Out of Africa: a little less blurred?

DNA from the mitochondria of humans who live on all the habitable continents shows such a small variability that all of us must have had a common maternal ancestor, and she lived in Africa about 160 ka ago. Since this was first suggested by Rebecca Cann, Mark Stoneking and Allan Wilson of the University of California, Berkeley in 1987 there has been a stream of data and publications – subsequently using Y-chromosome DNA and even whole genomes – that both confirm an African origin for Homo sapiens and illuminate it. Analyses of the small differences in global human genetics also chart the routes and – using a ‘molecular clock’ technique – the timings of geographic and population branchings during migration out of Africa. As more and better quality data emerges so the patterns change and become more intricate: an illustration of the view that ‘the past is always a work in progress’. The journal Nature published four papers online in the week ending 25 September 2016 that demonstrate the ‘state of the art’.

Three of these papers add almost 800 new, high-quality genomes to the 1000 Genomes Project that saw completion in 2015. The new data cover 270 populations from around the world including those of regions that have previously been understudied for a variety of reasons: Africa, Australia and Papua-New Guinea. All three genomic contributions are critically summarized by a Nature News and Views article (Tucci, S & Akey, J.L. 2016. A map of human wanderlust. http://dx.doi.org/10.1038/nature19472). The fourth paper pieces together accurately dated fossil and archaeological findings with data on climate and sea-level changes derived mainly from isotopic analyses of marine sediments and samples from polar ice sheets (Timmermann, A & Friedrich, T. 2016. Late Pleistocene climate drivers of early human migration. Nature, doi:10.1038/nature19365). Axel Timmermann and Tobias Friedrich of the University of Hawaii have attempted to simulate the overall dispersal of humans during the last 125 ka according to how they adapted to environmental conditions; mainly the changing vegetation cover as aridity varied geographically, together with the opening of potential routes out of Africa via the Straits of Bab el Mandab and through what is now termed the Middle East or Levant. They present their results as a remarkable series of global maps that suggest both the geographic spread of human migrants and how population density may have changed geographically through the last glacial cycle. Added to this are maps of the times of arrival of human populations across the world, according to a variety of migration scenarios. Note: the figure below estimates when AMH may have arrived in different areas and the population densities that environmental conditions at different times could have supported had they done so. Europe is shown as being possibly settled at around 70-75 ka, and perhaps having moderately high densities for AMH populations. Yet no physical evidence of European AMH is known before about 40 ka. Anatomically modern humans could have been in Europe before that time but failed to diffuse towards it, or were either repelled by or assimilated completely into its earlier Neanderthal population: perhaps the most controversial aspect of the paper.

Estimated arrival time since the last continuous settlement of anatomically modern human migrants from Africa (top); estimated population densities around 60 thousand years ago. (Credit: Axel Timmermann University of Hawaii)

The role of climate change and even major volcanic activity – the 74 ka explosion of Toba in Indonesia – in both allowing or forcing an exodus from African homelands and channelling the human ‘line of march’ across Eurasia has been speculated on repeatedly. Now Timmermann and Friedrich have added a sophisticated case for episodic waves of migration across Arabia and the Levant at 106-94, 89-73, 59-47 and 45-29 ka. These implicate the role of Milankovich’s 21 ka cycle of Earth’s axial precession in opening windows of opportunity for both the exodus and movement through Eurasia; effectively like opening and closing valves for the flow of human movement. The paper is critically summarised by a Nature News and Views article (de Menocal, P.B. & Stringer, C. 2016. Climate and peopling of the world. Nature, doi:10.1038/nature19471.

This multiple-dispersal model for the spread of anatomically modern humans (AMH) finds some support from one of the genome papers (Pangani, L. and 98 others 2016. Genomic analyses inform on migration events during the peopling of Eurasia. Nature (online). http://dx.doi.org/10.1038/nature19792). A genetic signature in present-day Papuans suggests that at least 2% of their genome originates from an early and largely extinct expansion of AMH from Africa about 120 ka ago, compared with a split of all mainland Eurasians from African at around 75 ka. It appears from Pangani and co-workers’ analyses that later dispersals out of Africa contributed only a small amount of ancestry to Papuan individuals. The other two genome analyses (Mallick, S. and 79 others 2016. The Simons Genome Diversity Project: 300 genomes from 142 diverse populations. Nature (online) http://dx.doi.org/10.1038/nature18964; Malaspinas, A.-S. and 74 others 2016. A genomic history of Aboriginal Australia. Nature (online). http://dx.doi.org/10.1038/nature18299) suggest a slightly different scenario, that all present-day non-Africans branched from a single ancestral population. In the case of Malaspinas et al. an immediate separation of two waves of AMH migrants led to settlement of Australasia in one case and to the rest of Mainland Eurasia. Yet their data suggest that Australasians diverged into Papuan and Australian population between 25-40 ka ago. Now that is a surprise, because during the lead-up to the last glacial maximum at around 20 ka, sea level dropped to levels that unified the exposed surfaces of Papua and Australia, making it possible to walk from one to the other. These authors appeal to a vast hypersaline lake in the emergent plains, which may have deterred crossing the land bridge. Mallick et al. see an early separation between migrants from Africa who separately populated the west and east of Eurasia, with possible separation of Papuans and Australians from the second group.  These authors also show that the rate at which Eurasians accumulated mutations was about 5% faster than happened among Africans. Interestingly, Mallick et al. addressed the vexed issue of the origin of the spurt in cultural, particularly artistic, creativity after 50 ka that characterizes Eurasian archaeology. Although their results do not rule out genetic changes outside Africa linked to cultural change, they commented as follows:

‘… however, genetics is not a creative force, and instead responds to selection pressures imposed by novel environmental conditions or lifestyles. Thus, our results provide evidence against a model in which one or a few mutations were responsible for the rapid developments in human behaviour in the last 50,000 years. Instead, changes in lifestyles due to cultural innovation or exposure to new environments are likely to have been driving forces behind the rapid transformations in human behaviour …’.

Variations in interpretation among the four papers undoubtedly stem from the very different analytical approaches to climate and genomic data sets, and variations within the individual sets of DNA samples. So it will probably be some time before theoretical studies of the drivers of migration and work on global human genomics and cultural development find themselves unified. And we await with interest the pooling of results from all the different genetics labs and agreement on a common data-mining approach.

Large-animal extinction in Australia linked to human hunters

Diprotodon optatum, Pleistocene of Australia. ...
Artist's impression of a giant Australian wombat (Diprotodon) (credit: Wikipedia)

In North America, between 13 and 11.5 ka, around 30 species of large herbivorous mammals became extinct. Much the same occurred in Australia around 45 ka. Both cases roughly coincided with the entry of anatomically modern humans, where neither they nor earlier hominids had lived earlier. Such extinctions are not apparent in the Pleistocene records of Africa or Eurasia. An obvious implication is that initial human colonisation and a collapse of local megafaunas are somehow connected, perhaps even that highly efficient early hunting bands slaughtered and ate their way through both continents. But other possibilities can not be ruled out, including coincidences between colonisation and climate or ecosystem change. As many as thirteen different hypotheses await resolution, one that inevitably makes headline news repeatedly: that both the early Clovis culture and North American megafaunas met their end around the same time as the start of the Younger Dryas millennial cold snap because a meteorite exploded above North America (http://earth-pages.co.uk/2009/03/01/comet-slew-large-mammals-of-the-americas/). One problem in assessing the various ideas is accurately dating the actual extinctions, partly because terrestrial environments rarely undergo the continual sedimentation that builds up easily interpreted stratigraphic sequences. Another is that it is not easy to prove, say, that all giant kangaroos died in a short period of time because of the poor record of preservation of skeletons on land. A cautionary take concerns the demise of the woolly mammoth that roamed the frigid deserts of northern Eurasia and definitely was hunted by both modern humans and Neanderthals. It was eventually discovered that herds still survived on Wrangell Island until the second millennium BC. There is a need for a proxy that charts indirectly the fate of megafaunas plus accurate estimates of the timing of human colonisation. In North America there is a candidate for the first criterion: traces of a fungus (Sporormiella – see Fungal clue to fate of North American megafauna in EPN of January 2010) that exclusively lives in the dung of large herbivores. Fungal spores get everywhere, being wind-dispersed, and in NE US lake cores they fell abruptly at about 13.7 ka. Sporormiella needs to pass through the gut of herbivores to complete its life cycle.

Aboriginal Rock Art, Anbangbang Rock Shelter, ...
Aboriginal Rock Art, Kakadu National Park, Australia (Photo credit: Wikipedia)

The same genus of fungus breaks down dung in Australia. Measuring spore content in sediment on the floor of a Queensland lake shows the same abrupt decline in abundance at between 43 to 39 ka before present (Rule, S. et al. 2012. The aftermath of a megafaunal extinction: ecosystem transformation in Pleistocene Australia. Science, v. 335, p. 1483-1486). Moreover, the fungal collapse is accompanied by a marked increase in fine-grained charcoal – a sign of widespread fires – and is followed by a steady increase in pollen of scrub vegetation at the expense of that of tropical rain forest trees. The shifts do not correlate with any Southern Hemisphere climatic proxy for cooling and drying that might have caused ecosystem collapse. That still does not mark out newly arrived humans as the culprits, as the early archaeological record of Australia, as in North America, is sparse and only estimated to have started at around 45 ka. Yet this is quite strong circumstantial evidence. The 20 or more animals – marsupials, birds and reptiles – with a mass more than 40 kg that formerly inhabited the continent would probably have been ‘naive’ as regards newly arrived, organised, well-armed and clever new predators, as would those of North America and much later in New Zealand, and would have been ‘easy prey’. Incidentally, faunas of both Africa and Eurasia are extremely wary of humans, possibly as a result of a far longer period of encounters with human hunter-gatherers.  In Australia’s case, the use of deliberate fire clearing to improve visibility of game may have had a major role, although it is equally likely that the demise of large herbivores would have left large amounts of leaf litter and dry grasses to combust naturally. Yet the Earth as a whole around 40 ka was slowly cooling and drying towards the last glacial maximum around 20 ka, so human influence may merely have pushed the megafauna towards extinction, such is the fragility of Australia’s ecosystems.