Reply to Barton et al: signatures of natural selection during the Black Death.

Autor: Vilgalys TP; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA., Klunk J; McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9.; Daicel Arbor Biosciences, Ann Arbor, MI, USA., Demeure CE; Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France., Cheng X; Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA., Shiratori M; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA., Madej J; Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France., Beau R; Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France., Elli D; Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA., Patino MI; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA., Redfern R; Centre for Human Bioarchaeology, Museum of London, London, UK, EC2Y 5HN., DeWitte SN; Department of Anthropology, University of South Carolina, Columbia, SC, USA., Gamble JA; Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, R3T2N2., Boldsen JL; Department of Forensic Medicine, Unit of Anthropology (ADBOU), University of Southern Denmark, Odense S, 5260, Denmark., Carmichael A; History Department, Indiana University, Bloomington, IN, USA., Varlik N; Department of History, Rutgers University-Newark, NJ, USA., Eaton K; McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9., Grenier JC; Montreal Heart Institute, Faculty of Medicine, Université de Montréal, Montréal, Quebec, Canada, H1T 1C7., Golding GB; McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9., Devault A; Daicel Arbor Biosciences, Ann Arbor, MI, USA., Rouillard JM; Daicel Arbor Biosciences, Ann Arbor, MI, USA.; Department of Chemical Engineering, University of Michigan Ann Arbor, Ann Arbor, MI, USA., Yotova V; Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada, H3T 1C5., Sindeaux R; Centre Hospitalier Universitaire Sainte-Justine, Montréal, Quebec, Canada, H3T 1C5., Ye CJ; Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.; Institute for Human Genetics, University of California, San Francisco, CA, USA., Bikaran M; Division of Rheumatology, Department of Medicine, University of California, San Francisco, CA, USA.; Institute for Human Genetics, University of California, San Francisco, CA, USA., Dumaine A; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA., Brinkworth JF; Department of Anthropology, University of Illinois Urbana-Champaign, Urbana, IL, USA.; Carl R Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA., Missiakas D; Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA., Rouleau GA; Montreal Neurological Institute-Hospital, McGill University, Montréal, Quebec, Canada, H3A 2B4., Steinrücken M; Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.; Department of Human Genetics, University of Chicago, Chicago, IL, USA., Pizarro-Cerdá J; Institut Pasteur, Université Paris Cité, CNRS UMR6047, Yersinia Research Unit, Microbiology Department, F-75015 Paris, France., Poinar HN; McMaster Ancient DNA Centre, Departments of Anthropology, Biology and Biochemistry, McMaster University, Hamilton, Ontario, Canada L8S4L9.; Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.; Department of Microbiology, Ricketts Laboratory, University of Chicago, Lemont, IL, USA., Barreiro LB; Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.; Centre for Human Bioarchaeology, Museum of London, London, UK, EC2Y 5HN.; Department of Anthropology, University of South Carolina, Columbia, SC, USA.; Department of Anthropology, University of Manitoba, Winnipeg, Manitoba, R3T2N2.
Jazyk: angličtina
Zdroj: BioRxiv : the preprint server for biology [bioRxiv] 2023 Apr 07. Date of Electronic Publication: 2023 Apr 07.
DOI: 10.1101/2023.04.06.535944
Abstrakt: Barton et al . 1 raise several statistical concerns regarding our original analyses 2 that highlight the challenge of inferring natural selection using ancient genomic data. We show here that these concerns have limited impact on our original conclusions. Specifically, we recover the same signature of enrichment for high F ST values at the immune loci relative to putatively neutral sites after switching the allele frequency estimation method to a maximum likelihood approach, filtering to only consider known human variants, and down-sampling our data to the same mean coverage across sites. Furthermore, using permutations, we show that the rs2549794 variant near ERAP2 continues to emerge as the strongest candidate for selection (p = 1.2×10 -5 ), falling below the Bonferroni-corrected significance threshold recommended by Barton et al . Importantly, the evidence for selection on ERAP2 is further supported by functional data demonstrating the impact of the ERAP2 genotype on the immune response to Y. pestis and by epidemiological data from an independent group showing that the putatively selected allele during the Black Death protects against severe respiratory infection in contemporary populations.
Competing Interests: Competing interest declaration JK, ADe, and J-MR declare financial interest in Daicel Arbor Biosciences, who provided the myBaits hybridization capture kits for this work. All other authors declare no competing interests.
Databáze: MEDLINE
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