DNA analysis – Earth-logs

The hobbits of Flores: An update

Published on August 10, 2018 by zooks7771 Comment

In October 2004 the world’s news media headlined the discovery of fossil remains of a tiny adult human on the Indonesian island of Flores, dated at around 18 ka. At only 1 m tall, with a brain cavity around a third the size of ours, yet having used stone tools and fire she was a sensational find. Someone so tiny and with such a small brain seemed highly unlikely to some palaeoanthropologists. Others claimed she was of a different species altogether. Homo floresiensis was also challenged as a new species and attributed to some congenital cause of small stature in a modern human – H. sapiens had first colonised Flores between 50 and 35 ka. But the subsequent discovery of remains of nine more individuals revealed skeletal details that were definitely un-human, with a suggestion of greater affinity to H. erectus. Her stature even suggested to a few anthropologists that she may have descended from migrant H. habilis, previously known only from 2 Ma ago in East Africa. The issue of relatedness was partly resolved by further dating of the cave strata that entombed the ‘hobbit’ which pushed her back to between 190 to 50 ka, beyond the earliest date of modern human colonisation. Further fragmentary fossil finds in more easily dated sediments on Flores showed the earliest known H. floresiensis lived around 700 ka ago. Stone tools and butchered prey remains on the island go back to 1 Ma, when the hominin trail goes cold.

A plausible theory for these human’s ‘hobbit’-like size is an evolutionary process known as island dwarfism, akin to that which produced the tiny elephants (Stegodon) on which they preyed. Such dramatic size reduction may arise through the influence of stringently limited food resources on the evolution of descendants from a restricted founder population, genetically cut-off from larger, more widespread populations. It now appears that such dwarfism has also affected a modern human population living on Flores (Tucci, S and 14 others 2018. Evolutionary history and adaptation of a human pygmy population of Flores Island, Indonesia. Science, v. 361, p. 511-516; doi: 10.1126/science.aar8486). A group of people of diminished stature live within shouting distance of the Liang Bua cave in which Homo floresiensis was first discovered. On average adults in the village are about 1.45 m tall. They certainly are not relict H. floresiensis, just significantly smaller than other Indonesian people living on Flores.

Serena Tucci and colleagues analysed the DNA of 32 adult pygmies from the village of Rampasasa. They show no sign of DNA from any other archaic human population than the Neanderthal and Denisovan traces that every living person outside of Africa carries – the pygmies are not descendants of H. floresiensis and are little different from other Indonesians and the rest of us. The analysis does show, however, that their ancestors carried a mixture of DNA from East Asia and New Guinea; perhaps a result of several waves of migration between 50 and 5 ka. They also carry significantly more DNA segments that are linked to short stature than do other East Asians. This suggests natural selection favored existing genes for shortness while the pygmies’ ancestors were on Flores; in other words they display an example of island dwarfism akin to that probably explaining the ‘hobbits’. Moreover, the people of Rampasasa show signs of an evolutionary adaptation to an almost exclusively meat and seafood diet, possibly arising after they migrated to Flores and had to depend on the available fauna but little in the way of plant foods.

A fully revised edition of Steve Drury’s book Stepping Stones: The Making of Our Home World can now be downloaded as a free eBook

Neanderthal news

Published on February 28, 2016 by zooks777Leave a comment

Note: Earth-Pages will be closing as of early July, but will continue in another form at Earth-logs

Increasingly sophisticated analysis of existing genomes from Neanderthal and Denisovan fossil bone, together with new data on single-chromosome DNA extracted from Croatian and Spanish Neanderthals continues to break new ground.

Artistic reconstruction of Neanderthal woman (credit: Natural History Museum, http://www.nhm.ac.uk/natureplus/blogs/tags/human_evolution)

According to genome comparison between a Siberian specimen and modern humans, a population from which Neanderthals emerged separated from that which led to anatomically modern humans (AMH) sometime between 550 and 765 ka, although the fossil record can only confirm that divergence was before 430 ka. The comparison famously showed that Neanderthals contributed to modern, non-African humans between 47 and 75 ka, that is after the exodus of AMH from Africa that spread our species throughout all continents except Antarctica. This genetic exchange is thought to have taken place somewhere in the Middle East, which seems to have been a major staging post for our spread further east and also westward to Europe. A similar indication of liaison between Denisovans and AMH migrants is restricted to modern Melanesians, and probably took place in eastern Asia before 45 ka, when modern people began crossing from Eurasia to New Guinea and Australia. Neanderthal-Denisovan comparison suggests that those distinct groups separated between 380 and 470 ka ago (recently revised from an earlier estimate).

In both cases the gene flow was from the older groups to humans. Further examination of Siberian Neanderthal genomes now indicates that a reverse exchange occurred more than 100 ka ago (Kuhlwilm, M. and 21 others 2016. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature, v. 530, p. 429-433). But the single-chromosome DNA from Croatian and Spanish Neanderthals shows no such sign This instance of two-way exchange is significant in another way: it took place before direct evidence of the generally accepted departure of African migrants to populate the rest of the world. At about 100 ka there is fossil evidence of possible AMH-Neanderthal cohabitation of the Levant, followed by a period with fossil evidence for Neanderthal presence there but not modern humans. Because stone tools from northern Arabia are dated as far back as 125 ka and closely resemble those associated with archaic modern humans, there is a possibility that AMH migration was far earlier than previously thought and passed through the Levant en route to points east.

Another tantalizing aspect of Neanderthal-modern human genetics is the tangible legacy of interbreeding with non-African humans. The first sign was that the gene (mc1r) that confers red hair on those of us blessed, or otherwise, with it may have Neanderthal origins, thus making us extremely proud of that heritage. The same gene is implicated in northern modern humans having developed pale skin, which might embarrass ‘white supremacists’! Similar studies in Svante Paabo’s lab at the Max Planck Institute for Evolutionary Anthropology in Leipzig also suggested 15 genome regions that include those involved in energy metabolism, possibly associated with type 2 diabetes; cranial shape and cognitive abilities, perhaps linked to Down’s syndrome, autism and schizophrenia; wound healing; skin, sweat glands, hair follicles and skin pigmentation; and barrel chests. There is more…

Joshua Akey of the University of Washington, Seattle, and evolutionary genomicist Tony Capra of Vanderbilt University in Nashville hit on the idea of ‘mining’ archived genetic information from more than 28 thousand living people for traces of 6000 Neanderthal DNA variants and comparing the results with physical traits and diseases logged in the human database (reported by Gibbons, A. 2016. Neanderthal genes linked to modern diseases. Science, v. 351, p. 648-9). On the plus side, Neanderthal ancestry may help boost immune responses to fungi, parasites and bacteria. Inheritance of enhanced blood coagulation, although greatly assisting recovery from wounds and hemorrhage when giving birth, confers a proclivity to heart attacks and strokes. Neanderthals also passed on ‘weak bladders’, solar keratoses that confer skin cancer risk, a tendency to malnutrition from modern diets low on meat and nuts, depression triggered by jet lag(!) and even a tendency to nicotine addiction. But a ‘pure’ line of modern human descent, shared by most Africans, also has its positive and negative heritable traits.

More on Neanderthals, Denisovans and anatomically modern humans

Surprising modern-human migrations into China and Africa

Published on October 23, 2015 by zooks777Leave a comment

Caves figure highly in discoveries of hominin remains, fossil riches from those near Johannesburg in South Africa and at Atapuerca in northern Spain having set the world of palaeoanthropology reeling in the last few months. As often as not the caves chosen by hominins for day-to-day living, refuge or ritual, places where carnivores dragged some of our early relatives, or into which they fell accidentally, formed in limestones. There are few places so well endowed with karst features than southern China, a fair number of caves in them having rich deposits of bat guano to which farmers have beaten well-trodden paths to dig it out for fertiliser. One such is Fuyan Cave in Daoxian County, Hunan. Manure mining there had done a great deal of the heavy work faced by archaeologists, having stopped when it reached a hard layer of calcite speleothem or flowstone that underpaves more or less the entire cave floor. Initial trial investigations found three clearly human teeth at the surface, encouraging further work. Digging through the flowstone revealed sediments rich in fossils, mainly teeth which preserve better than other remains in humid conditions. As well as teeth from a variety of mammals, large and small, 47 human teeth emerged. Close study revealed dental features that are irrefutably those of anatomically modern humans (Liu, W. and 13 others 2015. The earliest unequivocally modern humans in southern China. Nature, doi:10.1038/nature15696). Remarkably, many of the teeth are in far better condition than my own, and those of many living people with access to dental expertise.

Some of the Daoxian human teeth. (Credit: Song Xing and Xiu-jie Wu of the 1Key Laboratory of Vertebrate Evolution and Human Origins at the Chinese Academy of Sciences)

The true significance of the excavation emerged only when ²³⁰Th dating revealed the age of the flowstone cap to the old cave sediments. A small stalagmite protruding from its surface yielded a minimum age of ~80 ka: by far the oldest date for anatomically modern human remains outside of Africa and the eastern Mediterranean. The dating produced older ages around 120 ka with equally good precision. Before this discovery the date of migration of Africans to populate Eurasia was thought to be about 60 ka from imprecise dating based on genetics of a range of living Eurasians and Africans – a ‘molecular clock’ – and the earliest sign of humans found in Australia. Consequently, finds in South India of artefacts beneath 74 ka ash from the super-eruption of the Mount Toba caldera have been regarded by many, other than the finders, as having been made by Homo erectus. Dates of 100 ka for modern human occupation of the Levant were thought to represent a failed attempt at migration out of Africa by a northern route. Both these important findings now take on renewed significance. Yet a 30 to 40 ka time gap between the Fuyan people and the previous dates for the earliest signs of migration into China, Borneo and Australia (40-50 ka) begs the question, ‘Did this early group of far-travelled migrants survive to become ancestors of modern Chinese people?’ There are many possible scenarios that only future discoveries might validate: simply goiung extinct; failure to survive the encounter with earlier migrants, such as H. erectus or the Denisovans; assimilation into those older populations.

Mitochondrial DNA-based chart of large human m... — Mitochondrial DNA-based chart of large human migrations: the consensus before these new data. Numbers are millennia before present. ( credit: Wikipedia)

As if to counter this, a multinational group of collaborators have sequenced and analysed the genome from a 4500 year-old male skeleton discovered in the Mota Cave of the Gamo highlands of southern Ethiopia (Llorente, M.G. and 18 others 2015. Ancient Ethiopian genome reveals extensive Eurasian admixture throughout the African continent. Science, DOI: 10.1126/science.aad2879). Comparison with what is now a virtual library of living human genomes showed that this man’s genetic make-up most closely matched that of the Ari, a tribe living in the area today. What was most interesting is that part of the modern Ari genome – between 4 to 7% – is not present in the 4500 year-old sequence. Instead, it matches those of modern Sardinians and a prehistoric German farmer. Yet it occurs in people living not only in Ethiopia, but also in central, western and southern Africa to varying degrees. There seems to have been a ‘backflow’ of people into the whole of Africa from Eurasia, estimated to have occurred some 3500-4000 years ago and probably involving a large influx. By that time farming was already established in Africa, so the migrants may have had some advantage, either culturally or physically, to encourage their wide spread through the continent.

In tropical climates, DNA is likely to break down quickly and little if any fossil DNA has been recovered from prehistoric Africans. In this case, burial in a cave at high elevation may have helped preserve it, but also the target for extraction was the petrous bone from the inner ear whose density seems to allow DNA a better change of long-term survival. With continually improving DNA analysis and sequencing techniques more news is surely going to emerge from past African populations.

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