The genetic prehistory of southern Africa (1207.5552v2)

Abstract: Southern and eastern African populations that speak non-Bantu languages with click consonants are known to harbour some of the most ancient genetic lineages in humans, but their relationships are poorly understood. Here, we report data from 23 populations analyzed at over half a million single nucleotide polymorphisms, using a genome-wide array designed for studying human history. The southern African Khoisan fall into two genetic groups, loosely corresponding to the northwestern and southeastern Kalahari, which we show separated within the last 30,000 years. We find that all individuals derive at least a few percent of their genomes from admixture with non-Khoisan populations that began approximately 1,200 years ago. In addition, the east African Hadza and Sandawe derive a fraction of their ancestry from admixture with a population related to the Khoisan, supporting the hypothesis of an ancient link between southern and eastern Africa

• The paper presents comprehensive genomic evidence showing historical admixture among Khoisan groups, with population divergence estimated to have occurred within the last 30,000 years.
• The study employs high-density SNP genotyping alongside PCA, ADMIXTURE, f3/f4 tests, and TreeMix analyses to robustly infer evolutionary dynamics and admixture events.
• The findings uncover a unique mix of indigenous, East African, and Eurasian genetic inputs, offering new insights into the migration and gene flow shaping southern Africa’s prehistory.

Analysis of the Genetic Prehistory of Southern Africa

The research paper explores the genetic prehistory of southern Africa, employing a comprehensive genomic analysis to elucidate the historical relationships and admixture events between diverse populations in the region. This paper leverages high-resolution genotypic data procured from various African populations and integrates it with robust statistical methods to infer evolutionary dynamics and population structure.

Genomic Methods and Analyses

The paper employs a wide array of genomic tools to dissect the complex demography of southern African populations. High-density SNP genotyping, performed on the Human Origins array, forms the basis of this analysis. Principal Component Analysis (PCA) and ADMIXTURE analysis, alongside allele frequency spectra, provide insights into the genetic structure and historical admixture events.

Key methods include the usage of three- and four-population tests, informed by $f_3$ and $f_4$ statistics, to robustly infer admixture and population history. The relationship of the Nama's European ancestry is corroborated using ROLLOFF analyses, revealing recent admixture approximately five generations ago. Additionally, TreeMix is utilized to construct phylogenetic trees, which are subsequently analyzed for admixture events to highlight complex ancestries.

Noteworthy Findings

The genomic analysis confirms substantial admixture across various Khoisan groups, which are classified broadly into the northwestern and southeastern Kalahari groups. The temporal estimates derived suggest a population divergence within the last 30,000 years, albeit these are potentially overestimated due to non-Khoisan admixture. ADMIXTURE analysis further reveals genetic continuities and distinctions between historically foraging populations such as the Taa, Ju|’hoan, and Dinka.

One striking result is the identified intrusion of a western Eurasian genetic component, particularly prominent in the Sandawe and, to a lesser extent, the Hadza, dated back about 2000 to 2500 years. This reflects either direct introgression from Eurasian populations or more likely, through intermediation with an East African population that had previously interacted with Eurasian groups.

Furthermore, the data underpinning the TreeMix analyses reveal that the Hadza and Sandawe possess a unique admixture profile, consistent with a shared genetic history linked to southern African Khoisan populations and an additional gene flow from northeastern Africa.

Implications and Future Directions

The implications of these findings are multifaceted. Practically, they enrich the understanding of the complex genetic landscape of southern Africa, informing contemporary discussions on human migration and gene flow. Theoretically, the analyses provide a foundation for assessing the impact of demography on genetic diversity, contributing to broader evolutionary narratives.

Future research could extend these methodologies to finer scale geographic sampling and deeper exploration into the linkage disequilibrium patterns, which may offer unprecedented insights into ancestral gene flow and diversification processes. Additionally, ongoing developments in ancient DNA retrieval techniques and computational innovations are poised to complement these findings, potentially unlocking intricate details of human prehistory across the African continent.

In conclusion, this paper provides a granular and context-rich evaluation of southern African genetic landscapes, painting a detailed picture of historical population movements and interactions that shaped the region's genetic heritage.