This must be the place: deep learning local adaptation https://www.biorxiv.org/content/10.64898/2026.09.16.752190v1
Pai Kusuma
@paikusuma.bsky.social
SRO | SVI Melbourne | Hunter-gatherer; Genomics; Evolution; Transition
New online! Genomic insights into natural selection in recent human history
Genomic insights into natural selection in recent human history
Nature Reviews Genetics, Published online: 11 September 2026; doi:10.1038/s41576-026-01010-9Advances in genome-wide selection scans and ancient DNA have greatly expanded our ability to study human evolution. This Review discusses the conceptual and statistical challenges in identifying and interpreting selection signals, and how recent approaches are reshaping our understanding of human evolution over the past 10,000 years.
dlvr.it
Rapid evolution can select for fitness tradeoffs in fluctuating environments https://www.biorxiv.org/content/10.64898/2026.09.01.748641v1
This is neat
Yun Deng@yundeng.bsky.social · 2mo agoThe 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
New preprint out! The Punan of Borneo offer rare windows into what happens molecularly when a hunter-gatherers transitions to a settled lifestyle, and the answer is: a lot and fast. Deep gratitude to the communities for their trust & participation. Feedback welcome 🙏 www.biorxiv.org/content/10.6...
Rapid convergence toward an agriculturalist regulatory landscape following lifestyle transition in Bornean hunter-gatherers
The transition from hunter-gatherer to agricultural lifestyles is one of the landmarks in the history of human societies, but its phenotypic and immediate molecular consequences remain poorly understo...
biorxiv.org
Causal inference clarifies the roles of background selection and mutation rate variation in shaping human genetic diversity https://www.biorxiv.org/content/10.64898/2026.06.02.727906v1
Happy to share that this is now out in Cell Genomics and a featured paper for Multi-Journal Submission from @cellpress.bsky.social — many thanks to the editorial team + our reviewers! Short recap + some further thoughts on the paper ⬇️ [1/7] www.cell.com/cell-genomic...
Matthew Aguirre@aguirre404.bsky.social · last yr.Thrilled to share the second half of my PhD work here! We show how data on expression quantitative trait loci (eQTL) relates to the structure of gene regulatory networks (GRN). Much of the GRN / eQTL picture is unmapped, but what we do have says a lot… (1/) doi.org/10.1101/2025...
Why do schizophrenia GWAS signals look so flat across the genome? In our recent preprint, we explored why psychiatric disorders — and, more broadly, brain-related traits involving the central nervous system — appear to have unusual genetic architectures. 🧵1/n
I am sorry, I would like to see a rematch please. I trust this article more than the narrator. 😭😭😭 #2026MMM
Lara Durgavich@ldurgavich.bsky.social · 6mo agoCOMMON HIPPO DEFEATS ASIAN ELEPHANT!!!! #2026MMM
I got full score last battle! Ready for Library Legends arena #2026MMM
March Mammal Madness@mmmletsgo.bsky.social · 7mo ago#2026MMM MONEY MAMMALS ROUND 1 WINNERS: Humpback Whale, Eastern Gorilla, Giraffe, Indian Rhinoceros, Bornean Orangutan, Hippopotamus, Oryx, Asian Elephant Please join us TOMORROW (Thursday 3/12) at 8PM EST for Library Legends Round 1!
I'm excited to present this new model to detect positive selection on regulatory sequences, which has been 3 years in the making! Thanks to Alexandre Laverré and @Phylogenetrips for their amazing work on this project. 😃 https://doi.org/10.1101/2025.11.26.690685 #bioinformatics #molecularEvolution
We posted a preprint on Zenodo: “The important role of community engagement in genetic research: Lessons from the study of Bornean contemporary hunter–gatherers” (zenodo.org/records/1875...). We present a practical, field-tested approach to doing genomics with Indigenous communities. 1/
The important role of community engagement and equal collaboration in population genetic research: Lessons from Bornean contemporary hunter-gatherers
Abstract - Population and medical genetics can provide valuable information about human history and health. However, research involving Indigenous and vulnerable communities often raises ethical issue...
zenodo.org
demografr: A toolkit for simulation-based inference in population genetics https://www.biorxiv.org/content/10.64898/2025.12.18.694482v1
Gene expression changes aren’t just about mean shifts — variability shifts matter too, especially for aging. We're thrilled to introduce QRscore, a flexible non-parametric framework for detecting shifts in mean and variance across conditions. doi.org/10.1016/j.cr...
SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution https://www.biorxiv.org/content/10.1101/2025.09.01.673541v1
Invasion preferences suggest a possible role for Plasmodium falciparum parasites in the expansion of Duffy negativity in West and Central Africa https://www.biorxiv.org/content/10.1101/2025.07.09.663497v1
My first PhD paper on the importance of populations in small islands for the survival of megafaunas is out! In sum, the ~100 whole genome sequences of anoa & babirusa, forest cover & climate model of their habitat, all agree that small-island pops are dope. #consgen www.pnas.org/doi/10.1073/...
When should adaptation arise from a polygenic response versus few large effect changes? https://www.biorxiv.org/content/10.1101/2025.05.15.654234v1
Thrilled with the release of this Terra Australis volume about the West New Guinea, exploring the rich human past of this fascinating region. Honored to have contributed chapters to this volume.
ANU Press@anupress.bsky.social · 2y agoThe latest volume in the Terra Australis series explores the human past in West New Guinea. It describes the environmental and cultural history of the area and the boundary-making that has formed West New Guinea in the recent past. Available now doi.org/10.22459/TA5...
Do mutations that drive evolution improve many traits or few? Does this change over the course of evolution? Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵 doi.org/10.1371/jour...
A high-resolution two-step evolution experiment in yeast reveals a shift from pleiotropic to modular adaptation
Evolution is expected to involve mutations that are small and modular in effect, but recent findings suggest that mutations early in an adaptive process can have strong and pleiotropic effects. This s...
doi.org
Excited to share a new preprint with @jnovembre.bsky.social ! We use a combination of population genetic theory, simulation, and data analysis to ask: how does study design in genetic studies (including biobanks) impact the discovery of rare, deleterious variants?
bioRxiv Genetics@biorxiv-genetic.bsky.social · 2y agoStudy design and the sampling of deleterious rare variants in biobank-scale datasets https://www.biorxiv.org/content/10.1101/2024.12.02.626424v1
Just your regular reminder how awesome this review on inbreeding depression is. www.nature.com/articles/nrg...
The genetics of inbreeding depression - Nature Reviews Genetics
The genetic basis of inbreeding depression and of the related phenomenon, heterosis, has been a puzzle for many decades. Based on recent studies in many species, the authors argue that both phenomena ...
nature.com
🚨 This will become a curated list of awesome tools for complex trait genetics, **add yours**! it may become a review in which case those who contribute are invited as co-authors.
GitHub - MichelNivard/awesome-complex-trait-genetics: A list of awesome tools for complex trait genetics.
A list of awesome tools for complex trait genetics. - MichelNivard/awesome-complex-trait-genetics
github.com
It's a common knowledge that EPAS1 is enriched, and pos selected, in Himalayan highlanders. But i keep being astonished by the peaked frequency in the Himalayan highlander population given relatively recent split with the Han. Do we know the selection coefficient of these EPAS1 alleles in the pop?
bioRxiv Genomics@biorxiv-genomic.bsky.social · 2y agoHimalayan whole-genome sequences provide insight into population formation and adaptation https://www.biorxiv.org/content/10.1101/2024.11.26.625458v1
Oh the landscape block will surely come in handy 👍
Quarto@quarto.org · 2y agoQuarto 1.6 is out! 🎉 Download it here: quarto.org/docs/download/ Quarto 1.6 supports unified branding across formats, updates to RevealJS, a new shortcode to reorder content, a landscape page block, and more. Blog post: quarto.org/docs/blog/po...
Optimist: The cup is half full. Pessimist: The cup is half empty. Population geneticist teaching drift: Sample with replacement the atoms of water in this cup until the next cup is full and assume the total number of atoms stays constant.
Graham Coop@gcbias.bsky.social · 2y agoOptimist: The cup is half full. Pessimist: The cup is half empty. Population geneticist: The cup is either a quarter full or overflowing and I can never remember whether there's a factor of two for haploids or diploids. bsky.app/profile/hutc...