Christopher Wheat

rambaut/figtree Automatically exported from code.google.com/p/figtree - rambaut/figtree

The first version of FigTree was released nearly 20 years ago and it is still widely used (including by me). But there are currently 85 issues on the GitHub repo (github.com/rambaut/figt...) and some of them I don’t really like the look of.

Just found reviewer from @simonpcouch.com: Human-scale LLM code review, as if a member of the tidyverse team were there with you to workshop your code for reproducibility, readability, and resilience. Note it's still very experimental. #Rstats github.com/simonpcouch/...

Super excited about these results and new system.

Mapping, Expression, Loss-of-Function

I'm floored by how this locus seem to integrate all the spatial info to sketch the minute details of the phenotype, and how this is prone to evol tweaks

Large hyperdiverged haplotype without an inversion.

Something I’ve learned - the best research environments aren't sterile. They're alive with creativity and warmth, with huge fish murals and dogs who have no idea what a p-value is but show up to lab meeting anyway. Science is a human endeavour and humans need to be inspired by their surroundings.

New pre-print with some updates on ivory:miR193 in a highly polymorphic moth.

www.biorxiv.org/content/10.6...

We mapped ivory (again!?) this time controlling aspects of camouflage in Anticarsia gemmatalis. Mapping, SVs, Expression and Function.

Comments/suggestions welcome!

A group of researchers and participants gather at night in a mountain landscape around a glowing blue light trap used for collecting moths. The scene is illuminated by the bright light, with trees and dark mountain silhouettes in the background. The group is examining specimens and taking notes during fieldwork. Photo credit: Alena Suchackova.

(1/2) Applications are open for the second field workshop of WG 2: Specimen collection for genomic work
📍 Vlahi, Pirin Mountains (Bulgaria)
📅 15–19 June 2026
We’re bringing together Lepidoptera taxonomists, enthusiasts, bioinformaticians, and students for real hands-on learning and exchange.
⬇️ ⬇️

Expectations for Mendelian randomization research in PLOS One

After working with our community, @plosone.org has introduced stringent requirements for publishing Mendelian randomization studies.

Our experiences with this study type and expectations for authors are published in this Editorial:

journals.plos.org/plosone/arti...

Use as directed? A comparison of software tools intended to check rigor and transparency of published work The causes of the reproducibility crisis include lack of standardization and transparency in scientific reporting. Checklists such as ARRIVE and CONSORT seek to improve transparency, but they are not ...

Manuscript checks are a time-consuming and oft overlooked aspect of the publication process [no reviewers do not "do all the work"...]. Automating these should reduce costs, but how good is the software? doi.org/10.1371/jour...

Screenshot of the COI Pond webpage: Upload your academic CV and generate a draft NSF Collaborators and Other Affiliations (COA) Form to submit with your NSF grant proposals. COI Pond parses your CV to extract: Coauthors of articles published, in the last 48 months Collaborators on funded projects, in last 48 months Past PhD advisees & your own PhD advisor(s) Editorial roles, in last 24 months After extraction, you can edit the draft COA form before downloading a final version (in xslx format) that you can submit to NSF. COI Pond is a free tool* from Cevian Labs.

Today we’re excited to announce a new product: COI Pond is a tool for faculty and grant staff that converts an academic CV into a draft NSF Collaborators and Other Affiliations (COA) Form. COA forms are tedious work, and COI Pond makes it a snap. Try it for free, here cevianlabs.io/coipond/start/ /1

GBE Special Section on de novo gene evolution

We are happy to release our new Special Section on de novo Gene evolution!

Special Section: de novo Gene
🔗 academic.oup.com/gbe/pages/special-section-de-novo-gene

#genome #evolution #denovo

No animal alive today is ‘primitive’ – why are so many still labeled that way? All species alive today, from chimpanzees to bacteria, are cousins that each have equally long lineages, rather than ancestors or descendants of one another.

The idea that humans sit atop an evolutionary hierarchy dates back to 1866, when a scientist drew the first tree of life with "Man" at the top. This inaccurate view still shapes how we think of the animal world, despite decades of genomic evidence proving evolution has no hierarchy.

buff.ly/055hdSo

This this this this this this this

And in case people have not read it - this is worth a read www.cell.com/neuron/fullt... .. by @deevybee.bsky.social and others

Should biology put complexity first? The dictum “Everything should be made as simple as possible, but no simpler” poses a problem for biology. How simply can it be told without doing dama…

Terrific essay on unavoidable complexity by @philipcball.bsky.social
"It is not yet clear what a curriculum—not to mention both a public and a professional narrative—that begins [w/pleiotropy + polygenicity] would look like. But it would surely look more like real biology.
doi.org/10.1016/j.ce...

Evolution, genomics and conservation of butterflies and moths - Nature Reviews Biodiversity Butterflies and moths are key indicators of functioning and healthy ecosystems around the world. This Review describes the evolutionary history of the order Lepidoptera and tracks shifts in researcher...

Now online! In this review, we cover four major topics on butterflies and moths: their evolutionary history and diversification dynamics, genomics, global diversity patterns, and conservation 🦋🌏 (1/8) @natrevbiodiv.nature.com
www.nature.com/articles/s44...

Opinion | I Just Returned From China. We Are Not Winning.

I wouldn’t put it this way for research, as science isn’t about winning. But I also returned last week from China with similar sentiments about Chinese prowess.

www.nytimes.com/2026/02/10/o...

We are taking applications for our 2026 international Conservation Genetics course. This year the course will be in Brazil at the Vale Natural Reserve on Aug 3-13. See congenglobal.org/brazil2026/en for details. #conservation #genomics #course #handson #brazil #apply #biodiversity #bioinformatics

Degradation of fish food webs in the Anthropocene The decrease in body size driven by the selective species turnover is widely altering fish food web topology and function.

New paper out examining fish food web degradation in the Anthropocene. We show the structure of aquatic food webs are changing-- even when species richness doesn’t. These signals are strongly associated with decreases in body size within fish communities. www.science.org/doi/10.1126/... 🌐🐠🐡🦈🐟

Postdoctoral Fellow in Eco-evolutionary Modelling and Machine Learning The Department of Ecology, Environment and Plant Sciences (DEEP) at Stockholm University is located in the Arrhenius Laboratories on the Frescati campus. Currently, approximately 100 people, including

Please help me spread this postdoc position with me at Stockholm University, Sweden!!!! su.varbi.com/en/what:job/...

For the past two weeks, we've hosted Paty Machado & Jessie Pereira from the University of Campinas.

Together with Mar Repullés, Paty analysed genome-wide variation in Heliconius erato across the Atlantic Forest and Amazonia.

Paty's visit was possible thanks to @10klepgenomes.bsky.social

Comparison of read mappings at HG002 chr4:40,294,825-40,295,700, showing conventional (pbmm2) read mappings (above) and portello mappings (below). The same set of unaligned input reads were input into each mapping process.

What if you could improve small variant accuracy, CNV inference, and interpretability of your HiFi WGS data by taking a different approach to read mapping? Our new preprint describes portello, a method which demonstrates the potential for such improvements. (1/5)

To add one thing: if you have the data to run both classic dN/dS tests and MK tests, choose the latter. dN/dS tests are blind to positive selection in the important, constrained proteome, while MK test will work regardless of constraint, if DFE well estimated.
#evolution #adaptation #popgen

Participants of the workshop during Charlotte's presentation. Many screens show Hi-C maps being curated in real time.

(1/3) The 2nd Genome Curation Workshop continues!

Today, participants explored Merian elements and chromosome evolution in #Lepidoptera in a fantastic talk by @charlottewright.bsky.social

More info below 👇🦋

Hey genomics colleagues: are they any software programs you wish still worked on your modern OS? I’m trying to get a list of dead software that lost support and fell out of fashion, not due to method but due to software support. #genomics #evosky #evolbio #popgen #Evolution

Mechanisms linking cytoplasmic decay of translation-defective mRNA to transcriptional adaptation Transcriptional adaptation (TA) is a genetic robustness mechanism through which mutant messenger RNA (mRNA) decay induces sequence-dependent up-regulation of so-called adapting genes. How cytoplasmica...

This is a fascinating paper that reveals defined and clear mechanism for a phenomenon that for some seemed unbelievable- the up regulation of genes paralogous to those with specific types of inactivating mutations. This is called transcriptional adaptation 1/ www.science.org/doi/10.1126/...

Morphological innovation without gene co-option: the Drosophila sex comb evolved via changes in developmental tempo and energy metabolism https://www.biorxiv.org/content/10.64898/2026.02.13.705815v1

I unfortunately have a different story. I served on a hiring committee which initially failed. A late candidate then emerged with a superb publication record. There were reports of sexual misbehavior as a PhD student circulating but they were now married with kids. I voted yes 1/n

I voted “no” on hiring a former colleague at my prior institution who we hired against my recommendation.

My chair wanted to know why I voted no.

I replied that the candidate thought they were smarter than everyone else and that would come back and hurt us.

Hello Bluesky!

Does Nₑ really explain mutation rate (μ) or genome size (GS) in vertebrates?

We find the apparent Nₑ–μ link in Bergeron et al. (2023) is a “back-door” path via generation time, and GS is decoupled from both Nₑ and life-history traits.

www.pnas.org/doi/10.1073/...

#evobio #PNAS

If this is how you’re using Claude .. I don’t think there’s help for you.