Dang Liu
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dangliu.bsky.social
Dang Liu
@dangliu.bsky.social
Postdoc @ Universität Zürich | genomics & genetics | human evolutionary & adaptive history | dangliu.github.io
Reposted by Dang Liu
The preprint from my first postdoc is finally out! I had a blast working on this project with such an amazing team!
New pre-print out! 🎉 With @mathilde-andre.bsky.social + team we traced spatio-temporal shifts in genetically regulated #transcription across 10,000 years of Western Eurasia, fine-mapping regulatory features targeted by #selection! 👉 doi.org/10.1101/2025... ! #popgen #genomics
doi.org
November 23, 2025 at 9:21 AM
Reposted by Dang Liu
Origins of language, one of humanity’s most distinctive traits, may be best explained as a unique convergence of multiple capacities each with its own evolutionary history, involving intertwined roles of biology & culture. This framing can expand research horizons. A 🧵 on our @science.org paper.🧪1/n
What enables human language? A biocultural framework
Explaining the origins of language is a key challenge in understanding ourselves as a species. We present an empirical framework that draws on synergies across fields to facilitate robust studies of l...
www.science.org
November 23, 2025 at 11:54 AM
Reposted by Dang Liu
The 2026 EMBL symposium 'Reconstructing the human past using ancient and modern genomics' is live with a fantastic invited speaker lineup!

Abstract deadline 9 June. If work is ongoing, plan for Heidelberg in September😉.

Organised by Maanasa Raghavan, @matejahajdi.bsky.social, Choongwon Jeong & me.
November 19, 2025 at 1:41 PM
Reposted by Dang Liu
If you're interested in how advances in human genomics are transforming our understanding of the biology of spoken & written language abilities, please do check out my new peer-reviewed "tutorial" article, just published.
🗣️🧬🧪
[Will also make a Bsky explainer 🧵 on it next week when I get some time🙂.]
Genomic Investigations of Spoken and Written Language Abilities: A Guide to Advances in Approaches, Technologies, and Discovery
Purpose: The aim of this tutorial is to show how the rise of molecular technologies and analytical methods in human genetics yields exciting new ...
pubs.asha.org
October 30, 2025 at 3:49 PM
Reposted by Dang Liu
Séminaire sur les apports récents de la génomique à l'histoire évolutive humaine au cours des derniers dix millénaires
Etienne Patin - L'histoire d'Homo sapiens à la lumière de la génomique
YouTube video by Institut Pasteur EDUCATION
www.youtube.com
October 22, 2025 at 9:20 AM
Reposted by Dang Liu
The most surprising insight is that the Jomon, early inhabitants of the Japanese Archipelago, have much less Denisovan ancestry than all other East Asians - thus the Jomon (partially) descend from a lineage that predates the gene flow between modern-humans and Denisovans
October 20, 2025 at 6:14 PM
Reposted by Dang Liu
🎉The 1st paper in our special issue "Population Genomics Methods and Software" is now published!!

“SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution”
www.pivotscipub.com/hpgg/5/4/000...

Many more exciting papers to come - stay tuned!
www.pivotscipub.com/hpgg/special...
SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution
SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution
www.pivotscipub.com
October 16, 2025 at 7:05 AM
Reposted by Dang Liu
FLARE2: local ancestry inference with poorly-matched reference panels https://www.biorxiv.org/content/10.1101/2025.10.13.681993v1
October 14, 2025 at 5:34 PM
Reposted by Dang Liu
Selection scans and downstream analysis with selscan https://www.biorxiv.org/content/10.1101/2025.10.10.681670v1
October 13, 2025 at 5:32 AM
Reposted by Dang Liu
Method works from simple and complex scenarios in jointly estimating epoch time, population size, migration rate (symmetric or asymmetric), growth rate, and admixture proportion. Software integrated with msprime, demes, tsinfer/tsdate, relate, and singer. github.com/aprilweilab/...
October 8, 2025 at 2:48 PM
Reposted by Dang Liu
Inference of complex demographic history using composite likelihood based on whole-genome genealogies https://www.biorxiv.org/content/10.1101/2025.10.07.680347v1
October 8, 2025 at 1:33 AM
Reposted by Dang Liu
We have a few remaining seats left in the “Programming for Evolutionary Biologists” course - 10th edition, Berlin, Feb 17 to Mar 6
evop.bioinf.uni-leipzig.de

A highly motivated and experienced team is waiting for you with an updated curriculum!
Programming for Evolutionary Biology School (EVOP) | February 18th – March 5th 2026
evop.bioinf.uni-leipzig.de
October 7, 2025 at 9:55 AM
Reposted by Dang Liu
What's that? The story of East Asian pig domestication as told through ancient DNA? Yes please! Congrats to everyone on such a fantastic and overdue story! Pigs are so great.
doi.org/10.1093/molb...
Ancient Genomics Reveals the Origin, Dispersal, and Human Management of East Asian Domestic Pigs
Abstract. Pigs are the most commercially important modern livestock animal in East Asia. Numerous aspects of their domestication history remain unclear, ho
doi.org
September 26, 2025 at 11:30 AM
Reposted by Dang Liu
Parental haplotypes reconstruction in up to 440,209 individuals reveals recent assortative mating dynamics https://www.biorxiv.org/content/10.1101/2025.09.24.678243v1
September 26, 2025 at 4:32 PM
Reposted by Dang Liu
Alba Bossoms Mesa: ‘From rock art to cave walls: exploring new sources of ancient human DNA’
Can we get aDNA from cave art 😍??
Test: 11 sites from Iberia (300 libraries!)
5 cases w HUMAN mtDNA !!!
Nuclear DNA ongoing: but suggestion of male/female diffs on use of pigments; + pop ID (WHG)
September 25, 2025 at 7:56 AM
Reposted by Dang Liu
📣New paper alert

doi.org/10.1007/s109...

How did populations in tropical regions cope with the global climatic change around the LGM?

While the tropics are often perceived as having been less impacted by the LGM, we show that -as is often the case - it is more complex than it seems!
The Last Glacial Maximum in the Tropics: Human Responses to Global Change, 30–10 ka - Journal of World Prehistory
The world at 18,000 BP, published by Gamble and Soffer (The world at 18,000 BP. Vol. 2: low latitude, Unwin Hyman, 1990), represents the first, and so far the only, attempt at characterising and discussing the impact of the Last Glacial Maximum (LGM) on human societies on a global scale. At the time, they highlighted that research and data on the LGM in southern latitudes and the tropics in particular were scant. Since 1990, however, many sites dated to the LGM and located in tropical latitudes have been published. Many paradigms have changed regarding the peopling of the Americas, which allows the archaeology of this continent to be integrated into global scale studies of the LGM. The development of Pleistocene archaeology in tropical contexts, in parallel with methodological advances in cultural, geosciences and palaeoenvironmental studies have strongly reshaped what we know of the antiquity of human occupation in tropical regions and specific human–environment interactions. This article provides for the first time a pan-tropical perspective on the impact of the LGM on human groups living within the tropical latitudes, drawing from case studies in Southeast Asia, Africa and South America, specifically regions which have up until now never been discussed together. To this end, we focus on six different tropical regions between 30 and 10 ka. We present the archaeological and paleoenvironmental data available in these areas, along with proposed relationships for variations in these two records. Finally, we discuss at the regional scale the presence or absence of human changes (site density and techno-cultural change or continuity) before, during and immediately after the LGM.
doi.org
September 24, 2025 at 8:52 AM
Reposted by Dang Liu
We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics.
www.biorxiv.org/content/10.1...
(1/n)
September 22, 2025 at 5:29 AM
Reposted by Dang Liu
Delighted to see this paper with @anaignatieva.bsky.social now published in Genetics!
academic.oup.com/genetics/adv...

We tackle a thorny issue arising in statistical tests for genetic interactions (epistasis) using ancestral recombination graphs (ARGs)... 🧵
Phantom epistasis through the lens of genealogies
Abstract. Phantom epistasis arises when, in the course of testing for gene-by-gene interactions, the omission of a causal variant with a purely additive ef
academic.oup.com
September 10, 2025 at 4:31 PM
Reposted by Dang Liu
Brilliant paper by Visscher et al.

Populations differ in traits/disease burden. Are these differences due to genetics?

Comparing single variants or polygenic scores between populations is biased due to environmental confounders correlated with the variants.

1/3

www.medrxiv.org/content/10.1...
Direct effect of genetic ancestry on complex traits in a Mexican population
Human populations differ in disease prevalences and in average values of phenotypes, but the extent to which differences are caused by genetic or environmental factors is unknown for most complex trai...
www.medrxiv.org
September 11, 2025 at 5:57 AM
Reposted by Dang Liu
SINGER, our ARG inference method, is finally published and freely available online:

doi.org/10.1038/s415...

It was a long journey – 16 months from initial submission to acceptance. Is it just me, or has peer review gotten more arduous lately? 4+ rounds of review isn't so unusual these days...
Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes - Nature Genetics
SINGER is a method for creating ancestral recombination graphs to understand the genealogical history of genomes. The method has increased speed, and thus scalability, without sacrificing accuracy.
doi.org
September 11, 2025 at 3:50 AM
Reposted by Dang Liu
Announcing SimHumanity, a baseline SLiM 5.0 model of the full human genome, replete with demographic history, autosomes, X/Y, and mtDNA. A shared starting point for reproducible evolutionary simulations. We’d love your feedback! #SLiM #evolution #genomics www.biorxiv.org/content/10.1...
SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution
The reconstruction of human evolutionary history has undergone repeated advances, each made possible by methodological innovations. In recent decades, genetic and genomic data played a central role in...
www.biorxiv.org
September 3, 2025 at 3:27 AM
Reposted by Dang Liu
Great new paper: Patterns of genetic admixture reveal similar rates of borrowing across diverse scenarios of language contact

#linguistics #language
www.science.org/doi/10.1126/...
Patterns of genetic admixture reveal similar rates of borrowing across diverse scenarios of language contact
Human population contact leads to consistently similar rates of linguistic borrowing, but effects vary across linguistic features.
www.science.org
August 30, 2025 at 2:44 AM
Reposted by Dang Liu
🧬 The MOOC “Human Population and Evolutionary Genetics” is open for registration!!
👉 bit.ly/4fw3Zje
💀🌍 Where do we come from? What was the migration history of our species? What role does the Neanderthal genome play in our genetic heritage? How has our species adapted to different environments?
Human Population and Evolutionary Genetics
This Mooc aims to provide basic knowledge on population genetics and the help of genetics in the study of human migrations and human adaptation to extreme conditions.
bit.ly
August 25, 2025 at 11:14 AM
Reposted by Dang Liu
Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.

🔗 arxiv.org/abs/2508.03958

1/6
tskit_arg_visualizer: interactive plotting of ancestral recombination graphs
Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent brea...
arxiv.org
August 19, 2025 at 2:12 PM