phylonatworks.bsky.social
Nat Walker-Hale
@phylonatworks.bsky.social
690 followers 540 following 15 posts
PDRA in the Chomicki group, Department of Biosciences, Durham University. Mostly phylo stuff, sometimes NZ pol, sometime just pol
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phylonatworks.bsky.social
Nat Walker-Hale @phylonatworks.bsky.social · May 6
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 🧵
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
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Reposted by Nat Walker-Hale
aprilwei.bsky.social
April Wei @aprilwei.bsky.social · 18h
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
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Reposted by Nat Walker-Hale
newphyt.bsky.social
New Phytologist @newphyt.bsky.social · 9d
✨ 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.
Fig. 8 Lithium in plants: Summary. (a) Li+ uptake occurs through nonselective cation channels (NSCCs).
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tomopfuku.bsky.social
tomomi parins-fukuchi @tomopfuku.bsky.social · Sep 5
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...
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
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Reposted by Nat Walker-Hale
thalia.bsky.social
Thalia, PhD @thalia.bsky.social · Aug 25
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 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
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Reposted by Nat Walker-Hale
larsostergaard.bsky.social
Lars Østergaard @larsostergaard.bsky.social · Aug 25
👉 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
'
my.corehr.com
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Reposted by Nat Walker-Hale
yjluo.bsky.social
Yi-Jyun Luo @yjluo.bsky.social · Aug 18
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...
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
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Reposted by Nat Walker-Hale
molbioevol.bsky.social
Molecular Biology and Evolution @molbioevol.bsky.social · Aug 18
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
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
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Reposted by Nat Walker-Hale
molbioevol.bsky.social
Molecular Biology and Evolution @molbioevol.bsky.social · Aug 13
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
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
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Reposted by Nat Walker-Hale
jamesbpease.bsky.social
James Pease @jamesbpease.bsky.social · Aug 7
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
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Reposted by Nat Walker-Hale
ajhgnews.bsky.social
The American Journal of Human Genetics @ajhgnews.bsky.social · Aug 13
📣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
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
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Reposted by Nat Walker-Hale
carriezhu.bsky.social
carriezhu.bsky.social @carriezhu.bsky.social · Aug 6
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
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Reposted by Nat Walker-Hale
siluwang.bsky.social
Silu Wang (she/her)🇨🇦 @siluwang.bsky.social · Jul 29
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
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Reposted by Nat Walker-Hale
larusnz.bsky.social
Jamie Wood @larusnz.bsky.social · Jul 24
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
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Reposted by Nat Walker-Hale
heineikeb.bsky.social
Ben Heineike @heineikeb.bsky.social · Jul 25
Nice work by @maxhaase.bsky.social about the strange history of yeast centromeres - got to see him present it at #yeast2025
maxhaase.bsky.social
Max Haase @maxhaase.bsky.social · Apr 25
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
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
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Reposted by Nat Walker-Hale
fungage-lab.bsky.social
Aaron Vogan @fungage-lab.bsky.social · Mar 7
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...
Illustration depicting the ways in which fungi can exchange genetic material with each other. Starship mediated HGT is confirmed experimentally in this preprint.
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Reposted by Nat Walker-Hale
profsimonfisher.bsky.social
Simon Fisher @profsimonfisher.bsky.social · Jul 23
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
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Reposted by Nat Walker-Hale
evobioclio.bsky.social
Charikleia Karageorgiou (Clio) @evobioclio.bsky.social · Jul 23
www.biorxiv.org/content/10.1...
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
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Reposted by Nat Walker-Hale
vandepoelelab.bsky.social
Vandepoele lab @vandepoelelab.bsky.social · Jul 16
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
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Reposted by Nat Walker-Hale
chenxinli2.bsky.social
Chenxin Li, PhD @chenxinli2.bsky.social · Jul 16
Enzymatic epimerization of monoterpene indole alkaloids in kratom by @oconnorlab.bsky.social

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
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Reposted by Nat Walker-Hale
aldpaleo.bsky.social
Anne-Laure D 🌿 @aldpaleo.bsky.social · Jul 15
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...
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.
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sishuowang.bsky.social
Sishuo Wang @sishuowang.bsky.social · Jul 11
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
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
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Reposted by Nat Walker-Hale
epigenci.bsky.social
Hanbin Lee @epigenci.bsky.social · Jul 11
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....
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Reposted by Nat Walker-Hale
frankelab.bsky.social
FrankeLab @frankelab.bsky.social · Jul 10
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
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....
rdcu.be
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Reposted by Nat Walker-Hale
seedrevolutionlab.bsky.social
Andy Plackett @seedrevolutionlab.bsky.social · Jul 10
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
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.
www.jobs.ac.uk
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Reposted by Nat Walker-Hale
devoevomed.bsky.social
Vincent J Lynch 🐘🦣🦥 🦇🐋🐢🐍 @devoevomed.bsky.social · Jul 9
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...
The Extinction of Truth
Or, a Colossal Pile of Bullshit
substack.com
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