'DNA time capsule' reveals birthplace of modern humans

A Sydney-led study has found that the earliest ancestors of anatomically modern humans (Homo sapiens sapiens) emerged in a southern African ‘homeland’ and thrived there for 70 thousand years.

The breakthrough findings published today in the journal Nature today.

The authors propose that changes in Africa’s climate triggered the first human explorations, which initiated the development of humans’ genetic, ethnic and cultural diversity.

The findings provide a window into the first 100 thousand years of modern humans’ history.

DNA as a time capsule

The study uniquely combined the disciplines of genetics, geology and climatic physics to rewrite our earliest human history.

“It has been clear for some time that anatomically modern humans appeared in Africa roughly 200 thousand years ago. What has been long debated is the exact location of this emergence and subsequent dispersal of our earliest ancestors,” says study lead Professor Vanessa Hayes from the University of Sydney and Garvan Institute of Medical Research; the South African by birth is also an Extraordinary Professor at the University of Pretoria.

“Mitochondrial DNA acts like a time capsule of our ancestral mothers, accumulating changes slowly over generations. Comparing the complete DNA code, or mitogenome, from different individuals provides information on how closely they are related,” says Professor Hayes, from the Sydney Medical School.

In the study, Professor Hayes and her colleagues collected blood samples to establish a comprehensive catalogue of modern human’s earliest mitogenomes from the so-called ‘L0’ lineage.

“Our work would not have been possible without the generous contributions of local communities and study participants in Namibia and South Africa, which allowed us to uncover rare and new L0 sub-branches,” says study author and public health Professor Riana Bornman from the University of Pretoria.

“We merged 198 new, rare mitogenomes to the current database of modern human’s earliest known population, the L0 lineage. This allowed us to refine the evolutionary tree of our earliest ancestral branches better than ever before,” says first author Dr Eva Chan from the Garvan Institute of Medical Research, who led the phylogenetic analyses.

By combining the L0 lineage timeline with the linguistic, cultural and geographic distributions of different sub-lineages, the study authors revealed that 200 thousand years ago, the first Homo sapiens sapiens maternal lineage emerged in a ‘homeland’ south of the Greater Zambezi River Basin region, which includes the entire expanse of northern Botswana into Namibia to the west and Zimbabwe to the east.

University of Sydney Vice-Chancellor and Principal Dr Michael Spence congratulated Professor Hayes and her team on the discovery.

“This is an outstanding result for Australian research, providing fascinating insights into our ancestry,” Dr Spence said.

“This goes to show what can be achieved when people collaborate globally for a shared purpose; it’s also an exemplary example of academic endeavour – a leading genetic expert recognising the potential of the genetic clues in our cells to answer big questions in anthropology and human origin.”

A homeland perfect for life to thrive

Investigating existing geological, archeological and fossil evidence, revealed that the homeland region once held Africa’s largest-ever lake system, Lake Makgadikgadi.

“Prior to modern human emergence, the lake had begun to drain due to shifts in underlying tectonic plates. This would have created, a vast wetland, which is known to be one of the most productive ecosystems for sustaining life,” says geologist Dr Andy Moore, from Rhodes University, who was part of the study.

The first migrations of modern humans

The authors’ new evolutionary timelines suggest that the ancient wetland ecosystem provided a stable ecological environment for modern humans’ first ancestors to thrive for 70 thousand years.

“We observed significant genetic divergence in the modern humans’ earliest maternal sub-lineages, that indicates our ancestors migrated out of the homeland between 130 and 110 thousand years ago,” explains Professor Hayes.

“The first migrants ventured northeast, followed by a second wave of migrants who travelled southwest. A third population remained in the homeland until today.”

“In contrast to the northeasterly migrants, the southwesterly explorers appear to flourish, experiencing steady population growth,” says Professor Hayes.

The authors speculate that the success of this migration was most likely a result of adaptation to marine foraging, which is further supported by extensive archaeological evidence along the southern tip of Africa.

Climate effects

To investigate what may have driven these early human migrations, co-corresponding author Professor Axel Timmermann, Director of the IBS Center for Climate Physics at Pusan National University, analysed climate computer model simulations and geological data, which capture Southern Africa’s climate history of the past 250 thousand years.

“Our simulations suggest that the slow wobble of Earth’s axis changes summer solar radiation in the Southern Hemisphere, leading to periodic shifts in rainfall across southern Africa,” says Professor Timmermann.

 “These shifts in climate would have opened green, vegetated corridors, first 130 thousand years ago to the northeast, and then around 110 thousand years ago to the southwest, allowing our earliest ancestors to migrate away from the homeland for the first time.”

“These first migrants left behind a homeland population,” remarks Professor Hayes. “Eventually adapting to the drying lands, maternal descendants of the homeland population can be found in the greater Kalahari region today.”

Featured image: Professor Vanessa Hayes learning how to make fire with Juǀ’hoansi hunters in the now dried homeland of the greater Kalahari of Namibia. From left to right: Nǂamce Sao, ǀkun Nǂamce, Vanessa Hayes and ǀkun ǀkunta. Credit: Chris Bennett, Evolving Picture. 

Declaration

The research was supported by an Australian Research Council Discovery Project grant (DP170103071) and the Institute for Basic Science (IBS-R028-D1). Professor Vanessa Hayes holds the Sydney University Petre Chair of Prostate Cancer Research.

This study was conducted in consultation with the local African communities, approval from community leaders and ethics approval from the Ministry of Health and Social Services in Namibia, the University of Pretoria Human Research Ethics Committee and St Vincent’s Hospital, Sydney.

Participants for this study were recruited within the borders of South Africa and Namibia. The study was reviewed and approved by the Ministry of Health and Social Services (MoHSS) in Namibia (#17-3-3), with additional local approvals from community leaders, and the University of Pretoria Human Research Ethics Committee (HREC #43/2010 and HREC #280/2017), including US Federal-wide assurance (FWA00002567 and IRB00002235 IORG0001762).