Everyone says AI will accelerate science. I don't think it will -- at least not in biology, and at least not soon. New post where I explain why, and how the productivity paradox can be resolved: blekhman.substack.com/p/why-ai-wil...

Why AI will not speed up science (yet)

You can see AI everywhere except in the productivity statistics

blekhman.substack.com

FERAL 1.0 is out! Just to remind you: FERAL is an open-source toolkit for supervised animal behaviour segmentation directly from videos with no pose estimation needed. We made it much easier to install and run FERAL First, to install FERAL: pip install feral www.biorxiv.org/content/10.1... 🧵

FERAL: A Supervised Video-Understanding System for Direct Video-to-Behavior Mapping

Quantifying animal behavior often requires segmenting continuous actions into discrete, interpretable states, yet most automated pipelines infer actions from keypoint dynamics and are limited by keypo...

biorxiv.org

🔥 Does switching to a pangenome reference actually improve your association study? We tested it, and the answer is yes, measurably. Our preprint is online now: "Pangenome-based human genome analysis improves trait association and genomic prediction": doi.org/10.64898/202...

Pangenome-based human genome analysis improves trait association and genomic prediction

The Human Pangenome Reference Consortium has generated 462 open-access reference genomes and a variation graph that represents differences among them, providing a substrate for pangenome-based analysi...

doi.org

Hari Sridhar hs a nice bew paper on the role of natural history in ecology and evolution www.journals.uchicago.edu/doi/10.1086/...

Spark, Scaffold, Substrate: The Multiple Hidden Roles of Natural History in Ecology and Evolutionary Biology | The American Naturalist: Vol 0, No 0

AbstractOver the last 30 years, as ecology and evolutionary biology (EEB) has become more theoretical, experimental, and data driven, there has been a growing worry that the space for natural history ...

journals.uchicago.edu

Comparing reproductive isolation across species has been harder than it should be. The new Reproductive Isolation Ontology (RIO) provides a common framework to standardize RI estimates across the tree of life. academic.oup.com/evlett/advan...

A standardised framework for classifying estimates of reproductive isolation

Abstract. Understanding reproductive isolation (RI) between lineages is a central goal of speciation research. While the strength of RI has been estimated

academic.oup.com

Animal Behaviour Collective has been doing amazing work! Read all about it here:

Animal Behaviour Collective@abcmicrogrants.bsky.social · 4w ago

Our paper is out now! 🎉📝 We describe how we work to address barriers faced by students and early-career researchs in the animal behaviour field, through our mentorships and microgrants. We hope that this can inspire and provide practical resources for others hoping to do the same!

Our paper is out! 📣 we find that molecular measures of genetic variation do not predict heritable genetic variation across species - important implications for the application of genomic data for conservation! www.pnas.org/doi/10.1073/...

Nucleotide diversity is a poor predictor of short-term adaptive potential | PNAS

The capacity to adapt is essential for a population to avoid extinction in a changing world and is recognized as a global conservation priority. Ad...

pnas.org

THANK YOU, EDOUARD!! (Free until the zombie apocalypse starts - Open Access!)

Edouard Machery@edouardmachery.bsky.social · last mo.

from the great @smellosopher.bsky.social free to download for 2 weeks

So excited to announce that I will be starting the Chen Lab at EMBL Rome in September 2026 🎉 ! The Chen Lab will investigate the genetics + evolution of innate behavior w/ high-throughput sequencing + computational methods across diverse rodent species. Stay tuned for upcoming opportunities...

We are learning during sleep. This is also the case for songbirds. 🐦🎶 A key hormone whose concentration fluctuates over the day is melatonin. Scientists from Manfred Gahr's lab show that melatonin affects spontaneous and auditory responses of song control neurons. link.springer.com/article/10.1...

Nightly changes in neural activity and auditory processing of song control neurons depend on melatonin - Journal of Comparative Physiology A

Birdsong, as many complex behavioral patterns, needs to be acquired, maintained and adjusted throughout life. In songbirds, these tasks are held by a specialized neural network, the song control syste...

link.springer.com

How good is MiniBWA, the successor to BWA? To test it, I ran MiniBWA on sequencing from 76 different species, comparing mapping speed, rate and accuracy with BWA MEM. In short, it's really good. If you map short reads, it's well worth your time. andrewcarroll.github.io/2026/06/30/t...

Our paper on olfactory evidence accumulation is now officially published with the final clean version! With @luxorboero.bsky.social, Hao Wu, @josephdzak.bsky.social, @paulmasset.bsky.social, Farhad Pashakhanloo, @siddjakes.bsky.social, @btolooshams.bsky.social & Demba Ba.

🧵 New paper! We’re excited to release OPTICS: software that immediately predicts color sensitivity from any opsin protein sequence. In other words: give OPTICS any opsin sequence, and it predicts the wavelength of light the pigment is most sensitive to 🌈👁️ academic.oup.com/mbe/advance-...

Accessible and Robust Machine Learning Approaches to Improve the Opsin Genotype-Phenotype Map

Abstract. Predicting phenotypes from genetic variation is a central challenge in biology. Here, machine learning (ML) offers great promise, but its use is

academic.oup.com

Minibwa is a hybrid of bwa-mem and minimap2 and the successor of bwa-mem for short-read mapping. ~4X/2.5X as fast as bwa-mem/bwa-mem2 for WGS reads at comparable accuracy. Native support of directional bisulfite-seq. Applicable to long reads. Preprint at arxiv.org/abs/2606.15357

Excited to share a new paper on sex-aware genome-wide assessment of de novo variants (DNVs) in autism. The complete DNV callset and supplementary analyses are available in the Supplement to the paper. link.springer.com/article/10.1... #genomics #genetics #denovo #autism @washugenetics.bsky.social

Sex-aware genome-wide assessment of de novo variants in autism across coding and noncoding regions - Human Genomics

Human Genomics - Autism spectrum disorder (ASD) shows a consistent sex bias, yet how sex shapes de novo variant (DNV) risk across coding and noncoding sequence remains unclear. I analyzed DNVs...

link.springer.com

Low-Coverage Genome Sequencing Outperforms Target Enrichment Phylogenomics https://www.biorxiv.org/content/10.64898/2026.06.05.730492v1

DipSkmer: Reference-free population genomics with diploid genome skims https://www.biorxiv.org/content/10.64898/2026.06.05.730460v1

T2T assemblies for nearly all major Y chromosome haplogroups courtesy of a collab between @humanpangenome.bsky.social and HGSVC! What was once the hardest human chromosome to finish can now be routinely assembled thanks to ONT + Verkko www.biorxiv.org/content/10.6...

🚨 My last PhD chapter is out now in @jexpbiol.bsky.social 🚨 🦎 We compared the climbing abilities and kinematics of different species of salamanders. Surprisingly, all could climb well but climbing specialists do better. Let me tell why this is interesting (see thread)! doi.org/10.1242/jeb....

If you are interested in collecting specimens for chromosomal genomes and/or generating chromosomal reference genomes from specimens that were not cold-chain preserved, please read on and share this thread.

🧨 New publication out (I think this one is 🌶️ ): Cerca & @stelkens.bsky.social - "The identity crisis of speciation genomics". academic.oup.com/evolinnean/a...

Very happy to announce a big new paper from the lab, led by grad students @smishra677.bsky.social and Laia Pomar-Pallarès (in collaboration with @roblanfear.bsky.social). We introduce a new way to study introgression, with accompanying software (DAFT) 1/n 🧵 www.biorxiv.org/content/10.6...

Twenty five years on from Dolph Schluter's book "The Ecology of Adaptive Radiation" that reshaped the way adaptive radiation was studied, this review revisits key questions raised to evaluate the progress made over the past quarter century, 8 of which remain unresolved...🌍🧪👇

‘The ecology of adaptive radiation’ revisited: A 25-year reflection

Abstract. Twenty-five years ago, the book The Ecology of Adaptive Radiation by Dolph Schluter presented a testable framework that integrated ecology, genet

doi.org

The @systbiol.bsky.social Mentorship Program is back for 2026-2027! The program pairs off mentees with mentors based on shared interests in systematics and biodiversity research. Low effort, high reward! 12 virtual monthly meetings. More info: www.systbio.org/mentorship-p... Apply by June 12th!

Mentorship Program

Last updated May 14, 2025

systbio.org

Abstract deadline for Midwest Pop Gen 2026 extended to June 12th! Aug 21-22 at UChicago — free, trainee-oriented meeting with talks, posters + Friday BBQ at Promontory Point. Chicago in August doesn't get better than this... jkreinz.github.io/mwpg2026

Finally! BOOK 2 OUT SOON -- THIS AUGUST (e-book will be Open Access/free): THE SENSES: PERCEPTION AND EXPERIENCE (Cambridge University Press, Elements in Philosophy of Mind, ed. by @keithfrankish.com ) www.cambridge.org/gb/universit...

The Senses | Cambridge University Press & Assessment

cambridge.org

Wong et al. present IQ-TREE version 3, with new features including mixture models, gene and site concordance factors, integration with phylogenomic divergence time estimation, and a fully featured sequence simulator. 🔗 doi.org/10.1093/molbev/msag117 #evobio #molbio #compbio

Happy to announce the release of TOGA2 data for 68 turtle genomes, generated with a cryptodiran and a pleurodiran turtle reference. The combined TOGA2 annotation consistently improves annotation completeness compared with RefSeq. All data at genome.senckenberg.de/download/TOGA2. Genome browsers ...

Do you record multimodal data? For our experiments with the singing mice, @cshlnews.bsky.social graduate student @xmikezheng20.bsky.social set up a fantastic acquisition pipeline, which has now become THE standard for all rigs in my lab. He published a detailed protocol today! Check it out. 👇

Mike Zheng@xmikezheng20.bsky.social · 3mo ago

I’m happy to share a protocol we’ve been working on for building modular, synchronized multimodal data acquisition systems for systems neuroscience behavior rigs. @mbd1mbd1.bsky.social @arkarupbanerjee.bsky.social dx.doi.org/10.17504/pro...

Revamped the teaching materials site. Light/dark mode switch at the top. More consistent, compact presentation of all the materials. + Icons and such! www.langmead-lab.org/teaching.html