Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0

Abstract

We developed a method, ArchaicSeeker 2.0, to identify introgressed hominin sequences and model multiple-wave admixture. The new method enabled us to discern two waves of introgression from both Denisovan-like and Neanderthal-like hominins in present-day Eurasian populations and an ancient Siberian individual. We estimated that an early Denisovan-like introgression occurred in Eurasia around 118.8–94.0 thousand years ago (kya). In contrast, we detected only one single episode of Denisovan-like admixture in indigenous peoples eastern to the Wallace-Line. Modeling ancient admixtures suggested an early dispersal of modern humans throughout Asia before the Toba volcanic super-eruption 74 kya, predating the initial peopling of Asia as proposed by the traditional Out-of-Africa model. Survived archaic sequences are involved in various phenotypes including immune and body mass (e.g., ZNF169), cardiovascular and lung function (e.g., HHAT), UV response and carbohydrate metabolism (e.g., HYAL1/HYAL2/HYAL3), while “archaic deserts” are enriched with genes associated with skin development and keratinization.

Genetic Connections and Convergent Evolution of Tropical Indigenous Peoples in Asia

“…For instance, the only putative DPA shared by the four representative TIA populations, MTHFD1 -rs138662720-T, is related to different haplotypes between Africans and TIAs. The haplotypes in TIAs are similar to the Altai Neanderthal sequences and were inferred to be introgressed haplotypes by ArchaicSeeker 2.0 ( Yuan et al 2021 ). They were clustered on an independent basal branch in the haplotype network, whereas those in Africans were on the shared branches with other Eurasians ( fig.…”

sstar: A Python package for detecting archaic introgression from population genetic data with S*

“…Several methods also have been developed to detect ancient admixture. Some of these depend on knowledge of the source genome to infer introgressed fragments (Sankararaman et al 2014; Peter 2020), while others identify highly discordant regions in the genome (Skov et al 2018; Yuan et al 2021) similar to S *. These methods are often available as public packages that can be easily applied to new datasets.…”

“…Using approximate history (Supplementary Figure S10–S13), our results suggest that sstar performed similarly when compared with those using the full history (Figure 1B–1E). For two-source introgression, we compared sstar with SPrime, and ArchaicSeeker2.0 (Yuan et al 2021; Zhang et al 2022), another HMM-based tool. In the Human-Neanderthal-Denisovan model with large datasets, SPrime performed well, though both sstar and SPrime performed better when identifying Denisovan fragments than identifying Neanderthal fragments (Figure 1F and 1G).…”

Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0

“…The protocol below describes the analytic steps for the application of ArchaicSeeker 2.0 into analysis of example data of the Han Chinese population. For complete details on the use and execution of this protocol, please refer to Yuan et al. (2021) .…”

“…For complete details on the use and execution of this protocol, please refer to Yuan et al. (2021) .…”