Leaving Africa: When did our species first move out of Africa?

Update #8 to Human Origins: How diet, climate and landscape shaped us

John S. Compton (www.johnscompton.com)

A fossil jaw bone recovered from Misliya Cave on the western slopes of Mount Carmel in Israel suggests that modern humans (Homo sapiens) were living there sometime between 194 and 177 thousand years ago (Hershkovitz and others, 2018). This is significantly earlier than the previously oldest evidence, dated to between 120 and 90 thousand years ago, of when our species first resided outside Africa. The estimated age range appears to be robust as it is based on multiple dating techniques applied both directly to the fossil and indirectly to material encrusting the fossil. It is the only human fossil yet to be recovered from the site after a century of excavation and it fills a critical gap in the archaeological record of when our ancestors left Africa.

Whose jaw is it?

The upper jaw bone fragment has 7 intact teeth along with parts of the surrounding cheekbone and roof of the mouth. The fossil was scrutinised using high-resolution CT-scanning, which allowed for a virtual reconstruction and a detailed analysis of all of its exterior and interior features. By comparing many of its measurable features to other fossil jaw bones and teeth, the authors conclude that the fossil is most similar to modern humans and not Neanderthals. Their conclusion is strongly supported by the data and it is a critical distinction because Neanderthals, but not modern humans, were known to be living in Eurasia already at this time. But what is meant by ‘modern humans’?

Misliya jaw bone

Fossil jaw bone on the right and its virtual reconstruction on the left, from Hershkovitz and others (2018).

A recent paper argued that our species (Homo sapiens) extends back to around 300 thousand years based on fossils dated from Jebel Irhoud, Morocco (Hublin and others, 2017). However, the Jebel Irhoud fossils are considered by some to represent an earlier species, with enough anatomical and behavioural differences separating them from our species. Unfortunately, the features, and hence name, of this species that immediately preceded our own are not well defined. Some refer to the Jebel Irhoud, and similarly aged fossils known from Africa, as ‘early’ modern humans, while I refer to them in my book Human Origins as our ‘predecessor’ species. (For a more detailed discussion on this topic see my blog “New ages from Jebel Irhoud, Morocco”).

Therefore, the fossil jaw could belong to an ‘early’ modern human, a member of our predecessor species, or it could belong to a modern human, a member of our species. The detailed analysis of the jaw bone and teeth is unable to differentiate clearly between these possibilities. This is not surprising considering the variability in physical traits commonly associated with speciation events, and that the fossil’s age overlaps with when our species first emerged in Africa 200 to 160 thousand years ago. Resolving whether the jaw belongs to our species or to our predecessor species may not be possible, but there are other intriguing aspects about the fossil.


Why the fossil is important

We humans evolved in Africa and that our ancestors would rapidly expand beyond Africa given half a chance doesn’t come as a surprise considering how quickly they filled the varied habitats of the African continent. The archaeological record tells us that our ancestor Homo erectus left Africa soon after they evolved over 1.85 million years ago, as did Homo heidelbergensis, a species intermediate between H. erectus and us, around 400 thousand years ago.  What is surprising in light of these earlier exits out of Africa is the apparent delay between when our species emerged in Africa around 200 thousand years ago and when our species left Africa. Previously, the earliest evidence was from the Skhul and Qafzeh caves dated to 120 to 90 thousand years ago. This latest fossil find from Misliya Cave, a cave close by to the Skhul and Qafzeh caves, tells us that our species (or possibly our predecessor species) was living outside of Africa much earlier, at a time that overlaps with when our species first appeared in the fossil record in East Africa. Occupation of the Levant (modern day Israel, Syria, Lebanon and Jordan) is significant because it is the closest habitable region to Africa, located just across the Sinai Peninsula, the sole land bridge linking Africa and Eurasia. However, the archaeological record suggests that the Levant was not continuously occupied. Instead our ancestors appear to have left Africa in episodic pulses, many of which were limited to the Levant where, even there, they did not last for long.

One possible explanation for episodic exchange across the Sinai is the dynamic of the Sahara-Arabian Desert. Normally this severe desert is a barrier to movement. However, there is evidence of brief, wetter periods when the Sahara-Arabian Desert turned green with grass making it habitable. Greening of the desert tends to occur during the transition from glacial to interglacial periods, and most likely coincides with expansion of animals (including humans chasing after them) out of Africa. For example, movement into the Levant 120 to 90 thousand years ago appears to coincide with multiple greening events interspersed throughout the MIS 5 interglacial period (5e, 5c and 5a), which followed on from the MIS 6 glacial period during which severe desert likely prevented any exchange.

G-IG dispersals Misliya Cave MR

Plot showing time periods when the Sahara may have greened and humans may have moved out of Africa associated with major glacial to interglacial climate variations spanning the last 300 thousand years (adopted from Compton, 2016).

The MIS 6 glacial period was preceded by the MIS 7 interglacial period, which like the MIS 5 interglacial had several warmer and wetter intervals designated 7e (242 ka), 7c (220 ka) and 7a (205 ka). Greening during any of these three wetter intervals, all of which predate the age of the fossil jaw bone, may have allowed movement beyond Africa into the Levant. Although the Skhul and Qafzeh caves are nearby the Misliya Cave, there is no evidence that the area was continuously occupied. Instead, those living in the Levant during the warm MIS 7 interglacial period probably didn’t survive the long and severe MIS 6 glacial period. This would imply that those who came after the MIS 6 glacial during greening events associated with the MIS 5 interglacial period represent separate pulses out of Africa.

Episodic occupation of the Levant is supported by the archaeological evidence, which indicates significant differences in the cultures of those who frequented the Misliya Cave compared to those who later frequented the nearby Skhul and Qafzeh caves. Although the jaw bone is so far the only human fossil found, the bones of other animals, fire hearths and over a thousand stone tools give an indication of how those in the Misliya Cave lived.  They were skilful hunters capable of taking down prime-aged prey, which they mostly butchered in the field and carried back to the cave to cook over a fire. They hunted in nearby woodland and savanna habitats and hunted mostly fallow deer and mountain gazelle, as well as other antelope, auroch (feral cows), ostrich, tortoise and hare. Their stone tools are dominated by Levallois flakes, points and blades made from local flint nodules. Levallois refers to a technique for making stone tools of uniform size and shape struck from a specially prepared stone core. The prepared Levallois core acted like a die and ensured consistent production of quality stone tools. The Levallois technique has deep roots but its full development is associated with the transition to early modern humans (our predecessor species) around 300 thousand years ago, about the same time that the first throwing spears with Levallois points emerged in East Africa (Sahle and others, 2013).

Levallois tools

The Levallois technique involves preparing cores from which stone tools, such as points or blades, can be struck.

The major difference in the archaeological records is not so much reflected in the stone tools, but rather in the extent of symbolic cultural artifacts. The exceptional fossils from the Skhul and Qafzeh include several skulls that clearly are those of modern humans. Not only did their bones look like ours, they also behaved modern in that they buried their dead with symbolic burial goods, such as antler horn, used ochre body paint, and made some of the earliest shell jewellery. The stone tools used and the animals hunted were largely similar, but none of the symbolic artifacts, so strongly associated with modern human behaviour has yet been reported from the Misliya Cave. Those who frequented the Misliya Cave either never possessed these symbolic cultures or somehow lost them along the way.

Therefore, the jaw bone from Misliya Cave suggests movement of either members of our species or our predecessor species out of Africa during earlier greening events associated with the MIS 7 interglacial period. Such movement out of Africa as far as the Levant is not surprising because the Afro-Arabian mix of animals (fossil and living) indicates that the Levant is part of the transition zone between North Africa and the Arabian Peninsula. Animals, including humans, can move back and forth along the narrow land bridge of the Sinai Peninsula that tethers the two when the Sahara-Arabian Desert becomes habitable, and retreat or fade away upon return of severe desert. The jaw bone from Misliya Cave helps fill the gap of the anticipated movement of our ancestors associated with the wet and habitable intervals of the MIS 7 interglacial period.

The more intriguing movements are those that carry on beyond the Levant, when our ancestors managed to expand into the broad spectrum of habitats that exist throughout the vast Eurasian continent. The first to make the crossing and expand into much of Eurasia was Homo erectus, followed by Homo heidelbergensis, who would evolve into the Neanderthals and Denisovans, while those who remained in Africa evolved into us Homo sapiens. There is evidence that our species expanded as far as China during the MIS 5 interglacial period, but otherwise our species does not appear to have amounted to much outside of Africa during either the MIS 7 or MIS 5 interglacial periods. The reason why is perhaps because Eurasia had become occupied by our cousins, the Neanderthals and Denisovans, whose populations were possibly too formidable for us to displace. It would take the later expansion by those possessing the equivalent of modern-day hunter-gatherer cultures around 60-50 thousand years ago, the so-called Great Expansion, before our species would effectively conquer the world.

Great expansionThe Great Expansion when our species went global (ages in thousand of years ago, ka).


Further reading

Callaway, E., 2018. Israeli fossils hint at early migration. Nature 554, 15-16.

Compton, J.S., 2016. Human Origins, How diet, climate and landscape shaped us. Earthspun Books, www.johnscompton.com.

Compton blog: https://johnscomptonblog.wordpress.com/2017/08/07/new-ages-from-jebel-irhoud-morocco/

Hershkovitz, I., and others, 2018. The earliest modern humans outside Africa. Science 359, 456–459. DOI: 10.1126/science.aap8369

Hublin, J.-J., and others, 2017. New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens. Nature 546, 289-292. http://dx.doi.org/10.1038/nature22336.

Misliya Cave site, for details visit: http://misliya.haifa.ac.il/archaeology/archaeology.html

Sahle Y., Hutchings W.K., Braun D.R., Sealy J.C., Morgan L.E., et al., 2013. Earliest stone-tipped projectiles from the Ethiopian Rift date to >279,000 years ago. PLoS ONE 8(11): e78092. doi:10.1371/journal.pone.0078092.

Stringer, C., and Galway-Witham, J., 2018. When did modern humans leave Africa? Science 359, 389-390. DOI: 10.1126/science.aas8954

© John S. Compton (www.johnscompton.com)

What happened to the Neanderthals?

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

John S. Compton (www.johnscompton.com)

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.’

Great expansion

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?

cousins in EurasiaPossible 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.

Neanderthal v people

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.


peopling of Europe

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 adaptions 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 susceptibly 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).

© John S. Compton (www.johnscompton.com)


First Animals

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

John S. Compton (www.johnscompton.com)

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 of oxygen

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?

red algae fossils

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

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.

early life synopsis

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

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)



First Life (Inevitable Life?)

Update #5 to Human Origins: How diet, climate and landscape shaped us

John S. Compton (www.johnscompton.com)

Several recent papers present evidence that life was established early on, soon after Earth’s fiery and cataclysmic assembly had ended and its surface had cooled down into a watery world capable of sustaining life. Such an early start implies that life, rather than being unique to Earth may be, if not inevitable, then at least a highly likely outcome here as well as on other Earth-like planets. Give life half a chance and it will rise up and thrive. A result which perhaps shouldn’t come as too big a surprise considering the tenacity with which life has persisted and diversified over the many billions of years since it first emerged. One way to ascertain if life on Earth was a highly likely or inevitable outcome is to find it elsewhere. The recent discovery of thousands of distant planets (exoplanets) orbiting within the watery, and hence potentially habitable zone of their stars is a promising sign that we may be closing in on evidence that life does exists out there in the great beyond. Confirming life on just one exoplanet would imply that our universe is home to a multitude of living worlds peppered across its enormous expanse. This is a mind-boggling concept even if our chances of ever directly interfacing with life elsewhere is remote given the distances involved. As our search for life on distant planets continues, we can also look long and hard for evidence of the earliest life here on Earth. Establishing when life first appeared on Earth can provide us with valuable insights into how life might have come about, but finding convincing evidence of life in the ancient rock record is a difficult task.

The first problem is that most life never leaves even a hint of its existence in the rock record. Life is fragile and readily decomposes such that most living things upon death rapidly vanish, recycled back into the world of non-living elements. Hence, fossil remains of life are rarely preserved in rocks of any age, never mind long ago when the abundance and types of life forms were far more limited than today. The other problem is that older rocks become increasingly difficult to find the further back in time you go. This is because Earth is dynamic, with the movement of its crustal plates (plate tectonics) constantly recycling older rocks into younger rocks. The evidence of life can only be found in the rock record and, therefore, the oldest rocks define the limit of how far back we can potentially detect life. And even for those oldest rocks that we are lucky enough to find and that once harboured fossils, most have since been subjected to intense pressures and temperatures over the dynamic history of their long existence. Such abuse is likely to obscure, if not destroy, whatever original fossil evidence the now transformed rocks may have once contained. Despite these problems, what does the rock record reveal about the earliest life on Earth?

The oldest rocks yet found are around 4 billion years old and occur in Canada and Greenland. We know from the age and composition of meteorites that our solar system formed initially 4.56 billion years ago. It was at this time that Earth’s assembly began by the collision of the many small rocky and metallic bits circling the Sun in our planet’s orbit. Initially gravity pulled in surrounding dust and rock to form small planets (planetissmals) and then these collided gradually to form larger planets. The final, major planetissmal collision that went into the making of Earth occurred 4.44 billion years ago. Our Moon formed from the debris of this collision and the force of the collision transformed Earth into a magma ball, too hot to sustain life. Life could have conceivably been established once the magma ball had cooled and crusted over, and the water vapour had condensed to form the oceans. Conditions on Earth however remained challenging to life as it had to contend with periods of intense bombardment by the sweeping up of the remaining rocky bits. This time of heavy meteorite bombardment is known as the Hadean, named after Hades, god of the underworld. The intense bombardment and the Hadean ended 4 billion years ago to give way to the Archean. To whatever extent life may have started during the Hadean, it was only by the start of the Archean that Earth presented a relatively stable setting for life to persist.

hellish hadean

Archean Earth
The Hadean (top) was a hellish period of intense meteorite bombardment and vaporised oceans, conditions that were generally not favourable to life, while the Archean world (bottom) included oceans of water and conditions suitable for the earliest microbial life forms.


The oldest, direct fossil evidence of life is in the form of stromatolites. Stromatolites are mound-shaped structures that form from the activities of microbial mat communities. Stromatolites are common throughout much of the early rock record and some still form today in places like Shark Bay, Western Australia. The minute microorganisms themselves are rarely preserved, but the layered stromatolite structures they build as a result of their activities often are preserved. The distinctive features of stromatolites rule out alternative, non-biological origins for the layered structures, such as the deposition of mineral crusts. The oldest stromatolites were recently discovered in rocks from Greenland 3.7 billion years old (Nutman and others, 2016), significantly older than the previously oldest stromatolites known from Australia dated to 3.48 billion years.

1-Nutman stromatolites
Small conical-shaped mounds (dashed lines) in rocks from Greenland 3.7 billion years old are interpreted to be stromatolites formed by microbial communities (photo by Allen Nutman adapted from Allwood, 2017).

Going back beyond 3.7 billion years, the evidence of life relies on the chemical signature of what is interpreted to be the remains of once living organisms as well as possible fossils. Life on Earth is carbon based and hence most organisms are made up of a significant amount of carbon. For life that grows by taking up carbon directly as CO2, the lighter carbon isotope (carbon 12) is taken up preferentially to the heavier isotope (carbon 13) (the heaviest isotope (carbon 14) is radioactive and has a short life span). The preferential uptake of the light isotope gives life a distinct, negative carbon isotopic composition. When organisms die and their organic matter decomposes, most of the other elements besides carbon, such as nitrogen, phosphorus, oxygen and hydrogen are lost and eventually all that remains is carbon. When heated up under pressure the remaining organic carbon can form the mineral graphite (a soft, grey mineral that is familiar to us as pencil lead). At extreme pressures graphite can transform to diamond. Some have found organic matter in rocks from Greenland greater than 3.7 billion years old that still contains some oxygen, hydrogen, nitrogen and phosphorus because it was preserved as inclusions within the metamorphic mineral garnet (Hassenkam and others, 2017). But in most cases all that remains is pure carbon in the form of graphite. Graphite from rocks in Labrador Canada greater than 3.95 billion years old have carbon isotope values that suggest the carbon was originally part of living organisms. Some of the graphite takes on globular shapes common to some microorganisms (Tashiro and others, 2017). Structures in rocks at least 3.77 billion year old from Quebec Canada interpreted to represent fossil microorganisms suggest that mid-ocean ridge submarine hydrothermal vents or ‘black smokers’ are a potential setting in which early life evolved on Earth (Dodd and others, 2017). Unfortunately, the structures interpreted to be fossil bacteria and the carbon isotope values of graphite interpreted to indicate life processes can both be produced by reactions that do not involve living organisms. Therefore, the indications of life earlier than the 3.7-billion-year-old stromatolites are compelling, but remain ambiguous.

3.95 Ga graphite spheres

black smoker
Cluster of globular graphite in quartz chert from Canada is suggestive of fossilised microbial organisms (top, from Tashiro and others, 2017). A modern submarine volcanic vent or ‘black smoker’ is a possible setting where life first emerged on Earth (image from NOAA).


The oldest known rocks are around 4 billion years old, so how can we say anything about earlier periods of Earth history? Some younger rocks contain mineral grains derived from the erosion of older rocks. Zircon is a highly durable mineral that often ends up being eroded out of older rocks but is not destroyed by weathering and ends up being recycled into younger rocks. In fact, the oldest known mineral is zircon dated to as old as 4.38 billion years in rocks from Jack Hills, Western Australia. A small number of these zircon grains have minute inclusions of graphite. The graphite in a zircon grain dated to 4.1 billion years has a carbon isotope signature consistent with a biological origin, but again not unambiguously (Bell and others, 2015). Therefore, the recent evidence pushes back the earliest life on Earth from around 1000 million years to at least 700 million and possibly 300 million years following the final major collisional event 4.44 billion years ago. Assuming it took on the order of 100 million years for Earth to become habitable after the final major collisional event, reduces the time span of life’s emergence to between 600 and 200 million years.

timeline early Earth
Timeline of early Earth history from its formation as a molten, magma ball, through the hellish Hadean and into the Archean. Oldest direct fossil evidence of life is from stromatolites in rocks 3.7 billion year old and indirect chemical evidence of life comes from rocks around 4 billion year old and from graphite inclusions in zircon minerals 4.1 billion years old.

What is the significance of the suggested narrowing of the time it took life to emerge on Earth? The more rapidly life was established, the less difficult or improbable it would appear to be. The origin of life remains a major unknown. We know that early Earth likely had an enormous diversity of chemical compounds to work with including amino acids, which are the building blocks of all life today. But whether life was inevitable or even highly likely to come about is open to debate, because it remains unclear how these compounds became organised into self-replicating, evolving organisms. It could be that the emergence of life is simply too slow a process for us to replicate in the lab. Even the simplest of life forms, bacteria, involve an incredibly complex array of biochemical reactions and processes that would have taken time to evolve from the diverse pool of chemical compounds available. Although less than previously thought, several hundred million years is still a long span of time over which life could have gradually emerged.

It seems unlikely that the rock record will allow us to refine the timing much more or to push it back much further. Thus, the implied ease at which life can emerge on a place like Earth will perhaps have to wait for the discovery of life on another planet. Just what form life will take on other planets is unknown, but if at all like Earth, life is most likely to be dominated by diverse yet small, simple microbial organisms. Perhaps quick to get started, life on Earth appears to have remained fairly simple for a long period of time. It took around a billion years before the more complex eukaryotic cells evolved and another two billion years or so after that before animals evolved. The delay in the evolution of animals has been attributed to the need of an oxygen-rich atmosphere.  For the latest ideas on what may have controlled oxygen levels in the atmosphere and how the level became high enough for animals, check out my next blog update #6: First Animals.

Further reading

Allwood, A.C., 2016. Evidence of life in Earth’s oldest rocks. Nature 537, 500-501 (doi:10.1038/nature19429).

Bell, E.A., and others, 2015. Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon. PNAS 112, 14518–14521 (www.pnas.org/cgi/doi/10.1073/pnas.1517557112).

Dodd, M.S., and others 2017. Evidence for early life in Earth’s oldest hydrothermal vent precipitates. Nature 543, 60-64 (doi:10.1038/nature21377).

Hassenkam, T., and others, 2017. Elements of Eoarchean life trapped in mineral inclusions. Nature 548, 78-81 (doi:10.1038/nature23261).

Nutman, A.P., and others, 2016. Rapid emergence of life shown by discovery of 3,700-million-year-old microbial structures. Nature 537, 535-538 (doi:10.1038/nature19355).

Tashiro, T., and others, 2017. Early trace of life from 3.95 Ga sedimentary rocks in Labrador, Canada. Nature 549, 516-518 (doi:10.1038/nature24019).

© John S. Compton (www.johnscompton.com)


The first Australians

Update #4 to Human Origins: How diet, climate and landscape shaped us

John S. Compton (www.johnscompton.com)

Australia is home to some of our species’ most ancient roots outside of Africa. When the first of our human (Homo) lineage arrived in Australia has long been debated. Although early members of our lineage (Homo erectus, for example) were living nearby on the island of Java as early as 1.7 million years ago, it was only much later that humans entered Australia. Dated archaeological sites suggest that our species, Homo sapiens was the first to arrive by around 50 thousand years ago (50 ka) and that we had become widespread throughout the continent by 45 ka (Hamm and others, 2016). This chronology generally fits with the proposed timing of the ‘Great Expansion,’ when our species rapidly spread out of Africa around 60 to 50 ka and effectively conquered the world. Our species had earlier forays out of Africa prior to the Great Expansion, but these never appear to have amounted to much. In my book Human Origins I refer to those who left Africa prior to the Great Expansion as anatomically modern humans (AMHs) and those that left as part of the Great Expansion as people having cultures on a par with modern hunter-gatherers. Our species evolved in Africa 200 to 160 ka, but appears to have only slowly acquired cultures equivalent to modern hunter-gatherers between 100 and 70 ka while in Africa. This may explain, in part, why earlier exits were relatively unsuccessful: the Great Expansion had to wait until modern hunter-gatherers had emerged in Africa and their movement beyond Africa, in turn, had to wait until the Sahara-Arabian Desert became sufficiently green to let them out 60 to 50 ka. However, a recent study by Clarkson and others (2017) proposes that modern people had arrived in Australia by at least 59.3 ka and possibly as early as 70 ka. Such an early arrival of people in Australia would be at odds with the Great Expansion scenario.

Great expansion

Going global: possible pathways and timing of the Great Expansion, when modern people conquered the world.

The study by Clarkson and others revisited and expanded upon earlier work carried out at the Madjedbebe rock shelter located in northern Australia. From the lowest and oldest layers of human occupation they recovered over 10,000 artefacts that, in addition to an in place hearth, included many stone flakes, ground ochre (associated with mica), edge-ground hatchets and a grinding stone. The age of the deposit was determined by optically stimulated luminescence (OSL), a method by which the measured luminescence of many individual sand grains is related to the time it took for them to accumulate their luminescence from exposure to radioactivity in the surrounding sediment. The artefacts and their associated OSL ages establish that the sequence of layers at the site has not been significantly disturbed or mixed and indicate, quite convincingly, that our species was in Australia as early as 65±5 ka. Such an early arrival of modern hunter-gatherers is inconsistent with all other archaeological evidence indicating that the peopling of the Eurasian continent occurred between 55 and 45 ka.

A critical question is who were these first Australians? If they were part of one of the earlier waves of our species (AMHs) that expanded out of Africa between 130 and 80 ka, then there is no problem with the timing of their arrival. Instead, the potential problem is with their cultural artefacts, which appear to be inconsistent with those associated with earlier waves of our species out of Africa. On the other hand, if they were part of the exodus from Africa of modern hunter-gatherers that successfully filled the world, then the problem lies not with their artefacts but with the time of their arrival, which would appear too early relative to other sites. At this stage, the best explanation appears to be that the first to arrive were AMHs from an earlier exodus out of Africa that had developed some cultural artefacts similar to modern hunter-gatherers. Despite their cultural artefacts, these early arrivals in Australia, as elsewhere, appear to have had a limited presence in the archaeological record and were largely replaced by the later arrival of modern hunter-gatherers by around 50 ka as part of the Great Expansion.

The authors of the paper argue that those living at the Madjedbebe rock shelter were behaviourally modern people based on the presence of an edge-ground hatchet, a grinding stone and ochre (a red coloured pigment) mixed with highly reflective mica flakes. The use of ochre dates back to our predecessor species, already widespread in Africa by 230 ka. However, these earlier ochre occurrences are not associated with highly reflective mica flakes, for which the Madjedbebe site is the earliest known example. Ground hatchets and a grinding stone at the site may also be the earliest occurrences known, but the lack of fine stone tools (such as backed microlithic stone tools for spear or bow and arrow), along with art or jewellery (micaceous ochre aside) suggest that these earliest arrivals were perhaps not yet in possession of a complete modern hunter-gatherer culture.

Interpreting the significance of these artefacts is difficult because cultures evolve over time and can be lost. Loss of cultures may result if specific cultural items are no longer needed or if groups are too small to sustain them. There is evidence that humans living in Southeast Asia developed different cultures to those elsewhere in Eurasia, with a lack of stone tools in particular. The lack of stone tools may reflect their use of wood (bamboo), which is much less likely to be preserved than stone tools. There is evidence that those associated with the Great Expansion were innovative, using fire ash to detoxify yams and tree nuts by 46 ka in Borneo, as well as artistic, making some of the earliest cave paintings 40 ka on Sulawesi (Aubert and others, 2014). What the archaeological record suggests in Australia is that the first to cross over did not arrive with the typical modern hunter-gatherer toolkit but managed to reinvent it over time, with bone points appearing by 40 ka and backed microliths by 30 to 20 ka (Hamm and others, 2016).

If Homo erectus was already in Java by 1.7 Ma, why did it take so long for humans to cross over to Australia? The difficulty in reaching Australia is that it requires crossing over water to get there. This is true today as well as in the past when many of the islands were joined into one large landmass during periods of lowered sea level when ice sheets built up in the Northern Hemisphere. Homo erectus survived in Southeast Asia until around 300 ka. Some among them managed to cross narrow, calm seaways to reach the island of Flores, where they underwent island dwarfism to become the one-metre tall ‘hobbit’ (Homo floresiensis) who lived there until around 50 ka. But crossing the larger seaways required to reach New Guinea – Australia (collectively called Sahul) was apparently too great for earlier members of our lineage to manage. There is evidence that our species was living in Sumatra sometime between 78 and 58 ka, but unfortunately no cultural items were found associated with the fossil evidence (Westaway and others, 2017). Perhaps these were AMHs for an earlier exit and among those who the first to successfully navigate their way as far as Australia.


Humans could expand into Southeast Asia when sea level was lower (pale blue areas of Sunda) but had to island-hop their way through Wallacea to reach the connected landmasses of New Guinea and Australia (Sahul).

Therefore, it would appear that the first arrivals in Australia were AMHs from an earlier exit out of Africa. As elsewhere in Eurasia, the AMHs who arrived in Australia had a relatively subdued impact and were largely displaced by the later arrival of modern hunter-gatherers as part of the Great Expansion who reached Australia by around 50 ka. This Great Expansion scenario is supported by genetic studies which indicate that all people today outside of Africa descend from a single population that exited out of Africa and that they acquired DNA from intermingling with Denisovans and Neanderthals along the way between 53 to 45 ka. DNA studies of indigenous Australians (aborigines) indicate that those who arrived with the Great Expansion rapidly colonized the continent by 45 ka (Tobler and others, 2017). To whatever extent earlier expansions of our species may have taken place prior to the Great Expansion, none feature strongly in either the archaeological or genetic evidence, their existence appears to have been swamped out by the rapid peopling of the world during the Great Expansion. However, the earlier forays of our species out of Africa were perhaps not completely erased, with some genetic studies suggesting that a few percent of the DNA from these earlier expansions survives in modern populations (Pagani and others, 2016).


Further reading

Aubert, M., and others, 2014. Pleistocene cave art from Sulawesi, Indonesia. Nature 514, 223-227. doi:10.1038/nature13422

Clarkson, C., and others, 2017. Human occupation of northern Australia by 65,000 years ago. Nature 547, 306-310. doi:10.1038/nature22968

Gibbon, A., 2017. The first Australians arrived early. Science 357, 238-239. doi: 10.1126/science.357.6348.238

Hamm, G., and others, 2016. Cultural innovation and megafauna interaction in the early settlement of arid Australia. Nature 539, 280-283. doi:10.1038/nature20125

Marean, C.W., 2017. Early signs of human presence in Australia. Nature 547, 285-287.

Pagani, L., and others, 2016. Genomic analyses inform on migration events during the peopling of Eurasia. Nature 538, 238-241. doi:10.1038/nature19792

Tobler, R., and others, 2017. Aboriginal mitogenomes reveal 50,000 years of regionalism in Australia. Nature 544, 180-184. doi:10.1038/nature21416

Westaway, K.E., and others, 2017. An early modern human presence in Sumatra 73,000–63,000 years ago. Nature 548, 322-325. doi:10.1038/nature23452


© John S. Compton (www.johnscompton.com)

The first humans in America

Update #3 to Human Origins: How diet, climate and landscape shaped us
John S. Compton (www.johnscompton.com)


A recent study presents evidence that members of our human (Homo) lineage were in North America around 130 thousand years ago (Holen and others, 2017; Wade, 2017a). This is a shocking claim because it is more than 100 thousand years before the previously established timing of 14 thousand years ago for when humans first entered the Americas. This latest report is not the first to argue for a much earlier presence of humans in the Americas, but it provides by far the most compelling and best dated evidence yet.

The evidence consists of scattered mastodon bones lying immediately adjacent to several large stones. The bed in which the bones and stones occur were recovered from a 12-m-thick succession of river deposits discovered at a construction site near San Diego, California. The mastodon is a distant relative of elephants and was common in North America (along with the woolly mammoth and other large animals) up until people hunted them to extinction by around 12 thousand years ago. The authors of the study argue that the physical damage of some mastodon bones and associated stones indicate that the stones were used as hammerstones and anvils to break open the large mastodon bones. Breaking of the bones was done most likely to access the oozing, nutrient-rich marrow inside. The large stones were locally sourced but, oddly, none was modified or shaped in any way by removal of smaller stone flakes. Although no human bones were found at the site, it is assumed that humans were responsible because no other animal capable of smashing large mastodon bones with large stones is known to have lived at this time in the Americas.


Many of the large animals shown here (including the mastodon, upper right) became extinct soon after people arrived in North America 14 thousand years ago (human with spear for scale).

The site was determined to be 130.7 ± 9.4 thousand years old based on the decay of the radioactive element uranium contained within the bones. There was no organic carbon left in the bones to date using radiocarbon methods and the application of optically stimulated luminescence (OSL) indicated that the sediment at the site was deposited at least 60 thousand years ago. The age uncertainty of plus/minus nearly ten thousand years reflects, in part, the model assumptions made in using the uranium-series disequilibrium method. However, the uranium-derived ages appear to be robust and indicate that the deposit most likely formed sometime between 140 and 120 thousand years ago.

The lack of human bones, as well as any other stone tools or cultural artefacts besides the hammerstones and anvils, make it difficult to say which member of our human lineage was active at the site. It is certainly conceivable that members of our lineage living in Eurasia may have crossed over to North America when the Beringia land bridge was exposed. The Beringia land bridge today is flooded by the Bering Sea, but the lowering of sea level at times in the past was sufficient to expose the Bering Sea as a land bridge connecting Eurasia and North America. For example, the Beringia land bridge could have been crossed roughly 134 to 131 thousand years ago, within the age window of the mastodon site. Any humans living in eastern Siberia at that time may have made the journey across on foot without necessarily making use of boats.


Siberia was connected to North America periodically when sea level was lowered by major ice build up. Humans living in Siberia could have crossed over to North America either by boat along a coastal route or on foot overland through ice-free corridors.

The highly successful crossing 14 thousand years ago was part of the Great Expansion of behaviourally modern people who left Africa around 60 to 50 thousand years ago. There are numerous archaeological sites that show modern people had entered and become widespread throughout the Americas, reaching the southern coast of Chile by around 14 thousand years ago. The timing of initial entry into the Americas is thought to be mostly determined by when people living in the Far East and eastern Siberia could cross over the Beringia land bridge connecting Eurasia and North America during the Last Glacial Maximum when sea level was lowered in response to the build-up of major ice sheets. Passage into North America from Beringia was delayed until the large ice sheet blocking the way had started to melt back with the onset of warmer climates 18 to 14 thousand years ago. There was a relatively brief window to pass over the land bridge before it was flooded by the rising sea as the ice sheets quickly melted. Most are sceptical that humans had crossed over before 14 thousand years ago, with the current debate centred on when people crossed over, where they came from and whether they travelled by canoe along a coastal route or overland on foot through ice-free corridors that opened as the large Laurentide ice sheet melted back (Wade, 2017b).

It is not too far-fetched that some of our ancestors living in Eurasia might have crossed over to the Americas much earlier than the well-documented crossing of people by 14 thousand years ago. This is because the Beringia land bridge was repeatedly exposed as Earth cycled through glacial and interglacial periods over the last million years. Any of our ancestors adapted to living at relatively high latitudes may have inadvertently crossed over Beringia in pursuit of game and, once across, they could expand and fill the virgin American landscapes.

SL and Beringia

Sea-level cycles over the last million years and the periodic exposure of the Beringia land bridge in the transition from glacial to interglacial periods when animals (including humans) may have crossed over to North America (brown columns). The mastodon archaeological site reported from southern California implies humans crossed over sometime prior to 134 to 131 thousand years ago during the MIS 6 glacial to MIS 5 interglacial transition (third brown column on the right) when Neanderthals and Denisovans, but probably not our species (Homo sapiens) or the ‘hobbit’ (H. floresiensis), were living at high latitudes in Eurasia.

Could it have been our species, Homo sapiens, who crossed over? This seems unlikely because, although our species had appeared in Africa by around 200 to 160 thousand years ago, the earliest evidence of when we left Africa is 131 to 113 thousand years ago (MIS 5). After crossing over, our species appears to have largely been confined to the Middle East region. There is, as yet, no evidence that they had expanded into Siberia as early as when the Beringia land bridge to the Americas was exposed 134 to 131 thousand years ago. So, if not our species, then what other member of our lineage may have crossed over prior to 140 to 120 thousand years ago?

We know that Neanderthals, Denisovans and the ‘hobbit’ (Homo floresiensis) were all living in Eurasia at this time. Homo erectus were widespread throughout Eurasia even earlier, but do not appear to have lived at high enough latitudes, above 40°N, to have crossed over the Beringia land bridge located at latitudes above 55°N. The ‘hobbit’ is only known from the Indonesian island of Flores where it lived from 700 up until 50 thousand years ago, whereas Neanderthals and Denisovans are known to have lived at high latitudes, including Siberia. However, it is unclear which of the two crossed over the Beringia land bridge because the only stone tools (hammerstones and anvils) yet to be recovered from the site are not shaped in any way. Almost all contemporaneous stone tools documented in Eurasia (and Africa) were intentionally shaped by the removal of stone flakes. The lack of shaped stone tools is an unusual, and difficult to comprehend, aspect of the mastodon site.

Another surprising aspect about the mastodon site besides its lack of shaped stone tools, is that there has been so little convincing evidence of an earlier human presence in the Americas before now. If humans did managed to cross over, then it is predicted that they would have rapidly spread into the virgin landscapes, landscapes never before occupied by humans and full of large animals relatively easy to hunt. The Americas are two enormous continents no more difficult for humans to thrive in than Eurasia. So why are traces of humans living there so difficult to see in comparison to the record in Eurasia? Has the abundance of archaeological sites younger than 14 thousand years old obscured older, less abundant evidence? Perhaps if people dig a bit deeper and consciously look for it, an older record of humans in the Americas will be revealed. Now that the first compelling site has been discovered, perhaps more will follow.

Further reading

Holen, S. R., and others, 2017. A 130,000-year-old archaeological site in southern California, USA. Nature 544, 479–483. doi:10.1038/nature22065

Wade, L., 2017a. Claim of very early humans in Americas shocks researchers. Science 356, 361. doi: 10.1126/science.356.6336.361

Wade, L., 2017b. On the trail of ancient mariners. Science 357, 542-545. doi: 10.1126/science.357.6351.542

© John S. Compton (www.johnscompton.com)



Surprisingly young age of the Homo naledi fossil site


Update #2 to Human Origins: How diet, climate and landscape shaped us

The age of the fossil-rich Homo naledi fossil site within the Rising Star cave system in the Cradle of Humankind World Heritage Site near Johannesburg, South Africa was frustratingly unknown until recently. The exceptionally large number of fossil bones scattered on the cave floor proved difficult to date, but an international team of scientists has applied several dating techniques (optically stimulated luminescence, uranium/thorium and palaeomagnetism) to constrain the age of the deposit to between 414 and 236 thousand years old (Dirks and others, 2017). This age is supported by the estimated age of several fossil teeth from the deposit, independently dated to between 335 and 183 thousand years old using a combination of uranium series and electron spin resonance (US-ESR) methods. The US-ESR methods directly date the fossils, but rely on a number of complex model assumptions that result in a large amount of uncertainty. Although not terribly precise, these ages are considered fairly robust and are surprisingly young for fossils whose features (or traits) suggest that they are much older. Prior to the age determinations, many estimated that the fossils, given their mix of australopith and early Homo features, would date to around when our genus Homo first appeared in the fossil record between 3 and 2 million years ago (Ma). How, then, is such a young age explained for fossils that retain so many old features?

A mosaic of features

One of the striking aspects of the Homo naledi fossils is the odd mix or mosaic of features they display. The amazingly rich fossil find from the Rising Star cave system includes a total of over 1500 bones from the Dinaledi Chamber alone (Berger and others, 2015), with more bones recently discovered in the separate Lesedi Chamber (Hawks and others, 2017). All of the bones recovered from both caves are considered to belong to Homo naledi and comprise a minimum of 15 individuals. Such a large number of bones provides a fairly complete skeleton of Homo naledi who stood 1.4-1.6 m high and weighed 40-55 kg. One of the most notable features is the small size of the skull, having an interior volume (endocranial capacity) of between 460 and 610 cc. This range in volume is based on three skulls and is intermediate between the mean skull size of the australopiths and the earliest Homo species for which skulls are available that date to around 2 Ma. Such a small skull suggested that Homo naledi represented one of the earliest members of our genus Homo, which branched from the australopiths around 2.8 to 2.3 Ma, based on fossil teeth and jaws from East Africa (Villmoare and others, 2015). In contrast, its foot shares many features similar to ours. Comparing Homo naledi to other species is difficult to do because for most other species there are simply not enough fossil bones to compare. However, overall, Homo naledi much more closely resembles early Homo (H. habilis and H. erectus) than it does us (H. sapiens) or our predecessor species (‘archaic’ H. sapiens). The close resemblance to early Homo suggested to many that the age of the deposit would be similar in age to when early Homo appeared circa 2.5 Ma and not the reported age of less than 0.5 Ma.

Hawks et al 2017 H naledi skull   Hawks et al 2017 H naledi endocranial LES1

Skull of Homo naledi (LES1) from the Lesedi Chamber (scale bar 5 cm) and the digital reconstruction of the endocranial volume of 610 cc, scale sphere is 10 mm (Hawks and others, 2017).

The most likely explanation is that Homo naledi represents one of the earliest members of our Homo lineage and that it managed to retain many features of early Homo up until at least 414 to 236 thousand years ago. While retaining many of its early features, it also appears to have acquired features that closely resemble later features, which either evolved independently (convergent evolution) or were acquired through interbreeding (hybridization) with other, later-evolved Homo species (but probably not our species, which only appeared by around 200 to 150 thousand years ago).

What is remarkable is that Homo naledi persisted for so long in a region occupied by other, later-evolved Homo species. For example, the skull from the Florisbad fossil site is thought to represent our predecessor species and was likely contemporary with Homo naledi, the two living within several hundred kilometres of one another. One possible explanation of their co-existence is that they occupied distinctly different habitats. Although their feet and aspects of their hands are similar to ours, Homo naledi’s fingers are curved. Curved fingers suggest that they were adapted for living in and moving about in trees. Therefore, they may have resided within heavily treed habitats, such as forest canopies, whereas our predecessor species was living primarily in more open grassland and savannah habitats. Although such niche partitioning may explain the co-existence of different species of Homo, it is remarkable that a species with so many early features, including such a small brain, managed to survive until just prior to when our species Homo sapiens evolved onto the scene.

Hangers on

Homo naledi is not the only member of our Homo lineage who managed to persist over such a long period of time. Homo erectus, for example, managed to survive in Asia long after they had become locally extinct in Africa, surviving up until around 300 thousand years ago in China and Java. And, in many respects, the suite of unusual features of Homo naledi reflect those of Homo floresiensis, the ‘hobbit”, which also retains features of early Homo (H. habilis and H. erectus) and lived up until just 50 thousand years ago on the island of Flores (Sutikna and others, 2016). The persistence of H. floresiensis on the somewhat remote island of Flores seems more plausible than a group within the African continent, but perhaps this reflects the fact that groups in Africa were adapted to specific habitats that effectively isolated them from other groups. Population densities were likely low and, along with the diversity of habitats, may have facilitated the survival of earlier groups for long periods of time. More recently evolved species might have been widely dispersed in part because of their big brain, sophisticated tools and control of fire, but were perhaps spread thinly enough over the landscape to have permitted pockets of earlier evolved groups to hang on. What the hobbit and Homo naledi seem to indicate is that among the more recently evolved members of our lineage, older groups managed to persist, either within distinct habitat or niche holdouts  ̶  perhaps culturally as much as physically isolated from other groups. The fossil record is so limited it may have hidden from us or we may have tended to underestimate the amount of variability in features, such as brain and body size that existed in the past.

Homo naledi culture?

Typically an archaeological site has hundreds to thousands of stone artefacts but very few if any fossil bones of those who made the artefacts. And whether or not any bones of the makers of the stone tools are found, it is common to find the bones of other animals at many archaeological sites. Hence, the Rising Star cave sites present the most unusual case: many bones of Homo naledi not in association with any stone tools or other cultural artefacts, nor any other large animal bones. Hence, although we know a lot about what Homo naledi looked like, we have very little idea of what they made or what other animals they lived among.

This lack of context makes it difficult to know much about the habitat in which they lived and how they lived. They most clearly did not live in the deep caves where they ended up as fossils. It is conceivable that they fell into or were washed down into the caves through surface openings connected to deep cave chambers. But in that case we would expect other large animals to have fallen in or been washed into the caves along with them. Some have proposed that they were intentionally disposed of into cave openings and that this disposal may indicate a type of ritual burial (Berger and others, 2017). Ritual burial is a cultural behaviour that has so far only been associated with our species, with the earliest hints (mortuary defleshing) dating to around 160 thousand years ago, and proper burials with grave goods not until around 100 thousand years ago. It is possible they disposed of their dead into the caves as a form of good housekeeping, but it is hard to imagine that small-brained Homo naledi had the mental ability to practice ritual burials, and evidence to substantiate ritual disposal into the caves remains lacking.

The complete absence of stone tools makes it difficult to know what stone tools, if any, were used by Homo naledi. They possess the wrists and hands capable of making and using stone tools, but did they? The age of the site falls within the Middle Stone Age (MSA), a time of regionally diverse stone tool industries throughout Africa. Some have suggested that Homo naledi may have been the maker of some of these stone tools (Berger and others, 2017), but so far there is no direct evidence to support this idea. The appearance of stone tool use has been dated as far back as 3.3 Ma and associated with australopiths having brains similar to or smaller sized than Homo naledi, but these early stone tools are a far cry from the diversity and sophistication of MSA stone tools that existed throughout much of Africa by 300 thousand years ago. Hopefully future finds of Homo naledi in association with cultural artefacts will shed some light on where and how they lived.

Lomekwian tool           MSA tools across Africa

A 3.3 Ma Lomekwian stone tool (left; Harmand and others, 2015) and regionally diverse MSA stone tools throughout Africa 300-100 thousand years ago (right).

Further Reading

Berger. L., and others, 2017. Homo naledi and Pleistocene hominin evolution in subequatorial Africa. eLife 2017;6:e24234. DOI: 10.7554/eLife.24234

Berger, L., and others, 2015. Homo naledi, a new species of the genus Homo from the Dinaledi Chamber, South Africa. eLife 2015;4:e09560. DOI: 10.7554/eLife.09560

Dirks, P., and others, 2017. The age of Homo naledi and associated sediments in the rising star Cave, South Africa. eLife 6:e24231. doi: 10.7554/eLife.24231

Harmand, S., and others, 2015. 3.3-million-year-old stone tools from Lomekwi 3, West Turkana, Kenya. Nature 521, 310–318.

Hawks, J., and others, 2017. New fossil remains of Homo naledi from the Lesedi Chamber, South Africa. eLife 6:e24232. DOI: 10.7554/eLife.24232

Sutikna, T., and others, 2016. Revised stratigraphy and chronology for Homo floresiensis at Liang Bua in Indonesia. Nature 532, 366–369.

Villmoare, B., and others, 2015. Early Homo at 2.8 Ma from Ledi-Geraru, Afar, Ethiopia. Science 347, 1352–1355.

New ages from Jebel Irhoud, Morocco

Update #1 to Human Origins: How diet, climate and landscape shaped us

John S. Compton

The date

New fossil finds and a better constrained age for the Jebel Irhoud fossil site in Morocco shed new light on our evolution. The new ages indicate that the site is approximately 315 thousand years old (315 ka), or nearly twice as old as the previous estimated age of 160 ka for the site. The new, older age was obtained by applying the thermoluminescence dating method, which estimates the amount of time lapsed since stone flint tools found from the same layer as the fossil bones had been heated by fires made by those living at the site. The thermoluminescence method measures the amount of light given off by the stones tools (the amount of luminescence) as they are heated to higher temperatures. The idea is that the fires at the site were hot enough to completely erase any luminescence trapped in the stones. Once cooled, and so long as they were never exposed to the heat of a fire again, the stones gradually accumulated stored luminescence through time from natural radiation received from the surrounding sediment. The present-day background radiation dose of the deposit was measured from where the stone tools were recovered and was assumed to have remained more or less constant back through time. Heating of the stone flints in the lab causes the stored luminescence to be released, and the amount released could be measured. Dividing the total released luminescence by the radiation dose rate measured at the site allows an age to be calculated.

Luminescence dating, both thermoluminescence and optically stimulated luminescence (or OSL), has revolutionized our ability to date archaeological sites beyond what was previoulsy limited to the last 50 thousand years by the radiocarbon method. The drawback to luminescence dating is that it too has limits in how far back it can reach because the amount of luminescence that can accumulate is limited. Once the stones have acquired maximum luminescence they can acquire no more, making it difficult to apply the method to samples older than 200 ka. So, the new age determined at Jebel Irhoud by thermoluminescence in excess of 300 ka is remarkable.

The other drawback with the thermoluminescence method is that the dates are not nearly as precise as those obtained by the radiocarbon dating method. The weighted average age of 14 samples from the fossil-bearing layer at Jebel Irhoud is 315 ka, but this age is associated with a fairly large uncertainty, with a 68% probability that the age of the site is between 349 ka and 281 ka, and a 95% probability that the age of the site is between 383 ka and 247 ka. The age range of 383 ka to 247 ka is consistent with both the range in age of a human tooth recovered from the site determined by a different method known as electron spin resonance (a far more complicated method than thermoluminescence that I will not try to explain here), and the known age ranges of fossil animals found at the site. Therefore, although not terribly precise, the new age is a huge improvement on previous ones for the site and, as we shall see, the new age provides valuable insights into the interpretation of the Jebel Irhoud fossils and their possible connection to other fossil sites in Africa.

The fossils

The Jebel Irhoud site has yielded a rich human fossil assemblage comprising skulls, jaws, teeth, leg and arm bones from at least five individuals, including a child and adolescent. Although the original location of all the fossils is not known, they are all assumed to have come from the same layer at the site associated with the new date of circa 315 ka. The face, jaw and teeth are considered to be similar to our own, although the jaw and teeth are unusually large, and the size of the browridge is variable. The most significant difference appears to be in the shape of the skull, being lower in height and more elongate (less bulbous) than ours (see figure below). The features of the skull resemble those of other skulls of similar age, such as the 260 ka skull from the Florisbad site in South Africa. These differences in the shape of the skull suggest that those living at Jebel Irhoud, and more broadly throughout Africa from around 330 to 230 ka, were not yet fully us (Homo sapiens).

The line of descent in our Homo lineage is thought to be from early Homo species (Homo habilis, for example) to Homo erectus to Homo heidelbergensis to our predecessor species, and finally, to us Homo sapiens. As I discuss in my book, the range of variations within a species and the complexity of speciation in a large continent such as Africa, makes it difficult from the limited number of fossils available to delineate species clearly. Some experts, the ‘lumpers’, view the changes in our lineage as gradational and refer to the Jebel Irhoud fossils as ‘archaic’ Homo sapiens. Other experts are ‘splitters’ and argue for stepwise evolution of distinct species. I believe there are enough physical differences and culture differences (see below) to support an intermediary species in the evolution of H. heidelbergensis to H. sapiens, an intermediary species that would take the place of the lumpers’ archaic Homo sapiens. However, this intermediary species lacks a generally accepted species name, and so I refer to it as our ‘predecessor’ species.

To my view, the new age indicates that the fossils at Jebel Irhoud represent some of the earliest members of our predecessor species and not, as implied by many of the news stories, that our species Homo sapiens now has an age range that extends back to around 300 thousand years. The oldest yet recovered fossils of our species Homo sapiens, ones that represent anatomically modern humans (AMHs) remain those found in East Africa that date to between 200 ka and 150 ka. The earliest members of our species most probably descended from our predecessor species, who were widespread throughout Africa by around 280 ka as represented by the fossil skulls found at Jebel Irhoud in Morocco, Florisbad in South Africa and Laetoli and Ileret in East Africa.

predecessor skulls.pngFossil skulls dated between 315 and 260 thousand years old that are possibly representative of our predecessor species intermediate between H. heidelbergensis and H. sapiens (from left to right: Florisbad, Laetoli (Smithsonian Institution) and Jebel Irhoud (Natural History Museum, London)).

Herto 1.png   Herto 2.png  modern skull 1.png  modern skull 2.png

Fossil skulls of our species Homo sapiens from 160 thousand years ago (Herto, two images on left; photos by David Brill (humanoriginsphotos.com)) and modern (two images on the right). Our species is largely defined by its bulbous shaped skull.


Cultural differences

The arrival of our predecessor species is associated with the major transition from the Earlier Stone Age to the Middle Stone Age (MSA), a transition marked by smaller, more regionally-diverse stone tools. Jebel Irhoud is now the oldest site known having a direct association of fossils with MSA tools. MSA tools are widespread throughout Africa from around 300 ka to 230 ka, but most often not associated with human fossil remains. Some of the MSA stone points recovered from Ethiopia have been interpreted from their edge damage to have been used as thrown spears by at least 279 ka. The stone points from Jebel Irhoud have not yet been interpreted as having been thrown as spears (javelins). Those living at Jebel Irhoud were competent hunters based on the animal bones found. It may be that they made effective use of sharpened wooden spears without stone armatures, something their predecessor Homo heidelbergensis was doing.


spear tips.png    San throwing.png

Obsidian projectile spear tips from Ethiopia dating to at least 279 ka (Sahle et al., 2013) and a photo of a !Kung San throwing a spear (photo courtesy of Neil Roach).


The presence of burnt bones and charcoal suggests they had control of fire. However, they do not appear to have used fire to intentionally heat the stones (pyrotechnology). The earliest evidence for intentional heating of stones to improve their work-ability dates from 164 ka at the Pinnacle Point site in South Africa, presumably made by H. sapiens. Heating was probably not necessary in the case of the raw stone material available at Jebel Irhoud and the heating of about a third of the stone tools there was likely because they inadvertently ended up beneath where later fires were made.

The other cultural artefact to appear for the first time in the MSA is ochre, an iron-rich rock used for, among other things, symbolic body painting based on the specific collection of the reddest coloured stones. The earliest use of ochre is in East Africa, but no ochre has been reported from the Jebel Irhoud site. The absence of thrown stone-tipped spears and ochre at Jebel Irhoud may indicate that these cultural innovations were only developed later among groups of our predecessor species. Alternatively, these cultural items may have been present among groups in sub-Saharan Africa but were lost by groups too small to sustain these cultures after they had expanded into North Africa where soon became isolated from other groups.

ochre.png  ochre powder.png

Ochre stones and grinding ochre into a red powder.


Speciation events

Do the fossils at Jebel Irhoud suggest that the geographical region of origin of our predecessor species was North Africa? I argue in my book that the Maghreb, located at the northernmost tip of Africa was a potential geographical region of origin for species within our human lineage. This was based primarily on the periodic isolation of the Maghreb, separated from the rest of Africa and Eurasia by the Sahara-Arabian Desert and the Mediterranean Sea. Relatively small groups living in isolation in the Maghreb over long periods of time may have evolved away from other groups. These substantial physical barriers would have made exchange highly unlikely, except during relative brief periods when the Sahara-Arabian Desert ‘greened’ by receiving enough rainfall for the transformation of the desert into grassland and lakes.

These greening events may have made it possible for the periodic mixing of previously isolated groups living in the Maghreb, sub-Saharan Africa and Eurasia. We know the Sahara-Arabian Desert greened most recently 9 to 6 ka, with large impacts on the movement and interaction of people throughout the region. There is also good evidence of widespread greening 130 to 120 ka go associated with the movement of our species out of Africa into the Levant, and possibly into North Africa as indicated by the first appearance there of distinctive Aterian stone tools. What the groups represented by Jebel Irhoud fossils had evolved into by the time of the 130 ka greening event and to what extent they may have intermingled with Homo sapiens coming from sub-Saharan Africa is unknown. There were other greening events, such as the one associated with when modern people left Africa as part of the Great Expansion 60 thousand years ago, but the timing and extent of past greening events remains poorly known.

The interglacial period that occurs within the dated range of the Jebel Irhoud fossil site of 383-247 ka that is most likely to have had a significant greening event is Marine Isotope Stage (MIS) 9  ̶̶   roughly 330 ka. The fossils at Jebel Irhoud may represent early members of our predecessor species who evolved there among small, isolated populations of H. heidelbergensis and then spread out into the African continent with the greening of the Sahara associated with the MIS 9 interglacial period. Alternatively, our predecessor species may have evolved from H. heidelbergensis somewhere in sub-Saharan Africa and moved into the Maghreb during the MIS 9 or another greening event. Unfortunately, the age resolution of archaeological sites and number of sites are not sufficient to determine at this stage where in Africa our predecessor species evolved.

MIS 9.png

Ochre, javelins and diverse Middle Stone Age regional cultures are associated with the evolution of our predecessor species from H. heidelbergensis in Africa. The age range of 383-247 ka of the Jebel Irhoud site places it around the time of the MIS 9 Interglacial period when a greening of the Sahara may have allowed movement of groups living in North Africa and sub-Saharan Africa.


What we know from the dated MSA stone tool assemblages in North Africa, East Africa Rift Valley and South Africa is that our predecessor species was widespread throughout Africa by around 280 ka, but from which of these areas they evolved into us Homo sapiens remains unresolved. In my book I suggest that the currently available information favors South Africa as our species’ geographical region of origin  ̶̶  check it out and see if you agree.


Further Reading

Richter, D. et al., 2017. The age of the Jebel Irhoud (Morocco) hominins and the origins of the Middle Stone Age. Nature http://www.nature.com/doifinder/10.1038/nature22335.

Hublin, J.-J. et al., 2017. New fossils from Jebel Irhoud, Morocco and the pan-African origin of Homo sapiens. Nature http://dx.doi.org/10.1038/nature22336.

Stringer, C. and Galway-Witham, J., 2017. On the origin of our species. Nature 456, 212-214.

Gibbons, A., 2017. Oldest members of our species discovered in Morocco. Science 356, 993-994. [doi: 10.1126/science.356.6342.993]

Compton, J.S., 2016. Human Origins, How diet, climate and landscape shaped us. Earthspun Books, www.johnscompton.com.

Sahle Y., Hutchings W.K., Braun D.R., Sealy J.C., Morgan L.E., et al., 2013. Earliest stone-tipped projectiles from the Ethiopian Rift date to >279,000 years ago. PLoS ONE 8(11): e78092. doi:10.1371/journal.pone.0078092.



First and forever a microbial world

They are so small, we rarely give them a thought and yet they are out there in numbers too enormous for us to comprehend. In fact, they are estimated to constitute no less than half of the total mass of all life on Earth. So, when you next look out over the landscape covered by plants and teeming with insects, birds and animals, think of the roughly equivalent mass of life that you don’t see. This invisible other half of life is the microbial world, made up of a great variety of microorganisms, so called because they typically measure only 0.5 to 5 micrometres across (that is about one-thousandth to one-hundredth the width of the 0.5 millimeter sized dot atop the letter i).  Although they are nearly everywhere, to see them requires a microscope (although some exceptionally large species are visible to our naked eye, such as Thiomargarita namibiensis, which lives by accumulating spheres of elemental sulphur in its elongate cells in shelf sediments offshore Namibia in southwest Africa).

For what they lack in size, microorganisms make up for by their ubiquitous multitudes: 10 to 1000 billion in every teaspoon of soil, a billion or so in every 20 drops (one millilitre) of water, and each of us hosts on the order of 40,000 billion microbes thriving inside our body and out. Microbes have evolved to eke out a living in nearly every habitat on Earth, even those we don’t normally associate with the living world: kilometres below the surface in deep rock fractures, and deep below the surface of massive ice sheets. Microbes can even survive in the vacuum of space, and include those left behind on the Moon by astronauts (most likely in a dormant, resting state). We tend to consider microbes as dangerous and something to kill off indiscriminately with antibiotics and disinfectants. Although some are pathogens, most microbes are benign and many others beneficial, if not essential to our well-being. We are only beginning to appreciate the roles played by the highly diverse microbes that thrive in our gut, our mouths and in every nook and cranny of our skin.


The bacteria Staphylococcus aureus (colourised from CDC/Matthew J. Arduino, DRPH/Photo Credit: Janice Haney Carr, scale bar is 1 micrometre).


Escherichia coli (E. coli) bacteria (credit: NIAID, each around 2 micrometres long)

Microorganisms are unicellular, with each individual consisting of a single cell whose features are either relatively simple or complex. Those with generally small, simple cells are referred to as prokaryotes and include two main groups: bacteria and archaea. Their simple cells contain a single, circular loose strand of DNA along with ribosomes housed within a cell wall and membrane. Those with generally bigger and more complex cells in which the DNA occurs tightly coiled within a separate nucleus enclosed by a membrane and, along with ribosomes, contain organelle structures are referred to as eukaryotes. The eukaryotes are thought to have evolved from the merging of different prokaryotes. For example, mitochondria organelles, which act as the energy furnace within eukaryotes, were once separate bacteria that were at some stage taken in by and subsumed by archaea. Bacteria and archaea evolved by around 3.5 billion years ago, while the eukaryotes only evolved later by around 2 to 1.5 billion years ago.  The evolution of eukaryotes was critical to the eventual evolution of all the big, visible organisms like plants and animals whose many cells are eukaryotic.


Even magnified under a microscope, the many different species of bacteria and archaea can be difficult to tell apart. Some species have many tiny hair-like cilia or long thread-like tails (flagella) to whip them about (see photo top from http://www.cdc.gov/ecoli/), while others can bind together to form filaments or thin-film colonies. But most individual cells are either spherical to elongate in shape and difficult to tell apart from outward appearances. And this partially explains why archaea were only recently appreciated as being different from bacteria. One way to tell them apart is by what they do chemically, for bacteria and archaea are extremely versatile in the ways in which they metabolise. Some reduce carbon dioxide to methane, others fix nitrogen into nitrate while others convert nitrate to nitrogen, some oxidize sulphur to sulphate while others reduce sulphate to sulphide, and so on…each occupying the chemical niche best suited to their way of life. In essence, bacteria and archaea run most global elemental cycles at Earth’s surface, accelerating the pace of chemical reactions so vital to all life forms big and small. Just how many species there are remains largely unknown, but the application of genetics has facilitated our ability to identify them, with thousands of species typically analysed within any given soil or water sample.


No sex please, we are prokaryotes! Bacteria and archaea reproduce by binary fission, where an individual makes an identical copy of itself and splits into two – a parent and its clone. They can also take up bits of DNA of interest that happen to be floating about in their surroundings or they can transfer specific bits of DNA among themselves. Such horizontal or lateral transfer of DNA helps them adapt to changes and to survive stressful times. They can also shut down and stay holed up as microbial cysts until better conditions return, even if that means remaining dormant for centuries or perhaps millions of years. Although microbes living today are probably not terribly different from the first of their kind that appeared 3.5 billion years ago, they can evolve rapidly. For example, so-called ‘superbugs’ evolve in hospitals by surviving the continuous onslaught of antibiotics and disinfectants.

Being the first to live on Earth, bacteria and archaea form the two deepest domains of life, and they are the life forms most likely to endure. Their small size, widespread distribution, genetic diversity and ability to shutdown make them far more likely than other organisms to survive whatever future catastrophes come along. As long as Earth is capable of supporting life it will always include a microbial world. In this sense, the meek shall inherit the earth, if the meekest among us are the smallest and simplest microorganisms. And if life exists on other Earth-like rocky planets orbiting within the wet and warm habitable zone of their stars, it too will most likely be microbial. When considering the abundance and amazing chemical promiscuity demonstrated by the element carbon on Earth, it seems reasonable to conjecture that microbes on other rocky planets are likely to be similar in many respects to our own. It is partly for this reason that we must take every precaution not to contaminate other worlds if we hope to determine unambiguously if life exists elsewhere.

©John S. Compton (www.johnscompton.com)       Earthspun logotan

Origin of life

How did life first came about? Our planet started out as a molten magma ball too hot for life, but the oldest fossils indicate that life was established soon after Earth had cooled sufficiently to be covered by oceans of water suitable for life. Evolutionary theory allows us to understand how life, once arrived, diversified over deep geological time into the abundant life forms we observe today. However, how life first evolved on Earth remains largely unknown. We have only ever observed life to spring from existing life, and we have yet to find convincing evidence that life exists elsewhere beyond our planet. And although we have extensively modified the DNA of existing organisms, including the synthesis of a simple microbe ( C. A. Hutchison III et al., Science 351, aad6253 (2016). DOI: 10.1126/science.aad6253), we have yet to synthesis life from scratch, from its basic organic molecular building blocks such as amino and nucleic acids.

All the diverse life forms on Earth today, including us, appear to be ultimately related to one another and to share a common ancestor. This gives rise to the concept that ‘all life is one,’ which stems from the fact that all life is based on DNA and RNA, the double and single helical molecules that contain the code of life. Similarities in genetic DNA and RNA make-up, as well as the many shared biochemical processes across many different organisms, suggest that we and all other life forms descend from a distant common ancestor. This shared great-great-greatest of grandparents to everything that is living today is known as life’s Last Universal Common Ancestor, or ‘LUCA’ for short.

Charles Darwin commented on this profound concept that ‘all life is one’ in his book On the Origin of Species, published in 1859:

‘It is a truly wonderful fact – the wonder of which we are apt to overlook from familiarity – that all animals and all plants throughout all time and space should be related to each other…Therefore I should infer from analogy that probably all the organic beings which have ever lived on this earth have descended from some one primordial form, into which life was first breathed.’

LUCA is Darwin’s ‘primordial form into which life was first breathed’ and from which all life forms on Earth descended. Hence, the myriad species we see today are each from a long line of descent that includes many now extinct ancestors over the eons of deep geological time and which converge all the way back to LUCA.

There have been many ideas put forth on where and how did LUCA evolved, but the upshot is we do not know. What we do know is that LUCA must have evolved sometime between when Earth had first become habitable (4 to 3.8 billion years ago) and the oldest fossil life forms yet found in rocks 3.4 billion years old.


The earliest fossil evidence of life on Earth comes from organic structures such as these observed in thin slices of rock 3.4 billion years old from Australia and South Africa (image 0.16 mm across, courtesy of Ken Sugitani; K. Sugitani, and others, 2015. Early evolution of large micro-organisms with cytological complexity revealed by microanalyses of 3.4 Ga organic-walled microfossils. Geobiology DOI: 10.1111/gbi.12148)

These oldest fossils reveal the overall cell morphologies, but tell us little about the biology of these early organisms. However, they are generally assumed to be representative of the simplest single-celled microorganisms living today. But even the simplest bacteria today include many complex organic structures (DNA, RNA and ribosomes) and intricate biochemical processes that occur within their cell-wall structures. Our general understanding of evolution suggests that the complex biology represented by these fossil organisms evolved gradually over the hundreds of millions of years available from the modification of existing, simpler structures. These first organic structures were not in themselves living entities, but they may have nevertheless evolved as molecules by way of random mutations and natural selection in much the same way that Darwin proposed species do today. These selective forces may have promoted the merging of different ‘molecular species’ in ways that enhanced their mutual stability and replication in what could be viewed as a continuum leading up to the first bona fide life forms, out of which LUCA would evolve to give rise to all life as we know it.

Earth’s surface had an abundance of all the elements necessary for life: carbon, nitrogen, oxygen, phosphorus, etc. It also included organic compounds, such as amino acids, sugar and sugar alcohols, either formed naturally on Earth or delivered by meteorites. Besides water, life forms are mostly made up of amino acids organized into many different proteins, which are the large, complexly folded, three-dimensional organic compounds that make up our blood, muscles, skin, hair, etc. Amino acids existed before life, but how did they become organized into complex proteins under the direction of DNA and RNA housed within cellular membranes?

One idea is that early organic compounds may have included simple, self-replicating molecules, with those that replicated the fastest or most accurately persisting instead of perishing. Gradually, compounds as complex as small RNA-type molecules may have emerged whose information-storage capabilities could code for different amino acids in the production of proteins essential for a broad spectrum of biochemical functions. For example, phospholipid protein molecules capable of forming impermeable bubbles may have been precursors to cell membranes providing barriers to the outside world. Over time, incremental Darwinian selection led to improvements in replication and the coordinated merging of different organic structures and protein enzymes into the first simple cellular ensembles capable of extracting energy to grow, replicate and evolve, which in a nutshell is what life does. Of course, much of the above generalized scenario is highly speculative and we are a long way from understanding the many intricate processes by which life arose on Earth.

Where on Earth might life have first evolved? A likely ‘primordial soup’ from which life was concocted is in the vicinity of volcanic hot springs located along the axis of the mid-ocean ridge mountain chain in the deep, dark ocean. These volcanic hot springs are called ‘black smokers’ (see image below), because they spew turbulent smoke-like billows of black sulfide particles through mounds and chimney-like columns. The mid-ocean ridge represents the most recently formed oceanic crust. The large temperature contrast between the newly emplaced, hot crustal rocks and cold, overlying seawater drives the intense circulation of seawater through the oceanic crust. Hot, altered seawater is eventually shot back out into the sea via black smoker vents. These and other ocean vents are home to thriving communities of organisms, such as tube worms, clams and shrimp. At the base of the vent food chain are chemosynthetic microbes, which derive their energy from chemical reactions associated with the vents rather than from sunlight energy as do algae and plants living today in the sunlit uppermost surface of the ocean. Support for a black smoker origin of life comes from the fact that some of the most primitive microbes (archaea) live there today in waters as hot as 113°C.


NOAA Ocean Explorer: Okeanos Explorer: Galapagos Rift Expedition

Is this where life began? Hydrothermal (hot water) vents, such as this one on the Galápagos Rift mid-ocean ridge, are host to a diverse community of organisms (mostly white and red tube worms in the photo above). The vibrant vent community ultimately exists from the energy available from chemical reactions. Some of these reactions are expressed in the precipitation of the dark sulfide minerals that give ‘black smokers’ their name.  (photo from NOAA PMEL Vents Program; source: http://oceanexplorer.noaa.gov/okeanos/explorations/ex1103/logs/july20/media/tubeworms_smokers.html)


The mid-ocean ridge forms a long, continuous submarine mountain chain (red) along which black smokers and other vent systems occur. Early Earth is likely to have included a mid-ocean ridge with black smokers, with the continents only forming later.

We don’t know how many variations on early life there were before LUCA had evolved. In fact, we know very little about LUCA itself, except that it likely included features of the simplest microbes found today residing in the vicinity of deep, dark ocean vents. Wherever and however LUCA first appeared, its descendants soon ventured out to other parts of the ocean and along the way evolved into many different types of microorganisms. These, in turn, gradually gave rise to the rich diversity of life we are familiar with today in the sea and on the continents.

©John S. Compton (www.johnscompton.com)                                                      Earthspun logotan