Thursday, 31 March 2016

Flores ‘hobbits’ died out much earlier than originally thought

Homo floresiensis extinct by 50,000 years ago

A new study published in Nature has suggested that Homo floresiensis became extinct much earlier than originally reported. The type specimen LB 1, recovered from Late Pleistocene sediments at Liang Bua, Flores in 2004 was claimed to be 18,000 years old, with other remains and associated stone tools dating from 74,000 to 95,000 years old. The dates were inferred from radiocarbon, thermoluminescence, uranium series and electron spin resonance dates on associated sedimentary material. No direct dates were obtained from the remains themselves for fear of damaging them. However, some authorities were dubious that the ‘hobbits’ could have survived for so long after modern humans reached Southeast Asia.

It has now been discovered that the hominin remains and artefacts were found in a stratigraphic sequence of older sediment forming a pedestal, which have been truncated by one or more phases of erosion and subsequently covered by later sediment. This was not recognised during the original excavations, hence making the accuracy of the inferred dates suspect.

The new dates have been obtained by dating the main stratigraphic units within the pedestal; and this time direct dating was also applied to the skeletal remains of Homo floresiensis. Radiocarbon, thermoluminescence, and uranium series methods were used. The revised dates suggest that the skeletal remains range from 60,000 to 100,000 years old and the associated stone tools range from 50,000 to 190,000 years old.

Parts of Southeast Asia may have been inhabited by Denisovans during this period, and modern humans reached Australia by 50,000 years ago. Whether either came into contact with Homo floresiensis or were connected to its demise is at this stage still unknown.

Sutikna, T.
et al., Revised stratigraphy and chronology for Homo floresiensis at Liang Bua in Indonesia. Nature, doi:10.1038/nature17179 (2016).

Saturday, 26 March 2016

Waterloo sunset

Taken at 18:32 on 25 March 2016 with iPhone 5.1/120th sec at f/2.4 ISO 80.

Sunday, 20 March 2016

Melanesian genomes reveal episodes of interbreeding with Neanderthals and Denisovans

Study demonstrates multiple encounters with archaic humans

In a new attempt to obtain genetic information about Neanderthals and Denisovans, researchers have analysed the genomes of 1,523 genetically-diverse individuals, including 35 Melanesians. Results were compared with known Neanderthal and Denisovan sequences. 1340 Mb of the Neanderthal genome and 304 Mb of the Denisovan genome were obtained.

The Melanesians show between 1.9 and 3.4 percent of Denisovan ancestry. They have an average 104 Mb of archaic sequences: 48.9 Mb of Neanderthal, 42.9 Mb of Denisovan, and 12.2 Mb of ambiguous sequence that could be either. By contrast, only 0.026 Mb (in Esan) to 0.5 Mb (in Luhya) of archaic sequences per individual were found in Africans. An average 65.0 Mb of archaic sequences were found in East Asians; 55.2 Mb in South Asians; and 51.2 Mb in Europeans. Most of these archaic sequences were Neanderthal in origin, although a small fraction (less than 1 percent) in East Asians and South Asians are predicted to be Denisovan. There was evidence for an additional pulse of Neanderthal admixture in Europeans, East Asians, and South Asians compared to Melanesians. The data suggests that there were at least three separate episodes of interbreeding between Neanderthals and modern humans, and one of modern humans interbreeding with Denisovans.

The study also found a statistically-significant overlap between regions depleted of Neanderthal and regions depleted of Denisovan genetic sequences, suggesting that archaic sequences in these regions were deleterious and were purged by the effects of purifying selection. Regions depleted of archaic lineages are contain large numbers of genes associated with specific regions of the brain, particularly in the developing cortex and adult striatum. A large region depleted of archaic sequences spans 11 Mb on chromosome 7 and contains the FOXP2 gene associated with speech and language, as well as genes associated with autism.

It is likely that further studies will reveal an increasingly complex picture of how modern humans have interbred with archaic humans throughout Eurasia. The depletion of archaic sequences from brain-related sequences of the genome might hint at cognitive differences between modern and archaic humans; or these regions might simply be more prone to adverse effects of horizontal gene transfer.

Vernot, B. et al., Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals (10.1126/science.aad9416) (2016).x

Friday, 18 March 2016

The mammoth diet of Neanderthals

Stable isotope evidence from three Belgian sites

Attempts to gain insight into Neanderthal diet have been many and various over the years. Methods have included consideration of dental microwear, tooth calculus, lithic use-wear and residues, and stable carbon and nitrogen isotope data. These studies have shown that the Neanderthal diet included the consumption of large herbivores, but the extent to which smaller mammals, birds, riverine and seafood was eaten remains uncertain.

To address these issues, researchers conducted carbon and nitrogen stable isotope analyses of collagen extracted from Neanderthal remains from the Belgian sites of Goyet and Spy. Results were compared with those from extensive faunal remains from Goyet, Spy and a third Belgian site, Scladina. These included mammoth, rhino, horse, reindeer, hyena, wolf, cave bear and cave lions. The proportion of the isotopes carbon-13 and nitrogen-15 reflect an animal’s place in the food chain: the highest levels are found in carnivores.

The results show that Neanderthal isotope levels and hence diet differed from that of any carnivore, indicating that they occupied a distinct ecological niche. The overall data suggested that while predators typically preferred smaller animals such as reindeer and horse, the Neanderthal focus was on large herbivores. Mammoth was the most important source of meat, accounting for around 30 to 40 percent of the Neanderthal diet. Reindeer and rhino accounted for lesser proportions, and plant food for about 20 percent.

Wißing, C. et al., Isotopic evidence for dietary ecology of late Neandertals in North-Western Europe. Quaternary International, (2015).x

Thursday, 17 March 2016

Genetic study suggests that Sima hominins were proto-Neanderthals

430,000-year-old nuclear genome sequences confirms affinities  

Sima de los Huesos (‘Pit of Bones’)is a small muddy chamber lying at the bottom of a 13 m (43 ft.) chimney, lying deep within the Cueva Mayor system of caves in the Sierra de Atapuerca of northern Spain. Hominin remains were first reported there in the 1970s, and to date the remains of 28 individuals have been recovered. The Sima hominins lived around 430,000 years ago and while conventionally described as Homo heidelbergensis, they share some derived features with Neanderthals. This has led some to suggest that they are very early Neanderthals.

In 2014, mitochondrial DNA was obtained from the thighbone of one of the Sima hominins. It was expected that it would show affinities to later sequences obtained from Neanderthals, but instead it suggested that the Sima hominins were more closely related to Denisovans. However, mitochondrial DNA does not reveal the full picture of relationships among populations, so researchers set about the more difficult task of obtaining nuclear sequences from the Sima remains.

Genetic material was recovered from an incisor and a molar tooth, a fragment of a thighbone and a shoulder blade. Useful sequences were obtained from the incisor tooth and the thighbone fragment. The results have shown that the Sima hominins were, after all, more closely related to Neanderthals than they were to Denisovans. The Sima hominins were thus either early Neanderthals or closely related to the ancestors of Neanderthals after diverging from a common ancestor shared with the Denisovans. The age of the Sima remains is compatible with earlier estimates that the Neanderthal/Denisovan split occurred between 381,000 and 473,000 years ago. Based on the correctness of these estimates, modern humans diverged from Neanderthals 550,000 to 765,000 years ago – too early for later examples of Homo heidelbergensis such as Arago or Petralona to belong to a population ancestral to both Neanderthals and modern humans. The true common ancestor may be Homo antecessor, which was present in Spain from 1.2 million to 800,000 years ago and might have been responsible for the hominin footprints discovered at Happisburgh, England, in May 2013. However, this species has yet to be identified in Africa and may be a European variant of Homo erectus that migrated from Asia.

The Denisovan affinities of the mitochondrial DNA are still unexplained. One possibility is that the common ancestor carried mitochondrial lineages present in both, but later eliminated from the Neanderthals. The authors noted that this requires an explanation for the presence of two deeply divergent mtDNA lineages in the same archaic group, one that later recurred in Denisovans but disappeared from the Neanderthals; and one that became fixed in Neanderthals. The required explanation might be later population bottlenecks that are known to have affected Neanderthal populations. However, the authors preferred explanation is that the mitochondrial genomes of later European Neanderthals was acquired by interbreeding with hominins from Africa. This might explain the absence of Neanderthal-derived morphological traits in some European Middle Pleistocene hominins such as Ceprano and Mala Balanica.

Meyer, M. et al., Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins. Nature (Published online) (2016).

Thursday, 10 March 2016

Meat-eating and food processing were major drivers of human evolution

Study shows how dietary changes and stone tools enabled reductions in size of teeth, jaws and gut

In comparison to earlier hominins, Homo erectus was bigger both in stature and brain size. As such, its energy requirements would have increased – but paradoxically the teeth and chewing muscles were smaller, maximum bite forces weaker and the gut size was reduced. It has long been assumed that this was made possible by increased meat consumption, slicing and pounding food with stone tools, and by cooking. However, the latter was uncommon until around 500,000 years ago. By these means, it is believed that Homo erectus and later humans reduced the both amount of chewing required for their food and workload of the gut in digesting it.

In a newly-published study, Zink and Lieberman report on a series of experiments intended to test these hypotheses. They measured chewing performance in adult human subjects fed size-standardized portions of meat and underground storage organs (roots, tubers, etc.) which are thought to have formed a major component of hominin diet. Goat meat, yams, carrots and beets were chosen for the test; goat is tougher than beef and therefore more similar to the wild game eaten by early hominins. The food was either unprocessed, processed by simple mechanical methods available in Lower Palaeolithic times (slicing and pounding), or roasted (the simplest form of cooking).

They found that the subjects were unable to chew the raw meat effectively, but slicing it resulted in substantial reductions in both the amount of chewing and bite forces required, and in smaller and more digestible meat particles were swallowed. Roasted meat required a greater chewing effort, but even smaller meat particles resulted. However, even unprocessed meat required considerably less masticatory effort than the raw USOs.

Although the advent cooking brought considerable benefits in terms of hygiene and increased energy yields, Zink and Lieberman believe that the reductions in dental size and jaw musculature observed in Homo erectus would have been made possible by the combined effects of eating more meat and mechanically processing both it and USOs. By eating a diet of one-third meat and two-thirds USOs, and slicing the meat and pounding the USOs with stone tools prior to eating, early humans would have reduced chewing by 17 percent and enabled a 26 percent reduction in bite forces.

Although it is possible that food processing and meat eating favoured evolutionary selection for smaller teeth and jaws, Zink and Lieberman believe that it is more likely that these relaxed the selective pressures maintaining robust masticatory anatomy, thus enabling selection to decrease facial and dental size for other functions such as speech production, locomotion, thermoregulation, and possibly even changes in the size and shape of the brain, so leading eventually to the modern condition of Homo. Regardless of what evolutionary factors favoured these changes, they would not have been possible without increased meat eating combined with food processing technology.

Zink, K. & Lieberman, D., Impact of meat and Lower Palaeolithic food processing techniques on chewing in humans. Nature (Published online) (2016).

Tuesday, 1 March 2016

Did Neanderthals use manganese dioxide to start fires?

Mineral might have been sought for its combustion enhancing properties rather than as black pigment

Manganese dioxide minerals have been found at a number of Neanderthals sites in Europe, including Pech-de-l’Azé I in the Dordogne region of southern France. The site is around 50,000 years old, predating the arrival of modern humans in Europe. Over the last sixty years, the site has yielded several hundred small ‘blocs’ of black mineral, thought to  be manganese dioxide, and totaling 750 gm in weight. The majority have been ground to obtain powder.

The long-standing view is that powdered manganese dioxide was used as a black pigment, but this view is challenged in a newly-published study. Although manganese dioxide minerals are reasonably abundant, it would have been far easier for Neanderthals to use charcoal and soot from their campfires as black pigment. Also, the evidence from other sites suggests that Neanderthals favoured manganese dioxide over other locally-available manganese minerals, even though the latter would yield equally-satisfactory black pigment. This led the researchers to consider uses for which only manganese dioxide would suffice.

Manganese dioxide is not combustible, but it is a powerful oxidising agent and thus aids the combustion of other materials. The researchers found that when industrial powdered manganese dioxide was mixed with wood turnings, the latter ignited at a temperature of 250 degrees Celsius, over a hundred degrees below the normal ignition temperature. Furthermore, the rate of charcoal combustion was substantially increased. As little as six percent by weight of manganese dioxide was required. The same results were obtained with powder obtained from the Pech-de-l’Azé I blocs.

Based on these experiments, the researchers concluded the Neanderthals’ chief use for manganese dioxide was for starting fires rather than pigment. With archaeological evidence for fireplaces and the production of manganese dioxide to powder, they suggest that the Neanderthals at Pech-de-l’Azé I were able to produce fire as required rather than having to make opportunistic use of lightning strikes and forest fires.

Heyes, P. et al., Selection and Use of Manganese Dioxide by Neanderthals. Scientific Reports 6 (22159 ), doi:10.1038/srep22159 (2016).