Statistical methods to detect archaic admixture and identify introgressed sequences

Liming Li, Joshua M. Akey

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Scopus citations


Genome-scale sequencing data sets from many taxa have shown that hybridization across leaky species boundaries is common in natural populations. This observation extends to our own species, as gene flow between anatomically modern humans and other hominins, such as Neanderthal and Denisovans, has been well established. In this chapter, we describe statistical approaches that have been used to test hypotheses of gene flow between species and identify introgressed sequences. These methods provide powerful tools to investigate population history, understand mechanisms of evolutionary change, and better understand the heritable basis of phenotypic variation.

Original languageEnglish (US)
Title of host publicationHandbook of Statistical Genomics
Number of pages19
ISBN (Electronic)9781119487845
ISBN (Print)9781119429142
StatePublished - Jul 29 2019

All Science Journal Classification (ASJC) codes

  • General Biochemistry, Genetics and Molecular Biology


  • Archaic admixture detection
  • D-statistics
  • F-statistics
  • Genetic drift
  • Genetically structured populations
  • Introgressed sequences
  • Rigorous probabilistic models
  • Statistical methods
  • Summary statistic


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