To unearth the secrets of our human origins, scientists are delving deep into the prehistoric record to find the last common ancestor of great apes and humans, while simultaneously looking in more recent history to define when and where modern humans (modern in terms of anatomy and behavior) first appeared. This endeavor, which has traditionally entailed years of painstaking digging for fossils and archaeological relics in often far-flung places, has lately received a welcome boost from the advent of novel genetic tools that enable the reconstruction of complete human genomes (a genome being the complete set of genetic material contained in an organism). Newly published work in the journals Nature [2] and Science [5] describing novel human fossils and genomes have now added to our small but growing appreciation of the complexity of our common evolutionary ancestries.

The Earliest Hominid Was Not Alone

For several decades, the consensus in the human evolutionary research community was that modern man, Homo sapiens, appeared nearly 200,000 years ago, descending more or less linearly from a succession of forebears who also belonged to the same group called Homo. At the base of this Homo lineage lay Homo habilis, a primitive species that was thought to give rise to Homo erectus, who dispersed out of Africa about 50,000 years ago and whose direct descendants included our own species, Homo sapiens (see Figure 1).

Figure 1. Timeline depicting the human “family tree,” adapted from

Muddying the waters surrounding this straight-line narrative linking H. habilis and H. sapiens is a curious skull specimen, KNM-ER 1470 (hereafter referred to as 1470), discovered by Meave Leakey and her colleagues in 1972 at the Koobi Fora near the shores of Lake Turkana in Kenya. Unlike the other H. habilis fossils uncovered at the Koobi Fora, 1470 has a flat, large, and upright face. Its facial morphology is sufficiently distinct that it prompted Leakey to christen it a new species, H. rudolfensis. However, 1470 lacks a lower jaw, and for many years no other anatomically similar fossils were found. Its status as a bona fide non-Homo habilis lineage has thus been a source of much debate amongst paleoanthropologists, some of whom contend that its large size and unique cranial features may simply reflect variation between the sexes within the H. habilis species [1]. This controversy may now be closer to a resolution with the discovery by Leakey and colleagues of three new fossils from Koobi Fora that manifest features closely resembling those of 1470 [2].

The three specimens include a well-preserved skull (KNM-ER 62000), a lower jaw (60000), and a fragmentary lower jaw (62003). 62000 belonged to a late juvenile individual and has a long, flat face  similar to that of 1470. Unlike 1470, 62000 retains its lower jaw and some teeth. Interestingly, the anatomy of the lower jaw of 62000 matches those of 60000 and 62003, and all are distinct from other H. habilis fossils. It thus seems unlikely that the founding H. rudolfensis specimen, 1470, represents a one-off event, a mere fluke of nature. Moreover, all three specimens date to between 1.78 and 1.95 million years old, the same time period when H. habilis was also living in East Africa. This means that our earliest Homo ancestors coexisted with at least one other hominid lineage two million years ago; the nature of this coexistence and its impact on ensuing human evolution begs more fascinating questions than answers.

Out of Africa and into Modernity: Our Relationship with Neandertals and Denisovans

While fossils of skulls and bones reveal anatomical changes, and archaeology reflects the development of abstract thought, language, and culture, genetics can tell us when and where different human populations arose and moved apart from one another, the size of the populations, and what early humans may have looked like. Over the last decade, rapid advances in genetic analytical techniques and the diminishing costs of these procedures have made the reconstruction of the whole genomes of both current humans and extinct hominid species possible.

In 2010, Svante Pääbo’s team in Germany presented the first reconstruction of the entire Neandertal genome derived from the bones of three female Neandertals to much enthusiasm from researchers and the public alike [3]. Perhaps the most surprising part of their findings was that present-day Europeans and Asians, but not Africans, share about 2.5 percent of their genome with the Neandertals. The researchers interpreted this as evidence for interbreeding between Neandertals and Homo sapiens just as modern humans were migrating out of Africa, such that those who remained in Africa did not pick up the genetic variants from the Neandertals [3]. This upended conventional thought that the relationship between Neandertals and modern humans was neutral or even antagonistic. However, conclusive proof of interbreeding between Neandertals and Homo sapiens is exceedingly difficult to obtain, and this hypothesis has been called into question by a recent study that suggested that the observed genetic overlap between the Neandertals and living Europeans and Asians could simply represent material inherited from a common ancestor [4].

Pääbo and colleagues have now improved upon their method of genomic analysis and successfully applied it to reconstruct in unprecedented detail the complete genome of the Denisovans, an archaic group of humans [5, 6]. But who exactly are the Denisovans?

The first (and so far only) Denisovan specimen was discovered in a cave in Siberia, and it comprises only a molar and a fragmentary finger bone. Early, lower quality genomic analysis on DNA extracted from the bone indicated that it belonged to a new species – later named after its site of discovery, the Denisova caves – distinct from both Neandertals and humans. Intriguingly, both Neandertal and human fossils were found in the Denisova caves and dated to 30,000 to 50,000 years ago. Did all three species co-exist at the same site? If so, how did they interact? Pääbo’s latest study suggests that archaic Denisovan DNA can still be found in Melanesians (a group of people living on various islands to the northeast of Australia) today, making up about 5 percent of their genome. This proportion is too large to be explained away as remnants of genetic material inherited from the ancient Africans who were the common ancestors of Denisovans and Homo sapiens. The researchers therefore concluded that our human ancestors not only interbred with the Neandertals, but also with the Denisovans [5, 6].

Celebrating Our Common Yet Diverse Origins

These hypotheses of early hominids living alongside Homo habilis and interbreeding between modern humans and their archaic cousins are not without their detractors and skeptics. A key reason is the relative dearth of complete human fossils and archaeological relics. Reconstruction of ancient DNA, often severely degraded and contaminated, is also technically challenging. Nonetheless, palaeoanthropological remains continue to turn up in previously unexplored sites, and genome analysis tools become increasingly better. The dust has yet to settle from the varying views of our evolutionary past, but we can be certain about one thing: our origin story is likely going to grow ever more complex, marked by multiple lineages coexisting and interacting with one another. We may carry in all of us a little bit of Neandertal, Denisovan, and Homo rudolfensis, and we should celebrate our diverse yet shared human ancestry.

Tze G. Tan is a graduate student at Harvard Medical School.


[1] John Noble Wilford, “New Fossils Indicate Early Branching of Human Family Tree”. New York Times. Aug 8, 2012.

[2] Meave G Leakey, Fred Spoor, M. Christopher Dean, Craig S. Feibel, Susan C. Anton, Christopher Kiarie & Louise N. Leakey (2012) New fossils from Koobi Fora in northern Kenya confirm taxonomic diversity in early Homo. Nature 488: 201-204.

[3] Anne Gibbons (2010) Close Encounters of the Prehistoric Kind. Science 328(5979): 680-684.

[4] “Research Raises Doubts About Whether Modern Humans and Neanderthals Interbreed”. ScienceDaily. Aug 13, 2012.

[5] Matthias Meyer, Martin Kircher, Marie-Theres Gansauge, et al. (2012) A High-Coverage Genome Sequene from an Archaic Denisovan Individual. Science 338 (6104): 222-226.

[6] Katherine Harmon. “New DNA Analysis Shows Ancient Humans Interbred with Denisovans”. Scientific American. Aug 30, 2012.

Further Reading

Smithsonian National Museum of Natural History. Human Evolution Evidence.

This site curated by the Smithsonian National Museum of Natural History contains links to a multitude of resources on various aspects of human evolution.

3 thoughts on “The Dawn of Homo Sapiens: Our Family Tree Grows Messier Still

  1. I should have been a scientist or anthropologist! When I watched the documentary that stated that Neanderthals did not interbreed with humans I knew that did not make sense. Even today different cultures and races interbreed. There is racism and then as time goes by the cultures interbreed with each other. That is what happened with the Neanderthals and other groups. I always loved science in school and laughed when the came back after the documentary and said we made a mistake Neanderthals did have children with humans at the time. Today we have about 4 percent in us. Now I read that a 9 million year old human tooth was found in Germany. How will that change the evolutionary tree. Can hardly wait to see that documentary.

    1. Homo Sapiens were not around 9 million years ago. Estimated 500,000 possibly longer but no way older than 2.5 million. 2.5 million is when homo ha ilia was around, that’s one of our ancestors. Can’t be alive before your ancestors, maybe do your own research. That’s what we use, we being me and my fellow anthropologists.

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