Nicolas Bierne

era2027.sciencesconf.orgERA 2027 - Evolutionary Responses to Anthropogenic drivers - Sciencesconf.orgSciencesconf.org

📢 Save the date, submit your abstract, spread the word! ERA 2027 - Evolutionary Responses to Anthropogenic Drivers 📅 20–21 April 2027 📍Nantes, France 🇫🇷 With a fantastic lineup of keynote speakers: @tatianagiraud.bsky.social, Daniel Streicker, Ophélie Ronce & Bruno Ernande! 🔗 era2027.sciencesconf.org

Two days exploring how human activities are profoundly reshaping the pace and direction of evolution across ecosystems.

biorxiv.orgParallel differentiation extends beyond chromosomal inversions to small genomic islands on a background of rampant gene flow in the European flat oyster (Ostrea edulis)Heterogeneous genomic landscapes of differentiation can reveal evolutionary processes acting over different timescales. Whereas genetic structure in the European flat oyster, Ostrea edulis , is mainly...

A new preprint from my former PhD student Lila Colston-Nepali: “Parallel differentiation extends beyond chromosomal inversions to small genomic islands on a background of rampant gene flow in the European flat oyster Ostrea edulis” www.biorxiv.org/content/10.6... #PopGen #MarEvol #ParallelEvolution

Especially when rampant gene flow has made most of the genome amnesic, leaving only a few barrier loci that still retain the signal of past divergence.

Also keep in mind that modern sliding-window genome scans would almost certainly miss the locally adaptive Drosophila ADH polymorphism.

5/ Our hypothesis is that a northern/marginal lineage was pushed towards the edges of the range by the post-glacial expansion of the southern/central lineage. The intrinsic barriers that maintain differentiation may be the only parts of the genome that reveal this history amid rampant gene flow.

I’m not saying that this is always how parallel differentiation works. Just that we need to look beyond large inversions and properly test primary differentiation against secondary contact.

3/ When demographic reconstruction explicitly accounts for heterogeneity in gene flow across the genome, a history of divergence followed by postglacial secondary contact emerges, despite massive swamping by contemporary gene flow.

4/ Strikingly, two of the 12 islands map ATP synthase subunits, pointing to intrinsic incompatibilities as a likely source of barriers to gene flow.

1/ We find an unusual population structure. Most of the genome follows geography around Europe, but a few outliers, including two inversions, tell a different story: populations at the margins (North Sea and East Med) cluster together, against populations from the centre (Atlantic and West Med).

2/ When we look beyond the large inversions that dominate sliding-window scans, using a very simple but effective SNP-based approach, we find additional small islands of parallel differentiation. Some narrow down to a single gene, and even to a single nonsynonymous change.

biorxiv.orgAdaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalisAdaptive introgression, the transfer of beneficial alleles between species through hybridization, is increasingly recognized as an important source of adaptation to novel environments. However, the th...

New preprint from the team #AdaptiveIntrogression #Haplotagging #PopGen #MarEvol "Adaptive introgression in subdivided populations leaves distinct genomic footprints under global and local selection: a case study in Ciona intestinalis" www.biorxiv.org/content/10.6...

2- We tested this prediction in a well-characterized case of adaptive introgression, in the sea squirt Ciona intestinalis: Using haplotagging and local ancestry, we find no correlation between allele frequency and tract length, supporting local adaptation.

Not submitted yet, comments welcome! Congrats to first author and PhD student Manon Le Goff! 🎉

@pleunipennings.bsky.social

1- Combining allele frequency with introgressed tract lengths allows to test global vs. local adaptive introgression: -Traveling adaptive wave → positive correlation between frequency and tract length -Local selection → the correlation disappears because frequency reflects the direction of selection

Nicolas Bierne reposted

Pleuni Pennings

I am hiring a postdoc! Are you interested to work on population genetics/ drug resistance/ data? Want to work in Montpellier, France? Fastq files don't scare you? PhD required, start date hopefully Nov 1! (end date Sep 30 2028) Please share! abetterscientist.wordpress.com/2026/09/29/p...

abetterscientist.wordpress.comPostdoc position on drug resistance evolution in Montpellier, FranceI have some exciting news (again!). I got money from the region (Occitanie) to hire a postdoc (and later an engineer / technician) to work on drug resistance evolution in malaria (P. faciparum) and…

sfecologie.orgLauréats Grand Prix SFE - sfecologie.org

16 Sept

La SFE2 @sfecologie.bsky.social délivre cette année sont grand prix à 3 lauréats sur le thème de l’écologie et et de la biologie marine: Didier Gascuel, Henri Weimerskirch, et la seule et unique Fred Viard 🎉 #MarEvol sfecologie.org/actions/laur...

Didn't you miss hearing from #MusselsAreCool just a little bit? We had our AMMR2026 conference organised by Pierre de Wit at the Tjarno Marine Lab @cemeb.bsky.social, and it was a lot of fun. www.gu.se/en/event/int...

Students were able to benefit from Prof. Skibinski's boundless knowledge. We discussed sex determination and sex ratio for hours. Can you believe we still don't know how sex determation works in #MusselsAreCool?

The next AMMR is scheduled to take place in Greece in two years, stay tuned! #MusselsAreCool

We have learned that mussel farms have a very positive impact on biodiversity and provide a very low-carbon eco-friendly source of protein (good for your health, no animal welfare concerns, no inputs required, and production that emits very little CO2). #MusselsAreCool

We were even more amazed by the complexity of these beasts’ genomes, which exhibit insane structural variation. #MusselsAreCool

biorxiv.orgAllelic coverage analyses reveal a high proportion and uneven chromosomal distribution of SNPs associated with polymorphic duplications in the oyster Ostrea edulisMarine bivalves are known for their high genetic diversity and potentially high genetic load, as well as their structurally complex genomes. The European flat oyster, Ostrea edulis , is no exception. ...

30 Aug

A substantially revised V2 of our work on SNPs associated with rampant polymorphic duplications in the European flat oyster 🦪is out! ~15% of SNPs are associated with polymorphic duplications, with a striking concentration on 3 of the 10 chromosomes. #PopGen #MarEvol www.biorxiv.org/content/10.1...

Nicolas Bierne@couplingdmi.bsky.social

#PopGen New preprint of the team on the discovery of a very high rate of polymorphic duplication in a marine bivalve. Imagine looking at the distribution of the allelic coverage fraction at heterozygous calls in an indivdual and getting this distribution 👇 😱😱😱

Nicolas Bierne reposted

Urban Evolution & Ecology Conference

@urbanevoecoconf.bsky.social

24 Aug

Bienvenue chez la Dre Frédérique Viard, director of the CNRS at Université de Montpellier and coastal marine ecosystems evolutionary biologist, who will lead "Adaptation to Urban Environments". Review starts in Sept-apply soon! 1st GRC on Urban Evo & Eco www.grc.org/urban-evolut... #UrbanEvoEcoGRC

Nicolas Bierne reposted

Carl Zimmer

@carlzimmer.com

nyti.msDeep in This Lake, a Contagious Cancer Is Spreading (Gift Article)Transmissible tumors have been reported in a handful of animal species, but never before among fish. Is it possible in humans?

Did Thoreau encounter contagious cancer? A new study finds transmissible tumors in catfish--and raises questions about whether they could arise in humans someday. Gift link: nyti.ms/4whfi6v

go.nature.comRare contagious cancer discovered in wild catfishTransmissible tumours have been found in only a few types of animal, but there might be many more out there.

I find this new discovery of a transmissible cancer in catfish fascinating. As it’s described as the fourth example of contagious cancer, let me share this phylogenetic tree of species infected by such rarities.

Nature@nature.com

Researchers have discovered a contagious cancer in catfish – just the fourth example of tumour cells that spread naturally from one animal to another go.nature.com/4fsoLR3

@maxstammnitz.bsky.social

Not everyone knows that there’s more genetic divergence between a mussel and a clam than between a dog and a fish.

Nicolas Bierne reposted

Max Stammnitz

nature.comBrown bullhead catfish melanoma represents a novel transmissible cancer - NatureWhole-genome sequencing analysis of tumour and matched non-tumour host tissues of the brown bullhead catfish reveals a type of naturally occurring transmissible cancer.

Wow! A fourth class of transmissible cancers. CONTAGIOUS FISH MELANOMA, discovered in Lake Memphremagog (Vermont / Quebec) 🎣 🧬 😷 www.nature.com/articles/s41... @uvmvermont.bsky.social

Nicolas Bierne reposted

Julien Joseph

@jujoseph.bsky.social

7 July

Hi everyone, I just started a bluesky account to share my work and keep up with the work of others :) ! I am very pleased to share this review on the evolutionary causes behind the existence of meiotic recombination hotspots: doi.org/10.1371/jour... I hope it will be useful to some of you!

doi.orgWhy recombination hotspots?Meiotic recombination is the process by which DNA is exchanged between parental chromosomes during the production of gametes in eukaryotes. This phenomenon has important implications for fertility, ge...

Nicolas Bierne reposted

Michael Metzger

@metzgerm.bsky.social

23 June

I am excited to present our newest report on a severe outbreak of transmissible cancer in clams in the Pacific Northwest, with a lot of unexpected twists. Led by Sydney Weinandt and Zach Child. www.pnas.org/doi/10.1073/pnas.2611852123 1/14

pnas.orgAtlantic to Pacific: Outbreak of bivalve transmissible neoplasia detected in hybridizing soft-shell clams and eDNA in Puget Sound | PNASBivalve transmissible neoplasias (BTNs) are transmissible cancers that have arisen in multiple bivalve species, including Eastern soft-shell clam (...

Nicolas Bierne reposted

Claire Mérot

@clairemerot.bsky.social

21 May

Looking forward to our next STRiVE seminar by @aruizherrera.bsky.social

STRIVE@strivestn.bsky.social

🧬 Next STRiVE Seminar! Aurora Ruiz-Herrera (UAB) presents: "Structural variation through the lens of the 3D genome". 🗓️ Wed, June 3 | 3pm CEST / 9am EDT ✉️ Zoom link via mailing list: groupes.renater.fr/sympa/subscr... ℹ️ Info: structuralvariantsstn.github.io/about/

Nicolas Bierne reposted

Molly Przeworski

@mollyprz.bsky.social

15 May

Happy to highlight new findings by Vanesa Getseva and Lin Poyraz about the sources of variation in germline mutation rates among humans: www.biorxiv.org/content/10.6... Joint work with Anastasia Stolyarova and @ipsitaagarwal.bsky.social. 1/n

biorxiv.orgA sibling study of variation in parental mutation ratesPeople are born with variable numbers of de novo germline mutations (DNMs), depending primarily on the ages of their parents. To explore additional causes, we developed an approach to call DNMs from nucleotide differences between siblings in genomic regions inherited identical by descent from both parents. Applying it to whole genome sequences from 28,985 sibling pairs of diverse genetic ancestries present in the UK Biobank and All of Us datasets, as well as 2,330 trios, we identified >800K autosomal DNMs and characterized mutation phenotypes in 27,645 sets of parents. We found subtle shifts in the mutation spectrum but no differences in total DNM rates among genetic ancestry groups, or between smokers and non-smokers. Testing for associations between parental mutation phenotypes and their burden of loss-of-function and deleterious missense variants in a set of 180 DNA repair and maintenance genes, we discovered that disruptions in REV1 and LIG1 increase germline mutation rates, and thus that rare mutator alleles segregate in population cohorts. ### Competing Interest Statement The authors have declared no competing interest. NIH, R35 GM083098

Nicolas Bierne reposted

Vincent CASTRIC

@vincentcastric.bsky.social

29 Apr

Ever wondered what makes some alleles dominant (A) and others recessive (a) ? In our new paper, we explored how a series of recently discovered "dominance modifiers", genetic elements that have long remained elusive, achieve their regulatory function. journals.plos.org/plosgenetics...

journals.plos.orgDominance modifiers at the Arabidopsis self-incompatibility locus retain proto-miRNA features and act through non-canonical pathwaysAuthor summary Many plants avoid self-fertilization through a system of self-incompatibility, which allows them to recognize and reject their own pollen. In plants like those in the Arabidopsis family...

@gabnocgenomics.bsky.social

23 Apr

I gave a PopGen Vienna seminar on Tueaday. I was impressed by the quality and depth of the discussions I had the all day with all the students of the program. Thank you very much. I learned so much from you, far more than I was able to help you with my limited advice #PopGen youtu.be/kAEsLuuLuq0?...

youtu.beyoutu.be

Nicolas Bierne reposted

Gabriele Nocchi

doi.orgReplicated hybrid zones reveal genomic patterns of local adaptation and introgression in spruceAbstract. Hybridization between species can occur along repeated zones of contact, providing a natural laboratory for studying the interplay between migrat

Happy to share this paper with @samyeaman.bsky.social, now published in Molecular Biology and Evolution! Using replicated hybrid zones, we explored patterns of local adaptation and introgression in spruce and found strong signals even at very fine geographical scales! doi.org/10.1093/molb...

pnas.orgPNASProceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...

Evergreen debate over the stickleback narrative: recent, rapid, independent. One more piece on the “coupling” side: two timeframes (old adaptation, recent spatial redeployment), not so independent. www.pnas.org/doi/full/10....

"the origin of standing genetic variation in the sea is interesting and requires further stud" Isn't it simply a migration (of old variants that long persisted in freshwater populations) - selection balance?

I had finally come to acknowledge the "reuse" concept, but the constant push for the “rapid and independent” narrative is wearing me out.

pnas.orgReply to MacColl: Repeated evolution from standing genetic variation | PNASReply to MacColl: Repeated evolution from standing genetic variation

Reply "understanding early speciation requires recognizing the evidence that adaptation is rapid and repeatable" Really? www.pnas.org/doi/abs/10.1...

Nicolas Bierne reposted

James McCulloch

@jamesimcc.bsky.social

@robjohnnoble.bsky.social

Why do the chromosomes of cyperids (sedges & rushes) split and fuse so regularly on evolutionary timescales? Is it because they have so many centromeres? Our new preprint, the first major paper of my PhD, addresses this question. 🧵⬇️ 1/12 www.biorxiv.org/content/10.6...

Nicolas Bierne reposted

Rob Noble

4 Mar

Academics often lament that hardly any master’s projects get published. The student moves on. Other research takes priority. No one has time to do the final analyses. Here I tell how one master’s project was, through persistent teamwork, finally carried over the finish line: go.nature.com/4aKs7N3

go.nature.comOn the expansion and evolution of a master’s projectAcademics often lament that hardly any master’s projects – even the best ones – get published. The student moves on. Other research takes priority. No one has time to do the final analyses. Here I tel...

5 Mar

Un poste MCF en génomique évolutive / écologie moléculaire à ECOBIOP - Université de Pau #PopGen 👇 urlr.me/rVQmN6

urlr.meurlr.me

doi.orgThe core-pivotal index: a geometry-first approach to academic impactThe defining goal of the academic endeavor is to establish a single perfect value that completely summarizes entire careers’ achievements. Such an index wo

April Fools’ Day is coming early this year, but really, any day is a good day to poke fun at the system. Well done @russcd.bsky.social

Molecular Biology and Evolution@molbioevol.bsky.social

@russcd.bsky.social ushers in a new era of academic metrics with the core-pivotal author index, which assigns all credit to authors that occupy the exact center of the author list, while non-central peripheral authors receive no credit whatsoever. 🔗 doi.org/10.1093/molbev/msag026 #evobio #molbio

univ-reunion.fruniv-reunion.fr

Un poste MCF en évolution de la biodiversité marine à l'Université de La Réunion UMR Entropie #MarEvol 👇 www.univ-reunion.fr/wp-content/u...

Nicolas Bierne reposted

cfraisserios.bsky.social

@cfraisserios.bsky.social