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

Zhang, Rui; Yuan, Kai; Xu, Shuhua

doi:10.1016/j.xpro.2022.101314

Cited by 9 publications

(11 citation statements)

References 13 publications

(9 reference statements)

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“…For example, the adaptive EPAS1 haplotype was proven as a “borrowed fitness” from Denisovans [ 34 ]. To search for the genome-wide regions showing signatures of archaic introgression in the Tibetan genomes, we employed two widely used tools, ArchaicSeeker2.0 [ 35 ] and SPrime [ 36 ] (see the “ Methods ” section), which gave 599 and 670 candidate introgression regions, respectively. The detected genome-wide introgression levels (0.06–0.18% from Denisovan and 0.34–0.79% from Neanderthal) of Tibetans are similar to those reported in other East Asian populations [ 35 ].…”

Section: Resultsmentioning

confidence: 99%

Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans

Zheng

Guo

et al. 2023

Genome Biol

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Background Tibetans are genetically adapted to high-altitude environments. Though many studies have been conducted, the genetic basis of the adaptation remains elusive due to the poor reproducibility for detecting selective signatures in the Tibetan genomes. Results Here, we present whole-genome sequencing (WGS) data of 1001 indigenous Tibetans, covering the major populated areas of the Qinghai–Tibetan Plateau in China. We identify 35 million variants, and more than one-third of them are novel variants. Utilizing the large-scale WGS data, we construct a comprehensive map of allele frequency and linkage disequilibrium and provide a population-specific genome reference panel, referred to as 1KTGP. Moreover, with the use of a combined approach, we redefine the signatures of Darwinian-positive selection in the Tibetan genomes, and we characterize a high-confidence list of 4320 variants and 192 genes that have undergone selection in Tibetans. In particular, we discover four new genes, TMEM132C, ATP13A3, SANBR, and KHDRBS2, with strong signals of selection, and they may account for the adaptation of cardio-pulmonary functions in Tibetans. Functional annotation and enrichment analysis indicate that the 192 genes with selective signatures are likely involved in multiple organs and physiological systems, suggesting polygenic and pleiotropic effects. Conclusions Overall, the large-scale Tibetan WGS data and the identified adaptive variants/genes can serve as a valuable resource for future genetic and medical studies of high-altitude populations.

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Section: Resultsmentioning

confidence: 99%

Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans

Zheng

Guo

et al. 2023

Genome Biol

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“…The default was used for all parameters as suggested in protocol paper. 79 ArchaicSeeker 2.0 used a hidden Markov Model to detect archaic segments on each haplotype. We merged these segments and keep segments detected in all the East Asian subpopulations.…”

Section: Methodsmentioning

confidence: 99%

Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia

Ma¹,

Xu²

2022

iScience

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“…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).…”

Section: Figurementioning

confidence: 99%

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

Huang

Kuhlwilm

2022

Preprint

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S* is a widely used statistic for detecting archaic admixture from population genetic data. To apply S*, several previous studies used the freezing-archer repository, which is a compilation of Python 2 and R scripts originally developed to detect Neanderthal and Denisovan introgression into modern humans. When studying other species or populations, however, freezing-archer is not directly applicable. Here, we implemented a new Python 3 package named sstar, with better performance than freezing-archer. Reliability was also improved after fixing bugs in freezing-archer. Compared with freezing-archer, sstar is more user-friendly, versatile, and well-documented.

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

Cited by 9 publications

References 13 publications

Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans

Large-scale genome sequencing redefines the genetic footprints of high-altitude adaptation in Tibetans

Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia

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

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