(Y|G)iannis P.

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~

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.

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~

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.

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~

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.

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~

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.

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

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.

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

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

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.

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

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.

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...

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.

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...

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.

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...

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.

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...