the topic, alongside speakers Svante Pääbo, Priya Moorjani, @mathiesoniain.bsky.social and Lluis Quintana-Murci.

Nifty preprint led by @mathiesoniain.bsky.social comparing femur length as a proxy of stature to genetic variants linked to height today. Many key insights, but main one for me is that variants responsible for lactase persistence are strongly associated with height in ancient but not modern people.

My talk from this year's probgen is finally out.

Where do linear mixed models and random effects come from?

They emerge from *mutations* on Ancestral Recombination Graphs.

Two useful new reviews on ancestry inference in population genetics:

onlinelibrary.wiley.com/doi/10.1111/...
genomebiology.biomedcentral.com/articles/10....

A difficulty in scrutinising ancient DNA from the outside is that the original methods are discussed in arcane terms in separate papers cast across the innumerable winds of scientific publishing. Here are 2 papers which attempt to discuss collections of common methods with plainer language.

It started with a meeting between @mp-williams.bsky.social) and Robbi Davidson during the last @isbarchaeology.bsky.social conference (Tartu, 2023). I remember them sitting at the bar after lunch, engrossed in their discussion—that moment was even captured by the event photographer 🧵1/n

Get excited for ISBA11! The conference program is now online!
www.isba11.com/programme

#ISBA11 #biomoleculararchaeology #Archaeology #Archaeology #archaeologist
@isbarchaeology.bsky.social @archaeobiomics.bsky.social

👇 Make sure to register for our webinar happening next week!

Professur für Archäologie des antiken Mittelmeerraumes und seiner Umwelt (W2)

Open position at @unileipzig.bsky.social for professor of archaeology of the antique Mediterranean! www.uni-leipzig.de/stellenaussc...

I have an opportunity to hire a staff scientist for my lab. Looking for someone with outstanding skillset in ML/statistics, genomics applications; interest in mentoring, strong publication record, PD experience required.

Email CV to me+cc my assistant (see 'contact' on my website). Ad to follow.

🥳 We're back with a new edition of our HAAM-radio webinar series! Come and be part of the development from a reporting scheme for aDNA samples & seqdata!
#aDNA #workshop #humanDNA #sequencing

I have implemented VCF reading and writing support in pileupCaller and Poseidon https://www.stephanschiffels.de/posts/2025-05-14-vcf_post.html #adna #data