Going local with ancient DNA: A review of human histories from regional perspectives

Abstract

Ancient DNA (aDNA) has added a wealth of information about our species’ history, including insights on genetic origins, migrations and gene flow, genetic admixture, and health and disease. Much early work has focused on continental-level questions, leaving many regional questions, especially those relevant to the Global South, comparatively underexplored. A few success stories of aDNA studies from smaller laboratories involve more local aspects of human histories and health in the Americas, Africa, Asia, and Oceania. In this Review, we cover some of these contributions by synthesizing finer-scale questions of importance to the archaeogenetics field, as well as to Indigenous and Descendant communities. We further highlight the potential of aDNA to uncover past histories in regions where colonialism has neglected the oral histories of oppressed peoples.

Hunter–gatherer genetics research: Importance and avenues

“…At this point in time, genome-wide SNP genotypes exist for several hunter gatherer groups and whole genome sequences for a subset of these, mostly from populations in Africa (see Fan et al, 2023 for recent efforts). Increasing genomic coverage for more groups in addition to the sequencing of currently genotyped populations is likely to allow us to answer existing questions regarding the extent of human genetic variation, regarding human origins, geographical dispersals and adaptations to various ecosystems (Ávila-Arcos et al, 2023 ). Moreover, it will help remove bias from our interpretations by allowing us to build reference panels and estimate genetic parameters (such as recombination or mutation rates) that more accurately reflect human genetic diversity, and that are representative of more populations.…”

“…In addition, while population genetics research has traditionally focused on documenting ‘broad strokes’ of continental patterns of migrations and interactions between different populations or large demographic fluctuations, such patterns emerge from the local-scale behaviour of individuals and groups (He et al, 2019 ; Ávila-Arcos et al, 2023 ). Consequently, more sampling of individuals within regions and a coupling of genetic and anthropological data are required for understanding the local level processes that give rise to the observed continental level patterns (see Lansing et al, 2022 for examples).…”

Unraveling the diversity and cultural heritage of fruit crops through paleogenomics

“…In many respects it is a revolutionary field that has significantly expanded our understanding of human history, evolution, and environmental adaptation. The retrieval and analysis of ancient DNA from archaeological and paleontological remains has even offered insights into the genetic makeup of extinct and ancient populations [ 49 , 99 , 100 ], and ancient DNA data can help to address an array of questions in anthropology, evolutionary biology, and the environmental and archaeological sciences. Such data have, for example, been used to study archaic human groups such as Denisovans and Neanderthals [ 101 , 102 ], to unravel human migration patterns [ 103 , 104 ], and to shed light on domestication processes [ 105 ].…”

Testing Times: Challenges in Disentangling Admixture Histories in Recent and Complex Demographies

“…With the recent shift of aDNA research towards reconstructing admixture histories within sub-continental regions (Ávila-Arcos et al 2023), understanding the limits of rejecting false sources recently split from the true ancestral source is becoming increasingly pertinent. To investigate this, we explored the limits of differentiating between the sister clades of R1 and S1, and by symmetry S2 and R2, (Figure 3A) as false and true sources in qpAdm models.…”

“…No species has gained deeper insights from the aDNA revolution than humans, as it has significantly unraveled our complex evolutionary and migratory histories (Haber et al 2016;Slatkin and Racimo 2016;Fu et al 2016;Llamas et al 2017;Williams and Teixeira 2020;Liu et al 2021;Ávila-Arcos et al 2023). Much of the research in human paleogenomics during the early 2010s was focused on reconstructing human prehistory (dating back more than 5k years before the present (YBP)) (Figure 1A).…”