Milestones of Human Evolution from Paleontology & Bioinformatics

Ever since Darwin suggested that humans are closely related to apes [Figure 1], the question has arisen of how human beings evolved from apes.

What exactly were the factors that forced our early ape ancestors to adopt the traits peculiar to humans? To answer this queston, first we'll need to provide a list of human traits:

Figure 1. Man's place in the natural kingdom.

Although numerous hypotheses have been proposed over the last century and a half since Darwin to explain the origin of human traits, no one hypothesis has really suceeded, largely because of the lack of direct evidence for any of these hypotheses.

However, things have changed over the last few decades. Enough paleontological and, more suprisingly, bioinformatic discoveries have accumulated to determine a reasonably reliable chronological order in which our ancestors gained each of these human traits.

Here, I hope to provide a handy summary of these fascinating discoveries in chronological order.

6 million: last common human-ape ancestor

A good starting point is to know when humans last shared a common ancestor with our fellow apes.

This involves calculating differences between our genomes and the genomes of other apes. Different biological measurements have been used from DNA binding affinities, expressed protein sequences to messenger RNA. A phylogenetic tree can then be constructed that respects the differences between all the genomes. The structure of this tree can be used to estimate the time between branching.

Phylogentic trees have been constructed that suggests that the human-ape split occurred 4-8 million years ago (Patterson et. al, 2006, Nature 441:1103, pdf). Reconstruction of paleotological climate suggests that this period corresponded to a harsh global ice age from 10-5 million years ago. This would have shrunk the tropical forests of our forest-dwelling last common ape ancestors lived in, forcing adaptions amongst their descendents.

Looking at the phylogentic tree Figure 2, chimpanzees and bonobos are our closest relatives, followed by gorillas, and then orangantans. For a long time, bonobos (also known as pygmy chimps) were not recognized as a distinct species. However, they are as closely related to humans as are chimpanzees (Prufer et al, 2012, Nature 486:527), which is important because bonobos have suprisingly different behavior to chimpanzees. This is to highlight that conclusions about our last common ancestor cannot be taken solely from comparison to chimmpanzees but should also include bonobos. In particular, bonobos have been observed to walk, using a rather awkward but nevertheless bipedal gail, which free their hands to carry objects Figure 3.

Figure 2. A phylogenetic tree of closest apes (from Bonobo: Friends of Bonobos)
Figure 3. Walking Bonobo

4.4 million - climbing woodland ape

The oldest human ancestor that's more than a few bones dates from 4.4 million years ago. Ardipithecus Ramidus possesed a fascinating mix of human and ape features - bipedal walking but also a tree climber.

Figure 4. Ardipithecus Ramidus. A fairly good skeleton of Ardipethus and a great comparative anatomical drawing.

Ardi is a rather recent found, with the skeleton found in 1994 but reported in 2009 in a special issue of Science. We are fortunate to have a partial skeleton Figure 4, with a complete skull, hands, pelvis and legs, as well as fossils of other animals from the same strata.

Although bipedal, the foot of Ardipithecus had large opposable toes Figure 5, which meant that Ardi could grip trees quite well. Ardipithecus had small canines with a small brain, about the same size as apes. By careful analysis of the teeth, and also the skeletons of hundreds of other animals found in the same strata, it's clear that Ardipithecus lived in woodlands (White et al. 2009, Science 361:87), and ate a fibrous vegetarian diet.

Figure 5. Foot bones of Ardipithecus Ramidus showing an opposable toe. Ardi was oriented to walk, but could climb trees like chimpanzees.

3.9 million - Australopithecus everywhere

The fossils of the Australopithecus lineage stretches from 3.9 to 1.4 million years ago. Australopithecus is quite ape-like with a small head, long arms and short legs. Australopithecus appears to be even better adapted to walking than Ardipithecus. Fossil footprints Figure 6 show that the big toe points forward.

Figure 6. Fossil imprint of footporints from 3.9 million years ago attributed to Australopithecus.

There is quite a variety of Australopithecus fossil records and they have been split into two populations:

  1. Robust, or vegetarian Australopithecus with big jaws designed for chewing tough fibrous vegetation.

  2. Gracile, or omnivore, Australopithecus, with thinner jaws and skulls, probably ate all sorts of diet.

Perhaps the most celebrated was a young Australopithecus Afarensis, discovered in 1974, who existed somewhere around the 3.2 million year mark, with a pretty good skeleton known as Lucy Figure 7. A later find in 2006 includes a beautiful intact skull Figure 8 from 3.3 million years ago. This is now known as Lucy's child Figure 9.

Figure 7. Skeleton of Lucy from the Smithsonian
Figure 8. The intact skull of Lucy's baby.
Figure 9. Reconstruction of Baby Lucy by Viktor Deak from National Geographic.

Australopithecus was highly dimorphic: males typically appear 50% larger than females, which suggests a aggressive male-dominated society. Ian Tattersall (Masters of the Planet, 2013) speculates that Australopithecus may have lived in large herds like baboons on the plains, as opposed to small tribes like chimpanzees.

Walking as well

One of the great reviews of human biomechanics comes from Daniel Lieberman (Bramble & Lieberman, 2004, Nature 432:345 pdf), which is a thorough analysis of the many factors involved in walking and running in humans and their ancestors Figure 10.

Figure 10. Anatomic comparison of Humans, Erectus, and Australopithecus and Chimpanzee

To summarise, our ancestors from Ardipithecus to Homo Habilis were efficient walkers, but could not run (Lieberman, 2014, "The Story of the Human Body"). Homo Erectus was our first ancestor to display the features of running in their skeletons.

Nevertheless, Erectus, like us, was not that fast. Chimpanzees can easily outrun us over short distances, and Erectus would not have been able to outrun savannah predators, or chase down savannah ungulates.

3-4 million years - nakedness, divergence of head and pubic lice

Nakedness, or the loss of fur, is one of the most puzzling trait of humans. Losing body fur is a tactic that few mammals have taken, even on the savannah plains. As fur is not preserved in the paleological record, the origins of nakedness has been completely open to interpretation, indeed most reconstruction of human ancestors assumes a furry covering.

However, a 2007 paper finally describes a method to estimate when our ancestors lost their body hair (Reed et al. 2007 BMC Biology 5:7). This paper observes that humans have two kinds of hair lice: one for the head and one for the groin (crabs) Figure 11. In contrast, gorillas and chimpanzess have only one type of lice, and so presumably did our last common human-ape ancestor. Turns out that pubic hair lice diverged from gorilla lice approximately 3-4 million years ago, when presumably it jumped across species to humans.

Figure 11. Head lice (left) and pubic lice (right) diverged from each other 3-4 million years ago.

The hypothesis then is that head-hair lice diverged from pubic-hair lice which our ancestors lost our body hair and evolved the thicker more gorilla-like pubic hair (Weiss, 2009, J Biol 8:20). This date is quite close to the age of Ardipitehcus and coexistent with Australopithecus, suggesting that our ancestors from Ardipitehcus on were relatively hairless, like us.

Speculation: naked walking woodland ape: water-wader.

The discoveries here strongly bracket the origin of bipedalism in our ancestors. The thorough analysis by Liebermann has now shown that bipedalism evolved for walking in woodlands but not running (Liebermann 2014, The Origin of the Human Body). And nakedness evolved around this time. As we now know that bipedalism appeared well before large brains, complex tools, hunting of meat, cooking, language, and adaptations for the hot savannah plains, any hypotheses requiring these traits must be eliminated, as it would be directly refuted by the fossil record.

The only remaining hypothesis that provides a specific utility for slow walking on two legs is the wading ape theory of Algis Kuliukis, a modern variant of the aquatic-ape theory of Alister Hardy and expounded by Elaine Morgan. The aquatic ape theory in its original form has been quite unpopular, as it tries to explain many human traits with this one hypothesis. Instead the wading water ape theory only postulates that a period of semi-aquatic life induced bipedalism. But more importantly, the water-wading theory is the only hypothesis that provides a functional hypothesis for the early evolution of nakedness, well before the savannah plains, mainly as an aid to semi-aquatic life.

Daniel Libermann, who demonstrated that Ardipithecus was a slow bipedal walker, is skeptical of the water-wading theory, arguing that water-wading apes would have been vulnerable to water-based predators. The irony of this skepticism is that in Liebermann's own schema, our slow-walking ancestors would eventually migrate to the savannah plains, where they would run the risk of fast-running savannah predators. This did not prevent them from adapting to this envioronment, as the existence of predators does not automatically negate the advantages of moving into a new ecological niche.

Indeed most of near relatives have been observed to both walk bipedally, and swim in water. Here is some footage of baboons wading bipedally through flooded plains to find food. Bonobos, our very closest relative have been observed to enjoy wading and playing in water Figure 12. Their body morphology is quite similar to Australopithecus, and we could easily imagine Australopithecus as a bonobo that decided to spend more time in water, with less body hair.

Figure 12. Bonobos have been frequently observed to enjoy wading and playing in water.

2.33 million - tools and growing brain - meat eating ape

The next step in the fossil record at 2.33 million years, is Homo Habilis, Handy Man, one of the first human ancestor discovered in 1964 by the great Louis Leakey (Leakey et al. 1964 Nature 4927:7).

What makes Habilis special was that the fossil was discovered with stone tools, in the area known as the Olduwan Industrial Complex Figure 13. The appearance of stone tools and cuts in bone fragments suggests hunting and eating meat, which is something that chimpanzees sometimes indulge in Figure 14.

Figure 13. On Oldawun scraper from
Figure 14. Chimpanzees hunting

At the time of discovery, tool-using was considered the essential feature of Homo Sapiens, and thus Habilis was classified under Homo. Compared to older ancestors, the face has begun to flatten and the nose poking out Figure 15. The brain is somewhat larger than Australopithecus but still about half the size of ours. However, Ian Tattersall and even the son of Louis Leakey, Richard Leakey, have argued that Habilis is not that much different to Australopithecus, with their short 4 ft height, long arms, and short legs, and should probably be classed as a variety of Australopithecus.

Figure 15. Skull of Homo Habilis from Wikipedia

2 million years ago - endurance running and hunting

At 2 million years, we find the first ancestor that is most agreed to be considered in the human family: Homo Erectus.

The body proportions of Homo Erectus has the hallmarks of an endurance runner Figure 16 (Bramble & Lieberman, 2004, Nature 432:345 pdf): long legs, arched feet, broad shoulders and short arms and a flat face Figure 17. These are anatomical adaptations that increase the efficiency of running as opposed to walking Figure 10.

Figure 16. Skeleton of Homo Erectus
Figure 17. Reconstruction of Homo Erectus by Kennis & Kennis

Nevertheless, Erectus could not run fast, especially compared to large four-legged predators that live in the savannah plains, such as lions and tigers. Indeed, over short distances, chimpanzees can gallop faster than humans. Instead, Habilis appears to be optimized for endurance running at moderate speeds over long distances.

What could this be useful for? Well, it turns out that there is an ancient method of hunting that requires endurance running, persistence hunting, which is still practiced by Kalahari Bushmen (MacDougall, 2009, "Born to Run"). As in this footage of a persistence hunt, the hunters, in the hot noonday sun, run for several hours, tracking and chasing a single animal until it is heat exhausted, and then closing in to kill the collapsing animal.

As the African continent dried up into hot savannah plains in this period, this suggests that Homo Erectus moved to the savannah planes and carried out persistence hunting on grazing animals of the savannah plains (Liebenberg 2006 Current Anthropology 47:1017).

1.2 million - universal black pigmentation

What color was the skin of our ancestors? One bioinformatic study (Rogers et al. Current Anthropology 2004 45:105) can at least pinpoint a time when all of our ancestors had black skin. The key gene is MC1R, a melanocortin receptor gene Figure 18 that is activated in indigenous Africans and inactivated in people outside Africa.

Figure 18. Homology model of the MC1R receptor from SWISSMODEL.

The concept used here is genetic drift. When a version of a gene becomes universal, presumably due to environmental pressure, it sweeps across all surviving members as exactly the same gene. But as time goes on, bits of the gene varies in ways that does not affect the function of the gene.

The amount of such neutral variation can be used to deduce the last point of universality, giving a date of 1.2 million when the activated MC1R gene for black skin was universal.This period coincides with a drier period and the expansion of Homo Erectus throughout Europe and Asia.

The authors of this study have gone on to argue that this indicates when our ancestors became naked, which is a rather indirect argument - first, that black skin was due to hot weather, and second, that hot weather must have caused a host of adaptations that include the loss of hair. Instead, the head/pubic lice split argument referred to above, directly links a speciation event with changes in ancestral hair covering.

200,000 years ago - speech, long hair and modern skeletons

The first skeletons of our ancestors that resemble modern human beings - modern day Africans - are found from 200,000 years ago.

Coincidentally, a gene involved in speech defects, Foxp2 (Lai et al. 2001, Nature 413:519), had its last universal sweep at 200,000 years ago (Enard et al. 2002 Nature 418:869).

Another interesting gene that had a universal sweep around 200,000 is the Phi-hHaA gene, which is an inactivated gene in humans (Winter et al. 2001 Human Genetics 108:37). In gorillas and chimps, the Phi-hHaA gene is activate and produces a keratin protein involved in hair growth. It's hypothesized that inactivation of Phi-hHaA in humans 200,000 years ago corresponded to the beginning of uncontrolled hair growth on the head, which is postulated to have adapted to more complex grooming and body decoration.

It's really hard to date when our ancestors first used fire but there is enough evidence to suggest that fire was widely used by this time.

So the modern human skeletal form appears about the same time that a potential language development occurred and hair started growing long.

72,000 years ago - clothing

In terms of understanding the cultural development of our ancestors, when our ancestors started wearing clothing might be an important event.

The key turns out to be, once again, lice. There are in fact three major types of human lice - head lice, pubic lice and body lice Figure 19. Body lice, however, attaches to human clothing.

By analyzing the differences between human body lice and human head lice, Mark Stoneking has been able to estimate that they split about 72,000 years ago, suggesting this was when our ancestors started wearing clothes (Kittler et al. 2004, Current Biology 14:2309).

Figure 19. The 3 kinds of human lice - head, pubic and body, from U. Nebraska

50,000 years ago - leaving Africa

There is now diverse evidence that modern humans originated in Africa. So when did humans leave? One strand of evidence is analyzing the distribution of mutations across geographical regions.

The work of Chris Stringer has focused, amongst other things, the male Y-chromosome mutation known as the M168 mutation in non-African men (Stringer 2000 Nature 405:24). By carefully correlating these mutation patterns in the genome, a date of 50,000 years is given to when modern humans first left Africa and began the process of displacing the other human species in the rest of the world.

This date of 50,000 years also coincides with the appearance of complex tools such as bone flutes, refined missiles, and fishing tools. Paul Mellars argues that this increased complexity implies also some key development in the complexity of language.

16,000 years ago - domestication of dog, white skin - cold adaptation

Around 16,000 years ago, probably the coldest part of the last glacial age between 100,000 to 10,500 years ago, several things happened.

Analysis of the divergence of dog genomes from wolves suggest that dogs domesticated around 15,000 years ago (Larson et al., 2012, PNAS 109:8878). How this happened is unclear, but one hypothesis is that humans made the pivotal jump to permanent settlements, which allowed the domestication of wolves, eventually leading to dogs.

Coincendentally, at 16,000 years ago is when mongoloid and caucasian skulls started appearing (Wade, 2007, "Before the Dawn"). It has been estimated that the entire caucasian population could be traced to a concentrated bottleneck of several thousand individuals around this time. The idea is that the harsh conditions of northern Europe lead to fast adapation of a small cold-adapted tribe. Similarly the Mongoloid population is hypothesized to descend from another cold-adapted population in northeastern Asia.

Something in these populations allowed them to overrun Europe and Asia to the south, once the temperature started to warm up.

10,000 years ago - settlement and warmth

The ice age ends at 10,000 and we start seeing the evidence of human settlements. The oldest large-scale settlement known is Catalhoyuk in Turkey, and dates back some 9,000 years ago Figure 20. This city is composed entirely of domestic buildings with no obvious public buildings. The entrance is from the roof and bodies were buried inside the building. Analysis of the food remains suggests that the population were still hunter/gatherers, and not farmers.

Figure 20. The dig at Catalhoyuk, oldest city in the world.

From here on in, paleontology dovetails with history, as the Rig Vedas and Old Testament carry traces of events from this period.


Following Ian Tattersall, there were 3 distinct phases in human evolution:

  1. 6-2 million years ago, climbing walking woodland ape
    • woodlands/rivers
    • tree-climbing
      • long arms
      • narrow shoulders
      • short legs
      • curved fingers
    • small brains
    • dimorphic body sizes
    • omnivorous, mostly fibrous vegeation
    • legs adapted for bipedal walking
    • naked
    • ocassional stone tools
  2. 2-0.2 million years ago, running/hunting savannah ape
    • hot savannah plains
    • endurance running
      • long legs
      • short arms
      • narrow hips
    • growing brains
    • persistence hunting
    • meat/foraging diet
    • complex tools
    • fire
  3. 200,000 years ago, symoblic tool-using humans
    • modern proportions and skulls
    • long hair
    • clothing
    • language

Theories about why this occured must respect the order in which the traits have been observed in the fossil record.

    ~ Bosco Ho, 8/6/2014


Some more recent books on human evolution that discuss these findings in much greater detail:


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