PhD. Working with sedimentary ancient DNA at the Centre for Palaeogenetics (@cpgsthlm.bsky.social), Stockholm University
Ernst Johnson
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🧬 New paper in Cell!
Analysis of 12 cave lion genomes shows that cave lions and modern lions may have diverged more than three times earlier than previously thought – as early as 1.7 million years ago!
AND…they interbred when temperatures dropped!
Paper: www.cell.com/cell/fulltex...
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Ernst Johnson
Isabelle Feinauer is currently defending their PhD thesis on the genomic consequences of postglacial recolonization of Scandinavian mammals with Morten Tange Olsen as the opponent.
Good luck, Isa!
Centre for Palaeogenetics
Centre for Palaeogenetics
4/6 metaJAM can also be used for other purposes, such as identification of "mystery bones" where bone morphology has not given a definitive species assignment, or metagenomic analysis of archaeological artefacts. Any shotgun-sequenced sample could be processed, who knows what might be found in it!
3/6 Metagenomic analyses can be overwhelming, especially with larger sample sets. The output of metaJAM will provide the user with an overview of the dataset, ready for interpretation and identification of potential "hot-spots" in large datasets to target for additional down-stream analyses.
The biggest challenge during my PhD within sedimentary ancient DNA was to figure out how to bioinformatically process several hundreds of sequenced samples. This workflow is optimised for identification of eukaryotes from metagenomic shotgun data. Let me introduce the preprint of metaJAM! 1/6
5/6 We wanted the workflow to be reproducible and easy to install and setup across different HPC systems. That's why we chose to code it in Nextflow, and make use of a containerised approach. Check out what else is needed to run it on the Github readme and wiki: github.com/NathanACO/me...
6/6 And the name? (me) Johnson, (Jamie) Alumbaugh and (Nathan) Martin designed the workflow and so we named it after our surname initials. @chenyu.bsky.social and @benjaminguinet.bsky.social were also crucial parts of this @cpgsthlm.bsky.social collaboration, another of my PhD chapters!
2/6 metaJAM has three main modules: 1) Pre-processing, 2) Mapping against extensive reference databases and 3) Authentication. Starting from raw fastq-files, it outputs several diagnostic plots and metrics, including heatmaps of read counts of identified taxa and aDNA damage across the dataset.
Ancient DNA reveals a wandering #bear. 🐻🧬 A 9,600-year-old genome from Swedish lake #sediments shows a southern brown bear migrating north during #post-glacial recolonization.
www.pnas.org/doi/10.1073/...
#MetagenomicsMonday #SPAAM #aDNA #sedaDNA #biodiversity
Ernst Johnson
Ernst Johnson
Ernst Johnson
Ernst Johnson
Ernst Johnson
Ernst Johnson
www.pnas.org
#CPGStlhm 's PhD candidate @officialernst.bsky.social is currently defending his thesis on using metagenomics sedimentary DNA to reconstruct past ecosystems 🧬🏞️ in Sweden with Laura Epp as opponent.
Good luck, Ernst!
After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two direc...
