Bonobos and Chimpanzees had a Human/Neandertal Like Fling

A new whole-genome analysis of chimpanzees and bonobos reveals that these two great ape species likely interbred several hundred thousand years ago. A better understanding of the genetic flow between humans' closest living relatives could shed light on processes that might have played a recurring role in great ape evolution. While chimpanzees and bonobos are known to interbreed in captivity, the historic genetic flow between the two species in the wild is less clear. To gain better insights into possible historical gene flow between them, Marc de Manuel et al. analyzed the complete genomes of 10 bonobos and 65 chimpanzees. Significantly, more chimpanzees were included in their analysis, and from various regions in Africa, because previous genetic studies have suggested that four distinct species of chimpanzee exist. Following their analysis, the researchers observed clear evidence for gene flow between the two species, occurring between 200 and 550 thousand years ago, they estimate. Central, eastern, and Nigeria-Cameroon chimpanzees share significantly more genetic information with bonobos than do western chimpanzees, they report. What's more, similar to Neanderthal genetic patterns in humans, some background bonobo genetic information has been deleted in the chimpanzee genome, suggesting that some bonobo genes may have been disadvantageous for chimpanzees.

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New Evidence Suggestions Modern Human, Neandertals Interbred Much Earlier Than Previously Thought

Using several different methods of DNA analysis, an international research team has identified an interbreeding event between Neanderthals and modern humans that occurred an estimated 100,000 years ago, which is tens of thousands of years earlier than other such events previously documented. They suggest that some modern humans left Africa early and mixed with Neanderthals. These modern humans later became extinct and are therefore not among the ancestors of present-day people outside Africa who left Africa about 65,000 years ago.

"We knew from Neanderthal DNA found in the genomes of humans outside Africa that Neanderthals and humans have interbred. This interbreeding is estimated to have happened less than 65,000 years ago, around the time that modern human populations spread across Eurasia from Africa. We now find evidence for a modern human contribution to the Neanderthal genome. This is likely the result of much earlier interbreeding", says Sergi Castellano from the Max Planck Institute for Evolutionary Anthropology, who co-led the study.

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Neandertal Genes IDed as Important to Modern Human's Immunity Systems

When modern humans met Neanderthals in Europe and the two species began interbreeding many thousands of years ago, the exchange left humans with gene variations that have increased the ability of those who carry them to ward off infection. This inheritance from Neanderthals may have also left some people more prone to allergies.

The discoveries reported in two independent studies in the American Journal of Human Genetics on January 7 add to evidence for an important role for interspecies relations in human evolution and specifically in the evolution of the innate immune system, which serves as the body's first line of defense against infection.

"We found that interbreeding with archaic humans--the Neanderthals and Denisovans--has influenced the genetic diversity in present-day genomes at three innate immunity genes belonging to the human Toll-like-receptor family," says Janet Kelso of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany.

"These, and other, innate immunity genes present higher levels of Neanderthal ancestry than the remainder of the coding genome," adds Lluis Quintana-Murci of the Institut Pasteur and the CNRS in Paris. "This highlights how important introgression events [the movement of genes across species] may have been in the evolution of the innate immunity system in humans."

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Mammoth Evolution and Dispersal Across the Northern Hemisphere

Evolution and dispersal of mammoths across the Northern Hemisphere

Authors:

Lister et al

Abstract:

le of species origins and dispersal, but understanding has been impeded by taxonomic confusion, especially in North America. The Columbian mammoth Mammuthus columbi was thought to have evolved in North America from a more primitive Eurasian immigrant. The earliest American mammoths (1.5 million years ago), however, resemble the advanced Eurasian M. trogontherii that crossed the Bering land bridge around that time, giving rise directly to M. columbi. Woolly mammoth M. primigenius later evolved in Beringia and spread into Europe and North America, leading to a diversity of morphologies as it encountered endemic M. trogontherii and M. columbi, respectively. In North America, this included intermediates (“M. jeffersonii”), suggesting introgression of M. primigenius with M. columbi. The lineage illustrates the dynamic interplay of local adaptation, dispersal, and gene flow in the evolution of a widely distributed species complex.

Eurasian Farmers "Invaded" Africa at Least 4,500 Years ago, 4 to 7% of African Genome is Eurasian

Geneticists have sequenced the first prehistoric genome from Africa: that of Mota, a hunter-gatherer man who lived 4500 years ago in the highlands of Ethiopia. Named for the cave that held the remains, the Mota genome gives scientists their first glimpse into what an African genome looked like prior to many recent migrations in Africa. This ancient Ethiopian highlander is most closely related to the Ari, an ethnic group that speaks Omotic languages in the Ethiopian highlands today. And when researchers compared Mota's genome to that of other Africans, Europeans, and Asians, they got a surprise: Africa is usually seen as a source of outward migrations, but the genomes suggest a major migration into Africa by farmers from the Middle East, possibly about 3500 years ago. These farmers' DNA reached deep into the continent, spreading even to groups considered isolated such as the Khoisan of South Africa and the pygmies of the Congo.

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Oase-1: This man was 10% Neandertal

To Erik Trinkaus, the jaw of the oldest modern human found in Europe has always looked strange. Its huge wisdom teeth and hefty, buttressed lower jaw reminded him of Neandertals, and he argued that this fossil, 37,000 to 42,000 years old, was the product of generations of mixing between modern humans and our extinct cousins. “It wasn't a popular idea,” admits Trinkaus, a paleoanthropologist at Washington University in St. Louis. Other paleoanthropologists insisted that the young man whose remains were found in 2002 in Peştera cu Oase cave in Romania was just a chunky example of our own species.

Now, 15 years later, Trinkaus has been vindicated by ancient DNA. The young Oase man inherited as much as one-tenth of his DNA from a Neandertal ancestor, and that ancestor lived only 200 years or so previously, according to a talk this month at Cold Spring Harbor Laboratory in New York. “One of Oase's ancestors—its great-great-great-grandparent—is Neandertal,” reported Qiaomei Fu, a geneticist at the Chinese Academy of Sciences–Max Planck Society Joint Laboratory for Human Evolution in Beijing and a postdoc in the lab of population geneticist David Reich at Harvard Medical School. The finding is “important as the first direct evidence of a very recent admixture event in Europe,” says population geneticist Laurent Excoffier of the University of Bern.

Europe just after the arrival of modern humans has long seemed a likely setting for such close encounters, given that Neandertals and modern humans overlapped there about 45,000 to 39,000 years ago. But until now, ancient DNA pointed to a different time and place for such a liaison. By sequencing the genomes of fossil Neandertals and comparing them with today's human genomes, paleogeneticists had found that living Europeans and Asians—but not Africans—have inherited just 1% to 4% of their DNA from Neandertals. DNA from fossils of two modern humans from what is now Russia also suggested that their Neandertal heritage was faint (see http://scim.ag/RussDNA). So researchers proposed that modern humans and Neandertals had rare and relatively early encounters, perhaps in the Middle East, when moderns swept out of Africa 60,000 to 50,000 years ago.

The DNA from Oase 1, a lower jaw without a skull, complicates that picture, Fu reported at the Biology of Genomes meeting. Working in a team led by paleogeneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, she and her colleagues captured 2.2 million base pairs of the fossil's DNA. Then, they sequenced 78,055 locations where the genomes of Neandertals and modern humans are known to differ. They found that the Oase man had far more Neandertal DNA—composing 4.8% to 11.3% of his genome—than either the ancient modern humans from Russia or living Europeans and Asians, Fu said.

What's more, the young man had inherited the Neandertal DNA in “large chunks,” including several segments more than 50 million base pairs long; one chunk spanned half the length of chromosome 12. Those unbroken stretches of Neandertal DNA suggest that the interbreeding must have been just four to six generations back. If the mixing had been more ancient, the long DNA segments would have been broken up by the reshuffling of chromosomes that takes place every generation. “This is quite amazing,” Fu said in her talk. “We're quite excited about that.”

If modern humans and Neandertals had several successful matings, why do living humans' genomes record only the earlier event?

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Khoisan People Show No (!!!) Admixture With Other Humans Since Calabrian Pleistocene Quaternary (150kya)

New genetic research reveals that a small group of hunger-gatherers now living in Southern Africa once was so large that it comprised the majority of living humans during most of the past 150,000 years. Only during the last 22,000 years have the other African ethnicities, including the ones giving rise to Europeans and Asians, become vastly most numerous. Now the Khoisan (who sometimes call themselves Bushmen) number about 100,000 individuals, while the rest of humanity numbers 7 billion. Their lives and ways have remained unaltered for hundreds of generations, with only recent events endangering their hunter-gatherer lifestyles. The study's findings will be published in the journal Nature Communications on 4 December 2014.

By comparing nearly all the genes of these individuals -- their genomes -- with the genomes of 1,462 people from around the world, the researchers discovered that the inflow of new genes into the Khoisan peoples has been quite restricted the past 150,000 years, indicating that this large hunter-gatherer culture was physically isolated for most of its history and that its men typically did not take wives from outside the group.

"Khoisan hunter-gatherers in Southern Africa always have perceived themselves as the oldest people" said Stephan Schuster, a former Penn State University professor, now at Nanyang Technological University in Singapore and a leader of the research team, which includes scientists at Penn State and other research universities in the United States, Brazil, and Singapore. The Nature Communication paper analyzes five study participants from different tribes in Namibia. The study investigated 420,000 genetic variants across 1,462 genomes from 48 ethnic groups in populations worldwide. These analyses reveal that Southern African Khoisans are genetically distinct not only from Europeans and Asians, but also from all other Africans. The paper's first author Hie Lim Kim, formerly at Penn State and now at Nanyang Technological University, said "It is fascinating to unravel the population history of humankind over the last 150,000 years."

By conducting extensive computational analyses, the team demonstrated that two of the sequenced individuals showed no signs of having inherited any genetic material from members of other ethnic groups. Interestingly, these individuals are the oldest members of the Ju/'hoansi tribe, which still live in protected areas of Northwest Namibia. "This and previous studies show that the Khoisan peoples and the rest of modern humanity shared their most recent common ancestor approximately 150,000 years ago, so it was entirely unexpected to find that this group apparently did not intermarry with non-Khoisan neighbors for many thousand years," said Webb Miller, professor of Bioinformatics at Penn State and a member of the research team. "The current Khoisan culture and tradition, where marriage occurs either among Khoisan groups or results in female members leaving their tribes after marrying non-Khoisan men, appears to be long-standing."

The cultural and genetic persistence of the Ju/'hoansi tribe is intriguing, the researchers say, because genetic and genomic analysis of ancient hominid lineages such as the Neanderthals, as well as non-African humans, have shown that intermarrying does occur frequently in these groups and is traceable over the entire time span of 150,000 history during which anatomically modern humans have lived. "We also observed gene flow for some of the other Khoisan groups, as defined by their largely varying language, but a key finding of this study is that, even today, individuals without genes from other communities can be identified within the Ju/'hoansi population and possibly others," Schuster said.

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The damned important question is whether or not the  Khoisan have the introgressed genes proposed to be Neandertal and Denisovan in origin.  If they do and the conclusion the Khoisan have been genetically isolated for that long, it throws into question the recent admixture is really what it is.

Horses, Equids Have a Complicated Evolutionary History

Speciation with gene flow in equids despite extensive chromosomal plasticity

Authors:

Jónsson et al

Abstract:

Horses, asses, and zebras belong to a single genus, Equus, which emerged 4.0–4.5 Mya. Although the equine fossil record represents a textbook example of evolution, the succession of events that gave rise to the diversity of species existing today remains unclear. Here we present six genomes from each living species of asses and zebras. This completes the set of genomes available for all extant species in the genus, which was hitherto represented only by the horse and the domestic donkey. In addition, we used a museum specimen to characterize the genome of the quagga zebra, which was driven to extinction in the early 1900s. We scan the genomes for lineage-specific adaptations and identify 48 genes that have evolved under positive selection and are involved in olfaction, immune response, development, locomotion, and behavior. Our extensive genome dataset reveals a highly dynamic demographic history with synchronous expansions and collapses on different continents during the last 400 ky after major climatic events. We show that the earliest speciation occurred with gene flow in Northern America, and that the ancestor of present-day asses and zebras dispersed into the Old World 2.1–3.4 Mya. Strikingly, we also find evidence for gene flow involving three contemporary equine species despite chromosomal numbers varying from 16 pairs to 31 pairs. These findings challenge the claim that the accumulation of chromosomal rearrangements drive complete reproductive isolation, and promote equids as a fundamental model for understanding the interplay between chromosomal structure, gene flow, and, ultimately, speciation.

45,000 Year Old Siberian Man had Significantly More Neandertal Genes Than Modern People

Genome sequence of a 45,000-year-old modern human from western Siberia

Authors:

Fu et al

Abstract:

We present the high-quality genome sequence of a ~45,000-year-old modern human male from Siberia. This individual derives from a population that lived before—or simultaneously with—the separation of the populations in western and eastern Eurasia and carries a similar amount of Neanderthal ancestry as present-day Eurasians. However, the genomic segments of Neanderthal ancestry are substantially longer than those observed in present-day individuals, indicating that Neanderthal gene flow into the ancestors of this individual occurred 7,000–13,000 years before he lived. We estimate an autosomal mutation rate of 0.4 × 10−9 to 0.6 × 10−9 per site per year, a Y chromosomal mutation rate of 0.7 × 10−9 to 0.9 × 10−9 per site per year based on the additional substitutions that have occurred in present-day non-Africans compared to this genome, and a mitochondrial mutation rate of 1.8 × 10−8 to 3.2 × 10−8 per site per year based on the age of the bone.

Now we know when Neandertals got the Sapiens drunk enough for the first beer goggles.  

Did Tibetans Get Hemoglobin Gene From Denisovan Hominins?

Tibetans were able to adapt to high altitudes thanks to a gene picked up when their ancestors mated with a species of human they helped push to extinction, according to a new report by University of California, Berkeley, scientists.

An unusual variant of a gene involved in regulating the body's production of hemoglobin – the molecule that carries oxygen in the blood – became widespread in Tibetans after they moved onto the high-altitude plateau several thousand years ago. This variant allowed them to survive despite low oxygen levels at elevations of 15,000 feet or more, whereas most people develop thick blood at high altitudes, leading to cardiovascular problems.

"We have very clear evidence that this version of the gene came from Denisovans," a mysterious human relative that went extinct 40,000-50,000 years ago, around the same time as the more well-known Neanderthals, under pressure from modern humans, said principal author Rasmus Nielsen, UC Berkeley professor of integrative biology. "This shows very clearly and directly that humans evolved and adapted to new environments by getting their genes from another species."

This is the first time a gene from another species of human has been shown unequivocally to have helped modern humans adapt to their environment, he said.

Nielsen and his colleagues at BGI-Shenzhen in China will report their findings online July 2 in advance of publication in the journal Nature.

The gene, called EPAS1, is activated when oxygen levels in the blood drop, triggering production of more hemoglobin. The gene has been referred to as the superathlete gene because at low elevations, some variants of it help athletes quickly boost hemoglobin and thus the oxygen-carrying capacity of their blood, upping endurance. At high altitude, however, the common variants of the gene boost hemoglobin and its carrier, red blood cells, too much, increasing the thickness of the blood and leading to hypertension and heart attacks as well as low-birth-weight babies and increased infant mortality. The variant or allele found in Tibetans raises hemoglobin and red blood cell levels only slightly at high elevation, avoiding the side-effects seen in most people who relocate to elevations above 13,000 feet.

"We found part of the EPAS1 gene in Tibetans is almost identical to the gene in Denisovans and very different from all other humans," Nielsen said. "We can do a statistical analysis to show that this must have come from Denisovans. There is no other way of explaining the data."

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Neandertals Were as Capable as Mesolithic Modern Humans From Africa

An analysis of the archaeological records of Neandertals and their modern human contemporaries has found that complex interbreeding and assimilation may have been responsible for Neandertal disappearance 40,000 years ago, in contrast to many current theories, according to results published April 30, 2014, in the open access journal PLOS ONE by Paola Villa from the University of Colorado Museum and Wil Roebroeks from Leiden University in the Netherlands.

Neandertals thrived in Eurasia for more than 300,000 years but vanished around 40,000 years ago, around the same time that modern humans entered Europe. Archaeologists have developed many theories to explain their disappearance, and many of these suggest that modern-day humans were superior in a wide range of ways, including weaponry and subsistence strategies. This superiority may have eventually led to the demise of Neandertals. However, new evidence, including genetic data, suggest that differences between Neandertals and modern humans in Africa may not be so clear as previously thought.

In this study, scientists systematically tested the strength of some of the archaeologically derived explanations for Neandertal extinction, such as the Neandertals' supposed lack of complex language, inferior capacity for innovation, inferior hunting ability, and smaller social networks, as well as other environmental explanations, including harsh climate or volcanic eruptions that occurred at the time of their decline.

If the Neandertal record is compared to that of African Middle Stone Age human contemporaries, instead of the modern humans that succeeded them, the differences between them and humans in their capacities, like weaponry, subsistence, and use of symbols are too small to explain their demise in terms of cognitive or behavioral inferiority. Instead, the authors argue, genetic data recently obtained from Neandertal skeletal remains suggest that complex and drawn-out processes of interbreeding and assimilation may have been responsible for the disappearance of the specific Neandertal morphology from the fossil record.

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Just How Neandertal are YOU?!

Technical objections to the idea that Neandertals interbred with the ancestors of Eurasians have been overcome, thanks to a genome analysis method described in the April 2014 issue of the journal GENETICS. The technique can more confidently detect the genetic signatures of interbreeding than previous approaches and will be useful for evolutionary studies of other ancient or rare DNA samples.

"Our approach can distinguish between two subtly different scenarios that could explain the genetic similarities shared by Neandertals and modern humans from Europe and Asia," said study co-author Konrad Lohse, a population geneticist at the University of Edinburgh.

The first scenario is that Neandertals occasionally interbred with modern humans after they migrated out of Africa. The alternative scenario is that the humans who left Africa evolved from the same ancestral subpopulation that had previously given rise to the Neandertals.

Many researchers argue the interbreeding scenario is more likely, because it fits the genetic patterns seen in studies that compared genomes from many modern humans. But the new approach completely rules out the alternative scenario without requiring all the extra data, by using only the information from one genome each of several types: Neandertal, European/Asian, African and chimpanzee.

The same method will be useful in other studies of interbreeding where limited samples are available. "Because the method makes maximum use of the information contained in individual genomes, it is particularly exciting for revealing the history of species that are rare or extinct," said Lohse. In fact, the authors originally developed the method while studying the history of insect populations in Europe and island species of pigs in South East Asia, some of which are extremely rare.

Lohse cautions against reading too much into the fact that the new method estimates a slightly higher genetic contribution of Neandertals to modern humans than previous studies. Estimating this contribution is complex and is likely to vary slightly between different approaches.

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Evidence of Eurasian Introgression in Southern and Eastern African Populations

Ancient west Eurasian ancestry in southern and eastern Africa

Authors:

Pickrell et al

Abstract:

The history of southern Africa involved interactions between indigenous hunter–gatherers and a range of populations that moved into the region. Here we use genome-wide genetic data to show that there are at least two admixture events in the history of Khoisan populations (southern African hunter–gatherers and pastoralists who speak non-Bantu languages with click consonants). One involved populations related to Niger–Congo-speaking African populations, and the other introduced ancestry most closely related to west Eurasian (European or Middle Eastern) populations. We date this latter admixture event to ∼900–1,800 y ago and show that it had the largest demographic impact in Khoisan populations that speak Khoe–Kwadi languages. A similar signal of west Eurasian ancestry is present throughout eastern Africa. In particular, we also find evidence for two admixture events in the history of Kenyan, Tanzanian, and Ethiopian populations, the earlier of which involved populations related to west Eurasians and which we date to ∼2,700–3,300 y ago. We reconstruct the allele frequencies of the putative west Eurasian population in eastern Africa and show that this population is a good proxy for the west Eurasian ancestry in southern Africa. The most parsimonious explanation for these findings is that west Eurasian ancestry entered southern Africa indirectly through eastern Africa.

hm.  I wonder how this intersects with the lack if Neandertal genetic components in African populations.

(genetic) Results of Getting it on With Neandertals

There was a veritable storm yesterday of posts on online for the implications of the latest implications of what bits of our genome are Neandertalic.

At D-brief, the implication is the genes helped us tolerate cold better. Amongst other, ahem, ball games.

In a press release, it turns out that Asians are more Neandertal than Europeans! it also claims that Neandertals were barely able to interbreed with Homo sapiens: there are no X chromosomes which have genes from Neandertals and implies male hybrids were sterile. This would strongly support the idea Neandertals were a separate species.

A related press release, it is also suggested that diabetes, Crohn's Disease and lupus might be related to the intermixing and that we didn't just get

In another press release also associated with a paper, one which seems on the extraordinary claim side of things, there is a claim that 20% of the Neandertal genome survives in modern populations. This contrasts wildly with the above paper and previous results placing the total modern genome being less than 5%.  

Considering how complicated things are and how we are still sorting this out, expect radical wind changes in the future.

Siberian Skeleton Hints Native Americans Have Some PreColumbian, PreViking European Roots

Where did the first Americans come from? Most researchers agree that Paleoamericans moved across the Bering Land Bridge from Asia sometime before 15,000 years ago, suggesting roots in East Asia. But just where the source populations arose has long been a mystery.

Now comes a surprising twist, from the complete nuclear genome of a Siberian boy who died 24,000 years ago—the oldest complete genome of a modern human sequenced to date. His DNA shows close ties to those of today's Native Americans. Yet he apparently descended not from East Asians, but from people who had lived in Europe or western Asia. The finding suggests that about a third of the ancestry of today's Native Americans can be traced to "western Eurasia," with the other two-thirds coming from eastern Asia, according to a talk at a meeting* here by ancient DNA expert Eske Willerslev of the University of Copenhagen. It also implies that traces of European ancestry previously detected in modern Native Americans do not come solely from mixing with European colonists, as most scientists had assumed, but have much deeper roots.

"I'm still processing that Native Americans are one-third European," says geneticist Connie Mulligan of the University of Florida in Gainesville. "It's jaw-dropping." At the very least, says geneticist Dennis O'Rourke of the University of Utah in Salt Lake City, "this is going to stimulate a lot of discussion."

Researchers have been trying to parse the origins of the first Americans for decades. Most agree that people moved across Beringia, via a vast ice age land bridge (see map p. 410), and began spreading through the Americas, reaching Chile by 14,500 years ago. But the origins of the source populations are not clear, and some archaeologists have even suggested that ancient Europeans crossing the Atlantic were part of the mix (Science, 16 March 2012, p. 1289). Others have contended that early skeletons found in the Americas, such as the 9000-year-old Kennewick Man, show some European features (Science, 10 April 1998, p. 190). In his talk, Willerslev argued that the ancient genome "can actually explain a lot of these inconsistencies," by offering glimpses of prehistoric populations before more recent migrations and other demographic events blurred the picture.

The genome comes from the right upper arm bone of a boy aged about 4 years, who lived by Siberia's Belaya River. Those who buried him adorned his grave with flint tools, pendants, a bead necklace, and a sprinkling of ochre. In the 1920s, Russian archaeologists discovered the burial and other artifacts near a village called Mal'ta, which gave the celebrated site its name. Willerslev and co-author Kelly Graf of Texas A&M University in College Station, traveled to the State Hermitage Museum in St. Petersburg, Russia, where the boy's remains are housed, and took a bone sample.

Willerslev reported that the team was able to sequence the boy's genome, and also to radiocarbon date the bone. The team then used a variety of statistical methods to compare the genome with that of living populations. They found that a portion of the boy's genome is shared only by today's Native Americans and no other groups, showing a close relationship. Yet the child's Y chromosome belongs to a genetic group called Y haplogroup R, and its mitochondrial DNA to a haplogroup U. Today, those haplogroups are found almost exclusively in people living in Europe and regions of Asia west of the Altai Mountains, which are near the borders of Russia, China, and Mongolia.

One expected relationship was missing from the picture: The boy's genome showed no connection to modern East Asians. DNA studies of living people strongly suggest that East Asians—perhaps Siberians, Chinese, or Japanese—make up the major part of Native American ancestors. So how could the boy be related to living Native Americans, but not to East Asians? "This was kind of puzzling at first," Willerslev told the meeting. But there seemed little doubt that the finding was correct, he said, because nearly all Native Americans from North and South America were equally related to the Mal'ta child, indicating that he represented very deep Native American roots.

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Did the Denisovans Cross the Wallace Line to Australia?

Scientists have proposed that the most recently discovered ancient human relatives -- the Denisovans -- somehow managed to cross one of the world's most prominent marine barriers in Indonesia, and later interbred with modern humans moving through the area on the way to Australia and New Guinea.

Three years ago the genetic analysis of a little finger bone from Denisova cave in the Altai Mountains in northern Asia led to a complete genome sequence of a new line of the human family tree -- the Denisovans. Since then, genetic evidence pointing to their hybridisation with modern human populations has been detected, but only in Indigenous populations in Australia, New Guinea and surrounding areas. In contrast, Denisovan DNA appears to be absent or at very low levels in current populations on mainland Asia, even though this is where the fossil was found.

Published today in a Science opinion article, scientists Professor Alan Cooper of the University of Adelaide in Australia and Professor Chris Stringer of the Natural History Museum in the UK say that this pattern can be explained if the Denisovans had succeeded in crossing the famous Wallace's Line, one of the world's biggest biogeographic barriers which is formed by a powerful marine current along the east coast of Borneo. Wallace's Line marks the division between European and Asian mammals to the west from marsupial-dominated Australasia to the east.

"In mainland Asia, neither ancient human specimens, nor geographically isolated modern Indigenous populations have Denisovan DNA of any note, indicating that there has never been a genetic signal of Denisovan interbreeding in the area," says Professor Cooper, Director of the University of Adelaide's Australian Centre for Ancient DNA. "The only place where such a genetic signal exists appears to be in areas east of Wallace's Line and that is where we think interbreeding took place -- even though it means that the Denisovans must have somehow made that marine crossing."

"The recent discovery of another enigmatic ancient human species Homo floresiensis, the so-called Hobbits, in Flores, Indonesia, confirms that the diversity of archaic human relatives in this area was much higher than we'd thought," says Professor Stringer, Research Leader in Human Origins, Natural History Museum, in London. "The morphology of the Hobbits shows they are different from the Denisovans, meaning we now have at least two, and potentially more, unexpected groups in the area.

"The conclusions we've drawn are very important for our knowledge of early human evolution and culture. Knowing that the Denisovans spread beyond this significant sea barrier opens up all sorts of questions about the behaviours and capabilities of this group, and how far they could have spread."

"The key questions now are where and when the ancestors of current humans, who were on their way to colonise New Guinea and Australia around 50,000 years ago, met and interacted with the Denisovans," says Professor Cooper.

I'd think there are probably far better explanations.  So consider me setting my skeptical bit.

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