We find diverse ancestry in Punic sites 600-200 BCE - with a main component of Greek-Sicilian-like ancestry. Also North African ancestry was widespread across Punic sites on a narrow admixture cline - but remains a minority component (including in Carthage). (3/4)

We could generate genome-wide data of >100 human remains from prominent Punic necropolis in Iberia, Tunisia, Sicily, and the islands of Ibiza and Sardinia. That includes important urban centers, such as the former Phoenician colony Carthage itself. (2/4)

Check out our ancient DNA paper on the maritime Punic civilization! 🦴🧬🌊

We find that their Levantine Phoenician cultural ancestors contributed surprisingly little ancestry to Punic sites in the central and western Mediterranean! (1/4)

doi.org/10.1038/s415...

#aDNA #PopGen #Punic #Phoenician

Finally, we detect only modest amounts of parental relatedness (measured by so-called ROH). We fit an effective size Ne~1,000. That is a considerable recent mating pool, not a crashing population!
Notably, the ROH also allowed us to quantify a lack of contaminating DNA by other humans. (6/7)

There are only a few Neandertal segments—around 10x less than out-of-Africa populations. This supports the idea that most ancestors of this lineage were not part of the out-of-Africa population that mixed with Neandertals, but rather stayed in Africa. (4/7) 🌍

Their ancestry resembles that of other ancient North Africans, including the 15ky-old Tafforalt group from Morocco. However, the Takakori individuals are much less admixed with Levantine-like ancestry.
This appears to be a deep lineage, previously undescribed in that form. (3/7)

Deep in the SW Libyan desert, the Takakori rock shelter preserved human remains and, despite the extreme climatic conditions, even small amounts of human DNA. Cutting-edge archaeogenetic methods let us squeeze out enough sequences from two individuals for various population genetic analyses. (2/7)

I am with Shai here @aylwyn-scally.bsky.social

For older MRCAs more recombinations spots can start an IBD (increasing their total number). Your model does not account for this bias.

There is a history of analytical theory (perfectly fitting the sim.), e.g. SI here:
www.nature.com/articles/s41...

Yes you definitely get meaningful signal down to 2-4cM! ✅️ But is it still accurate IBD segments rather than some similarity measure? But that does matter mostly only for explicit modelling (e.g. timing).

Ralph&Coop did a careful copying in true IBD and checking their inference - a great plot:

Wait - detecting longer IBD segments should be much, much easier (higher power and lower FP) - modulo some gap merging, perhaps.

<6-8cm is where the trouble with lower power and higher error rates should start.

See e.g. the IBIS IBD caller paper
www.sciencedirect.com/science/arti...

Huge congratulations to the awesome Dr. Yilei Huang on his stellar PhD defense! 🌟👏🎉

Supervising one's first PhD student is truly special, and I got so incredibly lucky to have worked with Yilei (and the entire Archaeogenetics department @MPI-EVA Leipzig).

IBS segment sharing is not about nearest neighbors in a sample though - so not inherently biased for admixture modelling ;)

Fascinating technical aspect: Imputing & ancIBDing 45ky-old human genomes works well. With modern ref panels and down to 0.1x WGS coverage! We used downsampling of the two high coverage genomes to prove that. 🎯 That direct experiment showcases the application range of those tool. ✅️✅️ (3/3)

Generally all Ranis individuals share very high background relatedness in form of long IBD (within Ranis and equally to ZK): We modelled an effective pop size of only Ne~200. These early European modern humans were small and mobile Europea hunter gatherer populations! (2/3)

👏👏 @arevsumer.bsky.social ! Contains our IBD analysis led by Yilei Huang: Multiple really long 20cm++ IBD segments link the two record 45ky-old sequenced modern human sites Zlatý kůň (Czechia) and Ranis (Germany). Showing they are closely related - within few generations! 😮😮 (1/3) #PopGen #aDNA

It is large mass Graves embedded in a large urban Medieval cemetery - Black Death victims mostly lined up before decomposition. While there are no burial goods, we will make a detailed map of each individuals position (see Black shades in the map - those are the skeletons! ⬇️ )

PhD opportunity in computational population genetics at @MPI_EVA_Leipzig:
Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬
Please spread the word! 📢🙌 #aDNA #PopGen

www.eva.mpg.de/de/karriere/...

Help my "quiet posters" feed is broken 😅