Funk Lab Photo credit: David Herasimtschuk

The Funk Lab (funklab.colostate.edu) is finally here on bluesky! 🥳

This is the kind of studies I like to see. Great job 👍

Conservation genomics and assisted introgression is saving the American chestnut from extermination by invasive non-native pathogens. #consgen

Awesome study!

Thought exactly the same when I read the title of the post

📣📣📣 CONSERVATION GENETICS WORKSHOP -
Few more spaces left!

ConGen Population Genomic Data Analysis Course
🧬💻💡
University of Pretoria, South Africa 🌍
7-14 December + field trip to Kruger NP!
🦁🐃🐘🐆🦏

More info & registration here: www.umt.edu/congen/africa/

PopGLen—A Snakemake pipeline for performing population genomic analyses using genotype likelihood-based methods AbstractSummary. PopGLen is a Snakemake workflow for performing population genomic analyses within a genotype-likelihood framework, integrating steps for r

Happy to see my former @nbis.se advisory program student Zach Nolen's new pipeline PopGLen for analyses of short-read data using genotype-likelihood based methods out!

Github: github.com/zjnolen/PopG...
Paper: academic.oup.com/bioinformati...

Neat job alert 🧬🐺🦌

Montana Fish Wildlife & Parks is hiring a wildlife conservation geneticist based in Missoula, MT. The position is joint with @umontana.bsky.social, working with Dr. Ryan Kovach on lots of neat wildlife #consgen projects. Reach out to Ryan with questions.

pangenome 'expansion' curves for cotton and soybean

Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts.

We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...

Opinion: Why Sex‐Based Genomic Differentiation Should Not Be Overlooked in Population Genetics Sex-specific genomic differentiation is a crucial yet frequently overlooked factor in population genetics. In this opinion piece, we leverage the substantial genomic resources available for the great...

onlinelibrary.wiley.com/doi/full/10....

Catching Biodiversity in the Wind: How a Simple Dust Cloth Revolutionizes Airborne eDNA Monitoring Post provided by Meng Yao Biodiversity is disappearing at an alarming rate worldwide. To protect it, we first need to monitor it—but tracking species traditionally requires significant time, expert…

Go check out our new post on the Methods Blog!

Find out how a simple dust cloth might revolutionize airborne eDNA monitoring 🧬 🌍 🧪

buff.ly/BhIKcKq

Interested in how new sex chromosomes evolve in birds? Our NSF-funded collaborative work with the (Daven) Presgraves lab at @urochester.bsky.social is out this week in @pnas.org. Check it out!

www.pnas.org/doi/10.1073/...

Aah ok. But just as reminder, the original post was between NovaseqX and Novaseq6000 ☺️

I believe both technologies use a two colour chemistry, and they both tend to have an increase in Poly-G

Let me know if you manage, having struggles myself...

Help! Is anyone else finding batch effects between whole genome sequences generated with Illumina NovaSeq6000 vs NovaSeqX?
Any suggestions or solutions would be hugely appreciated! 🙏
#PopGen #ConGen #Bioinformatics #Genomics 🧬🖥️🧪

Downsize reads depth, and also use the option in AGSD to make PCA instead of using PCAngsd

Yup, I have found it. I am now inspecting bamqc in my different batches. I have a few things considered: poly-G removal with improved code in fastP (done but does not remove the batch effect)

Still ongoing. I have however encountered a big issue in the form of batch effects and have suffered some drawbacks from poor tissue quality. Bioinformatic corrections exist, but so many headaches could be afforded with good standard fieldwork for genetic work

Past conservation efforts reveal which actions lead to positive outcomes for species journals.plos.org/plosbiology/...

#consgen authority Fred Allendorf cries out in despair for American science in the Missoulian newspaper. It’s terrifying to watch this destruction unfold day by day. My heart goes out to my American colleagues and friends. Stay strong and fight.