On the origins of our species

As families go ours is pretty amazing. You have ancient cousins who effortlessly chomped through the toughest of roots and hardest of seeds. Another relative was the first of our family to make it all the way to China around 1.7 million years ago. Each individual human alive today belongs to the same family as all of our extinct relatives, the Hominidae. Our kinship runs deeper than geographical boundaries.

What is truly spectacular is that we are still discovering incredible fossils today that are adding detail to our complex family history. Just last year, a new twig on the family tree was added with the remarkable discovery of Homo naledi. Recently, a strange structure was discovered at a Neanderthal site in France: our sister species was building things 170,000 years ago. Let’s not forget our quirky second cousin, the hobbit Homo florensiensis, with recent finds suggesting they evolved around 700,000 years ago from Homo erectus.

Our family is large! Hominins have a long hsitory, dating back to at least 7 million years ago. (Image from Wiki Commons)

We are learning more each year about our incredible family. But what about us: what can we say about the origins of our species?

Until relatively recently, our species, Homo sapiens was the only known species of human. In 1859 when Charles Darwin wrote his masterpiece On the Origin of Species, there was no solid evidence for any other human species. (Although Neanderthal fossils were known, they were thought to be remains of humans with disease. It wasn’t until 1864 until they were named as a separate species.) For such an important, ground shaking book, Darwin gave just one sentence to human evolution: “Light will be thrown on the origin of [hu]man[s] and [their] history.”

Some years later in The Descent of Man, Darwin writes a little more about how humans are related to other animals. With just the Neanderthal finds, there was little to include about evidence from the fossil record. Nevertheless, Darwin still made a prediction about where one should look for human ancestors:

“In each great region of the world the living mammals are closely related to the extinct species of the same region. It is, therefore, probable that Africa was formerly inhabited by extinct apes closely allied to the gorilla and chimpanzee; and as these two species are now [hu]man’s nearest allies, it is somewhat more probably that our early progenitors lived on the African continent than elsewhere.”

So by 1871 Darwin was advocating looking for our ancestors in Africa but this wasn’t the consensus view. The great German naturalist, Ernst Haekel, for example, argued strongly that human ancestors would be found in Indonesia (presumably because of the other great ape living there, the orang-utan). Remarkably hominin fossils were found there in 1891 by Eugène Dubois, which he saw as a species intermediate between apes and humans (though this ‘Java Man’ was later identified as Homo erectus). It wasn’t until 1924 that the first hominin fossil was found in Africa, with Raymond Dart’s discovery of the first Australopithecus africanus specimen. Since then, numerous hominin fossils have been found across Africa, Europe and Asia.

Original fossils of ‘Java Man’. The thick broken skull at the back, with the big femur at teh front. (Image by Peter Mass, Public Domain)

We know hominins evolved in Africa, but with so many fossils being discovered across the continents, there have been huge debates about where our species, Homo sapiens, originated. Two main theories have dominated: the Out of Africa (or Recent African Origin) and the Multiregional origin. Out of Africa proposes that there was a single origin for anatomically modern humans. This theory says that the first modern humans arose on Africa soil around 100,000 years ago before spreading out to populate the rest of the world replacing existing human groups. The Multiregional theory instead suggests that rather than arising in Africa the modern form arose in multiple parts of the globe with constant gene flow between existing human species: so all modern humans alive today are a mixture of Homo sapiens, H. neanderthalensis, and H. erectus. (There is another theory, which often gets confused with the multiregional model. The Candelabra theory suggests that after leaving Africa and migrating to other regions of the world our very early ancestor H. erectus evolved modern features independently (without any gene flow between other species of Homo) and at multiple times.)

Are we a species that arose in Africa or in multiple regions round the globe? Did we leave Africa once and replace all other species of Homo, or did we bump into and have a little fun with other species we met on the way? Where did our species leave Africa from and what route did they take? A recent paper took a very detailed look at the publications on this subject to try to get a clearer picture. As well as fossils, climate and radiocarbon dates they advocate genetics as another tool in helping us to discover the true origins of Homo sapiens.

It turns out that by using genetic evidence we can disregard the Multireigonal and Candelabra theories rather quickly. Genetic studies using mitochondrial DNA, which traces genetic information down the female Homo sapiens line, point to all regions tracing their line back to Africa. Later Y chromosome studies, which looked at the male line, also suggested an African common ancestor. What is more, using information from our other 22 non-sex chromosomes genetic diversity was found to decrease predictably the further away you go from Africa. Given our ancestors must have been genetically more diverse than us this is pretty convincing evidence for an African origin.

These studies agree strikingly well with the fossil record. In 1967, Richard Leakey discovered the oldest anatomically modern human fossils in Ethiopia. Known as the Omo remains, these fossils date to between 200,000 and 190,000 years ago. Some more very old Homo sapiens fossils, known as the Herto skulls, were also found in Ethiopia in 2003, dating to between 160,000 and 154,000 years ago. The oldest fossils of our species have been found in Africa.

One of the Herto Skulls. One of the earlierst Homo sapiens fossils, around 160,000 years old. (Image Public Domain)

When and where our species left Africa is another hot topic for researchers. Outside of Africa, the oldest fossils of our species found so far are the Skhul/Qafzeh fossils in the Levant (where Israel is today), dating to around 100,000 years old. Originally thought of as a failed exodus, some believe the Skhul/Qafzeh fossils may represent a more successful distribution with stone tools on the Arabian Peninsula dating to between 100,000 and 80,000 years old. The location of these fossils falls in line with a Northern route out of Africa, through Egypt and Sinai. The other possible direction is a Southern route out of Africa through Ethiopia and the Bab el Mandeb strait across the Red Sea, following the coastline towards the Arabian Peninsular, heading to India.

The earliest anatomically modern humans out of Africa around 100,000 years ago, Skhul/Quafzeh Skull number 5. (Image Public Domain)

Given little in the way of archaeological evidence geneticists have attempted to track our ancestors African exit using DNA from people alive today. A number of studies have attempted to do this using different datasets and techniques but on the whole they run in to difficulties. It turns out people alive today are pretty bad representatives of those first humans leaving the African continent due to people having mixed extensively through history. Trying to figure out who mixed with whom, accounting for the mixed DNA in some way and then making any assumption that the DNA left looks anything like the DNA of those first ancestors is fraught with difficulties. This is particularly problematic in Africa where migrations of people ‘back to Africa’ have resulted in the DNA of modern day Africans being composed of high levels of non-African ancestry, muddying the signal further. One way around these problems is instead to analyse DNA extracted from people who lived many thousands of years ago (ancient DNA), allowing direct assessment of the genetic make up of past populations. With increasing improvements in the techniques used to recover DNA from human remains and account for damage as it has degraded through time, ancient DNA research is becoming a viable next option in answering these questions. However obtaining DNA from sufficient samples and in the right places (very tricky in Africa where the hot climate speeds up DNA damage) may be a limiting factor.

The movement out (and back into) Africa based on the fossil and genetic evidence to date. (image from Lopez, van Dorp & Hellenthal, 2016)

The timing of when bands of Homo sapiens left Africa is also not easy to pinpoint. There are two main dates that are proposed based on DNA evidence, between 130, 000 and 100,000 years ago, or between 60,000 and 50,000 years ago. Many researchers support the later date but recent finds are shaking this idea up a bit. Last year fossil finds in China dated between 120,000 and 80,000 years old, showing that H. sapiens had made it to China much earlier than previously thought. Did these individuals just die out like has been suggested for Skhul and Qafzeh? Or did they make a contribution to the gene pool of humans alive today? Dating our African exit using DNA is not precise because it relies on having a good estimate of when mutations have occurred in the genome through time and often assumes clear splits between groups when the reality is likely somewhat noisier. One approach to mitigate these difficulties is using ancient DNA from different points in history as a genetic ruler to calibrate the speed at which mutations have occurred. Using timescales revised in this way genetic reconstructions date our African departure to fit the range of this more recent date: 95,000 – 62,000 years ago.

Exactly when and where we left Africa is proving to be a little difficult to determine. Maybe we will never pinpoint the exact date, or the exact place we left. Maybe there were a number of small groups leaving at different times and places. What we do know is that some of these groups met other species of humans. And we mated with them. Successfully. Some of the pioneering work on ancient DNA showed that modern humans share a detectable amount of DNA (1.5-4%) with Neanderthals, revising our idea of the Out of Africa model existing without any intermixing. And it’s not just the Neanderthals. Another species we had intimate relations with were the Denisovans, a mysterious species characterised solely from genetic material extracted from a sliver of finger bone. Even 40,000 year old secrets can be revealed.

A cast of a the tiny finger bone. The orginal was destroyed for DNA anaylsis. (Image Thilo Parg, Public Domain)

No field of science is more personal than the study of our own origins. With more finds every year, the details challenge what we know and often create more questions than answers. When we left Africa, where did we travel first and whom we met are all key questions, which we are beginning to answer by integrating archaeology, climatic and genetic evidence. Our species origins lie in Africa, illustrated by both the fossil record and genetic studies. We left Africa at least on two separate occasions, and travelled the world. We met, and slept with, other species of humans: the evidence of our promiscuity forever written in our DNA. The origins of us is a beautiful, but complicated story.

Written by Lucy van Dorp (@LucyvanDorp) and Jan Freedman (@JanFreedman)

This post is based on the following research:

Lopez, S, van Dorp, L, & Hellenthal, G. (2016). ‘Human Dispersal Out of Africa: A Lasting Debate.’ Evolutionary Bioinformatics. 11 (S2). pp.56-68. [Full article]

Further reading:

Blome MW, et al. (2012). ‘The environmental context for the origins of modern human diversity: a synthesis of regional variability in African climate 150,000–30,000 years ago.’ J Hum Evol. 62. pp.563–92. [Abstract only]

Cann, R. L, Stoneking, M, & Wilson, A. (1987), ‘Mitochondrial DNA and human evolution’, Nature. 325(6099). pp.31-36. [Abstract only]

Cooper, A & Stringer, C. B, (2013), ‘Did the Denisovans cross the Wallace line?’ Science. 342(6156). pp.321-323. [Abstract only]

Darwin, C. (1859). ‘On the origin of species by means of natural selection’. Murray. [Book]

Darwin C. (1871). ‘The Descent of Man, and Selection in Relation to Sex’. London: John Murray; 1871. [Book]

Gibbons, A. (2012), ‘Ancient DNA. A crystal-clear view of an extinct girl’s genome’, Science. 337(6098). pp.1028-1029. [Full article]

Goldstein D B, & Chikhi L. (2002) ‘Human migrations and population structure: what we know and why it matters.’ Annu Rev Genomics Hum Genet. 3. pp.129–152. [Abstract only]

Gunz P, et al. (2009). ‘Early modern human diversity suggests subdivided population structure and a complex out-of-Africa scenario.’ Proc Natl Acad Sci U S A. 106. pp.6094–6098. [Full article]

Krause, J, et al. (2010), ‘The complete mitochondrial DNA genome of an unknown hominin from southern Siberia’, Nature. 464(7290). pp.894-897. [Abstract only]

Lowery R. K, et al. (2013) ‘Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms.’ Gene. 530. pp.83–94. [Abstract only]

Pennisi, E, (2013), ‘More genomes from Denisova Cave show mixing of early human groups’, Science. 340(6134). pp.799. [Abstract only]

Prüfer, K, et al. (2013), ‘The complete genome sequence of a Neanderthal from the Altai Mountains’, Nature, 505(7481). pp.43-49. [Abstract only]

Reich, D, et al. (2011), ‘Denisova Admixture and the first modern human dispersals into Southeast Asia and Oceania’, The American Journal of Human Genetics. 89. pp.516-528. [Abstract only]

Roberts, A. (2009) ‘The Incredible Human Journey.’ Bloomsbury. [Book]

Sankararaman S, et al. (2014) ‘The genomic landscape of neanderthal ancestry in present-day humans.’ Nature. 507. pp.354–357. [Full article]

Stringer C. B, & Andrews, P. (1988) ‘Genetic and fossil evidence for the origin of modern humans.’ Science. 239. pp.1263–1268. [Abstract only]

Tattersall I. (2009) ‘Human origins: out of Africa.’ Proc Natl Acad Sci U S A. 106. pp.16018–16021. [Full article]

Templeton A. R. (2007) ‘Genetics and recent human evolution.’ Evolution. 61: pp.1507–1519. [Abstract only]

Thomson R, et al. (2000). ‘Recent common ancestry of human Y chromosomes: evidence from DNA sequence data.’ Proc Natl Acad Sci U S A. 97. pp.7360–7365. [Full article]

Wu X. (1981) ‘The well preserved cranium of an early Homo sapiens from Dali, Shanxi.’ Sciencia Sinica. 2 pp.200–206. [Full article]