New paper showing clustering of the many traits across reproductive strategies of angiosperms. Lots of interesting discussions that gave raise to this piece. But only possible thanks to the hard work of Andrew Helmstetter, Sylvain Glémin, and Jos Käfer. nph.onlinelibrary.wiley.com/doi/abs/10.1...

An angiosperm‐wide perspective on reproductive strategies and floral traits

Flowering plants have many modes of sexual reproduction, notably varying from selfing to outcrossing, and from bisexual flowers to individuals with separate sexes (dioecy). These reproductive modes ...

nph.onlinelibrary.wiley.com

Hi all. I am very excited that after 6 years I finally got my phylogenetic comparative methods book and online exercises online. Feel free to use and share. The book is here: nhcooper123.github.io/pcm-primer/. Note that it is not finished, we had to abandon it before the sunk costs fallacy broke us

MutaPhy: A clade-based framework to detect genotype-phenotype associations on phylogenetic trees https://www.biorxiv.org/content/10.64898/2026.04.19.719535v1

Choosing the right tree matters. Phylograms outperform chronograms for neutral traits but not for detecting selection. By @phylogenetrips.bsky.social et al. doi.org/10.1093/evle...

Phylograms better fit neutrally evolving traits than chronograms

Many species are characterized by trait differences between each other. For example, the brain size of different primate and human lineages varies. The que

doi.org

New paper out from @hoehna.bsky.social Lab, led by the brilliant @bjorntko.bsky.social! We applied the Pesto software (Kopperud & Höhna, 2025) to look at lineage-specific shifts in diversification rate on large, densely-sampled phylogenies across the Tree of Life doi.org/10.1093/evle...

GLADE: Accurate inference of Gains, Losses, Ancestral genomes, and Duplication Events for comparative genomics https://www.biorxiv.org/content/10.64898/2026.01.27.702036v1

Nature research paper: Dated gene duplications elucidate the evolutionary assembly of eukaryotes go.nature.com/4azJDF8

Dated gene duplications elucidate the evolutionary assembly of eukaryotes - Nature

Analysis of eukaryotic gene sequences using a relaxed molecular clock methodology indicate that eukaryotes emerged 3.0–2.25 billion years ago as a result of mitochondrial endosymbiosis with complex archaea that already possessed an elaborated cytoskeleton, membrane trafficking, endomembrane, phagocytotic machinery and a nucleus.

go.nature.com

Check out our review/perspective piece on phylogenetic diversification analysis, intended for the 75th anniversary of @systbiol.bsky.social. I had the privilege of working with great coauthors, @fhenaodiaz.bsky.social, @tvasconcelos.bsky.social and @roszenil.bsky.social! doi.org/10.1093/sysb...

🌿Excited to share our new study in New Phytologist! 🌿 Polyploidy is a major force in plant evolution, but is understudied in the tropics. We find that polyploidy evolved multiple times in Inga, a characteristic Neotropical tree radiation (1/n) 🧵. Full paper🔗: tinyurl.com/msnffhs8

Symbiotic diversification relies on an ancestral gene network in plants doi.org/10.1101/2025...

Symbiotic diversification relies on an ancestral gene network in plants

Symbioses have been fundamental to colonization of terrestrial ecosystems by plants and their evolution. Emergence of the ancient arbuscular mycorrhizal symbiosis was followed by the diversification o...

doi.org

I cannot believe our work is finally out there and in @journal-evo.bsky.social ! This was an enormous group effort! We provide an updated estimate of the number of buzz pollinated angiosperm species, genera, and families, look at consequences for diversification, number of transitions, and more!

Mario Vallejo-Marin@nicrodemo.bsky.social · 10mo ago

How many plant species are buzz pollinated? After more than six years in the making, our paper on the convergent evolution of buzz pollinated flowers is out in @journal-evo.bsky.social. Thanks @draverbee.bsky.social @roszenil.bsky.social and all co-authors for your hard work! doi.org/10.1093/evol...

We are excited to share GPN-Star, a cost-effective, biologically grounded genomic language modeling framework that achieves state-of-the-art performance across a wide range of variant effect prediction tasks relevant to human genetics. www.biorxiv.org/content/10.1... (1/n)

🌸 FLOWERING NEWSLETTER REVIEW 🌸 🧬 Since the discovery of the first plant sex-determining gene, more than 20 other genes have been identified. Here Marais et al. review what this tells us about the evolution of separate sexes (dioecy) in angiosperms 🌸 🔗 doi.org/10.1093/jxb/... #PlantScience 🧪

Delighted that our paper about the distribution of genomic spans of clades/edges in genealogies (ARGs), and using this for detecting inversions and other SVs (and other phenomena that cause local disruption of recombination) is out in MBE academic.oup.com/mbe/article/... (1/n)

The Length of Haplotype Blocks and Signals of Structural Variation in Reconstructed Genealogies

Abstract. Recent breakthroughs have enabled the accurate inference of large-scale genealogies. Through modelling the impact of recombination on the correla

academic.oup.com

New preprint led by grad student, Yu Mo! We introduce new software to calculate evolutionary rates of quantitative characters in the presence of discordance 1/ www.biorxiv.org/content/10.1...

Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees

Quantitative traits provide insights into how phenotypes evolve across species. However, standard comparative methods often assume a single species tree and overlook the discordant gene tree histories...

biorxiv.org

Evolutionary and functional dynamics of chimeric pseudogenes ({varphi}genes) https://www.biorxiv.org/content/10.1101/2025.10.01.679709v1

Life-history evolution under artificial selection in a clonal plant https://www.biorxiv.org/content/10.1101/2025.10.01.679824v1

Estimating the rate of quantitative trait evolution in the presence of gene tree discordance by calculating likelihoods across trees https://www.biorxiv.org/content/10.1101/2025.10.06.680724v1

Excited to share the latest from the #eFLOWERproject: a morphospace study of angiosperm flowers led by Andrea López-Martínez and Marion Chartier! Angiosperm flowers reached their highest morphological diversity early in their evolutionary history nph.onlinelibrary.wiley.com/doi/10.1111/...

Unsolicited listicle: My list of the most criminally underused/underappreciated phylogenetic comparative methods. Note, I am not involved in ANY of these methods; but I see them as things people are often asking of comparative data but have been surprised at how infrequently they have been cited.

"To plan for the future, it’s sometimes necessary to look to the past." Nice highlight of our work synthesizing temporal, taxonomic, and spatial trends in botanical collections to facilitate new research avenues @emlombardi.bsky.social @softcorebotany.bsky.social

From Liam Revell et al. Testing for heterogeneous rates of discrete character evolution on phylogenies 🧪 academic.oup.com/jeb/article-...

Testing for heterogeneous rates of discrete character evolution on phylogenies

Abstract. Many hypotheses in the field of phylogenetic comparative biology involve specific changes in the rate or process of trait evolution. This is part

academic.oup.com

13. How to prepare a high-quality manuscript PDF Download www.cell.com/action/showP...

15. Tips on How to Write ‘Good’ "Develop your own voice and writing habits." bsky.app/profile/scin...

Science News@scinews.bsky.social · 2y ago

Tips on How to Write ‘Good’ #Matter PDF download www.cell.com/action/showP...

A new interpretable #MachineLearning approach to identify plant traits associated with #PlantAdaptation to divergent ecoregions New in #AppsPlantSci by Sambadi Majumder & Chase Mason (@plantevoecophys.bsky.social) bsapubs.onlinelibrary.wiley.com/doi/full/10.... #ecophysiology #Helianthus #botany

Genetic diversity matters because it determines species' capacity to adapt, persist, & recover onlinelibrary.wiley.com/doi/10.1111/... #biodiversity #genomics

Future Projections of Biodiversity Under Global Change Need to Include Genetic Diversity

This perspective argues that current methods for predicting biodiversity loss from future land use and climate change models are incomplete without incorporating projections of genetic diversity. Wit...

onlinelibrary.wiley.com

Chromosome-scale Genome Assemblies of Two Allopolyploid Cuscuta Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid Evolution doi.org/10.1101/2025... Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions doi.org/10.1017/qpb....

Chromosome-scale Genome Assemblies of Two Allopolyploid Cuscuta Species Uncover Genomic Signatures of Parasitic Lifestyle and Polyploid Evolution

Dodders (Cuscuta spp.) is an obligated parasitic plant, which lost a large part of photosynthetic genes but gained host genes through parasitism-mediated horizontal gene transfer (HGT). Their migrator...

doi.org

Important modification... from the FAQ, it seems that students who are beginning their PhDs in Fall 2025 can apply (as long as matriculation date is August 1, 2025 or after). Awards start in Fall 2026. www.simonsfoundation.org/grant/simons...

Simons Graduate Fellowships in Ecology and Evolution

The purpose of these awards is to provide support for students entering U.S.-based Ph.D. programs with a plan to perform research in ecology and evolution. While we will consider all projects in ecolo...

simonsfoundation.org

Joshua Weitz@joshuasweitz.bsky.social · last yr.

Get the word out far and wide. New opportunity from the Simons Foundation in the Eco-Evo space. 2026 Simons Graduate Fellowship in Ecology and Evolution Awards, due July 31, 2025, only for incoming PhD students who plan to start their PhDs in Fall 2026. www.simonsfoundation.org/grant/simons...

Partial retention of ancient function increases genetic pleiotropy in grass evolution https://www.biorxiv.org/content/10.1101/2025.08.22.670905v1

I’m proud to present the main work from my postdoc, 3+ years in making from scratch, my ultimate #MimulusPropaganda up till now: The Moment That Symmetry Breaks. #plantscience #development #imaging #microscopy 🧪🌸🔬 w. Captain Yaowu & @biancatash.bsky.social www.biorxiv.org/content/10.1...