A Primer on the Population Genetic Analysis of Ancient Genomes
The genetic analysis of ancient biological remains is increasingly relying on next generation sequencing and genome-wide data it produces. In addition to bioinformatics processing of high-throughput data produced by next generation sequencing, downstream
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Contents Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Relatedness and Recent Consanguinity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Population Structure and Data Overview . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Modeling of Population Relationship: F-Statistics and Their Extensions . . . . . . . . . . . . . . . . . . . . . . . Conclusion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Cross-References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .
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Abstract
The genetic analysis of ancient biological remains is increasingly relying on next generation sequencing and genome-wide data it produces. In addition to bioinformatics processing of high-throughput data produced by next generation sequencing, downstream population genetic analyses are critical to fully utilize rich evolutionary information stored in genomic variation data. In this chapter, I summarize representative population genetic methods that are applied to genomewide data from ancient sources, such as mummies. They aim at detecting genetic relatives, overviewing the genetic profile of the analyzed individuals in the context of worldwide genetic diversity, and formally testing population relationship. For each method, I outline its general principle and provide practical guidance for conducting it. Keywords
Mummy genomics · Population genetics · Genetic relatedness · Principal component analysis · ADMIXTURE · F4 statistics · qpAdm
C. Jeong (*) School of Biological Sciences, Seoul National University, Seoul, Republic of Korea e-mail: [email protected] © Springer Nature Singapore Pte Ltd. 2021 D. H. Shin, R. Bianucci (eds.), The Handbook of Mummy Studies, https://doi.org/10.1007/978-981-15-1614-6_49-1
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C. Jeong
Introduction The study of ancient genomes provides a window to directly observe genetic profiles of individuals and populations who lived in the past, stretching back to as far as hundreds of thousands of years (Krause and Pääbo 2016). Archaeogenetic studies of our own species are at the forefront of this trend, and findings from the study of ancient human genomes, especially those obtained from mummies or naturally mummified soft tissues, revolutionized our understanding of human history in various temporal and spatial scales (Rasmussen et al. 2010; Rasmussen et al. 2011; Schuenemann et al. 2017). For example, the geneti
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