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What happened to the Neanderthals?

Update #7 to Human Origins: How diet, climate and landscape shaped us

We have long been fascinated by the Neanderthals and for good reason. All of us, outside of sub-Saharan Africa, are a bit Neanderthal. This is because we carry a small fraction of the Neanderthal genome acquired long ago when our ancestors left Africa. A relatively small group of our ancestors with cultures equivalent to modern-day hunter-gatherers left Africa around 60 to 50 thousand years ago. Upon leaving they rapidly multiplied and spread throughout Eurasia and then the Americas  ̶  a peopling of the world referred to as the ‘Great Expansion.’

photo of front cover of the book Human Origins by John Compton

People emerged in southern Africa with cultures on a par with modern hunter-gatherers by 70 thousand years ago (70 ka) and eventually spread throughout Africa and the world.

Upon leaving Africa and entering Eurasia, our ancestors soon encountered the Neanderthals. We share a common ancestor with Neanderthals that left Africa long ago, with the Neanderthals (Homo neanderthalensis) evolving in Eurasia while our species (Homo sapiens) evolved separately in Africa. We know from the DNA extracted from Neanderthal bones that these encounters included intermingling (i.e., sex) and production of offspring. Just how romantic or not such intermingling was is unknown. What is known is that it took place on more than one occasion up until when the Neanderthals became extinct around 40 thousand years ago.

 

The offspring of these unions had an equal mixture of our species’ and Neanderthal’s DNA. Some of these offspring then mated with others and passed Neanderthal genes down the line. However, the amount of Neanderthal DNA became greatly diminished over time, with most people today outside of sub-Saharan Africa having only between 1.8% and 2.6% Neanderthal DNA. The loss of Neanderthal DNA from our genome reflects the fact that the Neanderthals became extinct and many of their genes carried by people were selected against, with those having them not successfully passing them along to the next generation. Although any individual has a small percentage Neanderthal DNA, the specific Neanderthal DNA that each person carries is not the same, such that if everyone’s different bits are added up then roughly 20% to 30% of the Neanderthal genome survives scattered among people living today.

 

But 20% to 30% of a genome scattered about the population does not a species make and the Neanderthals, along with all our other cousins living in Eurasia became extinct during the course of the Great Expansion. Prior to the Great Expansion there were as many as five different co-existing species in our human family tree. Why did all the others, including the Neanderthals become extinct and not us?

 

Possible distribution of our cousins living in Eurasia at the time of the Great Expansion. People exiting Africa most likely first encountered Neanderthals in the Middle East and continued to interbreed with them until they became extinct by around 40 thousand years ago.

Some argue that the Neanderthals were already in decline when we arrived; others claim that our arrival is what ultimately did them in. But how the extinction of the Neanderthals unfolded remains unclear. The Neanderthals were a successful species, having a long history of surviving the highly variable climate cycles of Europe. They hunted in cooperative groups using stone tipped spears, made use of body paint and buried their dead. They had a brain similar in size to ours (approximately 1500 cc) at the time of their extinction, but we know little about how their brain was structured. One way to gain insights into how the brains of Neanderthals and people differ is to compare their social organisation and culture. Several recent papers on DNA extracted from fossil bones shed some new light on how the social organisation of Neanderthals compares to people living in Eurasia soon after the Neanderthals became extinct.

Both Neanderthals (left, red) and people (right, blue) independently evolved big brains, but differences in social organisation and culture suggest significant differences in structure (image Philipp Gunz/Max Plank Institute for Evolutionary Anthropology).

The first paper by Kay Prüfer and others (2017) presents a high-quality Neanderthal genome assembled from DNA extracted from a female’s fossil bones from Vindija Cave in Croatia dated to around 50 thousand year ago. The only other high-quality Neanderthal genome is for an individual from the Altai region of southern Siberia. The DNA from Croatia did not show the extreme inbreeding of the Altai individual, but was found to contain a third fewer gene variations than present-day Eurasians. The low level of gene variation (low heterozygosity) found in fossil bones from both Croatia and southern Siberia suggests that Neanderthal population sizes were relatively small and geographically isolated and included instances of extreme inbreeding.

 

The second paper by Martin Sikora and others (2017) presents the DNA sequence extracted from fossil bones of a number of people (Homo sapiens) from the Sunghir site located 190 km east of Moscow and dated to 34 thousand years ago. The four individuals studied from Sunghir are associated with burials containing grave goods such as heavily beaded clothing, with many beads stained black and red (the site was covered in red ochre). The artefacts suggest that those living at Sunghir had cultures on a par with modern-day hunter-gatherers.

 

The genomes indicate small population size, but in contrast to the small, geographically isolated populations of the Neanderthals, the genomes of the Sunghir people suggest that they were connected to wider social networks. These results suggest that the people living in Eurasia soon after the extinction of the Neanderthals had already established social organisations similar to modern-day hunter-gatherers. The large amount of gene variation (high heterozygosity) among the Sunghir individuals suggest that these groups mated (married) outside of their groups (exogamy), which implies greater mobility and cultural exchange among groups. These groups likely travelled over large areas seasonally and by exchanging mates with other far-ranging groups they were able to minimise inbreeding. This social behaviour is consistent with that observed among modern hunter-gatherers, which helps them to sustain low genetic relatedness among members of their small groups.

 

The spread of people into Europe having the equivalent of modern hunter-gatherer cultures replaced the resident Neanderthals by around 40 ka, but not before some interbreeding took place (ka = thousands of years ago).

These latest DNA results indicate a greater degree of social networking in people compared to the Neanderthals and this may have been a key factor to our species successful replacement of the Neanderthals along with other established groups living in Eurasia. Strong social networks would have facilitated the spread and retention of innovative cultures, while reducing genetic relatedness among individuals in small, mobile groups. Widespread social networks ensured genetic mixing to avoid inbreeding and spread cultural adaptations that allowed people to move successfully into many different and new environments. The Neanderthals and presumably our other cousins established in Eurasia lacked these traits, a lack which perhaps only became critical in competition with people as they spread across the landscape.

 

The successful interbreeding between people and Neanderthals suggests that hybridisation was important throughout human evolution. Hybridisation is when two species successfully breed to produce viable offspring, offspring capable of breeding and having offspring of their own. In biology, many of us learned that two different species by definition cannot produce viable offspring. But biology is messy and it turns out that some closely related species can interbreed. Primates, the large group of animals to which we belong are known for interbreeding, for example among closely related species of monkeys and baboons.

 

A zorse is a horse-zebra hybrid. The fossil DNA record indicates that human species could interbreed to produce hybrids (photo: Christine and David Schmitt).

Our last shared common ancestor with the Neanderthals lived in Africa 630 to 520 thousand years ago (Prüfer and others, 2017). And even though the group that moved into Eurasia to evolve into the Neanderthals were isolated from those who remained in Africa to evolve into us for at least 400 thousand years, we were still able to successfully interbreed. Interbreeding (hybridisation) is important because it increases gene flow. By successfully interbreeding with Neanderthals, the newcomers were able to acquire new genes. Many of the new genes were beneficial because they had been modified by natural selection to be useful traits for Neanderthals living in Eurasia as opposed to Africa. For example one of the retained genes from Neanderthals allowed us to adapt to low UV radiation in the northern hemisphere where there is less sunlight. Other adaptations involved properties of the skin to the generally colder and drier climates of Eurasia. However, hybridisation is a random mixed bag and along with the good genes were the not so good genes, such as those associated with lupus and Crohn’s disease and greater susceptibility to diabetes.

 

The interbreeding of our species with the Neanderthals provides strong evidence that hybrids were likely common throughout the millions of years of human evolution. Groups isolated at times either through cultural differences or physical barriers would have evolved separately and diverged away from other groups.  When barriers fell, previously isolated groups were reunited.  Successful interbreeding during these reunions would have facilitated evolution by mixing closely related but different gene pools. Thus, rather than the traditional linear branching of species leading up to us, one can imagine a far more complex scenario where many closely related but geographically and genetically distinct groups are periodically mixed and through interbreeding give rise to new traits.

 

Further reading

Bergström, A. and Tyler-Smith, C., 2017. Paleolithic networking. Science 358, 586-587 (doi: 10.1126/science.aaq0771).

 

Prüfer, K., and others, 2017. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 358, 655-658 (doi: 10.1126/science.aao1887).

 

Sikora, M. and others, 2017. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 358, 6595-662 (doi: 10.1126/science.aao1807).

 

First Animals

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Update #6 to Human Origins: How diet, climate and landscape shaped us

The sudden, but relatively late appearance of animals in the rock record has both fascinated and puzzled scientists for years. Simple bacteria emerged as early as 4000 million years ago, soon after Earth had become habitable (refer to my previous blog: First Life), but complex animals appeared only around 600 million years ago and burst onto the scene from 541 million years ago as part of the ‘Cambrian Explosion.’ The delay in the evolution of animals is usually attributed to low levels of oxygen gas in Earth’s atmosphere, which had to first rise above a threshold value before animals could proliferate. This idea finds support from rock record, which indicates that the arrival of animals coincides broadly with when oxygen levels increase sharply. But why did oxygen levels remain so low for so long, and what was it that led to our oxygen-rich atmosphere and the rapid evolution of diverse animal life?

 

Rise in oxygen in Earth's atmosphere from JS Compton's book Human Origins
Earth initially had no oxygen gas in its atmosphere, and oxygen remained at low levels (<0.1%) during the ‘boring billion’ years before it rapidly increased between 600 and 500 million years ago coinciding with the appearance of the earliest animals (adapted from Sperling and others, 2015).

In my book I state that we animals may owe thanks to the algae for our existence. This concept finds support in a recent paper by Brocks and others (2017), in which they show that the transition to an animal world corresponds to when algae suddenly became the dominant primary producers. Primary producers form the base of the food chain by using sunlight to grow by photosynthesis.  Oxygen gas is a by-product of photosynthesis, a biological process that is ultimately responsible for our oxygen-rich atmosphere. They propose that greater availability of the nutrient phosphorus in the world’s oceans allowed algae to dominate for the first time over bacteria as primary producers. Algae are significantly larger and more complex than bacteria, and as a result algae are more likely to end up buried in sediment before they react with oxygen and are converted back into carbon dioxide. Hence, the ‘rise of algae’ resulted in a rise in oxygen levels through enhanced burial of organic matter. The scenario they propose is a good example of how interactions between the living and non-living worlds may have promoted ecological transformations that ultimately led to the emergence of the vast animal kingdom to which we belong. What is the evidence for the rise of algae?

 

There are a number of ways in which life can leave evidence of its existence in the rock record. Body fossils are the preserved remains of the actual animal and they most commonly consist of hard parts, such as teeth, bone or shell. In rare cases the rapid draping of fine sediment soon after death can preserve soft tissue structures (Lagerstätte). Trace fossils, such as footprints, burrows or tooth marks can also provide evidence, although linking them to a specific animal can be difficult. Molecular fossils are distinct chemical compounds made by organisms referred to as biomarkers. Biomarker molecules, if stable can indicate the existence of an organism or group of similar organisms even in the absence of any other fossil evidence. For example, compounds derived from steroids or sterols (called steranes) have been used to indicate when the first sponges appeared (Love and others, 2009).  Sterane biomarkers specific to algae were used by Brocks and others (2017) to document when algae became abundant in the rock record. Importantly, their methods were designed to minimise contamination by petroleum products.

 

What the biomarker record of Brocks and others (2017) suggests is that, although algae had first appeared by around 1800 million years ago, algae only became dominant much later by 659-645 million years ago. Algae have far more complex, eukaryotic cells compared to bacteria (prokaryotic cells) and by 1600 to 1200 million years ago algae were the earliest multicellular organisms, having specialised cells for attachment, vertical elements and reproduction. These features represent major evolutionary innovations, and yet for all their innovativeness the algae do not appear to have displaced the bacteria as primary producers. Why not? In modern oceans bacteria tend to dominate in nutrient-poor waters, whereas algae take over once nutrients become more abundant. So, one possibility is that the early ocean had few nutrients, such as phosphorus, and that algae struggled to compete with bacteria until the nutrient content of the oceans increased. If this scenario is correct, then what could have increased the nutrient content of the oceans allowing algae to out compete bacteria?

 

Fossil red algae 1200 million years ago grew in vertical filaments attached to a firm substrate and had reproductive structures (two images on the right) (images courtesy of Nicholas Butterfield).

Snowball Earth is an appropriate name for a most unusual period of Earth history, the Cryogenian, when our planet experienced extreme climate cycles of cold, near complete icing over to hot climates when all the ice rapidly melted. Significant variations in ice and climate are known from the past, but none was nearly as intense as the hot and cold cycles of the Cryogenian. Prior to Snowball Earth oxygen levels were steady and low (<0.1% compared to 21% today) from roughly 1800 to 800 million years ago, a period referred to as the ‘boring billion’ when Earth was locked into a low-oxygen atmosphere. A low-oxygen atmosphere may partly explain why the nutrient content of the ocean was also kept low for so long. Under low oxygen conditions, the ocean has more iron and iron can keep surface, sunlit surface waters where photosynthesis occurs low in phosphorus by removing it through adsorption to iron oxides. Whatever the reasons for its long stability, the ‘boring billion’ finally came to an end with the onset of Snowball Earth. The large ice sheets ground large amounts of rock into fine powder that then underwent intense chemical weathering in the ice-free hot climates that ensued. If this weathering released large amounts of phosphorus to the ocean, then it may have spurred on the algae who, having waited patiently in the wings for so long could now take off and displace bacteria as the dominant primary producers.

Snowball Earth cycle figure from Compton's book Human Origins
Snowball Earth is when our planet cycled between cold, ice-covered intervals (centre) and hot, ice-free climates (far left and right). The position of the continents was different then compared to today, with most positioned near the equator where intense weathering may have contributed to initiating Snowball Earth. Input of carbon dioxide, a greenhouse gas, by volcanoes (dark streaks in centre image) eventually warmed Earth and the ice melted.

The dominance of algae as primary producers was a major event and one that has endured ever since, most probably because it established a powerful feedback loop that rapidly led to an oxygen-rich atmosphere. Snowball Earth cycles released more nutrients, more nutrients fuelled more growth of large multicellular algae, some parts of which were more resistant to degradation than others and were more easily buried. Burial of more algal organic matter in turn allowed more oxygen to remain in the atmosphere. Higher oxygen levels resulted in an iron-poor, but nutrient-rich ocean, which promoted the growth and burial of algae and a continued rise in oxygen, rapidly exceeding the threshold level at which animals could thrive. Algae also promoted the evolution of animals by providing a large source of food. Single-celled animals feed on tiny bacteria but large, multicellular animals could fed on algae as well as on other animals consuming the algae. The result was a major global ecological shift to far more complex and intricate food chains cascading up from the algal primary producers.

 

The timing fits nicely with the rock record. The increase in algal biomarkers occurs between the major icing over episodes of the Cryogenian and coincides with a large, positive carbon isotope shift indicating more efficient organic matter burial just prior to the emergence of the earliest animals. The earliest animals include sponges, jelly fish and odd, pillow-like animals of the Ediacaran fauna that evolved around 600 million years ago and that by 541 million years ago were joined by diverse bilaterian animals, the dominant animals on Earth ever since. Thus, it took a major disruptor in the form of Snowball Earth to knock the biosphere into a new level of complexity driven by a greater flux of nutrients, more organic matter burial, an oxygen-rich atmosphere and more diverse, multicellular animals. If this scenario is correct then we humans, along with all the other animals living today owe thanks to the algae, who waited patiently for the conditions to arrive that allowed them to proliferate and in so doing ushered in the animal world.

 

Synopsis of early evolution of life on Earth from Compton's book Human Oriigins
Synopsis of the major events in the early evolution of life on Earth up to the emergence of complex animals (time is shown on the far right in billions of years ago).

Further reading

download this blog (PDF)

Brocks, J.J., and others, 2017. The rise of algae in Cryogenian oceans and the emergence of animals. Nature 548, 578-581 (doi:10.1038/nature23457). Butterfield, N.J., 2002. Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26, 386-404. Knoll, A.H., 2017. Food for early animal evolution. Nature 548, 528-530. Love, G.D., and others, 2009. Fossil steroids record the appearance of Demospongiae during the Cryogenian period. Nature 457, 718-721 (doi:10.1038/nature07673). Sperling, E.A. and others, 2015. Statistical analysis of iron geochemical data suggests limited late Proterozoic oxygenation. Nature 523, 451-454-721 (doi:10.1038/nature14589). © John S. Compton (www.johnscompton.com)

© John S. Compton

John S. Compton
Earthspun Books logo
photo of front cover of the book Human Origins by John Compton Update #7 to Human Origins: How diet, climate and landscape shaped us
Update #6 to Human Origins: How diet, climate and landscape shaped us
Rise in oxygen in Earth's atmosphere from JS Compton's book Human Origins
Earth initially had no oxygen gas in its atmosphere, and oxygen remained at low levels (<0.1%) during the ‘boring billion’ years before it rapidly increased between 600 and 500 million years ago coinciding with the appearance of the earliest animals (adapted from Sperling and others, 2015).
Fossil red algae 1200 million years ago grew in vertical filaments attached to a firm substrate and had reproductive structures (two images on the right) (images courtesy of Nicholas Butterfield).
Snowball Earth cycle figure from Compton's book Human Origins
Snowball Earth is when our planet cycled between cold, ice-covered intervals (centre) and hot, ice-free climates (far left and right). The position of the continents was different then compared to today, with most positioned near the equator where intense weathering may have contributed to initiating Snowball Earth. Input of carbon dioxide, a greenhouse gas, by volcanoes (dark streaks in centre image) eventually warmed Earth and the ice melted.
Synopsis of early evolution of life on Earth from Compton's book Human Oriigins
Synopsis of the major events in the early evolution of life on Earth up to the emergence of complex animals (time is shown on the far right in billions of years ago). Brocks, J.J., and others, 2017. The rise of algae in Cryogenian oceans and the emergence of animals. Nature 548, 578-581 (doi:10.1038/nature23457). Butterfield, N.J., 2002. Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26, 386-404. Knoll, A.H., 2017. Food for early animal evolution. Nature 548, 528-530. Love, G.D., and others, 2009. Fossil steroids record the appearance of Demospongiae during the Cryogenian period. Nature 457, 718-721 (doi:10.1038/nature07673). Sperling, E.A. and others, 2015. Statistical analysis of iron geochemical data suggests limited late Proterozoic oxygenation. Nature 523, 451-454-721 (doi:10.1038/nature14589). © John S. Compton (www.johnscompton.com)
Earthspun Books logo
John S. Compton
Earthspun Books logo
Update #7 to Human Origins: How diet, climate and landscape shaped us
photo of front cover of the book Human Origins by John Compton
Update #6 to Human Origins: How diet, climate and landscape shaped us
Rise in oxygen in Earth's atmosphere from JS Compton's book Human Origins
Earth initially had no oxygen gas in its atmosphere, and oxygen remained at low levels (<0.1%) during the ‘boring billion’ years before it rapidly increased between 600 and 500 million years ago coinciding with the appearance of the earliest animals (adapted from Sperling and others, 2015).
Fossil red algae 1200 million years ago grew in vertical filaments attached to a firm substrate and had reproductive structures (two images on the right) (images courtesy of Nicholas Butterfield).
Snowball Earth cycle figure from Compton's book Human Origins
Snowball Earth is when our planet cycled between cold, ice-covered intervals (centre) and hot, ice-free climates (far left and right). The position of the continents was different then compared to today, with most positioned near the equator where intense weathering may have contributed to initiating Snowball Earth. Input of carbon dioxide, a greenhouse gas, by volcanoes (dark streaks in centre image) eventually warmed Earth and the ice melted.
Synopsis of early evolution of life on Earth from Compton's book Human Oriigins
Synopsis of the major events in the early evolution of life on Earth up to the emergence of complex animals (time is shown on the far right in billions of years ago). Brocks, J.J., and others, 2017. The rise of algae in Cryogenian oceans and the emergence of animals. Nature 548, 578-581 (doi:10.1038/nature23457). Butterfield, N.J., 2002. Bangiomorpha pubescens n. gen., n. sp.: implications for the evolution of sex, multicellularity, and the Mesoproterozoic/Neoproterozoic radiation of eukaryotes. Paleobiology 26, 386-404. Knoll, A.H., 2017. Food for early animal evolution. Nature 548, 528-530. Love, G.D., and others, 2009. Fossil steroids record the appearance of Demospongiae during the Cryogenian period. Nature 457, 718-721 (doi:10.1038/nature07673). Sperling, E.A. and others, 2015. Statistical analysis of iron geochemical data suggests limited late Proterozoic oxygenation. Nature 523, 451-454-721 (doi:10.1038/nature14589). © John S. Compton (www.johnscompton.com)
photo of front cover of the book Human Origins by John Compton