Image by Aaron Logan
Roughly 6 million years ago, the Hominini subtribe of the Hominidae family tree (the so-called â€œgreat apesâ€) diverged into two known branches, with one branch (genus Pan ) resulting in modern-day Chimpanzees and Bonobos, and the other branch (genus Homo) resulting in modern-day humans.
Since there has only been 6 million years of divergent evolution, Chimpanzees/Bonobos and Humans share a great deal of DNA sequence in common (although estimates vary widely and typically depend on what, exactly, is being considered in the comparison).
The Close Cousins DNA Project
On May 31, 2008, the Close Cousins DNA Project was launched by Bill Davenport as a result of a discussion on the Genealogy-DNA mailing list regarding the relatedness of human and chimpanzee Y-DNA.Â From the launching post:
An international team of researchers have concluded that humans entered the Americas from Asia along at least two different paths.Â By studying two rare mtDNA haplogroups found in Native Americans â€“ D4h3 and X2a â€“ the researchers conclude that D4h3 spread into the Americans along the Pacific coast while X2a entered through the ice-free corridor between the Laurentide and Cordilleran ice sheets.
From the Press Release:Â â€œSix major genetic lineages account for 95 percent of Native American mtDNA and are distributed everywhere in the Americas,â€ said first author Ugo Perego, director of operations at SMGF. â€œSo we chose to analyze two rare genetic groups and eliminate that â€˜statistical background noise.â€™ In this way, we found patterns that correspond to two separate migration routes.â€
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I received the following press release today from SMGF:
SALT LAKE CITY (Dec. 30, 2008)â€”Genetic research by the Sorenson Molecular Genealogy Foundation (SMGF) and scientists from ten organizations in Europe and the U.S. shows human groups with the deepest roots in southeastern Europe were not pushed out by an incoming wave of farmer-colonists as agriculture first spread into Europe. Instead, indigenous Europeans with a hunting and gathering lifestyle adopted agriculture when it was introduced by settlers from the Middle East. The study was published in the Dec. 24, 2008 online issue of European Journal of Human Genetics.
Scientists have long debated the question of how agriculture spread into Europe from its birthplace in the Fertile Crescent region of the Middle East. But the evidenceâ€”primarily archaeologicalâ€”is inconclusive.
Last week I had the opportunity to attend a lecture by Spencer Wells, director of the Genographic Project from National Geographic and IBM.
The talk was a Syracuse Symposium event, and the first big event ever to be held in Syracuse University’s new $110 million Life Sciences Center.Â I thought it was fitting that the first event to celebrate the future of the new life sciences building was a lecture that examined the collective genetic journey of mankind.
Dr. Wells began by giving the audience a very brief introduction about DNA and genetic genealogy.Â He included a great quote that “The question of origin is actually a question about genealogy.”Â For those that are not familiar with the Genographic Project, it was launched in 2005 and includes three primary missions:
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Ötzi the Iceman is the popular name for a 5,000 year-old mummy discovered frozen in the ice of the Alps in 1991. Studies of the Iceman has revealed an immense amount of information about him, including details of his life, his death, and his culture.
Although Ötzi’s mtDNA has previously been studied, researchers had only examined short segments which suggested that his mtDNA belonged to Haplogroup K. A new paper in Current Biology (subscription only darn it) details Ötzi’s full mtDNA genome for the first time:
"Using a mixed sequencing procedure based on PCR amplification and 454 sequencing of pooled amplification products, we have retrieved the first complete mitochondrial-genome sequence of a prehistoric European. We have then compared it with 115 related extant lineages from mitochondrial haplogroup K. We found that the Iceman belonged to a branch of mitochondrial haplogroup K1 that has not yet been identified in modern European populations."
I’ve been meaning to write about recent two papers, one in Current Biology and one in Nature, that attempt to identify and characterize a relationship between genetic sequence or SNP and geography. Amazingly, both papers found a very strong correlation between genetics and geography.
From a news article regarding the paper in Nature (note that I haven’t verified that the paper supports the statement; HT: Yann Klimentidis’ Weblog):
"The map was so accurate that when Novembre’s team placed a geopolitical map over their genetic "map", half of the genomes landed within 310 kilometres of their country of origin, while 90% fell within 700 km."
Although there are some caveats, for example in one of the papers all of an individual’s grandparents had to have similar geographic origins in order for the method to identify ancestry, these types of studies will continue to discover and refine the methods and findings. As Kambiz stated at Anthropology.net, "With higher resolution GeneChips, ideally full genomes, and larger samples, we’ll be able see much more accurate genetic-geographic separations of populations."
See the new article at Seed Magazine “Inheriting Confucius,” which discusses efforts to generate a family tree containing the 2 million+ descendants of Confucius.
Kong De-Yong, a 77th(!) generation descendant of Confucius, has been compiling the tree for the last 10 years.Â Although the Committee is accepting submissions from women and other previously excluded groups, it is not accepting DNA contributions.Â According to the article, this “hints at the limits of Chinese engagement with the age of genomics, and demonstrates how high cultural stakes can constrain science.”Â Unfortunately, as the author of the article suggests, many people might be afraid of the results of such DNA testing: “Given the potential implications of genetic knowledge for long-presumed members of the [Confucius] family, they think it better not to know.”
GenomeWeb Daily News published a story on Friday entitled “En route to Neandertal Genome, Researchers Analyze Its Complete Mitochondrial Genome” which revealed the results of recent Neanderthal mtDNA analysis.
On Thursday May 9th, Svante PÃ¤Ã¤bo spoke at the Biology of Genomes meeting at Cold Spring Harbor Laboratory. PÃ¤Ã¤bo’s group, along with 454 Life Sciences, is currently engaged in a project to sequence the Neanderthal genome. The researchers have been able to sequence the complete Neanderthal mtDNA genome with 35-fold coverage. The genome is approximately 16 kilobases long and differs from the CRS at 133 positions. From what I’ve been able to find online, it doesn’t appear that the actual sequencing results have been released to the public. Given current estimates of mtDNA mutation rates, the number of differences between human and Neanderthal mtDNA suggests that the branches diverged approximately 600,000 years ago.
Around the year 1700, a relatively healthy young hunter was walking along a glacier in land that would one day be British Columbia in Canada. He wore a robe of 95 animal skins, perhaps gopher or squirrel, stitched together with sinew, and carried a walking stick, iron-blade knife, and spear thrower. For some reason, the young man, aged 17 to 22, died on the glacier and was quickly incorporated into the ice. There he remained, frozen, for the next 300 years.
In August 1999, three hikers noticed a walking stick, fur, and bone lying on a melting glacier (60′ N 138′ W). The young hunter, renamed KwÃ¤day DÃ¤n Tsâ€™Ã¬nchi in the Southern Tutchone language of the Champagne and Aishihik First Nations, was removed by scientists for analysis (see the NY Times article, and the Journal of Canadian Archaeology article). From an article in the Sydney Morning Herald:
Yesterday, a very interesting paper was published in the American Journal of Human Genetics by the Genographic Project Consortium entitled “The Dawn of Human Matrilineal Diversity.” The results of the study, which examined the 624 mtDNA genomes from sub-saharan Haplogroup L lineages, suggests that humanity once split into two small groups with one group in eastern Africa and the other in southern Africa, and that humanity bottlenecked into a relatively small number of individuals (as few as 2,000 based on results from a previous study). Note, as always, that these are hypotheses based upon the results of this and other studies, and will require further research to support or refute.
Two mtDNA Branches
The human mtDNA tree has two main branches, the L0 branch which includes individuals concentrated in southern and eastern Africa, and the L1’2’3’4’5’6′ branch (aka the L1’5 branch), which includes the entire remainder of humanity including non-Africans (see the figure to the left). Based upon the analysis of the 624 genomes, the researchers hypothesized that the L0 and L1’5 branches diverged into two small populations around 140,000 to 210,000 years ago, with one group settling in eastern Africa (the L1’5 branch) and the other settling in southern Africa (the L0 branch). Interestingly, the results also suggest that there was little to no intermingling of these branches for the next 50,000 to 100,000 years!