As slight as these finds are, scientists know quite a bit about these ancient hominins. In 2010, a team of scientists isolated and sequenced DNA from that finger bone fragment and discovered that it belonged to a young girl of an extinct Homo species described as Denisovan—after the Denisova cave in Siberia where the remains were found.

Unfortunately, the sequencing wasn’t reliable enough to do further studies. ScienceNOW explains:

But these genomes were too low quality to produce a reliable catalog of differences. Part of the problem was that ancient DNA is fragmentary, and most of it breaks down into single strands after it is extracted from bone.

Enter Matthias Meyer, a postdoc from Germany who developed a new way of sequencing. His novel technique splits the DNA double helix so that each of its two strands can be used for sequencing. This allowed the same team of scientists to sequence every position in the Denisovan genome about 30 times over ensuring that each nucleotide was in the correct spot.

The technique provides 99.9% accuracy—a quality similar to genomes that have been determined from present-day humans!

The much-improved genome furthers our understanding of the 50,000 year-old individual and population. The young girl had brown hair, eyes and skin and the genetic variation of Denisovans was extremely low—suggesting their population was never very large for long periods of time.

In addition, studies of the genome enhance our comprehension of human evolution. They describe the divergence between Denisovans and modern-day humans and confirm that modern populations from the islands of southeastern Asia (like Papua New Guinea) share genes with the Denisovans.

“This research will help determine how it was that modern human populations came to expand dramatically in size as well as cultural complexity while archaic humans eventually dwindled in numbers and became physically extinct,” says study co-author Svante Pääbo.

The findings were published last week in Science.

Image: Max Planck Institute for Evolutionary Anthropology

The authors of the paper sequenced the entire genomes of five members of each of the following hunter-gatherer populations: forest-dwelling, short-statured Pygmies from Cameroon, and click-speaking Hadza and Sandawe individuals from Tanzania.

The fascinating findings tell us more about human origins and prove to be a bit controversial, so I wanted to get more information from the Academy’s expert in human evolution, Zeray Alemseged. Zeray’s studies of early human remains have been published in prominent journals and garnered him worldwide attention. (PBS’s NOVA filmed an extensive interview with him here last spring, in addition to being on the covers of Nature and National Geographic.)

Zeray says these populations are not well studied and their isolation offers a new view on the human genome. Their unique diets, stature and culture also enable scientists to potentially link specific attributes to genetic markers, he adds.

The researchers used an in-depth method that involves sequencing each strand of DNA more than 60 times on average. This redundancy makes the sequencing highly accurate, giving the geneticists confidence that any mutations they identify are real and not errors.

Their results suggest that different human populations evolved distinctly in order to reap nutrition from local foods and defend against infectious disease. They also identify new candidate genes that likely play a major role in making Pygmies short in stature.

Scanning these sequences, the researchers found 13.4 million genetic variants or mutations—locations in the genome where a single nucleotide differed from other human sequences—and astonishingly, 3 million are new to science.

These new variants can represent the gene expressions unique to these populations, Zeray explains. This study is quite significant in making these genetic links to function and attributes that are phenotypic.

Zeray reminds us that these genetic studies aren’t just for mapping our ancestry, but also for mapping our future. He offers two separate examples—first, personalized medicine could tailor to specific gene regions. Second, “If we can link variants to diet, isolation and environment,” Zeray says, citing this current study’s examples, “then we can also understand what future climate change might look like for our species and how to prepare for it.”

Finally, the study finds genetic evidence that these direct ancestors of modern humans may have interbred with members of an unknown ancestral group of hominins. Zeray remarks that this particular finding—of a potential new species—reminds us why, in this technological age, paleoanthropology is a transdisciplinary endeavor requiring both fossil discovery AND genetic research.

So he’ll wait for more evidence, along with the rest of us…

The jaws discussed in the study are likely 1.8 to 2 million years old. But the story begins much more recently—in 1964, when Mary and Louis Leakey found a skull. They described it as Homo habilis, one of the oldest species of the Homo genus and possibly the first stone tool-maker.

Then in 1972, another skull was discovered. This one was somewhat similar to H. habilis, but larger, and seemingly with a flatter face. Many researchers attributed it to a separate species, Homo rudolfensis.

But not all paleoanthropologists agreed. Some thought it was just a larger version of H. habilis, perhaps showing the male-female sized difference known as sexual dimorphism that is common in primates. They also believed that the flattened aspect of H. rudolfensis’ face wasn’t indicative of its true shape—that it wasn’t flat after all. These scientists argued this skull didn’t belong to a separate species.

And the arguments have continued for 40 years. However, with the new study, researchers report on a discovery of another skull (face, actually) and two jaws. These fossils provide more evidence, it seems, for the existence of H. rudolfensis as a separate species.

Not that this ends the arguments. Instead, it seems to have provided more fuel for the fire! (See headlines above.)

Why does it matter so much? Because it all centers on human evolution—determining where we come from and where we go to from here. Some scientists look at human evolution as a linear straight line. But with H. habilis and H. rudolfensis (and a third species, Homo erectus) potentially co-existing at the same time, what does that say about our lineage? We shouldn’t be surprised, Zeray says, especially if we consider the way in which plants and other animals have evolved—it simply means that we are part of them and diverse. The possibilities are intriguing!

Image: Fred Spoor/National Museums of Kenya

Hominid fossils always make big news, and the interest extends to older primate fossils as well. Remember the big media splash Ida made at the announcement of her discovery? The European Darwinius masillae fossil, touted as the missing link in primate evolution back in 2009, had a book deal, documentary, and website. All for one fossil!

Primates are divided into two categories: lemurs and anthropoids (monkeys, apes, and humans). Ida, at 47 million years old, seems to lie at the beginning of the branch for anthropoids. Despite looking lemur-ish, Ida was missing a grooming claw: anthropoids have nothing but toenails and fingernails, while lemurs have a distinctive grooming claw.

At the time, dissention broke out in the scientific ranks, with many people arguing that too much hoopla had erupted over one fossil—and that Ida may be a “link” in human evolution, but not the “missing” one.

Well, last week, scientists published an article about Ida’s North American cousin, Notharctus tenebrosus (also 47 million years old).  While studying its fossil, researchers discovered an odd-shaped second toe. It has claw-like features near the base, but the tip is more flat, much like a modern monkey nail.

So what kind of link is Notharctus? Where does it fit in the family tree? Good question, says a new article about the fossil in PLoS One.

Study co-author Doug Boyer of Brooklyn College says the primate was “either in the process of evolving a nail and becoming more like humans, apes and monkeys, or in the process of evolving a more lemur-like claw.”

He also questions the origin of both nails and claws in the primate family tree. “I now believe it’s more likely that nails were the starting point and grooming claws developed as a functional trait.”

Lead author Stephanie Maiolino of Stony Brook University is unsure that claws and nails are even that significant. “It’s not clear that lacking a grooming claw means a species is related to anthropoids.” Take that, Ida!

One of the authors of the Ida study has already expressed disagreement with some of the findings of this current study. We can expect more to come on this lemur-anthropoid battle… Nature might be “red in tooth and claw,” but we hope the paleoanthropologists will settle this nail-biting mystery without much violence.

Image: PLoS One

Catching glimpses into our fossil ancestors’ daily lives is a tricky business. Fossil remains of our ancestors can only tell us so much concrete information, and tracing our DNA backwards in time can only get us so far.

But bones and teeth hold more clues than you’d think, if you just know how to extract them. In a new research paper published in the journal Nature, evolutionary anthropologists harnessed cutting-edge chemical tools and analyses to uncover the social patterns of our earliest ancestors and in so doing, discovered that males weren’t too keen on leaving their childhood homes.

The study, led by Sandi Copeland of the Max Planck Institute for Evolutionary Anthropology, looked at fossilized teeth from South Africa: eight Australopithecus africanus (2.2 million years ago) individuals and 11 individuals belonging to the Paranthropus robustus (1.8 million years ago) species. Using a laser, the team extracted a key element from the tooth enamel called strontium.

The strontium found in tooth enamel is like a snapshot into where the person lived during childhood, when permanent teeth developed. The various types of strontium, called isotopes, can be connected with specific geographical regions. “The strontium isotope ratios are a direct reflection of the foods these hominids ate, which in turn are a reflection of the local geology,” Copeland explains.

The research team divided sets of teeth for both species into male and female based on size (male teeth are generally larger). They then performed strontium isotope analysis on each, looking for clues into the each specimen’s childhood geographical landscape. They found that a large majority of male specimens – nearly 90% – grew up in the same general area where the fossilized teeth were uncovered. They were born, grew up, and died in pretty much the same place: the prehistoric equivalent of their hometown.

But analysis of female strontium isotopes revealed a different history. Over 50% of female remains trace to further afield, away from the dolomite cave systems that so many males grew up near. It seems that many females spent their formative years elsewhere, only arriving in the area once they reached adulthood.

Chimpanzees, our closest living primate relatives, exhibit a similar social structure. Male chimps are highly territorial, and will not leave their home base, even upon reaching adulthood. To prevent inbreeding, females are often forced to leave their childhood groups in search of new mating partners in other groups. Copeland’s strontium-isotope analysis lends support to the idea that early hominids might have done the same. If this structure exists in both chimpanzees and early hominids, perhaps its origins extend much further back in time.

“One of our goals was to try to find out something about early hominin landscape use. Here we have the first direct glimpse into the geographic movements of early hominids,” says Copeland.

The study not only provides insight into previously unknown aspects of ancient hominin social structure, it also highlights exactly how much new information can be squeezed out of a fossil specimen. As Julia Lee-Thorp, one of the study’s co-authors, explains, “Studies like these really bring home that finding and describing fossils is not the end of the story. Thoughtful application of these new analytical methods can tell us such a lot more about the details and lives of the distant past.”

Anne Holden, a docent at the California Academy of Sciences, is a PhD trained genetic anthropologist and science writer living in San Francisco.

Image: Darryl de Ruiter

There’s been much to say over the past few years about the possibility of significant interactions – and even interbreeding – between early members of our species, Homo sapiens, and our evolutionary cousins, Neanderthals. But now, new analysis of Neanderthal remains from western Russia casts doubt on the notion that we coexisted at all. Instead, the Neanderthals of western Russia appear to have died out before we even arrived. Results of this study were reported in last week’s online edition of the Proceedings of the National Academy of Sciences.

The research team, led by archaeologist Ron Pinhasi of University College Cork, questioned the analysis of two Neanderthal infants excavated over 10 years ago. The infants were found in the Mezmaiskaya Cave near the Caucasus Mountains of western Russia. Using carbon-14 dating, along with traditional stratigraphic methods (comparing ages of surrounding sediment layers), these infants were originally dated to about 30,000 years ago, just when humans were making their way into the region. This led many to wonder whether the two species ever came into contact, and to what extent.

But Pinahsi and his team were unconvinced the dating techniques were accurate. Central to their skepticism was the fact that the layers of sediment between which the infants were found were themselves dated incorrectly, skewing the original results.

But archaeological dating techniques have improved vastly over the past decade. So Pinhasi and his team put these new techniques to the test, by reanalyzing the Neanderthal infant remains directly. Specifically, Pinhasi harnessed the expertise of Thomas Hingham of Oxford University. Hingham has developed a new method of filtering samples that removes contaminants such as dirt, leaves, and collagen recovered from bone. This can give a far more accurate radiocarbon reading.

According to Hingham, “Previously, research teams provided younger dates which we now know are not robust, possibly because the fossil has become contaminated with modern particles. This latest dating evidences sheds further light on the extinction dates for Neanderthals in this key region.”

When putting the infant bone samples through the filter and dating them again, they found the infants to be 39,000 year old—9,000 years older than previously thought.

These infant remains had been strong evidence that humans and Neanderthals could have interacted with each other in western Russia. Now it is clear they were dead 9,000 years before humans showed up. Could this same story play out in other parts of the Europe and Asia?

“It now seems much clearer that Neanderthals and anatomically modern humans did not co-exist in the Caucasus, and it is possible that this scenario is also true for most regions of Europe,” says Pinhasi. He points to many instances of problematic dates for other archaeological sites excavated over the past several decades.

The western plains of Russia, like the Near East, were a prehistoric crossroads for early humans and our fossil ancestors. The revised analysis of the Mezmaiskaya Cave infants highlights the vast uncertainties we still hold surrounding the early expansions of our species, and our interactions with Neanderthals. But it also opens the door to new discoveries.

Anne Holden, a docent at the California Academy of Sciences, is a PhD trained genetic anthropologist and science writer living in San Francisco.

Image: Luna04/Wikimedia

The origin of our species was once firmly rooted in eastern Africa, but a new discovery may have shifted those roots much further to the south.

Exactly when and from where our species, Homo sapiens, first evolved and left Africa has been the subject of fierce debate. Most fossil and genetic evidence placed these origins in eastern Africa between 150,000 and 200,000 years ago. But a new study published earlier this month online in the Proceedings of the National Academy of Sciences reveals that our species may have evolved in southern, not eastern Africa.

Most Africans south of the Sahara are descended from early farmers spreading from western Africa about 8,000 years ago. But nestled within this vast dispersal of farmers are pockets of hunter-gatherers: The Khomani Bushmen of the Namibian Desert, the Pygmies of the central African rainforests, and the click-speaking Hadza and Sandawe of Tanzania. These peoples’ anatomy, culture, and language are distinct from their neighbors, and many believe that they offer a window into our species’ earliest days. But genetic data of these groups has been limited, and many questions on their origins remain.

The study’s authors, led by Brenna Henn of Stanford University, sought to fill in the gaps. “We started [this] project because southern Africa has been poorly sampled. Very few other studies have ever published on them in the last decade, certainly never with more than a dozen individuals,” says Henn.

Henn and colleagues analyzed over 55,000 individual points on the genomes of people from six hunter-gatherer populations, comparing them alongside other African populations. The team used this data to construct a genetic map of prehistoric Africa.

Not only had the hunter-gatherers been genetically isolated from the farming groups for thousands of years, they were also genetically distinct from each other.

In addition, long before the farmers swept across the continent, these hunter-gatherer groups were already well-established in their respective locales.

How does this relate to modern human origins? By using genomic data and a computer model, the team found the most likely starting point to be closest to the most ancient populations: southern Africa. Other experts have hypothesized this to be the case, and recent archaeological discoveries and climatic evidence have lent additional support to the fact that this region of Africa hosted our most ancient ancestors.

But the team has many questions left to answer. Henn and her colleagues also detected rapid evolutionary change among the groups, which may trace back thousands of years. They found that the Hadza of Tanzania have been going through a rapid decline, called a bottleneck, but have yet to understand why. “We would like to know when this bottleneck started – did it happen when the agriculturalists moved in?  Why don’t all hunter-gatherer populations show this signature?” says Henn.

Anne Holden, a docent at the California Academy of Sciences, is a PhD trained genetic anthropologist and science writer living in San Francisco.

Image of the Khomani courtesy of Brenna Henn