Charlie Hale

Postdoctoral Researcher - Evolutionary Genomics and Population Genetics Position Title: Postdoctoral Researcher - Evolutionary Genomics and Population Genetics Appointment Type: Post Doc/Trainee Job Description: Summary of Duties and Responsibilities: We are seeking a Pos...

Postdoc in evolutionary genetics with @mbhufford.bsky.social isu.wd1.myworkdayjobs.com/IowaStateJob...

www.biorxiv.org/content/10.6...

"TSS-proximal TFBSs are implicated in rapid, tissue-wide transcriptional stress responses....distal upstream regions contain conserved TF clusters that overlap rare cell type-specific accessible chromatin"

American climate science is losing federal support right when we need it most.

Project Drawdown is stepping up: launching the Climate Science Serving America Fellowship for early/mid-career PhD scientists to do good science that does good.

🗓️ Apply by April 17
👉 https://bit.ly/4kx2J1Q

Widespread turnover of a conserved cis-regulatory code across 589 grass species Abstract. The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation thro

Hale et al. analysed >500 grass genomes to support a “stable motifs, variable binding sites” model of cis-regulatory evolution that involves turnover of thousands of individual binding sites while preserving TF binding preferences.

🔗 doi.org/10.1093/molbev/msaf324

#evobio #molbio #PlantSky

“Natural History, Crowdsourced,” an article in Arnoldia by Patrick McKenzie. The article begins with an image of a ruby-throated hummingbird visiting Lobelia cardinalis.

Quiet hours in the sun, meditating with the bugs, plants, and birds, are my inspiration as an evolutionary biologist.

I wrote in the most recent issue of Arnoldia about using @inaturalist.bsky.social and, more generally, about the continuing role of natural history in motivating questions in evo bio + my excitement about community science for unlocking new scales of analysis: arboretum.harvard.edu/arnoldia-sto...

Year 1 data on congestion pricing in Manhattan…

* Vehicle traffic: -11%
* Foot traffic: +3.4%
* Storefront vacancy: -0.9%
* Pollution: -22%
* Revenue for mass transit: $548M

So YES this has been a huge success.

Big thank you to my labmates and collaborators who helped make this ambitious project possible. Including but not limited to @marand-lab.bsky.social @aimeejschulz.bsky.social @taelder.bsky.social @mbhufford.bsky.social @arnstrm.bsky.social @mcstitzer.bsky.social @mohamedel-walid.bsky.social

Our paper is out in MBE! doi.org/10.1093/molb...

We tracked TF binding site evolution across 589 grass species, and found that while binding preferences are pretty stable over 80 million years of evolution, individual binding sites have turned over a lot.

Thread here: bsky.app/profile/char...

Widespread turnover of a conserved cis-regulatory code across 589 grass species Abstract. The growing availability of genomes from non-model organisms offers new opportunities to identify functional loci underlying trait variation thro

"cis-regulatory evolution involves turnover of thousands of individual binding site instances while largely preserving transcription factors’ binding preferences."

From: academic.oup.com/mbe/advance-...

Identification of Freezing Tolerance QTLs in Tripsacum dactyloides Using Open-Pollinated Bulk Segregant Analysis https://www.biorxiv.org/content/10.64898/2025.12.10.693030v1

Made a site comparing the sizes of living things :)

The great Julius Csotonyi spent 5 months painting over 60 illustrations for the site, no ai used

> neal.fun/size-of-life/

Are you planning to attend Botany 2025? Consider applying to be a PLANTS mentor! You'll be paired with another mentor to help your mentee network, comprehend talks, and discuss grad school and careers, all while making them feel welcome in the botany community. (1/2)

Lineage-specific evolution of regulatory landscapes in polyploid plant and its diploid progenitors https://www.biorxiv.org/content/10.64898/2025.12.04.692133v1

The origins and adaptive consequences of polyploidy in a dominant prairie grass Polyploidy is ubiquitous across North American prairies, which provide essential ecosystem services and rich soil for agriculture. Yet the mechanism driving polyploid abundance is unclear. Multiple hy...

Super proud of @alyssa-phillips.bsky.social 's paper, now out on biorxiv! She resolves the origin(s) of polyploid big blue-stem, a dominant species in the midwest tall-grass prairie. Her common garden analysis also informs on environmental adaptation and hints at the impacts of polyploidy.

Available now in @asn-amnat.bsky.social ! Taking on some big-scale natural history: processed >40k @inaturalist.bsky.social images of Monarda fistulosa using computer vision to query for flower presence and phenotype flower color: doi.org/10.1086/739413

@chenxinli2.bsky.social I'd guess TCP

To quote my friend @drkatemarvel.bsky.social, climate change won't make humanity extinct but we can do better than "not extinct". Raise your standards people!

We are seeking speakers for #pag33 hosted in San Diego: Jan 9th at 10:30am. Talk to us about your current/planned efforts to develop genomic resources for threatened/endangered species! @ebpgenome.bsky.social - hosted by @uconneeb.bsky.social @nanoporetech.com Abstracts by Oct 27th! 🧬 🦜 🌱 🐛 🐢

Most public transit systems depend largely on fare revenue to fund basic operations, but ridership never recovered after the pandemic. I wrote about 3 major transit systems that are facing a fiscal cliff, and the somewhat lackadaisical political response to the crisis. heatmap.news/politics/chi...

MBE | Genotype by Environment Interactions in Gene Regulation Underlie the Response to Soil Drying in the Model Grass Brachypodium distachyon

Yun et al. leveraged RNA-seq data to model gene expression variation in the grass Brachypodium distachyon and its response to soil drying, identifying genotypic, environmental, and G×E effects on physiological, metabolic, and gene expression traits.

🔗 doi.org/10.1093/molbev/msaf218

#evobio #molbio

@prereview.bsky.social is a great model for broadening participation in the review process!

Our paper showing that variation in transcription factor binding sites underlies the majority of additive genetic variance for phenotypic variation in maize is finally out!

Sadly they didn't use our suggested cover image below (made by the inimitable Andi Kur).

www.nature.com/articles/s41...

SPEECHLESS duplication in grasses expands potential for environmentalregulation of stomatal development https://www.biorxiv.org/content/10.1101/2025.07.29.667563v1

Recruitment, rewiring and deep conservation in flowering plant gene regulation - Nature Plants A highly scalable approach is used to generate 3,000 genome-wide maps of transcription factor binding in ten flowering plants, along with multi-species single-nucleus RNA-seq atlases. Together, the re...

"We found that TF orthologues from distant species retain
nearly identical binding preferences, while on the same timescales the gain and loss of TFBSs are widespread."

From: www.nature.com/articles/s41...

Conservation of chromatin states and their association with transcription factors in land plants https://www.biorxiv.org/content/10.1101/2025.07.12.664529v1

So grateful to be one of the 500+ early-career scientists returning to their roots this month. The SNAP team behind this campaign has been such a blast to work with! @snapcoalition.bsky.social

Check out my piece in the Marietta Daily Journal, as well as other national coverage: bit.ly/3HXlfB4

Polling data from Harris & Associates 1966. Q: Do you approve of what Freedom Riders are Doing? 22% approve 61%disapprove18%no opinion.

I just like to post these data from time to time to puncture the mythological aura of mid 20th c protests. They were less popular than pretty much any 21st c mass action & people criticizing them used the same lines. Protest is about people coming together, shaping narratives, & building power.

We're excited to share PlantCAD browser tracks: a new, unpublished dataset integrating AI techniques for plant genome analysis. Explore it here: github.com/andorfc/Plan...
We welcome the community's feedback and innovative use cases for this data!

URGENT: FlyBase has lost practically all its funding overnight; even user fees are tied up in denied grant funding. 🤬🤯

Any lab using @flybase.bsky.social please donate using the link in post below.

This incredible community, on whose backs our #Drosophila labs depend, can't be left out to dry.

A chart showing cancelled NIH grants

“I would like to cure brain cancer. I think that's not particularly controversial.” Be that as it may, the NIH terminated that scientist's grant. Here's a huge survey of the 2,500 grants that NIH has killed or delayed...so far. Gift link: nyti.ms/43Jz1yJ