Earliest interbreeding event between ancient human populations discovered

Neanderthal-Denisovan ancestors interbred with a distantly related hominin 700,000 years ago

UNIVERSITY OF UTAH

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IMAGE: AN EVOLUTIONARY TREE INCLUDING FOUR PROPOSED EPISODES OF GENE FLOW. THE PREVIOUSLY UNKNOWN EVENT 744,372 YEARS AGO (ORANGE) SUGGESTS INTERBREEDING OCCURRED BETWEEN SUPER-ARCHAICS AND NEANDERTHAL-DENISOVAN ANCESTORS IN EURASIA.... view more 

CREDIT: ADAPTED FROM ALAN ROGERS

For three years, anthropologist Alan Rogers has attempted to solve an evolutionary puzzle. His research untangles millions of years of human evolution by analyzing DNA strands from ancient human species known as hominins. Like many evolutionary geneticists, Rogers compares hominin genomes looking for genetic patterns such as mutations and shared genes. He develops statistical methods that infer the history of ancient human populations.

In 2017, Rogers led a study which found that two lineages of ancient humans, Neanderthals and Denisovans, separated much earlier than previously thought and proposed a bottleneck population size. It caused some controversy--anthropologists Mafessoni and Prüfer arguedthat their method for analyzing the DNA produced different results. Rogers agreed, but realized that neither method explained the genetic data very well.

"Both of our methods under discussion were missing something, but what?" asked Rogers, professor of anthropology at the University of Utah.

The new study has solved that puzzle and in doing so, it has documented the earliest known interbreeding event between ancient human populations--a group known as the "super-archaics" in Eurasia interbred with a Neanderthal-Denisovan ancestor about 700,000 years ago. The event was between two populations that were more distantly related than any other recorded. The authors also proposed a revised timeline for human migration out of Africa and into Eurasia. The method for analyzing ancient DNA provides a new way to look farther back into the human lineage than ever before.

"We've never known about this episode of interbreeding and we've never been able to estimate the size of the super-archaic population," said Rogers, lead author of the study. "We're just shedding light on an interval on human evolutionary history that was previously completely dark."

The paper was published on Feb. 20, 2020, in the journal Science Advances.

Out of Africa and interbreeding

Rogers studied the ways in which mutations are shared among modern Africans and Europeans, and ancient Neanderthals and Denisovans. The pattern of sharing implied five episodes of interbreeding, including one that was previously unknown. The newly discovered episode involves interbreeding over 700,000 years ago between a distantly related "super-archaic" population which separated from all other humans around two million years ago, and the ancestors of Neanderthals and Denisovans.

The super-archaic and Neanderthal-Denisovan ancestor populations were more distantly related than any other pair of human populations previously known to interbreed. For example, modern humans and Neanderthals had been separated for about 750,000 years when they interbred. The super-archaics and Neanderthal-Denisovan ancestors were separated for well over a million years.

"These findings about the timing at which interbreeding happened in the human lineage is telling something about how long it takes for reproductive isolation to evolve," said Rogers.

The authors used other clues in the genomes to estimate when the ancient human populations separated and their effective population size. They estimated the super-archaic separated into its own species about two million years ago. This agrees with human fossil evidence in Eurasia that is 1.85 million years old.

The researchers also proposed there were three waves of human migration into Eurasia. The first was two million years ago when the super-archaics migrated into Eurasia and expanded into a large population. Then 700,000 years ago, Neanderthal-Denisovan ancestors migrated into Eurasia and quickly interbred with the descendants of the super-archaics. Finally, modern humans expanded to Eurasia 50,000 years ago where we know they interbred with other ancient humans, including with the Neanderthals.

"I've been working for the last couple of years on this different way of analyzing genetic data to find out about history," said Rogers. "It's just gratifying that you come up with a different way of looking at the data and you end up discovering things that people haven't been able to see with other methods."

Arnhem Land, Australia: arliest evidence of Homo sapiens use of plant foods outside Africa and the Middle East.

Australia's first plant foods -- eaten by early populations 65,000 years ago -- have been discovered in Arnhem Land.

Preserved as pieces of charcoal, the morsels were recovered from the debris of ancient cooking hearths at the Madjedbebe archaeological site, on Mirarr country in northern Australia.

University of Queensland archaeobotanist Anna Florin said a team of archaeologists and Traditional Owners identified 10 plant foods, including several types of fruits and nuts, underground storage organs ('roots and tubers'), and palm stem.

"By working with Elders and co-authors May Nango and Djaykuk Djandjomerr, the team was also able to explain how the plants were likely used at Madjedbebe," Ms Florin said.

"Many of these plant foods required processing to make them edible and this evidence was complemented by grinding stone technology also used during early occupation at the site."

"The First Australians had a great deal of botanical knowledge and this was one of the things that allowed them to adapt to and thrive in this new environment.

"They were able to guarantee access to carbohydrates, fat and even protein by applying this knowledge, as well as technological innovation and labour, to the gathering and processing of Australian plant foods."

Madjedbebe is a sandstone rock shelter at the base of the Arnhem Land escarpment, and is Australia's oldest documented site.

Excavation director Professor Chris Clarkson from UQ's School of Social Science said he was surprised and delighted by the quantity of archaeobotanical evidence recovered from the site.

"Madjedbebe continues to provide startling insights into the complex and dynamic lifestyle of the earliest Australian Aboriginal people," Professor Clarkson said.

The oldest occupation layer at Madjedbebe also holds evidence for the oldest edge ground stone axes in the world, the earliest grindstone technology outside Africa, the early shaping of stone spearheads, many kilograms of ground ochre, and the first recorded use of reflective pigments in the world.

"The site is an important cultural place to Mirarr people today who strive to protect their heritage from numerous threats, including mining," Ms Florin said.

Justin O'Brien, CEO of Gundjeihmi Aboriginal Corporation which represents the Mirarr Traditional Owners, said that research on country -- working in meaningful partnership with Traditional Owners -- was a powerful way to share Mirarr's enduring culture with a broader audience.

Discovery at 'flower burial' site could unravel mystery of Neanderthal death rites

CAPTION

The Neanderthal skull, flattened by thousands of years of sediment and rock fall, in situ in Shanidar Cave, Iraqi Kurdistan.

CREDIT

Graeme Barker

The first articulated Neanderthal skeleton to come out of the ground for over 20 years has been unearthed at one of the most important sites of mid-20th century archaeology: Shanidar Cave, in the foothills of Iraqi Kurdistan.

Researchers say the new find offers an unparalleled opportunity to investigate the "mortuary practices" of this lost species using the latest technologies.

Shanidar Cave was excavated in the 1950s, when archaeologist Ralph Solecki uncovered partial remains of ten Neanderthal men, women and children.

Some were clustered together, with clumps of ancient pollen surrounding one of the skeletons. Solecki claimed this showed Neanderthals buried their dead and conducted funerary rites with flowers.

The 'flower burial' captured the public imagination, and prompted a reappraisal of a species that - prior to Shanidar Cave - was thought to have been dumb and animalistic.

It also sparked a decades-long controversy over whether evidence from this extraordinary site did actually point to death rituals, or burial of any kind, and if Neanderthals were really capable of such cultural sophistication.

More than 50 years later, a team of researchers have reopened the old Solecki trench to collect new sediment samples, and discovered the crushed skull and torso bones of another Shanidar Neanderthal.

The discovery has been named Shanidar Z by researchers from Cambridge, Birkbeck and Liverpool John Moores universities.

The work was conducted in conjunction with the Kurdistan General Directorate of Antiquities and the Directorate of Antiquities for Soran Province. The find is announced today in a paper published in the journal Antiquity.

"So much research on how Neanderthals treated their dead has to involve returning to finds from sixty or even a hundred years ago, when archaeological techniques were more limited, and that only ever gets you so far," said Dr Emma Pomeroy, from Cambridge's Department of Archaeology, lead author of the new paper.

"To have primary evidence of such quality from this famous Neanderthal site will allow us to use modern technologies to explore everything from ancient DNA to long-held questions about Neanderthal ways of death, and whether they were similar to our own."

Ralph Solecki died last year aged 101, having never managed to conduct further excavations at his most famous site, despite several attempts.

In 2011, the Kurdish Regional Government approached Professor Graeme Barker from Cambridge's McDonald Institute of Archaeology about revisiting Shanidar Cave. With Solecki's enthusiastic support, initial digging began in 2014, but stopped after two days when ISIS got too close. It resumed the following year.

"We thought with luck we'd be able to find the locations where they had found Neanderthals in the 1950s, to see if we could date the surrounding sediments," said Barker. "We didn't expect to find any Neanderthal bones."

In 2016, in one of the deepest parts of the trench, a rib emerged from the wall, followed by a lumbar vertebra, then the bones of a clenched right hand. However, metres of sediment needed carefully digging out before the team could excavate the skeleton.

During 2018-19 they went on to uncover a complete skull, flattened by thousands of years of sediment, and upper body bones almost to the waist - with the left hand curled under the head like a small cushion.

Early analysis suggests it is over 70,000 years old. While the sex is yet to be determined, the latest Neanderthal discovery has the teeth of a "middle- to older-aged adult".

Shanidar Z has now been brought on loan to the archaeological labs at Cambridge, where it is being conserved and scanned to help build a digital reconstruction, as more layers of silt are removed.

The team is also working on sediment samples from around the new find, looking for signs of climate change in fragments of shell and bone from ancient mice and snails, as well as traces of pollen and charcoal that could offer insight into activities such as cooking and the famous 'flower burial'.

Four of the Neanderthals, including the 'flower burial' and the latest find, formed what researchers describe as a "unique assemblage". It raises the question of whether Neanderthals were returning to the same spot within the cave to inter their dead.

A prominent rock next to the head of Shanidar Z may have been used as a marker for Neanderthals repeatedly depositing their dead, says Pomeroy, although whether time between deaths was weeks, decades or even centuries will be difficult to determine.

"The new excavation suggests that some of these bodies were laid in a channel in the cave floor created by water, which had then been intentionally dug to make it deeper," said Barker. "There is strong early evidence that Shanidar Z was deliberately buried."

CT-scans in Cambridge have revealed the petrous bone - one of the densest in the body; a wedge at the base of the skull - to be intact, offering hope of retrieving ancient Neanderthal DNA from the hot, dry region where "interbreeding" most likely took place as humans spilled out of Africa.

Added Pomeroy: "In recent years we have seen increasing evidence that Neanderthals were more sophisticated than previously thought, from cave markings to use of decorative shells and raptor talons.

"If Neanderthals were using Shanidar cave as a site of memory for the repeated ritual interment of their dead, it would suggest cultural complexity of a high order."

Ancient engravings were likely produced with aesthetic intent and marked group identity.

Symbolic behaviour - such as language, account keeping, music, art, and narrative - constitutes a milestone in human cognitive evolution. But how, where and when did these complex practices evolve? This question is very challenging to address; human cognitive processes do not fossilize, making it very difficult to study the mental life of our Stone Age ancestors. However, in a new study published in the Proceedings of the National Academy of Sciences journal PNAS, an interdisciplinary team of cognitive scientists and archaeologists from Denmark, South Africa and Australia takes up the challenge. They used engravings on ochre nodules and ostrich eggshells made between about 109 000 and 52 000 years ago in a series of five cognitive science experiments to investigate their potential symbolic function.

The engravings originate from the South African Middle Stone Age sites of Blombos Cave and Diepkloof Rock Shelter, and are considered among the earliest examples of human symbolic behaviour. They were found in different layers of the cave sediments, which has made it possible to reconstruct the approximate time and order in which they were produced. Lead scientist Kristian Tylén, Associate Professor at the Department of Linguistics, Cognitive Science and Semiotics and at the Interacting Minds Centre, Aarhus University, Denmark, explains:

"It is remarkable that we have a record of a practice of making engravings spanning more than 40 000 years. This allows us to observe how the engraved patterns have been developed and refined incrementally over time to become better symbols - that is - tools for the human mind, similar to the way instrumental technologies, such as stone tools, are honed over time to do their job more efficiently".

In the experiments, participants were shown the engraved patterns while the researchers measured their responses in terms of visual attention, recognition, memory, reaction times, and discrimination of patterns belonging to different points in time. The experiments suggest that over the period of more than 40 000 years, the engravings evolved to more effectively catch human visual attention, they became easier to recognize as human-made, easier to remember and reproduce, and they evolved elements of group-specific style. However, they did not become easier to discriminate from each other within or between each of the two sites.

Several previous studies have presented speculations on the possible symbolic function of the Blombos and Diepkloof engravings. Some have suggested that they should be regarded as fully-developed symbols pointing to distinct meanings, more or less like written glyphs. This suggestion is, however, not supported by the present study:

"It is difficult to make well-grounded interpretations of these ancient human behaviours", says archaeologist and co-author Niels N. Johannsen, Associate Professor at the Department of Archaeology and Heritage Studies and at the Interacting Minds Centre, Aarhus University, "and we have been missing a more systematic, scientific approach. The main advantage of our experimental procedure is that we work directly with the archaeological evidence, measuring cognitive consequences of the changes that these engravings have undergone through time - and from these data, we argue, we are in a better position to understand the possible function of the engravings made by our ancestors tens of thousands of years ago."

The experimental findings suggest that the engravings from Blombos and Diepkloof were created and refined over time to serve an aesthetic purpose, for instance as decorations. However, they also evolved elements of style that could have worked to mark the identity of the group, that is, they could be recognized as coming from a particular group.

The experiments make use of contemporary participants and concerns could be raised that the measurements say little about cognitive processes unfolding in the minds of stone age humans 100 000 years ago.

Kristian Tylén explains:

"Previous investigations have relied exclusively on studies of archaeological artefacts, the size and shape of cranial casts, or the mapping of genes. These are very indirect measures of human cognitive processes. While our experimental approach is also indirect in the sense that we cannot travel back in time and directly record the cognitive processes of our Stone Age ancestors, it is, on the other hand, dealing directly with those basic cognitive processes critically involved in human symbolic behaviour."

The study can thus inform foundational discussions of the early evolution of human symbolic behaviour. Not unlike manual tools, the findings suggest that the engravings were incrementally refined over a period of more than 40 000 years to become more effective 'tools for the mind' as their producers became more skilled symbol makers and users. In the challenging pursuit of understanding human cognitive evolution, the approach and findings provide novel insights into the minds of our Stone Age ancestors that cannot be achieved through the traditional methods of archaeology and genetics, or by theoretical work alone.

Dog domestication during ice age

Analysis of Paleolithic-era teeth from a 28,500-year-old fossil site in the Czech Republic provides supporting evidence for two groups of canids - one dog-like and the other wolf-like - with differing diets, which is consistent with the early domestication of dogs.

The study, published in the Journal of Archaeological Science, was co-directed by Peter Ungar, Distinguished Professor of anthropology at the University of Arkansas.

The researchers performed dental microwear texture analysis on a sample of fossils from the Předmostí site, which contains both wolf-like and dog-like canids. Canids are simply mammals of the dog family. The researchers identified distinctive microwear patterns for each canid morphotype. Compared to the wolf-like canids, the teeth of the early dog canids - called "protodogs" by the researchers - had larger wear scars, indicating a diet that included hard, brittle foods. The teeth of the wolf-like canids had smaller scars, suggesting they consumed more flesh, likely from mammoth, as shown by previous research.

This greater durophagy - animal eating behavior suggesting the consumption of hard objects - among the dog-like canids means they likely consumed bones and other less desirable food scraps within human settlement areas, Ungar said. It provides supporting evidence that there were two types of canids at the site, each with a distinct diet, which is consistent with other evidence of early-stage domestication.

"Our primary goal was to test whether these two morphotypes expressed notable differences in behavior, based on wear patterns," said Ungar. "Dental microwear is a behavioral signal that can appear generations before morphological changes are established in a population, and it shows great promise in using the archaeological record to distinguish protodogs from wolves."

Dog domestication is the earliest example of animal husbandry and the only type of domestication that occurred well before the earliest definitive evidence of agriculture. However, there is robust scientific debate about the timing and circumstances of the initial domestication of dogs, with estimates varying between 15,000 and 40,000 years ago, well into the Ice Age, when people had a hunter-gatherer way of life. There is also debate about why wolves were first domesticated to become dogs. From an anthropological perspective, the timing of the domestication process is important for understanding early cognition, behavior and the ecology of early Homo sapiens.

Canaanite temple at Lachish: gold artifacts, cultic figurines, and oldest known etching of Hebrew letter 'Samech'

IMAGE: A CANAANITE STORAGE JAR WITH AN INSCRIPTION BEARING THE LETTER "SAMEK. " view more 

CREDIT: T. ROGOVSKI

"And the Lord delivered Lachish into the hand of Israel, which took it on the second day, and smote it with the edge of the sword, and all the souls therein..." -Joshua, 10:32

The Biblical Book of Joshua tells the story of the ancient Israelites' entry into the Promised Land after a 40-year sojourn in the desert. Now, a team of archaeologists led by Professor Yosef Garfinkel at the Hebrew University of Jerusalem's Institute of Archaeology and Professor Michael Hasel at Southern Adventist University in Tennessee, have opened a window onto the Canaanite society that inhabited the land during that era.

In a study published last month in Levant, Garfinkel and his co-authors revealed, for the first time ever, extensive ruins of a Canaanite temple dating to the 12th century BCE that they uncovered in National Park Tel Lachish, a large Bronze Age-era settlement near the present-day Israeli city of Kiryat Gat.

Lachish was one of the most important Canaanite cities in the Land of Israel during the Middle and late Bronze Ages; its people controlled large parts of the Judean lowlands. The city was built around 1800 BCE and later destroyed by the Egyptians around 1550 BCE. It was rebuilt and destroyed twice more, succumbing for good around 1150 BCE. The settlement is mentioned in both the Bible and in various Egyptian sources and was one of the few Canaanite cities to survive into the 12th century BCE.

"This excavation has been breath-taking," shared Garfinkel. "Only once every 30 or 40 years do we get the chance to excavate a Canaanite temple in Israel. What we found sheds new light on ancient life in the region. It would be hard to overstate the importance of these findings."

The layout of the temple is similar to other Canaanite temples in northern Israel, among them Nablus, Megiddo and Hazor. The front of the compound is marked by two columns and two towers leading to a large hall. The inner sanctum has four supporting columns and several unhewn "standing stones" that may have served as representations of temple gods. The Lachish temple is more square in shape and has several side rooms, typical of later temples including Solomon's Temple.

In addition to these archaeological ruins, the team unearthed a trove of artifacts including, bronze cauldrons, Hathor-inspired jewellery, daggers and axe-heads adorned with bird images, scarabs, and a gold-plated bottle inscribed with the name Ramses II, one of Egypt's most powerful pharaohs. Near the temple's holy of holies, the team found two bronze figurines. Unlike the winged cherubs in Solomon's Temple, the Lachish figurines were armed "smiting gods".

Of particular interest was a pottery sherd engraved with ancient Canaanite script. There, the letter "samek" appears, marked by an elongated vertical line crossed by three perpendicular shorter lines. This makes it the oldest known example of the letter and a unique specimen for the study of ancient alphabets.

Only time will tell what treasures still remain to be uncovered in the ancient city of Lachish.

Canaanite temple uncovered in Lachish, a city destroyed by Joshua

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A Canaanite temple and many artifacts have been uncovered in a city that, according to the Bible, was destroyed by the Israelites when they entered the Land of Israel after 40 years in the desert. The discovery shed light on the extensive ruins of a structure dating back to the 12th century BCE in Lachish, the Hebrew University of Jerusalem announced Monday.
 

 

“Joshua proceeded with all Israel to Lachish; he encamped against it and attacked it. God delivered Lachish into the hands of Israel. They captured it on the second day and put it and all the people in it to the sword,” reads Joshua 10:31-32.
 

Among the crucial findings were a pottery shard featuring the Hebrew letter samekh, which represents the oldest-known engraving of the letter, gold artifacts and cultic figurines, including figurines depicting the warrior god Ba’al, who is mentioned dozens of times in the Bible – including several instances where the Israelites turn to its cult in spite of the commandments of God.
 

The site of Lachish was first identified in 1929 by William Foxwell Albright, who is considered the founding father of Biblical archaeology.

 

The city was a major Canaanite center city, as we know from historical sources. There is no other site in this region as prominent. It is the right location, the right place, and the name ‘Lachish’ was found on some inscriptions found there.”

 

The square-shaped layout of the building featured a compound in the front marked by two columns and two towers leading to a large room, as well as an inner sanctum with four supporting columns and several unhewn “standing stones” that might have represented the different gods worshiped. In addition, it presented numerous side rooms.
 

One of the research questions the team pursued in Lachish was connected to the time of the Kingdom of Judah, specifically whether the Bible contains historical memories about the 10th century BCE and whether King David can be considered an historical figure.

The Bible says that Rehoboam, the grandson of David, fortified 15 cities, including Lachish. The first researchers examining the site did not manage to uncover fortifications from the period, prompting many scholars to doubt the validity of the description presented in the Biblical book of Chronicles II.
 

However, archaeologists were able to locate the fortification from the relevant period, also discovering houses, floors and pottery inside the city, whose dating was confirmed by carbon dating at around the late 10th century BCE.
 

They also managed to locate some inscriptions at the site for the first time in 40 years, along with an especially rich collections of objects such as daggers and ax-heads adorned with bird images, bronze cauldrons, jewelry, scarabs and a gold-plated bottle featuring the name of Egyptian Pharaoh Ramses II.