Extra Gene Copies Were Enough To Make Early Humans' Mouths Water

Source: University of California - Santa Cruz
Date: September 14, 2007


Science Daily.... To think that world domination could have begun in the cheeks. That's one interpretation of a discovery, published online September 9 in Nature Genetics, which indicates that humans carry extra copies of the salivary amylase gene.

Humans have many more copies of this gene than any of their ape relatives, the study found, and they use the copies to flood their mouths with amylase, an enzyme that digests starch. The finding bolsters the idea that starch was a crucial addition to the diet of early humans, and that natural selection favored individuals who could make more starch-digesting protein.

"Extra gene copies are an easy way for evolution to ramp up expression of a protein," said Nathaniel Dominy, assistant professor of anthropology at University of California, Santa Cruz, and one of the paper's authors. "Why wait for chance mutations to improve gene function? Natural selection can favor duplicate copies of a gene that already works well, and enzyme production will increase."

Other primates eat mainly ripe fruits containing very little starch. A new ability to supplement the diet with calorie-rich starches could have fed our large brains and opened up new food supplies that fueled our unrivaled colonization of the planet, Dominy said.

The researchers sampled saliva from 50 European-American undergraduates and found as many as 15 copies of the amylase gene per person. By comparison, all 15 chimpanzees they sampled had exactly two copies each. Students with more copies of the gene also had higher concentrations of the enzyme in their spit.

Next, the team studied groups of humans with differing diets. They found a similar correspondence between the amount of starch in a group's diet and the average number of amylase gene copies its individuals possessed. For example, the Yakut of the Arctic, whose traditional diet centers around fish, had fewer copies than the related Japanese, whose diet includes starchy foods like rice, Dominy said. The same pattern existed for two Tanzanian tribes--the Datog, who raise livestock, and the Hadza, who primarily gather tubers and roots.

"Even though they're closely related genetically and live close to each other geographically, still there are big differences in the average number of copies in these populations," Dominy said. "So we felt like geography and relatedness are not driving these differences. It's got to be diet."

For Dominy and his coauthors, the finding goes beyond the mouth. In pondering human origins, Dominy said, anthropologists have long been stumped by the sudden, nearly simultaneous increases in our brain size, body size, and geographic range, while other apes changed little. Early humans simply must have found some source of better nutrition to make it all possible, they reasoned.

"That's the big mystery of paleoanthropology," Dominy said. "What changed? Why did our earliest human ancestors deviate from the pattern we see in living apes to evolve this incredibly large brain, which is very energetically expensive to maintain, and to become a much more efficient bipedal organism?"

For years, the answer was thought to be the growing importance of meat in the diet, as early humans learned to hunt. But, Dominy pointed out, "Even when you look at modern human hunter-gatherers, meat is a relatively small fraction of their diet. They cooperate with language, use nets; they have poisoned arrows, even, and still it's not that easy to hunt meat. To think that, two to four million years ago, a small-brained, awkwardly bipedal animal could efficiently acquire meat, even by scavenging, just doesn't make a whole lot of sense."

Some anthropologists have begun to suspect the new source of food consisted of starches, stored by plants in the form of underground tubers and bulbs--wild versions of modern-day foods like carrots, potatoes, and onions. Once early humans learned to recognize tuber-forming plants, they opened up a food source unknown to other apes.

"It's kind of a goldmine," Dominy said. "All you have to do is dig it up."

Tubers may have been especially critical for the first widely successful humans, known as Homo erectus, who may have learned to cook with fire. Since this idea was proposed, about a decade ago, researchers have been looking for evidence to support or refute it--no easy task for a theory that concerns highly perishable food consumed two million years ago. But in work earlier this year, Dominy and his colleagues found that animals eating tubers and bulbs produce body tissues with an isotopic signature that matches what has been measured in early fossilized humans.

The new discovery is a separate line of evidence pointing to the importance of starch in human beginnings, Dominy said. When early humans mastered fire, cooking starchy vegetables would have made them even easier to eat, he added. At the same time it would have made extra amylase gene copies an even more valuable trait.

"We roast tubers, and we eat French fries and baked potatoes," Dominy said. "When you cook, you can afford to eat less overall, because the food is easier to digest. Some marginal food resource that you might only eat in times of famine, now you can cook it and eat it. Now you can have population growth and expand into new territories."

Dominy's coauthors include George Perry, Katrina Claw, John Werner, Rajeev Misra, and Anne Stone of Arizona State University; Arthur Lee and Charles Lee of Brigham and Women's Hospital in Boston, Mass.; Heike Fiegler, Richard Redon, and Nigel Carter of the Wellcome Trust Sanger Institute in Hinxton, UK; Fernando Villanea, a former graduate fellow at UCSC who is now at the University of Costa Rica; and Joanna Mountain of Stanford University.

Note: This story has been adapted from a news release issued by University of California - Santa Cruz.

New Evidence On The Role Of Climate In Neanderthal Extinction

Source: University of Leeds
Date: September 13, 2007


Science Daily... The mystery of what killed the Neanderthals has moved a step closer to resolution after an international study led by the University of Leeds has ruled out one of the competing theories -- catastrophic climate change -- as the most likely cause.

The bones of more than 400 Neanderthals have been found since the first discoveries were made in the early 19th century. The finds suggest the Neanderthals, named after the Neander Valley near Düsseldorf, where they were first recognized as an extinct kind of archaic humans, inhabited Europe and parts of western Asia for more than 100,000 years.

The causes of their extinction have puzzled scientists for years -- with some believing it was due to competition with modern humans, while others blamed deteriorating climatic conditions. But a new study recently published in Nature has shown that the Neanderthal extinction did not coincide with any of the extreme climate events that punctuated the last glacial period.

The research was led by Professor Chronis Tzedakis, a palaeoecologist at the University of Leeds, who explained: "Until now, there have been three limitations to understanding the role of climate in the Neanderthal extinction: uncertainty over the exact timing of their disappearance; uncertainties in converting radiocarbon dates to actual calendar years; and the chronological imprecision of the ancient climate record."

The team's novel method -- mapping radiocarbon dates of interest directly onto a well-dated palaeoclimate archive -- circumvented the last two problems, providing a much more detailed picture of the climate at the possible times of the Neanderthal disappearance.

The researchers applied the new method to three alternative sets of dates for the timing of the Neanderthal extinction from Gorham's Cave, Gibraltar, a site which is thought to have been occupied by some of the latest surviving Neanderthals:

• a set of generally accepted but older dates (around 30-32,000 radiocarbon years ago)
• newly-suggested younger dates (around 28,000 radiocarbon years ago)
• more contentious dates (around 24,000 radiocarbon years ago).

The team showed that during the first two sets of dates, Europe was experiencing conditions similar to the general climatic instability of the last glacial period -- conditions the Neanderthals had already proved able to survive.

The much more controversial date of around 24,000 radiocarbon years ago placed the last Neanderthals just before a large expansion of ice sheets and the onset of cold conditions in northern Europe. "But at that time, Gibraltar's climate remained relatively unaffected, perhaps as a result of warm water from the subtropical Atlantic entering the western Mediterranean," explained palaeoceanographer Isabel Cacho of the University of Barcelona.

"Our findings suggest that there was no single climatic event that caused the extinction of the Neanderthals," concludes palaeonthropologist Katerina Harvati of the Max Planck Institute for Evolutionary Anthropology. "Only the controversial date of 24,000 radiocarbon years for their disappearance, if proven correct, coincides with a major environmental shift. Even in this case, however, the role of climate would have been indirect, by promoting competition with other human groups."

The work also has wider implications for other studies, as paleoclimatologist Konrad Hughen of the Woods Hole Oceanographic Institution explained: "Our approach offers the huge potential to unravel the role of climate in critical events of the recent fossil record as it can be applied to any radiocarbon date from any deposit."

The article Placing late Neanderthals in a climatic context (Tzedakis, P.C., Hughen, K.A., Cacho, I. & Harvati, K) is published in Nature on September 13. The study was conducted by Chronis Tzedakis (University of Leeds); Konrad Hughen (Woods Hole Oceanographic Institution); Isabel Cacho (University of Barcelona); Katerina Harvati (Max Planck Institute for Evolutionary Anthropology).

Note: This story has been adapted from a news release issued by University of Leeds.

Ancient 'Escape Tunnel' Discovered In Israel

Source: Israel Antiquities Authority
Date: September 10, 2007

Science daily.... In excavations the Israel Antiquities Authority is conducting in the City of David in order to expose the main road of Jerusalem from the time of the Second Temple period, the city’s main drainage channel was discovered. According to the writings of Josephus Flavius, the residents of the city fled to this channel at the time of the revolt in order to hide from the Romans.

In excavations the Israel Antiquities Authority is jointly carrying out with the Elad Association in the Walls around Jerusalem National Park, approximately 70 meters of Jerusalem’s main drainage channel from the time of the Second Temple period have been exposed so far. The channel is located along the route from the Temple Mount to the Shiloah Pool. The channel, which passes beneath the main road of the city and apparently continues to Nahal Kidron on its way to the Dead Sea, drained the rainfall of ancient Jerusalem; the Jewish quarter, the western region of the City of David and the Temple Mount.

The channel is built of ashlar stones and is covered with heavy stone slabs that are actually the paving stones of the street. In some places the channel reaches a height of about 3 meters and is one meter wide, so that it is possible to walk in it comfortably.

According to the excavation directors, Professor Ronny Reich of the University of Haifa and Eli Shukron of the Israel Antiquities Authority, in the last two thousand years the valley has become blocked with thick layers of alluvium and collapse. Therefore the Israel Antiquities Authority was asked to excavate some 10 meters for the purpose of uncovering the main road of Jerusalem and the channel below it.

“There is evidence in the writings of Josephus Flavius, the historian who described the revolt, the conquest and the destruction of Jerusalem, that numerous people took shelter in the channel and even lived in it for a period until they succeeded to flee the city through its southern end”, they added.

Pottery shards, fragments of vessels, and coins from the end of the Second Temple period, prior to the destruction of Jerusalem by the Romans in the year 70 CE, were discovered inside the channel.

The northern part of the channel, which is still unexcavated, apparently reaches the area of the Western Wall where in the past a large drainage channel was found that is the continuation of the channel that was exposed in the southern part of the City of David. The construction of the channel is characterized by its advanced technology. The further south one goes in the channel the deeper it is below the surface level so as to allow the rainwater to flow to Nahal Kidron.

Note: This story has been adapted from a news release issued by Israel Antiquities Authority.

Physics Reveals The Secrets Of Saint Francis

Source: Istituto Nazionale di Fisica Nucleare
Date: September 11, 2007


Science Daily....The tunic believed to have been worn by Saint Francis of Assisi preserved in the Church of Saint Francis in Cortona (Province of Arezzo) dates back to the period in which the saint lived, whereas the tunic preserved in the Church of Santa Croce in Florence was made after his death.

Carbon 14 measurements, which allow a relic to be dated, show that the tunic in Santa Croce dates back to some time between the late 13th century and late 14th century and thus could not have belonged to the “Poor Man of Assisi”, who died in 1226. These and other discovers were made possible through the analysis of the relics with a tandem particle accelerator, which was performed by the Laboratory of Nuclear Techniques for Cultural Heritage (LABEC) of the INFN of Florence.

The results of the study were presented in Florence at the European Conference on Accelerators in Applied Research and Technology (ECAART) and will be published in the volume “L’eredità del Padre: le reliquie di San Francesco a Cortona” (which will be released in a few weeks by Edizioni Messaggero di Sant’Antonio). The volume will include the complete results of an interdisciplinary investigation which included both scientific and humanist research and which was promoted by the Tuscany Province Chapter of the Franciscan Order “Friars Minor Conventual”.

The analyses were conducted with a radiocarbon method, measuring the radiocarbon using Accelerator Mass Spectrometry (AMS). From each tunic, researchers took from 5 to 7 samples of fabric, each of which was smaller than one square centimetre and weighed around 10 milligrams. Multiple samples were taken to avoid doubts or ambiguities (due to, for example, the presence of patches that were added to the tunic at a later time), thus increasing the analysis’ validity.

Each sample of wool was then treated so as to extract only the carbon, obtaining a small graphite pellet weighing about 0.8 milligrams. The pellet was then placed in the accelerator’s chamber, where it was exposed to a beam of cesium ions, “scratching” the pellet’s surface and extracting carbon isotopes 12, 13, and 14. The accelerator used by the INFN separately measured the quantity of the three isotopes. Relics are dated by calculating the ratio of carbon 14 to carbon 12, the quantities of which are “counted” in the accelerator’s detectors. Both great delicacy and exceptional sensitivity are required for taking these measurements; in fact, the ratio of carbon 14 to carbon 12 is only around one to one trillion, or even lower.

The analysis of the tunic preserved in the Basilica of Santa Croce in Florence showed that it dates back to a period between the end of the 1200s and the end of the 1300s, revealing that it was made at least 80 years after Saint Francis’ death and thus could not have belonged to him.

By contrast, the dates of all of the fragments taken from the tunic in the church in Cortona coincide with the period of Saint Francis’ life (the average results show that the tunic was made between 1155 and 1225). The tunic is one of three Franciscan relics, which also include a finely embroidered cushion and a book of gospels believed to have been brought to Cortona by Friar Elia, Saint Francis’ first successor as leader of the order.

LABEC researchers also analysed the composition of the precious metal thread used to embroider the cover of the cushion on which the Saint’s head was placed upon his death, and they used the carbon 14 method to date the fabric of the cushion itself. Moreover, the book of gospels was subjected to in-depth codicological and paleographic investigations by researchers at the University of Siena. Based on both the scientific evidence and humanistic research, the cushion and the book of gospels were also found to date back to the period in which Saint Francis lived.

Note: This story has been adapted from a news release issued by Istituto Nazionale di Fisica Nucleare.

Ancient Human DNA Extracted From Yucca Leaves Spat Out

Source: Harvard University


Science Daily In a groundbreaking study, two Harvard scientists have for the first time extracted human DNA from ancient artifacts. The work potentially opens up a new universe of sources for ancient genetic material, which is used to map human migrations in prehistoric times.

Before this, archaeologists could only get ancient DNA from relics of the human body itself, including prehistoric teeth, bones, fossilized feces, or — rarely — preserved flesh. Such sources of DNA are hard to find, poorly preserved, or unavailable because of cultural and legal barriers.

By contrast, the genetic material used in the Harvard study came from two types of artifacts — 800 to 2,400 years old — that are found by the hundreds at archaeological sites in the American Southwest.

“Quids” — small fibrous bundles of stripped yucca leaves — are the spit-out remnants of a kind of ancient chewing gum. Cells from long-dried saliva yield usable DNA. And “aprons” were thong-like woven garments worn by women. They are stained with traces of apparent menstrual blood, a source of DNA.

The Harvard study, featured in the summer 2007 issue of the Journal of Field Archaeology, “opens up the possibility of utilizing a much larger variety of human-handled artifacts” for DNA evidence, said project co-director Steven LeBlanc, director of collections at Harvard’s Peabody Museum of Archaeology and Ethnology.

Among the likely future sources of ancient DNA, he said, are “sandals, textiles, and cane cigarettes,” a reedlike smoke favored by early humans. LeBlanc’s co-director in the project was Thomas Benjamin, a professor of pathology at Harvard Medical School.

LeBlanc and others sampled 48 quids from four Southwestern archaeological sites — some of them on Harvard museum shelves for nearly 100 years — and 18 aprons found in Canyon de Chelly, a National Park Service site in Arizona still occupied by the Navajo Nation.

Aprons, and especially quids, are very common in archaeological collections, and are recovered from rock shelters or caves in the Southwest, Utah, Texas, California, and central Mexico. The DNA is preserved by the extreme dryness of such sites.

The Harvard study brings other good news for historians of ancient times. LeBlanc said the DNA captured from quids and aprons shows — in a preliminary way — that early farming populations in the Southwest descended from farmers in what is now central Mexico. That helps answer an old question among those who study the ancient Southwest: Was the idea of farming imported, or was it adopted by indigenous populations?

More broadly, archaeologists interested in migration patterns anywhere now have a new source for the DNA that can be used to track the movement of ancient people — though LeBlanc cautioned that the methods have to be retested and refined.

The origins of the earliest North American farmers are still officially a puzzle, and center on a now-lost tribe known as the Western Basketmakers. More than 2,000 years ago, these indigenous Americans started growing corn in what is now southeastern Utah and northern Arizona.

In what is now a boon to archaeologists who look at DNA, early farmers rested in the shade of rock formations, and spit out quids of chewed yucca leaves.

“The team was as surprised as everyone else that we could learn something about a possible migration over 2,000 years ago from ancient spit,” said LeBlanc. “Every artifact that we recover from such ancient sites now needs to be thought of in a new light, and handled in new ways, to ensure we preserve this DNA for future studies.”

To make sure the DNA was from ancient farmers and not from modern handlers, samples were taken from the cores of the quids and not from their surfaces.

Peabody Museum experts say future studies of ancient DNA from quids, aprons, and other appropriate artifacts are needed to test and refine Harvard’s preliminary findings.

The study was a collaborative project. Harvard researchers worked with genetic anthropologist Shawn W. Carlyle at the University of Utah; pathologist Lori S. Cobb Kreisman at Case Western Reserve University School of Medicine; curator Anna N. Dhody at the Mütter Museum at the College of Physicians of Philadelphia; anthropologist Brian M. Kemp at Vanderbilt University; and Francis E. Smiley, an anthropologist at Northern Arizona University. Ancient DNA expert David Glenn Smith offered his advice and the use of his laboratory at the University of California, Davis.

Some of the artifacts used in the DNA analysis were from collections at the Brooklyn Museum of Art, the Southwest Museum, and Northern Arizona University.

The study was supported by the Provost’s Fund for Interfaculty Collaboration at Harvard University and by the Peabody Museum of Archaeology and Ethnology.

Note: This story has been adapted from a news release issued by Harvard University.

Note: This story has been adapted from a news release issued by Harvard University.