Abstract
The archaic ancestry present in the human genome has captured the imagination of both scientists and the wider public in recent years. This excitement is the result of new studies pushing the envelope of what we can learn from the archaic genetic information that has survived for over 50,000 years in the human genome. Here, we review the most recent ten years of literature on the topic of archaic introgression, including the current state of knowledge on Neanderthal and Denisovan introgression, as well as introgression from other as-yet unidentified archaic populations. We focus this review on four topics: 1) a reimagining of human demographic history, including evidence for multiple admixture events between modern humans, Neanderthals, Denisovans, and other archaic populations; 2) state-of-the-art methods for detecting archaic ancestry in population-level genomic data; 3) how these novel methods can detect archaic introgression in modern African populations; and 4) the functional consequences of archaic gene variants, including how those variants were co-opted into novel function in modern human populations. The goal of this review is to provide a simple-to-access reference for the relevant methods and novel data, which has changed our understanding of the relationship between our species and its siblings. This body of literature reveals the large degree to which the genetic legacy of these extinct hominins has been integrated into the human populations of today.
Highlights
As anatomically modern human (AMH, Box 1) populations began to expand outside of Africa around 50,000– 100,000 years before present (YBP, Karmin et al 2015), they encountered other archaic humans—Neanderthals and Denisovans—and admixture between AMH and these populations left a lasting impact on modern human genomes
Our goal is to review the expansion of admixture-related methods and show how newly identified archaic genetic variation has been used to develop a more complex map of archaic admixture between human populations of the past
The ability to trace the origin of genomic segments allows ARGWeaver-D to ascribe specific ancestry to genomic segments in modern human genomes, as well as in Neanderthal and Denisovan genomes, even identifying portions of the Denisovan genome which originated from an unknown, superarchaic human population
Summary
As anatomically modern human (AMH, Box 1) populations began to expand outside of Africa around 50,000– 100,000 years before present (YBP, Karmin et al 2015), they encountered other archaic humans—Neanderthals and Denisovans—and admixture between AMH and these populations left a lasting impact on modern human genomes. Advances in genomic sequencing and detection methods have provided researchers with a better understanding of archaic populations, as well as evidence for multiple admixture events between Neanderthals, Denisovans, and AMH. New evidence supports admixture with more distantly related “super-archaic” individuals from populations that diverged prior to the split between AMH and Neanderthals-Denisovans, for which we have no direct genome data (Mondal et al 2019; Ragsdale and Gravel 2019; Wall et al 2019; Durvasula and Sankararaman 2020; Hubisz and Siepel 2020; Wang, Mathieson, et al 2020). Our goal is to review the expansion of admixture-related methods and show how newly identified archaic genetic variation has been used to develop a more complex map of archaic admixture between human populations of the past. We discuss in detail the stateof-the-art methods used to identify archaic genome ancestry, and how those methods have allowed us to infer a more complete demographic history of modern humans, in the African continent, and explore functional consequences of archaic introgression in modern humans
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
