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

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...

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!

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)

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...

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-...

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...

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

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....

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...

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...

The unique morphological basis & repeated evolutionary origins of personate flowers in #Penstemon New #AJB research by @trinitydepatie.bsky.social & @carriewessi.bsky.social doi.org/10.1002/ajb2... #botany #plantscience #phylogenomics #evolution #snapdragon

OrthoFinder just dropped a major update It’s faster, more accurate, and ready for thousands of genomes Let’s break it down (1/10) github.com/OrthoFinder/... www.biorxiv.org/content/10.1...

Plasticity in climate change responses - just published in Biological Reviews What in the role of phenotypic plasticity as an adaptive response to climate change? Looking at mechanisms from the subcellular to the community and ecosystem levels. With Stollewerk, @davidboukal.bsky.social, et al.

🚨 Our GW paper is out in Nature Methods!🥲 GW is a fast genomics browser (up to 100x faster!) github.com/kcleal/gw Also, just released a Python interface for GW github.com/kcleal/gwplot 📝 nature.com/articles/s4159…#Genomicsc#Bioinformaticscs

Loss-of-function mutations cannot simply eliminate some paralogous genes. Duplicated genes encoding homomeric proteins interfere with each other, leading to negative selection on the paralogs, even if they are fully redundant. See our new findings here: www.biorxiv.org/content/10.1...

A new paper in Nature Ecol & Evol by @rosafernandez.bsky.social et al. shows a #punctuated burst of genome evolution in #annelids as they transitioned from marine to land and freshwater habitats.

Mesquite 4 beta released! Many new features, esp. phylogenomic. Check out the trailer and longer video on the home page: www.mesquiteproject.org, and use the download link there to get a copy. Feedback welcome! Ask and discuss on our new Google Group (groups.google.com/g/mesquite-p...).

🚨🎉 New paper "Ten quick tips to get you started with Bayesian statistics", hope you'll like it 😇🤗 ✍🏽 w/ Andy Royle, Marc Kéry and Chloé Nater 🔗 dx.plos.org/10.1371/jour... @plos.org @cnrsecologie.bsky.social @cnrsoccitanieest.bsky.social @umontpellier.bsky.social

🚨New #phylo paper alert!🚨 🌲+🔥= speciation? This one has been a bit of a journey, but thanks to lead author Dan Turck's expertise on #conifers it has turned out as quite the treasure-trove of conifer evolution! (reading-access link on my website)

The recording of last week's #PolyploidyWebinar featuring @raymondcast.bsky.social and @erichagen.bsky.social is now up! youtu.be/zmUyTO3jN6s

1️⃣ 🌍 Fresh out in #Science! The Asian tropics are among the most biodiverse places on Earth, but where does all that diversity come from? 🤔🔍 We used 🌴 phylogenomics and 🦴 new fossils to unravel the roles of different regions in generating and distributing species! 🌱 #Evolution

My new preprint (with Matt Pennell & Lauren Sallan), which is my first at OIST, is now online! Finally, something cheerful in this depressing period... Thread 🧵 ahead:

Shifting, expanding, or contracting? Range movement consequences for biodiversity 🌎🌐🧪 www.cell.com/trends/ecolo...

Expanding plant trait databases using large language model: A case study on flower color extraction https://www.biorxiv.org/content/10.1101/2025.02.11.637746v1

1st paper from my lab this year. Chelsea & Erica showed that self-incompatible plants of this little groundcherry change to self-compatible as they get old, but they are only passable selfers, making less than half the number of seeds as plants are fixed for self-compatibility rdcu.be/d7ZM8

My favourite papers yield more questions than answers. This one is like that. Fascinating! www.biorxiv.org/content/10.1...

🧵𝐀 𝐭𝐡𝐫𝐞𝐚𝐝 𝐰𝐢𝐭𝐡 𝐟𝐞𝐚𝐭𝐮𝐫𝐞𝐝 𝐥𝐚𝐛 𝐩𝐮𝐛𝐥𝐢𝐜𝐚𝐭𝐢𝐨𝐧𝐬: 🧵 #1️⃣ Hofstatter, Thangavel, Lux et al. 2022 𝘊𝘦𝘭𝘭: 𝗥𝗲𝗽𝗲𝗮𝘁-𝗯𝗮𝘀𝗲𝗱 𝗵𝗼𝗹𝗼𝗰𝗲𝗻𝘁𝗿𝗼𝗺𝗲𝗿𝗲𝘀 𝗶𝗻𝗳𝗹𝘂𝗲𝗻𝗰𝗲 𝗴𝗲𝗻𝗼𝗺𝗲 𝗮𝗿𝗰𝗵𝗶𝘁𝗲𝗰𝘁𝘂𝗿𝗲 𝗮𝗻𝗱 𝗸𝗮𝗿𝘆𝗼𝘁𝘆𝗽𝗲 𝗲𝘃𝗼𝗹𝘂𝘁𝗶𝗼𝗻 www.cell.com/cell/fulltex... @gokilavani.bsky.social #PlantSciences #Chromosome #Genomics #Meiosis4eva #Centromere 🌱🧬🔬

Happy to share our Tansley insight published in @newphyt.bsky.social nph.onlinelibrary.wiley.com/doi/epdf/10.... #plantscience #chromosome #centromere #meiosis

Happy to announce the beta release of #BiGSCAPE2! This is the result of a great effort by Arjan Draisma, Catarina Loureiro and Nico Louwen, who worked tirelessly to improve the code from the ground up! Also major kudos to @marnixmedema.bsky.social for his leadership 💪 github.com/medema-group...

"One of the great tragedies of mankind is that morality has been hijacked by religion. So now people assume that religion and morality have a necessary connection. But the basis of morality is really very simple and doesn't require religion at all." -- Arthur C. Clarke, born #OTD 1917

Evolution: Morphological complexity fuels rapid species turnover: authors.elsevier.com/a/1kH973QW8S... #paleontology #paleobiology #evolution #fossils #ammonoids

There are now 24 step-by-step guides, explaining how to create these ⬇️ data visualizations with R/ggplot2 - I hope this is a useful resource. Find them all here: joachimgoedhart.github.io/DataViz-prot...

(it’s a fig tree)

The Missouri Botanical Garden (MBG) is seeking a Scientist to join our Latin America Program! The successful candidate will establish a collaborative research program, with a focus on the Tropical Andes or other regions where MBG is engaged. Apply here: jobs.dayforcehcm.com/en-US/mbg/CA...

Come join us in Tucson!! I am excited to announce a tenure track faculty position on the genomics of resilience @uofa-eeb.bsky.social! Read more about the position in the updated link below! We will begin reviewing applications on December 9! arizona.csod.com/ux/ats/caree...