Using Variable Window Sizes for Phylogenomic Analyses of Whole Genome Alignments https://www.biorxiv.org/content/10.64898/2026.03.04.709403v1
07.03.2026 03:50
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Using Variable Window Sizes for Phylogenomic Analyses of Whole Genome Alignments https://www.biorxiv.org/content/10.64898/2026.03.04.709403v1
Fig. 1 Simulating the pathway from life history to branching history.
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.
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📖 nph.onlinelibrary.wiley.com/doi/10.1111/...
#LatestIssue @mortonarboretum.bsky.social #PlantScience
Species and gene trees showing expected sequence divergence under ingroup versus ghost lineage introgression models.
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!
Flyer for the "Application of Genetics and Genomics for Large-scale Breeding Programs" session at PAG 33 Monday in room Pacific C at 12:50pm
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...
The allotetraploid lycophyte Selaginella rupincola growing among the boulders at Cochise Stronghold in the Dragoon Mountains southeast of Tucson, Arizona.
Xanthisma spinulosum growing outside a gym in Tucson, Arizona.
Selaginella arizonica X eremophila hybrid zone at Alamo Canyon in Organ Pipe National Monument.
A Dieteria sp. being visited by a skipper in the White Mountains of Arizona.
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…
#Genomics #Bioinformatics
Logo for the Genomic History Inference Strategies Tournament
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
If you want to try something that doesn't include the phasing stuff (I'm not sure if it does multiallelic genotyping though), there's updog:
github.com/dcgerard/updog
3. Unfortunately, I think ~50x coverage may not be enough to distinguish between all of the different possible heterozygous states in a hexaploid, so the model could also be having trouble finding the best genotype estimates
2. In addition to the combinatorial issues, there's an implicit assumption of autopolyploidy (randomly sampled alleles), so things like fixed heterozygosity can really throw off the probability calculations
If I had to guess, I think these could be the main causes:
1. Freebayes models multiallelic genotypes, and uses locally phased windows to share information. For a hexaploid, considering all of the combinations of multiallelic genotypes at multiple sites can get really massive
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.)
Rust and serde really are amazing tools for data. I’m curious if you’ve tried pydantic – it looks interesting but I haven’t spent the time to learn it well yet. It’s not the level of static validation that the compiler gives but maybe with mypy and type hints it could make things better in Python?
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
1. When will the Award Cash Management Service (ACM$) be restored to allow disbursements on active awards? Access to ACM$ has been restored and the system is available to accept payment requests as of 12:00 PM ET on February 2, 2025. 2. On Friday, January 31, 2025, a Federal Court issued a Temporary Restraining Order (TRO) directing Federal grant-making agencies, including the U.S. National Science Foundation (NSF), to"..not pause, freeze, impede, block, cancel, or terminate... awards and obligations." What is NSF doing to comply with this TRO? NSF has restored access to the ACM$ system as of 12:00 PM ET on February 2, 2025 and is in compliance with the TRO.
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...
A flyer announcing the next polyploidy webinar on February 5, 2025, at 11 AM PST. Links to sign up for the zoom at barkerlab.net/polyweb. Featuring Charity Goeckeritz from the HudsonAlpha Institute on Genomics of triploid apples narrow the search for the genetic basis of apomixis in Malus, and Christoph Rosche from the University of Halle on Herbarium specimens reveal a cryptic invasion of polyploid Centuarea stoebe in Europe.
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