Ancestor Arguments

Our genus Homo is thought to have evolved a little more than 2 million years ago from the earlier Australopithecus. But there are few fossils that provide detailed information. ¹

But whether the new hominins are Homo ancestors or a side branch of late-surviving australopithecines, researchers agree that because of their completeness—including a skull and many postcranial bones—the fossils offer vital new clues to a murky area in human evolution. “This is a really remarkable find,” says paleontologist Meave Leakey of the National Museums of Kenya in Nairobi, who thinks it's an australopithecine. “Very lovely specimens,” says biological anthropologist William Kimbel of Arizona State University (ASU), Tempe, who thinks they are Homo.

Such different views of how to classify these fossils reflect a still-emerging debate over whether they are part of our own lineage or belong to a southern African side branch. The oldest Homo specimens are scrappy and enigmatic, leaving researchers unsure about the evolutionary steps between the australopithecines and Homo. Some think that the earliest fossils assigned to that genus, called H. habilis and H. rudolfensis and dated to as early as 2.3 million years ago, are really australopithecines. “The transition to Homo continues to be almost totally confusing,” says paleoanthropologist Donald Johanson of ASU Tempe, who has seen the new fossils. So it is perhaps no surprise that the experts disagree over whether the new bones represent australopithecines or early Homo. And for now, at least, they don't seem to mind the uncertainty. “All new discoveries make things more confusing” at first, says anthropologist Susan Antón of New York University. ²

I asked White whether Ardi's transitional form might justify calling Ar. ramidus a "missing link." He bristled at the very question.

"That term is wrong in so many ways, it's hard to know where to begin," he said. "Worst of all is the implication that at some point there existed something halfway between a chimp and a human. That's a popular misconception that has plagued evolutionary thought from the beginning, and one Ardi should bury, once and for all."

If the Middle Awash team is right in its interpretation, Ar. ramidus is indeed nothing at all like a modern chimp or gorilla. Of course apes and humans derive from a common ancestor. But their lineages have been evolving in separate, and quite different, directions ever since. ³

The study of human origins has been marked by lively—sometimes vicious—sparring over the identity of the original human ancestor. The battle royal is best symbolized by world-famous Lucy, a 3.2 million-year-old fossil Australopithecus afarensis originally unearthed in 1974 and put forth as the original biped leading to us. The furor over Lucy’s pedigree embroiled researchers of the 1980s and remains unresolved, but proof could be beside the point. “I frankly do not care,” says Stony Brook paleoanthropologist William Jungers. “She allows us to understand what our precursors looked like: sexually dimorphic, small-brained bipeds retaining the ability to climb trees.”

Recent discoveries offer a deeper and broader view of human ancestry. One stunner: Early humans mated with Neanderthals, according to evolutionary geneticist Svante Pääbo and colleagues at the Max Planck Institute for Evolutionary Anthropology in Germany. Through an analysis of DNA fragments from Neanderthal bones, Pääbo traced the interbreeding back 60,000 years to the Middle East. Today 1 to 4 percent of the human genome outside Africa is Neanderthal. Another shock came last year when Tim White of the University of California, Berkeley, and the Middle Awash Team unveiled Ardipithecus ramidus (“Ardi”), a 4.4 million- year-old fossil female hominid. Bipedal on the ground but efficient at moving through trees, Ardi suggests the common ancestor we share with chimpanzees was an ape with monkeylike traits. Finally, in 2004, in a cave on the island of Flores in Indonesia, bones of a human relative no larger than a modern-day 4-year-old were discovered by archaeologist Michael Morwood of the University of Wollongong in Australia and his team. The bones are 14,000 years old, but tools nearby date back as much as a million years. After furious debate, most paleoanthropologists now agree that Homo floresiensis, nicknamed the hobbit, is a genuine ancient human with a teensy brain folded in ways that increased its complexity—enough for hobbits to hunt cooperatively, knap their own tools, and thrive on an island for more than a million years. ⁵

For the first time a hominin has been described, not from the morphology of its fossilized bones, but from the sequence of its DNA.

The DNA comes from a piece of finger bone discovered in Denisova Cave in the Altai Mountains of southern Siberia. This cave was intermittently occupied by humans for 125,000 years. It is rich in stone tools and bone implements, but has yielded few human bones, most of them isolated finds such as that used in this study. With such incomplete specimens, the morphological information needed to identify the species to which a human bone belongs is impossible.

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By comparing the sequence of the Denisova mtDNA with those of Neanderthals and modern humans, Krause et al were able to draw a family tree showing the three species' evolutionary relationships. The tree revealed that the common ancestor of the species dates to about 1 million years ago. If modern humans evolved in Africa, then this ancestor must also have been in Africa, making it impossible for the Denisova hominin to be descended from the H. erectus populations that moved to Europe 900,000 years earlier. The Denisova sequence is also distinct from that of the immediate ancestors of Neanderthals, which split away from the lineage leading to modern humans some 450,000 years ago, much later than the branch leading to Denisova. Left with few alternatives, Krause et al. make the logical deduction that the Denisova DNA sequence represents an unknown type of hominin that left Africa in a previously unsuspected migration about 1 million years ago, and that survived in at least some parts of Eurasia until 40,000 years ago or later. ⁶

Her approximately 3-billion-letter nuclear genome, reported in this issue of Nature, now provides a more telling glimpse into this mysterious group. It also raises previously unimagined questions about its history and relationship to Neanderthals and humans. "The whole story is incredible. It's like a surprising Christmas present," says Carles Lalueza Fox, a palaeogeneticist at Pompeu Fabra University in Barcelona, Spain, who was not involved in the research. ⁷

Until recently, genetic data and interpretation of the fossil record seemed to favour a complete-replacement model, in which all human species trace all of their genetic ancestry to a single origin in one or more African populations of moderate size some 200,000 years ago. However, the Denisovan nuclear genome sequence, along with that of Homo neanderthalensis published by some of the same authors, suggest that the out-of-Africa population history of Homo sapiens is probably much more intertwined than previously thought, with more intertwining in some parts of the world than others. ⁸

Most anthropologists think that our species, H. sapiens, first evolved in sub-Saharan Africa about 200,000 years ago and began migrating out of Africa between 70,000 and 50,000 years ago, eventually colonizing the globe. And although the expansion has often been considered a single migration, many researchers are beginning to suspect that moderns left Africa in two or more waves.

Some of these early migrants may have gone east, across the Red Sea and along the southern coast of Arabia. But the earliest known modern human fossils outside Africa suggest a northern route, perhaps through the Nile Valley: Modern human skulls and other bones discovered in the early 20th century in the Skhul and Qafzeh caves in Israel are now dated to between 100,000 and 130,000 years ago, although researchers debate whether these early colonizers traveled any farther at that early date (Science, 9 October 2009, p. 224).

Despite this early connection to the Middle East, not so long ago most experts thought that modern humans occupied North Africa itself relatively late. ⁹

So ancient DNA, too, argued against the idea of mixing between Neandertals and moderns. Over the years the replacement model became the leading theory, with only a stubborn few, including Wolpoff, holding to multiregionalism.

Yet there were a few dissenting notes. A few studies of individual genes found evidence of migration from Asia into Africa, rather than vice versa. Population geneticists warned that complete replacement was unlikely, given the distribution of alleles in living humans. And a few paleoanthropologists proposed middle-of-the-road models. Smith, a former student of Wolpoff's, suggested that most of our ancestors arose in Africa but interbred with local populations as they spread out around the globe, with archaic people contributing to about 10% of living people's genomes. At the University of Hamburg in Germany, Gunter Brauer similarly proposed replacement with hybridization, but with a trivial amount of interbreeding. But neither model got much traction; they were either ignored or lumped in with multiregionalism. “Assimilation got kicked so much,” recalls Smith. ¹⁰

Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. ¹¹