Christopher Wheat
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chriswheat.bsky.social
Christopher Wheat
@chriswheat.bsky.social
1.9K followers 370 following 68 posts
Ecological & Evolutionary Functional Genomics, mostly butterflies. Biology Professor, Stockholm University.
Posts Replies Media Videos
Reposted by Christopher Wheat
pnas.org
Medieval agricultural and trade practices in southwestern Germany boosted plant diversity for centuries, with biodiversity peaking around 1000 CE and declining only when human activity contracted during the Black Death. In PNAS: https://ow.ly/Q6ca50XxIvC
Woodcut illustration to Michael Beuther’s Calendarium Historicum, published in Frankfurt by David Zephelius in 1557. Image shows a person pollarding a tree and another person sowing seeds. CREDIT: The Trustees of the British Museum. Shared under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) license.
November 25, 2025 at 7:01 PM
Reposted by Christopher Wheat
nclark.bsky.social
Wow A good explanation!
sashagusevposts.bsky.social Sasha Gusev @sashagusevposts.bsky.social · 4d
I wrote a little bit about the "missing heritability" question and several recent studies that have brought it to a close. A short 🧵
The missing heritability question is now (mostly) answered
Not with a bang but with a whimper
theinfinitesimal.substack.com
November 22, 2025 at 4:36 AM
Reposted by Christopher Wheat
sinamajidian.bsky.social
Our trilogy of orthology publications is online!
Review on Hierarchical Orthologous Groups doi.org/10.1007/s00239-025-10277-1

OrthoXML-Tools doi.org/10.1007/s00239-025-10271-7

A great community effort on Quest for Orthologs in the era of Data Deluge and AI doi.org/10.1007/s00239-025-10272-6
https://link.springer.com/article/10.1007/s00239-025-10277-1 Conceptual overview of hierarchical orthologous groups. An example of one HOG, or gene family. A Species tree with four taxa: plant (green), fish (blue), human (orange), and mouse (yellow), each with one or more genes. B The implied gene tree, dubbed “HOG tree,” and inferred nested HOG composition. Duplication nodes (red) can be deduced based on the species tree topology and clusters of homologous genes at each level. Ancestral genes from which the HOGs descended are shown in gray. C HOGs returned at different taxonomic levels. Consider a gene family that was present in the last eukaryotic common ancestor (LECA). At this level, a single HOG encompasses all genes descending from that ancestral gene. At the Vertebrata level, this gene underwent duplication, leading to two distinct copies, i.e., HOGs. At the Mammalia level, a second duplication further subdivides one of these HOGs, showing how deeper HOGs split into nested subHOGs at more recent levels. The HOG composition implies that a loss event occurred after the mammalian speciation https://link.springer.com/article/10.1007/s00239-025-10272-6 Summary of the QfO8 meeting. a Hot topics and future directions in method development and applications within the QfO community, namely artificial intelligence, protein domains, protein structure, RNA and splicing isoforms. b Definition of orthology and paralogy, including various paralogous subtypes (e.g. in-paralogs and out-paralogs). c Duplications and functional divergence. d Applications of orthology https://link.springer.com/article/10.1007/s00239-025-10271-7 Overview of the OrthoXML File Format (simplified). A schematic representation of an OrthoXML file, a standardized XML-based format for representing orthology data. OrthoXML follows a hierarchical structure where elements are enclosed within opening < tag > and closing </tag > tags. < orthoXML > is the root element enclosing other elements. The < species > element contains information about genes. An OrthoXML file can include a < taxonomy > element, which specifies the species tree used to generate the file. Additionally, the < groups > element encapsulates the orthology and paralogy relationships among genes
November 21, 2025 at 4:26 PM
Reposted by Christopher Wheat
pavelmatosm.bsky.social
Had a great workshop on population and conservation genomics with Kay Lucek. We revisited key concepts and metrics, and streamlined our ongoing projects in Czechia 🦋
November 20, 2025 at 9:30 AM
Reposted by Christopher Wheat
blekhman.bsky.social
I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field

open.substack.com/pub/blekhman...
The Autism-Microbiome Hypothesis Is Falling Apart
Why this new review paper should be required reading for every microbiome researcher
open.substack.com
November 19, 2025 at 5:12 PM
Reposted by Christopher Wheat
elisabethbik.bsky.social
SG: The 'forgotten' curve - the problem of p values. The chance that your replicate experiment of an experiment with p=0.05 will be reproducible is only 0.5 - it's a toss up!

Science publication is Darwinian: a survival pressure to publish.
royalsocietypublishing.org/doi/full/10....
#IRICSydney
Slide showing the forgotten curve Goodman 1992: https://onlinelibrary.wiley.com/doi/abs/10.1002/sim.4780110705 Curran-Everett 2017:
November 16, 2025 at 10:02 PM
Reposted by Christopher Wheat
nature.com
Nature research paper: An ancient recombination desert is a speciation supergene in placental mammals

go.nature.com/47UiBWa
An ancient recombination desert is a speciation supergene in placental mammals - Nature
Deep learning methods identified a large and evolutionarily conserved X-linked low recombination region in placental mammals that serves as both a barrier to gene flow in hybridizing lineages and an accurate phylogenomic marker.
go.nature.com
November 14, 2025 at 2:03 PM
chriswheat.bsky.social
Chatty for grant title brainstorming .. is off the chart this morning ... I just had to share the gem of the pile:

BUTTER-SEQ
November 15, 2025 at 8:39 AM
Reposted by Christopher Wheat
marcinwiorek.bsky.social
It was great to be there and collect Lepidoptera in the Italian Alps for @projectpsyche.bsky.social @10klepgenomes.bsky.social, and it's amazing to see it once again through the stunning photos by Luigi Avantaggio in Glenn Zorpette's article in @spectrum.ieee.org 👇
spectrum.ieee.org IEEE Spectrum @spectrum.ieee.org · 21d
In July, our reporter traveled to the Italian Alps and to Barcelona, Spain, to observe researchers capturing moths and butterflies and then sequencing their genomes. It was all part of the most ambitious biology project ever: to sequence every species on Earth.
The Genome Revolution Takes Flight: Mapping the DNA of Europe’s Lepidoptera
An expedition in the Italian Alps unleashes advanced genome sequencing
spectrum.ieee.org
November 12, 2025 at 7:17 PM
Reposted by Christopher Wheat
evolvwing.bsky.social
It's out, Minos transgenesis in the pantry moth by
@donyaniyaz.bsky.social
@lucalivraghi.bsky.social

High efficient, glowing eye and silk gland markers

peerj.com/articles/202...
@peerj.bsky.social
November 12, 2025 at 2:40 PM
Reposted by Christopher Wheat
itaiyanai.bsky.social
This is a such an inspiring book about the art of improvisation and how it applies to our lives in general. I think it’s also very relevant also for what it’s like to do science. It was a pleasure to talk with Stephen about it on the Night Science podcast! open.spotify.com/episode/165i...
November 12, 2025 at 4:47 PM
Reposted by Christopher Wheat
theorecol.bsky.social
We're now using this scale as part of all assignment instructions.
Students can use AI in (some) assessments, but we would expect a higher level of insight in those.
Get them to save/include all prompts & outputs to show how they've extended the AI slop.

leonfurze.com/2024/08/28/u...
Updating the AI Assessment Scale
Thanks for visiting! Before you read on, please make sure you visit our new website at https://aiassessmentscale.com/. It’s the new home for all of the AIAS related materials, publications, and resour...
leonfurze.com
November 11, 2025 at 5:16 PM
Reposted by Christopher Wheat
samjakeengland.bsky.social
Do you work (/want to work) with caterpillars? Or sensory systems? Or BOTH?! Well good golly do we have the paper for you! We explain the senses that caterpillars have, what they use them for, and how anthropogenic sensory pollution might be messing it all up 🐛 doi.org/10.1007/s003...
The sensory ecology of caterpillars - Journal of Comparative Physiology A
Caterpillars (larval Lepidoptera) are one of the most ecologically and evolutionarily significant taxa on Earth. As both feeders and food, they shape the dynamics of enumerate ecosystems on land. Key ...
doi.org
November 10, 2025 at 3:24 PM
Reposted by Christopher Wheat
phylogenomics.bsky.social
Yes, some people's legacies are complicated. For example, Watson. After all, though he was racist, don't forget his other traits. For example, he was also sexist. And also anti-semitic. And a data / idea thief. So let's not forget all the different facets.
November 8, 2025 at 12:52 AM
Reposted by Christopher Wheat
flybehaviour.bsky.social
A really good thread on adjusting your bsky filter settings, which you might not know are set to be fully on by default!
astridoverthere.bsky.social I said abolish and I fucking meant it @astridoverthere.bsky.social · 19d
Wondering why no one likes your posts anymore, even among your friends? It's because @jay.bsky.team and team have decided to hide a huge amount of content from all of our feeds by default.

Here's how to turn it off.

First go to the hamburger menu in the upper left corner
Screenshot of the top of a Bsky feed, with a red circle around the hamburger menu in the top left.
November 7, 2025 at 2:35 PM
Reposted by Christopher Wheat
10klepgenomes.bsky.social
👇Check out this article about our work in the Italian Alps and Barcelona, where we’re studying moth and butterfly genomes as part of @projectpsyche.bsky.social ’s goal to sequence every species in Europe 🦋🧬

#10kLepGenomes #Genomics #Lepidoptera
spectrum.ieee.org IEEE Spectrum @spectrum.ieee.org · 21d
In July, our reporter traveled to the Italian Alps and to Barcelona, Spain, to observe researchers capturing moths and butterflies and then sequencing their genomes. It was all part of the most ambitious biology project ever: to sequence every species on Earth.
The Genome Revolution Takes Flight: Mapping the DNA of Europe’s Lepidoptera
An expedition in the Italian Alps unleashes advanced genome sequencing
spectrum.ieee.org
November 6, 2025 at 10:06 AM
Reposted by Christopher Wheat
ergabiodiv.bsky.social
We are excited to welcome new members to our network of affiliated initiatives!
🦋 @projectpsyche.bsky.social aims to sequence the genomes of all butterflies and moths of Europe, supporting their conservation, protection and driving innovation.

🦋 Learn more: www.projectpsyche.org #Lepidoptera
November 7, 2025 at 1:40 PM
Reposted by Christopher Wheat
danielbolnick.bsky.social
I hadnt seen this particular take on this story till now. A minimalist apology. Not impressed.
nationalnews.co.uk/news/shamed-...
Shamed Scientist Apologises For The First Time About The Academic Scandal That Destroyed His Career And Shocked The World
An ecologist who shot to fame after discovering that spiders have human-like personalities has made an emotional apology after being
nationalnews.co.uk
November 6, 2025 at 8:31 PM
Reposted by Christopher Wheat
clauswilke.com
I think I understand how it can be that LLMs are both exceptionally good and quite terrible at programming. It's because there are two entirely different skillsets that we both call "good at programming." LLMs have only one of them.
blog.genesmindsmachines.com/p/llms-excel...
LLMs excel at programming—how can they be so bad at it?
My explanation for the mystery of why LLMs can be both exceptionally good and quite terrible at programming.
blog.genesmindsmachines.com
November 6, 2025 at 3:43 PM
Reposted by Christopher Wheat
molbioevol.bsky.social
Community competitions help benchmark approaches in computational biology. Struck et al. now present GHIST 2024 - The First Genomic History Inference Strategies Tournament, for the inference of evolutionary history from genome data.

🔗 doi.org/10.1093/molbev/msaf257

#evobio #molbio #compbio #popgen
MBE | GHIST 2024: The First Genomic History Inference Strategies Tournament
November 6, 2025 at 3:20 PM
Reposted by Christopher Wheat
jbyoder.org
Species invasions often create a "founder effect" that makes it hard to see effects of adaptation to the invaded habitat— genomic signals of a rapid post-bottleneck expansion look a lot like signals of adaptation. This study of European starlings teases those signals apart! 🌿🪶

buff.ly/4RopxHb
A flock of starlings, brown-black passerines, in flight over a body of water. Photo by Julio Mulero on Flickr.
November 4, 2025 at 3:54 PM
Reposted by Christopher Wheat
etkayapar.bsky.social
It is so nice to finally see the first paper of my PhD published! It was possible thanks to invaluable contributions of Andrea Chiocchio, @mariaheikkila.bsky.social, @jadrankarota.bsky.social, Lauri Kaila, and @lepphylo.bsky.social.
October 31, 2025 at 9:51 PM
Reposted by Christopher Wheat
jlsteenwyk.bsky.social
At the workshop on #Phylogenomics and #Evolutionary Genomics, @nclark.bsky.social will be giving a lecture and lab on linking #genotype-to-phenotype in a #phylogenetic framework

Space is limited - register today to ensure your attendance!
Registration link: evomics.org/apply-worksh...
October 30, 2025 at 6:48 PM
Reposted by Christopher Wheat
genomebiolevol.bsky.social
@guyleonard.bsky.social et al. report a near-complete genome and transcriptome sequence dataset for green algae host Paramecium bursaria, an endosymbiotic model system.

🔗 doi.org/10.1093/gbe/evaf183

#genome #evolution
De Novo Genome Sequence Assembly of the RNAi-Tractable Paramecium bursaria 186b: An Endosymbiotic Model System
Abstract. How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a use
doi.org
October 31, 2025 at 10:54 AM
Reposted by Christopher Wheat
paulhoskisson.bsky.social
Incredible paper - Genomic architecture of eggmimicry and its consequencesfor speciation in parasitic cuckoos www.science.org/doi/epdf/10.... and a great commentary here www.science.org/doi/epdf/10.... @btobirds.bsky.social
Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos
Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...
www.science.org
October 31, 2025 at 9:31 AM