Source: https://wileyearthpages.wordpress.com/tag/dna/
Timestamp: 2019-04-22 09:12:41+00:00

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Whatever controversies still linger about when they arrived in the Americas, there can be little doubt that humans crossed what are now the Bering Straits from NE Asia using the landmass of Beringia exposed by sea-level fall during the last ice age. Of course, there have been controversies too about who they were; probably of East Asian origin but the waters muddied by the celebrated case of 9300 year-old Kennewick Man whose skull bears close resemblance to those of modern Europeans but also to those of the Ainu of northern Japan. Genetic studies of Y-chromosome DNA suggested that all early Americans stemmed from 4 separate colonising populations who may have entered via Beringia by different routes (coastal and across the interior of North America) and at different times. Now, perhaps unsurprisingly, a new kind of data seems set to stir things up immeasurably.
After the triumphs of reconstruction of the Neanderthal and Denisovan genomes and the corollary that both interbred with anatomically modern humans, it was only a matter of time before the palaeogenetics of humans would be pushed back in time. The oldest remains to yield DNA are those of a boy from near Lake Baikal in Siberia excavated by Soviet archaeologists along with a rich trove of cultural remains, including female effigies. Such figurines are rare in Siberia, most being known from western Eurasia. Radiocarbon dating of the bones gave an age of around 24 ka, just before the last glacial maximum. The genetic information, specifically mtDNA and Y-chromosome DNA are potentially revolutionary (Raghavaan and 30 others 2013. Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans. Nature online doi:10.1038/nature12736).
The mtDNA (passed down the female line) places the individual in haplogroup U, but with little relation to living members with that ‘signature’. Modern haplogroup U is mainly confined to people now living in North Africa, the Middle East, south and central Asia, Europe and western Siberia up to the area where the skeleton was found but rare further to the northeast. The male-specific Y-chromosome DNA is related to haplogroup R widely spread today among men living in western Eurasia, south Asian and in the vicinity of the find. When the data were subject to statistical tests routinely used in distinguishing existing p[populations and lineages within them (principal component analysis) a surprise emerged. The boy plots separately from all living populations but halfway between modern Europeans and the genetic trend of native Americans: i.e. descendants from the population to which he belonged could have evolved towards both extant groups but certainly not to East Asians. Plotted on a map, the degree of shared genetic history of the ice-age south Siberian boy to modern humans shows links westward to Europeans and eastwards to northeastern Siberians and hence to native Americans. Up to 38% of native American ancestry may have originated by gene flow from the population to which the boy belonged, similarly for Europeans as a whole.
The research helps explain traces of European genetic ‘signatures’ in native Americans rather than the commonly held view that this resulted from post-Columbian admixture with European invaders. It also links with the European-looking skulls of a number of early Americans which do not resemble those of East Asians once thought to be their forebears.
One of the oddities of using human genetic material passed down the male (from Y chromosomes) and female lines (from mitochondria) to assess when fully modern humans originated is that they have hitherto given widely different dates: 50 to 115 ka and 150 to 240 ka respectively. Twice to three-times the age for a putative ancestral ‘mother’ compared with such a ‘father’ for humanity raised all kinds of problematic issues for palaeoanthropology, such as a possibly greater ‘turnover’ of lines of descent among males perhaps due to riskier lifestyles. Y-chromosome data limited speculation on the timing of human colonisation outside of Africa to a maximum of 60 ka, even though there is fossil and archaeological evidence for a much earlier presence in the Levant and India. The difference also questions the validity of molecular-clock approaches to evolutionary matters. Two new studies have lessened the phylogenetic strains.
One examines Y chromosomes in 69 males from nine diverse populations from Africa, Eurasia and Central America (Poznik, G.D. and 10 others 2013. Sequencing Y chromosomes resolves discrepancy in time to common ancestors of males versus females. Science, v. 341, p. 562-565). The US-French team applied sophisticated statistics as well as the elements of a molecular clock approach to both Y-chromosome and mitochondrial DNA, discovering in the process a hitherto unresolved feature in the African part of the male ‘tree’. The outcome is a significant revision of both male and female paths of descent: 120 to 156 ka and 99 to 148 ka to the last common ancestor in both lines. The upper limit is somewhat lower than the age of fossil evidence for the earliest anatomically modern humans.
The second study zeros-in on the European story, by examining the Y-chromosome data of 1200 men from Sardinia (Francalacci, P. and 38 others. Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny. Science, v. 341, p. 565-569) calibrated to some extent by the date when Sardinia was first colonised (7.7 ka). It too revealed new detail that enabled the Italian-US-Spanish team to refine the time when features of Sardinian Y-chromosome DNA would coalesce with those from the rest of the world. In this case the date for a last common paternal ancestor goes back to between 180 to 200 ka, more similar to the old dates for ‘African Eve’ and the earliest modern human fossils than to either that for male or female lines arrived at by Posnik et al. (2013), which are significantly younger.
Equally interesting are the comments on both papers in the Perspectives section of the issue of science in which they appear (Cann, R.L. 2013. Y weigh in again on modern humans. Science, v. 341, p. 465-7).Rebecca Cann of the University of Hawaii Manoa considers the two sets of results from Y-chromosomes potentially capable of refining models for the migration times of modern humans out of Africa and their interactions with the archaic populations that they eventually displaced from Europe and central and southern Asia (Neanderthals, Denisovans and Homo erectus respectively). She believes that will include signs of earlier excursions that the generally accepted diaspora between roughly 60 and 50 ka seemingly constrained by the previous 50 to 115 ka estimate for the last common paternal ancestor. That would help explain the presence of modern humans in India at the time of the Toba eruption (71 ka).
Harvey was an imaginary, 2 m tall rabbit which befriended Elwood P. Dowd in Mary Chase’s 1944 comedy of errors named after the said rabbit, filmed in 1950 and starring James Stewart as the affable though deranged Dowd. Though not so tall, a giant fossil rabbit (relative to modern rabbits) weighing it at 12 kg has emerged from the prolific Late Neogene cave deposits of Minorca (Quintana, J. Et al. 2011. Nuralagus rex, gen. et sp. nov., an endemic insular giant rabbit from the Neogene of Minorca (Balearic Islands, Spain). Journal of Vertebrate Paleontology, v. 31, p. 231-240). At about 3 times heavier than Barrington my lagomorphophagic (rabbit-eating to the uninitiated) cat, this would have been, to him, a beast best avoided, as the name N. rex might suggest. So unexpected was a gigantic rabbit that, interestingly, it was first mistaken for a fossil tortoise, albeit one lacking a carapace.
Island faunas have long been recognized as havens for peculiar trends in evolutionary successions, either towards dwarfism as in the case of the tiny elephants on which H. floresiensis preyed until quite recently on the Indonesian island of Flores or gigantism as in this remarkable case. As the authors infer, on account of the creature’s ‘…(short manus and pes with splayed phalanges, short and stiff vertebral column with reduced extension/flexion capabilities), and the relatively small size of sense-related areas of the skull (tympanic bullae, orbits, braincase, and choanae)…’ this was a rabbit which sadly could not hop. This un-rabbit-like locomotion may well have been a result of it not having needed to hop, being so large as to challenge seriously the largest Neogene predators on the island – lizards – and thereby saving energy. For much the same evolutionary logic, neither did N. rex have long ears, having less need to detect a stealthy nemesis.
The demise of Late Neogene megafaunas in general has often been ascribed to human intervention. Though N. rex became extinct at around 3 Ma and avoided human predation, later giants did not fare so well. A case in point is the celebrated wooly mammoth, the last of the steppe mammoths, that first appeared in the fossil record of Siberia around 750 ka ago (Nicholls H. 2011. Last days of the mammoth. New Scientist, v. 209 (26 March 2011), p. 54-57). DNA evidence from hairs preserved in permafrost suggests that ancestors of the steppe mammoth line diverged with that of Asian elephants from African elephant ancestors around 5 Ma. Interestingly, ancestral steppe mammoths – without shaggy coats but having the archetypical curved tusks – roamed Africa until 3 Ma when they disappear to reappear in Europe and Asia, yet without adaptation to cold until the onset of northern glaciations around 2.5 Ma. At that point the true steppe mammoths evolved increased tooth enamel needed for a diet of mainly silica-rich grasses to resist wear. The family spread to North America when sea-level fell to expose the sea floor of the Bering Straits. The woolly mammoth is the star partly because specimens periodically turn up almost perfectly preserved in permafrost. This has allowed almost half of a full DNA sequence to be restored. Preserved haemoglobin from a woolly mammoth shares with that from modern musk oxen an ability to release oxygen at temperatures well below zero so that they could function even if their extremities became chilled.
Astonishingly, all elephants urinate so copiously that they soak their range lands in DNA, though it only lingers in ultra cold climes. This bizarre fact encouraged a large team of palaeobiologists to comb frozen soils in an alluvium section in Arctic Alaska for mammoth DNA (Haile, J and 17 others, 2009. Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proceedings of the National Academy of Sciences of the USA, v. 106, p. 22352–22357). Mammoth DNA turned up in soils as young as 10.5 ka. Moreover mammoth overlapped with human occupation for several millennia, casting doubt on theories that mammoth extinction resulted either from human predation or the introduction of epidemic disease that might have felled mammoths quickly: they declined gradually. Yet the empirical fact that steppe mammoths in general and the woolly mammoth in particular survived through at least 8 major glacial-interglacial transitions only to become extinct at the start of the current Holocene interglacial period at the same time as humans recolonised the frigid desert of Arctic latitudes, where woolly mammoths could survive except at the last glacial maximum surely points to some influence that arose from human activity.

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