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Pai Kusuma

@paikusuma.bsky.social
44 followers 113 following 19 posts

SRO | SVI Melbourne | Hunter-gatherer; Genomics; Evolution; Transition

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Reposted by Pai Kusuma
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 19/09/2026
This must be the place: deep learning local adaptation www.biorxiv.org/content/10.64898/20…
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Reposted by Pai Kusuma
Nature Reviews Genetics @natrevgenet.nature.com · 11/09/2026
New online! Genomic insights into natural selection in recent human history
dlvr.it
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.
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Reposted by Pai Kusuma
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 05/09/2026
Rapid evolution can select for fitness tradeoffs in fluctuating environments www.biorxiv.org/content/10.64898/20…
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Pai Kusuma @paikusuma.bsky.social · 15/08/2026
This is neat
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Pai Kusuma @paikusuma.bsky.social · 14/08/2026
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...
biorxiv.org
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...
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Reposted by Pai Kusuma
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 03/06/2026
Causal inference clarifies the roles of background selection and mutation rate variation in shaping human genetic diversity www.biorxiv.org/content/10.64898/20…
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Reposted by Pai Kusuma
Matthew Aguirre @aguirre404.bsky.social · 23/05/2026
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...
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Pai Kusuma @paikusuma.bsky.social · 05/05/2026
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Reposted by Pai Kusuma
Huisheng (Julie) Zhu @huishengzhu.bsky.social · 30/03/2026
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
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Pai Kusuma @paikusuma.bsky.social · 26/03/2026
I am sorry, I would like to see a rematch please. I trust this article more than the narrator. 😭😭😭 #2026MMM
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Pai Kusuma @paikusuma.bsky.social · 13/03/2026
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Pai Kusuma @paikusuma.bsky.social · 12/03/2026
I got full score last battle! Ready for Library Legends arena #2026MMM
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Pai Kusuma @paikusuma.bsky.social · 10/03/2026
Not a favourable start ...
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Reposted by Pai Kusuma
Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 03/12/2025
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. 😃 doi.org/10.1101/2025.11.26.690685 #bioinformatics #molecularEvolution
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.
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Pai Kusuma @paikusuma.bsky.social · 24/02/2026
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/
zenodo.org
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...
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Reposted by Pai Kusuma
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 19/12/2025
demografr: A toolkit for simulation-based inference in population genetics www.biorxiv.org/content/10.64898/20…
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Reposted by Pai Kusuma
fandingzhou.bsky.social @fandingzhou.bsky.social · 05/09/2025
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...
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Reposted by Pai Kusuma
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 02/09/2025
SimHumanity: Using SLiM 5.0 to run whole-genome simulations of human evolution www.biorxiv.org/content/10.1101/202…
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Reposted by Pai Kusuma
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 12/07/2025
Invasion preferences suggest a possible role for Plasmodium falciparum parasites in the expansion of Duffy negativity in West and Central Africa www.biorxiv.org/content/10.1101/202…
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Reposted by Pai Kusuma
Sabhrina Aninta @sagitaninta.bsky.social · 10/07/2025
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/...
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.
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Reposted by Pai Kusuma
bioRxiv Evolutionary Biology @biorxiv-evobio.bsky.social · 17/05/2025
When should adaptation arise from a polygenic response versus few large effect changes? www.biorxiv.org/content/10.1101/202…
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Pai Kusuma @paikusuma.bsky.social · 09/04/2025
A hot take. #ethics #DireWolf #CRISPR but in both cases, "science" won.
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Pai Kusuma @paikusuma.bsky.social · 20/02/2025
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.
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Reposted by Pai Kusuma
Grant Kinsler @grantkinsler.bsky.social · 05/12/2024
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...
doi.org
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...
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Reposted by Pai Kusuma
Maggie Steiner @maggiesteiner.bsky.social · 04/12/2024
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?
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Reposted by Pai Kusuma
Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 04/12/2024
Just your regular reminder how awesome this review on inbreeding depression is. www.nature.com/articles/nrg...
nature.com
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 ...
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Reposted by Pai Kusuma
Michel Nivard @michelnivard.bsky.social · 28/11/2024
🚨 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.com
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
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Pai Kusuma @paikusuma.bsky.social · 28/11/2024
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?
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Pai Kusuma @paikusuma.bsky.social · 25/11/2024
Oh the landscape block will surely come in handy 👍
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Pai Kusuma @paikusuma.bsky.social · 25/11/2024
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.
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Pai Kusuma @paikusuma.bsky.social · 25/11/2024
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.
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