Christopher Wheat

Promoting the use of phylogenetic multinomial generalised mixed-effects model to understand the evolution of discrete traits Abstract. Phylogenetic comparative methods (PCMs) are fundamental tools for understanding trait evolution across species. While linear models are widely us

NEW METHODS ARTICLE: Phylogenetic GLMMs open doors to study evolution of discrete traits. We show how binary models extend to ordinal & nominal traits, using bird data, and provide tutorials to make these methods accessible to evolutionary biologists:

doi.org/10.1093/jeb/...
Mizuno et al.

🚀 Join our online course “Species Distribution & Ecological Niche Modelling in R” with @ambarbosa.bsky.social from Jan 19–23! Learn SDM & ENM concepts with hands-on R practice—no advanced skills needed. Save your spot now! 🌿👉 www.physalia-courses.org/courses-work...

Infographic with AI slop published in Nature Scientific Reports

"Runctitiononal features"? "Medical fymblal"? "1 Tol Line storee"? This gets worse the longer you look at it. But it's got to be good, because it was published in Nature Scientific Reports last week: www.nature.com/articles/s41... h/t @asa.tsbalans.se

Causal modelling of gene effects from regulators to programs to traits - Nature Approaches combining genetic association and Perturb-seq data that link genetic variants to functional programs to traits are described.

GWAS has been an incredible discovery tool for human genetics: it regularly identifies *causal* links from 1000s of SNPs to any given trait. But mechanistic interpretation is usually difficult.

Our latest work on causal models for this is out yesterday:
www.nature.com/articles/s41...
A short🧵:

Pangenomics transforms evolutionary biology | Royal Society This Theo Murphy meeting organised by Dr Joana Meier, Dr Henry North and Dr Charlotte Wright, will showcase cutting-edge pangenome tools, applied uses of pangenomes which are transforming health and a...

Are you excited about pangenomics? If so, join us in Edinburgh on 8-9th June to discuss the latest methods & insights from using these approaches across biodiversity! More details here:

royalsociety.org/science-even...

Organised together with @henrylnorth.bsky.social & @joanameier.bsky.social!

Don't ask “when is it coevolution?”—ask “how?” Abstract. Coevolution has come to be widely understood as specific, simultaneous, reciprocal adaptation by pairs of interacting species. This strict-sense

It's in print! My opinionated dive into the definition of "coevolution" is officially out in the December issue of @journal-evo.bsky.social

doi.org/10.1093/evol...

Such an awesome paper! Go @alexrob.bsky.social, @alisonfeder.bsky.social and Ben Kerr! At times less is more.

www-nature-com.stanford.idm.oclc.org/articles/s41...

YouTube video by Cells4PlanetaryHealth Insights from Dr. Jan Ellenberg: Why Global Cooperation is Key to Tackling Climate Change?

Watch Jan Ellenberg @scilifelab.se on the importance of #PlanetaryCellBiology and opportunities for ECRs. Join the discussion tomorrow Dec 7 | 8:30-9:45 AM EST CellBio2025 @ascbiology.bsky.social @embo.org. www.youtube.com/watch?v=KgRW... and/or join our community docs.google.com/forms/d/e/1F...

Helixer: ab initio prediction of primary eukaryotic gene models combining deep learning and a hidden Markov model - Nature Methods By leveraging both deep learning and hidden Markov models, Helixer achieves broad taxonomic coverage for ab initio gene annotation of eukaryotic genomes from fungi, plants, vertebrates and invertebrat...

🚀 Big news in genome annotation! The latest Nature Methods paper presents Helixer. Developed as part of the @denbi.bsky.social infrastructure, Helixer makes high-quality genome annotations more accessible and efficient for the community.
🔗 nature.com/articles/s41592-025-02939-1

Accurate Runs of Homozygosity Estimation From Low Coverage Genome Sequences in Non‐Model Species Runs of homozygosity (ROH) are increasingly being analysed using whole genome sequences in non-model species as a measure of inbreeding and to assess demographic history, thus providing useful inform...

Accurate Runs of Homozygosity Estimation From Low Coverage Genome Sequences in Non-Model Species
#popgen #consgen
doi.org/10.1111/1755...

Very proud to see this work highlighted by the journal! Publishing in Evolution has always meant something special to me. Congrats to the first author Sylvain Pouzet who found the energy to keep on working on his master project during his PhD.

RegEvol: detection of directional selection in regulatory sequences through phenotypic predictions and phenotype-to-fitness functions https://www.biorxiv.org/content/10.1101/2025.11.26.690685v1

Fast and Memory-Efficient Dynamic Programming Approach for Large-Scale EHH-Based Selection Scans Abstract. Haplotype-based statistics are widely used for finding genomic regions under positive selection. At the heart of many such statistics is the comp

Rahman, Smith & Szpiech present selscan v2.1, a dynamic programming algorithm to improve runtime and memory usage in the calculation of extended haplotype homozygosity.

🔗 doi.org/10.1093/molbev/msaf275

#evobio #molbio #compbio

MBE | Mitonuclear Discordance of Beetles Shaped by Incomplete Lineage Sorting and Introgression Under Loose Interaction Mechanism

Zhao et al. analysed phylogenetic signal in OXPHOS genes, mtDNA genes and nuclear genes in 53 beetle species, detecting two major cases of mitonuclear discordance caused by introgressive hybridization and incomplete lineage sorting.

🔗 doi.org/10.1093/molbev/msaf291

#evobio #molbio

Robust and Efficient Confidence Limits for Phylogenomic Inference of Organismal Relationships Abstract. Phylogenomic data are indispensable for establishing reliable relationships needed to build a robust Tree of Life. The superalignment approach co

Sharma & Kumar present the Net Bootstrap Support (NBS) approach that accounts for phylogenetic variation in the estimates of bootstrap confidence.

🔗 doi.org/10.1093/molbev/msaf296

#evobio #molbio #phylogenetics

Democratizing protein language model training, sharing and collaboration www.nature.com/articles/s41... (read free: rdcu.be/eOikv) 🧬🖥️🧪 github.com/westlake-rep...

Better monitoring to support restoration of EU pollinators The Commission has adopted a new Pollinator Monitoring Scheme to help reverse the decline of pollinator populations by 2030.

The EU has published rules for the Pollinator Monitoring Scheme. Butterflies, moths, bees and hoverflies will all be monitored by every Member State. Target to reverse decline in Pollinators by 2030 and increase pops. A big step in conserving biodiversity environment.ec.europa.eu/news/better-...

plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics www.biorxiv.org/content/10.1... 🧬🖥️🧪 R package meyer-lab-cshl.github.io/plinkQC/ #Rstats

A shorthair domestic cat gazes upward.

The domestic cat may be a far more recent arrival to Europe than previously thought, a new Science study. finds. The results offer new insight into one of humanity’s most enigmatic animal companions and identify North Africa as the cradle of the modern housecat.

Learn more: https://scim.ag/44kov1S

1,000 butterfly and moth genomes to investigate evolution, climate change resilience, and tackle food security issues These freely available genomes can be used to answer evolutionary questions, inform conservation and improve food security around the world.

The DNA of butterflies & moths is supporting conservation, shedding light on evolution, and could find new ways to stop pests 🦋
1,000 genomes have been released, and @projectpsyche.bsky.social aims to continue until all 11,665 European species have been sequenced🧬

www.sanger.ac.uk/news_item/10...

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.

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

Wow A good explanation!

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

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

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 🦋

The Autism-Microbiome Hypothesis Is Falling Apart Why this new review paper should be required reading for every microbiome researcher

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...

Slide showing the forgotten curve Goodman 1992: https://onlinelibrary.wiley.com/doi/abs/10.1002/sim.4780110705 Curran-Everett 2017:

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

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.

Nature research paper: An ancient recombination desert is a speciation supergene in placental mammals

go.nature.com/47UiBWa

2nd best:

FLUTTER-GEN

Chatty for grant title brainstorming .. is off the chart this morning ... I just had to share the gem of the pile:

BUTTER-SEQ

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 👇