Ancient genomes from southern Africa pushes modern human divergence beyond 260,000 years ago

Abstract

30Southern Africa is consistently placed as one of the potential regions for the evolution of Homo sapiens. 31To examine the region's human prehistory prior to the arrival of migrants from East and West Africa or 32 Eurasia in the last 1,700 years, we generated and analyzed genome sequence data from seven ancient 33 individuals from KwaZulu-Natal, South Africa. Three Stone Age hunter-gatherers date to ~2,000 years 34 ago, and we show that they were related to current-day southern San groups such as the Karretjie People. 35Four Iron Age farmers (300-500 years old) have genetic signatures similar to present day speakers. The genome sequence (13x coverage) of a juvenile boy from Ballito Bay, who lived ~2,000 37 years ago, demonstrates that southern African Stone Age hunter-gatherers were not impacted by recent 38 admixture; however, we estimate that all modern-day Khoekhoe and San groups have been influenced 39 by 9-22% genetic admixture from East African/Eurasian pastoralist groups arriving >1,000 years ago, 40 including the Ju|'hoansi San, previously thought to have very low levels of admixture. Using traditional 41 and new approaches, we estimate the population divergence time between the Ballito Bay boy and other 42 groups to beyond 260,000 years ago. These estimates dramatically increases the deepest divergence 43 amongst modern humans, coincide with the onset of the Middle Stone Age in sub-Saharan Africa, and 44 coincide with anatomical developments of archaic humans into modern humans as represented in the 45 local fossil record. Cumulatively, cross-disciplinary records increasingly point to southern Africa as a 46 potential (not necessarily exclusive) 'hot spot' for the evolution of our species. 47. CC-BY-NC-ND 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/145409 doi: bioRxiv preprint first posted online Jun. 5, 2017; African indigenous groups, and push the emergence of modern humans back to >260 kya. 75We sequenced the genomes of three Stone Age hunter-gatherers and four Iron Age farmers, directly 76 radiocarbon dated to ~2 kya and 0.5-0.3 kya respectively, to between 0.01x and 13.2x genome coverage 77( Figure 1, Table 1, SI 1 for archaeological contexts, and SI 2-3 for sampling and laboratory procedures). 78The DNA-sequence data display all features characteristic of ancient DNA (e.g. 21 , short DNA fragments was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/145409 doi: bioRxiv preprint first posted online Jun. 5, 2017; 4 haplotype (SI Section 5.1), common among modern-day Khoe-San 17 . 90To assess population affinities among the ancient individuals and their relations to modern-day groups, 91we merged the ancient southern African genome data wit...

Microbial symbiosis and coevolution of an entire clade of ancient vertebrates: the gut microbiota of sea turtles and its relationship to their phylogenetic history

“…In contrast, the human microbiota has diverged rapidly from our closest relatives [89], and among populations of humans, continues to rapidly evolve [90]. Sea turtles are among the most ancient species on Earth, with the leatherback existing in its current form for nearly 70 million years [15], while modern humans first appeared around 350,000 to 260,000 years ago [91]. These seemingly marked differences in rate of evolution of microbiotas, may be reflective of broad differences in rates of evolution between taxa, and warrants further investigation.…”

Archaic Hominin Introgression in Africa Contributes to Functional Salivary MUC7 Genetic Variation

“…2016 ), as well as the unexpectedly old human remains ( Hublin etal. 2017 ) and lineages ( Schlebusch etal. 2017 ).…”

Counterbalancing the time-dependence effect on the Human Mitochondrial DNA Molecular Clock

“…These older dates were genetically confirmed in a study of ancient African genomes that estimated modern human divergence at 350 to 260 kya. [3] Another controversial milestone of the mtDNA molecular clock was the dating, based on the coalescence age of macrohaplogroup L3, of the dispersal of modern humans out of Africa 50 to 70 kya [4]. This is against the presence of early modern human remains in the Levant at the Skhul and Qafzeh caves dated at about 80-120 kya [5], the presence of middle stone age industries in the Arabian peninsula with similar dates around 80-130 kya [6][7][8], the recent discovery in southern China of unequivocally modern human teeth dated to 80-120 kya [9], or the lately reported detection of an ancient gene flow from early modern humans into the ancestors of eastern Neanderthals more than 100 kya [10] .…”