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Raphael Gollnisch

@rgollnisch.bsky.social
1.1K followers 769 following 8 posts

Evolutionary genetics of calcifying protists Postdoc at University of Oxford

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Reposted by Raphael Gollnisch
Casey Dunn @caseywdunn.bsky.social · 25/08/2026
My new book, Phylogenetic Biology, is now published. Available online for free at dunnlab.org/phylogenetic... . Physical copies can be purchased at shop.lightningsource.com/b/085?params... or your favorite bookstore.
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The Guardian @theguardian.com · 15/08/2026
It’s the SUV tyranny: where have all the normal family cars gone? | Coco Khan
theguardian.com
It’s the SUV tyranny: where have all the normal family cars gone? | Coco Khan
They rule the roads and, in their wake, even old-style saloons have been supersized. It’s an illusion of consumer choice, says writer and podcaster Coco Khan
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David Ho @davidho.bsky.social · 15/08/2026
19-year-old British cyclist Finlay Tarling, the brother of cycling star Josh Tarling, died after a head-on collision with a car driven by someone not associated with the race during stage 8 of the Volta a Portugal. 🤬
velo.outsideonline.com
19-Year-Old Development Racer Finlay Tarling Dies in Crash at Volta a Portugal
Initial reports indicate a car unaffiliated with the race was involved in the incident.
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Jeffrey Ross-Ibarra @jrossibarra.bsky.social · 15/06/2026
People. @ksamuk.bsky.social and others have made this argument before. There’s good software to do this right. Here’s the argument again: Invariant sites matter! They’re not in your standard vcf and many programs pretend they are anyway. academic.oup.com/gbe/article/...
academic.oup.com
A Recipe for a Good π. How to Properly Estimate Population Genetics Summary Statistics and Why we Should Systematically Report Them
Abstract. Many long-standing questions in population genomics can now be addressed through comparative analyses and by leveraging the vast amount of genomi
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Ryan Gutenkunst @ryangutenkunst.bsky.social · 01/06/2026
The 2026 Genomic History Inference Strategies Tournament is live! ghist.bio Today was the kickoff tutorial at the Modeling and Theory in Population Biology workshop at @icerm.bsky.social . Looking forward to summer workshops at PEQG @genetics-gsa.bsky.social and at SMBE @official-smbe.bsky.social .
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Julie Meilland @juliemeilland.bsky.social · 29/05/2026
We got our first common paper out #theLifeOfRetaria with @sandinmm.bsky.social , @raphaelmorard.bsky.social, @nicolecoots.bsky.social, @mattgr3co.bsky.social, Nicolaas Glock and Natalia Llopis-Monferrer - first product of our seminar series! check it out! onlinelibrary.wiley.com/doi/abs/10.1...
onlinelibrary.wiley.com
Unifying Retaria Research: A Common Framework for Studying Foraminifera and Radiolaria
Research on Foraminifera and Radiolaria has predominantly focused on their fossil remains. This synthesis identifies the “Big Five” disciplines of a unified Retaria research: diversity and evolution,...
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David Ho @davidho.bsky.social · 04/03/2026
Scientific American has updated the figure, now grouped into swimmers, fliers, walkers/runners, and vehicles. A person on a bicycle remains the most efficient way to travel, compared to all forms of biological locomotion and mechanical transport. www.scientificamerican.com/article/a-hu...
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Pedro Brandão-Dias F Pinto @pedrobd.bsky.social · 13/02/2026
🧬 My haplotype paper is out! We show that deviations between within-sample and population-level haplotype frequencies can be used to estimate how many individuals contributed to an eDNA sample. No tissue references needed, just metabarcoding data and some population genetics. #eDNA #PopGen
onlinelibrary.wiley.com
Estimating Organism Abundance Using Within‐Sample Haplotype Frequencies of eDNA Data
Environmental DNA (eDNA) provides powerful insights into species presence and community composition but remains limited in its capacity to infer species abundance or population structure. Here, we sh...
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Matthew Hahn @3rdreviewer.bsky.social · 08/01/2026
Final version of paper with @smishra677.bsky.social now published in a wonderful issue of GENETICS! academic.oup.com/genetics/art...
academic.oup.com
Estimating recombination using only the allele frequency spectrum
Abstract. Standard methods for estimating the population recombination parameter, ρ, are dependent on sampling individual genotypes and calculating various
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Genome Biology and Evolution @genomebiolevol.bsky.social · 08/01/2026
In a new GBE Review, @david-peede.bsky.social et al. overview the SMC model and extensions, discuss examples of discoveries made with the help of SMC-based inference, and comment on the assumptions, benefits, and drawbacks of various methods. 🔗 doi.org/10.1093/gbe/... #genome #evolution #compbio
doi.org
Not Just Ne Ne-More: New Applications for SMC from Ecology to Phylogenies
Abstract. Genomes contain the mutational footprint of an organism’s evolutionary history, shaped by diverse forces including ecological factors, selective
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Maximilian Ganser @mhganser.bsky.social · 27/12/2025
Finally, we’ve solved a long-standing mystery: what tintinnid shells are actually made of: A new class of biomaterial formed by remarkable structural proteins unique to tintinnids. A major milestone after 3 years of work! Read about it in our preprint: doi.org/10.64898/202... #ProtistsOnSky
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Trends in Ecology & Evolution @cp-trendsecolevo.bsky.social · 15/12/2025
Online now: Genomic insights into the origin of ecotypes
dlvr.it
Genomic insights into the origin of ecotypes
A century after Turesson introduced ecotypes as locally adapted subunits of species, their origins and nature remain debated. Recent advances in molecular ecology have breathed new life into the ecotype concept and significantly expanded our understanding of how ecotypes form. Here, we clarify how ecotypes can be distinguished from other forms of local adaptation, outline criteria for their recognition, and synthesise evidence on the ecological and evolutionary processes that give rise to them. We then evaluate what genomics has uncovered about the origin of ecotypes, revealing pronounced roles of pre-existing variation, large-effect loci, structural variants, gene regulation, and complex demographic histories. Our framework refines Turesson’s concept and highlights outstanding questions about the predictability, persistence, and evolutionary significance of ecotypes.
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Ryan Gutenkunst @ryangutenkunst.bsky.social · 15/12/2025
Congratulations to the winners of the 2025 Genomic History Inference Strategies Tournament challenges! Among the 9 challenges, we had five winners: @alwaysrong.bsky.social, @adaigle.bsky.social, @andrewhvaughn.bsky.social, @thymelicus.bsky.social, @rgollnisch.bsky.social
GHIST logo
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Justin Merondun @merondun.bsky.social · 30/10/2025
Our new @science.org paper is out! Cuckoos and hosts are locked in a coevolutionary arms race over egg mimicry. But how are these egg types inherited, and could this drive speciation? We sequenced hundreds of genomes to find out! doi.org/10.1126/scie... 🧵1/6
doi.org
Genomic architecture of egg mimicry and its consequences for speciation in parasitic cuckoos
Host-parasite arms races facilitate rapid evolution and can fuel speciation. Cuculus cuckoos are deceptive egg mimics that exhibit a broad diversity of counterfeit egg phenotypes, representing host-ad...
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Yuki Haba @yukihaba.bsky.social · 25/10/2025
How does life evolve to adapt to modern cities? Out now in Science, my PhD work with @lindymcbr.bsky.social uncovers the ancient origin of the “London Underground mosquito” – one of the most iconic examples of urban adaptation. 🧵(1/n) @science.org www.science.org/doi/10.1126/science.ady4515
science.org
Ancient origin of an urban underground mosquito
Understanding how life is adapting to urban environments represents an important challenge in evolutionary biology. In this work, we investigate a widely cited example of urban adaptation, Culex pipie...
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Meg Daly @megdaly.bsky.social · 23/10/2025
This is an INCREDIBLE advance in our understanding of coral diversification. 🪸🎉 Fantastic new work led by @claudiavaga.bsky.social www.nature.com/articles/s41...
nature.com
A global coral phylogeny reveals resilience and vulnerability through deep time - Nature
The most recent common ancestor of the stony coral Scleractinia dates to about 460 million years ago and was probably a solitary, heterotrophic and free-living organism.
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José Aguilar-Rodríguez @jaguilarrod.bsky.social · 22/10/2025
One of the most exciting works of my career, years in the making. We used high-throughput precision genome editing to test the fitness effects of thousands of natural variants. Our findings challenge the long-held assumption that common variants are inconsequential. www.biorxiv.org/content/10.1...
biorxiv.org
Massively parallel interrogation of the fitness of natural variants in ancient signaling pathways reveals pervasive local adaptation
The nature of standing genetic variation remains a central debate in population genetics, with differing perspectives on whether common variants are almost always neutral as suggested by neutral and n...
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Ellinor Alseth @ellinoralseth.bsky.social · 08/10/2025
Obsessed with this Journal of Immaterial Science article 🔥
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Audald Lloret-Villas @audald.bsky.social · 04/10/2025
Low-coverage sequencing (LCS) + genotype imputation is a cost-effective approach to genotype hundreds of samples at a full-genome level. But how do different imputation tools perform across populations with varying relatedness and inbreeding?
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Mahwash Jamy @mjamy.bsky.social · 03/09/2025
Check out our new paper on adopting a trait-based framework for protist diversity! We make the case for a unified protist trait database, how to build it, and how it could transform research on protist ecology and evolution. #protistsonsky
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Anton Suvorov @antonsuvorov.bsky.social · 24/08/2025
My very first post on here. I am stoked to share lab's latest paper led by @ethantolman.bsky.social. Ethan developed a highly scalable pipeline to differentiate between various gene flow models, including ghost introgression in phylogenomic datasets. Check it out! www.biorxiv.org/content/10.1...
biorxiv.org
GhostParser: A highly scalable phylogenomic approach for the identification of ghost introgression
A growing body of empirical research shows that interspecific gene flow is a widespread biological force that shapes evolutionary histories across the Tree of Life. Computational approaches designed t...
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Laura Bertola @lauradbertola.bsky.social · 09/08/2025
The molecular evolutionary basis of species formation revisited www.cell.com/trends/genet...
cell.com
The molecular evolutionary basis of species formation revisited
How do new species arise? This is among the most fundamental questions in evolutionary biology. The first genetic model for how reproductive barriers lead to the origin of new species was proposed nea...
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Vasily Zlatogursky @zlatogursky.bsky.social · 24/07/2025
Promethea = PROvora + MEteora + HEmimastigophora. The new supergroup, unifying previously “orphan” lineages with gene-rich mitogenomes. Position of #telonemids is still uncertain. #protistsonsky tinyurl.com/yk9xkt49
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Alex Lipp @alexlipp.github.io · 31/07/2025
eartharxiv.org/repository/v... In our new preprint we describe in detail the software & workflows behind www.SewageMap.co.uk! One for the open environmental data nerds out there :) 💩 🧑‍💻 🏞️
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Jon Puritz @jonpuritz.marineevoeco.com · 05/07/2025
I haven’t read the paper yet, but this looks interesting! www.nature.com/articles/s41... #PopGen
nature.com
Accounting for population structure and data quality in demographic inference with linkage disequilibrium methods - Nature Communications
Accurate estimation of effective population size is critical for understanding population history but is often confounded by structure and data quality. Here, the authors show that GONE2 and currentNe...
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Matthew Hahn @3rdreviewer.bsky.social · 28/06/2025
Cool new paper on pop gen and machine learning: www.biorxiv.org/content/10.1...
biorxiv.org
Coalescence and Translation: A Language Model for Population Genetics
Probabilistic models such as the sequentially Markovian coalescent (SMC) have long provided a powerful framework for population genetic inference, enabling reconstruction of demographic history and an...
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Ana Catalán @anaevolcatalan.bsky.social · 24/06/2025
This work shows the first overview on the population genetics and demographic history of the big European firefly, **Lampyris noctiluca**. Feeling very happy this work is out :) academic.oup.com/mbe/article/...
academic.oup.com
Sex-biased Migration and Demographic History of the Big European Firefly Lampyris noctiluca
Abstract. Differential dispersion between the sexes can impact the colonization process and demographic history of a species. Here, we explored the demogra
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Jürgen Strassert @strassert.bsky.social · 13/06/2025
Happy to have contributed to this great article: #Protist genomics: key to understanding eukaryotic evolution. Congrats Alexandra Schoenle et al. #ProtistsOnSky authors.elsevier.com/sd/article/S...
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Joseph W. Brown @josephwb.bsky.social · 03/05/2025
Estimates of the Mutation Rate per Year Can Explain Why the Molecular Clock Depends on Generation Time academic.oup.com/mbe/article/... 🧪
academic.oup.com
Estimates of the Mutation Rate per Year Can Explain Why the Molecular Clock Depends on Generation Time
Abstract. Rates of molecular evolution are known to vary across species, often deviating from the classical expectation of a strict molecular clock. In man
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ASM @asm.org · 23/04/2025
Introducing Eukfinder! A bioinformatics pipeline that identifies eukaryotic sequences from metagenomic data. The tool is valuable for reference-independent and cultivation-free studies of eukaryotic microbial genomes from environmental samples. #mBio: asm.social/2nl
Schematic representation of Eukfinder workflows. Eukfinder is a taxonomic classification-based bioinformatics approach to retrieve microbial eukaryotic nuclear and mitochondrial genomes from WGS metagenomic sequencing data. Eukfinder has two different workflows based on the input files. (a) Eukfinder_short utilizes Illumina short reads, and the first round of classification assigns reads into 1 of 5 distinct taxonomic categories (Archaeal, Bacterial, Viral, Eukaryotic, and Unknown). Next, Eukaryotic and Unknown reads are assembled into contigs which undergo a second round of classification to generate potential eukaryotic sequences. (b) Eukfinder_long uses assembled contigs or long-read sequencing data and only performs one round of classification to select Eukaryotic and Unknown contigs. The potential eukaryotic contigs can then be further separated into MAGs by a separate binning workflow to generate draft eukaryotic nuclear and mitochondrial genomes.
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Philipp Bayer @philippbayer.bsky.social · 23/04/2025
My nightmare in #eDNA is to detect a rare or threatened species that turns out to be a false positive, so we set out to evaluate some of the commonly used taxonomic classifiers. The results are finally out: onlinelibrary.wiley.com/doi/full/10.... 1/3
onlinelibrary.wiley.com
A Comprehensive Evaluation of Taxonomic Classifiers in Marine Vertebrate eDNA Studies
Environmental DNA (eDNA) metabarcoding is a widely used tool for surveying marine vertebrate biodiversity. To this end, many computational tools have been released and a plethora of bioinformatic app...
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Jelena Godrijan 🫧❾🌊🦋 @godi.bsky.social · 18/04/2025
​🌊 New research reveals that coccolithophore blooms significantly enhance carbon export by increasing particle fluxes. This finding underscores their vital role in oceanic carbon sequestration and has important implications for climate models. www.researchsquare.com/article/rs-6...
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Tara Oceans Science @taraoceans-science.bsky.social · 12/04/2025
Hot off the press, the most comprehensive survey ever performed of diatom distributions, abundances, and diversity in the global ocean. All enabled by the famous schooner@fondationtaraocean.bsky.social and lots of hard work from the Tara Oceans team! www.nature.com/articles/s41...
nature.com
Patterns and drivers of diatom diversity and abundance in the global ocean - Nature Communications
Using the Tara Oceans dataset, this study describes global patterns of diatom diversity, abundance and adaptation. The authors identify 25 distinct communities, with the Arctic as a hotspot, and highl...
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Cameron Thrash @jcamthrash.bsky.social · 11/04/2025
Eukfinder: a pipeline to retrieve microbial eukaryote genome sequences from metagenomic data journals.asm.org/doi/full/10.... #jcampubs
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Rob Waterhouse @rmwaterhouse.bsky.social · 06/04/2025
How #genome-wide sequence divergence maps to species status www.pnas.org/doi/10.1073/... #biodiversity #genomics
pnas.org
Genomic divergence across the tree of life | PNAS
Nucleotide sequence data are being harnessed to identify species, even in cases in which organisms themselves are neither in hand nor witnessed. Bu...
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del Campo Lab @delcampolab.bsky.social · 02/04/2025
We are glad to announce that #MidweekMicrobe is back!🥳 Today we are celebrating the International Children's Book Day coinciding with Hans Christian Andersen's birthday. A creative mind, Hans published the tale The Drop of Water in 1847, available at andersen.sdu.dk/vaerk/hersho....
andersen.sdu.dk
Hans Christian Andersen : The Drop of Water
Hans Christian Andersen: life and works - research, texts and information
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Fabien Burki @fburki.bsky.social · 28/03/2025
On hidden protist diversity (unfortunately the data is not available yet) #protistsonsky www.biorxiv.org/content/10.1...
biorxiv.org
Global Metagenomics Reveals Hidden Protist Diversity
Protists, defined as unicellular eukaryotes distinct from animals, plants, and fungi, are a polyphyletic group that predominates the eukaryotic tree of life, exhibiting significant phylogenetic divers...
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EMBRC (European Marine Biological Resource Centre) @embrc.eu · 27/03/2025
#Event2025 I 👉 AtlantECO #hackathon The Marine Training Unit (Embrc Belgium) is organising the One Ocean, One Health: Multi-Omics Hackathon to address questions using Mission Microbiomes AtlantECO data 📍 Azores 📅 Sept 8-12 ⌛ Register by 10 Apr 🔗 www.marinetraining.eu/node/6150
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BES Aquatic Ecology Group @bes-aquaticgroup.bsky.social · 19/03/2025
Have you registered yet for our #BESAG2025 Annual meeting in London? this year we are joining forces with the @bes-microbialgroup.bsky.social to give you a great #aquatic conference! #freshwater #marine #aquatic 🧪🌏🐋🦐🦪🐠💧🌊Registration link: www.eventbrite.co.uk/e/besag2025-...
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SAME18-BCN @same18-bcn.bsky.social · 22/03/2025
🌊 Save the Date! 🌍 #SAME18 — Aquatic Microbiomes on a Changing Planet 📍 Barcelona, Spain | 🗓️ Sept 28 – Oct 3, 2025 At the iconic PRBB 🧬🌿 Join us to explore the frontiers of aquatic microbial ecology. 📢 Stay tuned for more info and follow us on Bluesky! #MicrobialEcology #MarineMicrobiology #SAME18
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Will Ratcliff @wcratcliff.bsky.social · 19/03/2025
1/35 New paper out! @jamesTstroud and I dive into why long-term studies are crucial for understanding evolution. They reveal processes impossible to detect in short timescales and capture rare events that transform our understanding of evolutionary dynamics. www.nature.com/articles/s41...
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Tamlin Pavelsky @globalhydro.bsky.social · 19/03/2025
Do you work on lakes globally? Check out what is, to my mind, the most complete global database of lakes (~6M) and associated attributes, newly published in WRR. Also the basis for SWOT lake data. agupubs.onlinelibrary.wiley.com/doi/full/10....
Map of global lake distribution, colored by the number of SWOT overpasses per 21 day cycle. There are many lakes with a high number of SWOT overpasses at high northern latitudes, but there are also tens of thousands to more than a million lakes on every continent. Lakes are graphed by latitude and longitude on the edges of the figure.
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Alex Mackintosh @thymelicus.bsky.social · 12/12/2024
My and Derek Setter's work on gene flow is now published in the latest issue of Genetics. We show that it is possible to detect past gene flow between two populations by summarising the asymmetry in pop-specific external branch lengths. 1/2 tinyurl.com/5ff8ch9e
tinyurl.com
Genealogical asymmetry under the isolation with migration model and a two-taxon test for gene flow
Abstract. Methods for detecting gene flow between populations often rely on asymmetry in the average length of particular genealogical branches, with the A
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James McInerney @jomcinerney.bsky.social · 18/03/2025
Splitting and merging in human ancestry. www.nature.com/articles/s41...
nature.com
A structured coalescent model reveals deep ancestral structure shared by all modern humans - Nature Genetics
The cobraa model extends the pairwise sequentially Markovian coalescent to identify structured population history by examination of the model transition matrix. Applied to human polymorphism data, cob...
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Javier del Campo @fonamental.bsky.social · 26/02/2025
Bamboozle: A Bioinformatic Tool for Identification and Quantification of Intraspecific Barcodes
onlinelibrary.wiley.com
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Seth Bordenstein @symbionticism.bsky.social · 24/02/2025
It wasnt easy for #phylosymbiosis to get off the ground, but it is now. Here is the first study to suggest that phytoplankton have phylosymbiotic microbiomes. On a personal note, it’s fulfilling to watch the term, the concepts, and approaches broadly take flight. www.biorxiv.org/content/10.1...
biorxiv.org
Phytoplankton recruitment of specific microbial assemblages and phylosymbiotic patterns
Phytoplankton and bacteria represent two major pillars of the carbon cycle in marine ecosystems. While their interactions are known to be tightly linked, the specific mechanisms underlying these inter...
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Richard Lenski @relenski.bsky.social · 21/02/2025
I just posted "Some Experiments Work, and Some Don't." It features this new paper from Paul Rainey's group, along with a *failed* experiment that Paul Sniegowski and I ran in the 1990s trying to test the same idea. telliamedrevisited.wordpress.com/2025/02/21/s...
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Bohao Fang @fangbohao.bsky.social · 14/02/2025
How do SVs, satellite DNA & gene content shape avian genome evolution? We analyzed 45 HiFi genomes across 3 Scrub-Jay species with distinct population sizes. Grateful to be on this incredible team led by Scott Edwards! "Comparative population pangenomes" www.biorxiv.org/content/10.1...
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Sam Macaulay @samuelmacaulay.bsky.social · 11/02/2025
How can mesocosms help tackle grand ecological challenges in aquatic ecosystems? 🌊🌍 Check out our open-access Oikos Forum article, out today: 🔗 doi.org/10.1111/oik.... @oikosjournal.bsky.social
doi.org
Addressing grand ecological challenges in aquatic ecosystems: how can mesocosms be used to advance solutions?
Rapid and drastic anthropogenic impacts are affecting global biogeochemical processes and driving biodiversity loss across Earth's ecosystems. In aquatic ecosystems, species distributions are shiftin...
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