Scientists used the full DNA sequences of Schistosoma mansoni parasites from Africa and the French Caribbean to discover the fluke's origins, map its historic transmission and identify the secrets of its success. Their findings, published in Scientific Reports, show how the global slave trade transported the disease from Senegal and Cameroon to Guadeloupe. Further genomic comparison with a closely related schistosome species that infects rodents reveals how the parasite has adapted to infecting human beings.

Schistosoma mansoni is a blood fluke (flatworm) that infects more than 250 million people worldwide and causes more than 11,000 deaths each year. Six years ago the Sanger Institute published the parasite's first full DNA sequence (genome); this latest study used that 'genetic map' to construct and compare the genomes of S. mansoni parasites gathered from across Africa and the New World, the majority of which were held at the Schistosomiasis Collection in the Natural History Museum, London.

By analysing the differences between the human-infecting S. mansoni and its close relative, the rodent-infecting S. rodhaini, the scientists calculated that the two species evolved from a common ancestor approximately 107,000 to 148,000 years ago in East Africa. This finding suggests that the species is much 'younger' than previously thought.

"The timing of the separation of the two species coincidences with the first archaeological evidence of fishing in Africa," explains Thomas Crellen, first author of the study from Imperial College London, the Sanger Institute and the Royal Veterinary College London. "The parasite develops in freshwater and infects people by burrowing through their skin. The introduction of fishing would have meant that people spent more time in the water, greatly increasing their chances of being infected."

Analysing the differences between genomes from different locations also revealed the darker side of human history.

"Comparing the S. mansoni genomes suggests that flukes in West Africa split from their Caribbean counterparts at some point between 1117AD and 1742AD, which overlaps with the time of the 16th-19th Century Atlantic Slave Trade," says Professor Joanne Webster from Imperial College London and the Royal Veterinary College. "During this period more than 22,000 African people were transported from West Africa to Guadeloupe by French slave ships, and the fluke was carried with them."

Comparing the genomes of S. mansoni with S. rodhaini also revealed the genetic variations that have been positively selected over time in the human-infecting fluke and have been "fixed" into its DNA. It is likely that these variations are the evolutionary adaptations that have occurred to enable the fluke to successfully tunnel into, and thrive within, human beings.

"When we looked for the differences between human-infecting S. mansoni DNA and its rodent infecting cousin S. rodhaini, we found two important variations. We found that changes to two genes in S. mansoni's DNA -- VAL21 and an elastase gene -appear to be important in allowing the fluke to enter and live in humans," says Dr James Cotton, senior author of the study from the Sanger Institute. "VAL genes produce proteins that cause allergic responses, so it is possible that the variation in VAL21 helps the fluke to hide from our immune systems. The elastase gene helps the parasite to burrow in to the body, by breaking down elastin -- a major component of human skin."

It is hoped that exploring the genetic makeup of the fluke it will be possible to discover more about the processes the parasite relies on to infect humans and offer new opportunities to develop preventive and therapeutic interventions.

Source: Wellcome Trust Sanger Institute [February 17, 2016]

Human teeth discovered in southern China provide evidence that our species left the African continent up to 70,000 years earlier than prevailing theories suggest, a study published on Wednesday said.

Homo sapiens reached present-day China 80,000-120,000 years ago, according to the study, which could redraw the migration map for modern humans.

"The model that is generally accepted is that modern humans left Africa only 50,000 years ago," said Maria Martinon-Torres, a researcher at University College London and a co-author of the study.

"In this case, we are saying the H. sapiens is out of Africa much earlier," she told the peer-reviewed journal Nature, which published the study.

While the route they travelled remains unknown, previous research suggests the most likely path out of East Africa to east Asia was across the Arabian Peninsula and the Middle East.

The findings also mean that the first truly modern humans -- thought to have emerged in east Africa some 200,000 years ago -- landed in China well before they went to Europe.

There is no evidence to suggest that H. sapiens entered the European continent earlier than 45,000 years ago, at least 40,000 years after they showed up in present-day China.

The 47 teeth exhumed from a knee-deep layer of grey, sandy clay inside the Fuyan Cave near the town of Daoxian closely resemble the dental gear of "contemporary humans," according to the study.

They could only have come from a population that migrated from Africa, rather than one that evolved from an another species of early man such as the extinct Homo erectus, the authors said.

The scientists also unearthed the remains of some 38 mammals, including specimens of five extinct species, one of them a giant panda larger than those in existence today.

No tools were found.

"Judging by the cave environment, it may not have been a living place for humans," lead author Wu Liu from the Chinese Academy of Science in Beijing told AFP.

The study, published in the journal Nature, also rewrites the timeline of early man in China.

Up to now, the earliest proof of H. sapiens east of the Arabian Peninsula came from the Tianyuan Cave near Beijing, and dated from no more than 40,000 years ago.

The new discovery raises questions about why it took so long for H. sapiens to find their way to nearby Europe.

"Why is it that modern humans -- who were already at the gates -- didn't really get into Europe?", Martinon-Torres asked.

Wu and colleagues propose two explanations.

The first is the intimidating presence of Neanderthal man. While this species of early human eventually died out, they were spread across the European continent up until at least some 50,000 years ago.

"The classic idea is that H. sapiens... took over the Neanderthal empire, but maybe Neanderthals were a kind of ecological barrier, and Europe was too small a place" for both, Martinon-Torres said.

Another impediment might have been the cold.

Up until the Ice Age ended 12,000 years ago, ice sheets stretched across a good part of the European continent, a forbidding environment for a new species emerging from the relative warmth of East Africa.

"H. sapiens originated in or near the tropics, so it makes sense that the species' initial dispersal was eastwards rather than northwards, where winter temperatures rapidly fell below freezing," Robin Dennell of the University of Exeter said in a commentary, also in Nature.

Martinon-Torres laid out some of the questions to be addressed in future research, using both genetics and fossil records.

"What are the origins of these populations, and what was their fate? Did they vanish? Could they be the ancestors of later and current populations that entered Europe?"

She also suggested there might have been "different movements and migrations" out of Africa, not just one.

Besides the prehistoric panda, called Ailuropoda baconi, the scientists found an extinct species of a giant spotted hyaena.

An elephant-like creature called Stegodon orientalis and a giant tapir, also present, were species that may have survived into the era when the Chinese had developed writing, some 3500 years ago.

The cache of teeth nearly went unnoticed, Wu told AFP.

He and his Chinese colleagues discovered the cave -- and its menagerie of long-deceased animals -- in the 1980s, but had no inkling that it also contained human remains.

But 25 years later, while revisiting the site, Wu had a hunch.

"By thinking about the cave environment, we realised that human fossils might be found there," he told AFP by email. "So we started a five-year excavation."

Author: Marlowe Hood | Source: AFP [October 14, 2015]

Uplift associated with the Great Rift Valley of East Africa and the environmental changes it produced have puzzled scientists for decades because the timing and starting elevation have been poorly constrained.

Now paleontologists have tapped a fossil from the most precisely dated beaked whale in the world -- and the only stranded whale ever found so far inland on the African continent -- to pinpoint for the first time a date when East Africa's mysterious elevation began.

The 17 million-year-old fossil is from the beaked Ziphiidae whale family. It was discovered 740 kilometers inland at an elevation of 620 meters in modern Kenya's harsh desert region, said vertebrate paleontologist Louis L. Jacobs, Southern Methodist University, Dallas.

At the time the whale was alive, it would have been swimming far inland up a river with a low gradient ranging from 24 to 37 meters over more than 600 to 900 kilometers, said Jacobs, a co-author of the study.

The study, published in the Proceedings of the National Academy of Sciences, provides the first constraint on the start of uplift of East African terrain from near sea level.

"The whale was stranded up river at a time when east Africa was at sea level and was covered with forest and jungle," Jacobs said. "As that part of the continent rose up, that caused the climate to become drier and drier. So over millions of years, forest gave way to grasslands. Primates evolved to adapt to grasslands and dry country. And that's when -- in human evolution -- the primates started to walk upright."

Identified as a Turkana ziphiid, the whale would have lived in the open ocean, like its modern beaked cousins. Ziphiids, still one of the ocean's top predators, are the deepest diving air-breathing mammals alive, plunging to nearly 10,000 feet to feed, primarily on squid.

In contrast to most whale fossils, which have been discovered in marine rocks, Kenya's beached whale was found in river deposits, known as fluvial sediments, said Jacobs, a professor in the Roy M. Huffington Department of Earth Sciences of SMU's Dedman College of Humanities and Sciences. The ancient large Anza River flowed in a southeastward direction to the Indian Ocean. The whale, probably disoriented, swam into the river and could not change its course, continuing well inland.

"You don't usually find whales so far inland," Jacobs said. "Many of the known beaked whale fossils are dredged by fishermen from the bottom of the sea."

Determining ancient land elevation is very difficult, but the whale provides one near sea level.

"It's rare to get a paleo-elevation," Jacobs said, noting only one other in East Africa, determined from a lava flow.

Beaked whale fossil surfaced after going missing for more than 30 years

The beaked whale fossil was discovered in 1964 by J.G. Mead in what is now the Turkana region of northwest Kenya.

Mead, an undergraduate student at Yale University at the time, made a career at the Smithsonian Institution, from which he recently retired. Over the years, the Kenya whale fossil went missing in storage. Jacobs, who was at one time head of the Division of Paleontology for the National Museums of Kenya, spent 30 years trying to locate the fossil. His effort paid off in 2011, when he rediscovered it at Harvard University and returned it to the National Museums of Kenya.

The fossil is only a small portion of the whale, which Mead originally estimated was 7 meters long during its life. Mead unearthed the beak portion of the skull, 2.6 feet long and 1.8 feet wide, specifically the maxillae and premaxillae, the bones that form the upper jaw and palate.

The researchers reported their findings in "A 17 million-year-old whale constrains onset of uplift and climate change in East Africa" online at the PNAS web site.

Modern cases of stranded whales have been recorded in the Thames River in London, swimming up a gradient of 2 meters over 70 kilometers; the Columbia River in Washington state, a gradient of 6 meters over 161 kilometers; the Sacramento River in California, a gradient of 4 meters over 133 kilometers; and the Amazon River in Brazil, a gradient of 1 meter over 1,000 kilometers.

Source: Southern Methodist University [March 17, 2015]

On the outskirts of Beijing, a small limestone mountain named Dragon Bone Hill rises above the surrounding sprawl. Along the northern side, a path leads up to some fenced-off caves that draw 150,000 visitors each year, from schoolchildren to grey-haired pensioners. It was here, in 1929, that researchers discovered a nearly complete ancient skull that they determined was roughly half a million years old. Dubbed Peking Man, it was among the earliest human remains ever uncovered, and it helped to convince many researchers that humanity first evolved in Asia.

Since then, the central importance of Peking Man has faded. Although modern dating methods put the fossil even earlier—at up to 780,000 years old—the specimen has been eclipsed by discoveries in Africa that have yielded much older remains of ancient human relatives. Such finds have cemented Africa's status as the cradle of humanity—the place from which modern humans and their predecessors spread around the globe—and relegated Asia to a kind of evolutionary cul-de-sac.

But the tale of Peking Man has haunted generations of Chinese researchers, who have struggled to understand its relationship to modern humans. "It's a story without an ending," says Wu Xinzhi, a palaeontologist at the Chinese Academy of Sciences' Institute of Vertebrate Paleontology and Paleoanthropology (IVPP) in Beijing. They wonder whether the descendants of Peking Man and fellow members of the species Homo erectus died out or evolved into a more modern species, and whether they contributed to the gene pool of China today.

Keen to get to the bottom of its people's ancestry, China has in the past decade stepped up its efforts to uncover evidence of early humans across the country. It is reanalysing old fossil finds and pouring tens of millions of dollars a year into excavations. And the government is setting up a US$1.1-million laboratory at the IVPP to extract and sequence ancient DNA.

The investment comes at a time when palaeoanthropologists across the globe are starting to pay more attention to Asian fossils and how they relate to other early hominins—creatures that are more closely related to humans than to chimps. Finds in China and other parts of Asia have made it clear that a dazzling variety of Homo species once roamed the continent. And they are challenging conventional ideas about the evolutionary history of humanity.

"Many Western scientists tend to see Asian fossils and artefacts through the prism of what was happening in Africa and Europe," says Wu. Those other continents have historically drawn more attention in studies of human evolution because of the antiquity of fossil finds there, and because they are closer to major palaeoanthropology research institutions, he says. "But it's increasingly clear that many Asian materials cannot fit into the traditional narrative of human evolution."

Chris Stringer, a palaeoanthropologist at the Natural History Museum in London, agrees. "Asia has been a forgotten continent," he says. "Its role in human evolution may have been largely under-appreciated."

Evolving story

In its typical form, the story of Homo sapiens starts in Africa. The exact details vary from one telling to another, but the key characters and events generally remain the same. And the title is always 'Out of Africa'.

In this standard view of human evolution, H. erectus first evolved there more than 2 million years ago. Then, some time before 600,000 years ago, it gave rise to a new species: Homo heidelbergensis, the oldest remains of which have been found in Ethiopia. About 400,000 years ago, some members of H. heidelbergensis left Africa and split into two branches: one ventured into the Middle East and Europe, where it evolved into Neanderthals; the other went east, where members became Denisovans—a group first discovered in Siberia in 2010. The remaining population of H. heidelbergensis in Africa eventually evolved into our own species, H. sapiens, about 200,000 years ago. Then these early humans expanded their range to Eurasia 60,000 years ago, where they replaced local hominins with a minuscule amount of interbreeding.

A hallmark of H. heidelbergensis—the potential common ancestor of Neanderthals, Denisovans and modern humans—is that individuals have a mixture of primitive and modern features. Like more archaic lineages, H. heidelbergensis has a massive brow ridge and no chin. But it also resembles H. sapiens, with its smaller teeth and bigger braincase. Most researchers have viewed H. heidelbergensis—or something similar—as a transitional form between H. erectus and H. sapiens.

Unfortunately, fossil evidence from this period, the dawn of the human race, is scarce and often ambiguous. It is the least understood episode in human evolution, says Russell Ciochon, a palaeoanthropologist at the University of Iowa in Iowa City. "But it's central to our understanding of humanity's ultimate origin."

The tale is further muddled by Chinese fossils analysed over the past four decades, which cast doubt over the linear progression from African H. erectus to modern humans. They show that, between roughly 900,000 and 125,000 years ago, east Asia was teeming with hominins endowed with features that would place them somewhere between H. erectus and H. sapiens, says Wu.

"Those fossils are a big mystery," says Ciochon. "They clearly represent more advanced species than H. erectus, but nobody knows what they are because they don't seem to fit into any categories we know."

The fossils' transitional characteristics have prompted researchers such as Stringer to lump them with H. heidelbergensis. Because the oldest of these forms, two skulls uncovered in Yunxian in Hubei province, date back 900,000 years >^{1, 2}>, Stringer even suggests that H. heidelbergensis might have originated in Asia and then spread to other continents.

But many researchers, including most Chinese palaeontologists, contend that the materials from China are different from European and African H. heidelbergensis fossils, despite some apparent similarities. One nearly complete skull unearthed at Dali in Shaanxi province and dated to 250,000 years ago, has a bigger braincase, a shorter face and a lower cheekbone than most H. heidelbergensis specimens>3, suggesting that the species was more advanced.

Such transitional forms persisted for hundreds of thousands of years in China, until species appeared with such modern traits that some researchers have classified them as H. sapiens. One of the most recent of these is represented by two teeth and a lower jawbone, dating to about 100,000 years ago, unearthed in 2007 by IVPP palaeoanthropologist Liu Wu and his colleagues>4. Discovered in Zhirendong, a cave in Guangxi province, the jaw has a classic modern-human appearance, but retains some archaic features of Peking Man, such as a more robust build and a less-protruding chin.

Most Chinese palaeontologists—and a few ardent supporters from the West—think that the transitional fossils are evidence that Peking Man was an ancestor of modern Asian people. In this model, known as multiregionalism or continuity with hybridization, hominins descended from H. erectus in Asia interbred with incoming groups from Africa and other parts of Eurasia, and their progeny gave rise to the ancestors of modern east Asians, says Wu.

Support for this idea also comes from artefacts in China. In Europe and Africa, stone tools changed markedly over time, but hominins in China used the same type of simple stone instruments from about 1.7 million years ago to 10,000 years ago. According to Gao Xing, an archaeologist at the IVPP, this suggests that local hominins evolved continuously, with little influence from outside populations.

Politics at play?

Some Western researchers suggest that there is a hint of nationalism in Chinese palaeontologists' support for continuity. "The Chinese—they do not accept the idea that H. sapiens evolved in Africa," says one researcher. "They want everything to come from China."

Chinese researchers reject such allegations. "This has nothing to do with nationalism," says Wu. It's all about the evidence—the transitional fossils and archaeological artefacts, he says. "Everything points to continuous evolution in China from H. erectus to modern human."

But the continuity-with-hybridization model is countered by overwhelming genetic data that point to Africa as the wellspring of modern humans. Studies of Chinese populations show that 97.4% of their genetic make-up is from ancestral modern humans from Africa, with the rest coming from extinct forms such as Neanderthals and Denisovans>5. "If there had been significant contributions from Chinese H. erectus, they would show up in the genetic data," says Li Hui, a population geneticist at Fudan University in Shanghai. Wu counters that the genetic contribution from archaic hominins in China could have been missed because no DNA has yet been recovered from them.

Many researchers say that there are ways to explain the existing Asian fossils without resorting to continuity with hybridization. The Zhirendong hominins, for instance, could represent an exodus of early modern humans from Africa between 120,000 and 80,000 years ago. Instead of remaining in the Levant in the Middle East, as was thought previously, these people could have expanded into east Asia, says Michael Petraglia, an archaeologist at the University of Oxford, UK.

Other evidence backs up this hypothesis: excavations at a cave in Daoxian in China's Hunan province have yielded 47 fossil teeth so modern-looking that they could have come from the mouths of people today. But the fossils are at least 80,000 years old, and perhaps 120,000 years old, Liu and his colleagues reported last year>6. "Those early migrants may have interbred with archaic populations along the way or in Asia, which could explain Zhirendong people's primitive traits," says Petraglia.

Another possibility is that some of the Chinese fossils, including the Dali skull, represent the mysterious Denisovans, a species identified from Siberian fossils that are more than 40,000 years old. Palaeontologists don't know what the Denisovans looked like, but studies of DNA recovered from their teeth and bones indicate that this ancient population contributed to the genomes of modern humans, especially Australian Aborigines, Papua New Guineans and Polynesians—suggesting that Denisovans might have roamed Asia.

Maria Martinon-Torres, a palaeoanthropologist at University College London, is among those who proposed that some of the Chinese hominins were Denisovans. She worked with IVPP researchers on an analysis>7, published last year, of a fossil assemblage uncovered at Xujiayao in Hebei province—including partial jaws and nine teeth dated to 125,000–100,000 years ago. The molar teeth are massive, with very robust roots and complex grooves, reminiscent of those from Denisovans, she says.

A third idea is even more radical. It emerged when Martinon-Torres and her colleagues compared more than 5,000 fossil teeth from around the world: the team found that Eurasian specimens are more similar to each other than to African ones>8. That work and more recent interpretations of fossil skulls suggest that Eurasian hominins evolved separately from African ones for a long stretch of time. The researchers propose that the first hominins that left Africa 1.8 million years ago were the eventual source of modern humans. Their descendants mostly settled in the Middle East, where the climate was favourable, and then produced waves of transitional hominins that spread elsewhere. One Eurasian group went to Indonesia, another gave rise to Neanderthals and Denisovans, and a third ventured back into Africa and evolved into H. sapiens, which later spread throughout the world. In this model, modern humans evolved in Africa, but their immediate ancestor originated in the Middle East.

Not everybody is convinced. "Fossil interpretations are notoriously problematic," says Svante Paabo, a palaeogeneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. But DNA from Eurasian fossils dating to the start of the human race could help to reveal which story—or combination—is correct. China is now making a push in that direction. Qiaomei Fu, a palaeogeneticist who did her PhD with Paabo, returned home last year to establish a lab to extract and sequence ancient DNA at the IVPP. One of her immediate goals is to see whether some of the Chinese fossils belong to the mysterious Denisovan group. The prominent molar teeth from Xujiayao will be an early target. "I think we have a prime suspect here," she says.

Fuzzy picture

Despite the different interpretations of the Chinese fossil record, everybody agrees that the evolutionary tale in Asia is much more interesting than people appreciated before. But the details remain fuzzy, because so few researchers have excavated in Asia.

When they have, the results have been startling. In 2003, a dig on Flores island in Indonesia turned up a diminutive hominin>9, which researchers named Homo floresiensis and dubbed the hobbit. With its odd assortment of features, the creature still provokes debate about whether it is a dwarfed form of H. erectus or some more primitive lineage that made it all the way from Africa to southeast Asia and lived until as recently as 60,000 years ago. Last month, more surprises emerged from Flores, where researchers found the remains of a hobbit-like hominin in rocks about 700,000 years old>10.

Recovering more fossils from all parts of Asia will clearly help to fill in the gaps. Many palaeoanthropologists also call for better access to existing materials. Most Chinese fossils—including some of the finest specimens, such as the Yunxian and Dali skulls—are accessible only to a handful of Chinese palaeontologists and their collaborators. "To make them available for general studies, with replicas or CT scans, would be fantastic," says Stringer. Moreover, fossil sites should be dated much more rigorously, preferably by multiple methods, researchers say.

But all agree that Asia—the largest continent on Earth—has a lot more to offer in terms of unravelling the human story. "The centre of gravity," says Petraglia, "is shifting eastward."

Author: Jane Qiu | Source: Nature 535, 22–25 (14 July 2016) doi:10.1038/535218a [July 15, 2016]

Various specimens of Africa’s earliest coelacanth have been found in a 360 million year-old fossil estuary near Grahamstown, in South Africa’s Eastern Cape.

More than 30 complete specimens of the new fossil species, Serenichthys kowiensis, were collected from the famous Late Devonian aged Waterloo Farm locality, by palaeontologist Dr Robert Gess and described by him in collaboration with Professor Michael Coates of the University of Chicago.

Gess did the research whilst he was completing his PhD at the Evolutionary Studies Institute at the University of the Witwatersrand. An article describing the new species will be published in the in the prestigious Zoological Journal of the Linnean Society of London on Monday, 21 August.

“Remarkably, all of the delicate whole fish impressions represent juveniles. This suggests that Serenichthys was using a shallow, waterweed-filled embayment of the estuary as a nursery, as many fish do today,” says Gess.

The fossils come from black shales originally disturbed by road works at Waterloo Farm. These shales are the petrified compacted remains of mud, which was deposited in the quiet reaches of an estuary not unlike some of those along the Eastern Cape coast today.

“This earliest known record of a coelacanth nursery foreshadows a much younger counterpart, known from the 300 million year old Mazon Creek beds of Illinois in the United States,” says Gess.

“This glimpse into the early life history of ancient coelacanths raises further questions about the life history of the modern coelacanth, Latimeria, which is known to bear live young, but whether they, too, are clustered in nurseries remains unknown,” explains Coates.

360 million years ago, Africa was part of the southern supercontinent Gondwana, made up of Africa, India, Australia, Antarctica and South America. At that time, the rocks of Waterloo Farm were forming along the shores of the semi-enclosed Agulhas Sea, not far from the South Pole.

Gess originally identified coelacanth remains from the locality whilst carrying out excavations at Waterloo Farm in the mid-1990s under the supervision of Dr Norton Hiller, of the Rhodes University Geology Department. These fossils were not, however, well enough preserved to be reconstructed and described. His painstaking excavation of tons of shale salvaged during subsequent roadworks has now shed light on dozens more specimens, a few of which are preserved in exquisite detail.

These were prepared under a microscope and have allowed the species to be reconstructed in minute detail. They prove to be a new genus and species.

Coelacanths are believed to have arisen during the Devonian Period (about 419.2 ± 3.2 million years ago), however only five species of reconstructable Devonian coelacanths have previously been described, in addition to a number of very fragmentary remains. None of these came from Africa, but rather from North America, Europe, China and Australia. The new species gives important additional information on the early evolution of coelacanths.

“According to our evolutionary analysis (conducted by Gess and Coates), it is the Devonian species that most closely resembles the line leading to modern coelacanths,” says Gess.

The new species was discovered a mere 100km from the mouth of the Chalumna River, off which the type specimen of Latimeria chalumnae (the first discovered modern coelacanth) was caught in 1938.

Furthermore, the Geology Department at Rhodes, where Gess was based when he found his first fossil coelacanth, is on the site of the former Chemistry Department where Latimeria was first described. In keeping with the naming of its living relative (after an Eastern Cape river), the species name of the new fossil form, kowiensis, is after the Kowie River which rises among the hills where it was found, and the genus name, Serenichthys, honours Serena Gess, who provided land for the storage of more than 70 tons of black shale rescued from roadworks for ongoing research – in which all the new material was found.

All specimens have been deposited in the palaeontological collection of the Albany Natural History Museum, in Grahamstown, Eastern Cape Province, South Africa.

Source: University of the Witwatersrand [September 21, 2015]

By comparing the genes of current-day North and South Americans with African and European populations, an Oxford University study has found the genetic fingerprints of the slave trade and colonization that shaped migrations to the Americas hundreds of years ago.

The study published in Nature Communications found that:

• While Spaniards provide the majority of European ancestry in continental American Hispanic/Latino populations, the most common European genetic source in African-Americans and Barbadians comes from Great Britain.

• The Basques, a distinct ethnic group spread across current-day Spain and France, provided a small but distinct genetic contribution to current-day Continental South American populations, including the Maya in Mexico.

• The Caribbean Islands of Puerto Rico and the Dominican Republic are genetically similar to each other and distinct from the other populations, probably reflecting a different migration pattern between the Caribbean and mainland America.

• Compared to South Americans, people from Caribbean countries (such as the Barbados) had a larger genetic contribution from Africa.

• The ancestors of current-day Yoruba people from West Africa (one of the largest African ethnic groups) provided the largest contribution of genes from Africa to all current-day American populations.

• The proportion of African ancestry varied across the continent, from virtually zero (in the Maya people from Mexico) to 87% in current-day Barbados.

• South Italy and Sicily also provided a significant European genetic contribution to Colombia and Puerto Rico, in line with the known history of Italian emigrants to the Americas in the late 19th and early 20th century.

• One of the African-American groups from the USA had French ancestry, in agreement with historical French immigration into the colonial Southern United States.

• The proportion of genes from European versus African sources varied greatly from individual to individual within recipient populations.

'We found that the genetic profile of Americans is much more complex than previously thought,' said study leader Professor Cristian Capelli from the Department of Zoology.

The research team analysed DNA samples collected from people in Barbados, Columbia, the Dominican Republic, Ecuador, Mexico, Puerto Rico and African-Americans in the USA.

They used a technique called haplotype-based analysis to compare the pattern of genes in these 'recipient populations' to 'donor populations' in areas where migrants to America came from.

'We firstly grouped subsets of people in Africa and Europe who were genetically similar and used this fine scale resolution to find which combinations of these clusters resulted in the sort of mixtures that we now see in people across the Americas', said the study's first author, Dr Francesco Montinaro from the Department of Zoology.

'We can see the huge genetic impact that the slave trade had on American populations and our data match historical records', said study author Dr Garrett Hellenthal from the UCL Genetics Institute, 'The majority of African Americans have ancestry similar to the Yoruba people in West Africa, confirming that most African slaves came from this region. In areas of the Americas historically under Spanish rule, populations also have ancestry related to what is now Senegal and Gambia. Records show that around a third of the slaves sent to Spanish America in the 17th Century came from this region, and we can see the genetic evidence of this in modern Americans really clearly.'

These genetic findings also uncover previously unknown migration. ‘We found a clear genetic contribution from the Basques in modern-day Maya in Mexico’, said Professor Capelli. ‘This suggests that the Basque also took part in the colonisation of the Americas, coming over either with the Spanish conquistadores or in later waves of migration’.

'The differences in European ancestry between the Caribbean islands and mainland American population that we found were also previously unknown. It is likely that these differences reflect different patterns of migration between the Caribbean and mainland America.'

'These results show just how powerful a genetic approach can be when it comes to uncovering hidden patterns of ancestry. We hope to use the same approach to look at other populations with diverse genetic contributions, such as Brazilians,' said Professor Capelli.

Source: University of Oxford [March 24, 2015]

The forests of Central Africa could be home to up to 920,000 Pygmies, according to researchers from UCL, Manchester Metropolitan University and the University of Malaga, who have conducted the first measured estimate of the population and distribution of these indigenous groups.

Up until now it has not been possible to determine the numbers and actual geographic ranges of Pygmy communities, because of their location in remote forest areas, mobility, lack of census data, and imprecise and partial sources of information. Pygmy communities live in rainforests across nine countries in Central Africa—an area of some 178 million hectares—where they make up a very small minority of the total population.

Despite the Pygmies' significance to humanity's cultural diversity as the largest group of active hunter-gatherers in the world, the new study, published in >PLOS ONE, is the first to predict how many Pygmies are likely to be found in the vast expanse of tropical forests in Central Africa. The study maps their distribution and identifies which areas are of ecological importance.

Dr Jerome Lewis (Hunter-Gatherer Resilience Project, UCL Anthropology), co-author of the paper, said: "This is a very underprivileged and neglected group of people many of whom have already lost their forest land, livelihoods and whose rich cultural traditions are seriously threatened in many regions.

"Information on their locations and population numbers are crucial for developing appropriate human rights, cultural and land security safeguards for them, as for other indigenous peoples."

Using a compilation of evidence collected by an unprecedented number of researchers, the authors generated the largest database of Pygmy camp locations throughout their known range.

As there are no known accurate censuses of Pygmy population the researchers used a statistical method, developed by paper co-author Dr Jesus Olivero (University of Malaga), to forecast the distribution of Pygmies in Central Africa. Based on species distribution models that investigate the relationship between environmental conditions and the distribution of organisms, the study is the first to apply this method to human societies and their cultural diversity.

Dr Olivero said: "By using tried and tested animal and plant distribution models we hope to promote a greater awareness of the importance of these too often ignored and marginalized groups in this region."

Professor John Fa (Manchester Metropolitan University), co-author, explained that understanding where and how Pygmy communities live is an important first step in supporting them and safeguarding their rights.

"It's important for all of the countries involved to come together to help support Pygmies' cultures and human rights to make sure they are respected and understood.

"At the end of the day, 900,000 people living in small groups in such a vast area can very easily be ignored, leading to their cultural extinction, and given the extraordinary role they have played in the human story since well before antiquity, we don't want that."

Source: University College London [January 15, 2016]

Modern humans have been blamed for killing off the Neanderthals by out competing them, breeding with them and even outright murdering them.

But new research suggests it may actually have been infectious diseases carried by our modern ancestors as they migrated out of Africa that finished them off.

Scientists studying the latest genetic, fossil and archaeological evidence claim that Neanderthals suffered from a wide range of diseases that still plague us today.

They have found evidence that suggests our prehistoric cousins would have been infected by diseases such as tuberculosis, typhoid, whooping cough, encephalitis and the common cold.

But anthropologists from Cambridge University and Oxford Brookes University say that new diseases carried by modern humans may have led to the downfall of Neanderthals.

They speculate that pathogens like Heliocbacter pylori, the bacteria that causes stomach ulcers, were brought to Europe by modern humans from Africa and may have infected Neanderthals, who would have been unable to fight off these new diseases.

However, Neandethals may have also helped modern humans by passing on slivers of immunity against some diseases to our ancestors when they interbred.

Dr Simon Underdown, a principal lecturer in anthropology at Oxford Brookes University and co-author of the study, said: 'As Neanderthal populations became more isolated they developed very small gene pools and this would have impacted their ability to fight off disease.

'When Homo sapiens came out of Africa they brought diseases with them.

'We know that Neanderthals were actually much more advanced than they have been given credit for and we even interbred with them.

'Perhaps the only difference was that we were able to cope with these diseases but Neanderthals could not.'

The findings add to a growing body of evidence that Neanderthals were not as different from modern humans as was originally thought.

Recent discoveries have suggested that rather than being brutish cavemen, Neanderthals had sophisticated culture, were master tool makers and may even have had their own language.

The new study suggests that Neanderthals also suffered from many of the same afflictions and complaints that modern humans experience.

Indeed, there is some evidence from caves that early humans may have burned their bedding in a bid to rid themselves of infestations of lice or bed bugs.

Dr Underdown and his colleague Dr Charlotte Houldcroft, a researcher in infectious diseases at Cambridge University and University College London, analysed recent genetic studies on Neanderthals and other early humans.

They also examined recent genetic research on common human pathogens that have aimed to trace their origins and combined it with fossil and archaeological evidence.

Most evidence from the fossil record suggest that Neanderthals tended to suffer traumatic injuries as a result of their hunter gatherer lifestyle, but there are also signs of inflammation and infection.

Their study, which is published on the open source database bioRxiv, contradicts the common view that infectious diseases only really became a problem for humans in the Holocene about 11,000 years ago when humans began living in dense settlements and farming livestock.

Instead, they say many of the diseases we see around us today were common during the pleistocene when Neanderthals dominated much of Europe and Asia between 250,000 and 45,000 years ago, when they disappeared.

They say pathogens like TB, typhoid and Crimean fever that were thought to be zoonoses caught from herd animals may have actually originated in humans and were only passed to animals during the rise of farming around 8,000 years ago.

Genetic sequencing of Neanderthal and Denisovan - another early human ancestor - DNA has shown that modern humans have inherited a number of genes from these extinct species.

These include genes that provide immunity to viral infections such as tick-borne encephalitis.

Dr Underdown said this virus would probably have been common in the forested areas of northern Europe that Neanderthals inhabited and so immunity would have been an advantage.

Other genes found in modern Papua New Guineans that are involved in the immune response against viruses like dengue and influenza may have come from Neanderthals.

Analysis of ancient DNA has also shown that Neanderthals carried genes that would have protected them against bacterial blood poisoning, or sepsis.

Dr Underdown said: 'There are genetic signals in the Neanderthal genome that suggest quite clearly that they were exposed to these types of diseases but also developed some resistance to them.

'It had been thought that many of these diseases began infecting humans with the population increases that came with domestication of animals and permanent settlements.

'Be here we have got Neanderthals being infected by these diseases long before those developments.'

Author: Richard Gray | Source: Daily Mail Online [April 03, 2015]

Placental mammals consist of three main groups that diverged rapidly, evolving in wildly different directions: Afrotheria (for example, elephants and tenrecs), Xenarthra (such as armadillos and sloths) and Boreoeutheria (all other placental mammals). The relationships between them have been a subject of fierce controversy with multiple studies coming to incompatible conclusions over the last decade leading some researchers to suggest that these relationships might be impossible to resolve.

There are thus many outstanding questions such as which is the oldest sibling of the three? Did the mammals go their separate ways due to South America and Africa breaking apart? And if not, when did placentals split up?

"This has been one of the areas of greatest debate in evolutionary biology, with many researchers considering it impossible to resolve," said lead author Dr Tarver of Bristol's School of Earth Sciences. "Now we've proven these problems can be solved -- you just need to analyse genome-scale datasets using models that accurately reflect genomic evolution."

The researchers assembled the largest mammalian phylogenomic dataset ever collected before testing it with a variety of models of molecular evolution, choosing the most robust model and then analysing the data using several supercomputer clusters at the University of Bristol and the University of Texas Advanced Computing Centre. "We tested it to destruction," said Dr Tarver. "We threw the kitchen sink at it."

"A complication in reconstructing evolutionary histories from genomic data is that different parts of genomes can and often do give conflicting accounts of the history," said Dr Siavash Mirarab at the University of California San Diego, USA. "Individual genes within the same species can have different histories. This is one reason why the controversy has stood so long -- many thought the relationships couldn't be resolved."

To address the complexities of analysing large numbers of genes shared among many species, the researchers paired two fundamentally different approaches -- concatenated and coalescent-based analyses -- to confirm the findings. When the dust settled, the team had a specific family tree showing that Atlantogenata (containing the sibling groups of African Afrotheria and the South American Xenarthra) is the sister group to all other placentals.

Because many conflicting family trees have already been published, the team then gathered three of the most influential rivals and tested them against each other with the same model. All of the previous studies suddenly fell into line, their data agreeing with Tarver and colleagues.

With the origins of the family tree resolved, what does this mean for placental mammals? The researchers folded in another layer -- a molecular clock analysis. "The molecular clock analysis uses a combination of fossils and genomic data to estimate when these lineages diverged from each other," said author Dr Mario Dos-Reis of Queen Mary London, UK. "The results show that the afrotherians and xenarthrens diverged from one another around 90 million years ago."

Previously, scientists thought that when Africa and South America separated from each other over 100 million years ago, they broke up the family of placental mammals, who went their separate evolutionary ways divided by geography. But the researchers found that placental mammals didn't split up until after Africa and South America had already separated.

"We propose that South America's living endemic Xenarthra (for exmaple, sloths, anteaters, and armadillos) colonized the island-continent via overwater dispersal," said study author Dr Rob Asher of the University of Cambridge, UK.

Dr Asher suggests that this isn't as difficult as you might think. Mammals are among the great adventurers of the animal kingdom, and at the time the proto-Atlantic was only a few hundred miles wide. We already know that New World monkeys crossed the Atlantic later, when it was much bigger, probably on rafts formed from storm debris. And, of course, mammals repeatedly colonised remote islands like Madagascar.

"You don't always need to overturn the status quo to make a big impact," said Dr Tarver. "All of the competing hypotheses had some evidence to support them -- that's precisely why it was the source of such controversy. Proving the roots of the placental family tree with hard empirical evidence is a massive accomplishment."

The findings are published in Genome Biology and Evolution journal.

Source: University of Bristol [February 15, 2016]

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The leopard (Panthera pardus), one of the world's most iconic big cats, has lost as much as 75 percent of its historic range, according to a paper >published in the scientific journal PeerJ. Conducted by partners including the National Geographic Society's Big Cats Initiative, international conservation charities the Zoological Society of London (ZSL) and Panthera and the International Union for Conservation of Nature (IUCN) Cat Specialist Group, this study represents the first known attempt to produce a comprehensive analysis of leopards' status across their entire range and all nine subspecies.

The research found that leopards historically occupied a vast range of approximately 35 million square kilometers (13.5 million square miles) throughout Africa, the Middle East and Asia. Today, however, they are restricted to approximately 8.5 million square kilometers (3.3 million square miles).

To obtain their findings, the scientists spent three years reviewing more than 1,300 sources on the leopard's historic and current range. The results appear to confirm conservationists' suspicions that, while the entire species is not yet as threatened as some other big cats, leopards are facing a multitude of growing threats in the wild, and three subspecies have already been almost completely eradicated.

Lead author Andrew Jacobson, of ZSL's Institute of Zoology, University College London and the National Geographic Society's Big Cats Initiative, stated: "The leopard is a famously elusive animal, which is likely why it has taken so long to recognize its global decline. This study represents the first of its kind to assess the status of the leopard across the globe and all nine subspecies. Our results challenge the conventional assumption in many areas that leopards remain relatively abundant and not seriously threatened."

In addition, the research found that while African leopards face considerable threats, particularly in North and West Africa, leopards have also almost completely disappeared from several regions across Asia, including much of the Arabian Peninsula and vast areas of former range in China and Southeast Asia. The amount of habitat in each of these regions is plummeting, having declined by nearly 98 percent.

"Leopards' secretive nature, coupled with the occasional, brazen appearance of individual animals within megacities like Mumbai and Johannesburg, perpetuates the misconception that these big cats continue to thrive in the wild—when actually our study underlies the fact that they are increasingly threatened," said Luke Dollar, co-author and program director of the National Geographic Society's Big Cats Initiative.

Philipp Henschel, co-author and Lion Program survey coordinator for Panthera, stated: "A severe blind spot has existed in the conservation of the leopard. In just the last 12 months, Panthera has discovered the status of the leopard in Southeast Asia is as perilous as the highly endangered tiger." Henschel continued: "The international conservation community must double down in support of initiatives — protecting the species. Our next steps in this very moment will determine the leopard's fate."

Co-author Peter Gerngross, with the Vienna, Austria-based mapping firm BIOGEOMAPS, added: "We began by creating the most detailed reconstruction of the leopard's historic range to date. This allowed us to compare detailed knowledge on its current distribution with where the leopard used to be and thereby calculate the most accurate estimates of range loss. This research represents a major advancement for leopard science and conservation."

Leopards are capable of surviving in human-dominated landscapes provided they have sufficient cover, access to wild prey and tolerance from local people. In many areas, however, habitat is converted to farmland and native herbivores are replaced with livestock for growing human populations. This habitat loss, prey decline, conflict with livestock owners, illegal trade in leopard skins and parts and legal trophy hunting are all factors contributing to leopard decline.

Complicating conservation efforts for the leopard, Jacobson noted: "Our work underscores the pressing need to focus more research on the less studied subspecies, three of which have been the subject of fewer than five published papers during the last 15 years. Of these subspecies, one—the Javan leopard (P. p. melas)—is currently classified as critically endangered by the IUCN, while another—the Sri Lankan leopard (P. p. kotiya)—is classified as endangered, highlighting the urgent need to understand what can be done to arrest these worrying declines."

Despite this troubling picture, some areas of the world inspire hope. Even with historic declines in the Caucasus Mountains and the Russian Far East/Northeast China, leopard populations in these areas appear to have stabilized and may even be rebounding with significant conservation investment through the establishment of protected areas and increased anti-poaching measures.

"Leopards have a broad diet and are remarkably adaptable," said Joseph Lemeris Jr., a National Geographic Society's Big Cats Initiative researcher and paper co-author. "Sometimes the elimination of active persecution by government or local communities is enough to jumpstart leopard recovery. However, with many populations ranging across international boundaries, political cooperation is critical."

Source: PeerJ [May 03, 2016]

The transition from hunter-gatherer to sedentary farming 10,000 years ago occurred in multiple neighbouring but genetically distinct populations according to research by an international team including UCL.

“It had been widely assumed that these first farmers were from a single, genetically homogeneous population. However, we’ve found that there were deep genetic differences in these early farming populations, indicating very distinct ancestries,” said corresponding author Dr Garrett Hellenthal, UCL Genetics.

The study, published today in >Science and funded by Wellcome and Royal Society, examined ancient DNA from some of the world’s first farmers from the Zagros region of Iran and found it to be very different from the genomes of early farmers from the Aegean and Europe. The team identified similarities between the Neolithic farmer’s DNA and that of living people from southern Asia, including from Afghanistan, Pakistan, Iran, and Iranian Zoroastrians in particular.

“We know that farming technologies, including various domestic plants and animals, arose across the Fertile Crescent, with no particular centre” added co-author Professor Mark Thomas, UCL Genetics, Evolution & Environment.

“But to find that this region was made up of highly genetically distinct farming populations was something of a surprise. We estimated that they separated some 46 to 77,000 years ago, so they would almost certainly have looked different, and spoken different languages. It seems like we should be talking of a federal origin of farming.”

The switch from mobile hunting and gathering to sedentary farming first occurred around 10,000 years ago in south-western Asia and was one of the most important behavioural transitions since humans first evolved in Africa some 200,000 years ago. It led to profound changes in society, including greater population densities, new diseases, poorer health, social inequality, urban living, and ultimately, the rise of ancient civilizations.

Animals and plants were first domesticated across a region stretching north from modern-day Israel, Palestine and Lebanon to Syria and eastern Turkey, then east into, northern Iraq and north-western Iran, and south into Mesopotamia; a region known as the Fertile Crescent.

“Such was the impact of farming on our species that archaeologists have debated for more than 100 years how it originated and how it was spread into neighbouring regions such as Europe, North Africa and southern Asia,” said co-author Professor Stephen Shennan, UCL Institute of Archaeology.

“We’ve shown for the first time that different populations in different parts of the Fertile Crescent were coming up with similar solutions to finding a successful way of life in the new conditions created by the end of the last Ice Age.”

By looking at how ancient and living people share long sections of DNA, the team showed that early farming populations were highly genetically structured, and that some of that structure was preserved as farming, and farmers, spread into neighbouring regions; Europe to the west and southern Asia to the east.

“Early farmers from across Europe, and to some extent modern-day Europeans, can trace their DNA to early farmers living in the Aegean, whereas people living in Afghanistan, Pakistan, Iran and India share considerably more long chunks of DNA with early farmers in Iran. This genetic legacy of early farmers persists, although of course our genetic make-up subsequently has been reshaped by many millennia of other population movements and intermixing of various groups,” concluded Dr Hellenthal.

Source: University College London [July 14, 2016]

A DNA analysis of four ancient Roman skeletons found in London shows the first inhabitants of the city were a multi-ethnic mix similar to contemporary Londoners, the Museum of London said on Monday.

Two of the skeletons were of people born outside Britain -- one of a man linked genealogically to eastern Europe and the Near East, the other of a teenage girl with blue eyes from north Africa.

The injuries to the man's skull suggest that he may have been killed in the city's amphitheatre before his head was dumped into an open pit.

Both the man and the girl were suffering from periodontal disease, a type of gum disease.

The other two skeletons of people believed to have been born in Britain were of a woman with maternal ancestry from northern Europe and of a man also with links through his mother to Europe or north Africa.

"We have always understood that Roman London was a culturally diverse place and now science is giving us certainty," said Caroline McDonald, senior curator of Roman London at the museum.

"People born in Londinium lived alongside people from across the Roman Empire exchanging ideas and cultures, much like the London we know today," she said.

The museum said in a statement that this was "the first multidisciplinary study of the inhabitants of a city anywhere in the Roman Empire".

The Romans founded Britain's capital city in the middle of the first century AD, under the emperor Claudius.

Britain's University of Durham researched stable isotopes from tooth enamel to determine migration patterns.

A tooth from each skeleton was also sent to McMaster University in Canada for DNA analysis that established the hair and eye colour of each individual and identified the diseases they were suffering from.

McMaster University also examined the mitochondrial DNA (mtDNA) to identify maternal ancestry.

The exhibition of the four skeletons, entitled "Written in Bone", opens on Friday.

Source: AFP [November 24, 2015]

Analysis of the first fossil bee nest from the Plio-Pleistocene of South Africa suggests that the human ancestor Australopithecus africanus lived in a dry savannah environment, according a study published in the >open-access journal PLOS ONE by Jennifer Parker from University College London, United Kingdom, and colleagues.

Little paleoecological information is available for the site in South Africa where the first Au. africanus fossil—the 'Taung Child'—was discovered. However, insect-related fossils, abundant at the discovery site, can yield insights into the paleoenvironment. Bees, for example, tend to build characteristic nests in characteristic conditions. Parker and colleagues analyzed CT scans of a fossil bee nest that was discovered near the Taung Child site to determine its internal structure and thus the kinds of bees that built it.

The fossil nest was exceptionally well preserved, and the structure of its cells and tunnels suggested that it was made by a ground-nesting solitary bee. These bees typically nest on bare, light, dry soil that is exposed to the sun, which bolsters other recent evidence that Au. africanus lived in dry savannahs. Insect-related fossils are common but largely overlooked at sites where human ancestors lived, the researchers said, and their work underscores the contribution such fossils can make to understanding the environments where human ancestors lived.

"When Raymond Dart published his description of the 'Taung Child' in 1925 he profoundly changed our understanding of human evolution," says study co-author Philip Hopley. "In the 90 years following his discovery, attention of anthropologists has moved to other African sites and specimens, and research at Taung has been hampered by the complex geology and uncertain dating. New research at Taung is helping to reconstruct the environment in which this enigmatic little hominin lived and died."

Source: Public Library of Science [September 29, 2016]

In the summer of 430 B.C., a mass outbreak of disease hit the city of Athens, ravaging the city’s population over the next five years. In his History of the Peloponnesian War, the historian Thucydides, who witnessed the epidemic, described victims’ “violent heats in the head,” “redness and inflammation in the eyes,” and tongues and throats “becoming bloody and emitting an unnatural and fetid breath.” Patients would experience hot flashes so extreme, he wrote, that they “could not bear to have on [them] clothing or linen even of the very lightest description.” In the later stages of infection, the disease would end with “violent ulceration” and diarrhea that left most too weak to survive.

More than 2,000 years later, the Plague of Athens remains a scientific mystery. Thucydides’ account—the only surviving description of the epidemic—has been the basis for dozens of modern-day theories about its cause, including bubonic plague, cholera, typhoid fever, influenza, and measles. And in June, an article in the journal Clinical Infectious Disease suggested another answer: Ebola.

The article, written by the infectious-disease specialist Powel Kazanjian, is the latest in a string of papers arguing that Athens was once the site of an Ebola outbreak. The surgeon Gayle Scarrow first raised the suggestion in The Ancient History Bulletin in 1988. Eight years later, the epidemiologist Patrick Olson published a letter in Emerging Infectious Diseases, a journal of the Centers for Disease Control and Prevention, comparing the symptoms of the Athens plague to those of Ebola, which had broken out in the Democratic Republic of Congo (then Zaire) and Sudan in 1976. “The profile of the ancient disease,” he concluded, “is remarkably similar.”

But not everyone was on board with Olson’s theory. In a 1996 interview with the The New York Times, the epidemiologist David Morens argued that Thucydides wasn’t the most reliable source: Unlike his contemporary, Hippocrates, he wasn’t a physician, and many of the terms he used to describe the disease’s symptoms were ambiguous. For example, the ancient Greek phlyktainai could refer to either blisters or callouses. Noting Thucydides’ claim that the epidemic had originated “in the parts of Ethiopia above Egypt” (today’s sub-Saharan Africa), Morens also questioned how people with Ebola, a highly contagious and deadly disease, could make it all the way to Greece without dying along the way.

The duration of the Athens epidemic also presented another problem: At five years, it was much longer than any known Ebola outbreaks, the majority of which lasted less than a year. And finally, Morens asked, if Ebola had made it out of Africa millennia ago, why were there no other accounts of the disease re-appearing anywhere on Earth until 1976?

Unfortunately for both Olson and Morens, however, neither had a more concrete way to back up their arguments. Their efforts to identify the Plague of Athens, like all the other efforts before them, could only rely on the written record left by Thucydides, which made confirmation more or less impossible.

This, in a nutshell, is the challenge of ancient pathology: With DNA testing, it’s often possible to identify the cause of an epidemic that took place centuries or even millennia ago. Finding remains of those victims to test, though, is another story.

Sometimes, scientists get lucky. In 2001, for example, a mass grave was uncovered at a construction site in Vilnus, Lithuania. Based on uniform fragments found in the grave, the bodies were identified as belonging to soldiers in Napoleon’s army—somewhere between 2,000 and 3,000 of them, hurriedly buried during the retreat from Moscow. When a team of anthropologists examined dental pulp taken from the bodies, they found that around one-third of them had died of typhus, a finding confirmed by tests of dead lice found at the site (the disease is transmitted through lice). Researchers had long suspected that typhus had contributed to Napoleon’s eventual defeat, but because knowledge of the disease was scant during his lifetime, historical accounts alone had never been enough to confirm it.

For the Plague of Athens, it seemed like a similar turning point had arrived in 1994, when during excavations for a planned Athens metro station at Kerameikos, an ancient graveyard used from the early Bronze age through Roman times. The excavators uncovered thousands of previously undiscovered tombs—including a set of seemingly hurried, unceremonious mass burials dating to 430 B.C., the year of the Plague of Athens.

Control of the site was turned over from the construction company to the Greek Ministry of Culture, which handles the discoveries of ancient ruins. In 2000, archaeologists turned over three teeth found at the site to a University of Athens team led by Manolis Papagrigorakis, an orthodontist and professor of dentistry, for DNA testing. Examining the dental pulp found in the teeth, Papagrigorakis’ team ran tests for seven diseases that had previously been suggested by other scholars: plague, typhus, anthrax, tuberculosis, cowpox, cat-scratch disease, and typhoid fever. The only match they identified on all three teeth was with the pathogen for typhoid fever. The researchers published the findings from their analysis in the International Journal of Infectious Diseases in 2006.

Far from solving the mystery, though, Papagrigorakis’s team only muddled it further. In a letter to the editor in the same journal, zoologists from Oxford University and the University of Copenhagen argued that Papagrigorakis’s methodology was flawed because he failed to do a phylogenetic analysis (a way of examining evolutionary relationships) on the teeth. Using the DNA data published in Papagrigorakis’s study, they conducted their own phylogenetic analysis, concluding that the DNA of the tooth bacteria was related to, but not the same as, that of the pathogen for typhoid fever. “The Athens [DNA] sequence and typhoid would have shared a common ancestor in the order of millions of years ago,” they wrote.

The authors also suggested another possibility: that the DNA found in the teeth wasn’t from the Plague of Athens pathogen at all. “While we cannot exclude the possibility that the Athens sequence is a previously unidentified infectious agent,” they concluded, “it is quite reasonable to assume that the sequence is actually that of a modern, free-living soil bacterium, a possibility that could have been explored by extracting DNA from surrounding soil samples as additional negative controls.”

Papagrigorakis currently has a new study underway, using more modern techniques and a greater number of tooth samples, that he hopes will help to settle the debate. In the decade since he published his Athens study, advancements in DNA-sequencing technology have enabled scientists to answer a number of lingering questions about ancient epidemics, making new discoveries from very old tooth samples. In 2011, for example, scientists used teeth taken from bodies in one of London’s so-called “plague pits” to sequence the genome of the bacterium y. pestis, the source of the Black Death epidemic that had swept Europe in the 14th century. By comparing the old genome to modern-day strains, the researchers were able to reconstruct the bacterium’s evolutionary path over the centuries, finding support for the idea that the 14th-century pathogen was likely the root of the evolutionary tree leading to more recent outbreaks.

And in a 2014 study published in the Lancet Infectious Diseases, scientists were able to prove for the first time that the Plague of Justinian—which killed about 50 million people in Europe and the Byzantine Empire between 600 and 800 A.D.—was actually a strain of y. pestis, making it the first known outbreak. The team made its discovery by sequencing DNA from teeth taken from human remains that had been found in a German graveyard and dated to the time of the epidemic.

Even when ancient specimens are available, though, they may not be enough to identify a disease. Bacteria, like typhoid and plague, can be identified through DNA sampling, but this isn’t always the case with viruses. Many of them, including the viruses for Ebola, influenza, and measles, require an RNA sample for positive identification—and thus far, the oldest preserved RNA viral genome belongs to a 700-year-old specimen of caribou feces, much more recent than the Athens samples from in the 5th century B.C. The structure of RNA makes it much more unstable—and therefore more prone to degradation—than DNA, meaning that if the Plague of Athens was viral rather than bacterial, its source may remain a mystery.

“If Ebola virus was there, we will never know,” said Vinent Racaniello, a professor of microbiology at Columbia University professor and the host of the podcast This Week in Virology. “For that, we’ll need a time machine to bring us back to get samples.”

Partially due to these limitations, Kazanjian’s recent study doesn’t delve into dental-pulp analysis data. His argument is based on the similarity between the symptoms of the Plague of Athens and those of Ebola, an argument that he believes is strengthened by observations from the latest Ebola outbreak. The paper ends with a chart of the symptoms described by Thucydides, listed side-by-side against the symptoms of eight modern diseases that had previously been floated as possible explanations; of all of them, the symptoms for Ebola have the most overlap.

Even so, Kazanjian cautioned against referring to Ebola as a “probable” or even a “likely” cause. “The most accurate statement is that the cause remains unknown, and there are several possibilities,” he said, including that the Plague of Athens may have been a now-extinct disease with Ebola-like symptoms.

He also acknowledges the difficulty of making rigorous comparisons between Thucydides’s descriptions and modern-day medical knowledge: “I try not to get into the trap of saying what the most likely thing is,” he said.

But for Kazanjian—also a historian—solving the puzzle of the Plague of Athens is less compelling than exploring all the possibilities. The inquiry is “clearly fun to do,” he said, “no matter what your background is.”

Author: Simon Davis | Source: The Atlantic [September 16, 2015]

Research published in the American Geophysical Union's journal >Global Biogeochemical Cycles shows that recent rises in levels of methane in our atmosphere is being driven by biological sources, such as swamp gas, cow burps, or rice fields, rather than fossil fuel emissions.

Atmospheric methane is a major greenhouse gas that traps heat in our atmosphere, contributing to global warming. Its levels have been growing strongly since 2007, and in 2014 the growth rate of methane in the atmosphere was double that of previous years, largely driven by biological sources as opposed to fossil fuel emissions.

Conventional wisdom refuted

The study, led by researchers at Royal Holloway, University of London shows that methane emissions have been increasing, particularly in the tropics. Researchers discovered that biological sources, such as methane emissions from swamps, make up the majority of increase.

"Our results go against conventional thinking that the recent increase in atmospheric methane must be caused by increased emissions from natural gas, oil, and coal production. Our analysis of methane's isotopic composition clearly points to increased emissions from microbial sources, such as wetlands or agriculture" said lead author Euan Nisbet from Royal Holloway, University of London's Department of Earth Sciences.

Methane growth rate doubles

Professor Nisbet says "Atmospheric methane is one of the most potent greenhouses gases. Methane increased through most of the 20th century, driven largely by leaks from the gas and coal industries."

He continued, "At the beginning of this century it appeared that the amount of methane in the air was stabilising, but since 2007 the levels of methane have started growing again. The year 2014 was extreme, with the growth rate doubling, and large increases seen across the globe."

Tropics identified as key source

The research shows that in recent years, the increase in methane has been driven by sharp increases in the tropics, in response to changing weather patterns. It is possible that the natural processes that remove methane from the atmosphere have slowed down, but it is more likely that there's been an increase of methane emission instead, especially from the hot wet tropics.

Professor Nisbet and his team, together with the US The National Oceanic and Atmospheric Administration (NOAA), have been looking at measurements and samples of air taken from places like Alert in the Canadian Arctic; Ascension, a UK territory in the South Atlantic; Cape Point, South Africa.

International collaboration leads to new conclusions

The research has been carried out by an international team of atmospheric scientists, led by Euan Nisbet, from Royal Holloway, University of London. Ed Dlugokencky, from the NOAA, Martin Manning from Victoria University, Wellington, New Zealand and a team from the University of Colorado's Institute of Arctic and Alpine Research, led by Jim White, have been working with collaborators from the UK, France, Canada, and South Africa.

Source: University of Royal Holloway London [September 27, 2016]

In a remarkable technical feat, researchers have sequenced DNA from fossils in Spain that are about 300,000 to 400,000 years old and have found an ancestor—or close relative—of Neanderthals. The nuclear DNA, which is the oldest ever sequenced from a member of the human family, may push back the date for the origins of the distinct ancestors of Neanderthals and modern humans, according to a presentation here yesterday at the fifth annual meeting of the European Society for the study of human evolution.

Ever since researchers first discovered thousands of bones and teeth from 28 individuals in the mid-1990s from Sima de los Huesos (“pit of bones”), a cave in the Atapuerca Mountains of Spain, they had noted that the fossils looked a lot like primitive Neanderthals. The Sima people, who lived before Neanderthals, were thought to have emerged in Europe. Yet their teeth, jaws, and large nasal cavities were among the traits that closely resembled those of Neanderthals, according to a team led by paleontologist Juan-Luis Arsuaga of the Complutense University of Madrid. As a result, his team classified the fossils as members of Homo heidelbergensis, a species that lived about 600,000 to 250,000 years ago in Europe, Africa, and Asia. Many researchers have thought H. heidelbergensis gave rise to Neanderthals and perhaps also to our species, H. sapiens, in the past 400,000 years or so.

But in 2013, the Sima fossils’ identity suddenly became complicated when a study of the maternally inherited mitochondrial DNA (mtDNA) from one of the bones revealed that it did not resemble that of a Neanderthal. Instead, it more closely matched the mtDNA of a Denisovan, an elusive type of extinct human discovered when its DNA was sequenced from a finger bone from Denisova Cave in Siberia. That finding was puzzling, prompting researchers to speculate that perhaps the Sima fossils had interbred with very early Denisovans or that the “Denisovan” mtDNA was the signature of an even more ancient hominin lineage, such as H. erectus. At the time, researchers at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who had obtained the mtDNA announced that they would try to sequence the nuclear DNA of the fossils to solve the mystery.

After 2 years of intense effort, paleogeneticist Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology has finally sequenced enough nuclear DNA from fossils of a tooth and a leg bone from the pit to solve the mystery. The task was especially challenging because the ancient DNA was degraded to short fragments, made up of as few as 25 to 40 single nucleotides. (Nucleotides—also known as base pairs—are the building blocks of DNA.) Although he and his colleagues did not sequence the entire genomes of the fossils, Meyer reported at the meeting that they did get 1 million to 2 million base pairs of ancient nuclear DNA.

They scanned this DNA for unique markers found only in Neanderthals or Denisovans or modern humans, and found that the two Sima fossils shared far more alleles—different nucleotides at the same address in the genome—with Neanderthals than Denisovans or modern humans. “Indeed, the Sima de los Huesos specimens are early Neanderthals or related to early Neanderthals,” suggesting that the split of Denisovans and Neanderthals should be moved back in time, Meyer reported at the meeting.

Researchers at the meeting were impressed by this new breakthrough in ancient DNA research. “This has been the next frontier with ancient DNA,” says evolutionary biologist Greger Larson of the University of Oxford in the United Kingdom.

The close affinity with Neanderthals, but not with Denisovans or modern humans, suggests that the lineage leading to Neanderthals was separate from other archaic humans earlier than most researchers have thought. That means that the ancestors of modern humans also had to split earlier than expected from the population that gave rise to Neanderthals and Denisovans, who were more closely related to each other than they were to modern humans. (Although all three groups interbred at low levels after their evolutionary paths diverged—and such interbreeding may have been the source of the Denisovan mtDNA in the first Sima fossil whose DNA was sequenced.) Indeed, Meyer suggested in his talk that the ancestors of H. sapiens may have diverged from the branch leading to Neanderthals and Denisovans as early as 550,000 to 765,000 years ago, although those results depend on different mutation rates in humans and are still unpublished.

That would mean that the ancestors of humans were already wandering down a solitary path apart from the other kinds of archaic humans on the planet 100,000 to 400,000 years earlier than expected. “It resolves one controversy—that they’re in the Neanderthal clade,” says paleoanthropologist Chris Stringer of the Natural History Museum in London. “But it’s not all good news: From my point of view, it pushes back the origin of H. sapiens from the Neanderthals and Denisovans.” The possibility that humans were a distinct group so early shakes up the human family tree, promising to lead to new debate about when and where the branches belong.

Author: Ann Gibbons | Source: ScienceMag/AAAS [September 11, 2015]

The Piltdown Man scandal is arguably the greatest scientific fraud ever perpetrated in the UK, with fake fossils being claimed as evidence of our earliest ancestor.

Published 100 years on from Dawson's death, new research reveals that the forgeries were created using a limited number of specimens that were all constructed using a consistent method, suggesting the perpetrator acted alone.

It is highly likely that an orang-utan specimen and at least two human skeletons were used to create the fakes, which are still kept at the Natural History Museum.

Between 1912 and 1914 Museum palaeontologist Arthur Smith Woodward and the amateur antiquarian Charles Dawson announced the discovery of fossils from Piltdown in Sussex. These were supposedly a new evolutionary link between apes and humans. They indicated a species with both an ape-like jaw and a large braincase like a modern human. Before he died in 1916, Dawson claimed to have discovered further evidence at a second site.

The forgeries helped misdirect the study of anthropology for decades. While doubts were raised from the start, it took 40 years for the scientific community to recognise that the remains had been altered to seem ancient and had been planted in the sites.

The new research, published in >Royal Society Open Science, was undertaken by a multi-disciplinary team from institutions in Liverpool, London, Cambridge and Canterbury. They used the latest scientific methods to test the Piltdown specimens to uncover more about how the forgery was done.

DNA analyses show that both the canine from the first Piltdown site and the molar from the second site probably came from one orang-utan, related most closely to orang-utans now occupying south-west Sarawak (Borneo). In addition, the shape and form of the molar from the second Piltdown site was almost certainly from the other side of the jawbone planted in the first site.

3D X-ray imaging (Micro-CT scans) show that many of the bones and a tooth were filled with Piltdown gravel and the openings plugged with small pebbles. Holes in the skull bones were filled with dental putty, which was also used to re-set the teeth in the jaw and to reconstruct one of the teeth that fell apart while it was being ground down.

Dr Laura Buck co-author on the paper from the Division of Biological Anthropology, University of Cambridge commented on the project's importance. "Even today, over a hundred years after the Piltdown fraud was perpetrated, it remains relevant because of the huge impact it had on the course of Palaeoanthropological research at the beginning of the twentieth century."

"Fossil human remains from Africa, such as the Taung child from South Africa, were largely ignored when first found because they didn't fit with preconceptions of what an early human relative would look like, based on Piltdown Man. This serves as an important reminder to researchers today to study what is there and not what we think should be there," Buck said.

Dr Isabelle De Groote from Liverpool John Moores University and lead author on the paper, thinks the results point to a clear conclusion: "Although multiple individuals have been accused of producing the fake fossils, our analyses to understand the modus operandi show consistency between all the different specimens and on both sites. It is clear from our analysis that this work was likely all carried out by one forger: Charles Dawson."

Source: University of Cambridge [August 11, 2016]

An international research partnership is revealing the first mosasaur fossil of its kind to be discovered in Japan. Not only does the 72-million-year-old marine reptile fossil fill a biogeographical gap between the Middle East and the eastern Pacific, but also it holds new revelations because of its superior preservation. This unique swimming lizard, now believed to have hunted on glowing fish and squids at night, is detailed in an article led by Takuya Konishi, a University of Cincinnati assistant professor of biological sciences. The article is published in the Journal of Systematic Palaeontology, a publication of the Natural History Museum in London.

The fossil marine reptile, Phosphorosaurus ponpetelegans (a phosphorus lizard from an elegant creek), existed during the Late Cretaceous Period just before the last of the dinosaurs such as Tyrannosaurus and Triceratops. Compared with some of their mosasaur cousins that could grow as large as 40 feet, this species is relatively small, about 3 meters, or 10 feet long. This unique discovery in a creek in the town of Mukawa in northern Japan reveals that they were able to colonize throughout the northern hemisphere.

"Previous discoveries of this particular rare mosasaur have occurred along the East Coast of North America, the Pacific Coast of North America, Europe and North Africa, but this is the first to fill the gap between the Middle East and the Eastern Pacific," explains Konishi, a member of the research team that also was represented by the Royal Tyrrell Museum of Palaeontology (Canada), University of Alberta, Brandon University, Hobetsu Museum (Japan), Fukuoka University and the town of Mukawa.

Because the fossil was so well preserved, the creature revealed it had binocular vision -- its eyes were on the front of the face, providing depth perception. This was a new discovery for this fossil species. The discovery reveals that the eye structure of these smaller mosasaurs was different from their larger cousins, whose eyes were on either side of their large heads, such as the eye structure of a horse. The eyes and heads of the larger mosasaurs were shaped to enhance streamlined swimming after prey that included fish, turtles and even small mosasaurs.

"The forward-facing eyes on Phosphorosaurus provide depth perception to vision, and it's common in birds of prey and other predatory mammals that dwell among us today," says Konishi. "But we knew already that most mosasaurs were pursuit predators based on what we know they preyed upon -- swimming animals. Paradoxically, these small mosasaurs like Phosphorosaurus were not as adept swimmers as their larger contemporaries because their flippers and tailfins weren't as well developed."

As a result, Konishi says it's believed these smaller marine reptiles hunted at night, much like the owl does compared with the daytime birds of prey such as eagles. The binocular vision in nocturnal animals doubles the number of photoreceptors to detect light. And, much like owls with their very large eyes to power those light receptors, the smaller mosasaur revealed very large eye sockets.

Also, because fossils of lantern fish and squid-like animals have been found from the Late Cretaceous Period in northern Japan, and because their modern counterparts are bioluminescent, the researchers believe that Phosphorosaurus may have specifically targeted those glowing fish and squids at night while their larger underwater cousins hunted in daytime.

"If this new mosasaur was a sit-and-wait hunter in the darkness of the sea and able to detect the light of these other animals, that would have been the perfect niche to coexist with the more established mosasaurs," says Konishi.

Painstaking Preservation

The fossil, enclosed in a rock matrix, was first discovered in 2009, in a small creek in northern Japan. Revealing what was inside the matrix while protecting the fossil was a painstaking process that took place at the Hobetsu Museum in Mukawa. The calcareous nodule would be dipped at night in a special acid wash, and then carefully rinsed the next day, as the two-year process freed the bones from the matrix. To further protect the fossil, special casts were made of the bones so that the researchers could piece together the remains without damaging the fossil.

"It's so unusually well-preserved that, upon separating jumbled skull bones from one another, we were able to build a perfect skull with the exception of the anterior third of the snout," says Konishi. "This is not a virtual reality reconstruction using computer software. It's a physical reconstruction that came back to life to show astounding detail and beautiful, undistorted condition."

Future Research

Konishi says future research will examine how this new mosasaur fits in the evolutionary family tree of mosasaurs.

Author: Dawn Fuller | Source: University of Cincinnati [December 08, 2015]

Industrialized nations that view wildfire as the enemy have much to learn from people in some parts of the world who have learned to live compatibly with wildfire, says a team of fire research scientists.

The interdisciplinary team say there is much to be learned from these "fire-adaptive communities" and they are calling on policy makers to tap that knowledge, particularly in the wake of global warming.

Such a move is critical as climate change makes some landscapes where fire isn't the norm even more prone to fire, say the scientists in a new report published in a special issue of the >Philosophical Transactions of the Royal Society B.

"We tend to treat modern fire problems as unique, and new to our planet," said fire anthropologist Christopher Roos, Southern Methodist University, Dallas, lead author of the report. "As a result, we have missed the opportunity to recognize the successful properties of communities that have a high capacity to adapt to living in flammable landscapes—in some cases for centuries or millennia."

One such society is the ethnically Basque communities in the French Western Pyrenees, who practice fire management to maintain seasonally flammable grassland, shrub and woodland patches for forage and grazing animals. But the practice is slowly being lost as young people leave farming.

Additionally, Aboriginal people in the grasslands of Western Australia use fire as part of their traditional hunting practices. Children begin burning at a very young age, and the everyday practice is passed down. These fires improve hunting successes but also reduce the impact of drought on the size and ecological severity of lightning fires.

Social institutions support individual benefits, preserve common good

Fire-adaptive communities have social institutions in place that support individual benefits from fire-maintained landscapes while preserving the common good, said Roos, whose fire research includes long-term archaeological and ecological partnerships with the Pueblo of Jemez in New Mexico.

"These institutions have been shaped by long-histories with wildfire, appropriate fire-use, and the development of social mechanisms to adjudicate conflicts of interest," said Roos, an associate professor in the SMU Department of Anthropology. "There is a wealth of tried and tested information that should be considered in designing local fire management."

The authors note that globally, a large number of people use fire as a tool to sustain livelihoods in ways that have been handed down across many generations. These include indigenous Australians and North Americans, South Asian forest dwellers, European farmers, and also hunters, farmers and herders in tropical savannahs.

Global Warming will likely bring new fire problems, more flammable landscapes

Global Warming will likely bring new fire problems, such as making some landscapes more flammable, Roos said. More effort will be required to balance conflicting fire management practices between adjacent cultures. Currently most fire-related research tends to be undertaken by physical or biological scientists from Europe, the United States and Australia. Often the research treats fire challenges as exclusively contemporary phenomena for which history is either absent or irrelevant.

"We need national policy that recognizes these dynamic challenges and that will support local solutions and traditional fire knowledge, while providing ways to disseminate scientific information about fire," Roos said.

The authors point out that one of the greatest policy challenges of fire on a warming planet are the international consequences of smoke plumes and potential positive feedbacks on climate through carbon emissions. Most infamously, wildfire smoke plumes have had extraordinary health impacts during Southeast Asian "haze" events, which result in increased hospitalization and mortality in the region.

Not all fire is a disaster; we must learn to live with and manage fire

Carbon emissions from wildfires can be as much as 40 percent of fossil fuel emissions in any given year over the last decade. Although only deforestation fires and land conversion are a net carbon source to the atmosphere, the contribution of wildfires to global carbon emissions is non-trivial and should be a formal component of international climate dialogs.

"It is important to emphasize that not all fire is a disaster and we must learn how to both live with as well as manage fire," said co-author Andrew Scott, earth sciences professor at Royal Holloway University of London.

The report, "Living on a flammable planet: interdisciplinary, cross-scalar and varied cultural lessons, prospects and challenges," was published May 23, 2016 by The Royal Society, the U.K.'s independent scientific academy.

Authors call for holistic study of fire on Earth

The authors are from the United States, Great Britain, Canada, Australia, South Africa and Spain. The synthesis emerged from four days of international meetings sponsored by the Royal Society - the first of its kind for fire sciences.

The authors advocate for greater collaboration among researchers studying all aspects of fire.

Pyrogeography—the holistic study of fire on Earth, "may be one way to provide unity to the varied fire research programs across the globe," the authors write.

"Fire researchers across disciplines from engineering, the natural sciences, social sciences and the humanities need to develop a common language to create a holistic wildfire science," said Roos. "The magnitude of the wildfire challenges we face on a warming planet will demand greater collaboration and integration across disciplines, but our job won't be done unless we are also able to translate our research for policymakers, land managers, and the general public."

Source: Southern Methodist University [June 01, 2016]