13.03.2026 00:42
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I got full score last battle! Ready for Library Legends arena #2026MMM
Not a favourable start ...
Graphical summary of the evolutionary model, in 4 rows, A to D. A: left, bell shaped distribution of phenotypic changes; right, observed substitutions between an ancestral sequence and a modern one, using an outgroup. B: 4 fitness landscapes: no selection, alpha=beta=1, uniform distribution; stabilizing selection, alpha=beta≠1, bell shape; directional selection, either alpha>beta, curve skewed right, or alpha<beta, curve skewed left. C: 4 distributions which are the product of the distribution in A and each of the fitness landscapes. Observed subtitutions are mapped onto them, falling outside of the high density area except for the third, i.e. directional selection alpah>beta. D: cartoon likelihood indicating that only the third fitness landscape is supported.
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
Read the preprint: zenodo.org/records/1875...
(doi: 10.5281/zenodo.18750555). If you’ve had experience doing community-engaged genomics, I’d appreciate a short comment on what worked, what didn’t, or resources worth adding. #PopulationGenomics #CommunityEngagement #IndigenousData #Ethics 5/5
The paper argues for budgeting engagement in grants, co-designing research questions with communities, and planning for the return of results and subsequent sustainable stewardship. We welcome feedback from colleagues, esp. Indigenous scholars, community partners, funders, and ethics committees. 4/
We discuss historical harms and current risks (e.g., extractive “helicopter” science, research fatigue, etc.), then show how community-centered practice improves data quality, interpretation, and trust, which enables long-term research that is richer and ethically sound. 3/
The paper presents a concise community engagement protocol and targeted recommendations on governance, consent, benefit-sharing, and capacity building. All derived from the outcomes that emerged from sustained partnership with the Punan Batu community (since 2018). This is a model that works. 2/
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/
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
An image of Sulawesi Island that consist of four connecting peninsula shaping the island into something that looks like a letter "K" with adjacent small islands, annotated with colored circles and triangles marking the location of anoa (circle) and babirusa (triangle) from three types of region across the islands. Each region is accompanied by an art piece of the head of anoa and babirusa to mark the presence of one or both taxa in the region. There are both in the northern and southeastern peninsula of Sulawesi, only anoa in Buton south of the southeastern peninsula, and only babirusa in the Togean south of northern peninsula. In the right side of the head art, there are DNA icon with breakage illustrating "deleterious mutations" and a forest icon illustrating "habitat quality". An arrow going down, up, and left accompanying each icon to mark whether the abundance of each icon are high or low relative to the focal populations, which is marked with arrow pointing right to illustrate stability in magnitude. For both Buton and Togean, the amount of deleterious mutations are low relative to the larger island's peninsula, while it has better habitat quality relative to the larger island. This graphical abstract is an oversimplification of the work, I hope you read the paper for more elaboration.
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
A hot take.
#ethics #DireWolf #CRISPR
but in both cases, "science" won.
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.
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...
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?
Just your regular reminder how awesome this review on inbreeding depression is. www.nature.com/articles/nrg...
🚨 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.
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?
Oh the landscape block will surely come in handy 👍
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.
Noob here. Migrating from Black to Blue.
1st intro post with 0 follower
Hello world! My name is Pai. A Wellcome Int'l Training Fellow at MR Institute Indonesia and an Honorary Research Assoc at McDonald Inst for Archaeological Research, Uni Cambridge.
Looking forward to a more peaceful life here.