#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

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

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

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

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

“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

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

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

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

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

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

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 👇 😱😱😱

#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 👇 😱😱😱

#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...

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...

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

#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

#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

#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

#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

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

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

🚨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

🚨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

In a paper led by J. Pekar now available online, we revisit claims made last year by Lv et al. about early SARS-CoV-2 sequences. We find that their two T/T genomes were sampled too late to be likely evolutionary intermediates between A and B lineages, and are instead likely derived. ▫️1/ #PopGen

Recently reported SARS-CoV-2 g...

In a paper led by J. Pekar now available online, we revisit claims made last year by Lv et al. about early SARS-CoV-2 sequences. We find that their two T/T genomes were sampled too late to be likely evolutionary intermediates between A and B lineages, and are instead likely derived. ▫️1/ #PopGen

Recently reported SARS-CoV-2 g...

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