Geography And History Shape Genetic Differences In Humans

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ScienceDaily (June 5, 2009) — New research indicates that natural selection may shape the human genome much more slowly than previously thought. Other factors -- the movements of humans within and among continents, the expansions and contractions of populations, and the vagaries of genetic chance – have heavily influenced the distribution of genetic variations in populations around the world.

The study, conducted by a team from the Howard Hughes Medical Institute, the University of Chicago, the University of California and Stanford University, is published June 5 in the open-access journal PLoS Genetics.
In recent years, geneticists have identified a handful of genes that have helped human populations adapt to new environments within just a few thousand years—a strikingly short timescale in evolutionary terms. However, the team found that for most genes, it can take at least 50,000-100,000 years for natural selection to spread favorable traits through a human population. According to their analysis, gene variants tend to be distributed throughout the world in patterns that reflect ancient population movements and other aspects of population history.
"We don't think that selection has been strong enough to completely fine-tune the adaptation of individual human populations to their local environments," says co-author Jonathan Pritchard. "In addition to selection, demographic history -- how populations have moved around -- has exerted a strong effect on the distribution of variants."
To determine whether the frequency of a particular variant resulted from natural selection, Pritchard and his colleagues compared the distribution of variants in parts of the genome that affect the structure and regulation of proteins to the distribution of variants in parts of the genome that do not affect proteins. Since these neutral parts of the genome are less likely to be affected by natural selection, they reasoned that studying variants in these regions should reflect the demographic history of populations.
The researchers found that many previously identified genetic signals of selection may have been created by historical and demographic factors rather than by selection. When the team compared closely related populations they found few large genetic differences. If the individual populations' environments were exerting strong selective pressure, such differences should have been apparent.
Selection may still be occurring in many regions of the genome, says Pritchard. But if so, it is exerting a moderate effect on many genes that together influence a biological characteristic. "We don't know enough yet about the genetics of most human traits to be able to pick out all of the relevant variation," says Pritchard. "As functional studies go forward, people will start figuring out the phenotypes that are associated with selective signals," says lead author Graham Coop. "That will be very important, because then we can figure out what selection pressures underlie these episodes of natural selection."
But even with further research, much will remain unknown about the processes that have resulted in human traits. In particular, Pritchard and Coop urge great caution in trying to link selection with complex characteristics like intelligence. "We're in the infancy of trying to understand what signals of selection are telling us," says Coop, "so it's a very long jump to attribute cultural features and group characteristics to selection."
Journal reference:
Coop G, Pickrell JK, Novembre J, Kudaravalli S, Li J, et al. The Role of Geography in Human Adaptation. PLoS Genetics, 2009; 5 (6): e1000500 DOI: 10.1371/journal.pgen.1000500
Adapted from materials provided by Public Library of Science, via EurekAlert!, a service of AAAS.

Ancient Human DNA Extracted From Yucca Leaves Spat Out

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http://www.sciencedaily.com/releases/2007/09/070905161208.htm

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.

Fausto Intilla

www.oloscience.com