Did Neolithic switch to agriculture drive selection for lighter skin colour in Europeans?

Study finds evidence of strong positive selection for skin, eye and hair pigmentation over last 5,000 years.

Why do people living in the tropics have dark skin whereas those living in higher latitudes have lighter skin? The traditional explanation is that is an evolutionary balancing trick between protection from skin cancer on one hand and the synthesis of Vitamin D by skin cells on the other. Dark skin results from higher levels of the pigment melanin: for those living nearer the equator, higher melanin levels provides a better protection from the sun’s more intense UV radiation; conversely, for those living at latitudes where UV radiation is weaker, the protection is not required and high melanin levels would block the production of Vitamin D.

However, things may not be quite so straightforward. A study carried out in 2012 at the University of Porto in Portugal considered alleles (variants) of four genes known to be associated with pigmentation, using samples taken from present-day Portuguese and sub-Saharan Africans. The evolutionary history of the four genes was estimated using a statistical model (Monte Carlo) to simulate the effects of genetic drift, natural selection and mutation. It was found that three of the alleles linked to lighter pigmentation did not start to sweep through European populations until around 11,000 to 19,000 years ago – at least 40,000 years after modern humans left Africa (Beleza, et al., 2012).

Two recently-published studies have investigated ancient DNA extracted from prehistoric human remains in Europe. The first study, published in the journal Nature, considered the pigment genes of DNA obtained from human remains found at the Mesolithic cave site of La Braña-Arintero, near León, Spain. The remains were identified as those of a male hunter-gatherer, who lived 7,000 years ago. He was found to have been dark-skinned and blue-eyed. Although present-day Spaniards are darker-skinned than northern Europeans, they are far paler than Africans (Olalde, et al., 2014). The result again suggests that paler skin colour was a fairly late development.

The second study, published in the journal PNAS, considered the pigment genes TYR, HERC2 and SLC45A2. TYR produces the enzyme tyrosinase, which is used as a catalyst in the production of melanin. HERC2 is responsible for determining eye colour; and SLC45A2 is involved in the distribution and processing of tyrosinase and other pigment-producing enzymes. The various alleles of these genes are responsible for different colours of skin, hair and eyes. Researchers extracted ancient DNA from 63 Chalcolithic (6500 to 5000 years old) and Bronze Age (5000 to 4000 years old) individuals from Ukrainian sites on the Pontic-Caspian steppe. 43 individuals yielded DNA from which the pigment genes could be sequenced, and these were compared with those of present-day Ukrainians.

The researchers found that the pigmentation of the prehistoric population differed from that of the present-day Ukrainians. The latter have 8.5 times as many alleles of TYR related to light skin colour as did their prehistoric forbears. Alleles of HERC2 related to blue eye colour were also far more common in the present-day population. However, none of these lighter pigmentation alleles are present in African populations. Thus it seems that the shift to lighter pigmentation was underway in the Chalcolithic and Bronze Ages, but it was at that stage incomplete – despite the immense passage of time since modern humans had left Africa. Computer simulations showed that these effects could not be explained by genetic drift alone, and that natural selection must have been a factor (Wilde, et al., 2014).

The team speculated that selection for lighter skin colour was related to the change in diet following the arrival of agriculture. The diet of hunter-gatherers was more likely than that of the farmers to include items rich in Vitamin D, such as fish and liver. To make up the difference, individuals needed to be able to synthesise it more efficiently – hence a lighter skin colour. At the same time, the trend to lighter hair and eye colour may have been the result of sexual selection: the initially-unusual colouring might have been more attractive to the opposite sex (the researchers noted that this phenomenon has been documented in guppies).

References:
1.  Beleza, S. et al., The timing of pigmentation lightening in Europeans. Molecular Biology and Evolution 30 (1), 24-35 (2012).

2.  Olalde, I. et al., Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European. Nature 507, 225-228 (2014).

3.  Wilde, S. et al., Direct evidence for positive selection of skin, hair, and eye pigmentation in Europeans during the last 5,000 y. PNAS (Early Edition) (2014).

Advertisements

Deep Impact?

Why an asteroid impact is unlikely to have caused the Late Quaternary mass extinction.

The Pleistocene world was dominated by large mammals, flightless birds and reptiles. These included mammoths, mastodons, giant ground sloths, camels, sabre-tooth cats, giant beavers, and giant deer with antlers spanning 3 m (10 ft.). In Australia, there lived the hippopotamus-sized Diprotodon optatum that weighed in at 2.8 tonnes, and was the largest marsupial of all time. These animals are collectively known as the megafauna, a term applied to animals with an adult weight of 45 kg (100 lb.) or more. Between 50,000 and 10,000 years ago, many of these great beasts vanished in one of the largest extinction events since the demise of the dinosaurs. Australia and the Americas were hardest hit, but no habitable continent remained unscathed. Overall, about 180 large mammal species and over 100 entire genera perished (Barnosky, et al., 2004; Lyons, et al., 2004; Koch & Barnosky, 2006; Barnosky, 2008). Usually referred to as the Late Quaternary extinction event, it was recognised by early geologists towards the end of the eighteenth century.

The cause of this mass extinction has long been debated and there remains a lack of consensus to this day. Climate change and human activity were put forward as possible causes as far back as the early nineteenth century, and both are hotly championed to this day. One of the more controversial theories, first proposed in 2007, is that around 12,900 years ago, Earth suffered multiple airbursts and surface impacts from fragments of a comet or asteroid that had previously broken up in space. In North America, the bombardment caused devastating shock-waves and continent-wide forest fires that brought about the extinction of the megafauna. While the overall effects were far less severe than those of the impact now believed to have killed off the dinosaurs, they were still sufficient to trigger a global ‘impact winter’. This in turn precipitated Younger Dryas climatic downturn.

Evidence for the supposed impact was claimed in the form of a 12,900-year-old carbon-rich layer or ‘black mat’. The layer has been identified at around fifty Clovis sites in North America. It is said to contain material consistent with an impact, including magnetic mineral grains, soot, carbon spherules and so-called nanodiamonds. The latter are minute diamonds formed when carbon particles are subjected to intense heat and pressure by an explosion (Firestone, et al., 2007; Haynes, 2008; Kennett, et al., 2009). More recently, evidence for impacts has also been claimed from Younger Dryas boundary sites in Mexico, Belgium, the Netherlands, Germany and Syria (Israde-Alcántara, et al., 2012; Bunch, et al., 2012). Anomalous levels of platinum, said to be due to the impact of a large iron meteorite, have also been reported from Greenland ice core samples dating to the Younger Dryas boundary (Petaev, et al., 2013).

In theory this is all sounds highly feasible, but in practice the timing is a little suspicious. Other factors were in play at the time, and it is not necessary to invoke an extraterrestrial impact to explain the onset of the Younger Dryas. Named for the arctic-alpine flowering plant Dryas octopetala that flourished in the northern tundra at that time, the Younger Dryas marks the final stage of the Pleistocene. It lasted from 12,900 until 11,600 years ago and both its onset and termination were fairly abrupt (Taylor, et al., 1997; Severinghaus, et al., 1998). During the preceding Bølling-Allerød warm period, the North American ice sheets retreated. The resulting meltwater formed a vast glacial lake known as Lake Agassiz, larger than all the modern Great Lakes put together. Beginning 13,000 years ago, Lake Agassiz released a series of freshwater discharges into the Arctic Ocean, through what is now the drainage basin of the Mackenzie River (Murton, et al., 2010). The conventional view is that the great volume of freshwater disrupted the Gulf Stream, halting the flow of warm seawater from the tropics to higher latitudes. The result was to plunge the Northern Hemisphere back into glacial conditions. Effects in the Southern Hemisphere are less certain, though evidence of cooling has been found there also (Moreno, et al., 2001).

That an extraterrestrial impact should occur at more or less the same time as the freshwater discharge strikes me as being a rather implausible coincidence. It should also be noted that other studies have failed to find evidence for the nanodiamonds (Daulton, et al., 2010), and that there is no evidence for the continent-wide conflagration supposedly triggered by the impact. Evidence for burning is better attributed to climate change-generated increases in natural wildfires (Marlon, et al., 2009). Similarly, the magnetic grains can be accounted for by a constant influx of micrometeorites from space (Surovell, et al., 2009). The ‘black mats’ do not occur throughout the whole of North America, but rather are located predominantly in the west. They may be algal mats or ancient soils associated with regional increases in moisture (Gill, et al., 2012). The source of platinum anomaly may be extraterrestrial, but this remains unproven and more evidence is needed. All in all, I am sceptical about the impact theory, although it certainly cannot be ruled out.

References:

1. Barnosky, A., Koch, P., Feranec, R., Wing, S. & Shabel, A., Assessing the Causes of Late Pleistocene Extinctions on the Continents. Science 306, 70-75 (2004).

2. Lyons, K., Smith, F. & Brown, J., Of mice, mastodons and men: human-mediated extinctions on four continents. Evolutionary Ecology Research 6, 339–358 (2004).

3. Koch, P. & Barnosky, A., Late Quaternary Extinctions: State of the Debate. The Annual Review of Ecology, Evolution, and Systematics 37, 215–250 (2006).

4. Barnosky, A., Megafauna biomass tradeoff as a driver of Quaternary and future extinctions. PNAS 105 (Suppl. 1), 11543–11548 (2008).

5. Firestone, R. et al., Evidence for an extraterrestrial impact 12,900 years ago that contributed to the megafaunal extinctions and the Younger Dryas cooling. PNAS 104 (41), 16016–16021 (2007).

6. Haynes, V., Younger Dryas ‘‘black mats’’ and the Rancholabrean termination in North America. PNAS 105 (18), 6520–6525 (2008).

7. Kennett, D. et al., Nanodiamonds in the Younger Dryas Boundary Sediment Layer. Science 323, 94 (2009).

8. Israde-Alcántara, I. et al., Evidence from central Mexico supporting the Younger Dryas extraterrestrial impact hypothesis. PNAS 109 (13), E738-E747 (2012).

9. Bunch, T. et al., Very high-temperature impact melt products as evidence for cosmic airbursts and impacts 12,900 years ago. PNAS 109 (28), E1903-E1912 (2012).

10. Petaev, M., Huang, S., Jacobsen, S. & Zindler, A., Large Pt anomaly in the Greenland ice core points to a cataclysm at the onset of Younger Dryas. PNAS 110 (32), 12917-12920 (2013).

11. Taylor, K. et al., The Holocene–Younger Dryas Transition Recorded at Summit, Greenland. Science 278, 825-827 (1997).

12. Severinghaus, J., Sowers, T., Brook, E., Alley, R. & Bender, M., Timing of abrupt climate change at the end of the Younger Dryas interval from thermally fractionated gases in polar ice. Nature 391, 141-146 (1998).

13. Murton, J., Bateman, M., Dallimore, S., Teller, J. & Yang, Z., Identification of Younger Dryas outburst flood path from Lake Agassiz to the Arctic Ocean. Nature 464, 740-743 (2010).

14. Moreno, P., Jacobson, G., Lowell, T. & Denton, G., Interhemispheric climate links revealed by a late-glacial cooling episode in southern Chile. Nature 409 , 804-808 (2001).

15. Daulton, T., Pinter, N. & Scott, A., No evidence of nanodiamonds in Younger–Dryas sediments to support an impact event. PNAS 107 (37), 16043-16047 (2010).

16. Marlon, J. et al., Wildfire responses to abrupt climate change in North America. PNAS 106 (8), 2519–2524 (2009).

17. Surovell, T. et al., An independent evaluation of the Younger Dryas extraterrestrial impact hypothesis. PNAS 106 (43), 18155-18158 (2009).

18. Gill, J. et al., Paleoecological changes at Lake Cuitzeo were not consistent with an extraterrestrial impact. PNAS 109 (34), E2243 (2012).

Return from Beringia

Linguistic study suggests Ice Age groups migrated back to Central Asia from Bering land bridge.

The New World was the last habitable part of the globe to be settled by humans. Today, Alaska is separated from eastern Siberia by the Bering Strait, which is 55 km (18 miles) wide, but this has not always been the case. Throughout the period from 25,000 years ago until as late as 10,000 years ago, sea levels were so low that the strait and parts of the adjoining Chukchi and Bering Seas became dry land. The result was a landmass stretching from the Verkhoyansk Range in eastern Siberia to the Mackenzie River in northwestern Canada (Hoffecker, et al., 1993). Known as Beringia, this so-called ‘land bridge’ was 1,600 km (1,000 miles) from north to south and linked Asia to North America. The region remained dry and cold, but free of ice. It is thought to have been an open landscape covered with grasses and herbaceous tundra and steppe vegetation (Guthrie, 2001; Zazula, et al., 2006). It is via the Beringia land bridge that humans are long believed to have first reached the New World, but the number of migrations and their timing have been hotly debated for many decades.

Much of our understanding of these migrations has come from archaeological and genetic data. The genetic results suggest that the New World was populated in three migrations: a major migration associated with the First Americans or Paleoindians; a second migration associated with Na-Dene language speakers distributed mainly in northwestern Canada, Alaska and along the Pacific Coast; and a third migration associated with Eskimo-Aleut language speakers, who are restricted to the Aleutian Islands and the Arctic (Reich, et al., 2012).

A third approach to understanding prehistoric migrations is comparative linguistics. In 1986, the American linguist Joseph Greenberg (1986) used this method in an attempt to identify the number of migrations into the New World. It has long been known that languages evolve over time, and that there are language ‘families’ or groups of languages that share common origins. Greenberg began by assuming each group of migrants spoke their own language and that over time a language family arose from each founding language. In earlier work going back to the 1960s, Greenberg claimed that there were three language families: Amerind, Na-Dene and Aleut-Eskimo. His conclusion – now vindicated by genetics – is that there were three migrations.

Up until now, however, linguists have been unable to link the three language groups to those in Asia. It has long been suspected that there is a linguistic connection between the Na-Dene languages and the Yeniseian languages of Siberia, but it remains unproven. A new study has investigated the possible relationship, using phylogenetic methods to build up a linguistic family tree. In the last decade, computational phylogenetic tools developed primarily to study relationships in evolutionary biology have been adapted for use in the field of historical linguistics. These new techniques have been used to study prehistoric migrations and language classifications as far back as the latter part of the last Ice Age.

The researchers applied the technique to 40 languages spoken across North America and Asia. The resulting family tree was used to test various migration hypotheses. The results suggested that there was an early dispersal of Na-Dene populations along the North American coast and a Yeniseian migration back into Siberia. This was followed by a dispersal of Na-Dene languages into the North American interior. The study does not contradict the widely-accepted scenario that the New World was settled from Beringia, but complicates it with the insight that some groups in Beringia migrated back in the opposite direction (Sicoli & Holton, 2914).

References:

1. Hoffecker, J., Powers, R. & Goebel, T., The Colonization of Beringia and the Peopling of the New World. Science 259, 46-53 (1993).

2. Guthrie, D., Origin and causes of the mammoth steppe: a story of cloud cover, woolly mammal tooth pits, buckles, and inside-out Beringia. Quaternary Science Reviews 20, 549-574 (2001).

3. Zazula, G. et al., Vegetation buried under Dawson tephra (25,300 14C years BP) and locally diverse late Pleistocene paleoenvironments of Goldbottom Creek, Yukon, Canada. Palaeogeography, Palaeoclimatology, Palaeoecology 242, 253–286 (2006).

4. Reich, D. et al., Reconstructing Native American population history. Nature 488, 370–374 (2012).

5. Greenberg, J., Turner, C. & Zegura, S., The Settlement of the Americas: A Comparison of the Linguistic, Dental, and Genetic Evidence. Current Anthropology 27 (5), 477-497 (1986).

6. Sicoli, M. & Holton, G., Linguistic Phylogenies Support Back-Migration from Beringia to Asia. PLoS One 9 (3), e91722 (2914).

Chauvet cave paintings may be far more recent than generally believed

French archaeologists claim that prehistoric artwork thought to be 36,000 years old is actually 10,000 years younger.

Chauvet Cave is located near the village of Vallon-Pont-d’Arc, Ardèche in southern France. The cave was discovered in 1994 by a team of cavers led by Jean-Marie Chauvet, for whom the site was named. It was the most important cave painting find since the discovery of Lascaux by a group of teenagers during World War II. Unlike the 18,000-year-old Lascaux cave paintings, which became a major tourist attraction after the war and deteriorated badly as a result, Chauvet was rapidly taken over by the French government and a strict conservation program was put in hand.

The artwork comprises 425 panels, depicting rhinoceroses, lions, bears, mammoths, horses, bison, ibex, reindeer, red deer, aurochs, muskoxen, panthers, and the earliest-known representation of an owl turning its head through 180 degrees. Hand prints, red dots and a partial image of a woman associated with a bison have also been discovered.

Radiocarbon dates indicating that the paintings are around 36,000 years old are widely accepted. This would date them to the late Aurignacian period, and make them twice as old as Lascaux. Put another way, the radiocarbon dates suggest that Lascaux is separated from Chauvet by the same interval of time that separates it from the first landing on the Moon. However, archaeologists Jean Combier and Guy Jouve have cast doubt on the great antiquity of the Chauvet paintings.

They argue that on stylistic grounds, the Chauvet artwork cannot be associated with the Aurignacian period. Instead, they claim, the artwork shows affinities to that of the more recent Gravettian and Solutrean periods. Therefore the oldest paintings at Chauvet cannot be more than 26,000 years old. The later ones might even be contemporary with Lascaux.

That Chauvet dates to the Solutrean period was the initial impression of Jean Clottes, one of France’s most eminent prehistorians. Clottes made his assessment in 1995, before any radiocarbon dates were available. His dating of the artwork on purely stylistic grounds was subsequently dismissed as ‘foolhardy’ – but could it be that relying purely on radiocarbon dates is equally unwise?

When first introduced in the 1950s, radiocarbon dating revolutionised archaeology and Willard Libby, the American chemist who pioneered the technique, was awarded the Nobel Prize in Chemistry in 1960. However, radiocarbon dating is not infallible. For example, it is very easy for a sample to become contaminated with more recent organic material that will slew results.

In the case of Chauvet, radiocarbon dates were obtained from wood charcoal used as black pigment. However, Combier and Jouve suggest fossil carbon was used as well as charcoal. This was available at Vagnas, a village not far from Vallon-Pont-d’Arc, where there was a quarry yielding lignite and bitumen. A pigment comprising a mixture of fresh charcoal and fossil carbon would present as being significantly older than one containing fresh charcoal alone.

Combier and Jouve note that such a mixture would also have a different isotopic signature to that of pure wood charcoal, i.e. the proportions of the stable carbon isotopes carbon-12 and carbon-13 would differ between the two. It would thus be possible to show whether or not the Chauvet dates were suspect. Such an anomaly has been detected at another cave site, Candamo Cave in Spain, although in this case the ‘old’ carbon leeched into the pigment from the limestone walls of the cave through the action of bacteria.

Accordingly, Combier and Jouve suggest that fresh radiocarbon dates should be obtained for Chauvet, and they believe that it extremely important that more than one laboratory carries out the work.

References:

1. Clottes, J., Cave Art (Phaidon, New York, 2008).
2. Combier, J. & Jouve, G., Chauvet cave’s art is not Aurignacian: a new examination of the archaeological evidence and dating procedures. Quartär 59, 131-152 (2012).
3. Combier, J. & Jouve, G., Nouvelles recherches sur l’identité culturelle et stylistique de la grotte Chauvet et sur sa datation par la méthode du 14C. L’Anthropologie ( (in press) doi:10.1016/j.anthro.2013.12.001) (2014).
4. Mellars, P., A new radiocarbon revolution and the dispersal of modern humans in Eurasia. Nature 493, 931-935 (2006).

Study provides insight into diet of early Pacific colonists

Lapita people relied on foraging as well as agriculture; men enjoyed a more varied diet than women.

Between 1400 and 800 BC, Polynesian colonists associated with the Lapita culture spread out into the Pacific from Island Southeast Asia, eventually settling the islands of central and eastern Melanesia and western Polynesia. The word ‘Lapita’ is a Western mispronunciation of Xapeta’a, the native Kanak name for the site in New Caledonia that gave its name to the culture. The Lapita culture is noted for its distinctive pottery, which was typically red-slipped, and decorated with small-toothed (‘dentate’) bone or shell chisels.

By around 1300 to 1200 BC, Early Lapita communities were established over a wide area of the Bismarck Archipelago. The dispersed communities formed a network of societies that maintained regular contact with one another, and were probably related by kinship and marriage. The clearest evidence for these long-distance interactions is the trade in obsidian from New Britain and the Admiralty Islands, and parallel changes in pottery styles over the region up until around 1000 BC. After that time, inter-island contacts seem to have dropped off markedly. In the meantime, by around 1200 to 1100 BC, Lapita people had moved beyond the Bismarck Archipelago and settled parts of Remote Oceania. In just 600 years, the Lapita people spread through Melanesia to the Central Pacific, reaching Vanuatu by 1000 BC, Fiji and Tonga by 900 BC, and Samoa by 700 BC. It was here that the migration paused after covering some 5,500 km (3,400 miles), one of the fastest movements of a prehistoric colonising population on record.

The Lapita colonists brought with them domesticated pigs, chickens and dogs, and crops including yams, taro, breadfruit, coconut, sago and bananas. However, the extent to which they relied upon this ‘agricultural package’ for sustenance remains uncertain, and in particular there are questions about how settlers sustained themselves during the initial stages of colonisation of each island.

A powerful technique for understanding the diets of prehistoric peoples is stable isotope analysis. The ratios in which isotopes of certain elements occur in human remains are dependent on what individuals ate while they were alive. Investigations have focussed on stable (i.e. non-radioactive) isotopes of carbon and nitrogen and, more recently, sulphur.

In the case of the Lapita people such investigations have been hampered by a scarcity of human remains, despite around 250 sites being known throughout the western Pacific. However, a cemetery at the site of Teouma, on Efate Island, Vanuatu has yielded 68 burials – the largest number of human remains from the Lapita period ever found. The cemetery dates to the earliest known settlement of Central Vanuatu, around 1000 BC. As such, it can provide information about the settlers’ diet during the initial stages of Lapita colonisation.

The researchers obtained isotopic ratios for bone collagen from 51 adult Lapita people. They then obtained a comprehensive isotopic dietary baseline made up of both modern plants and animals, and prehistoric animal remains from the site. By comparing the two sets of results, they found that the settlers’ diet included reef fish, marine turtles, and fruit bats in addition to domesticated pigs and chickens. Rather than rely solely on their ‘transported landscape’ of domesticated crops and animals, the settlers were practicing a mixed subsistence that included significant quantities of native wildlife, as well as domestic animals.

Dietary differences were found between men and women. The men enjoyed a more varied diet, which included greater access to pigs, chicken and tortoises. Such foods are considered to be of high status in present-day Pacific island societies, and the difference may reflect a higher status for men in Lapita society.

The results are consistent with the view that a newly-established colony would not be able to produce enough food to support itself, and would have to rely to an extent on foraging. This is also supported by an analysis of the remains of domestic pigs and chickens, which suggested that they were reared as free range animals. Such a system of husbandry would reduce demand for the limited amount of plant food that was available.

Reference:
1. Kinaston, R. et al., Lapita Diet in Remote Oceania: New Stable Isotope Evidence from the 3000-Year-Old Teouma Site, Efate Island, Vanuatu. PLoS One 9 (3), e90376 (2014).