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...

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)...

biorxiv.org

I saw this while playing with eGRM and thought my program had a bug. Turns out to be a feature rather than a bug, and the paper gives clear reasons behind the phenomenon. Lovely work.

Yun Deng@yundeng.bsky.social · 2d ago

In a model with sequential population split, a previous site-based statistics, eGRM, still shows population differentiation in ancestral populations. In contrast, the coalescent-based statistics faithfully capture the different clustering patterns over time. 8/n

The first manuscript from my postdoc is out (doi.org/10.64898/202...)! We introduce 𝐭𝐢𝐦𝐞-𝐬𝐭𝐫𝐚𝐭𝐢𝐟𝐢𝐞𝐝 𝐬𝐭𝐚𝐭𝐢𝐬𝐭𝐢𝐜𝐬 for studying population structure change over time, with the temporal resolution of Ancestral Recombination Graphs (ARGs). Joint with @jkpritch.bsky.social and @jeffspence.github.io. 1/n

Coalescent-Based Time-Stratified Statistics Reveal Population Structure Dynamics using the Ancestral Recombination Graph

Many questions in population genetics are concerned with reconstructing evolutionary history through time, such as inferring how population structure has changed throughout the past. Yet, many existing approaches have only an implicit temporal component, using quantities such as allele frequency or haplotype length as rough proxies for age. Recent advances in the inference of Ancestral Recombination Graphs (ARGs) have made it possible to estimate the entire sequence of local genealogies along the genome. These genealogies explicitly encode how samples are related to each other at different time points in the past, enabling the inference of how population structure has changed over time. To this end, recent work has used ARGs to define time-stratified versions of widely-used population genetics summary statistics in an attempt to capture the population structure present within a particular time window. Here, we show that naive approaches result in statistics that cannot be interpreted solely in terms of the population structure present within the time window they are targeting. To address this problem, we introduce a framework of coalescent-based time-stratified statistics, which use coalescence probabilities to partition classical summary statistics into interval-specific contributions. Using coalescent simulations, we demonstrate that these statistics accurately isolate population structure at different temporal depths and avoid spurious signals. Our results highlight the necessity of integrating coalescent theory into ARG-based temporal analyses and provide a principled and practical foundation for studying the dynamics of population structure through time. ### Competing Interest Statement The authors have declared no competing interest. National Human Genome Research Institute, https://ror.org/00baak391, R01HG014005

google.com

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...

On Fermi Problems in Human Genetics

and some very useful numbers about human genomes to get you started!

jkpritchard.substack.com

Highly recommend this, and it's a key element in most physics training. I'd add another trick that many biologists could benefit from, a small thing that makes a big difference: always use units. If you're unsure about the units of your number, chances are you don't properly understand it.

Jonathan Pritchard@jkpritch.bsky.social · last wk.

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...

www.biorxiv.org/content/10.6... ♡

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)...

biorxiv.org

New preprint: "A mathematical synthesis of genetics, development, and evolution". This work addresses the longstanding challenge of integrating these and finds a way. I think it has broad implications and offers exciting opportunities. Feedback welcome! www.biorxiv.org/content/10.6...

In advanced economies, only a small share of people work in agriculture.

Group Leader in Fundamental Biology of Legumes // John Innes Centre, Norwich www.jobs.ac.uk/job/DSG151/g... The John Innes Centre is seeking a junior or established researcher to lead a research programme in fundamental plant biology relevant to legumes or other rotation crops. #BotanyJobs

Group Leader in Fundamental Biology of Legumes at John Innes Centre, Norwich

An opportunity for an academic position as a Group Leader in Fundamental Biology of Legumes is available, as advertised on jobs.ac.uk. Apply now and explore other academic job openings.

jobs.ac.uk

How should we apply linear mixed models to populations under stabilizing selection? The first paper I wrote with my grad school advisor is published in Genetics. academic.oup.com/genetics/adv... 1/n

academic.oup.com/genetics/art...

Estimating recombination using only the allele frequency spectrum

Abstract. Standard methods for estimating the population recombination parameter, ρ, are dependent on sampling individual genotypes and calculating various

academic.oup.com

Martin Zuidhof: "You're familiar with this image ..." Yes, the most famous chicken image. www.sciencedirect.com/science/arti...

Genoio has a v0.2.0 release. Performance is better across the board, beating most other libraries or matching highly performance ones (but with a single interface in Python now). Check it out mancusolab.github.io/genoio/

In #GENETICS, @epigenci.bsky.social et al. present a collection of methods and #opensource software that use the ancestral recombination graphs (ARG) to efficiently fit linear mixed model to population phenotype data, for variance component estimation and genetic prediction. 🔗 buff.ly/9svg643

Ok, bc I don't know how to relax while on vacation, I put together a Python package for reading VCF/BCF, PLINK1/2, and BGEN genotype data into NumPy or SciPy sparse matrices. It’s Rust-backed for fast reads, with block/region iteration and composable variant filters. mancusolab.github.io/genoio

www.biorxiv.org/content/10.6...

This year’s Genomic History Inference Strategies Tournament includes challenges in inferring relatedness. ghist.bio. If you haven’t worked in this problem before, here’s a great resource to help you get started.

Laura Bertola@lauradbertola.bsky.social · 2mo ago

Genetic Estimates of Relatedness: Established Practices and New Opportunities Through Low Coverage Whole-Genome Sequencing onlinelibrary.wiley.com/doi/10.1111/...

postdoc alert 🚨! NIH-funded postdoc in my lab to work on Ancestral Recombination Graphs in space. Please spread the word widely in your networks, and please reach out if you're interested! (2-3yr position, start date flexible, pay/benefits good!). details here: careers.umich.edu/job_detail/2...

recruitment

Multiple positions available: ​ Postdoc PhD students

genescape.org

Bai et al. find that structural variants explain "at least 4.7% of the common genetic variation for complex traits", meaning about 1% of trait variance (on average across many traits). www.nature.com/articles/s41...

Genome-wide associations of structural variants with human traits through imputation from long-read assemblies - Nature Genetics

This study identifies structural variants (SVs) from long-read assemblies, develops a new reference panel and web application to impute SVs from single-nucleotide polymorphism-level data, and identifi...

nature.com

so called molecular heritability isn't even narrow sense heritability but in fact narrower narrow sense heritability as it's at most capturing genic variance and not additive variance.

Is there a software widely used that runs whatever stochastic process (OU, BM etc etc) on a tree?

Super excited to see this out! Fantastic collaboration with Luke O'Connor and trainees Amber Shen and Xinran Wang. Thread with details will come soon, but linear ARG provide a HIGHLY efficient representation of genotype data that can be treated as a linear operator www.biorxiv.org/content/10.6...

Highly efficient genotype compression leveraging genealogical relatedness https://www.biorxiv.org/content/10.64898/2026.04.29.721594v1

Something I increasingly recognize working on LD is that correlation betweem two loci at single time section, which is an accumulation of many steps prior to it is very different from a single step correlation which is truely due to linkage.

Please share! The USC Department of Quantitative and Computational Biology is searching for a full-time, teaching-track faculty member for the teaching of QBIO undergraduate statistics and computational biology courses. usccareers.usc.edu/job/los-ange...

This technology needs a health warning, like cigarettes: overuse of AI accelerates cognitive decline. www.bbc.com/future/artic...

AI chatbots could be making you stupider

As large language models take over more and more cognitive tasks, researchers are warning this mental outsourcing comes with a cost.

bbc.com

How to choose a "good tester" in testcrosses? 🎯🌾 ✓ Accuracy jumps most from 1 to 2 testers, though "noise" depends on dominance and pool structure. Next: Pareto framework to pick testers balancing GCA and complementarity! 🚀 Thanks to Daniel Tolhurst, @gregorgorjanc.bsky.social , Sven Weber and BASF!

Happy to share a new preprint, where we studied the expected outcomes of polygenic embryo screening in real-world IVF patients. Key conclusion: gains are very small for most infertility patients, with risk reductions under 5%. 🧵1/12 www.medrxiv.org/content/10.6...

academic.oup.com/genetics/adv... Good to see papers all presented in 2025 probgen appearing in one of the greatest venues.

Efficient Bayesian Phylogenetics under the Infinite Sites Model

Abstract. Bayesian inference of gene genealogies and evolutionary parameters from molecular sequences can provide key insights into the evolutionary histor

academic.oup.com

Why are Dutch people so tall? This has been a long-standing debate in genetics, with earlier studies questioned due to unaccounted for confounding. Great to be involved in a new study (link below) using within-family GWAS; we confirm that height has been under positive selection.