#popgen — Public Fediverse posts

Biello et al. present the first whole-genome analysis of Mediterranean fin whales, showing that although these form a distinct genetic cluster, they are not fully isolated from North Atlantic populations.

📷 Danny Kessler - dannykesslerphotography.com

🔗 https://doi.org/10.1093/gbe/evag084

#genome #evolution #popgen

Biello et al. present the first whole-genome analysis of Mediterranean fin whales, showing that although these form a distinct genetic cluster, they are not fully isolated from North Atlantic populations.

📷 Danny Kessler - dannykesslerphotography.com

🔗 https://doi.org/10.1093/gbe/evag084

#genome #evolution #popgen

I gave a PopGen Vienna seminar last week. 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 https://youtu.be/kAEsLuuLuq0?si=LUlB31eL6MruBcx5

I gave a PopGen Vienna seminar last week. 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 https://youtu.be/kAEsLuuLuq0?si=LUlB31eL6MruBcx5

“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

Any user of ANGSD on here has a trick to obtain the exact same set of sites per population when making subsets of individuals?
I can never retrieve the same sets and it is extremely annoying! This is basic popgen stuff.
The bare minimum would be to output missing data for sites impossible to analyze in this pop, so that output files can align between analyses.
(I use -sites without any filters)
#bioinformatics #popgen

Any user of ANGSD on here has a trick to obtain the exact same set of sites per population when making subsets of individuals?
I can never retrieve the same sets and it is extremely annoying! This is basic popgen stuff.
The bare minimum would be to output missing data for sites impossible to analyze in this pop, so that output files can align between analyses.
(I use -sites without any filters)
#bioinformatics #popgen

The August cover of Genome Biology and Evolution features the work of Watanabe et al., who uncover the evolutionary history of the Hondo red fox, an endemic subspecies from the Japanese Archipelago.

🔗 doi.org/10.1093/gbe/evaf152

📷 Kazuki Shibata

#genome #evolution #popgen

The August cover of Genome Biology and Evolution features the work of Watanabe et al., who uncover the evolutionary history of the Hondo red fox, an endemic subspecies from the Japanese Archipelago.

🔗 doi.org/10.1093/gbe/evaf152

📷 Kazuki Shibata

#genome #evolution #popgen

#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 👇 😱😱😱

#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 👇 😱😱😱

Four years ago, Jesse Bloom announced the recovery of SARS-CoV-2 sequences and suggested they could come from very early COVID-19 patients. Zach Hensel and I found out that Bloom's claim relied on the deliberate omission of a January 30, 2020 collection date contradicting his narrative. 🧪 #PopGen

A Critical Reexamination of Re...

#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

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

🎶 📣 - Our #HAAMsummerschool is happening again!
📅 - Application open: 17th of March 🧑‍💻
Keep your eyes and ears open for coming updates!
🔗 - haam-community.github.io/projects/haa...
#aDNA #PopGen #summerschool2025

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

Part of #ERC RegEvol
In #CEFE lab, Montpellier

🚨If you fancy evolutionary genomics, theory, my lab now offers *two* fully-funded #PhD #genomics #popgen #evolution
ℹ️One on sex-asex transitions with Christoph Haag bit.ly/4hp1q1A
ℹ️One 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

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

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

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

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

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

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 !

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 !

Another tool for detecting sex-linked genome sequences! SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering: https://doi.org/10.1111/1755-0998.13985

#genomics #evolution #popgen

Another tool for detecting sex-linked genome sequences! SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering: https://doi.org/10.1111/1755-0998.13985

#genomics #evolution #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

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

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

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

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

While analysing the GBS data for this study, we also uncovered an intriguing pattern in population structure potentially linked to another prehistoric uplift event:
https://doi.org/10.1098/rsif.2023.0105

#genomics #popgen #geology #evolution #ecology

Excited to share our new paper in Ecography, where we use population genomics to investigate the impact of the 2016 Kaikōura earthquake on Durvillaea bull kelp/rimurapa!

First genomic snapshots of recolonising lineages following a devastating earthquake: https://doi.org/10.1111/ecog.07117

#ecology #evolution #genomics #biogeography #kelp #algae #earthquake #biology #genetics #popgen

#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

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

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

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

#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

PhD positions in Population Genetics

Vienna Graduate School of Population Genetics

Join our international and fun #popgen team in #Vienna, one of the best places to live and start your research career in #evolution!

See the full job description on jobRxiv: https://jobrxiv.org/job/vienna-graduate-school-of-population-genetics-27778-phd-positions-in-population-ge...
https://jobrxiv.org/job/vienna-graduate-school-of-population-genetics-27778-phd-positions-in-population-genetics-6/?feed_id=72771

Nice preprint led by @benoitevol on counter intuitive relation between TE distribution and Ne measured by dN/dS https://www.biorxiv.org/content/10.1101/2024.02.26.582137v1 #PopGen #transposon

PhD positions in Population Genetics

Vienna Graduate School of Population Genetics

Join our international and fun #popgen team in #Vienna, one of the best places to live and start your research career in #evolution!

See the full job description on jobRxiv: https://jobrxiv.org/job/vienna-graduate-school-of-population-genetics-27778-phd-positions-in-population-ge...
https://jobrxiv.org/job/vienna-graduate-school-of-population-genetics-27778-phd-positions-in-population-genetics-6/?feed_id=71861