With @benoitevol.bsky.social, we developed our own strategy to properly estimate π (e.g. doi.org/10.1016/j.cu...) and I extended it to variable ploidy (doi.org/10.1093/gene...). But it's clearly not as user-friendly & computationally efficient as pixy for similar results ➡️Use pixy, forget VCFtools!😉

Thibault (Tibo) Leroy@tiboleroyinen.bsky.social · 6d ago

😍 pixy 😍 - "[...] implementations of new estimators of Watterson's θ and Tajima's D that are unbiased with respect to missing data. - [...] support for arbitrary ploidy and multiallelic sites. - [...] optimizations, including multicore execution" REPEAT AFTER ME: There is no reason not to use Pixy.

Congratulations to @sheilaroitman.bsky.social, postdoctoral researcher in Detlef Weigel’s department @plantevolution.bsky.social, on receiving the Women’s Postdoctoral Career Development Award in Science from the Weizmann Institute! Her research explores how viruses shape plant microbiomes.

Career Development Award for Sheila Roitman

bio.mpg.de

Avocados come in 2 varieties - A-types start each day female and switch to male midday. B-types do the reverse. In work just published from the last chapter of my PhD, we show this system evolved 40+million yrs ago and is regulated by alleles of 1 transcription factor www.pnas.org/doi/10.1073/...

Balanced polymorphism in a floral transcription factor underlies the ancient rhythm of daily sex alternation in avocado | PNAS

In avocado and certain wild relatives in Lauraceae, a highly synchronized daily rhythm of floral sex timing promotes cross-pollination between two ...

pnas.org

Simulating population pangenomes under coalescent demographic models with MSpangenome https://www.biorxiv.org/content/10.64898/2026.06.29.735168v1

Really incredible work from the Tcheandjieu Lab that finally helps us to decipher what is going on at the 9p21 locus and its association with coronary disease on different ancestral backgrounds. www.cell.com/ajhg/fulltex...

Linkage disequilibrium and allelic heterogeneity explain variation in coronary artery disease risk at 9p21 across populations and reduced effect in Africans

Using cross-ancestry fine-mapping across global and local ancestry groups, this study dissects the 9p21.3 coronary artery disease locus and shows how ancestry-specific haplotype structure shapes assoc...

cell.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...

Upshot: the pangenome is the inevitable solution to prokaryotic life under uncertainty. "Accessory" implies dispensable. The framework says they are essential, just not to every cell in every generation. A gene rarely needed is not a gene unneeded. It is insurance.

Happy 100th to a real one.

David Attenborough celebrates his 100th birthday

He was born before the Great Depression, came of age in WWII, and is still making wildlife documentaries. Brits call David Attenborough a national hero, as he celebrates his 100th birthday.

npr.org

A transcriptomic atlas of grass senescence reveals divergent underground sink networks limit nitrogen recycling in annuals https://www.biorxiv.org/content/10.64898/2026.05.05.723041v1

📢Out now on bioRxiv: We used Plant STARR-seq to characterize the species- and condition-specific enhancer activity of over 350,000 sequences derived from four plant species. For more, see below and read the paper at: www.biorxiv.org/content/10.6...

Woah www.pnas.org/doi/10.1073/...

Genome degradation in plant tissue culture | PNAS

Many plants, unlike most animals, can reproduce as clones [D. Kester, HortScience 18, 831–837 (1983), 10.21273/hortsci.18.6.831]. Cloning plants is...

pnas.org

Metabolic fingerprinting of 17 Brassicaceae species across three tissues https://www.biorxiv.org/content/10.64898/2026.04.17.719198v1

Blog post on "The AI Rewrite Dilemma": lh3.github.io/2026/04/17/t...

Getting close to a robust pipeline for ARG inference for messy genomes. 1. get a vcf. Align short reads to a reference and GATK and pray, or use whole genome assemblies and github.com/baoxingsong/... followed by github.com/RILAB/argprep

Excited to see our work out in Science today! Using machine learning to identify prokaryotic immune systems www.science.org/doi/10.1126/...

DefensePredictor: A machine learning model to discover prokaryotic immune systems

Antiphage defense systems protect bacteria from viral infection and have inspired important biotechnologies such as CRISPR-Cas9 while also revealing the evolutionary roots of eukaryotic innate immunit...

science.org

Peter DeWeirdt@pdeweirdt.bsky.social · 2y ago

Excited to share our work using machine learning to predict anti-phage defense systems! 1/n

Our new experimental evolution study across 30+ locations using the plant Arabidopsis thaliana —— we direct "see" adaptation and extinction to different climates at the genetic as it happens! Read it in Science dx.doi.org/10.1126/scie... @ucberkeleyofficial.bsky.social @hhmi-science.bsky.social

Clustering proteins using DIAMOND is out now @natmethods.nature.com www.nature.com/articles/s41...

Clustering the protein universe of life using DIAMOND DeepClust - Nature Methods

DIAMOND DeepClust provides an ultra-fast clustering method for organizing the protein universe of life at low sequence identity, enabling large-scale dimensionality reduction and improving downstream ...

nature.com

Now out! We show that TEs can be horizontally transferred between fungal species via Starships. Once transferred, these TEs can become active, changing the genome organization and affecting the lifestyle of the recipient fungus. www.nature.com/articles/s41... @oggenfussursula.bsky.social #TEsky

Transposable elements hitchhike on Starships across fungal genomes - Nature Communications

Large mobile genetic elements known as Starships act as vehicles for transferring transposable elements (TEs) between fungi. Here, Griem-Krey et al. show that these ‘hitchhiking’ TEs can drive rapid e...

nature.com

How much protein diversity can Life on Earth actually generate? With DIAMOND DeepClust, we show how billions of proteins across the tree of life can be clustered at low-identity for downstream analytics tasks. 📚Paper: www.nature.com/articles/s41... 💻Code: github.com/bbuchfink/di...

LongcallD: joint calling and phasing of small, structural and mosaic variants from long reads https://www.biorxiv.org/content/10.64898/2026.03.20.713111v1

Tandem and tandem

Science Magazine@science.org · 5mo ago

Wild rice is a perennial, creeping plant. The secret to its perennial growth habit lies in a developmental reversal directed by small RNAs. This image illustrates how combining perennial genes with prostrate growth genes allows cultivated rice to mimic wild rice. Learn more: https://scim.ag/40GOjDb

Excited to share my first preprint from my PhD w/ @justinmcrocker.bsky.social. We show that cell type-specific regulatory dominance promotes robustness and evolutionary innovation through interallelic transcriptional hubs, potentially expanding the mutational paths available to diploids. (1/18)

bioRxiv Evolutionary Biology@biorxiv-evobio.bsky.social · 5mo ago

Interallelic cis-regulatory dominance promotes robustness and evolutionary innovation https://www.biorxiv.org/content/10.64898/2026.03.17.712157v1

1/11 🔥 New preprint alert 🔥 We wanted to know what plants in the wild really care about. So we asked them 🎤. Here is what we learned: “Biotic-response networks are an important organizer of the transcriptome in wild Arabidopsis thaliana populations” www.biorxiv.org/content/10.6...

A deep-time landscape of plant cis-regulatory sequence evolution www.science.org/doi/10.1126/...

A deep-time landscape of plant cis-regulatory sequence evolution

Developmental gene function is often conserved over deep time, but cis-regulatory sequence conservation is difficult to identify. Rapid sequence turnover, paleopolyploidy, structural variation, and li...

science.org

@pratikkatte.bsky.social and I just released Lorax 🌲, a tool for interactive exploration of biobank-scale ancestral recombination graphs (ARGs). If you’ve ever wanted to scroll across the ancestries of thousands of genomes… this is for you.

Recently we're working with SNPs from whole genome assemblies to estimate ARGs. It's a pain to go from alignment files to vcf, keeping track of masked and invariant sites. So we wrote a snakemake/SLURM pipeline. Hope it's useful to others, and don't hesitate to post issues if there are problems!

Molecular and phenotypic footprints of climate in native Arabidopsis thaliana https://www.biorxiv.org/content/10.64898/2026.03.02.709013v1

We are very excited to share a new resource from our team: spatial subcellular proteome maps in plants! We developed an MS-based method that registers localizations of about 8000 proteins in Arabidopsis roots in a single experiment. (1/9) www.biorxiv.org/cgi/content/...

“Aneuploidy was identified in inbreeding and outbreeding populations of cultivated potato, with frequencies ranging from 14.8 to 24.0%, indicating notable genomic instability.” Plant genomes tolerate instability—more akin to human tumor evolution than stability. www.science.org/doi/10.1126/...

Human selection maintains karyotype integrity of highly unstable genomic cultivated autotetraploid potato (Solanum tuberosum)

Meiotic and genomic instabilities affect the reproductive fertility, genomic heterozygosity, and phenotypic plasticity of potato.

science.org

New paper alert: Paralog interference contributes to the preservation of genetic redundancy www.cell.com/current-biol...

Paralog interference contributes to the preservation of genetic redundancy

Duplicated self-interacting proteins can interact and interfere with each other’s function. Cisneros, Mattenberger, et al. show that selection against interfering loss-of-function alleles extends the ...

cell.com