NORMAN — Using advanced sequencing technologies, University of Oklahoma anthropologists demonstrate that human DNA can be significantly enriched from dental calculus (calcified dental plaque) enabling the reconstruction of whole mitochondrial genomes for maternal ancestry analysis — an alternative to skeletal remains in ancient DNA investigations of human ancestry.
Christina Warinner and Cecil M. Lewis, Jr., professors in the Department of Anthropology, OU College of Arts and Sciences, collaborated with researchers from Arizona State University and Pennsylvania State University on the capture, enrichment and high-throughput sequencing of DNA extracted from six individuals at the 700-year-old Oneota cemetery, Norris Farms #36.
“We can now obtain meaningful human, pathogen and dietary DNA from a single sample, which minimizes the amount of ancient material required for analysis,” said Warinner.
In recent years, dental calculus has emerged as an unexpected, but valuable, long-term reservoir of ancient DNA from dietary and microbial sources. This study demonstrates that dental calculus is also an important source of ancient human DNA. Very little dental calculus was required for analysis — fewer than 25 milligrams per individual. This makes it possible to obtain high quality genetic ancestry information from very little starting material, an important consideration for archaeological remains.
The results of this study provided high-resolution, whole mitochondrial genome information for the Oneota, a Native American archaeological culture that rose to prominence ca. AD 1000-1650, but declined sharply following European contact. “The analysis of mitochondrial DNA allows us to better understand the population history of ancient peoples,” said Anne Stone, professor in the School of Human Evolution and Social Change, Arizona State University.
Although dental calculus preserves alongside skeletal remains, it is not actually a human tissue. Dental calculus, also known as tartar, is a calcified form of dental plaque that acquires human DNA and proteins passively, primarily through the saliva and other host secretions. Once mineralized within dental calculus, however, human DNA and proteins can preserve for thousands of years. Dental calculus thus serves as an important non-skeletal reservoir of ancient human DNA.
New remains demonstrate early hominid’s adaptability
New fossils from Kenya suggest that an early hominid species — Australopithecus afarensis — lived far eastward beyond the Great Rift Valley: much farther than previously thought. An international team of paleontologists led by Emma Mbua of Mount Kenya University and Masato Nakatsukasa of Kyoto University report findings of fossilized teeth and forearm bone from an adult male and two infant A. afarensis from an exposure eroded by the Kantis River in Ongata-Rongai, a settlement in the outskirts of Nairobi.
“So far, all other A. afarensis fossils had been identified from the center of the Rift Valley,” explains Nakatsukasa. “A previous Australopithecus bahrelghazali discovery in Chad confirmed that our hominid ancestor’s distribution covered central Africa, but this was the first time an Australopithecus fossil has been found east of the Rift Valley. This has important implications for what we understand about our ancestor’s distribution range, namely that Australopithecus could have covered a much greater area by this age.”
A. afarensis is believed to have lived 3,700,000-3,000,000 years ago, as characterized by fossils like “Lucy” from Ethiopia.
Stable isotope analysis revealed that the Kantis region was humid, but had a plain-like environment with fewer trees compared to other sites in the Great Rift Valley where A.afaransis fossils had previously appeared. “The hominid must have discovered suitable habitats in the Kenyan highlands. It seems that A. afaransis was good at adapting to varying environments,” notes Nakatsukasa.
The team’s survey also turned up masses of mammal fossils, including a few that probably belong to new species of bovids or baboons.
The authors write that the Kantis site was first noted in a 1991 geological survey. At that time, a farmer said that he and his family had come across fossilized bones from Kantis in the 1970s, although they did not recognize their importance. Following airing of Kenyan television programs on paleontological research, locals gradually started to appreciate the fossils. Since then, Kantis and other sites have been identified thanks to fossil notifications from the local population.
The team welcomes this achievement not only for its academic implications, but also for the benefits to the local community. “Kantis is in the vicinity of Nairobi, a major city,” said Nakatsukasa. “We hope that the discovery of the new site and the fossils will aid in increasing tourism, and in improving educational awareness of the local community.”
(Text & Images’ Source: Kyoto University)
Forensic researchers have for the first time established science-based standards for identifying human remains based on X-rays of an individual’s spine, upper leg or the side of the skull.
“In the past, forensic experts have relied on a mixed bag of standards when comparing ante mortem and post mortem X-rays to establish a positive identification for a body – but previous research has shown that even experts can have trouble making accurate identifications,” says Ann Ross, lead author of a paper on the new standards and a professor of anthropology at North Carolina State University.
“We’ve created a set of standards that will allow for a consistent approach to identification – that can be replicated – and that allows experts to determine probabilities for an identification,” Ross says. “For example, you could say with 85 percent certainty that a body is a specific individual.”
The researchers compared ante mortem and post mortem lateral craniofacial (side of the skull) X-rays for 20 individuals, and did the same for X-rays of the vertebral column (spine) for 50 individuals, and X-rays of the proximal femur (upper leg) for 23 individuals. The researchers used these evaluations to develop location-specific standards for each skeletal region. The researchers focused on these skeletal regions because they are among the most frequently X-rayed in a clinical setting.
The researchers then used additional, unmatched X-rays to test the accuracy of the standards in two ways. First, they tested the standards to see how likely they were to accurately identify a body. Second, they ran separate analyses to see how likely the standards were to “misclassify” an identification – to provide a false-positive or false-negative result.
Production of butter from shea trees in West Africa pushed back 1,000 years University of Oregon anthropologists explore layers of households built atop of each other for 1,600 years and find shea nuts have been used since A.D. 100
EUGENE, Ore. — University of Oregon anthropologists have pushed back the history of harvesting shea trees in West Africa by more than 1,000 years earlier than previously believed.
Evidence for earlier use of the wild trees dating to A.D. 100 — reported in the March issue of the Journal of Ethnobiology — surfaced from excavations at the well-preserved archaeological site at Kirikongo in western Burkina Faso. Shea trees only grow in a narrow belt of fertile, well-drained soils in the savannah stretching from West Africa to East Africa.
Nuts from shea trees (Vitellaria paradoxa) are the source of thick ivory-colored vegetable butter — a staple used as cooking oil in the region. Shea butter, which is rich in antioxidants, also is used medicinally and exported for making soap, moisturizers and lotions. It occasionally is a substitute for cocoa butter. The tree’s termite-resistant wood also is used for construction and making implements.
The researchers analyzed thousands of carbonized fragments of nutshells found in multiple layers of households that had been built on top of each other for some 1,600 years.
“Our findings demonstrate the antiquity of the use of this particular resource,” said Daphne E. Gallagher, a researcher and lecturer in the UO Department of Anthropology. “It demonstrates the importance of wild foods in early agricultural diets, and that its importance has continued through time.”
Archaeologists at the University of York, leading a large international team, have revealed surprising new insights into why pottery production increased significantly at the end of the last Ice Age – with culture playing a bigger role than expected.
Investigating the use and expansion of hunter-gatherer pottery in Japan, home to some of the earliest pottery in the world, researchers analysed 143 ceramic vessels from Torihama, an ancient site in western Japan.
Pottery is thought to have originated in Japan around 16,000 years ago, but the numbers produced vastly increased 11,500 years ago, coinciding with a shift to a warmer climate. As resurgence in forests took place, an increase in vegetation and animals led to new food sources becoming available.
Previous thinking suggested that pottery use and production increased to accommodate different cooking and storage techniques for the wider variety of foodstuffs available at this time. However, new analysis reveals this not to be the case.
Performing molecular and isotopic analysis of lipids extracted from vessels spanning a 9000 year period, the researchers found that pottery was used largely for cooking marine and freshwater animal species – a routine that remained constant despite climate warming and new resources becoming available.
Finding surprisingly little evidence of plant processing in pottery, or cooking of animals such as deer, researchers found the only significant change to be the different types of fish consumed, such as an increase in freshwater fish.
University of Leicester archaeologists who discovered and helped to identify the mortal remains of King Richard III have created a 3D interactive representation of the grave and the skeleton of the king under the car park.
It is revealed today (Tuesday 22 March) on the first year anniversary of the reinterment of Richard III when the coffin bearing the mortal remains first emerged from the Fielding Johnson Building at the University of Leicester.
Following a procession through the county and city, the remains were handed to the care of Leicester Cathedral by archaeologist Richard Buckley and King Richard III was reinterred on 26 March 2015.
The team from University of Leicester Archaeological Services (ULAS) has now created a fully rotatable computer model which shows the king’s remains in-situ as they were found during the 2012 archaeological excavation.
Using photographs taken during the project, sophisticated photogrammetry software has been used to create an accurate representation of the grave and the skeleton.
The interactive model, which can be explored via the 3D sharing platform Sketchfab, graphically reveals in a new and immersive way the minimal reverence with which the king was buried.
Mathew Morris, Site Supervisor for University of Leicester Archaeological Services was the man who first discovered the remains of King Richard III- on the first day of the dig under the Leicester car park. He said: “Photographs and drawings of the grave, whilst dramatic, are only two-dimensional and do not always best show nuances in spatial relationships that a three-dimensional model can.
“Photogrammetry provides a fantastic analytical tool that allows us to examine the grave from angles that would have been physically difficult or impossible to achieve during the excavation, and gives us the ability to continue to examine the king’s grave long after the excavation has finished.”
More local adaptations in European genes were contributed by Stone Age hunters than farmers
Modern humans have adapted to their local environments over many thousands of years, but how genetic variation contributed to this adaptation remains debated. Using genomes from humans that lived between 45,000 and 7,000 years ago, researchers from the Max Planck Institute for Evolutionary Anthropology in Leipzig have shown that adaptation to local environments has resulted in genetic variants reaching high frequencies in European groups. Interestingly, most of the adaptive variants were present already in an early hunter-gatherer, but not in an early farmer. This suggests that hunter-gatherers, who lived in Europe for thousands of years before the arrival of farmers, were adapted to local environments and contributed adaptive genetic variants to present-day Europeans.
Humans have few genetic differences among individuals, and most of these differences have no effect on phenotype or fitness. The role of local adaptation in population differentiation thus remains unclear.
Using the genome of a 45,000 year old early modern Eurasian from Ust’-Ishim, researchers from the Max Planck Institute in Leipzig investigated the few genetic variants that have large frequency differences between Africans and non-Africans. “When we first heard about the Ust’-Ishim genome we got immediately excited. This individual is extremely useful in that it provides direct information on the genetics of a population that had experienced the out-of-Africa migration, but had not had much time to adapt to Eurasian environments”, says Aida Andrés, who led the scientific team.
Her team finds that about 70% of the genomic variants with large frequency differences between Africans and non-Africans are random changes that may have occurred during times of small population size, such as during the migration out of the African continent about 50,000 years ago. Less than 30% of the variants were found to have increased in frequency during or after the colonization of Europe. These are enriched in likely functional parts of the genome such as those that encode proteins and regulate the activity of genes. This suggests that some of them rose in frequency due to positive selection for locally adaptive traits.
Genetically more hunter than farmer
The genomes of additional ancient Europeans provided more detail on local adaptation in Europe. The team showed that an early hunter-gatherer carried more variants that have increased quickly in frequency in Europe than an early farmer. “It is quite striking that, while the Neolithic farming revolution brought a lifestyle to Europe that still persists today, the hunter-gatherers provided the majority of genetic adaptations to the local European environment”, says Felix Key, PhD student at the Max Planck Institute in Leipzig and first author of the paper. Eye pigmentation is among the traits likely influenced by hunter-gatherer variants, and the team speculates that these variants may be beneficial in populations living at high latitudes with limited exposure to UV light. However, Key is cautious, commenting that: ‘We have to note that our functional understanding of human genetic variants is still limited.’
Andrés sees great potential for this approach in the future: “Combining modern and ancient genomes improves our ability to understand local adaptation. The resolution of studies like ours will keep improving with the growing availability of high-quality ancient genomes.” She predicts that “With additional data we are likely to find similar evidence of genetic adaptations in other continents, too”.
(Text & Images’ Source: article by AA/FMK/SP, Max Planck Institute for Evolutionary Anthropology)
British anthropologist Professor Caroline Wilkinson had South African audiences at the edges of their seats with her fascinating work in facial reconstruction.
Wilkinson, a professor from Liverpool John Moores University, visited South Africa as a guest of the School of Anatomical Sciences at Wits University, with support from a National Research Foundation grant, to present various events, including a workshop for members of the South African Police Service.
While known for her expertise in forensic identification, Wilkinson is equally renowned for her contributions to archaeological investigations. Arguably her most famous case was her creation of a reconstruction of King Richard III’s head.
With a background in art and science and her research of art-science fusion, Wilkinson was appointed Director of the School of Art & Design at Liverpool John Moores University in October 2014. Her knowledge is diverse and extends to forensic art, human anatomy, medical art, face recognition, forensic science, anthropology, 3D visualisation, digital art and craniofacial identification.
She combines the latest medical and digital-imaging techniques to recreate faces from the past. Aside from King Richard III, her other famous facial reconstructions include Mary Queen of Scots (Queen of Scotland), Rameses II (ancient Egyptian), St Nicholas (historic 4th-century Christian saint) and Robert Burns (Scottish poet and lyricist).
Analysis of nuclear DNA from Sima de los Huesos hominins provides evidence of their relationship to Neandertals
Previous analyses of the hominins from Sima de los Huesos in 2013 showed that their maternally inherited mitochondrial DNA was distantly related to Denisovans, extinct relatives of Neandertals in Asia. This was unexpected since their skeletal remains carry Neandertal-derived features. Researchers of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, have since worked on sequencing nuclear DNA from fossils from the cave, a challenging task as the extremely old DNA is degraded to very short fragments. The results now show that the Sima de los Huesos hominins were indeed early Neandertals. Neandertals may have acquired different mitochondrial genomes later, perhaps as the result of gene flow from Africa.
Until now it has been unclear how the 28 400,000-year-old individuals found at the Sima de los Huesos (“pit of bones”) site in Northern Spain were related to Neandertals and Denisovans who lived until about 40,000 years ago. A previous report based on analyses of mitochondrial DNA from one of the specimens suggested a distant relationship to Denisovans, which is in contrast to other archaeological evidence, including morphological features that the Sima de los Huesos hominins shared with Neandertals.
“Sima de los Huesos is currently the only non-permafrost site that allow us to study DNA sequences from the Middle Pleistocene, the time period preceding 125,000 years ago”, says Matthias Meyer of the Max Planck Institute for Evolutionary Anthropology, lead author of an article that was published in Nature today. “The recovery of a small part of the nuclear genome from the Sima de los Huesos hominins is not just the result of our continuous efforts in pushing for more sensitive sample isolation and genome sequencing technologies”, Meyer adds. “This work would have been much more difficult without the special care that was taken during excavation”.
Residents of the remote equatorial islands of Melanesia share fragments of genetic code with two extinct human species. That’s the key finding of a new study published March 17 in the journal Science.
An international team contributed to the research, which compared the DNA sequences of 35 modern people living on islands off the coast of New Guinea with DNA drawn from two early human species: Denisovans, whose remains were found in Siberia, and Neandertals, first discovered in Germany.
“Substantial amounts of Neandertal and Denisovan DNA can now be robustly identified in the genomes of present-day Melanesians, allowing new insights into human evolutionary history,” they wrote. “As genome-scale data from worldwide populations continues to accumulate, a nearly complete catalog of surviving archaic lineages may soon be within reach.”
D. Andrew Merriwether, a molecular anthropologist at Binghamton University, collected the modern-day blood samples used in the study about 15 years ago in Melanesia. This is the first time full genomes from those samples have been sequenced.
“I’m surprised that these Neandertal and Denisovan genomes made it out to this remote place,” he said. “We know people have been there for at least 48,000 years because we find human remains that go back that far, but no one has ever been able to connect them to any other place. When you compare most of their genome sequences, they don’t cluster with any other group. They’ve been there and been isolated for a very, very long time.”
Earlier studies have revealed some genetic overlap (about 2 percent) between Neandertals and non-African populations and little or no Neandertal and Denisovan ancestry among Africans. This new research suggests Neandertals and modern human ancestors intersected at least three times. It also found an overlap of between 1.9 and 3.4 percent in the genetic codes of Denisovans and modern-day Melanesians.
Skepticism about the new findings is entirely appropriate, said Merriwether, who specializes in reconstructing the past using samples from contemporary populations and ancient DNA from the archaeological record.