human evolution

old-easter-island-genomes-show-no-sign-of-a-population-collapse

Old Easter Island genomes show no sign of a population collapse

A row of grey rock sculptures of human torsos and heads, arranged in a long line.

Rapa Nui, often referred to as Easter Island, is one of the most remote populated islands in the world. It’s so distant that Europeans didn’t stumble onto it until centuries after they had started exploring the Pacific. When they arrived, though, they found that the relatively small island supported a population of thousands, one that had built imposing monumental statues called moai. Arguments over how this population got there and what happened once it did have gone on ever since.

Some of these arguments, such as the idea that the island’s indigenous people had traveled there from South America, have since been put to rest. Genomes from people native to the island show that its original population was part of the Polynesian expansion across the Pacific. But others, such as the role of ecological collapse in limiting the island’s population and altering its culture, continue to be debated.

Researchers have now obtained genome sequence from the remains of 15 Rapa Nui natives who predate European contact. And they indicate that the population of the island appears to have grown slowly and steadily, without any sign of a bottleneck that could be associated with an ecological collapse. And roughly 10 percent of the genomes appear to have a Native American source that likely dates from roughly the same time that the island was settled.

Out of the museum

The remains that provided these genomes weren’t found on Rapa Nui, at least not recently. Instead, they reside at the Muséum National d’Histoire Naturelle in France, having been obtained at some uncertain point in the past. Their presence there is a point of contention for the indigenous people of Rapa Nui, but the researchers behind the new work had the cooperation of the islanders in this project, having worked with them extensively. The researchers’ description of these interactions could be viewed as a model for how this sort of work should be done:

Throughout the course of the study, we met with representatives of the Rapanui community on the island, the Comisión de Desarrollo Rapa Nui and the Comisión Asesora de Monumentos Nacionales, where we presented our research goals and ongoing results. Both commissions voted in favor of us continuing with the research… We presented the research project in public talks, a short video and radio interviews on the island, giving us the opportunity to inquire about the questions that are most relevant to the Rapanui community. These discussions have informed the research topics we investigated in this work.

Given the questionable record-keeping at various points in the past, one of the goals of this work was simply to determine whether these remains truly had originated on Rapa Nui. That was unambiguously true. All comparisons with genomes of modern populations show that all 15 of these genomes have a Polynesian origin and are most closely related to modern residents of Rapa Nui. “The confirmation of the origin of these individuals through genomic analyses will inform repatriation efforts led by the Rapa Nui Repatriation Program (Ka Haka Hoki Mai Te Mana Tupuna),” the authors suggest.

A second question was whether the remains predate European contact. The researchers attempted to perform carbon dating, but it produced dates that made no sense. Some of the remains had dates that were potentially after they had been collected, according to museum records. And all of them were from the 1800s, well after European contact and introduced diseases had shrunk the native population and mixed in DNA from non-Polynesians. Yet none of the genomes showed more than one percent European ancestry, a fraction low enough to be ascribed to a spurious statistical fluke.

So the precise date these individuals lived is uncertain. But the genetic data clearly indicates that they were born prior to the arrival of Europeans. They can therefore tell us about what the population was experiencing in the period between Rapa Nui’s settlement and the arrival of colonial powers.

Back from the Americas

While these genomes showed no sign of European ancestry, they were not fully Polynesian. Instead, roughly 10 percent of the genome appeared to be derived from a Native American population. This is the highest percentage seen in any Polynesian population, including some that show hints of Native American contact that dates to before Europeans arrived on the scene.

Isolating these DNA sequences and comparing them to populations from across the world showed that the group most closely related to the one who contributed to the Rapa Nui population presently resides in the central Andes region of South America. That’s in contrast to the earlier results, which suggested the contact was with populations further north in South America.

Old Easter Island genomes show no sign of a population collapse Read More »

indonesia’s-tiny-hobbits-descended-from-even-smaller-ancestors

Indonesia’s tiny hobbits descended from even smaller ancestors

Hobbit erectus? —

A 700,000-year-old humerus suggests small hominins have a long history on Flores.

Image of a small fossil bone in the palm of a person's hand.

Enlarge / Half of the upper arm bone of this species can fit comfortably in the palm of a modern human hand.

Yousuke Kaifu

The discovery of Homo floresiensis, often termed a hobbit, confused a lot of people. Not only was it tiny in stature, but it shared some features with both Homo erectus and earlier Australopithecus species and lived well after the origin of modern humans. So, its precise position within the hominin family tree has been the subject of ongoing debate—one that hasn’t been clarified by the discovery of the similarly diminutive Homo luzonensis in the Philippines.

Today, researchers are releasing a paper that describes bones from a diminutive hominin that occupied the island of Flores much earlier than the hobbits. And they argue that, while it still shares an odd mix of features, it is most closely related to Homo erectus, the first hominin species to spread across the globe.

Remarkably small

The bones come from a site on Flores called Mata Menge, where the bones were found in a large layer of sediment. Slight wear suggests that many of them were probably brought to the site by a gentle flood. Dating from layers above and below where the fossils were found limits their age to somewhere between 650,000 and 775,000 years ago. Most of the remains are teeth and fragments of jaw bone, which can be suggestive of body size, but not definitive. But the new finds include a fragment of the upper arm bone, the humerus, which is more directly proportional to body size.

The researchers argue that the bone is broken at roughly the mid-point of the humerus, meaning that the full-sized bone was twice its length. Based on the relationship between humerus length and body size, they estimate that the individual it came from was only a bit above a meter tall.

They also took a slice from the center of the sample and imaged the cells present in the bone when it fossilized. These suggest that the fossil came from a fully mature adult. That makes its dimensions, including the diameter of the bone, the smallest yet found. It is, to quote the paper, “smaller than LB1 (H. floresiensis) and any other adult individuals of small-bodied fossil hominins (Australopithecus and H. naledi.” So, even by the standards of small species, the new fossils belong to an extremely small individual.

As for what these individuals are related to, the answers are (once again) complicated. The morphology of the humerus is most closely related to the H. floresiensis individuals who resided on Flores hundreds of thousands of years later. Beyond that, it’s most similar to H. naledi. From there, its shape appears to be equally distant from various species, including both H. erectus and various species of Australopithecus. The teeth show a variety of affinities but are generally closest to members of the Homo genus.

So, the authors make two arguments. One is that the fossils come from the ancestors of the hobbits and belong to the same species, indicating that they inhabited Flores for at least half a million years. The second is that it’s a branch off the population of H. erectus, a species that was similar in stature to modern humans. The population would have evolved a shorter stature once isolated on Flores.

Nothing makes a lot of sense

That’s the argument, at least. There will undoubtedly be different opinions among paleontologists, however. Some had already argued that H. floresiensis was an offshoot of H. erectus and will be happy to accept this as new evidence. But the species is such a hodge-podge of features of earlier and contemporary species that it has been easy for others to make contrary arguments.

Even if those arguments were settled, there’s the issue of how it got there. Even at times of significantly lower sea levels, Flores would have required a significant ocean crossing from what is now Java, where H. erectus is known to have been present, and which was connected to Asia at the time. There’s no indication that any species that came before modern humans had developed boating technology, and some have suggested that the population was established on Flores after being swept there on tsunami debris. Once present, the island environment could have selected for a smaller body size.

But then there’s the issue of Homo luzonensis, which shared a similar body size but inhabited a very different island. That would seem to require a second event that was also unlikely: either a second ocean passage involving individuals from Flores or another ocean trip by H. erectus followed by similar evolution of smaller body size, despite a potentially different environment.

It’s clear that, while the new finds tell us something about the Flores population, they’re not going to settle any arguments.

Nature Communications, 2024. DOI: 10.1038/s41467-024-50649-7  (About DOIs).

Indonesia’s tiny hobbits descended from even smaller ancestors Read More »

much-of-neanderthal-genetic-diversity-came-from-modern-humans

Much of Neanderthal genetic diversity came from modern humans

A large, brown-colored skull seen in profile against a black background.

The basic outline of the interactions between modern humans and Neanderthals is now well established. The two came in contact as modern humans began their major expansion out of Africa, which occurred roughly 60,000 years ago. Humans picked up some Neanderthal DNA through interbreeding, while the Neanderthal population, always fairly small, was swept away by the waves of new arrivals.

But there are some aspects of this big-picture view that don’t entirely line up with the data. While it nicely explains the fact that Neanderthal sequences are far more common in non-African populations, it doesn’t account for the fact that every African population we’ve looked at has some DNA that matches up with Neanderthal DNA.

A study published on Thursday argues that much of this match came about because an early modern human population also left Africa and interbred with Neanderthals. But in this case, the result was to introduce modern human DNA to the Neanderthal population. The study shows that this DNA accounts for a lot of Neanderthals’ genetic diversity, suggesting that their population was even smaller than earlier estimates had suggested.

Out of Africa early

This study isn’t the first to suggest that modern humans and their genes met Neanderthals well in advance of our major out-of-Africa expansion. The key to understanding this is the genome of a Neanderthal from the Altai region of Siberia, which dates from roughly 120,000 years ago. That’s well before modern humans expanded out of Africa, yet its genome has some regions that have excellent matches to the human genome but are absent from the Denisovan lineage.

One explanation for this is that these are segments of Neanderthal DNA that were later picked up by the population that expanded out of Africa. The problem with that view is that most of these sequences also show up in African populations. So, researchers advanced the idea that an ancestral population of modern humans left Africa about 200,000 years ago, and some of its DNA was retained by Siberian Neanderthals. That’s consistent with some fossil finds that place anatomically modern humans in the Mideast at roughly the same time.

There is, however, an alternative explanation: Some of the population that expanded out of Africa 60,000 years ago and picked up Neanderthal DNA migrated back to Africa, taking the Neanderthal DNA with them. That has led to a small bit of the Neanderthal DNA persisting within African populations.

To sort this all out, a research team based at Princeton University focused on the Neanderthal DNA found in Africans, taking advantage of the fact that we now have a much larger array of completed human genomes (approximately 2,000 of them).

The work was based on a simple hypothesis. All of our work on Neanderthal DNA indicates that their population was relatively small, and thus had less genetic diversity than modern humans did. If that’s the case, then the addition of modern human DNA to the Neanderthal population should have boosted its genetic diversity. If so, then the stretches of “Neanderthal” DNA found in African populations should include some of the more diverse regions of the Neanderthal genome.

Much of Neanderthal genetic diversity came from modern humans Read More »

high-altitude-cave-used-by-tibetan-buddhists-yields-a-denisovan-fossil

High-altitude cave used by Tibetan Buddhists yields a Denisovan fossil

Eating in —

Cave deposits yield bones of sheep, yaks, carnivores, and birds that were butchered.

Image of a sheer cliff face with a narrow path leading to a cave opening.

Enlarge / The Baishiya Karst Cave, where the recently analyzed samples were obtained.

Dongju Zhang’s group (Lanzhou University)

For well over a century, we had the opportunity to study Neanderthals—their bones, the items they left behind, their distribution across Eurasia. So, when we finally obtained the sequence of their genome and discovered that we share a genetic legacy with them, it was easy to place the discoveries into context. In contrast, we had no idea Denisovans existed when sequencing DNA from a small finger bone revealed that yet another relative of modern humans had roamed Asia in the recent past.

Since then, we’ve learned little more. The frequency of their DNA in modern human populations suggest that they were likely concentrated in East Asia. But we’ve only discovered fragments of bone and a few teeth since then, so we can’t even make very informed guesses as to what they might have looked like. On Wednesday, an international group of researchers described finds from a cave on the Tibetan Plateau that had been occupied by Denisovans, which tell us a bit more about these relatives: what they ate. And that appears to be anything they could get their hands on.

The Baishiya Karst Cave

The finds come from a site called the Baishiya Karst Cave, which is perched on a cliff on the northeast of the Tibetan Plateau. It’s located at a high altitude (over 3,000 meters or nearly 11,000 feet) but borders a high open plain, as you can see in the picture below.

Oddly, it came to the attention of the paleontology community because the cave was a pilgrimage site for Tibetan monks, one of whom discovered a portion of a lower jaw that eventually was given to a university. There, people struggled to understand exactly how it fit with human populations until eventually analysis of proteins preserved within it indicated it belonged to a Denisovan. Now called the Xiahe mandible, it remains the most substantial Denisovan fossil we’ve discovered to date.

The Ganjia Basin borders the cliffs that contain the Baishiya Karst Cave.

Enlarge / The Ganjia Basin borders the cliffs that contain the Baishiya Karst Cave.

Dongju Zhang’s group (Lanzhou University)

Since then, excavations at the site had turned up a large collection of animal bones, but none that had been identified as Denisovan. Sequencing of environmental DNA preserved in the cave, however, revealed that the Denisovans had occupied the cave regularly for at least 100,000 years, meaning they were surviving at altitude during both of the last two glacial cycles.

The new work focuses in on the bones, many of which are too fragmentary to be definitively assigned to a species. To do so, the researchers purified fragments of proteins from the bones, which contain large amounts of collagen. These fragments were then separated according to their mass, a technique called mass spectrometry, which works well even with the incredibly small volumes of proteins that survive over hundreds of thousands of years.

Mass spectrometry relies on the fact that there are only a limited number of combinations of amino acids—often only one—that will produce a protein fragment of a given mass. So, if the mass spectrometry finds a signal at that mass, you can compare the possible amino acid combinations that produce it to known collagen sequences to find matches. Some of these matches will end up being in places where collagens from different species have distinct sequences of amino acids, allowing you to determine what species the bone came from.

When used this way, the technique is termed zooarchaeology by mass spectrometry, or ZooMS. And, in the case of the work described in the new paper, it identified nearly 80 percent of the bone fragments that were tested.

High-altitude cave used by Tibetan Buddhists yields a Denisovan fossil Read More »