Genomic sampling and population structure of farmer-maintained varieties reveal previously uncharacterized diversity of Theobroma cacao L. in Costa Rica https://www.biorxiv.org/content/10.64898/2026.03.30.715340v1

Spun off a lightweight python package “pedigraph-sim” for simulating meiosis on arbitrary pedigrees. It tracks how crossing over produces segments of local ancestry and contains convenience functions like exporting the tree sequence to tskit for analysis: github.com/pmckenz1/ped...

Was pointed to these Rust learning resources recently and have really enjoyed skimming through them. The 'Rust for Python Programmers' has been particularly good for connecting concepts between the two languages github.com/microsoft/Ru...

The Genomic Legacy of Ancient Polyploidy in Crop Domestication https://www.biorxiv.org/content/10.64898/2026.03.09.710542v1

Trait evolution with incomplete lineage sorting and gene flow: the Gaussian Coalescent model https://www.biorxiv.org/content/10.64898/2026.03.10.710880v1

Using Variable Window Sizes for Phylogenomic Analyses of Whole Genome Alignments https://www.biorxiv.org/content/10.64898/2026.03.04.709403v1

Simulating the pathway from life history to phylogeny 📖 nph.onlinelibrary.wiley.com/doi/10.1111/... 👆 A #Commentary by Kieran Althaus & Andrew Hipp on this article by Smith et al. 👇 📖 nph.onlinelibrary.wiley.com/doi/10.1111/... #LatestIssue @mortonarboretum.bsky.social #PlantScience

From the upcoming #AppsPlantSci special issue "Branching out: Resolving #PlantEvolution through #Phylogenetic Networks" Introducing ghostbuster: a new tool to detect cryptic ghost lineage introgression in genomic datasets (by Forsythe et al) bsapubs.onlinelibrary.wiley.com/doi/full/10.... #botany

Fun news! @gcbias.bsky.social and I are teaching a 2-week online population genetics workshop this summer to raise money for the Center for Population Biology at UC Davis. We're trying to gauge interest -- please fill this out if you might be interested! And please share broadly!

En route to San Diego for #PAG33 with several of my Bayer Crop Science colleagues. I'm excited to see what the genomics community has cooked up over the last year. Don't miss the Bayer-sponsored session on Monday! We have a great lineup of internal and external speakers

SNaQ.jl: Improved Scalability for Phylogenetic Network Inference https://www.biorxiv.org/content/10.1101/2025.11.17.688917v1

Hey Yaniv Brandvain is not on Bluesky but his most recent biostats ebook is live ybrandvain.github.io/biostats/. His stats resources have been so helpful to me as I develop my own stats course, so check it out. Github repo here: github.com/ybrandvain/b...

I'm recruiting PhD students for the Barker Lab @uofa-eeb.bsky.social We study plant evolutionary genomics - polyploidy, hybridization & machine learning for genome evolution. Work with Selaginella, Xanthisma, Brassica & more. Funding available via CAMBIUM Fellowships. Reach out if interested! 🧬🌵🤖

The #PolyploidyWebinar series is back for another season! 🧬 Join us for talks at 9AM Pacific on the second Thursday of each month. Are you working on something exciting in polyploidy? We'd love to have you speak! Sign up for open dates at the link below. Looking forward to the great research ahead!

Phylogenomic challenges in polyploid-rich lineages: Insights from orthology inference and reticulation methods using the complex genus Packera (Asteraceae: Senecioneae) https://www.biorxiv.org/content/10.1101/2025.09.14.676143v1

I'm hiring a computational biologist interested in complex trait genetics using deep learning approaches. Reach out to me, if interested.

We hope that these open educational resources can be useful to those who work with natural history collections! There are four modules that this paper walks through. All modules are available on QUBES HUB :https://qubeshub.org/community/groups/bceenet/teaching_resources

I'm hiring a postdoc to work in theoretical / computational phylogenomics! More info at tinyurl.com/63hb5ew8. Please share!

Please repost and amplify ! We are hiring a faculty position in Evolutionary Genetics in the Biology Department at U of South Carolina! Check us out and come be our colleague! sc.edu/study/colleg... Deadline for applications is Oct 1 #AcademicJobs #EvoBio

🚨 Our GW paper is out in Nature Methods!🥲 GW is a fast genomics browser (up to 100x faster!) github.com/kcleal/gw Also, just released a Python interface for GW github.com/kcleal/gwplot 📝 nature.com/articles/s4159…#Genomicsc#Bioinformaticscs

Excited to kick-off the 2025 Genomic History Inference Strategies Tournament tomorrow at my Evolution workshop! If you're at the meeting, grab a quick lunch and come to the Oconee River 2 room at 1:15 pm on Monday. No prior registration required. ghi.st #Evol2025

I had a blast chatting with JoeySantore on Crime Pays But Botany Doesn’t! We talked polyploidy, weird desert mustards, monotypic families, and Tiganophyton—a wild new species from Namibia. 🎧 www.podbean.com/ew/dir-en8pq... #Botany #Brassicales #PlantScience

Today, we’re announcing the preview release of ty, an extremely fast type checker and language server for Python, written in Rust. In early testing, it's 10x, 50x, even 100x faster than existing type checkers. (We've seen >600x speed-ups over Mypy in some real-world projects.)

ConfuseNN: Interpreting convolutional neural network inferences in population genomics with data shuffling https://www.biorxiv.org/content/10.1101/2025.03.24.644668v1

The collaborative paper on adding selection to stdpopsim is out! Learn about how to easily simulate realistic population genomic data with background selection and sweeps, plus some benchmarking of methods for demographic history, DFE, and sweep inference. www.biorxiv.org/content/10.1...

Low accuracy of complex admixture graph inference from f-statistics https://www.biorxiv.org/content/10.1101/2025.03.07.642126v1

The National Science foundation has just updated their FAQ to say they are complying with the court order and has restored access to funds and the ACM$ platform new.nsf.gov/executive-or...

“Access to the Award Cash Management Service (ACM$) has been restored and the system is available to accept payment requests as of 12:00 PM ET on February 2, 2025.” new.nsf.gov/executive-or...

Update on the NSF PRFB stipend situation: NSF is complying with the TRO. The money management system (ACM$) is back online as of today, and access to awarded funds has resumed. new.nsf.gov/executive-or...

Join us on Wednesday, February 5, at 11 AM PST for the next #PolyploidyWebinar! This month we have @cherrityg.bsky.social on apomixis and polyploidy in Malus and Christoph Rosche on herbarium specimens and invasive Centaurea! Sign up (if not already!) to get the zoom: www.barkerlab.net/polyweb

It would be fantastic if major federal institutions would acknowledge that the executive branch cannot legally unilaterally cancel or redistribute congressionally appropriated funding on ideological grounds and thus they have no legal obligation to comply with such directives

It’s official: all funding requests made on Tuesday by postdocs for their salaries have been unilaterally rejected by NSF.

Apparently all the PhD researchers holding prestigious NSF-funded research fellowships are having their salaries withheld until some unspecified time when the leadership figures out how to eliminate any grant funding that doesn’t align with the president’s political ideology.

I'm begging a major news org to cover the fact NSF is defying the courts to enact Trump's unconstitutional executive order

As of this AM, it is uncertain how NSF postdoc fellows will be impacted. If you are on an NSF PRFB and not a member of the slack group, send me a message.

NSF PRFB fellows: talk to your POs and transfer the remaining year’s balance of salary and research funds by 5pm today!! Dm me if you want to join the prfb slack where fellows are sharing info with each other #nsf #nsfprfb

NSF-funded ECRs -- if you haven't checked in on your funding situation, DO SO RIGHT NOW. Like, immediately. Finish up whatever you're doing and CALL THEM.

NSF PRFB POSTDOCS: Pull the remainder of this funding cycle’s stipend, all remaining research funds, and all remaining travel funds (if you have them). Do it before 5PM today. Per instructions from multiple NSF POs. If you’re not already on the PRFB slack, DM me and I’ll send you an invite

The consequences of polyploidy are... well, complicated. A deep dive into polyploidy in a massively successful tribe of grasses. A masterpiece led by Michelle Stitzer, representing the work of a lot of folks on the PanAnd project over last 7 years. www.biorxiv.org/content/10.1...

Our paper on fitting population genetic models to low-pass sequencing data is now out in Molecular Biology and Evolution! doi.org/10.1093/molb...

Long-Read Low-Pass Sequencing for High-Resolution Trait Mapping https://www.biorxiv.org/content/10.1101/2025.01.09.632261v1

Maize and wild relatives show distinct patterns of genome downsizing following polyploidy https://www.biorxiv.org/content/10.1101/2024.12.24.630189v1

As a long-time Python user, I think I've blocked out my early memories of wrestling with all the different options for package/project management. I'd heard of `uv`, but after watching this talk, I really do think that it's the future for Python: youtu.be/zOY9mc-zRxk?...

An ancient origin of the naked grains of maize https://www.biorxiv.org/content/10.1101/2024.12.02.626434v1

I'm pretty sure the 'reticulate' R package is magic. I've been working on a simulator that's built in Rust + Python and with reticulate it just works in R, converting polars/pandas dataframes and everything. Definitely some kind of sorcery

For #DataScience folks that like to work in the terminal, I highly recommend trying out Nushell.sh – it’s great for quickly exploring data, it’s scriptable, and it supports SQL-based operations directly on structured files (csv, json, etc). The more I learn, the more I’m impressed

I am recruiting graduate students this year to join my lab in Tucson! If you are interested in studying the evolution of plant diversity, polypoidy, and chromosomal evolution, please reach out about opportunities in my lab! Details about applying to EEB and our new CAMBIUM NRT in the thread below! 🧪

🥦 Hi! I’m Makenzie, and I study plant biodiversity, focusing on wild relatives of crops in the Brassica family—think cabbages, mustards, and leafy greens. My research explores how these plants adapt to diverse and often challenging environments, revealing insights into resilience and survival. (1/9)