Xinjun Zhang

I am thrilled to share this paper outlining some ideas I’ve been thinking about for a little while on a simple but powerful approach for predicting risk of inbreeding depression from long runs of homozygosity and non-ROH heterozygosity. 1/n @klohmueller.bsky.social doi.org/10.1016/j.tr...

I am seeking a postdoc for my group at UCLA. We work at the intersection of population genetics x microbiome (garud.eeb.ucla.edu). If interested, please message me!

Evaluating the roles of drift and selection in trait loss along an elevational gradient The evolutionary mechanisms underlying loss or retention of traits that have lost function are poorly understood. Short stamens in Arabidopsis thaliana pro

Sophie Buysse's paper on short stamen loss in Arabipsis is published in this month's Evolution issue!! academic.oup.com/evolut/artic... @journal-evo.bsky.social

Having major FOMO about #SMBE2025 in my hometown… but I’m very proud that my postdoc, Susanna Gutierrez, will be presenting our work on inferring the selection history of adaptive introgression candidates in Peruvians at poster S12-P19. Please visit her during poster session 3 if you're interested!

First ever skull from ‘Denisovan’ reveals what ancient people looked like Ancient proteins and calcified dental plaque identify heavy-browed fossil from China as a Denisovan.

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

The preliminary program of ProbGen 2026, which will be held at UC Berkeley, is now up: probgen2026.github.io

Sharing on behalf of Rasmus Nielsen who is not on this site. For more see his thread on that other site: x.com/ras_nielsen/...

Amazing!! Congratulations!!!

Thank you!

Thanks Bernard!!

n/n This was my last postdoc project that finally got completed with tremendous help from my postdoc mentors Kirk and Sriram, two UMich biostats MS students (Jiongxuan Yang and Lingxuan Zhu), and many colleagues and friends in MI and CA (esp. Jazlyn Mooney). Can't thank them all enough!

6/n Overall, we show that recessive deleterious mutations not only exist on the human genome, but also are not uniformly distributed and are mostly found in regions regulating metabolism and immune functions (our detected regions include the HLA cluster)

5/n We further investigated the biology of such regions and show they are 1) depleted of haploinsufficient genes, 2) depleted of long ROHs, 3) enriched with UKBB variants with evidence of fitting non-additive model, 4) experienced weaker historical BGS, and 5) more tolerant to LOF mutations

4/n we applied DominL to 7 non-African pops in 1KG, and show that approx. 3-9% of the human genome is enriched with recessive deleterious mutation! This is important because dominance is very understudied in humans due to many constraints with methodology (eg. can't distinguish h from hs compound)

3/n our method DominL shows decent power and robustness at finding genomic regions enriched with recessive deleterious muts (or close to fully recessive such as h<0.1; even if the model is trained using two extreme h values) at 1MB resolution, with exceptional accuracy in exon-dense regions

2/n we developed an ML approach using Neanderthal ancestry as one of the key features and trained 13 ML classifiers with simulations using fully recessive vs fully additive deleterious mutations. After a rigorous performance comparison and feature selection, we picked a winner ML model

1/n This is a spin-off of some earlier papers showing that recessive deleterious muts can confound adaptive introgression due to heterosis. And we ask a reverse-engineering Q: given the empirical archaic ancestry distribution, can we infer if any genomic region is enriched with recessive mutations?

Neanderthal introgressed ancestry reveals human genomic regions enriched with recessive deleterious mutations Negative natural selection on deleterious mutations plays a key role in shaping human genetic variation. Understanding the dominance of deleterious mutations is critical as it can fundamentally impact...

Super excited to share my latest preprint with @klohmueller.bsky.social! Here we leverage the unique signature that recessive deleterious variants can lead to an increase in archaic ancestry to tackle a classic question - the dominance distribution on the human genome www.biorxiv.org/content/10.1...

Superb!!! Congratulations Fernando!!!!

Congratulations!! That's a fantastic department and they are lucky to have you!

Repost w/ correct link!
The Dept of Human Genetics at the Univeristy of Utah is hosting a Rising Stars in Genetics & Genomics postdoc symposium. We are looking to feature postdocs doing cool science! Please self nominate or nominate an excellent postdoc! #ASHGtrainees docs.google.com/forms/d/e/1F...

Kirk Lohmueller

DominL uses patterns of archaic ancestry to infer degree of dominance. Provides statistical support for the presence of recessive deleterious mutations in the human genome. Up to 15% of the human genome may carry recessive deleterious mutations! 🧬

#HumanEvo25

Characterizing selection on complex traits through conditional frequency spectra Abstract. Natural selection on complex traits is difficult to study in part due to the ascertainment inherent to genome-wide association studies (GWAS). Th

a quick note on my paper with @jeffspence.bsky.social and @jkpritch.bsky.social on conditional frequency spectra, now out in a @genetics-gsa.bsky.social special issue: doi.org/10.1093/genetics/iyae210

Excited to share: "Addressing missing context in regulatory variation across primate evolution"

arxiv.org/abs/2504.02081

Whole-genome sequencing analysis of anthropometric traits in 672,976 individuals reveals convergence between rare and common genetic associations Genetic association studies have mostly focussed on common variants from genotyping arrays or rare protein-coding variants from exome sequencing. Here, we used whole-genome sequence (WGS) data in 672,...

A really nice paper by @drghawkes.bsky.social et al. argues that rare and common genetic associations converge on the same genes.

While this seems at odds with our recent work about how burden tests and GWAS prioritize different genes, our results agree (🧬🧪🧵 1/6)

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

A geographic history of human genetic ancestry Describing the distribution of genetic variation across individuals is a fundamental goal of population genetics. We present a method that capitalizes on the rich genealogical information encoded in g...

Really excited to see this work, led by Mike Grundler, published! It's a new method for inferring the geographic locations of shared genetic ancestors. In the paper, we and use it to infer the geographic history of human genetic ancestry

www.science.org/doi/10.1126/...

A geographic history of human genetic ancestry Describing the distribution of genetic variation across individuals is a fundamental goal of population genetics. We present a method that capitalizes on the rich genealogical information encoded in g...

Grundler et al propose a new method to infer the geographic position of all our genetic ancestors www.science.org/doi/10.1126/...
building on a method by Wohns et al www.science.org/doi/10.1126/....

My thoughts on the approach: www.science.org/doi/epdf/10.....

Congratulations Vince!!

Think of a polygenic score you care about. Are direct genetic effects driving variation among people in this predictor? Or perhaps other, confounding factors? We at the @arbelharpak.bsky.social & @docedge.bsky.social Labs developed a method to tackle this question. [1/n]

Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history Abstract. Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their

We are thrilled to share that our paper entitled "Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history" is officially out in MBE! academic.oup.com/mbe/advance-...

Thrilled to have been a part of this study led by @aidaandres.bsky.social that finds evidence of genetic adaptation in chimpanzees to different habitats. Most notably signatures of positive selection in chimpanzees underlie resistance to malaria in humans (GYPA and HBB).