Thursday, May 27, 2010

Genetic Data, Archaeology and Linguistics Used To Analyze African Population History

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Genetic researchers from the University of Pennsylvania have combined data from existing archaeological and linguistic studies of Africa with human genetic data to shed light on the demographic history of the continent from which all human activity emerged.

The study reveals not just a clearer picture of the continent’s history but also the importance of having independent lines of evidence in the interpretation of genetic and genomic data in the reconstruction of population histories.

The study is published in the current issue of the Proceedings of the National Academy of Sciences.

The results, according to Penn geneticist Sarah Tishkoff, a Penn Integrates Knowledge professor with joint appointments in the schools of Medicine and Arts and Science, is that genetic variation in Africa is structured geographically, and to a lesser extent, linguistically. The findings are consistent with the notion that populations in close geographic proximity that speak linguistically similar languages are more likely to exchange genes.

Furthermore, genetic variation in Africa appears consistent with the natural, geographic barriers that limit gene flow. In particular, there are geographic, and therefore genetic, distinctions between northern African and sub-Saharan African populations due to the vast desert that limited migration.

“Focusing on particular exceptions to these broad patterns will enable us to discern and fully appreciate the complex population histories that have contributed to extant patterns of genetic variation,” said Tishkoff, the David and Lyn Silfen University Associate Professor. “Disentangling past population histories is a formidably complicated task that benefits from the synthesis of archaeological, linguistic and genetic data.”

With this three-pronged approach, a clearer picture emerges.

Archaeology provides insights into ancient technology and culture, affording a timeline for the emergence of innovations. Historical linguistic data complement the archaeological record by contributing an independent phylogenetic analysis of language relationships and providing clues about ancient population migration and admixture events. Genetic data provide an independent data source to understand the biological relationships among modern peoples and likely points of origin and expansion of their ancestors.

“The details of modern human demography are complex and not well understood, so we have taken a cross-disciplinary approach to highlight broad patterns of population history in Africa,” said Laura Scheinfeldt of the Department of Genetics at Penn’s School of Medicine.

Patterns will continue to emerge as geneticists from Penn and elsewhere further analyze a mountain of genetic data acquired from these understudied populations.

The development of sequencing and genotyping technologies has advanced at an unprecedented rate and is allowing for the genotyping of millions of single-nucleotide polymorphisms and the sequencing of millions of nucleotides across populations.

This data, coupled with computational methods for inferring demographic parameters and testing demographic models – for example, maximum likelihood and approximate Bayesian computation -- can refine our understanding of African past population histories.

“The incorporation of archaeological and linguistic data will be important for establishing testable hypotheses and elucidating the evolutionary processes or forces that have shaped the genomic landscape in Africa,” Tishkoff said.

Analyzing patterns of population structure and ancestry in Africans illuminates the history of human populations and is critical for undertaking medical genomic studies on a global scale. Understanding ancestry not only provides insight into historical migration patterns and human origins and provides a greater understanding of evolutionary forces, it also allows researchers to examine disease susceptibility and pharmacogenic response and to develop personalized drugs and treatments, a frontier in public health.

Tishkoff’s prior work with this data set revealed genomic diversity among African and African-American populations far more complex than originally thought, reflecting deep historical, cultural and linguistic impacts on gene flow among populations.

The study was funded by the National Science Foundation, the National Institutes of Health and Tishkoff’s National Institutes of Health Pioneer Award.

Research was conducted by Tishkoff, joined by Scheinfeldt and Sameer Soi, of the Genomics and Computational Biology Graduate Group in Penn’s School of Arts and Sciences.

The paper was presented at the National Academy of Sciences’ Arthur M. Sackler Colloquium, “In the Light of Evolution IV: The Human Condition.”

The complete program and audio files of most presentations are available at www.nasonline.org/SACKLER_Human_Condition.

Early human habitat was savanna, not forest

Pre-humans living in East Africa 4.4 million years ago inhabited savannas -- grassy plains dotted with trees and shrubs -- according to a team of researchers that includes earth science Naomi Levin of The Johns Hopkins University's Krieger School of Arts and Sciences.

This conclusion is at odds with a theory – which holds that these early beings lived in a mostly forested environment – put forth by prominent University of California at Berkeley researcher Tim D. White and his team in a 2009 issue of the journal Science.

"Our team examined the data published by White and his colleagues last October and found that their data does not support their conclusion that Ardipithecus ramidus lived exclusively in woodlands and forest patches," said Levin, whose team published a commentary on the matter in today's issue of Science. "The White team's papers stress the wooded nature of A. ramidus's environment and say specifically that Ardi did not live in a savanna. Yet, the actual data they present are consistent with exactly that: a savanna environment with a mix of grasses and trees."

This criticism is important because the claim that the 4.4 million-year-old fossil nicknamed "Ardi" lived in woodlands and forest patches was used as an argument against a longstanding theory of human evolution known as the "savanna hypothesis." According to that premise, the expansion of savannas – grassy plains dotted with trees and shrubs – prompted our ape-like forebears to descend from trees and begin walking upright to find food more efficiently, or to reach other trees for resources or shelter.

Levin, an assistant professor of earth and planetary sciences at Johns Hopkins, was part of a team of eight geologists and anthropologists from seven universities led by Thure E. Cerling of the University of Utah. They used the White team's own data to draw very different conclusion about the environment inhabited by Ardi, an omnivorous, ape-like creature that stood about 4 feet tall and had a brain less than a quarter of the size of a modern day human's. This data was collected from ancient soils, plant fossils and other remains in the area now known as Aramis, in Ethiopia.

Levin's team found that tropical grasses, in fact, comprised between 40 and 60 percent of the biomass in Ardi's world.

Levin says her team's conclusion is noteworthy because, if scientists are to evaluate the environmental pressures that triggered the evolutionary success of some traits over others, they must clearly understand the environment itself.

"In their papers and summaries, White and his colleagues emphasize that A. ramidus had a mix of traits that suggest it was at ease both walking upright on the ground and moving through the trees on its palms," Levin explains. "If the habitat of A. ramidus was, in fact, a woodland with forest patches, where grasses were rare, then it's unlikely that the increased presence of grassy environments were the driving force behind the origin of upright walking in early human ancestors. However, if the habitat of A. ramidus included savannas where grasses were up to 60 percent of the available biomass, then we cannot rule out the possibility that open environments played an important role in human origins and, in particular, in the origins of upright walking. The scientific community and the public should not accept an exclusively woodland/forested habitat for A. ramidus and the origins of upright walking, because the data do not support it."

The critique concludes that although its authors do not judge the validity of the savanna hypothesis, the connection between human ancestors walking upright and the expansion of grasslands remains a viable idea.

A Magnificent Pagan Altar Found in Ashkelon

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The development work for the construction of a fortified emergency room at Barzilai Hospital, which is being conducted by a contractor carefully supervised by the Israel Antiquities Authority, has unearthed a new and impressive find: a magnificent pagan altar dating to the Roman period (first-second centuries CE) made of granite and adorned with bulls’ heads and a laurel wreaths. The altar stood in the middle of the ancient burial field.



According to Dr. Yigal Israel, Ashkelon District Archaeologist of the Israel Antiquities Authority, “The discovery further corroborates the assertion that we are dealing with a pagan cemetery. It is an impressive find that has survived 2,000 years. The altar is c. 60 centimeters tall and it is decorated with bulls’ heads, from which dangle laurels wreaths. There is a strap in the middle of each floral wreath and bull’s head. The laurel wreaths are decorated with grape clusters and leaves. This kind of altar is known as an “incense altar”. Such altars usually stood in Roman temples and visitors to the temple used to burn incense in them, particularly myrrh and frankincense, while praying to their idols. We can still see the burnt marks on the altar that remain from the fire. The altar was probably donated by one of the families who brought it to the cemetery from the city of Ashkelon”.

Dr. Israel adds that during the archaeological supervision of the development work burial structures were discovered, which served as family tombs, and cist tombs that were used for interring individuals. In addition a large limestone sarcophagus (stone coffin) with a decorated lid was also found. The sarcophagus stands 80 centimeters high is 60 centimeters wide and is 2 meters long. Part of the stone in the sarcophagus was left rather high in the spot where the head of the deceased was placed and resembles a kind of pillow.

2,000 Years of Water in Jerusalem

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Work on the city’s modern water infrastructure uncovered a section of Jerusalem’s ancient aqueduct. While the Gihon Corporation was working on the sewage infrastructure in the vicinity of the Sultan’s Pool in the “Walls around JerusalemNational Park”, a section of Jerusalem’s ancient aqueduct was discovered. In the wake of this discovery, the Israel Antiquities Authority conducted an excavation in which a spectacular arched bridge was revealed that was part of the very old aqueduct that conveyed water to the TempleMount.




According to Yehiel Zelinger, excavation director on behalf of the Israel Antiquities Authority, “The bridge, which could still be seen at the end of the nineteenth century and appears in old photographs, was covered over during the twentieth century. We were thrilled when it suddenly reappeared in all its grandeur during the course of the archaeological excavations”. Zelinger said, “The route of the Low Level aqueduct from the time of the Second Temple, beginning at Solomon’s Pools near Bethlehem and ending at the Temple Mount, is well known to scholars: substantial parts of it were documented along the edge of Yemin Moshe neighborhood and on the slope adjacent to the western wall of the Old City. The upper part of Gai Ben-Hinnom passes between the two sections of aqueduct where the Sultan’s Pool was built as a reservoir for flood water. In order to maintain the elevation of the path along which the water flowed, a bridge was erected above the ravine. Two of the original nine arches that were in the bridge were currently excavated to their full height of about 3 meters”.
“The bridge was built in 1320 CE (in the Mamluk period) by the sultan Nasser al-Din Muhammed Ibn Qalawun, as evidenced by the dedicatory inscription set in it; however, it was apparently constructed to replace an earlier bridge dating to the time of the Second Temple period that was part of the original aqueduct”.

The Israel Antiquities Authority, in cooperation with the Nature and Parks Authority, is working to expose the entire length of the arched bridge, conserve it and integrate it in the framework of the overall development of the Sultan’s Pool, as part of underscoring the importance of the water supply to Jerusalem in ancient times.

The Gihon Corporation, whose name preserves that of Jerusalem’s ancient source of water, is assisting in funding excavations that uncover Jerusalem’s ancient water systems of.

Mesoamerican people perfected details of rubber processing more than 3,000 years ago

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Great article, worth reading

Spanish explorers encountering an advanced civilization in Mesoamerica in the 16th century had plenty of things to be astonished about, but one type of object in particular was unlike anything they had ever seen before: rubber balls. No such stretchy, bouncy material existed in the Old World, and they had to struggle to find words to describe it.

New research from MIT indicates that not only did these pre-Columbian peoples know how to process the sap of the local rubber trees along with juice from a vine to make rubber, but they had perfected a system of chemical processing that could fine-tune the properties of the rubber depending on its intended use. For the soles of their sandals, they made a strong, wear-resistant version. For the rubber balls used in the games that were a central part of their religious ceremonies, they processed it for maximum bounciness. And for rubber bands and adhesives used for ornamental wear and for attaching blades to shafts, they produced rubber optimized for resilience and strength.

All of these, according to the research by Professor Dorothy Hosler and Technical Instructor Michael Tarkanian of MIT’s Department of Materials Science and Engineering, were most likely achieved by varying the proportions of the two basic ingredients, latex from rubber trees and juice from morning-glory vines, which were cooked together...

Thursday, May 13, 2010

It was brawn over beauty in human mating competition

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Male physical competition, not attraction, was central in winning mates among human ancestors, according to a Penn State anthropologist.

"There is sexual competition in many species, including humans," said David A. Puts, assistant professor of biological anthropology.

Many researchers have considered mate choice the main operator in human sexual selection. They thought that people's mating success was mainly determined by attractiveness; but for men, it appears that physical competition among males was more important. Puts sees humans as similar to many of the apes in using male competition to determine access to mates, the winning male choosing the women of his dreams. He reports his findings in the current issue of Evolution and Human Behavior.

"On average men are not all that much bigger than women, only about 15 percent larger," said Puts. "But, the average guy is stronger than 99.9 percent of women."

The problem is that men and women do not appear sexually dimorphic – different sexes having radically different sizes and weights. But Puts notes that women tend to store more body fat, while men have 60 percent more muscle mass than women.

Other traits indicate physical prowess was the major force in human mate competition through history. Men are far more aggressive than women, and approximately 30 percent of men in small-scale foraging communities die violently. Puts suggests that while a deep voice has been considered an appealing trait to women, it actually signals dominance.

"A deep voice makes men look dominant and older," said Puts. "A low voice's effect on dominance is many times greater than its effect on sexual attraction."

The main sticking point with human male competition compared to other species is that male humans do not possess inherent weapons.

"Other animals have antlers or long canines and claws," said Puts. "Why don't we have them?"

According to Puts, men do have weapons. They make them. Bows and arrows, spears, knives -- men have always manufactured weapons.

Other male traits also seem to imply competition. Males have thicker jawbones, which may have come from men hitting each other and the thickest-boned men surviving. Competition may explain why males have more robust skulls and brow ridges than women.

Another argument for male competition focuses on the environment. Puts suggests that species that live in three-dimensional space – birds and insects in the air or swimming creatures in the sea – tend not to compete for mates using physical competition because it would be very difficult for a male to defend females while fighting other males on all fronts. Species that live on the ground or the sea floor have it easier because there are only two dimensions to defend. Some insects that live in tunnels or burrows exhibit the most intense competition because it is impossible for the other male to get to the females except through the defender.

Male competition is rare among birds, occurring to a greater degree among large terrestrial species. Tree-living primates also show less physical competition. Humans living in a two-dimensional environment would experience substantial physical competition for mates.

According to Puts, humans and chimpanzees create male coalitions that are often strengthened by kinship. Coalitions can help males defend females from other males. However, when external forces are absent, these same males can compete with each other for mates.

These ideas may seem to paint a rather bleak picture of human nature with men duking it out among themselves for most of human evolution.

"Things are different for us now in many ways," said Puts. "It's heartening to think that human behavior is flexible enough that the right social institutions can increase equality and peace."

Wednesday, May 12, 2010

Easter Island discovery sends archaeologists back to drawing board

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Archaeologists have disproved the fifty-year-old theory underpinning our understanding of how the famous stone statues were moved around Easter Island.

Fieldwork led by researchers at University College London and The University of Manchester, has shown the remote Pacific island's ancient road system was primarily ceremonial and not solely built for transportation of the figures.

A complex network of roads up to 800-years-old crisscross the Island between the hat and statue quarries and the coastal areas.

Laying alongside the roads are dozens of the statues- or moai.

The find will create controversy among the many archaeologists who have dedicated years to finding out exactly how the moai were moved, ever since Norwegian adventurer Thor Heyerdahl first published his theory in 1958.

Heyerdahl and subsequent researchers believed that statues he found lying on their backs and faces near the roads were abandoned during transportation by the ancient Polynesians.

But his theory has been completely rejected by the team led by Manchester's Dr Colin Richards and UCL's Dr Sue Hamilton.

Instead, their discovery of stone platforms associated with each fallen moai - using specialist 'geophysical survey' equipment – finally confirms a little known 1914 theory of British archaeologist Katherine Routledge that the routes were primarily ceremonial avenues.

The statues, say the Manchester and UCL team just back from the island, merely toppled from the platforms with the passage of time.

"The truth of the matter is, we will never know how the statues were moved," said Dr Richards.

"Ever since Heyerdahl, archeologists have come up with all manner of theories – based on an underlying assumption that the roads were used for transportation of the moai, from the quarry at the volcanic cone Rano Raraku.

"What we do now know is that the roads had a ceremonial function to underline their religious and cultural importance.

"They lead – from different parts of the island – to the Rano Raraku volcano where the Moai were quarried.

"Volcano cones were considered as points of entry to the underworld and mythical origin land Hawaiki.

"Hence, Rano Ranaku was not just a quarry but a sacred centre of the island."

The previous excavation found that the roads are concave in shape –making it difficult to move heavy objects along them

And as the roads approach Rano Raraku, the statues become more frequent – which the team say, indicated an increasing grades of holiness.

"All the evidence strongly shows that these roads were ceremonial - which backs the work of Katherine Routledge from almost 100 years ago, " said Dr Sue Hamilton.

"It all makes sense: the moai face the people walking towards the volcano.

"The statues are more frequent the closer they are to the volcano – which has to be way of signifying the increasing levels of importance."

She added: "What is shocking is that Heyerdahl actually found some evidence to suggest there were indeed platforms.

"But like many other archaeologists, he was so swayed by his cast iron belief that the roads were for transportation – he completely ignored them."

Thursday, May 6, 2010

Neanderthal genome yields insights into human evolution and evidence of interbreeding

After extracting ancient DNA from the 40,000-year-old bones of Neanderthals, scientists have obtained a draft sequence of the Neanderthal genome, yielding important new insights into the evolution of modern humans.

Among the findings, published in the May 7 issue of Science, is evidence that shortly after early modern humans migrated out of Africa, some of them interbred with Neanderthals, leaving bits of Neanderthal DNA sequences scattered through the genomes of present-day non-Africans.

"We can now say that, in all probability, there was gene flow from Neanderthals to modern humans," said the paper's first author, Richard E. (Ed) Green of the University of California, Santa Cruz.

Green, now an assistant professor of biomolecular engineering in the Baskin School of Engineering at UC Santa Cruz, began working on the Neanderthal genome as a postdoctoral researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. Svante Pääbo, director of the institute's genetics department, leads the Neanderthal Genome Project, which involves an international consortium of researchers. David Reich, a population geneticist at the Broad Institute of MIT and Harvard, also played a leading role in the new study and the ongoing investigation of the Neanderthal genome.

"The Neanderthal genome sequence allows us to begin to define all those features in our genome where we differ from all other organisms on the planet, including our closest evolutionary relative, the Neanderthals," Pääbo said.

The researchers identified a catalog of genetic features unique to modern humans by comparing the Neanderthal, human, and chimpanzee genomes. Genes involved in cognitive development, skull structure, energy metabolism, and skin morphology and physiology are among those highlighted in the study as likely to have undergone important changes in recent human evolution.

"With this paper, we are just scratching the surface," Green said. "The Neanderthal genome is a goldmine of information about recent human evolution, and it will be put to use for years to come."

Neanderthals lived in much of Europe and western Asia before dying out 30,000 years ago. They coexisted with humans in Europe for thousands of years, and fossil evidence led some scientists to speculate that interbreeding may have occurred there. But the Neanderthal DNA signal shows up not only in the genomes of Europeans, but also in people from East Asia and Papua New Guinea, where Neanderthals never lived.

"The scenario is not what most people had envisioned," Green said. "We found the genetic signal of Neanderthals in all the non-African genomes, meaning that the admixture occurred early on, probably in the Middle East, and is shared with all descendants of the early humans who migrated out of Africa."

The study did not address the functional significance of the finding that between 1 and 4 percent of the genomes of non-Africans is derived from Neanderthals. But Green said there is no evidence that anything genetically important came over from Neanderthals. "The signal is sparsely distributed across the genome, just a 'bread crumbs' clue of what happened in the past," he said. "If there was something that conferred a fitness advantage, we probably would have found it already by comparing human genomes."

The draft sequence of the Neanderthal genome is composed of more than 3 billion nucleotides--the "letters" of the genetic code (A, C, T, and G) that are strung together in DNA. The sequence was derived from DNA extracted from three Neanderthal bones found in the Vindiga Cave in Croatia; smaller amounts of sequence data were also obtained from three bones from other sites. Two of the Vindiga bones could be dated by carbon-dating of collagen and were found to be about 38,000 and 44,000 years old.

Deriving a genome sequence--representing the genetic code on all of an organism's chromosomes--from such ancient DNA is a remarkable technological feat. The Neanderthal bones were not well preserved, and more than 95 percent of the DNA extracted from them came from bacteria and other organisms that had colonized the bone. The DNA itself was degraded into small fragments and had been chemically modified in many places.

The researchers had to develop special methods to extract the Neanderthal DNA and ensure that it was not contaminated with human DNA. They used new sequencing technology to obtain sequence data directly from the extracted DNA without amplifying it first. Although genome scientists like to sequence a genome at least four or five times to ensure accuracy, most of the Neanderthal genome has been covered only one to two times so far.

The draft Neanderthal sequence is probably riddled with errors, Green said, but having the human and chimpanzee genomes for comparison makes it extremely useful despite its limitations. Places where humans differ from chimps, while Neanderthals still have the ancestral chimp sequence, may represent uniquely human genetic traits. Such comparisons enabled the researchers to catalog the genetic changes that have become fixed or have risen to high frequency in modern humans during the past few hundred thousand years.

"It sheds light on a critical time in human evolution since we diverged from Neanderthals," Green said. "What adaptive changes occurred in the past 300,000 years as we were becoming fully modern humans? That's what I find most exciting. Right now we are still in the realm of identifying candidates for further study."

The ancestral lineages of humans and chimpanzees are thought to have diverged about 5 or 6 million years ago. By analyzing the Neanderthal genome and genomes of present-day humans, Green and his colleagues estimated that the ancestral populations of Neanderthals and modern humans separated between 270,000 and 440,000 years ago.

The evidence for more recent gene flow between Neanderthals and humans came from an analysis showing that Neanderthals are more closely related to some present-day humans than to others. The researchers looked at places where the DNA sequence is known to vary among individuals by a single "letter." Comparing different individuals with Neanderthals, they asked how frequently the Neanderthal sequence matches that of different humans.

The frequency of Neanderthal matches would be the same for all human populations if gene flow between Neanderthals and humans stopped before human populations began to develop genetic differences. But that's not what the study found. Looking at a diverse set of modern humans--including individuals from Southern Africa, West Africa, Papua New Guinea, China, and Western Europe--the researchers found that the frequency of Neanderthal matches is higher for non-Africans than for Africans.

According to Green, even a very small number of instances of interbreeding could account for these results. The researchers estimated that the gene flow from Neanderthals to humans occurred between 50,000 and 80,000 years ago. The best explanation is that the admixture occurred when early humans left Africa and encountered Neanderthals for the first time.

"How these peoples would have interacted culturally is not something we can speculate on in any meaningful way. But knowing there was gene flow is important, and it is fascinating to think about how that may have happened," Green said.

The researchers were not able to rule out one possible alternative explanation for their findings. In that scenario, the signal they detected could represent an ancient genetic substructure that existed within Africa, such that the ancestral population of present-day non-Africans was more closely related to Neanderthals than was the ancestral population of present-day Africans. "We think that's not the case, but we can't rule it out," Green said.

The researchers expect many new findings to emerge from ongoing investigations of the Neanderthal genome and other ancient genetic sequences. Pääbo's group recently found evidence of a previously unknown type of hominid after analyzing DNA extracted from what they had thought was a Neanderthal finger bone found in Siberia. Green is also taking part in that continuing investigation.