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Nat Walker-Hale

@phylonatworks.bsky.social
779 followers 667 following 36 posts

🇳🇿 PDRA in the Chomicki group, Department of Biosciences, Durham University. Mostly phylo stuff, sometimes NZ pol, sometime just pol

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Reposted by Nat Walker-Hale
Vaughn Cooper @vscooper.micropopbio.org · 27/09/2026
How do Burkholderia multivorans bacteria adaptively evolve during infections of the cystic fibrosis airway? A longtime collab and intensive study of 8 patients links bacterial adaptations to disease progression. Our findings also unite prior studies. www.biorxiv.org/content/10.6...
biorxiv.org
Convergent genetic evolution within Burkholderia multivorans chronic infections correlates with lung function decline in cystic fibrosis patients
The patterns and pathways of pathogen adaptation during chronic infections can reveal the gateways microbes must unlock to colonize and persist. In chronic lung infections of cystic fibrosis (CF) pati...
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Joseph W. Brown @josephwb.bsky.social · 26/09/2026
Early-diverging lineages provide little information about ancestors academic.oup.com/sysbio/advan... From @phylieu.bsky.social @sinkingdiatom.bsky.social @omearabrian.bsky.social
academic.oup.com
Early-diverging lineages provide little information about ancestors
Abstract. Large phylogenetic trees are often unbalanced near the root, with a species-depauperate lineage sister to a far more species-rich clade. The spec
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Boas Pucker @bpucker.bsky.social · 26/09/2026
Excited to share our new paper is out in TPJ! 🌱 "Out of the blue: family-wide loss of anthocyanin biosynthesis in Cucurbitaceae" We explore the anthocyanin biosynthesis gene loss through comparative genomics: doi.org/10.1111/tpj.... @nancy-choudhary.bsky.social @puckerlab.bsky.social #Evolution
Synteny analysis supports the loss of crucial genes in the anthocyanin biosynthesis across Cucurbitaceae. Details and figure reference: https://doi.org/10.1111/tpj.71136
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Mikko Kolkkala @xcsci.bsky.social · 23/09/2026
Retrotransposon has gained viral-like cell-to-cell transmission capability, further blurring the conventional boundaries between transposons and viruses www.cell.com/cell/fulltex... (Tiukkaa tekstiä, vaikka ois joskus tehnyt gradunsa retrotransposoneista niin kuin mä)
cell.com
Direct cell-to-cell transmission of retrotransposons
Retrotransposons can infect neighboring cells using a mechanism that relies on a small fusogen-like protein rather than on the envelope protein that is typically required for infection.
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Reposted by Nat Walker-Hale
Ben Parker @ben-parker.bsky.social · 21/09/2026
Excited that our new paper with @henrylabsymbio.bsky.social and Kerry Oliver is out @pnas.org! We show that mobile genetic elements can spread adaptive host-benefiting traits across heritable insect symbionts on eco-evolutionary timescales.🧵 www.pnas.org/doi/10.1073/...
pnas.org
Phenotypic divergence is driven by mobile genetic elements in a heritable insect symbiont | PNAS
Heritable microbes profoundly influence insect biology, yet the traits they confer often evolve rapidly and differ among closely related symbiont s...
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Dmitri Petrov @petrovadmitri.bsky.social · 17/09/2026
We are searching for an Assistant Professor in Evolutionary Biology! Looking for colleagues asking fundamental questions relating to evolutionary processes and drivers of evolutionary patterns. If you think it is you, please do apply! And please repost. facultypositions.stanford.edu/jobs/assista...
facultypositions.stanford.edu
Assistant Professor in Evolutionary Biology - Stanford University, California, United States
The Department of Biology at Stanford University seeks applicants for a tenure-track Assistant Professor in Evolutionary Biology. A successful candidate will conduct research that asks fundamental que...
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Dr. K. Lotterhos @drk-lo.bsky.social · 15/09/2026
I'm hiring a bioinformatician! Review of applications starts October 1 with a start date as soon as possible. 🧪 #Genomics #popGen #CompBio northeastern.wd1.myworkdayjobs.com/careers/job/...
northeastern.wd1.myworkdayjobs.com
Bioinformatician - Lotterhos Lab
About the Opportunity About the Center for Marine Ecological Genomics The successful candidate will be based at the Lotterhos Lab and the Center for Marine Ecological Genomics at Northeastern Marine S...
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Nature Ecology & Evolution @natecoevo.nature.com · 14/09/2026
Obituary: Robert Ricklefs (1943–2026) www.nature.com/articles/s41... Polymath ecologist whose research and textbooks integrating ecology and evolution have inspired generations of students. Free to read: rdcu.be/D33fLgYcv4Ba
nature.com
Robert Ricklefs (1943–2026) - Nature Ecology & Evolution
Polymath ecologist whose research and textbooks integrating ecology and evolution have inspired generations of students.
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Alexis Stamatakis @stamatak.bsky.social · 12/09/2026
The RAxML-NG v2.0 preprint is out: www.biorxiv.org/content/10.6... v2.0 features integrated model testing, fast branch support metrics, automatic parallelization, phylogenetic difficulty prediction, genotype evolution models, to name but the most important features. And it is A LOT FASTER of course
biorxiv.org
RAxML-NG 2: Automatic model selection, novel tree search heuristics, and fast branch support metrics
RAxML-NG is a widely used tool for maximum likelihood based phylogenetic inference. In the seven years since the last RAxML-NG publication, we have continuously improved and extended the code. Here, w...
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Fabian Blombach @fblombach.bsky.social · 11/09/2026
Gene duplication of initiation factor TFIIB drove eukaryotic inventions like the RNA polymerase I, II and III split and probably cyclins. With Kris Kuo and @buzzbaum.bsky.social, we show that the archaeal TFIIB paralogue TFB2 enables a regulated cell cycle in archaea. www.biorxiv.org/content/10.6...
biorxiv.org
A TFIIB paralog drives cyclic transcription to orchestrate the archaeal cell cycle
Cyclic transcription is a hallmark of the cell cycle. While transcriptional waves in eukaryotes are driven by oscillations in cyclin-dependent kinase (CDK) activity, many archaea have an ordered cell ...
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Graham Coop @gcbias.bsky.social · 10/09/2026
I’m looking to hire an NIH funded postdoc to join our lab here at Davis (please RT). Ongoing areas of interest include: 1) polygenic signals of selection from time series, ARGs, GWAS, etc 2) The interpretation of GWAS, polygenic scores, & sources of confounding
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beetle moses @beetlemoses.bsky.social · 10/09/2026
Two panel comic. Panel 1: a whale fall lies at the bottom of the ocean. The bones are covered in a variety of bottom feeders and ocean critters. Panel 2: closer up, the group of bottom feeders are holding red solo cups and chatting with each other. Among the group is a tiger prawn, who thinks to himself, “I needed this…”
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Chuliang Song @clsong.com · 10/09/2026
A wonderful review by Stefano on 100 years of Lotka–Volterra models. Don’t miss the incredibly detailed Supplement, truly the “War and Peace” of LV models. I really wish it had existed when I was a grad student! doi.org/10.1146/annu...
doi.org
One Hundred Years of Lotka–Volterra Models
Over the past century, the generalized Lotka–Volterra (GLV) model has grown from a mathematical curiosity to a cornerstone of theoretical ecology. Here we celebrate the enduring legacy of Lotka and Vo...
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Joint Genome Institute @jgi.doe.gov · 09/09/2026
Perspective: Pangenomes are Only as Powerful as their Annotation Method Are researchers wasting resources following false trails — due to variations in interpretative methods? 🖥️🧬 🌱 @tomasbruna.bsky.social Full story below⬇️
jgi.doe.gov
Perspective: Pangenomes are Only as Powerful as their Annotation Method | Joint Genome Institute
Researchers may be wasting resources following false trails due to variations in interpretative methods.
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Jessica Abbott @jessicakabbott.bsky.social · 05/09/2026
Are you a mathematical modeller in ecology and evolution looking for a job? My department has an opening! Please spread the word! lu.varbi.com/en/what:job/...
lu.varbi.com
Senior Lecturer in Computational Biology
Lund University welcomes applicants with different backgrounds and experiences. Gender equality, equal opportunities and diversity are fundamental principles in all parts of the University’s activit
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Nat Walker-Hale @phylonatworks.bsky.social · 04/09/2026
Now online at PNAS! www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Tatsuya Nobori @tatsuyanobori.bsky.social · 03/09/2026
Great work by Ingram & Zipfel labs. Congratulations, everyone! An embryo-derived peptide signal directs endosperm polarity in Arabidopsis www.science.org/doi/10.1126/...
science.org
An embryo-derived peptide signal directs endosperm polarity in Arabidopsis
Angiosperm seed formation requires the coordinated development of the products of double fertilization—the embryo and the endosperm. The endosperm mediates efficient nutrient transfer from surrounding...
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Ina Satokangas @inasatok.bsky.social · 01/09/2026
A cool bunch of new speciation papers out recently in Molecular Ecology, looking at divergence, hybridisation, recombination, genome architecture, and so on! Genomics of Speciation special issue: onlinelibrary.wiley.com/doi/toc/10.1... #speciation #divergence #hybridisation #recombination #genomics
onlinelibrary.wiley.com
Special Issue: Genomics of Speciation: Molecular Ecology
Molecular Ecology is an international journal for research using molecular genetic techniques to address questions in ecology, evolution, behavior and conservation.
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Lucy van Dorp @lucyvandorp.bsky.social · 01/09/2026
Our latest preprint 👉 www.biorxiv.org/content/10.6... 🦠🧬 We explore the genomic legacy of the Second Plague Pandemic across Northern Europe and the Caucasus, analysing 23 newly reconstructed ancient Yersinia pestis genomes from Sweden, Denmark, the Netherlands, Armenia and Iceland. 1/
biorxiv.org
The Genomic Landscape of Post-Black Death Epidemics in Northern Europe and the Caucasus
One of the most devastating events in human history, the Black Death (c.1347-1353), marked the beginning of the Second Plague Pandemic. After initially receding, plague returned in intermittent outbre...
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David Lowry @davidlowry.bsky.social · 31/08/2026
I am currently searching for a postdoc to work on the evolution of adaptations, cold acclimation, and freezing tolerance in switchgrass. The position entails lab, growth facility, bioinformatics, and fieldwork. careers.msu.edu/jobs/postdoc...
careers.msu.edu
Postdoctoral Scholar-Fixed Term - East Lansing, Michigan, United States
Position Summary The Lowry Lab at Michigan State University is searching for a postdoctoral research associate to conduct field and laboratory experiments to understand the causes of genetic variation...
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Pleuni Pennings @pleunipennings.bsky.social · 28/08/2026
I wrote a blog post about writing a grant but realized that I should also share the news that I got a permanent job in France! I will stay in Montpellier at @isemevol.bsky.social. 😁 abetterscientist.wordpress.com/2026/08/28/a...
abetterscientist.wordpress.com
A blog about a grant proposal but first some good news
I got a permanent research job in France! Starting in October I will be a CNRS researcher (directeur de recherche), which means I can spend all my time on research here in Montpellier at the ISEM i…
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lastpositivist.bsky.social @lastpositivist.bsky.social · 28/08/2026
It's being treated as a policy victory that we have less of the world's smart young people coming to learn from us, participate in our society and economy. This is just so depressing to me, it feels like a complete victory for know-nothing ignorant bigotry over enlightened sensibilities.
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Ulrich Hammes @uhammes.bsky.social · 28/08/2026
I‘ve witnessed this story develop first hand. Driven mainly by Lana this is a fascinating piece of work. Worth your while.
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Joe Gage @joegage10.bsky.social · 27/08/2026
New preprint 1 of 3! GxE is everywhere, but what causes it at the molecular level? @skdeb.bsky.social led this project using allele-specific expression in a B73xMo17 hybrid to test whether sequence variation changes TF binding & drives cis-reg GxE in gene expression. www.biorxiv.org/content/10.6...
biorxiv.org
Cis-regulatory variation and transcription factor binding contribute to allelic genotype-by-environment interactions for gene expression in maize
Genotype-by-environment interactions (GxE), or differences in how genotypes perform across varying environments, are a pervasive source of phenotypic variation and underlie differences in local adapta...
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Tony Gamble @tonygamble.eurosky.social · 27/08/2026
New collaborative paper from the lab on gecko sex chromosome and genome evolution! 🧪🦎 www.science.org/doi/10.1126/...
science.org
Genomic predisposition is associated with the direction of sex chromosome evolution
Sex chromosome evolution is among the most dynamic genomic innovations in vertebrates, yet why some lineages evolve XY while others evolve ZW remains unclear. Using chromosome-level genomes from 19 ge...
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Sam Yeaman @samyeaman.bsky.social · 27/08/2026
Very excited about SimGEA: a method for detecting genomic signatures of local adaptation developed by Takahiro Sakamoto. Unlike previous methods, it achieves good control of the false discovery rate (on simulated data) while maintaining reasonable power www.biorxiv.org/content/10.6...
Figure showing the false discovery rate for simGEA (green), kendall's tau (red), LFMM2 (purple), and Baypass (blue). Kendall's tau involves uniformly high false discovery, as expected. Both LFMM2 and Baypass incur substantial false discovery rates (even above 50% in some scenarios). SimGEA achieves a well controlled false discovery rate across all scenarios we tested.
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Eduardo Amorim @cegamorim.bsky.social · 26/08/2026
I’ll be teaching *Population Genomics Using Ancient DNA Data* with @arunsethuraman.bsky.social and @ppezov.bsky.social through @physaliacourses.bsky.social online September 21–25. More information and registration: www.physalia-courses.org/courses-work...
physalia-courses.org
Population genomics using ancient DNA data
21th-25th September 2026
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Ted Stankowich @tedstankowich.bsky.social · 25/08/2026
The bold stripes help potential predators learn to not attack skunks. Individual skunks can vary considerably, from narrow stripes to nearly all-white coats, but are more variable where there are fewer predators. #TautonymTuesday #TaxonomyTuesday #Systematics academic.oup.com/evolut/artic...
academic.oup.com
Predation risk drives aposematic signal conformity
Warning signals should be consistent across individuals to facilitate predator learning and reduce ambiguity about the presence of an unpleasant defense. T
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Luke Remage-Healey @healeylab.bsky.social · 25/08/2026
Come be our colleague!!! TT position in Evolution careers.umass.edu/jobs/assista...
careers.umass.edu
Assistant Professor - Evolutionary Biology - Amherst, Massachusetts, United States
Title: Assistant Professor - Evolutionary Biology Executive Area: Academic Affairs College/School/MBU: College of Natural Sciences Department: Biology Work Location: Amherst Schedule: Full Time Work A...
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Casey Dunn @caseywdunn.bsky.social · 25/08/2026
My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.
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Kathryn R Elmer @profkathrynelmer.bsky.social · 25/08/2026
We have a ca 1.5 yr postdoc available in our team, asking, 'what is the shape of the fitness landscape between oviparity and viviparity?' and 'what drives viviparity to evolve'? 🧬 using 🦎 as a model. closes 16 Sept. Details on EvolDir evoldir.net/brian/evoldi... @glasgow.ac.uk @sbohvm.gla.ac.uk
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Adaptive Evolution Lab @adaevo.bsky.social · 22/08/2026
PhD opening to study the Genomics of Adaptation in globally invasive ragweed. It will be a cross-continent venture, co-supervised between @johnstinchcombe.bsky.social at Toronto and us at Melbourne. Please circulate! findanexpert.unimelb.edu.au/opportunity/...
findanexpert.unimelb.edu.au
Genomic evolution of adaptive traits in the globally invasive weed Ambrosia artemisiifolia : Find an Expert : The University of Melbourne
<p> Ragweed is native to North America and is now a globally invasive weed whose pollen is extremely allergenic. Australian ragweed populations are restricted to parts of Queensland and New South Wales, potentially limited by the extent of genetic variation available for local adaptation that could facilitate its spread. Our modelling suggests that the supply of genetic variation from North America could dramatically help colonise Australia further. </p> <p> However, we have no empirical understanding of how functional variation is acquired by Australian ragweed and whether North American source populations might supply such variation in an ecological context. </p> <p> This project will connect field experiments in Toronto and genomically-informed niche modelling in Melbourne to assess the risk of ragweed becoming a superweed, able to combine multiple sources of genetic variation to expand its range. Ragweed plants from multiple origins, including Australia, planted at the University of Toronto’s field station will be characterised phenotypically and genomically to measure functional differentiation between ranges. </p> <p> Genetic mapping will identify adaptive loci, or regions of the genome involved in adaptive traits. A newly drafted pan-genome will be used to assess if these adaptive loci are found in genomic regions with high levels of structural variation, such as copy number variants or inversion, likely to reduce the effectiveness of gene flow between populations and ranges. </p> <p> This analysis will shed light on the process of adaptation to novel environments using a weed as model of accelerated evolution, and inform biosecurity models in the context of globalisation and enhanced invasion risk. </p>
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Dan Schrider @samurscicop.bsky.social · 21/08/2026
Ages ago I shared a preprint about how gene conversion can cause hard selective sweeps to look like soft sweeps by copying the adaptive allele onto different haplotypes. The accepted version is now published in GENETICS: academic.oup.com/genetics/adv...
academic.oup.com
Allelic gene conversion softens selective sweeps
Abstract. The prominence of positive selection, in which beneficial mutations are favored by natural selection and rapidly increase in frequency, is a subj
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bioRxiv Plant Bio @biorxiv-plants.bsky.social · 22/08/2026
From distyly to stigma-height dimorphism: phylogenetic insights into the evolutionary breakdown of distyly in Jasminum www.biorxiv.org/content/10.64898/20…
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Qagggy! @qagggy.bsky.social · 21/08/2026
UK transit nerds are next level.
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Rui Borges @ruiborges23.bsky.social · 19/08/2026
1/4 Excited to share that our paper "Phylogenetic inference with not-so-rare mutations and tiny organisms" has been accepted in Systematic Biology! 🧬🦠 academic.oup.com/sysbio/artic...
academic.oup.com
Phylogenetic inference with not-so-rare mutations and tiny organisms
Abstract. A common assumption in mathematical models of molecular evolution is that mutations are rare. One example is the boundary mutation assumption, wh
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Neil Hall @neilhall.bsky.social · 20/08/2026
Biological Databases are critical infrastructure - not projects. As so much effort is put into harnessing AI to solve all our problems, we are allowing the foundational data resources crumble. Treat biological databases as infrastructure, not projects www.nature.com/articles/d41...
nature.com
Treat biological databases as infrastructure, not projects
Letter to the Editor
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Mark Hibbins, Great Lakes Swashbuckler @rejectresubmit.bsky.social · 14/08/2026
New review from me and @stepheniwright.bsky.social! We argue the time is ripe for a phylogenomic approach to the study of plant sex chromosomes: doi.org/10.32942/X2S...
doi.org
Plant sex chromosome evolution in the phylogenomic era
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Darrin T. Schultz @dts.bsky.social · 19/08/2026
Our new paper in Science Advances asks how animals' genomes have changed since their origin from a common ancestor over 600 million years ago, and what patterns in their DNA have arisen in the churn of speciation and extinction. www.science.org/doi/10.1126/...
Five-panel diagram explaining fusion-with-mixing in chromosome evolution. Red and blue represent two different ancestral chromosomes throughout.

A, Fusion-with-mixing: a red chromosome and a blue chromosome fuse into one half-red, half-blue bar. Down the page, successive rows show inversions, drawn as X-shaped crossings between rows, progressively interleaving the two colors until the bottom bar is finely striped. A widening gray wedge labeled Entropy runs alongside an arrow marked Time plus evolution, pointing down.

B, Independent regulation: two separate chromosomes, one red and one blue. In each, a regulatory element, drawn as an oval, acts by an arrow on a gene within its own chromosome only.

C, FWM and novel regulation: on a fused, mixed chromosome, a red gene and a blue gene now sit next to each other across an inversion breakpoint. Red and blue arrows show regulatory elements reaching across it to act on the other chromosome's gene.

D, Regulatory entanglement: an extensively mixed chromosome, finely striped. Below it, a row of alternating red and blue genes is linked by a dense web of crossing curved arrows, so many overlapping regulatory connections that unmixing the chromosome would break them.

E, Emergence of entangled loci: a five-species phylogeny. A red and a blue chromosome fuse at an ancestral node, and helical icons on later branches mark continued mixing. Colored boxes mark four new red-blue regulatory interactions arising after inversions. Species A keeps its two chromosomes separate. In species B through E, the two earliest interactions, cyan boxes 1 and 2, are present in every descendant lineage, while later ones, yellow 3 and magenta 4, appear in fewer.
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Silvia Ramundo @sramundo.bsky.social · 19/08/2026
A stress response can be a great starting point for discovering new biology! By following genes regulated during the chloroplast unfolded protein response, we’re discovering novel factors involved in chloroplast homeostasis. Here’s the first one we characterized: www.pnas.org/doi/10.1073/...
pnas.org
VIA1 is a conserved regulator of thylakoid membrane integrity that acts through VIPP1 | PNAS
Thylakoid membranes are indispensable for oxygenic photosynthesis, yet the mechanisms that protect these membranes from photooxidative damage remai...
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Botanical Society of America @botsocamerica.bsky.social · 18/08/2026
Foliar salt spray exclusion & tissue tolerance underlie local adaptation to oceanic salt spray New #AJB research by @madisonplunkert.bsky.social, @pcdurant.bsky.social, @davidlowry.bsky.social & Katherine Egeler doi.org/10.1002/ajb2... #botany #plantscience #monkeyflower #Mimulus
The coastal perennial ecotype of Mimulus guttatus DC. (syn. Erythranthe guttata DC.) growing on a cliff at Montara State Beach, Montara, California, USA, with oceanic salt spray damage on the leaf margin. Coastal M. guttatus has delayed flowering, which contributes to a salt spray escape strategy by reducing the amount of salt spray reaching these plants. Still, some salt spray contacts the plant, so later-acting strategies that keep sodium from entering the leaves and prevent cell damage are also key for local adaptation to coastal habitat. (Credit: David Lowry)
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Evolution Letters @evolletters.bsky.social · 10/08/2026
Big evolutionary events can fool phylogenetic analyses. A new approach combines phylogenetic regression with eigenvectors to reduce false positives and better account for the history written in genomes. doi.org/10.1093/evle...
doi.org
Characterizing and mitigating confounding by unreplicated evolutionary events in phylogenetic regression
Abstract. When researchers want to test for a direct effect of one attribute on another using interspecific data, they need to account for the confounding
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Shelly Gaynor @shellygaynor.bsky.social · 17/08/2026
Extremely proud of @fkyeeb.bsky.social on receiving the Margaret Menzel Award for her #Botany2026 @botsocamerica.bsky.social talk! Keyi has accomplished so much this year, including finishing her PhD! Very proud to be part of her team! 🥳🎉
Keyi and her introduction slide, which reads "Improving Detection in Large-Scale Gene Family Expansions and Associated Phylogenomic Inference" by Keyi Feng, Shelly Gaynor, and Stephen Smith
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Joseph W. Brown @josephwb.bsky.social · 17/08/2026
Empirical evidence and robustness of clock models with spikes 🧪 www.biorxiv.org/content/10.6...
biorxiv.org
Empirical evidence and robustness of clock models with spikes
Time-calibrated phylogenies provide information on past macroevolutionary history. Time calibration can be obtained from fossil ages or node calibrations in combination with a clock model describing e...
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New Phytologist @newphyt.bsky.social · 14/08/2026
✨ Paper spotlight ✨ (🧵 1/7) Auxin Response Factors: from transcription factors to auxin effectors nph.onlinelibrary.wiley.com/doi/10.1111/...
Fig. 1 AUXIN RESPONSE FACTORs (ARFs) and the nuclear auxin pathway.
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Nat Walker-Hale @phylonatworks.bsky.social · 13/08/2026
I haven't dug into who is right about the Nature disruptiveness paper, but this is very funny regardless
Image of a paragraph that reads: "Simple keyword searches highlight the severity of the problem. The sample used by Holst et al.1 includes 456 For Dummies guides (among them, MySpace For Dummies, Raising Goats For Dummies and Existentialism For Dummies), 88 Complete Idiot’s Guides, 50 Dr. Seuss and Curious George books, and the Captain Underpants, Goosebumps, Berenstain Bears and Diary of a Wimpy Kid series—all of which are entries with zero references (Extended Data Table 1). These examples are from a handful of title searches, not a systematic audit. Captain Underpants and the Preposterous Plight of the Purple Potty People does not cite prior literature; Holst et al.1 computed its disruption score."
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Richard McElreath 🐈‍⬛ @rmcelreath.bsky.social · 13/08/2026
I am making my group read @kokkonut.bsky.social primer on continuous time models in ecology (doi.org/10.1111/2041...). Clearest presentation of Gillespie algorithm I've seen.
Comparison of deterministic and stochastic dynamics in the Lotka-Volterra predator–prey system. (a), four different limit cycles depicting deterministic predictions when starting the cycle at different densities for predators and prey, and (b–d) one run of a stochastic implementation of the same process using the Gillespie algorithm (starting at N1 = 1000, N2 = 100). The purple arrow in (a) exemplifies the problem with the Euler equation: Extrapolating from the current direction of change is prone to ‘miss the curve’. In (b–d), the first three cycles are in green, the next three in blue and the final three in red, to make it more visually clear that the system is not bound to always spiral outwards (from blue to red), the opposite can happen too (from green to blue), but the outwards movement is often observed last because it makes the population very prone to extinction. Other parameters: b = 2, B1 = 5, B2 = 1, a = 0.1, μ = 1, n = 150.
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Peter @notalawyer.bsky.social · 12/08/2026
there are weeks where you fuck around (bring the nail clipper to other rooms) and days where you find out (cannot locate nail clipper)
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