(Y|G)iannis P.
@ipatramanis.bsky.social
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.
I'm mostly interested in human history and evolution, but also more general: Bioinformatics, Population genetics, Phylogenetics, aDNA, Simulation tools and Palaeoproteomics.
Nice! I wasn't aware of the paper, I'll be taking a look!
April 15, 2025 at 8:58 PM
Nice! I wasn't aware of the paper, I'll be taking a look!
Well, thank you for reading it!
April 15, 2025 at 1:04 PM
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.
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.
April 15, 2025 at 11:06 AM
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.
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.
April 15, 2025 at 11:06 AM
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).
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).
April 15, 2025 at 11:06 AM
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).
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.
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.
April 15, 2025 at 11:06 AM
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 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).
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).
April 15, 2025 at 11:06 AM
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).
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.
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.
April 15, 2025 at 11:06 AM
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 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:
While this work still needs to go through peer review, here is a TLDR:
April 15, 2025 at 11:06 AM
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:
While this work still needs to go through peer review, here is a TLDR: