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...

FLARE2: local ancestry inference with poorly-matched reference panels https://www.biorxiv.org/content/10.1101/2025.10.13.681993v1

Selection scans and downstream analysis with selscan https://www.biorxiv.org/content/10.1101/2025.10.10.681670v1

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/...

Inference of complex demographic history using composite likelihood based on whole-genome genealogies https://www.biorxiv.org/content/10.1101/2025.10.07.680347v1

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!

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

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...

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

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)

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.

📣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!

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)

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

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)... 🧵

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...

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...

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.

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...

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...

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...

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.

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/...

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.

🧬 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?

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...

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

I'm pleased to share this new article by @svenkasser.bsky.social, Laura Fortunato @anthrolog.bsky.social, Marc Feldman and myself.

The article extends gene-culture coevolution to recognize evolutionary effects of culture arising through drift and migration.

onlinelibrary.wiley.com/doi/10.1002/...

The Oxford Handbook of Archaeology and Language Abstract. Linguists have long described their findings in an archaeological context, while archaeologists have been interested in what language can tell th

New volume on the interface between languages, human history, anthropology, archaeology and (a bit of) genetics, curated by M. Robbeets and M. Hudson. A very rich table of content for everyone interested in these multidisciplinary studies of the human past. I contributed two chapters:

Bridging theory and data: A computational workflow for cultural evolution | PNAS Cultural evolution applies evolutionary concepts and tools to explain the change of culture over time. Despite advances in both theoretical and emp...

Here's a paper with a skeleton of the idea, but there is really lots of research to do on the structure of workflow networks, now to make them robust, how to development diagnostics and calculi for steps within them. doi.org/10.1073/pnas...

Check out our dive into 50,000 years of Indian genetic history!🇮🇳
🧬~2,700 genomes
🦴Neanderthal/Denisovan DNA
🌾Hunter-gatherer, Iranian farmer & Steppe ancestry
🩺Health-linked, population-specific variants

@lauritsskov.bsky.social & Priya Moorjani
#Genomics #India #HumanEvolution #PopulationGenetics

Papua New Guinea's Genetic Past Through Ancient DNA Analysis A new study reveals the significance of regional dispersals and local interactions in coastal Papua New Guinea

Ancient #DNA reveals #Papua New Guinea's genetic past. Study @natecoevo.nature.com by an intl. team led by Kathrin Nägele @mpi-eva-leipzig.bsky.social shows the significance of regional dispersals & local interactions in coastal Papua New Guinea. tinyurl.com/2s3sc6ad & www.nature.com/articles/s41...

Happy to share a PhD opportunity in my new lab at the University of Zurich! Application deadline: June 30. Do not hesitate to contact me for any questions!

Elegant new theory on polygenic adaptation by Will Milligan, Laura Heyward, and Guy Sella.

Activate my 🦋 by thanking everyone, especially the organizers, at the #HumanEvo25 for a great conference, and by reposting the nice summaries of my talk by @martamlahr.bsky.social and @palaeotrails.bsky.social 😊

Why do Polynesians gave high risk of metabolic disease? Dang Liu tests the thrifty genotype vs population adaprive patterns (considering % Austronesian & Papuan ancestries), demographics (strong bottleneck in Eastern Polynesians!). Results: both!! BMI thrifty, HDL & others under drift & more!! 🤩

@dangliu.bsky.social

New genomic research reveals that genetic drift—not selection—likely shaped high risk of metabolic disorder in Polynesians, following ancient admixture and isolation. Unique variants underscore the value of studying diverse populations.

#HumanEvo25