@ipatramanis
Postdoctoral Researcher at Globe, University of Copenhagen, Denmark I'm mostly interested in human history and evolution, but also more general: Bioinformatics, Population genetics, Phylogenetics, aDNA, Simulation tools and Palaeoproteomics.
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!
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.
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.
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.
The final chapter of my PhD thesis, is finally published in GBE!
academic.oup.com/gbe/article/...
You can also read the earlier recommendation by PCI in a nice little summary here: evolbiol.peercommunityin.org/articles/rec...
#palaeoproteomics #phylogenetics
🦷 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
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...
Estén el pendiente y reserven la fecha 🤩🧬🇵🇪
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...
I'm hiring!⭐ As part of the DFF Sapere Aude-funded project MiddleEarth, I am looking for 1 postdoctoral researcher and 1 research assistant.
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
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!
Molecules from 20-million-year-old rhino-relative teeth are among the oldest ever sequenced
go.nature.com/4lFx4KN
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...
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!
I am delighted to share with you some new insights into the selection processes that shaped the Spanish population!
This work has been led by @ebosch1972.bsky.social @francesccalafell.bsky.social ( @upf.edu ) in collaboration with Rafael de Cid ( @igtp.bsky.social ) and @sabiagini.bsky.social
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Nice! I wasn't aware of the paper, I'll be taking a look!
Well, thank you for reading it!
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.
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.
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).
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.
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).
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.
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:
We’ve released a preprint on #palaeoproteomics and #phylogenetics !
Over the years, I’ve gotten multiple questions on the usefulness of ancient proteins in resolving phylogenetic questions. This is our attempt to provide some answers:
www.biorxiv.org/content/10.1...
Incredibly proud that our paper on the #palaeoproteomics analysis of the Penghu mandible, led by @tsutatsuta.bsky.social and in collaboration with Chun-Hsiang Chang, Enrico Cappellini and co, is out now in
@science.org! doi.org/10.1126/scie...
Hi
We contributed towards the South African Journal of Science Taung Centennial!
some links;
the special issue: issuu.com/sajs/docs/so...
our paper: sajs.co.za/article/view...
and I got featured on where I work from Nature Africa if you are interested in that: www.nature.com/articles/d44...
Paleoproteomics poster
Sequencing of ancient proteins is the only viable methodology today for retrieving the genetic data required to resolve evolutionary relations between vertebrate species that disappeared millions of years ago.
Paleoproteomics sheds light on million-year-old fossils 🏺🧪
www.nature.com/articles/s41...