A new inference method for detecting an ongoing selective sweep

Fujito, Naoko T.; Satta, Yoko; Hayakawa, Toshiyuki; Takahata, Naoyuki

doi:10.1266/ggs.18-00008

Cited by 15 publications

(37 citation statements)

References 60 publications

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“…The hallmark of an incomplete selective sweep is reduced intra-allelic variability (IAV) within a derived allele group relative to the total variability in the entire sample (Fujito et al, 2018;Satta et al, 2019). IAV may be expressed by numerous variables that are useful for detecting and classifying a selective sweep as well as for dating the onset of positive selection.…”

Section: Resultsmentioning

confidence: 99%

“…, HJ = jJ e ⁄ , HJ = jJ jJ ⁄ and = jJ / where Σ in H indicates that the summation is taken over a certain range of and (see Fujito et al, 2018 andSatta et al, 2019 13.4…”

Section: Discussionmentioning

confidence: 99%

“…The red points indicate the H or iSAFE value for the T allele at rs4988235. Needless to say, the ranking by H is in ascending order (Fujito et al, 2018), whereas that of iSAFE is in descending order (Akbari et al, 2018)…”

Section: Discussionmentioning

confidence: 99%

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Population genomics on the origin of lactase persistence in Europe and South Asia

Satta

Takahata

2020

Preprint

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AbstractThe C to T mutation at rs4988235 located upstream of the lactase (LCT) gene is the primary determinant for lactase persistence (LP) that is prevalent among Europeans and South Asians. Here, we review evolutionary studies of this mutation based on ancient and present-day human genomes with the following concluding remarks: the mutation arose in the Pontic Steppe somewhere between 23,000 and 5000 years ago, emigrated into Europe and South Asia in the Bronze Age via the expansion of the Steppe ancestry, and experienced local hard sweeps with their delayed onsets occurring in the last 3600 years. We also argue that the G to A mutation at rs182549 arose earlier than 23,000 years ago, the intermediate CA haplotype ancestral to the LP-related TA haplotype is still represented by samples from Tuscans, admixed Americans and South Asians, and the great majority of G to A mutated descendants have hitchhiked since the C to T mutation was favored by local selection.

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Section: Resultsmentioning

confidence: 99%

“…, HJ = jJ e ⁄ , HJ = jJ jJ ⁄ and = jJ / where Σ in H indicates that the summation is taken over a certain range of and (see Fujito et al, 2018 andSatta et al, 2019 13.4…”

Section: Discussionmentioning

confidence: 99%

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Population genomics on the origin of lactase persistence in Europe and South Asia

Satta

Takahata

2020

Preprint

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“…At least 1,000 replications were performed to obtain the distribution of F < c 7 . Needless to say, this F c -based method could unambiguously detect signals of selective sweep in such genes ( LCT , OCA2 , and EDAR ; [ 18 ]) that have been demonstrated as targets of positive selection [ 19 ].…”

Section: Methodsmentioning

confidence: 99%

Positive selection on schizophrenia-associated ST8SIA2 gene in post-glacial Asia

et al. 2018

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A number of loci are associated with highly heritable schizophrenia and the prevalence of this mental illness has had considerable negative fitness effects on human populations. Here we focused on one particular schizophrenia-associated gene that encodes a sialyltransferase (ST8SIA2) and is expressed preferentially in the brain with the level being largely determined by three SNPs in the promoter region. It is suggested that the expression level of the ST8SIA2 gene is a genetic determinant of schizophrenia risk, and we found that a geographically differentiated non-risk SNP type (-type) has significantly reduced promoter activity. A newly developed method for detecting ongoing positive selection was applied to the ST8SIA2 genomic region with the identification of an unambiguous sweep signal in a rather restricted region of 18 kb length surrounding the promoter. We also found that while the -type emerged in anatomically modern humans in Africa over 100 thousand years ago, it has increased its frequency in Asia only during the past 20–30 thousand years. These findings support that the positive selection is driven by psychosocial stress due to changing social environments since around the last glacial maximum, and raise a possibility that schizophrenia extensively emerged during the Upper Paleolithic and Neolithic era.

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“…We evaluated intra allelic variability (IAV) within a derived allele (D) group using 2D SFS (Φ i,j [ 34 ]) and its summary statistics, F c , G c0 , and L c0 [ 34 , 35 ]. The latter three summary statistics were designed to detect incomplete selective sweep signals when compared to the null distribution of each summary statistic.…”

Section: Methodsmentioning

confidence: 99%

Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population

Iwasaki

Ishiya

Kanzawa-Kiriyama

et al. 2020

Genes

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A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.

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A new inference method for detecting an ongoing selective sweep

Cited by 15 publications

References 60 publications

Population genomics on the origin of lactase persistence in Europe and South Asia

Population genomics on the origin of lactase persistence in Europe and South Asia

Positive selection on schizophrenia-associated ST8SIA2 gene in post-glacial Asia

Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population

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