Yun Deng

This derives from our SMBE 2025 symposium: “Gene Trees and Beyond: Genealogical Methods and Their Applications in Evolutionary Genetics”.

Tree Thinking in the Genomic Era: Unifying Models Across Cells, Populations, and Species The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and ...

With @szhan.bsky.social, @yulinzhang.bsky.social, Chao Zhang and Bingjie Chen, we wrote a Perspective about unifying the tree-based method across phylogenetics, population genetics and cell biology: arxiv.org/abs/2512.05499.

Reposts are greatly appreciated!

BAPG 2025 was a blast. Looking forward to seeing folks in Davis in Spring 2026! bapg2025.github.io/bapg2025stan...

Homo sapiens-specific evolution unveiled by ancient southern African genomes - Nature The genomes of 28 ancient southern African individuals dated to between 10,200 and 150 years before present offer insights into the evolution of Homo sapiens.

Our new ancient DNA paper has just been published!
We present 28 new genomes from southern Africa - several of them high-coverage whole genomes.
Exciting to be moving towards population-level representation of ancient southern African genetic diversity!

www.nature.com/articles/s41...

Observational epidemiological studies can mitigate genetic confounding with the genetic relatedness matrix Observational studies are commonly used in psychology and epidemiology to identify risk factors correlated with health outcomes. However, these studies are vulnerable to confounding when shared geneti...

Excited to share work from my postdoc with @docedge.bsky.social and collaborators Matt Pennell and @jgschraiber.bsky.social, newly out over the weekend: www.biorxiv.org/content/10.1... (1/6)

Genetic prediction with ARG-powered linear algebra Ancestral recombination graphs (ARGs) are an attractive means for quantitative genetic analysis of complex traits because they encode the realized genetic relatedness between a sample of individuals i...

www.biorxiv.org/content/10.1...

We finally submitted the earlier preprint to a journal after massive restructuring.
We've expanded the REML section for those interested in the method. We clarify that ARG-LMM estimates mutational variance and not additive variance.

Dissecting pleiotropy to gain mechanistic insights into human disease Nature Reviews Genetics - Genome-wide association studies of increasing scale have revealed the prevalence of pleiotropic genetic variants that affect multiple traits. In this Review, the authors...

Interested in pleiotropy dissection but not sure where to start, which methods are useful, which studies offer illustrative examples, or how to robustly validate your results? Look no further 👀 rdcu.be/eSfAZ

Biophysical constraints on mRNA decay rates shape macroevolutionary divergence in steady-state abundances Evolutionary changes to gene expression are understood to be a major driver of phenotypic divergence between species. Researchers have investigated the drivers of this divergence by fitting evolutiona...

We've got a really cool preprint out in collaboration with @lpachter.bsky.social's awesome student Cat Felce. Using biophysical models and RNA-seq data, we explore the mechanisms of selective constraint on mRNA abundance, finding constraint on decay rate www.biorxiv.org/content/10.1...

Work from my amazing undergrad @leyan-wang.bsky.social is just preprinted! TL;DR: If you worry that ARG methods might fail on unphased data due to phasing errors, you may not need to.

Check it out & consider reposting to support a great young scientist!

Complex patterns of local adaptation in teosinte Populations of widely distributed species often encounter and adapt to specific environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requi...

Hitting refresh on biorxiv for a paper to appear... realized my first biorxiv preprint was more than 12 years ago, and on arXiv two years before that! Preprinting sure seemed strange at the time, but it's become my favorite part of the process!
www.biorxiv.org/content/10.1...
arxiv.org/abs/1208.0634

GitHub - YunDeng98/POLEGON: Prior-Oblivious Length Estimation in Genealogies with Oriented Network Prior-Oblivious Length Estimation in Genealogies with Oriented Network - YunDeng98/POLEGON

The tool is available at github.com/YunDeng98/PO.... It should be usable generally for tskit formatted ARGs. Let me know if you have any questions! (n/n)

POLEGON can also accommodate mutation rate variation along the genome by taking a mutation map. We used a mutation rate estimation from Roulette and re-estimated the pairwise TMRCA in the HLA region. The trans-species polymorphism signal is stronger than what SINGER reports (C). (10/n)

With the help from @wsdewitt.github.io, we also improved the mutation rate estimation, by not assuming uniform placement of mutations on branches, which is incorrect when mutation rate changes over time. We implemented a new algorithm with better accuracy (A, B). (9/n)

It also led to good performance of population size history estimation of the CEU and YRI model in simulation benchmarks (A, B). Also when applied to the 1000 Genomes Project, it has led to similar results to other popular methods (C, D). (8/n)

We name our method POLEGON, and it is shown to improve the performance of SINGER on ARG inference accuracy in a few commonly used statistics: pairwise TMRCA, its distribution, local diversity, and local mutation density. (7/n)

The strategy of combining flat prior and ARG rescaling is shown to be adaptive to different demographic models, such as constant-size, CEU model (featuring OOA bottleneck), and YRI model (mainly expansion), when provided with simulated ARGs (C). (6/n)

Normally a coalescent prior is needed as the mutation data is sparse. Yet we figure out that we can perform MCMC only using the flat prior, and use ARG rescaling (introduced by SINGER) as an adjustment (A). This greatly simplifies the math. (5/n)

Goal here: tune the node ages such that branch lengths best match the number of mutations on them. We perturb the age of each node while fixing the others (C), to perform MCMC using a node-wise likelihood. The perturbation must not violate any parent-child ordering (D). (4/n)

The ARG can be viewed as a sequence of marginal trees (A). By merging the same node across trees (which must have the same age) we now have a Directed Acyclic Graph with mutations mapped to edges connecting these nodes (B). (3/n)

This project is joint with @wsdewitt.github.io , @yun-s-song.bsky.social and Rasmus Nielsen. (2/n)

The last work of my PhD is finally out: www.pnas.org/doi/10.1073/...! This work is about accurately estimating branch length in the Ancestral Recombination Graph (ARG), which is achieved by a really simple framework with minimal assumptions. (1/n)

In an earlier project simulating quantitative traits/stabilizing selection in a human-Neanderthal model, I became a bit curious about some observed fitness dynamics that I wasn’t expecting.

I’m not sure if this is all that interesting or relevant, but at least it’s short.

Looks super fun. Already applied!

How do genetic association studies rank genes? Genome-wide association studies and rare-variant burden tests reveal complementary aspects of trait biology.

@hakha.bsky.social and I wrote a Research Briefing (with a lay summary + "behind the scenes") of our paper on how genes are prioritized by GWAS and rare variant burden tests. 🧬🧪

www.nature.com/articles/d41...

SAVE THE DATE: the yearly NY Population Genetics meeting will be back on March 9 2026, generously hosted by the
@simonsfoundation.org. Details to follow. Please RT.

Insertion of an invading retrovirus regulates a novel color trait in swordtail fish For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...

I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A

Super excited that the bulk of my PhD work is now preprinted! Here we used whole-community competition, or coalescence, experiments to quantify selection acting on genetically diverged strains within larger communities. (1/n)
www.biorxiv.org/content/10.1...

An empirical approach to evaluating the prevalence of long-lived balancing selection in humans--and important limitations. Work by @hannahmm.bsky.social

Specificity, length and luck drive gene rankings in association studies - Nature Genetic association tests prioritize candidate genes based on different criteria.

How do GWAS and rare variant burden tests rank gene signals?

In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck!

🧬🧪🧵

www.nature.com/articles/s41...

Revisiting the Evolution of Lactase Persistence: Insights from South Asian Genomes Lactase persistence (LP), the ability to digest lactose from milk into adulthood, is a classic example of natural selection in humans. Multiple mutations upstream of the LCT gene are associated with L...

Exciting new study led by @ekerdoncuff.bsky.social and @meaghanmarohn.bsky.social on the evolution of Lactase Persistence in South Asia.
www.biorxiv.org/content/10.1...