Mike Barker

Tip rate estimates can predict future diversification, but are unreliable and context dependent https://www.biorxiv.org/content/10.1101/2025.10.06.680809v1

Restoring cytonuclear harmony: Distinct strategies in Arabidopsis auto‐ and allopolyploids Whole-genome duplication (WGD) disrupts cytonuclear balance by doubling nuclear content, requiring compensatory responses from organelles. In Arabidopsis auto- and allopolyploids, we found dynamic, o...

We’re excited to share our new work on how plants restore cytonuclear balance after whole-genome duplication. Using Arabidopsis auto- and allopolyploids, we uncover distinct, organelle-specific strategies in chloroplasts and mitochondria across generations.
doi.org/10.1111/tpj....

Assistant Professor Plant-Microbe Interactions We seek a creative, collaborative, and visionary plant biologist to establish an internationally recognized research program at the forefront of plant-microbe interactions aimed at understanding how t...

The Department of Biology at Colorado State University is hiring an Assistant Professor in the area of plant-microbe interactions! Please spread the word!

jobs.colostate.edu/postings/165...

Structure and sequence evolution in the pennycress (Thlaspi arvense) pangenome Summary · Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biod...

New — with @joannarifkin.bsky.social, @jotlovell.bsky.social, @spicybotrytis.bsky.social, and many more — we created seven new high-quality genomes and explored pangenomic variation in the emerging oilseed crop pennycress (Thlaspi arvense). 1/

Hybridization and introgression are major evolutionary processes. Since the 1940s, the prevailing view has been that they shape plants far more than animals. In our new study (www.science.org/doi/10.1126/...
), we find the opposite: animals exchange genes more, and for longer, than plants

Enhancing local meiotic crossovers in Arabidopsis and maize through juxtaposition of heterozygous and homozygous regions - Nature Plants This study discovered that locally confined DNA differences boost crossover rates in both Arabidopsis and maize, revealing a conserved mechanism that can accelerate plant breeding and trait introgress...

Breaking genetics news‼️🌱🌽 A natural DNA trick triples recombination in maize. What we first saw in Arabidopsis (@hendersi lab) a decade ago is now confirmed in crops—opening new doors for plant breeding. Published today in Nature Plants! More details 👉 www.nature.com/articles/s41...

Estimating waiting distances between genealogy changes under a Multi-Species Extension of the Sequentially Markov Coalescent Abstract. Genomes are composed of a mosaic of segments inherited from different ancestors, each separated by past recombination events. Consequently, genea

super excited to share this big project with @daeaton.bsky.social out now in Systematic Biology! We derived distributions for -- given an arbitrary species tree model -- how far you have to move along a genome before observing a change in the underlying genealogy: doi.org/10.1093/sysb...

Constraints on chromosome evolution revealed by the 229 chromosome pairs of the Atlas blue butterfly The genome of the Atlas blue butterfly contains ten times more chromosomes than most butterflies, and more than any other known diploid animal. Wright et al. show that this extraordinary karyotype is ...

How many chromosomes can an animal have?

In our paper out now in @currentbiology.bsky.social we show that the Atlas blue butterfly has 229 chromosome pairs- the highest in diploid Metazoa! These arose by rapid autosome fragmentation while sex chromosomes stayed intact.
www.cell.com/current-biol...

Our latest preprint led by @conjustover.bsky.social with fantastic undergraduate Sam Gibbon and @ryangutenkunst.bsky.social! Read Justin's thread below for more information on this fun project diving into mutation-selection balance in tetraploids! #polyploidy 🧪

So excited to be co-leading this special issue! Cannot wait to see all the innovative ways target enrichment sequencing is being used!

Don’t hesitate to reach out if you have any questions ☺️

Our latest preprint led by @conjustover.bsky.social with fantastic undergraduate Sam Gibbon and @ryangutenkunst.bsky.social! Read Justin's thread below for more information on this fun project diving into mutation-selection balance in tetraploids! #polyploidy 🧪

Bistable Mutation-Selection Equilibria and Violations of Fisher's Theorem in Tetraploids: Insights from Nonlinear Dynamics Polyploidy and whole genome duplication (WGD) are widespread biological phenomena with substantial cellular, meiotic, and genetic effects. Despite their prevalence and significance across the tree of ...

New Preprint! This one led by Sam Gibbon, an outstanding undergrad I've worked with for the past year. We take a look at whether segregation patterns in tetraploids (disomic v polysomic) affects mut-sel dynamics. We found some surprising results, and some subtleties: www.biorxiv.org/content/10.1...

Purple pollen visible in a dissected flower of Linum grandiflorum, flowering flax, an insect-pollinated species.

*Postdoc in Evolutionary genomics at Stockholm University*
We are recruiting a postdoc for a large interdisciplinary project to investigate evolutionary drivers and genomic consequences of pollen evolution in response to pollination mode shifts in flowering plants. 1/5

su.varbi.com/what:job/job...

Bistable Mutation-Selection Equilibria and Violations of Fisher's Theorem in Tetraploids: Insights from Nonlinear Dynamics https://www.biorxiv.org/content/10.1101/2025.08.28.672890v1

Atlanta Botanical Garden Inc - Research Scientist, Genetics The Atlanta Botanical Garden seeks a highly qualified scientist with training in plant population genetics to serve in the role of Research Scientist in Genetics within the Southeastern Center for Con...

We are recruiting a Research Scientist in Genetics trained in plant population genetics to run the Conservation Genetics Research Program! This is an incredible opportunity to work on a diverse and active team in a biodiversity hotspot!!! recruiting.paylocity.com/Recruiting/J...

📢🍄Job alert🍄📢
The Department of Plant Pathology of the University of Georgia is accepting applications for an Assistant/Associate Professor in Fungal Biology/Mycology. Anticipated start date of May 2026. Open until filled, so apply now!

www.ugajobsearch.com/postings/445...

I am recruiting graduate students to begin August 2026. Apply by Nov 15th!

MSU Plant Bio is hiring a new herbarium director! Our herbarium is a wonderful resource on campus and I'm excited to have the opportunity to make it even better by bringing in a new director. Details here: plantbiology.natsci.msu.edu/job-postings...

EdgeHOG: a method for fine-grained ancestral gene order inference at large scale - Nature Ecology & Evolution A new method to reconstruct ancestral genomes is used to estimate contigs of the last common ancestor of eukaryotes and to infer features such as the age of gene adjacencies and chromosome rearrangeme...

A new method to reconstruct ancestral genomes is used to estimate contigs of the last common ancestor of eukaryotes and to infer features such as the age of gene adjacencies and chromosome rearrangements

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

Graphic announcing a Computational Postdoctoral Fellow position. Text: Computational Postdoctoral Fellow – Plant Genomic Language Models (gLMs). JGI is seeking a Computational Postdoctoral Fellow to join a funded project at Berkeley Lab’s Joint Genome Institute applying genomic language models (gLMs) to unlock new biological insights in plants. Join one of the world’s leading genomics facilities to pioneer AI applications in plant biology, with access to cutting-edge computational resources and diverse genomic datasets. This project will focus on developing and exploring applications of gLMs to plant genomes, from identifying novel regulatory elements to revealing evolutionary patterns across species, with particular interest in cross-species and data-limited scenarios. In this role, you will design tasks and datasets to test and extend gLM capabilities, apply models to generate new biological hypotheses, and share findings through high-impact publications and presentations.

Postdoc opportunity with @tomasbruna.bsky.social here at @jgi.doe.gov @berkeleylab.lbl.gov:

Develop, benchmark, and apply Plant Genomic Language Models (gLMs) 🌿🧬💻

jobs.lbl.gov/jobs/computa...

#AI #PlantGenomics #gLMs #Postdoc

Out after peer review, collaborative study from Nordborg & Weigel labs with help from many others. Not the largest collection of new Arabidopsis thaliana genomes, but we hopefully put forward some good ideas for how to think about pangenomes and their analysis!
www.nature.com/articles/s41...

New Paper! In 2019, my first dissertation chapter revealed complicated polyploidies in the cotton family (Malvaceae) but we lacked the tools and genomes to truly understand it. Now with better genomes and improved methods, it's much more complicated than we thought. www.nature.com/articles/s41...

Notice Of Award for the renewal of our department's NIH T32 graduate student training grant arrived yesterday. Five years of funding for 8 students a year is a huge relief in this climate. Thank you to NIGMS staff for pushing out awards amidst all the upheaval! There are still good things happening.

Out today in @genetics-gsa.bsky.social #G3journal - our manuscript describing biases in summary statistics like genetic differentiation (Fst), diversity (pi), Tajima’s D, and estimates of theta, migration rates, and divergence times when not accounting for ghost gene flow. doi.org/10.1093/g3jo...

GHIST logo

I built a Gradio app to illustrate how selective sweeps can be detected from population genetic data: ryangutenkunst-sweep-detection-dpi.hf.space . It can help with your first submissions to the GHIST sweep detection challenges! ghi.st #GHIST

GHIST 2024: The 1st Genomic History Inference Strategies Tournament Evaluating population genetic inference methods is challenging due to the complexity of evolutionary histories, potential model misspecification, and unconscious biases in self-assessment. The Genomic...

Our manuscript describing the first Genomic History Inference Strategies Tournament is now on bioRxiv! Enjoy reading about the 2024 competition as you prepare your entries for the 2025 competition! ghi.st

tskit_arg_visualizer: interactive plotting of ancestral recombination graphs Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent brea...

Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.

🔗 arxiv.org/abs/2508.03958

1/6

ASTER: A Package for Large-Scale Phylogenomic Reconstructions Abstract. Many algorithms are available for inferring species trees from various input types while accounting for gene tree discordance. Several quartet-ba

C. Zhang, R. Nielsen and S. Mirarab integrate all ASTRAL-like methods into a single package called ASTER, comprising several tools that collectively enhance the scalability, accuracy, and versatility of species tree inference.

🔗 doi.org/10.1093/molbev/msaf172

#evobio #molbio #compbio

The genomic basis of local adaptation in the white x Engelmann spruce hybrid zone https://www.biorxiv.org/content/10.1101/2025.08.08.669264v1