Joe Walker

Glad to see this preprint is up doi.org/10.32942/X2C... describing what can be done to study UrbanEcoEvo using only publicly available data. Congrats to @shawn-anthony.bsky.social, and a great chance to collaborate with Natalie Love

Another exciting #SSB2026 workshop to highlight:

A Primer for Phylogenetic Causal Inference

with @oschwery.bsky.social & @pseudacris.bsky.social

Also, lots of new info on the website and more soon:

ssb2026.github.io

Follow for the latest updates!

@jembrown.bsky.social @systbiol.bsky.social

Not to shamelessly promote lab stuff, but if anyone is teaching evolution or phylogenetics, Karolis’ program has been great for students learning about trees. Its user interface is more like a basic calculator instead of a scientific calculator, which helps when learning. github.com/karolisr/tre...

There are many amazing tree viewers out there, and this is one the lab's developing for navigation of large trees, looking at you @blackrim.bsky.social. Karolis will be at Botany, so please see his talk or put any issues on GitHub for features you'd like. It’s early and is being actively developed.

Release v0.3.1 · karolisr/treehouse This is very much a work in progress. Currently: TreeHouse will only open files with .tre and .newick extensions, and will treat them as NEWICK (multi-tree files are supported). NEXUS support comi...

#phylogenetics Mac users alert: TreeHouse opens trees with >500k+ tips and it is very FAST. The initial version can open, sort, root/unroot, & save multitree newick files (Nexus+ coming soon). Karolis is soliciting features. Apple-certified installer here: github.com/karolisr/tre...

Sequencing historical RNA: unrealized potential to increase understanding of the plant tree of life Recent studies have demonstrated that it is a misconception that transcriptome sequencing requires tissue preserved at ultracold temperatures. Here, we outline the potential origins of this misconcept...

Glad to see this work by @atyszka.org published, and excited to see the Field Museum on the front of Trends in Plant Sciences this month. Also, a great chance for the lab to collaborate with Drew Larson. www.cell.com/trends/plant...

🚨 I’m thrilled to share that I am starting as an Assistant Professor at Wake Forest University this Fall!
👀 Opportunities coming soon as I re-root my research program in plant ecophysiology and evolution at Wake 🌿 🌲🌱
#NewPI #plantecophys #botany @wfubiology.bsky.social
@wakeforest.bsky.social

Awesome news, congrats!

Multiple transitions to high l‐DOPA 4,5‐dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales Many specialized metabolic pathways have evolved convergently in plants, but distinguishing multiple origins from alternative evolutionary scenarios can be difficult. Here, we explore the evolution .....

Excited to share a new paper with Sandra Guerrero-Rubio and @docbroc.bsky.social on the convergent evolution of betalains, now published in @newphyt.bsky.social! nph.onlinelibrary.wiley.com/doi/10.1111/.... A 🧵

New Postdoc position (2yrs) available in our #EvoMPMI lab @JohnInnesCentre. Come and work with on harnessing the diversity of immune mechanisms to protect plants. jobs.jic.ac.uk/Details.asp?va…

Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae Background and Aims: The flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite...

I’m extremely proud of all of our undergrads who undertook the difficult journey of producing scientific material and learning how to process transcriptomic data! Check out the culmination of our work on BioRxiv!! @evojfwalker.bsky.social

www.biorxiv.org/content/10.1...

Going green: Recycling transcriptomes to infer evolutionary relationships, gene duplication, gene tree conflict, and patterns of molecular evolution in the Apocynaceae Background and Aims: The flowering plant family Apocynaceae exhibits diverse adaptations with biological and pharmaceutical significance, many of which have been studied with RNA-seq. However, despite...

@shawn-anthony.bsky.social helped ~20 undergrads learn transcriptomics in this budget friendly investigation into the dogbane family. A fun way to investigate the molecular evolution of the group. Also, a chance to collaborate with @phylonatworks.bsky.social and Jarrad! doi.org/10.1101/2025...

Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants Robinson et al. identify pathogenic Pseudomonas viridiflava in wild Marchantia polymorpha liverworts and interrogate the mechanisms enabling virulence in non-flowering and flowering plants. Their resu...

Conserved effectors underpin the virulence of liverwort-isolated Pseudomonas in divergent plants

Very happy to share the published version of our work on natural Marchantia-Pseudomonas interactions.

Out now in Current Biology: www.cell.com/current-biol...

Congrats Stephen!

13 U-M faculty named as 2024 AAAS fellows Thirteen University of Michigan faculty members earned election to the American Association for the Advancement of Science in 2024.

I am honored to be elected an AAAS fellow! news.umich.edu/13-u-m-facul...

Pandora: A Tool to Estimate Dimensionality Reduction Stability of Genotype Data AbstractMotivation. Genotype datasets typically contain a large number of single nucleotide polymorphisms for a comparatively small number of individuals.

Are you analyzing genotype data via PCA or MDS, in particular including ancient DNA samples? Here is a novel easy-to-use tool to assess the stability of these analyses by bootstrapping the SNPs: academic.oup.com/bioinformati...

In recognizing that lots of students (undergrads and grads) are unaware of the dire situation created by the recent executive / DOGE actions, I am trying to compile a list of how these will impact folks so I can make materials and spread the word and get more advocates. 1/2

GitHub - ericbretz/transrate2 Contribute to ericbretz/transrate2 development by creating an account on GitHub.

Thanks! Yeah, TransRate is great. A grad student in my lab has made an updated version (github.com/ericbretz/tr...) to incorporate the newer mappers. Credit to Steve Kelly for the help on how all the stuff works. Snap can be a bit temperamental so HiSat and others can help with some of the issues.

🎙️Season 2 of our podcast is here! Kicking things off with the mind-blowing study below.
This research shatters the assumption that herbarium specimens are unsuitable for transcriptomics, successfully extracting mRNA from historical plant samples:
open.spotify.com/episode/1cqA...

RNA from herbarium specimens is more stable than you think. Cool new study from @atyszka.org @evojfwalker.bsky.social and team. @khongsamchia.bsky.social and I were happy to contribute by functionally validating an NLR immune receptor last expressed in 1956 : www.biorxiv.org/content/10.1...

Herbaria provide a valuable resource for obtaining informative mRNA While DNA has built the framework for molecular insights from museum collections, the utility of archival RNA remains largely unexplored. Likely a consequence of the known instability of RNA relative ...

Getting quality transcriptome assemblies from Herbarium samples is possible doi.org/10.1101/2025.... Work led by @atyszka.org. Another fun collaboration with @philcarella.bsky.social and @khongsamchia.bsky.social, who functionally validated an NLR immune receptor from a sample collected in 1956.

Semblans: automated assembly and processing of RNA-seq data AbstractMotivation. Recent advancements in parallel sequencing methods have precipitated a surge in publicly available short-read sequence data. This has e

A former undergraduate, Miles Woodcock-Girard, made a transcriptome assembly pipeline (doi.org/10.1093/bioi...) and is looking for features people may want. He’s a big advocate for maintaining software, so please reach out to him on GitHub if there’s anything you would find helpful.

A necrotizing toxin enables Pseudomonas syringae infection across evolutionarily divergent plants Grenz et al. interrogate the Pseudomonas syringae species complex for its capacity to infect evolutionarily divergent host plants. Their results demonstrate that broad host isolates from phylogroup 2 rely on the lipopeptide toxin syringomycin to promote host necrosis and enhance bacterial growth in plants.

Very happy to share the final version of our work on the evolution of broad host virulence in Pseudomonas out now @cellhostmicrobe It’s just in time for the holidays 🎄🦠 www.cell.com/cell-host-mi...

New pre-print from the lab on the natural history, phylogenomics, and allopolyploidy of North American Drosera. This work was from the pre-COVID field work graduate student Rebekah Mohn did in peatlands across the US and fell into muddy pits many, many times.