iiinova — where your digital self keeps evolving

Reposted by Ernst Johnson

ICP2026 Stockholm @palaeogenomics.bsky.social · 26/06/2026

What a fantastic conference dinner we had yesterday at the Golden Hall 🪙 of Stockholms City Hall! 🏫 Even the full-delegate (>380) conference group picture we thought we couldn't pull out, happened organically 📸🎉

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Ernst Johnson @officialernst.bsky.social · 27/06/2026

Happy to not wear orange potentially ever again with the 5-1 thrashing still fresh in memory, but what a fun conference this was! Enjoyed meeting old friends, and making new ones. Still buzzing from all the fantastic science presented! #ICP2026

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Reposted by Ernst Johnson

Centre for Palaeogenetics @cpgsthlm.bsky.social · 12/06/2026

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!

Isa and Morten discussing bear phylogenetic trees.

Isa at the beginning of her presentation.

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Reposted by Ernst Johnson

Centre for Palaeogenetics @cpgsthlm.bsky.social · 03/06/2026

🧬 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... 🧵 1/9

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Ernst Johnson @officialernst.bsky.social · 08/05/2026

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!

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Ernst Johnson @officialernst.bsky.social · 08/05/2026

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...

github.com

GitHub - NathanACO/metaJAM: Metagenomic Pipeline for ancient DNA analysis performed at the Centre for Palaeogenetics - Stockholm

Metagenomic Pipeline for ancient DNA analysis performed at the Centre for Palaeogenetics - Stockholm - NathanACO/metaJAM

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Ernst Johnson @officialernst.bsky.social · 08/05/2026

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!

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Ernst Johnson @officialernst.bsky.social · 08/05/2026

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.

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Ernst Johnson @officialernst.bsky.social · 08/05/2026

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.

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Ernst Johnson @officialernst.bsky.social · 08/05/2026

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

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Reposted by Ernst Johnson

ICP2026 Stockholm @palaeogenomics.bsky.social · 02/05/2026

Only ONE WEEK left to register for #ICP2026sthlm 👀 Deadline: 8th May Join us for an amazing week full of talks and networking on all things ancient DNA! Check the FULL conference program 👉 icp2026.palaeogenomics.org/wp-content/u... Register here 👉 icp2026.palaeogenomics.org/registration/

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Reposted by Ernst Johnson

Centre for Palaeogenetics @cpgsthlm.bsky.social · 22/04/2026

New paper alert 🚨 A study led by #CPGSthlm researchers found DNA from a bear in 9.6k year old lake sediments. This potentially rewrites the history of brown bears in Scandinavia! 🧬🐻🐾🏔️🧊 Check @officialernst.bsky.social thread 👉 bsky.app/profile/offi... OA article 👉 www.pnas.org/doi/10.1073/...

pnas.org

Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia | PNAS

After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two direc...

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Reposted by Ernst Johnson

Tom Higham @tommyhigham.bsky.social · 15/04/2026

It's wonderful to live in an era where you can extract ancient genomes from lake sediments and obtain this kind of information! Amazing what can be revealed with sedaDNA.

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Reposted by Ernst Johnson

Stockholm University @stockholm-uni.bsky.social · 14/04/2026

A single wandering male bear has provided crucial insights into the history of brown bears in Scandinavia after the last ice age. This is shown by DNA analysis of clay from a lake. New study from @cpgsthlm.bsky.social & @zoologysthlm.bsky.social published in @pnas.org www.su.se/english/news...

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Ernst Johnson @officialernst.bsky.social · 14/04/2026

7/7 This was such a fun study from start to finish with everyone at @cpgsthlm.bsky.social. Shared first co-author and brown bear expert Isabelle Feinauer, @carlregnell.bsky.social, @jcchacond.bsky.social, @gog1693.bsky.social, @lovedalen.bsky.social, @palaeopete.bsky.social, @bdotter.bsky.social

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Ernst Johnson @officialernst.bsky.social · 14/04/2026

6/7 We projected the genome onto a panel of modern and historical brown bear genomes in a PCA. With 145k SNPs, it has more affinity towards the southern population. This is also supported by F-statistics. More ancient genomes from especially northern Scandinavia would be needed to improve accuracy.

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Ernst Johnson @officialernst.bsky.social · 14/04/2026

5/7 ... to be due to the bidirectional postglacial recolonisation. It also has a unique SNP, separating it from other clade 3a bears. How come this bear was in the "wrong" place? Male bears are known to migrate, and we think this bear came from the south and walked northwards.

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Ernst Johnson @officialernst.bsky.social · 14/04/2026

4/7 Interestingly, the genome belongs to mitochondrial haplogroup 1a. Scandinavian brown bears are divided by a "contact zone", where haplogroup 1a populates the south of Scandinavia, and haplogroup 3a the north. This genome was found ~280 km north of the contact zone. This separation is thought...

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Ernst Johnson @officialernst.bsky.social · 14/04/2026

3/7 The genome most likely originates from one individual, instead of being a mosaic, despite being an environmental genome. We investigated the allele frequencies for each position in the mitochondrial genome, and if there were multiple contributing haplogroups to reach this conclusion.

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Ernst Johnson @officialernst.bsky.social · 14/04/2026

2/7 From less than 1 g of clay, we retrieved a 231x mitochondrial brown bear genome, and a whole-genome coverage of 0.05x. This allowed us to investigate the genome as we tried to get as much information as possible out of it. Based on the X-chromosome to autosomal ratio, we believe it is a male.

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Ernst Johnson @officialernst.bsky.social · 14/04/2026

Very excited to share our study of an ancient environmental genome extracted from lake sediment! It originates from a brown bear that lived around 9,600 years ago close to the last ice-sheet remains in northern Sweden, and has an unexpected mitochondrial haplogroup. 1/7 www.pnas.org/doi/10.1073/...

pnas.org

Ancient environmental genome reveals a migratory brown bear individual in Early Holocene Scandinavia | PNAS

After the last ice age, species migrated into a newly deglaciated Scandinavia. Brown bear recolonization is thought to have occurred from two direc...

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Ernst Johnson @officialernst.bsky.social · 02/10/2025

Submit your abstracts and come to Stockholm next summer!

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Reposted by Ernst Johnson

ICP2026 Stockholm @palaeogenomics.bsky.social · 27/05/2025

The FIRST International Conference on Palaeogenomics will happen in Stockholm, Sweden, June 23-26, 2026! Topics will encompass all corners of ancient DNA research, from humans to wildlife and sediments🧬🦣💀🦠 Save the dates ✅ Check the website icp2026.palaeogenomics.org and follow us for updates!

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Ernst Johnson @officialernst.bsky.social · 15/12/2024

Really enjoyed the Association for Environmental Archaeology conference at Keble College in Oxford, presenting some fresh sedaDNA results!

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