Cracks in the Out of Africa Theory?

The most exciting finding of the past two decades in biological anthropology has been, without a doubt, evidence for interbreeding between Homo sapiens, Neanderthals, Denisovans, etc. and the sheer multiplicity of new hominin species being uncovered.

Exactly where the lines between species lie is a bit of a matter of semantic debate–where exactly did our ancestors end and Homo sapiens begin? Should we classify Neanderthals and Sapiens as one species if we interbred? etc–but if we accept the current classifications as decent approximations, we have:

Source: Wikipedia

Sorry, I realized it would be much more efficient if I just grabbed the family tree off Wikipedia instead of copying it over bit by bit. The top part of the tree got cut off, so I’ll note that Homini (6.3 million years ago) includes us + chimps, while Hominina (5.7 million years ago) has no chimps, but includes australopithecines. Gorillas are way back in Homininae, with an e. Homo, our genus, includes all of the “human” species, but usually doesn’t include australopithecines.

There is further debate on exactly who descended from whom. We’re finding new fossils all the time, which is quite exciting, but our current record is not nearly as complete as we’d like it to be. So sometimes branches get moved around or re-categorized as more data comes to light.

The most recent notable additions to our genus are the Denisovans, Homo floresiensis, Homo luzonensis, Homo Naledi, Homo doesn’t have a name yet, and more Denisovans.

You have probably heard of the “hobbit,” Homo floresiensis. The remains we have uncovered of this diminutive hominin are remarkably good, including a skull in great condition (despite some damage caused after excavation.) They lived on the island of Flores from about 200,000 to 50,000 years ago (though their arrival may get pushed back considerably because there are stone tools on Flores that are much older–700,000 years old–we just don’t know yet who used them.)

The hobbits are remarkable in multiple ways. First, they lived in an area that was not connected to the mainland by any landbridges–that is, they had to swim, boat, or otherwise be carried to their island. I am skeptical of the idea of anyone surviving a tsunami as a means of populating an island, but they arrived in an era when, as far as we know, humans had yet to build boats. So perhaps their ancestors were among the first humans to build boats, and we just haven’t found the remains of their crafts (wood being a material that degenerates very quickly.)

Second, the Hobbits are most likely descended from Homo erectus, who lived nearby on mainland Indonesia (at the time, connected to the rest of Asia via a landbridge), but are morphologically very different. They are tiny–shorter than pygmies, Homo erectus, or even australopithecines.

There is much debate about whether they are descended directly from erectus, or part of a sister-clade to erectus that descended from a common ancestor. It was previously believed that erectus was the first hominin to leave Africa, but if Floresiensis is not descended from erectus, Flores could be the first.

Now a similarly diminutive hominin has turned up in the Philippines, also past a significant water barrier that would require some effort to cross. It has been dubbed Homo luzonensis. Not much is known, yet, about luzonensis, (we haven’t found as many of its bones), but what we do know is tantalizing:

It was soon apparent to Détroit that the remains featured a puzzling mosaic of traits both modern and ancient. “Each of the features [of Homo luzonensis] corresponds to some hominin or another,” he says. “But the combination makes for something really unique. There’s no known species with this same suite of features.”

They’re small, possibly even smaller than the Hobbits. Their feet resemble australopithecines, but australopithecines supposedly died out a couple million years before Luzonensis arrived on the scene. And their teeth were “remarkably uniform,” which probably sounds boring to anyone who isn’t a dentist, but provides strong evidence of them being a different species.

Two island dwelling species in the same area supports the idea that their ancestors either developed boats or were remarkably skilled at surviving tsunamis, and that southeast Asia was a remarkable hotspot of hominin diversity.

And then there are the Denisovans!

Denisovans are mysterious because we have so few of their bones–a chunk of skull was recently uncovered, but we have no jaws, no faces, no ribs, etc–so we don’t have a good idea of what they looked like. What we do have are Denisovan DNA (extracted from those fragments of skeletons) and traces of Denisovan DNA in modern humans.

Oddly, those Denisovan bones turned up in Siberia (a good place for preserving old bones, but not such a great place for humans adapted to warm climates) while the humans with Denisovan DNA live in modern Papua New Guinea and nearby areas.

The obvious answer to this puzzle is that both the Denisovans had a much broader range than one cave in Siberia and the ancestors of modern folks from PNG used to live in different areas than they do now.

A more detailed analysis of PNG DNA was recently released, which reveals three separate, significant groups of Denisovans who interbred with sapiens:

… modern Papuans carry hundreds of gene variants from two deeply divergent Denisovan lineages that separated [from each other] over 350 thousand years ago. Spatial and temporal structure among these lineages suggest that introgression from one of these Denisovan groups predominantly took place east of the Wallace line and continued until near the end of the Pleistocene. A third Denisovan lineage occurs in modern East Asians. This regional mosaic suggests considerable complexity in archaic contact, with modern humans interbreeding with multiple Denisovan groups that were geographically isolated from each other over deep evolutionary time.

The Wallace line is a place that’s too deep for a landbridge, and thus the area to the east was an island even during the Ice Age. In other words, it looks like Denisovans could use boats. (Or survive tsunamis, pfft.)

Next, we sought to retrieve dates of divergence between D1, D2, and the Altai Denisovan genome … to encompass two deeply divergent Denisovan-related components, our best fitting model indicates that D1 and D2 split from the Altai Denisovan approximately 283 kya … respectively (Figure 4B). While clearly branching off the Denisovan line, D2 diverged so closely to the Neanderthal-Denisovan split that it is perhaps better considered as a third sister group… For context, even the youngest of these divergence times is similar to the evolutionary age of anatomically modern humans … Our model implies substantial reproductive separation of multiple Denisovan-like populations over a period of hundreds of thousands of years. … 

The genetic diversity within the Denisovan clade is consistent with their deep divergence and separation into at least three geographically disparate branches, with one contributing an introgression signal in Oceania and to a lesser extent across Asia (D2), another apparently restricted to New Guinea and nearby islands (D1), and a third in East Asia and Siberia (D0). This suggests that Denisovans were capable of crossing major geographical barriers, including the persistent sea lanes that separated Asia from Wallacea and New Guinea. They therefore spanned an incredible diversity of environments, from temperate continental steppes to tropical equatorial islands.

(We will probably reclassify some of the older fossils from Asia as Denisovans once we figure out what they looked like.)

Then we have Homo naledi, from South Africa. Naledi lived around 250,000 years ago, about the same time as Homo sapiens were differentiating from their ancestors. We have a wonderful array of Homo naledi fossils, preserved in the bottom of a cave pit. If they were placed here intentionally, this was pretty advanced behavior, though I wonder if perhaps they just got lost in the cave from time to time and then died in the pit.

At about 5 ft tall, (male height) naledi was short, but not nearly as short as Floresiensis, and taller than some groups of sapiens. Its skull was significantly smaller than a modern skull, however, and I find it odd that, out of the thousands of bones and fragments discovered, we have not yet recovered much of the front of their faces. Perhaps their faces were shattered when they fell into the cave?

Naledi, like Floresiensis and Luzonensis, shares some more modern traits with other members of the homo genus, and some traits with the older australopithecines. Unlike them, we have yet to uncover evidence that Naledi used tools.

The we have a couple of unnamed hominins

These so-called “ghost populations” are known entirely from their presence in the DNA of modern humans. We don’t have any fossils from them, either because they lived in areas where the weather didn’t favor preservation, or the modern political climate makes searching for fossils difficult.

The pygmies and Bushmen derive about 2% of their DNA from an archaic population or two that we estimate split off from the rest of us about 700,000 years ago. They met and mated with these other hominins around 35,000 years ago.

More interesting is another ghost population that shows up in the genomes of west African groups like the Mende. Now, the average non-African has about 1-4% Neanderthal DNA, and Melanesians have about 4-6% Denisovan, but some tribes in west Africa, such as the Yoruba, Mende, Gambians, and Esan, may derive about 10% of their DNA from an otherwise unknown ghost population that split off before the Neanderthals! (Razib’s very nice article summarizing the paper.)


Oh, jeeze, it’s three am, let me finish this in the next post…



Recent Exciting Developments in Human Evolutionary History: Naledi and Flores

A reconstruction of Homo naledi’s head by paleoartist John Gurche, who spent some 700 hours recreating the head from bone scans. Image credit: John Gurche / Mark Thiessen / National Geographic. source:

Continuing with our series on recent exciting discoveries in human genetics/paleo anthropology:

  • Ancient hominins in the US?
  • Homo naledi
  • Homo flores
  • Humans evolved in Europe?
  • In two days, first H Sap was pushed back to 260,000 years,
  • then to 300,000 years!
  • Bell beaker paper

One of the most interesting things about our human family tree (the Homo genus and our near primate relatives, chimps, gorillas, orangs, gibbons, etc.) is that for most of our existence, “we” weren’t the only humans in town. We probably coexisted, mated with, killed, were killed by, and at times perhaps completely ignored 7 other human species–Homo erectus, floresiensis, Neanderthals, Denisovans, heidelbergensis, rhodesiensis, and now Naledi.

That said, these “species” are a bit controversial. Some scientists like to declare practically every jawbone and skull fragment they find a new species (“splitters”,) and some claim that lots of different bones actually just represent natural variation within a species (“lumpers.”)

Take the canine family: dogs and wolves can interbreed, but I doubt great danes and chihuahuas can. For practical purposes, though, the behavior of great danes and chihuahuas is similar enough to each other–and different enough from wolves’–that we class them as one species and wolves as another. Additionally, when we take a look at the complete variety of dogs in existence, it is obvious that there is actually a genetic gradient in size between the largest and smallest breeds, with few sharp breaks (maybe the basenji.) If we had a complete fossil record, and could reliably reconstruct ancient hominin behaviors and cultural patterns, then we could say with far more confidence whether we are looking at something like dogs vs. wolves or great danes vs. chihuahuas. For now, though, paleoanthropology and genetics remain exciting fields with constant new discoveries!

Homo naledi and homo Floresiensis may ultimately be small branches on the human tree, but each provides us with a little more insight into the whole.

Naledi’s story is particularly entertaining. Back in 2013, some spelunkers crawled through a tiny opening in a South African cave and found a chamber full of bones–hominin bones.

Anthropologists often have to content themselves with a handful of bones, sometimes just a fragment of a cranium or part of a jaw. (The recent claim that humans evolved in Europe is based entirely on a jaw fragment plus a few teeth.) But in the Rising Star Cave system, they found an incredible 1,500+ bones or bone fragments, the remains of at least 15 people, and they haven’t even finished excavating.

According to Wikipedia:

The physical characteristics of H. naledi are described as having traits similar to the genus Australopithecus, mixed with traits more characteristic of the genus Homo, and traits not known in other hominin species. The skeletal anatomy displays plesiomorphic (“ancestral”) features found in the australopithecines and more apomorphic (“derived,” or traits arising separately from the ancestral state) features known from later hominins.[2]

Adult males are estimated to have stood around 150 cm (5 ft) tall and weighed around 45 kg (100 lb), while females would likely have been a little shorter and weighed a little less. An analysis of H. naledi‘s skeleton suggests it stood upright and was bipedal.[2][22][23] Its hip mechanics, the flared shape of the pelvis are similar to australopithecines, but its legs, feet and ankles are more similar to the genus Homo.[2][24]

I note that the modern humans in South Africa are also kind of short–According to Time, the Bushmen average about 5 feet tall, (that’s probably supposed to be Bushmen men, not the group average,) and the men of nearby Pygmy peoples of central Africa average 4’11” or less.

The hands of H. naledi appear to have been better suited for object manipulation than those of australopithecines.[2][25] Some of the bones resemble modern human bones, but other bones are more primitive than Australopithecus, an early ancestor of humans. The thumb, wrist, and palm bones are modern-like while the fingers are curved, more australopithecine, and useful for climbing.[3] The shoulders are configured largely like those of australopithecines. The vertebrae are most similar to Pleistocene members of the genus Homo, whereas the ribcage is wide distally as is A. afarensis.[2] The arm has an Australopithecus-similar shoulder and fingers and a Homo-similar wrist and palm.[24] The structure of the upper body seems to have been more primitive than that of other members of the genus Homo, even apelike.[3] In evolutionary biology, such a mixture of features is known as an anatomical mosaic.

Four skulls were discovered in the Dinaledi chamber, thought to be two females and two males, with a cranial volume of 560 cm3 (34 cu in) for the males and 465 cm3 (28.4 cu in) for females, about 40% to 45% the volume of modern human skulls; average Homo erectus skulls are 900 cm3 (55 cu in). A fifth, male skull found in the Lesedi chamber has a larger estimated cranial volume of 610 cm3 (37 cu in) [6]. The H. naledi skulls are closer in cranial volume to australopithecine skulls.[3] Nonetheless, the cranial structure is described as more similar to those found in the genus Homo than to australopithecines, particularly in its slender features, and the presence of temporal and occipitalbossing, and the fact that the skulls do not narrow in behind the eye-sockets.[2] The brains of the species were markedly smaller than modern Homo sapiens, measuring between 450 and 610 cm3 (27–37 cu in). The teeth and mandiblemusculature are much smaller than those of most australopithecines, which suggests a diet that did not require heavy mastication.[2] The teeth are small, similar to modern humans, but the third molar is larger than the other molars, similar to australopithecines.[24] The teeth have both primitive and derived dental development.[26]

The overall anatomical structure of the species has prompted the investigating scientists to classify the species within the genus Homo, rather than within the genus Australopithecus. The H. naledi skeletons indicate that the origins of the genus Homo were complex and may be polyphyletic (hybrid), and that the species may have evolved separately in different parts of Africa.[27][28]

Because caves don’t have regular sediment layers like riverbeds or floodplains, scientists initially had trouble dating the bones. Because of their relative “primitiveness,” that is, their similarity to our older, more ape-like ancestors, they initially thought Homo naledi must have lived a long time ago–around 2 million years ago. But when they finally got the bones dated, they found they were much younger–only around 335,000 and 236,000 years old,[1][4] which means H naledi and Homo sapiens–whose age was also recently adjusted–actually lived at the same time, though not necessarily in the same place.

(On the techniques used for dating the bones:

Francis Thackeray, of the University of the Witwatersrand, suggested that H. naledi lived 2 ± 0.5 million years ago, based on the skulls’ similarities to H. rudolfensis, H. erectus, and H. habilis, species that existed around 1.5, 2.5, and 1.8 million years ago, respectively.[35][36] Early estimates derived from statistical analysis of cranial traits yielded a range of 2 million years to 912,000 years before present.[2][37][38]

Dirks et al. (2017) obtained a much more recent age range of between 335,000 and 236,000 years ago from dating fossil teeth, sediments encasing the fossils and overlying flowstone. They used a variety of dating techniques, including radiocarbon dating of teeth, optically stimulated luminescence of sediment, palaeomagnetic analysis of flowstone, and most conclusively, uranium-thorium dating of cave flowstone and teeth and electron spin resonance dating of teeth.[1][4] The latter two types of measurements of teeth were performed on blind duplicate samples by two different labs.[1])

H naledi is unlikely to be a major branch on the human family tree–much too recent to be one of our ancestors–but it still offers important information on the development of “human” traits and how human and ape-like traits can exist side-by-side in the same individual (a theme we will return to later.) (Perhaps, just as we modern Homo sapiens contain traits derived from ancestors who mated with Neanderthals, Denisovans, and others, H naledi owes some of its traits to hybridization between two very different hominins.) It’s also important because it is one more data point in favor of the recent existence of a great many different human varieties, not just a single group.

Flores Hobbit aka Homo floresiensis source

The Flores hominin, (aka the Hobbit,) tells a similar tale, but much further afield from humanity’s evolutionary cradle.

The island of Flores is part of the Indonesian archipelago, a surprisingly rich source of early hominin fossils. Homo erectus, the famous Java Man, arrived in the area around 1.7 million years ago, but to date no erectus remains have been discovered on the actual island of Flores. During the last Glacial Maximum, ocean levels were lower and most of Indonesia was connected in a single continent, called Sundaland. During one of these glacial periods, H erectus could have easily walked from China to Java, but Flores remained an island, cut off from the mainland by several miles of open ocean.

Stone tools appeared on Flores about 1 million years ago, though we don’t know yet who made them, nor how they developed the technology necessary to make the journey.

The diminutive Hobbits show up later, around 50,000 to 100,000 years ago, though stone tools recovered alongside their remains have been dated from 50,000 to 190,000 years ago. Homo erectus is generally believed to have lived between 2 million and 140,000 years ago, and Homo sapiens arrived in Indonesia around 50,000 years ago. This places Floresiensis neatly between the two–it could have interacted with either species–perhaps descended from erectus and wiped out, in turn, by sapiens. (Or perhaps floresiensis represents an altogether novel line of hominins who left Africa on a completely separate trek from erectus.)

Unlike H naledi, whose diminutive stature is still within the current human range (especially of humans in the area,) floresiensis is exceptionally small for a hominin. According to Wikipedia:

The first set of remains to have been found, LB1, was chosen as the type specimen for the proposed species. LB1 is a fairly complete skeleton, including a nearly complete cranium (skull), determined to be that of a 30-year-old female. LB1 has been nicknamed the Little Lady of Flores or “Flo”.[2]

LB1’s height has been estimated at about 1.06 m (3 ft 6 in). The height of a second skeleton, LB8, has been estimated at 1.09 m (3 ft 7 in) based on measurements of its tibia.[3] These estimates are outside the range of normal modern human height and considerably shorter than the average adult height of even the smallest modern humans, such as the Mbenga and Mbuti (< 1.5 m (4 ft 11 in)),[32] Twa, Semang (1.37 m (4 ft 6 in) for adult women) of the Malay Peninsula,[33] or the Andamanese (1.37 m (4 ft 6 in) for adult women).[34]

By body mass, differences between modern pygmies and Homo floresiensis are even greater. LB1’s body mass has been estimated at 25 kg (55 lb). This is smaller than that of not only modern H. sapiens, but also H. erectus, which Brown and colleagues have suggested is the immediate ancestor of H. floresiensis. LB1 and LB8 are also somewhat smaller than the australopithecines from three million years ago, not previously thought to have expanded beyond Africa. Thus, LB1 and LB8 may be the shortest and smallest members of the extended human family discovered thus far.[citation needed]

Aside from smaller body size, the specimens seem otherwise to resemble H. erectus, a species known to have been living in Southeast Asia at times coincident with earlier finds purported to be of H. floresiensis.[3]

There’s a lot of debate about whether floresiensis is a real species–perhaps affected by insular dwarfism–or just a hominin that had some severe problems. Interestingly, we have a find from about 700,000 years ago on Flores of another hominin, which we think was also a Hobbit, but is even smaller than Flo and her relatives.

Floresiensis, like Naledi, didn’t contribute to modern humans. Rather, it is interesting because it shows the breadth of our genus. We tend to assume that, ever since we split off from the rest of the great apes, some 7 or 8 million years ago, our path has been ever upward, more complex and successful. But these Hobbits, most likely descendants of one of the most successful human species, (Homo erectus, who mastered fire, was the first to leave Africa, spread across Asia and Indonesia, and lasted for over a million and half years, far longer than our puny 300,000 years,) went in the opposite direction from its ancestors. It became much smaller than even the smallest living human groups. Its brain shrank:

In addition to a small body size, H. floresiensis had a remarkably small brain size. The brain of the holotype LB1 is estimated to have had a volume of 380 cm3 (23 cu in), placing it at the range of chimpanzees or the extinct australopithecines.[2][40] LB1’s brain size is half that of its presumed immediate ancestor, H. erectus (980 cm3 (60 cu in)).[40] The brain-to-body mass ratio of LB1 lies between that of H. erectus and the great apes.[41]

Nevertheless, it still made tools, probably controlled fire, and hunted cooperatively.

Whatever it was, it was like us–and very much not like us.


More on Naledi: Another Awesome Twig on our Human Family Tree and Homo Naledi was Chipping its Teeth Amazingly Often.