9/9 TRACE reveals hidden layers of modern human evolution using only contemporary genomes. We would greatly appreciate any comments or suggestions!
github.com/YulinZhang98...
8/9 In Oceanians, Denisovan-introgressed segments are enriched for deep lineages (compared to Neanderthal-introgressed regions) that diverged ~1.8 million years ago, supporting evidence for “super-archaic” ancestry in modern humans and Denisovans.
7/9 Surprisingly, ghost ancestry persists in “archaic deserts”—regions thought to be modern human-specific, including the desert containing FOXP2 on chromosome 7, challenging interpretations of positive selection for modern human variants in these regions.
6/9 Ghost ancestry is enriched for immune and metabolic complexes. While there are ghost ancestry deserts in non-Africans, no ghost ancestry deserts were found in Africans.
5/9 Ghost segments are shared among modern human populations and show equal affinity to Neanderthals and Denisovans, suggesting an origin from an unsequenced lineage diverging ~830,000 years ago.
4/9 We recover patterns of Neanderthal and Denisovan ancestry in non-Africans. Surprisingly, we find ghost ancestry (0.5-1.1%) in *all* modern humans -- East Africans, West Africans, Europeans, East Asians, and South Asians.
3/9 We perform a range of simulations to show TRACE is reliable and has low false discovery rates using both true ARGs and inferred ARGs.
2/9 TRACE leverages footprints of archaic admixture in ancestral recombination graphs- specifically, long branches (deep coalescent events) and long haplotypes (differentiates ancestral variation from recent gene flow)
1/9 Jointly lead with @aabiddanda.github.io and in collaboration with @sarahaj34.bsky.social , Colm O'Dushlaine and Priya Moorjani, we developed a new method TRACE that detects archaic introgression without requiring archaic genomes — and reveals previously unresolved admixture events. 🧬💀
Have you ever wondered how many archaic populations contributed DNA to modern humans? We know about Neanderthals and Denisovans, but the fossil and genetic evidence suggests a much more complex history!
www.biorxiv.org/content/10.6...
With @szhan.bsky.social, @yulinzhang.bsky.social, Chao Zhang and Bingjie Chen, we wrote a Perspective about unifying the tree-based method across phylogenetics, population genetics and cell biology: arxiv.org/abs/2512.05499.
Reposts are greatly appreciated!
