iiinova — where your digital self keeps evolving

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Matthew Collins @matthewcollins.bsky.social · 28/08/2026

There is fun to be had in *not* reviewing a manuscript. @pciarchaeology.bsky.social @cos.io #openaccess

Thank you for your invitation to review a manuscript. While I value the scholarly community's efforts to disseminate research, I have growing concerns about the publishing model many commercial publishers, including Springer Nature, employ. In my view, the current system heavily relies on taxpayer-funded research, often conducted at public institutions, yet places the resulting work behind expensive paywalls. This practice limits access for scientists and the general public in the Global South, who often cannot afford subscription fees or open-access charges.

To put this in perspective, Springer Nature's most recent financial results (for the fiscal year ending December 2025) show total revenue of €1,926.4 million, adjusted operating profit of €543.6 million, and net income of €356 million. The Research division, which includes its journals, generated €1,517.2 million of that revenue. Shareholders received dividends of approximately €25.9 million, a significant increase from the previous year. These figures show that the current model is highly profitable, but much of that profit goes to investor returns rather than making research accessible to the global scientific community.

I have worked unpaid for you in the past, but this unpaid labour, combined with publicly funded research, generates enormous profits for a publishing industry that gives back relatively little to the public or to scientists in under-resourced regions. I do not believe this is fair or sustainable. I therefore have become a champion of Diamond Open Access and an editor at PCI.

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Matthew Collins @matthewcollins.bsky.social · 09/09/2026

@paastacommunity.bsky.social is developing #metadata standards for #palaeoproteomicis based upon ##USHUPO #Proteomics @us-hupo.org #mzPeak Join the debate on #PAASTA #element github.com/Palaeoprot/Z...

The Metadata Thread in the Paasta community

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Miren Iraeta Orbegozo @mireniraorb.bsky.social · 09/09/2026

Happy to share our new paper on DNA preservation in the Caribbean: Open access: doi.org/10.1098/rsos... 🌎 Summaries in Español, Français, Kreyòl Ayisyen and Kréyòl Gwadloup: shorturl.at/FMHNI 🧵👇 @jazminrm.bsky.social @bitesizedna.bsky.social

doi.org

Ancient DNA preservation in the Caribbean

Abstract. Ancient DNA (aDNA) analysis has transformed how we study human migration, species dispersals and environmental change, but poor preservation rema

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Marco Capodiferro @marcocapo.bsky.social · 04/09/2026

Our paper on archaic introgression in imputed ancient genomes is out. Imputation performs better in archaic regions, making Neanderthal and Denisovan segments detectable in low-coverage data. Thousands of archived genomes become usable. doi.org/10.1038/s414...

doi.org

Archaic ancestry inference in imputed ancient human genomes - Nature Communications

Genotype imputation enables accurate detection of Neanderthal and Denisovan ancestry in low-coverage ancient genomes and allows the identification of introgressed haplotypes as well as candidate genes...

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(Y|G)iannis P. @ipatramanis.bsky.social · 17/08/2026

I'd like to point out that the image is from the Greek revolution of 1821, not Chille or the Americas :P

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Arev P. Sümer @arevsumer.bsky.social · 15/08/2026

Our new study with @benmpeter.bsky.social is now on biorxiv! Here we present a new computational tool which makes it possible to conduct population genetic analyses from very contaminated and very low quality archaic human genomes. (1/7)

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(Y|G)iannis P. @ipatramanis.bsky.social · 14/08/2026

To some extend it should influence the tooth shape, indeed. Not sure how much tough. Keep in mind that some present day humans also have these archaic mutations today (due to past admxiture), so one could see what is the effect on their teeth if any!

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

It's a good question! I think its protein product mostly has to do with enamel tooth formation (see en.wikipedia.org/wiki/Amelobl... ). We're interested in it because it seems very resilient to degradation, so we find it in the teeth of these very old fossils!

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

8) We are aiming for an open review for our manuscript and are very much interested in hearing what the community thinks about this strange case. We of course expect that more data (proteins, genomes, morphology) and community effort will eventually solve this puzzle!

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

7) We think this work is important, given that AMBN is shaping up to be a useful marker for identifying Denisovans, Homo erectus and potentially other humans in the fossil record. A good understanding of this gene's genetic history will be essential.

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

6) While we think the scenario of AMBN introgressing from Homo erectus to Denisovans is now less likely, we still need to explain *why* these groups share a unique mutation on AMBN! We propose a number of models, from boring ILS to exciting hybridization!

Proposed alternative models. Different datatypes and analysis can support or reject some of them.

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

5) Denisova 25 is... stranger. Its AMBN copy is heterozygous for 17 SNPs, for which other archaics are fixed for one allele and moderns for the other. In fact, you can create two almost perfect archaic and modern haplotypes and place them phylogenetically. See discussion for our best guess for this.

Phylogenetic tree of archaic AMBN pseudohaploypes. Denisova 3 AMBN copies are clustering with Neanderthal copies, contrary to the expectation of super-archaic origin. Strangely, Denisova 25 copies can be seperated into a Archaic-Neanderthal-like haplotype and a modern-human-like haplotype.

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

4) In short, we do not find super-archaic evidence in either high coverage Denisovan for AMBN, leading us to think of alternative models for this gene (see below). For Denisova 3, AMBN looks fairly normal: a few derived mutations, placing its copies sister to the Neanderthal copies of AMBN.

Genome wide distributions of derived alleles per 20kb, non-overlapping windows for five high coverage archaic individuals. For each individual the placement of the window containing AMBN (A) and KRTAP-10_10 (B) within the distribution is shown with a dotted vertical line. For the same fragment length KRTAP-10_10 shows a signal of super-archaic introgression, while AMBN does not. AMBN has roughly the same number of derived mutations for either Neanderthals or Denisovans.

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

3) The model necessitates that the AMBN gene has a ‘super-archaic’ origin in the Denisovan genome. This is also what the original publication found evidence for. We wanted to test this for ourselves so we used the now 2 available high coverage Denisovan genomes.

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

2) To explain this result, the authors suggest a model of introgression of this mutation, from these Homo erectus into Denisovans. This model neatly fits with our current understanding of Denisovans, who have a super-archaic signal in their genomes, but -

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

1) A recent enamel palaeoproteomic study sampled 6 Homo erectus teeth, showing that they uniquely share an AMBN mutation with Denisovans! This is along another mutation on AMBN, that is unique to these samples.

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(Y|G)iannis P. @ipatramanis.bsky.social · 13/08/2026

We have a new preprint out :D www.biorxiv.org/content/10.6... Did Denisovans inherit their AMBN gene from Homo erectus? We have released a short preprint trying to answer this question! @lauritsskov.bsky.social @fridowelker.bsky.social ~Summary below~

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(Y|G)iannis P. @ipatramanis.bsky.social · 26/07/2026

Had a chance to present our work on assesing the potential of palaeoproteomics for the study of hominid evolution (doi.org/10.1093/gbe/...). Thank you to the @paastacommunity.bsky.social for inviting me and for recording the talk. Happy to be part of this community! :D

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Matthew Collins @matthewcollins.bsky.social · 15/07/2026

Copenhagen job alert 🚨 GLOBE (@ucph.bsky.social) is hiring a 21-mo Postdoc in #Bioinformatics & #ComputationalProteomics Work with @lindorfflarsen.bsky.social, @fridowelker.bsky.social, @brandtgroup.bsky.social & more mapping collagen/keratin diversity across 1000s of genomes. 📅 Deadline Aug 31

jobportal.ku.dk

Postdoc of Bioinformatics and Computational Proteomics

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PAASTA Community @paastacommunity.bsky.social · 06/07/2026

REMINDER: Next 🍝PAASTA🍝 talk this Wednesday! Message us for the link 🔗

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Palesa @palaeoprotpalesa.bsky.social · 25/06/2026

Hello Hello, If you have some downtime and want to read something excitingly odd, read on the enamel proteins of Homo naledi: www.cell.com/cell/fulltex... Working closely with Alberto, @clairekoenig.bsky.social, @ipatramanis.bsky.social, and the rest of our collaborators was just so wonderful.

cell.com

Proteomic analysis of dental enamel from 20 Homo naledi individuals shows no male markers

The morphological homogeneity of the middle Pleistocene hominin Homo naledi is reflected in its dental proteome, with no evidence supporting confident identification of male individuals, and the detec...

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(Y|G)iannis P. @ipatramanis.bsky.social · 17/05/2026

The data fit just fine if you assume these 6 samples being from a Denisovan subpopulation and not from a homo erectus relic population.

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(Y|G)iannis P. @ipatramanis.bsky.social · 17/05/2026

To me it's more likely that the 'homo erectus' variant emerged later, on top of the haplotype that carries the 'Denisovan-like' variant. So after an introgression event happened, if it did happen for this protein.

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(Y|G)iannis P. @ipatramanis.bsky.social · 17/05/2026

The two variants that are recovered are also found on the same protein! If they were introgressed from homo erectus, they likely would have been linked together due to their physical proximity on the genome, and Denisovans would have inherited both.

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(Y|G)iannis P. @ipatramanis.bsky.social · 17/05/2026

Interesting points! If you look at the protein data alone, there are no recovered variants that support these samples being very divergent from modern humans, e.g. 'H.erectus like'. For comparison, the H.antecessor enamel had a variant, placing it as an outgroup to nean, deni, and present day humans

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(Y|G)iannis P. @ipatramanis.bsky.social · 02/03/2026

Given the recent and upcoming recovery of ancient proteins from archaic human remains this would be something to keep in mind. The missmatch of autosomal, mitochondrial, Y chromosome and morphology-based trees is already complicated for these groups, proteins might add some to that complexity!

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(Y|G)iannis P. @ipatramanis.bsky.social · 02/03/2026

While we suspect incomplete lineage sorting as the main culprit for this result, an older admixture between Neanderthal and humans, a 'super-archaic' admixture into Denisovans or other scenarios could be at play.

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(Y|G)iannis P. @ipatramanis.bsky.social · 02/03/2026

In fact, in the trees of enamel, collagen and other bone/dentin proteins, humans and Neanderthals appear closer to eachother as often as Neanderthals appear closer to Denisovans. This persists even when only looking at sub-saharan African populations, who have limited archaic introgression.

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(Y|G)iannis P. @ipatramanis.bsky.social · 02/03/2026

In short we find that while only a few proteins are needed to resolve the tree between humans - chimpanzees - gorillas, the same cannot be said for the tree of modern humans - Neanderthals - Denisovans.

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Matthew Collins @matthewcollins.bsky.social · 22/02/2026

🦷 A new study by @marinemorvan.bsky.social High-throughput paleoproteomics method using MALDI-CASI-FTICR mass spectrometry to estimate biological sex from tooth enamel. Great success on 130 individuals from medieval Great Moravia. #Bioarchaeology #Archaeology #Proteomics #TooMS 😉 #Teammasspec

biorxiv.org

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Giulia Zampirolo @giuliazamp93.bsky.social · 23/02/2026

Seeing our work on videnskab.dk brings back memories of those fieldwork days. It was a great journey from sampling archaeological and old river sediments in Serbia to the ancient DNA labs in Copenhagen. Read more about the challenges and our findings in the original paper: doi.org/10.1038/s415...

doi.org

Ancient DNA reconstruction of Late Holocene ecosystems within the Carpathian Basin from paleo-meanders and archaeological deposits - Scientific Reports

The diverse ecology in the Carpathian Basin supported a variety of subsistence strategies throughout the Holocene, ranging from animal husbandry to the management of woodlands, grasslands, and wetland...

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VVillaIslas @vvillaislas.bsky.social · 20/02/2026

Estén el pendiente y reserven la fecha 🤩🧬🇵🇪

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Thomaz Pinotti @tpinotti.bsky.social · 26/11/2025

we made a tool! ybyra is a lightweight, flexible Y-chromosome haplogroup caller. It is faster, easier to tune and more robust than other tools particularly for low-coverage or ancient DNA data. And it has lots of detailed output – including plots! www.biorxiv.org/content/10.1...

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Frido Welker @fridowelker.bsky.social · 27/10/2025

I'm hiring!⭐ As part of the DFF Sapere Aude-funded project MiddleEarth, I am looking for 1 postdoctoral researcher and 1 research assistant.

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PAASTA Community @paastacommunity.bsky.social · 02/09/2025

Following a marvelous time at ISBA11 and our PAASTA conference, we're back to sharing the work of our community with you here! @ipatramanis.bsky.social PAASTA talk from March about PaleoProPhyler a tool for #phylogenies from ancient proteins is now live on our YouTube youtu.be/2gVEQyinL4A

youtu.be

PAASTA Seminar Series - Ioannis Patramanis

YouTube video by PAASTA community

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Laurits Skov @lauritsskov.bsky.social · 28/08/2025

Are you interested in doing a PhD in Copenhagen? Interested in studying Neanderthals and Denisovans which live on in our genomes? Than you are more than welcome to apply to join my group starting Jan 2026 :) candidate.hr-manager.net/ApplicationI... Please reach out if you have any questions!

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Nature @nature.com · 09/07/2025

Molecules from 20-million-year-old rhino-relative teeth are among the oldest ever sequenced go.nature.com/4lFx4KN

go.nature.com

Ancient proteins rewrite the rhino family tree — are dinosaurs next?

Molecules from 20-million-year-old teeth are among the oldest ever sequenced.

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Vincent J Lynch 🐘🦣🦥 🦇🐋🐢🐍 @devoevomed.bsky.social · 07/07/2025

The slander slanders on. Criticizing #ColossalBio and its co-founder Ben Lamm for their de-extinction #DisInformation campaign complete with #DeepFake dire wolves & woolly mammoths has unleashed a slew poorly written AI news stories about me, again 🙄 www.greenmatters.com/news/lynch-s...

greenmatters.com

Questioning Credibility: Lynch’s Stem Cell Shortcomings

Vincent Lynch, a researcher at the University at Buffalo, has publicly raised doubts about the value and feasibility of de-extinction efforts.

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(Y|G)iannis P. @ipatramanis.bsky.social · 30/05/2025

The Paranthropus paper is out! :D See the post from Palesa for a quick summary. Although technically small in scale (4 specimens🦷), this work took many years and many people to complete... Excited to see how the results we show will be applied to future sample sets, now that we know what works!

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(Y|G)iannis P. @ipatramanis.bsky.social · 15/04/2025

Nice! I wasn't aware of the paper, I'll be taking a look!

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(Y|G)iannis P. @ipatramanis.bsky.social · 15/04/2025

Lastly, We comment on the current state of paleo-phylo-proteomics, including recent works, similar to ours (see academic.oup.com/gbe/article/... & www.researchsquare.com/article/rs-5...) and how the field can move forward.

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(Y|G)iannis P. @ipatramanis.bsky.social · 15/04/2025

The reason why trees differ, likely has to do with the amount of information lost, when going from mixed DNA data, to coding only DNA data (due to selection), to then protein data (due to translation). We quantify and visualize that informational loss.

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(Y|G)iannis P. @ipatramanis.bsky.social · 15/04/2025

DNA vs Proteins Phylogenetic trees created using DNA or protein data can often differ from each other. But, does a tree generated from the protein and DNA data of the SAME LOCUS, differ? Turns out, yes, and in our small sample set, quite often (5 out of 12 genes).

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(Y|G)iannis P. @ipatramanis.bsky.social · 15/04/2025

What about more difficult relations? We performed the same test as above for Neanderthal, Denisovans and modern humans. We failed to confidently or accurately resolve the relations between these 3 groups, with these 12 proteins. We added 16 additional proteins, but failed again to resolve them.

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(Y|G)iannis P. @ipatramanis.bsky.social · 15/04/2025

How many proteins do I need? We see that around 3-4 proteins can give you enough variants to consistently discern between the 3 African great apes from one another (resolution) and around 9-10 proteins, accurately infer their phylogenetic relations, as we know them (accuracy).

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(Y|G)iannis P. @ipatramanis.bsky.social · 15/04/2025

How much phylogenetic information is in these proteins? We saw that these proteins can vary greatly, with collagen and amelogenin (AMELX) being quite conserved, but other proteins (ODAM,COL17A1 and even AMELY!) being far more variable.

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(Y|G)iannis P. @ipatramanis.bsky.social · 15/04/2025

Our manuscript focuses on 12 enamel and collagen proteins that have consistently been recovered in samples older than 1 million years. We use extant and extinct hominids as our test model. While this work still needs to go through peer review, here is a TLDR:

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