Nat Walker-Hale
@phylonatworks.bsky.social
PDRA in the Chomicki group, Department of Biosciences, Durham University. Mostly phylo stuff, sometimes NZ pol, sometime just pol
Pinned
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 .....
nph.onlinelibrary.wiley.com
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 🧵
Reposted by Nat Walker-Hale
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/...
nph.onlinelibrary.wiley.com/doi/10.1111/...
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...
nph.onlinelibrary.wiley.com
October 9, 2025 at 11:38 AM
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/...
nph.onlinelibrary.wiley.com/doi/10.1111/...
Reposted by Nat Walker-Hale
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...
w/ @yvdp.bsky.social
#PlantSci #Evolution
academic.oup.com/plcell/advan...
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
academic.oup.com
October 16, 2025 at 11:20 AM
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...
w/ @yvdp.bsky.social
#PlantSci #Evolution
academic.oup.com/plcell/advan...
Reposted by Nat Walker-Hale
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/
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/
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...
www.science.org
October 10, 2025 at 3:36 PM
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/
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/
Reposted by Nat Walker-Hale
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...
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...
Resetting the rules: Sex chromosome turnover as an escape hatch for mitonuclear conflict
ecoevorxiv.org
October 10, 2025 at 3:54 PM
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...
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...
Reposted by Nat Walker-Hale
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...
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...
www.biorxiv.org
October 8, 2025 at 2:48 PM
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...
Reposted by Nat Walker-Hale
✨ 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.
#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.
September 29, 2025 at 10:01 AM
✨ 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.
#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.
Reposted by Nat Walker-Hale
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...
academic.oup.com/evolut/advan...
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,
academic.oup.com
September 5, 2025 at 5:43 PM
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...
academic.oup.com/evolut/advan...
Reposted by Nat Walker-Hale
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...
"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...
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
doi.org
August 25, 2025 at 4:48 PM
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...
"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...
Reposted by Nat Walker-Hale
👉 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
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
'
my.corehr.com
August 25, 2025 at 9:42 AM
👉 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
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
Reposted by Nat Walker-Hale
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...
doi.org/10.1186/s130...
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...
doi.org
August 18, 2025 at 9:39 AM
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...
doi.org/10.1186/s130...
Reposted by Nat Walker-Hale
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
🔗 doi.org/10.1093/molbev/msaf172
#evobio #molbio #compbio
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
doi.org
August 18, 2025 at 7:13 AM
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
🔗 doi.org/10.1093/molbev/msaf172
#evobio #molbio #compbio
Reposted by Nat Walker-Hale
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
🔗 doi.org/10.1093/molbev/msaf179
#evobio #molbio
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
doi.org
August 13, 2025 at 5:13 PM
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
🔗 doi.org/10.1093/molbev/msaf179
#evobio #molbio
Reposted by Nat Walker-Hale
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/....
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 ...
onlinelibrary.wiley.com
August 7, 2025 at 3:12 PM
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/....
Reposted by Nat Walker-Hale
📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
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...
www.cell.com
August 13, 2025 at 2:40 PM
📣Online NOW!
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
📄Estimation of demography and mutation rates from one million haploid genomes
🧑🤝🧑 @jgschraiber.bsky.social @jeffspence.github.io @docedge.bsky.social
Reposted by Nat Walker-Hale
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...
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...
www.biorxiv.org
August 6, 2025 at 2:42 AM
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...
Reposted by Nat Walker-Hale
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.
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...
www.cell.com
July 24, 2025 at 6:40 PM
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.
Reposted by Nat Walker-Hale
Nice work by @maxhaase.bsky.social about the strange history of yeast centromeres - got to see him present it at #yeast2025
It’s out! The evolutionary origins of yeast point centromeres uncovered!
“Ancient co-option of LTR retrotransposons as yeast centromeres”
www.biorxiv.org/content/10.1...
“Ancient co-option of LTR retrotransposons as yeast centromeres”
www.biorxiv.org/content/10.1...
Ancient co-option of LTR retrotransposons as yeast centromeres
The evolutionary origins of the genetic point centromere in the brewer's yeast Saccharomyces cerevisiae, a member of the order Saccharomycetales, are still unknown. Competing hypotheses suggest that t...
www.biorxiv.org
July 25, 2025 at 7:43 AM
Nice work by @maxhaase.bsky.social about the strange history of yeast centromeres - got to see him present it at #yeast2025
Reposted by Nat Walker-Hale
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...
March 7, 2025 at 7:18 AM
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...
Reposted by Nat Walker-Hale
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. 👇🧬🧪
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.
www.nature.com
July 23, 2025 at 4:20 PM
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. 👇🧬🧪
Reposted by Nat Walker-Hale
Reposted by Nat Walker-Hale
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
Jobs | Vandepoele Lab
www.vandepoelelab.be
July 16, 2025 at 8:45 PM
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
Reposted by Nat Walker-Hale
Enzymatic epimerization of monoterpene indole alkaloids in kratom by @oconnorlab.bsky.social
From: www.nature.com/articles/s41...
#PlantScience #SecMet
From: www.nature.com/articles/s41...
#PlantScience #SecMet
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 ...
www.nature.com
July 16, 2025 at 2:58 PM
Enzymatic epimerization of monoterpene indole alkaloids in kratom by @oconnorlab.bsky.social
From: www.nature.com/articles/s41...
#PlantScience #SecMet
From: www.nature.com/articles/s41...
#PlantScience #SecMet
Reposted by Nat Walker-Hale
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...
#fossil #botany
www.sciencedirect.com/science/arti...
July 15, 2025 at 9:43 AM
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...
#fossil #botany
www.sciencedirect.com/science/arti...
Reposted by Nat Walker-Hale
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
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social
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…
sishuowang2022.wordpress.com
July 11, 2025 at 9:18 AM
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
sishuowang2022.wordpress.com/2025/06/19/n...
#phylo
@tweethinking.bsky.social @andrewjroger.bsky.social