Nat Walker-Hale

Interaction between floral rewards and floral symmetry shapes diversification dynamics in Amazonian trees Floral zygomorphy, or monosymmetry, is thought to have a positive effect on the diversification rates of angiosperms, but its true impact is still an open topic. Given the controversy surrounding th...

Happy to see this finally out! Diego is a brilliant student that took our grad course on Macroevolution during lockdown, and this eventually escalated to me becoming a co-author in his PhD chapter.

nph.onlinelibrary.wiley.com/doi/10.1111/...

Gene expression divergence following gene and genome duplications in spatially resolved plant transcriptomes After gene and genome duplications, expression divergence across cell types is not random, and it can be explained by a combination of gene age, gene funct

Our paper on the evolution (duplicated) gene expression divergence in spatially resolved plant transcriptomes is now out @theplantcell.bsky.social

w/ @yvdp.bsky.social

#PlantSci #Evolution

academic.oup.com/plcell/advan...

A cGAS-mediated mechanism in naked mole-rats potentiates DNA repair and delays aging Efficient DNA repair might make possible the longevity of naked mole-rats. However, whether they have distinctive mechanisms to optimize functions of DNA repair suppressors is unclear. We find that na...

This is so cool! Four amino acid changes in the naked mole rat cGAS turn it from a DNA repair inhibitor into an enhancer

www.science.org/doi/10.1126/...

What is going on in armadillos, which have lost the cGAS and STING genes‽ #PetosParadox #EvMed 🧪

pubmed.ncbi.nlm.nih.gov/40463121/

When sex chromosomes turnover, they can reset the rules of genomic conflict.
New preprint exploring how turnover reshapes barriers to gene flow through an “escape-hatch” model for mitonuclear conflict.
Any feedback would be welcome! ecoevorxiv.org/repository/v...

Inference of complex demographic history using composite likelihood based on whole-genome genealogies Accurate parametric inference on complex demographic models is a continuing challenge in population genetics. Ancestral recombination graphs (ARGs) provide richer information than simple population ge...

Excited to preprint our latest work (w/ Drew DeHaas, Zhibai Jia, Leo Speidel) on using ARGs for demographic inference. w/ applications using data from 1000 Genomes Project. www.biorxiv.org/content/10.1...

Fig. 8 Lithium in plants: Summary. (a) Li+ uptake occurs through nonselective cation channels (NSCCs).

✨ Paper spotlight ✨

#Lithium in plants
nph.onlinelibrary.wiley.com/doi/10.1111/...

(🧵 1/6) This #TansleyReview presents emerging insights into lithium’s role in #plants. Once thought to mimic sodium, lithium is now known to use distinct transport mechanisms and uniquely affect enzymes and DNA.

Sorting of ancestral polymorphism and its impact on morphological phylogenetics and macroevolution Abstract. Intraspecific phenotypic variation provides the basic substrate upon which the evolutionary processes that give rise to morphological innovation,

Excited to share a new paper! "Sorting of ancestral polymorphism and its impact on morphological phylogenetics and macroevolution". Part of some work I've been doing on modelling the evolution of polymorphic traits in fossil echinoderms.

academic.oup.com/evolut/advan...

The nature of mutation: a legacy of bacterial genetics Abstract. A central question in the fields of genetics and evolution was the nature and origin of spontaneous mutation. Bacterial genetic experiments throu

I cannot fully put into words what publishing this Review has meant to me, so I leave you with how we closed the paper.

"The humble bacterium is still a relevant tool for the study of the underlying mechanisms that are conserved throughout life."

🧪🧫🧬📚
doi.org/10.1093/gene...

👉 my.corehr.com/pls/uoxrecru...
Join us and be part of shaping the future of #plantscience at Oxford as we move to the new Life and Mind Building lifeandmind.web.ox.ac.uk/home (recognised for its potential to change the World edition.cnn.com/2025/01/01/s...) @biology.ox.ac.uk www.biology.ox.ac.uk

Conservation of bilaterian genome structure is the exception, not the rule - Genome Biology Species from diverse animal lineages have conserved groups of orthologous genes together on the same chromosome for over half a billion years since the last common ancestor of bilaterians. Although no...

Delighted to share the peer-reviewed version of our study led by @tomlewin.bsky.social now out in Genome Biology @bmc.springernature.com! We analyzed 64 chromosome-level genomes across 15 animal phyla and found that extensive genome rearrangements are the norm in bilaterians.
doi.org/10.1186/s130...

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

Convergent Molecular Evolution Associated With Repeated Transitions to Gregarious Larval Behavior in Heliconiini Abstract. Collective behavior forms the basis for many antipredator strategies. Within Lepidoptera, larval gregariousness has evolved convergently across m

Gregarious behaviour in butterfly larvae has evolved multiple times - Cicconardi, @ebablab.bsky.social et al. use genome data of 60 Heliconiini species, identifying signatures of convergent molecular evolution, on both coding and noncoding loci.

🔗 doi.org/10.1093/molbev/msaf179

#evobio #molbio

Differential gene reactions reveal drought response strategies in African acacias We studied the genetic basis of drought response in two well-known and widespread species of African acacia by analyzing gene expression reactions across a water deprivation experiment using a newly ...

Congrats to (newly graduated) Dr. Ellen Weinheimer for her new publication in @theplantjournal.bsky.social on drought responses in the iconic umbrella acacia of the African savannas using a "differential gene reaction" analysis developed for this project onlinelibrary.wiley.com/doi/10.1111/....

Estimation of demography and mutation rates from one million haploid genomes Samples of millions of genomes provide substantial information about recent demography and mutation, but standard population-genetic methods make assumptions not met in these data. We introduce DR EVI...

📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑‍🤝‍🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social

Escape from X inactivation drives sex differences and female trait variation X chromosome inactivation (XCI) partially balances gene dosage between sexes, yet expression from the inactive X (Xi) is variable across genes. In this study, we investigate whether gene-level Xi expr...

1/13 In a new preprint, we (with @xliaoyi.bsky.social‬ in the ‪@arbelharpak.bsky.social‬ lab) find that expression from the “inactivated” X (Xi) is consequential for both female-male differences in gene expression and variation among females in disease and physiology: www.biorxiv.org/content/10.1...

Check out our new special feature: Monitoring and Restoring Gene Flow in the Increasingly Fragmented Ecosystems of the Anthropocene www.pnas.org/topic/574 #biodiversity #evolution #ecology #popgen #ClimateEmergency

Long-term parasite decline associated with near extinction and conservation of the critically endangered kākāpō parrot Boast et al. analyze a unique fecal record of the endangered kākāpō parrot to reveal >800 years of changing parasite communities. Parasite losses occur during the species’ decline to near extinction a...

Parasite extinctions in threatened species may be far more prevalent than previous estimates suggest. Our new study of kākāpō dung spanning from ~1,500 years ago to present, finds >80% of parasite species were lost as the host species declined.

Nice work by @maxhaase.bsky.social about the strange history of yeast centromeres - got to see him present it at #yeast2025

Illustration depicting the ways in which fungi can exchange genetic material with each other. Starship mediated HGT is confirmed experimentally in this preprint.

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

Complex genetic variation in nearly complete human genomes - Nature Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.

Telomere-to-telomere DNA sequencing is set to transform the field of human genetics in coming years. For a flavour of what's coming, see this exciting work on nearly complete genomes of 65 individuals from diverse populations, out today in @nature.com by @glennislogsdon.bsky.social & colleagues. 👇🧬🧪

Segmental duplication-mediated rearrangements alter the landscape of mouse genomes Segmental duplications (SDs) are dynamic regions of mammalian genomes that drive structural variation and phenotypic diversity. However, genome-wide characterization of the SD landscape and the rearra...

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

We are hiring! If you have experience in plant genomics + AI, or promoter engineering + synthetic biology, check out our two open postdoc positions (computational + wetlab): www.vandepoelelab.be/Jobs please re-share RT #ERC

Enzymatic epimerization of monoterpene indole alkaloids in kratom - Nature Chemical Biology Monoterpene indole alkaloids are formed via a 3S stereoselective condensation between secologanin and tryptamine. Here the authors uncover the mechanism of epimerization behind uncommon 3R-containing ...

Enzymatic epimerization of monoterpene indole alkaloids in kratom by @oconnorlab.bsky.social

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

#PlantScience #SecMet

From the paper: Wood of Sphenophyllum with some fungal hyphae in transverse section (arrows)

From the paper : Detail of branching fungal hyphae within the wood of Sphenophyllum.

New accepted paper from @thibault-durieux.bsky.social's PhD reporting various fungal remains within the stem of a fossil plant from the Permian of France 🌿🍄⛏️ #paleobotany #paleomycology
#fossil #botany
www.sciencedirect.com/science/arti...

New Ways to Root Phylogenomic trees: the Smart, the symbiotic, the violent To root a phylogenomic tree is very important to study the evolutionary relationship between species. However, typically the substitution models (say GTR, LG, etc.) people use are time-reversible m…

some thoughts on new methods to root a phylogenomic tree: the smart, the symbiotic, the violent

sishuowang2022.wordpress.com/2025/06/19/n...

#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social

The paper is now online. The paper explains how even the simplest population genetic model can improve statistical power and explain the properties of admixed GWAS.

genomebiology.biomedcentral.com/articles/10....

Phylogenomics and metabolic engineering reveal a conserved gene cluster in Solanaceae plants for withanolide biosynthesis Nature Communications - Withanolides are plant steroids with potent bioactivities found in many medicinal plants including Withania somnifera, but their biosynthetic pathway is largely unknown....

Extremely happy to see our withanolide biosynthesis paper out in @natcomms.nature.com‬ rdcu.be/evHOF
Fantastic team effort with the Pucker group @bpucker.bsky.social‬ @puckerlab.bsky.social‬ at @unibonn.bsky.social and Heretsch, Herde and Witte groups at @unihannover.bsky.social. Funded by @dfg.de

Research Fellow (Postdoctoral) at University of Birmingham An opportunity for an academic position as a Research Fellow (Postdoctoral) is available, as advertised on jobs.ac.uk. Apply now and explore other academic job openings.

I have a Postdoctoral Research Fellow position starting in January to study the evolution of seed gene networks using the fern Ceratopteris! Interested? More info here:
www.jobs.ac.uk/job/DNU179/r...

Closing date 31st July. 🙂
#PlantScience
#PlantSciencejobs

The Extinction of Truth Or, a Colossal Pile of Bullshit

Re-upping given the moa deëxtinction nonsense from #ColossalBio and it’s cofounder Ben Lamm, it’s nominally about dire wolf “deëxtinction” but applies just as well to moas

substack.com/inbox/post/1...

A million shades of green: understanding and harnessing plant metabolic diversity
Rocky Payet, Anne Osbourn et al presents a step-by-step guide to starting a project that characterises plant secondary metabolites
www.embopress.org/doi/full/10....