Hot off the press!
We are sharing oligoN-design, an open-source tool to find specific probes and primers from large molecular datasets, without relying on specific databases, alignments or phylogenetic trees.
@mariescopy.bsky.social @rmassanam.bsky.social @beaplab.bsky.social
doi.org/10.1111/1755...
Our new article on #protist global distributions combining the #Mixoplankton and #metaPR2 databases with newly revised functional annotations.
rdcu.be/fanlx
My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵
🔁 🙏
#microSky #phagesky #UTIsky
@cnrs.fr
Llevo muchos años en esto y creo que es la mejor entrevista que he visto sobre el impacto real del accidente de Chernóbil.
Una fascinante conversación con @gorizaola.bsky.social, zoólogo, investigador y divulgador, que ha trabajado varios años en la zona de exclusión.
youtu.be/1fiJacjjW2s?...
No worries, it's impossible to keep up with all the literature at the moment ;)
Exactly! :) We discuss the dinoflagellate mucosphere (from Larsson et al) in our study. The problem (or charm!) studying Radiolaria is that they don't reproduce in culture, so much of their biology and ecology is based almost only on field observations.
In here they described it as "mucosphere" doi.org/10.1038/s414..., and in Radiolaria it's been traditionally used "gelatinous". I think it would be interesting to see what these "matrices" are all made of and their function!
Indeed! The Cambrian explosion reflects a change in the preservation of fossils or the sudden development of fossilizable structures (among other things). See our discussion on the "Sppil‐Rongis" effect and refs, for example. Or the development of skeleton in e.g. Radiolaria doi.org/10.1016/j.cu...
Looking forward! 🤓
In brief, all major eukaryotic supergroups were already established in the Proterozoic, and early eukaryote evolution was far more dynamic than directly read by the fossil record. For further details:
www.biorxiv.org/content/10.6...
This work started more than 5 years ago and combines molecular phylogenetics, diversification models, paleoecology and micropaleontology, requiring ~136 CPU-years 🧬💻! A lovely interdisciplinary collaboration with @phoebefossil.bsky.social, Hélèn Morlon and @fburki.bsky.social.
#ProtistsOnSky
We find steady diversification during the not-so-boring billion. Archaeplastida diversified early and remained the most diverse group, likely boosted by the first plastid endosymbiosis. Discoba, Amoebozoa and Rhizaria also diversified early, implying complex Proterozoic ecosystems and interactions.
New preprint out! Using ~75k environmental OTUs + 77 fossil calibrations, we reconstructed a Proterozoic timeline of eukaryote evolution. Our results show crown eukaryotes were already diversifying >1.6 Ga, long before the first undisputed fossils (~1.05 Ga).
🔗 DOI: www.biorxiv.org/content/10.6...
We find steady diversification during the not-so-boring billion. Archaeplastida diversified early and remained the most diverse group, likely boosted by the first plastid endosymbiosis. Discoba, Amoebozoa and Rhizaria also diversified early, implying complex Proterozoic ecosystems and interactions.
Built from and for ecologists, molecular biologists, and bioinformaticians working with high-throughput or environmental sequencing data, this tool will ease the tedious work of designing specific oligonucleotides at all different users expertise.
With just two FASTA files (targets & non-targets), oligoN-design identifies taxon-specific oligonucleotides. No alignments, phylogenetic trees, or reference databases required.
It integrates smoothly with tools like BLAST, VSEARCH, and MAFFT, and runs efficiently even on personal computers.
Oligonucleotide design meets big data:
We present oligoN-design, a simple, reproducible and versatile open-source tool to design specific primers and probes directly from large environmental DNA datasets.
🔗 DOI: doi.org/10.1101/2025...
👉 github.com/MiguelMSandi...
Now published in Peer Community Journal, #ecology section: On the quest for novelty in ecology
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.
With the « Life of Retaria » we do podcasts! Listen to the first one during which we interviewed @fabnot.bsky.social #protistsonsky
My friends in the Life of Retaria group decided to make a podcast! In the first episode, they interview @fabnot.bsky.social about his journey as a scientist. I loved the first episode, hope you do too! @juliemeilland.bsky.social @sandinmm.bsky.social et al.
thelifeofretaria.github.io/podcast.html
A lovely collaboration with @plannapus.bsky.social, Noritoshi & @fabnot.bsky.social, where we merged the extensive groundwork on the Polycystine fossil record with extant molecular diversity to trace the evolutionary history of Radiolaria from their appearance ~760 million years ago
Despite 150+ years of Radiolaria diversity research, we have just scratched the surface. Nearly half of Radiolaria diversity might be naked hiding in plain sight! We unveiled the diversity and evolution of Radiolaria beyond "the stars of the ocean"
doi.org/10.1016/j.cu...
Now published online in Current Biology! www.cell.com/current-biol...
Ah! And if you arrived until here and were wondering about the little golden dots, yes, they are photosynthetic symbionts identified as Scrippsiella. A common dinoflagellate found in symbioses with other planktonic groups like Acantharia (also Radiolaria) or the jellyfish Vellela
We hypothesize that such a trait could increase the effective volume to weight ratio favoring prey contact and capture, and provide an advantageous microenvironment for symbionts, enhancing ecological success in nutrient-depleted waters.
Pictures credit of @n-llopis-m.bsky.social, by the way!
Despite Phlebarachnium was rarely observed, metabarcoding analyses revealed a strong biogeographic affinity to oligotrophic water masses and co-occurrence with other gelatinous-bearing Radiolaria, reaching relative abundances of more than 13% to the total eukaryotic reads in specific samples
We introduce the first molecular characterization of Phlebarachnium, one of the few Radiolaria known to live within a gelatinous matrix besides Collodaria. Yet these lineages of Nassellaria developed independently the ability to produce the gelatinous matrix ∼150 million years ago
Why do some planktonic protists develop a gelatinous matrix? We suggest that this original adaptation is a strategy to cope with ocean oligotrophy: doi.org/10.1111/1462...
Led by @n-llopis-m.bsky.social, and thanks to all co-authors, I'm very happy to finally see it out!
#protistsonsky
