#popgen

100 downloads of my 'Genetic structure and relatedness of brown trout (Salmo trutta) populations in the drainage basin of the Ölfusá river, South-Western Iceland' article published in #OpenAccess journal @PeerJLife

#brownTrout #Myvatn #popgen #ecology #evolution #salmonid

https://peerj.com/articles/15985

Huh, folks. It seems that I don't get something about #Dryad
I'm looking for a code example for a bit exotic #popgen tool and 3 papers in a row (from 2021 - 2024) have "data and code available on Dryad", but doi gives an error and direct search on Dryad "dataset not available".
Is it just a sneaky way of authors to flip a bird to the #openScience practices required by the journal?
Does it make sense to poke @datadryad or it's journal's team who should sort this out with the authors?

Good reviews on "Gene flow and habitat heterogeneity shape coexistence dynamics of Arctic charr morphs in connected lakes" at Molecular Ecology

Rejected but encouraged resubmission (which I hate, its plain metric-playing)

The main result being #GeneticStructure of four sympatric morphs in #thingvallavatn #Iceland

#AcademicChatter #rejectResubmit #evolution #genetics #popgen #divergence #ArcticCharr #sympatry #ecology #metapopulation #SourceSink

https://www.authorea.com/users/588916/articles/1254729-gene-flow-and-habitat-heterogeneity-shape-coexistence-dynamics-of-arctic-charr-morphs-in-connected-lakes?commit=353eaa9510fc1c8dbdbdfa28e52c912447ca9fde

Tröllafoss spring 2021

Leirvogsá river runs from Leirvogur up to Lake Leirvogsvatn

Leir-vogur translates to clay-cove

Above the waterfall is the lake, and in it the brown trout with lowest level of genetic variation

#ecology #browntrout #popgen #colonization
#waterfall #Tröllafoss #salmonid #iceland #Thingvallavatn #Leirvogsvatn
https://peerj.com/articles/15985/

#PostDoc in #Montpellier on mussel transmissible cancers genomes. These weird cancers, microparasites with a mussel genome, have undergone genome doublings and aneuploidisation. You will play with PacBio and Nanopore data. Join the #HyperCan team in a joyfull environment. #TransCan #MarEvol #PopGen #MusselsAreCool #JobAlert https://euraxess.ec.europa.eu/jobs/333894

Harpy v2.0 is almost across the finish line, and I wrote a lil' post about what linked-read sequencing actually is and how we evaluate the data differently than standard short-read data. It's a quick and easy read (with pictures!), highly recommend
https://pdimens.github.io/harpy/blog/linked_read_data/

#genetics #PopGenomics #popgen

Gene flow and habitat heterogeneity shape coexistence dynamics of Arctic charr morphs in connected lakes. Han Xiao, et al
Submitted to Molecular Ecology,

preprint on Authorea.

#ecology #Evolution #popgen #charr #salmonid #diversity #geneticdiversity #metapopulation #speciation #geometricMorphometrics

https://www.authorea.com/users/588916/articles/1254729-gene-flow-and-habitat-heterogeneity-shape-coexistence-dynamics-of-arctic-charr-morphs-in-connected-lakes

If you fancy evolutionary genomics, theory, my lab now offers *two* fully-funded #PhD #genomics #popgen #evolution
One on sex-asex transitions with Christoph Haag bit.ly/4hp1q1A
One on allele-specific expression with Sylvain Glémin bit.ly/4iuKLuQ

Part of #ERC RegEvol
In #CEFE lab, Montpellier

Last week, I updated #adegenet on #CRAN. This is an important update as it fixes a memory overflow problem for SNP data that has existed since 2016.

If you use #PopGen packages that import adegenet (e.g. #poppr, #vcfR, or #dartR), then you should update.

https://cran.r-project.org/web/packages/adegenet/ChangeLog

#RStats

Gene flow and habitat heterogeneity shape coexistence dynamics of Arctic charr morphs in connected lakes

Han Xiao, Palsson, Jónsson, Snorrason

December 27, 2024.
DOI: 10.22541/au.173531304.47377188/v1
#evolution #popgen #metapopulation #fish #gbs #charr #Salmonid

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

@chasewnelson, some #popgen papers about this:

Kryazhimskiy and Plotkin, 2008, The Population Genetics of dN/dS

https://doi.org/10.1371/journal.pgen.1000304

Wolf, et al. 2009. Nonlinear dynamics of nonsynonymous (dN) and synonymous (dS) substitution rates affects inference of selection. Genome Biol Evol 1:308-319.

https://www.ncbi.nlm.nih.gov/pubmed/20333200

That time of year again: postdoc fellowships available at the Unviersity of Toronto. Get in touch if you want to apply to work with me on some evolutionary theory.

https://www.artsci.utoronto.ca/faculty-staff/research-supports-services/find-funding#as-postdoctoral-fellowship-program

#uoft #postdoc #evolution #popgen

3 years (and 2 kids) later, I finally revised the manuscript:

https://www.biorxiv.org/content/10.1101/2021.07.13.452277v2

we develop a #popgen method to locate genetic ancestors from tree sequences and apply it to arabidopsis thaliana.

software is ready to be applied to any dataset with Relate trees:
https://github.com/osmond-lab/spacetrees

check out our video to learn more: https://www.youtube.com/watch?v=4itER1uEKbQ

thanks for your patience @gcbias !

Population genetics: an introduction for physicists https://arxiv.org/abs/2408.02650 #genetics #physics #popgen

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

Sometimes we miss articles and don't understand how we missed them. I wouldn't normally miss an article by Thomas Wiehe. Fortunately, we always end up doing a more intensive bibliography on an issue we're interested in, and we end up finding the gems we missed. #MustRead #PopGen

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007426

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

The Australian Institute of Marine Science (Townsville, Australia) is advertising for an evolutionary modeller who can use models to forecast possible evolutionary trajectories for coral reef communities under various scenarios including restoration interventions. #Govjobs #academicjobs #PopGen

Deadline for applications: June 10, 2024

For full details and instructions: https://www.aims.gov.au/about/careers-aims