#popgen — Public Fediverse posts

“Here we reframe the inference of coalescence times as a problem of translation between two biological languages: the sparse, observable patterns of mutation along the genome and the unobservable ancestral recombination graph that gave rise to them.” #PopGen #PopulationGenetics

RE: https://bsky.app/profile/did:plc:dg7v6uxmmotprmirq7usk3bu/post/3mj5wsiyygc2h

Second day of the 3 day workshop/conference ARGEvol on Ancestral Recombination Graphs (ARG) in Porto. A great line up of speakers and workshops on understanding and using ARGs.
#ARG #PopGen #ARGEvol

If you're interested in population genetics and cooperation, you might be interested in our latest theory paper on the topic! Check it out!

⬇️ ⬇️
https://academic.oup.com/evolut/advance-article/doi/10.1093/evolut/qpae147/7821382
⬆️ ⬆️

#evolution #popgen #cooperation #altruism #recombination

Hi everybody,

I am pleased to share with you my latest work in collaboration with Augustin Cléssin and Nicolas Lartillot:

https://www.biorxiv.org/content/10.1101/2024.06.21.600052v1

GC-biased gene conversion (gBGC) is a process that distorts the segregation of heterozygous AT:GC polymorphisms during meiotic #recombination. This genome-wide non-Mendelian segregation has been shown to be a major source of #genetic load, earning the nickname of “Achille’s heel” of #genomes. (1/2)

#PopGen
#Evolution

Nice new work from Doc @edge on recovering polygenic scores from ancestral recombination graphs.

Scalability vs accuracy.

https://www.biorxiv.org/content/10.1101/2024.05.24.595829v1

#popgen #evol_gen #ARGs

Still open PhD position
#Job #phd #Evolution #Genomics #Cancer #TransCan #MarBiol #Polyploidy #PopGen #France
Here is an offer for a PhD (ERC HYPERCAN project) on the evolution of a transmissible cancer, with a focus on hyperploidy variations:
euraxess.ec.europa.eu/jobs/230401
Please boost

Still open PhD position
#Job #phd #Evolution #Genomics #Cancer #TransCan #MarBiol #Polyploidy #PopGen #France
Here is an offer for a PhD (ERC HYPERCAN project) on the evolution of a transmissible cancer, with a focus on hyperploidy variations:
euraxess.ec.europa.eu/jobs/230401
Please boost

Still open PhD position
#Job #phd #Evolution #Genomics #Cancer #TransCan #MarBiol #Polyploidy #PopGen #France
Here is an offer for a PhD (ERC HYPERCAN project) on the evolution of a transmissible cancer, with a focus on hyperploidy variations:
euraxess.ec.europa.eu/jobs/230401
Please boost

Still open PhD position
#Job #phd #Evolution #Genomics #Cancer #TransCan #MarBiol #Polyploidy #PopGen #France
Here is an offer for a PhD (ERC HYPERCAN project) on the evolution of a transmissible cancer, with a focus on hyperploidy variations:
euraxess.ec.europa.eu/jobs/230401
Please boost

Still open PhD position
#Job #phd #Evolution #Genomics #Cancer #TransCan #MarBiol #Polyploidy #PopGen #France
Here is an offer for a PhD (ERC HYPERCAN project) on the evolution of a transmissible cancer, with a focus on hyperploidy variations:
euraxess.ec.europa.eu/jobs/230401
Please boost

#PopGen #Hybridization #Introgression #HybridZones @zgompert and @disequilibber published their upgraded method and R package, bgchm, to analyse genomic clines in hyrid zones 👇
https://www.biorxiv.org/content/10.1101/2024.03.29.587395v1

#MathematicalBiology #evolution #evolutionarybiology #popgen #evolutionarydynamics #MathematicalModeling @Project_Telos

Hello everyone,

I'm glad to share this preprint:

https://www.biorxiv.org/content/10.1101/2024.03.06.583651v1

PRDM9 is a gene that determines the location of most meiotic #recombination events through local histone methylation in humans and mice. It is also one of the fastest evolving gene in mammals.

In this preprint, we show that its molecular function in #meiosis is the same in salmonids!

This suggests that PRDM9's rapid #evolution has been going on for hundreds of Mys.

#PopGen

Hello Mastodon people,

I wanted to mention that I have a new preprint out on bioRxiv:

https://www.biorxiv.org/content/10.1101/2024.01.16.575829v1

I think it could be really useful for people interested in the consequences of #Recombination on #Genome #Evolution, but more generally in interpreting DFEs, positive selection and dN/dS.

I will take the time to make a thread once the final paper is published (I hope it will).

For those who will take the time to read it, don't hesitate to give me feedback 😊

#Popgen

I am very pleased to share with the mastodon community the first part of my PhD work:

High prevalence of Prdm9-independent recombination hotspots in placental #mammals

https://www.biorxiv.org/content/10.1101/2023.11.17.567540v1

This work was done in collaboration with @djivanprentout Alexandre Laverré, Théo Tricou and @duret_lbbe. (1/8)

#Recombination #PopGen #Evolution #gBGC #PRDM9

A polygenic explanation for Haldane’s rule in butterflies
Xiong et al. (Jim Mallet's team)
#PopGen #Hybridization #Polygenic

"numerous small-effect factors on a single chromosome can appear as spurious large-effect loci. This mapping artifact persists even for large samples and dense markers and may cause underreporting of polygenicity from genetic crosses."

https://doi.org/10.1073/pnas.2300959120

The most interesting in a selective sweep is the shoulders.

New preprint by the team on the vanishing chromosomal footprint of an anthropogenic introgression of locally favoured foreign genes

Falling shoulders ahead: adaptive alien genes are maintained amid vanishing introgression footprint in sea squirts. https://www.biorxiv.org/content/10.1101/2023.09.21.558831v1

@darwin
#PopGen #AdaptiveIntrogression #SelectiveSweep #UrbanEvolution #Hybridization
#AnthropogenicHybridization #AnthropogenicIntrogression

Sex Unfolded Jacques Monod Conference. Third Edition in incredibly sunny Roscoff. Already 1 week ago. Thanks to all the participants! Many new ideas for the #evolutionofsex #recombination, #SexChromosomes #asexuality #evobio #popgen. 4th edition in 5 years by @KarineDoninck and Sylvain Glémin !

A new preprint by Hilde Schneeman and John Welch using FGM to explore what we can infer from introgression line data. Quite a lot of overdominance in the reanalysed datasets, but it may well be transient (background dependent) and thus fixable. Again, an important read for anyone interested in hybridization. #PopGen #Hybridization

Transient overdominance, coadaptation, and the fixability of heterosis
https://www.biorxiv.org/content/10.1101/2023.08.23.554444v1

A new strain of Penicillium roqueforti discovered in Termignon cheese, a cheese I can't wait to taste, and lots of interesting results from this new paper by Tatiana Giraud's team, published in #EvolutionaryApplications
https://onlinelibrary.wiley.com/doi/10.1111/eva.13578
going together with a short video summary explaining domestication of cheese fungi
https://youtu.be/iN0A6dudWqI
#PopGen #PopulationGenomics #Biodiversity #Domestication

#PopGen #EvolMol #ThalerConference #MustWatch #AlternativeSplicing #SplicingErrors #DriftBarrier Amazing talk by @duret_lbbe here on the SEEM youtube channel 👇

https://ecoevo.social/@couplingdmi/110860290160070455

#PopGen #EvolMol #ThalerConference #MustWatch #AlternativeSplicing #SplicingErrors #DriftBarrier Amazing talk by @duret_lbbe here on the SEEM youtube channel 👇

https://ecoevo.social/@couplingdmi/110860290160070455

#PopGen #EvolMol #ThalerConference #MustWatch #AlternativeSplicing #SplicingErrors #DriftBarrier Amazing talk by @duret_lbbe here on the SEEM youtube channel 👇

https://ecoevo.social/@couplingdmi/110860290160070455

#PopGen #EvolMol #ThalerConference #MustWatch #AlternativeSplicing #SplicingErrors #DriftBarrier Amazing talk by @duret_lbbe here on the SEEM youtube channel 👇

https://ecoevo.social/@couplingdmi/110860290160070455

Our latest paper on polyploid population genetics is now out at Genetics! Led by Paul Blischak with Ryan Gutenkunst and Mathews Sajan we develop models in dadi to infer the demographic history of polyploid species. Check it out here: https://academic.oup.com/genetics/advance-article-abstract/doi/10.1093/genetics/iyad107/7190362?redirectedFrom=fulltext

#polyploidy #genetics #PopGen

Happy to see this out! Not only because Martin Petr's tool #slendr is incredibly useful for anyone doing evolutionary #genetic simulations, but also because it's been peer reviewed though a system that doesn't profiteer off academic work, nor impose paywalls on its readers!

Thanks Emiliano Trucchi, Liisa Loog, 2 anonymous reviewers and @PeerCommunityIn !

https://evolbiol.peercommunityin.org/articles/rec?id=630

#EthicalPublishing #OpenScience #PeerReview #ScienceMastodon #PopGen #EcoEvo

Looking forward to attending this year's #SMBE2023! https://www.smbe2023.org

In addition to the research symposia, I'm particularly excited about the parallel events (https://www.smbe2023.org/parallelevents), which include a timely discussion on #EthicalPublishing and #diamondOA systems, and a workshop on non-violent #CivilResistance by @ScientistRebellion (special thanks to @SanjaHakala for orchestrating this!).

#ScienceMastodon #PopGen #Evolution #Ecology #EcoEvo #BiodiversityCrisis

Huiying Shang's preprint is now @PeerCommunityIn --recommended

"Drivers of genomic landscapes of differentiation across Populus divergence gradient"

In this study, we resequenced ~200 individuals from 8 related #species to comparatively investigate the #evolution of genomic landscapes of #diversity and #differentiation through time.

Take a look at it:
https://biorxiv.org/content/10.1101/2021.08.26.457771v6

#popgen #speciation #divergence #genomescan #Populus

Super interesting paper that analayzes one of the #LTEE populations that evolved stably coexisting #ecotypes from Joao Ascensao, Kelly Wetmore, Ben Good, Adam Arkin & Oskar Hallatschek. https://www.nature.com/articles/s41467-022-35677-5
#Microbiology #Evolution #ExperimentalEvolution #EcoEvo #popgen #PopulationDynamics #Genomics

@quantumlandbooks #evolutionaryecology, here I am! 😊 (but also #paleoecology, #popgen)

@quantumlandbooks #evolutionaryecology, here I am! 😊 (but also #paleoecology, #popgen)

@quantumlandbooks #evolutionaryecology, here I am! 😊 (but also #paleoecology, #popgen)

@quantumlandbooks #evolutionaryecology, here I am! 😊 (but also #paleoecology, #popgen)

@quantumlandbooks #evolutionaryecology, here I am! 😊 (but also #paleoecology, #popgen)

It's going to take ages to rebuild the #biology community I loved following on Twitter.

I'm keen to find anyone interested in anything below (or similar!):
#aotearoa
#algae
#bacteria
#bioinformatics
#conservation
#DNA
#ecology
#entomology
#evolution #evoeco
#EU
#fish
#fisheries
#genetics
#genomics
#ichthyology
#insects
#kelp
#LGBT #LGBTQIA #lgbtstem
#marinebiology
#molluscs
#newzealand #nz
#pathogens
#phylogenetics
#popgen
#snails
#UK
#USA
#wikipedia
#zoology

#newHere #hashtags

Some interests:

#singleCell #bayesian #stats #ancestry #genetics #popgen #geneRegulation #systemsGenetics #functionalGenomics #biology #immunology #vaccines #infection #viruses #influenza #tuberculosis #TB #malaria #NTDs #fitness #evolution #dominance #stress #aging #mosquitoes #mice #macaques

#academic #dei #diversity #equity #inclusion #blackLivesMatter #firstGen #asian #aapi #multi #access2meds #globalHealth #swarthmore #johnsHopkins #unc #chicago #washingtonDC #moco

For any #popgen #scientists, the 56th @popgroup meeting is still accepting abstracts until the 30th Nov: there are still talks & poster slots available!

It will be hybrid: attend from the comfort of your home or witness glorious #London 🌆

Read more at populationgeneticsgroup.org.uk

#populationgenetics #PopulationGenomics #populationgenetic #Genomics #EvolutionaryGenetics #EvolutionaryGenomics please recommend me more tags to get this spread!

:boost_ok: :boost_requested: :mastogrin:

Well, I guess I am on Mastodon now, so here is an #introduction post

- I run the #bioinformatics group at #harvard. We are a combination consulting group, training team, and computational research lab.

- My research interests are in #popgen, #bioinformatics, and #genomics, with a particular focus on #convergent #evolution, #genome #assembly and #annotation, and #software usability

- Outside of work, I #bird and play #dnd, mostly

Anyone out there in #PopGen #Populationgenomics #RNAseq or #Molecular biology have any leads on where to buy duplex-specific nuclease? Main provider is a Russian and unavailable to most because of sanctions. I have not been an alternative supplier or enzyme. Please boost!

#introduction (I love the idea!)

I am an associate professor at the #LBBE in Lyon

This means I teach for a significant part of my time (maths, genetics) at the #IUTLyon1

In my research I study #evolution with models (#popgen, #adaptivedynamics) more #mechanistic than usual – often this leads me to study #evolution in/of biological #networks

#Introduction again now that I have migrated to the evoeco instance. Some hashtags that align with my interests: #science
#evolution #popgen #biology #theory #proteins #bioinformatics #datascience #aging #prions #evolvability #robustness #astrobiology #epidemiology #COVID19 #economics #RiskAnalysis

Right, having moved servers: #Drosophila #Virus #Evolution #PopGen #Phylogeny #Genome #Insect #RNAi #Metagenomics #Fly #Preprint

An #introduction toot with my favorite hashtags: #PopGen #Evolution #Hybridization #Introgression #Speciation #Genome #EvolMol #MarBiol #TransCan #Cancer #Somatic #Mutations #Selection #adaptation #drift #GeneFlow #Coupling #UrbanEvolution #Biodiversity #MarineConnectivity and my flagship one #MusselsAreCool

So about this #introduction : I work on #statistics for #genetics at #INRAE in the #animal genetics division. I am interested in understanding the #evolution of quantitative traits in #livestock populations, with a specific interest for #recombination. I do #DataAnalysis and method development in #popgen and #QuantitativeGenetics. I like #programming in #python and playing with #R

The #Fediscience #mastodon instance kindly asks for an #introduction. Here it is:

I am an evolutionary biologist at #IDEEV (#CNRS #UniversiteParisSaclay, France). Wide interests in #Evolution, including #PopGen, #QuantitativeGenetics, #SystemsBiology, and #Genome evolution (in particular, #TransposableElements). Mostly #Theory and #DataAnalysis.

I am part of the recent #twitterMigration of #Academia, and very happy to find so many people #ESEBFolks here!

An #introduction toot with my favorite hashtags : #PopGen #Evolution #Hybridization #Introgression #Speciation #Genome #EvolMol #MarBiol #TransCan #Cancer #Somatic #Mutation #Selection #Adaptation #Drift #Coupling #UrbanEvolution #Biodiversity #MarineConnectivity and my flagship one #MusselsAreCool

Belated #introduction with some hashtags that align with my interests: #science
#evolution #popgen #biology #theory #proteins #bioinformatics #datascience #aging #prions #evolvability #robustness #astrobiology #epidemiology #COVID19 #economics #RiskAnalysis