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
#PopGen
Gene Flow and Habitat Heterogeneity Shape Coexistence Dynamics of Arctic Charr Morphs in Connected Lakes
We studied the phenotypic and genome-wide differentiation in Arctic charr (Salvelinus alpinus) in two Icelandic lakes: Thingvallavatn, known to harbour four distinct morphs, and a smaller downstream lake, Ulfljotsvatn. Our analyses confirm a single origin of charr polymorphism in this system, with all morphs present in both lakes.
#popgen #fish #charr #evolution
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
#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...
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
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
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/
🎶 📣 - 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
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
🚨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
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.
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
⬆️ ⬆️
@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.
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