Simion Paul

My entire team wrote an opinion paper about Common misconceptions of speciation research. Each section is written by 1-2 team members. The bulk of the writing happened during two writing retreats. It was a lot of fun and I am very happy with the result. academic.oup.com/evolinnean/art…

Exploring gene duplications! Our study reveals how duplicated genes diverge in function using structural and expression analysis across 36 species. Check out our paper: biorxiv.org/content/10.110… Thanks to @the_alexwv, @Gloveface, Paul Thomas, @cdessimoz #Genomics #Evolution

How #training and #education are crucial for #biodiversity protection. Read the article on Nature.com 👀 cetaf.org/elementor-1084… #taxonomy #BiodiversityMatters

NEW Publication!!😄 Phylogenomic analysis of Opisthokonta (#animals, #fungi, & relatives) reveals a largely robust #phylogeny, but uncovers orthology inference methods as a major contributor of #incongruence. This study provides a robust framework for studying the #Opisthokonts

Pretty strong evidence of negative mental health effects of doing a PhD. Recent working paper by @EvaRanehill, @annahsandberg, Sanna Bergvall, and Clara Fernström. Paper link: swopec.hhs.se/lunewp/abs/lun…

The value of ‘wasting time’ on deep thinking is often overlooked in a scientific ecosystem increasingly tainted by Wall Street’s productivity mindset. nature.com/articles/d4158…

Do grant proposal texts matter for funding decisions? A field experiment Spoiler alert...NO! #Grants #academia

MAST: Phylogenetic Inference with Mixtures Across Sites and Trees academic.oup.com/sysbio/advance… @systbiol

Worm Weds!🪱New preprint- The story of clitellate annelid genome evolution (earthworms, leeches) We found that they have extensive genome rearrangements, raising questions about how their gene regulation and development differs from other animals biorxiv.org/content/10.110… 1/10🧵

Interested in phylogenomics and plants ? We are still looking for candidates for a PhD thesis proposal at the University of Rennes about "Structural dynamics of plant genomes: Evolution of synteny in the context of polyploidy". t.ly/3gPDm Contact us for more info !

Very happy to announce the publication of our new SV genotyping tool for long read data: SVJedi-graph. Congrats to Sandra Romain for her first PhD student paper ! Come meet us and see Sandra present the method and its results at #ISMBECCB2023 #HiTSeq doi.org/10.1093/bioinf… 1/3

In our new study, we challenge this notion and show that for deep divergences DNA based tree inference is of similar accuracy to AA inferences 😱😱😱

@DanielTamarit Congratulations for this work! Quick curiosity question: do you results suggest that CAT models did not need FSR for Eukaryotes to be sister-clade to Hodarchaea ?

These results indicated a higher support for Hodarchaea, and not Njordarchaea, being the sister lineage of Eukaryotes. Hods are mesophiles and contain more ESPs in common with Eukaryotes. 10/

I am so very stoked that this study is finally out! So many years of work, now condensed in a few pages (+ extensive SI 😬). Don't miss @eme_laura's fantastic summary thread! Phylogenomics were central and painstaking. What did we do with 6 years of tree-making? 1/

The wonders of population genetics allow us to reveal the echoes of the tumultuous times our ancestors survived, forever imprinted in our genome. In this thread, I'll share my experience replicating one of my all-time favourite papers by @lh3lh3 and @richard_durbin

Using PAML to detect positive selection but need some guidance? @PKapli , @zihengyang , and I have been working on a protocol that we hope you find useful. The "Beginner's Guide on the Use of PAML to Detect Positive Selection" is now available! academic.oup.com/mbe/article/40… (1/n)

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Congratulations @tomodelmont et al nature.com/articles/s4158…