Chad Genetic Diversity Reveals an African History Marked by Multiple Holocene Eurasian Migrations

Abstract

Understanding human genetic diversity in Africa is important for interpreting the evolution of all humans, yet vast regions in Africa, such as Chad, remain genetically poorly investigated. Here, we use genotype data from 480 samples from Chad, the Near East, and southern Europe, as well as whole-genome sequencing from 19 of them, to show that many populations today derive their genomes from ancient African-Eurasian admixtures. We found evidence of early Eurasian backflow to Africa in people speaking the unclassified isolate Laal language in southern Chad and estimate from linkage-disequilibrium decay that this occurred 4,750-7,200 years ago. It brought to Africa a Y chromosome lineage (R1b-V88) whose closest relatives are widespread in present-day Eurasia; we estimate from sequence data that the Chad R1b-V88 Y chromosomes coalesced 5,700-7,300 years ago. This migration could thus have originated among Near Eastern farmers during the African Humid Period. We also found that the previously documented Eurasian backflow into Africa, which occurred ∼3,000 years ago and was thought to be mostly limited to East Africa, had a more westward impact affecting populations in northern Chad, such as the Toubou, who have 20%-30% Eurasian ancestry today. We observed a decline in heterozygosity in admixed Africans and found that the Eurasian admixture can bias inferences on their coalescent history and confound genetic signals from adaptation and archaic introgression.

Subsistence strategy was the main factor driving population differentiation in the bidirectional corridor of the African Sahel

“…Our data on uniparental markers, on the other hand, indicate differences in the population histories of male and female subpopulations. It has been well established that in the populations of eastern and central Sahel there is a discernible Eurasian genetic component introduced over a long period of time by numerous migration events from different non‐African regions (Galego Llorente et al, ; Haber et al, ; Pickrell et al, ). Successive waves of migration are clearly reflected in both maternal and paternal genetic pools (Bučková et al, ; Černý et al, ; Podgorná et al, ; Shriner & Rotimi, ) and also in autosomal datasets as shown by allele frequency based methods (Triska et al, ; Vicente et al, ).…”

A different view on fine-scale population structure in Western African populations

“…The study of population structure allows assigning individuals to distinct ethnic groups cohabiting a particular region (Liu et al 2018), investigating migrations from the origin of admixed populations (Haber et al 2016), and quantifying and characterising confounding due to shared genetic ancestry in association studies (Wang et al 2018). In humans, genetic variation is not randomly distributed across the world because of non-random mating between individuals, who tend to marry within their community, often driven by physical proximity (Schneider and Peischl 2011).…”

Continuity and admixture in the last five millennia of Levantine history from ancient Canaanite and present-day Lebanese genome sequences

“…Additionally, we sequenced whole-genomes of 99 present-day Lebanese individuals to ~8x coverage on an Illumina HiSeq 2500 using 2× 100 bp reads. We merged the low-coverage Lebanese data with four high-coverage (30x) Lebanese samples, 26 1000 Genomes Project phase 3 CEU, YRI, and CHB populations, 27 and sequence data previously published from regional populations (Egyptians, Ethiopians and Greeks). 1; 26 Raw calls were generated using bcftools (bcftools mpileup -C50 -pm3 -F0.2 -d10000 | bcftools call -mv, version 1.2-239-g8749475) and filtered to include only SNPs with the minimum of 2 alternate alleles in at least one population and site quality larger than 10; we excluded sites with a minimum per-population HWE and total HWE less than 0.01 28 and sites within 3bp of an indel.…”