Ancient human genome from southern Africa throws light on our origins

Professor Vanessa Hayes in the field.

The skeleton of a man who lived 2,330 years ago in the southernmost tip of Africa tells us about ourselves as humans, and throws some light on our earliest common genetic ancestry.

What can DNA from the skeleton of a man who lived 2,330 years ago in the southernmost tip of Africa tell us about ourselves as humans? A great deal when his DNA profile is one of the 'earliest diverged' -- oldest in genetic terms -- found to-date in a region where modern humans are believed to have originated roughly 200,000 years ago.

The man's maternal DNA, or 'mitochondrial DNA', was sequenced to provide clues to early modern human prehistory and evolution. Mitochondrial DNA provided the first evidence that we all come from Africa, and helps us map a figurative genetic tree, all branches deriving from a common 'Mitochondrial Eve'.
When archaeologist Professor Andrew Smith from the University of Cape Town discovered the skeleton at St. Helena Bay in 2010, very close to the site where 117,000 year old human footprints had been found -- dubbed "Eve's footprints" -- he contacted Professor Vanessa Hayes, an expert in African genomes.

At the time, Hayes was Professor of Genomic Medicine at the J. Craig Venter Institute in San Diego, California. She now heads the Laboratory for Human Comparative and Prostate Cancer Genomics at Sydney's Garvan Institute of Medical Research.

The complete 1.5 metre tall skeleton was examined by Professor Alan Morris, from the University of Cape Town. A biological anthropologist, Morris showed that the man was a 'marine forager'. A bony growth in his ear canal, known as 'surfer's ear', suggested that he spent some time diving for food in the cold coastal waters, while shells carbon-dated to the same period, and found near his grave, confirmed his seafood diet. Osteoarthritis and tooth wear placed him in his fifties.

Due to the acidity of the soil within the region, acquiring DNA from skeletons has proven problematic. The Hayes team therefore worked with the world's leading laboratory in ancient DNA research, namely that of paleogeneticist Professor Svante Pääbo at the Max Planck Institute for Evolutionary Anthropolgy in Leipzig, Germany, who successfully sequenced a Neanderthal.

The team generated a complete mitochondrial genome, using DNA extracted from a tooth and a rib. The findings provided genomic evidence that this man, from a lineage now presumed extinct, as well as other indigenous coastal dwellers like him, were the most closely related to 'Mitochondrial Eve'.

The study underlines the significance of southern African archaeological remains in defining human origins, and is published in the journal Genome Biology and Evolution, now online.

"We were thrilled that archaeologist Andrew Smith understood the importance of not touching the skeleton when he found it, and so did not contaminate its DNA with modern human DNA," said Professor Hayes.

"I approached Svante Pääbo because his lab is the best in the world at DNA extraction from ancient bones. This skeleton was very precious and we needed 
to make sure the sample was in safe hands."

"Alan Morris undertook some incredible detective work. He used his skills in forensics and murder cases to assemble a profile of the man behind the St Helena skeleton."

"Alan helped establish that this man was a marine hunter-gatherer -- in contrast to the contemporary inland hunter-gatherers from the Kalahari dessert. We were very curious to know how this man related to them."

"We also know that this man pre-dates migration into the region, which took place around 2,000 years ago when pastoralists made their way down the coast from Angola, bringing herds of sheep. We could demonstrate that our marine hunter-gatherer carried a different maternal lineage to these early migrants -- containing a DNA variant that we have never seen before."

"Because of this, the study gives a baseline against which historic herders at the Cape can now be compared."

While interested in African lineages, and how they interact with each other, Professor Hayes is especially keen for Africa to inform genomic research and medicine worldwide.

"One of the biggest issues at present is that no-one is assembling genomes from scratch -- in other words, when someone is sequenced, their genome is not pieced together as is," she said.

"Instead, sections of the sequenced genome are mapped to a reference genome. Largely biased by European contribution, the current reference is poorly representative of indigenous peoples globally."

"If we want a good reference, we have to go back to our early human origins."
"None of us that walk on this planet now are pure anything -- we are all mixtures. For example 1-4% of Eurasians even carry Neanderthal DNA"

"We need more genomes that don't have extensive admixture. In other words, we need to reduce the noise."

"In this study, I believe we may have found an individual from a lineage that broke off early in modern human evolution and remained geographically isolated. That would contribute significantly to refining the human reference genome."

Source: Garvan Institute of Medical Research

Oldest stone tool ever found in Turkey discovered

Stone tool approximately 1.2 million years old. Credit: Image courtesy of University of Royal Holloway London

Scientists have discovered the oldest recorded stone tool ever to be found in Turkey, revealing that humans passed through the gateway from Asia to Europe much earlier than previously thought, approximately 1.2 million years ago.

According to research published in the journal Quaternary Science Reviews, the chance find of a humanly-worked quartzite flake, in ancient deposits of the river Gediz, in western Turkey, provides a major new insight into when and how early humans dispersed out of Africa and Asia.

Researchers from Royal Holloway, University of London, together with an international team from the UK, Turkey and the Netherlands, used high-precision equipment to date the deposits of the ancient river meander, giving the first accurate timeframe for when humans occupied the area.

Professor Danielle Schreve, from the Department of Geography at Royal Holloway, said: "This discovery is critical for establishing the timing and route of early human dispersal into Europe. Our research suggests that the flake is the earliest securely-dated artefact from Turkey ever recorded and was dropped on the floodplain by an early hominin well over a million years ago."

The researchers used high-precision radioisotopic dating and palaeomagnetic measurements from lava flows, which both pre-date and post-date the meander, to establish that early humans were present in the area between approximately 1.24 million and 1.17 million years ago. Previously, the oldest hominin fossils in western Turkey were recovered in 2007 at Koçabas, but the dating of these and other stone tool finds were uncertain.

"The flake was an incredibly exciting find," Professor Schreve said. "I had been studying the sediments in the meander bend and my eye was drawn to a pinkish stone on the surface. When I turned it over for a better look, the features of a humanly-struck artefact were immediately apparent.

"By working together with geologists and dating specialists, we have been able to put a secure chronology to this find and shed new light on the behaviour of our most distant ancestors."

Source: University of Royal Holloway London

Scientists find 240-million-year-old parasite that infected mammals' ancestor

Scott Gardner. Credit: Craig Chandler, University Communications.

An egg much smaller than a common grain of sand and found in a tiny piece of fossilized dung has helped scientists identify a pinworm that lived 240 million years ago.

It is believed to be the most ancient pinworm yet found in the fossil record.

The discovery confirms that herbivorous cynodonts -- the ancestors of mammals -- were infected with the parasitic nematodes. It also makes it even more likely that herbivorous dinosaurs carried pinworms.

Scott Gardner, a parasitologist and director of the Harold W. Manter Laboratory of Parasitology at the University of Nebraska-Lincoln, was among an international group of scientists who published the study in the journal Parasites & Vectors.

"This discovery represents a first for our team and I think it opens the door to finding additional parasites in other species of fossil organisms," he said.

The team found the pinworm egg in a coprolite -- fossilized feces -- collected in 2007 at an excavation site in Rio Grande do Sul state in southern Brazil.

The coprolite was collected at a site with abundant fossilized remains of cynodonts. Previously, an Ascarid-like egg -- resembling a species of nematode commonly found in modern-day mammals -- was found in the coprolite.

The pinworm egg, representing an undescribed or "new species," was named Paleoxyuriscockburni, in honor of Aidan Cockburn, founder of the Paleopathology Association.

The structure of the pinworm egg placed it in a biological group of parasites that occur in animals that ingest large amounts of plant material. Its presence helped scientists deduce which cynodont species, of several found at the collection site, most likely deposited the coprolite.

Since the field of paleoparasitology, or the study of ancient parasites, emerged in the early 20th century, scientists have identified parasites of both plants and animals that date back as far as 500 million years ago.

The study of parasites in ancient animals can help determine the age of fossilized organisms and help establish dates of origin and diversification for association between host species and parasites. Coprolites are a key part of the study, enabling a better understanding of the ecological relationships between hosts and parasites.

Other members of the team were Jean-Pierre Hugot of the National Museum of Natural History in Paris; Victor Borba, Juliana Dutra, Luiz Fernando Ferreira and Adauto Araujo of Oswaldo Cruz Foundation in Rio de Janeiro; Prisiclla Araujo and Daniela Leles of Fluminense Federal University in Rio de Janeiro; and Atila August Stock Da-Rosa of the Federal University of Santa Maria in Rio Grande do Sul.

Source: University of Nebraska-Lincoln