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Very excited about this preprint on the high-coverage HGDP genomes, which includes a large part of my PhD work in @aylwyn_scally's group. Here's a thread summarizing what we learned about archaic admixtures in using this large and diverse panel: 1/n biorxiv.org/content/10.110…
We identified Neanderthal and Denisovan segments using an HMM. When we look at the total amount of archaic segments, the geographical pattern agrees with many previous studies, e.g. more Neanderthal ancestry in E. Asia than Europe, Denisovan ancestry enriched in Oceania 2/n 
When we compare various features of the archaic segments, it becomes clear that the Denisovan segments found in Oceania look quite different from Denisovan segments found elsewhere, while Neanderthal segments appear more similar across the world 3/n
For example, the heatmap showing the average diff. per bp between populations in the unadmixed part vs. Neanderthal part of the genome is largely symmetrical - diversity in Neanderthal segments mainly mirrors what is happening in the rest of the genome 4/n
But in the same plot targeting Denisovan regions, notice the brightest region in the upper triangle - the divergence between Oceanian pops and all other non-African pops in Denisovan segments really shoots up! 5/n
The large number of archaic segs even makes it possible to construct the relationship between archaic haplotypes spanning the same genomic region, in the form of haplotype networks. Again, Denisovan haps in Oceania frequently shows deep divergence to other regions 6/n
In the paper we also present other lines of evidence, including where N/D segs are found in the genome and their divergence to the sequenced archaic genomes. We conclude that N admixture happened in a single pulse, with mostly 2-4, but at times >10 introgressing N haps... 7/n
... while D admixture has a more complicated structure: one separate pulse into Oceania, and likely more than one pulses (supported by the divergence to archaic genomes) into the ancestral pop. of E. Asia and the Americas. 8/9
