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Gray and Atkinson analysed 87 languages from Irish to Afghan.
Rather than compare entire dictionaries, they used a list of 200 words that are found in all cultures, such as 'I', 'hunt' and 'sky'.
Spanish and Portuguese come out as sisters, for example - both are cousins to German, and Hindi is a more distant relation to all three.
All other Indo-European languages split off from Hittite, the oldest recorded member of the group, between 8,000 and 10,000 years ago, the pair calculates.
"We, including scientists, have considered ourselves as sort of the pinnacle of evolution," noted lead researcher Bruce Lahn, a University of Chicago geneticist whose studies appear in Friday's edition of the journal Science.
"There's a sense we as humans have kind of peaked," agreed Greg Wray, director of Duke University's Center for Evolutionary Genomics.
Aside from not knowing what the gene variants actually do, no one knows how precise the model Lahn used to date them is, Collins added.
Lahn's own calculations acknowledge that the microcephalin variant could have arisen anywhere from 14,000 to 60,000 years ago, and that the uncertainty about the ASPM variant ranged from 500 to 14,000 years ago.
"No matter how we [changed] the analysis or assumptions, we couldn't get a date of around 6,000 years," says Gray.
"This kind of study is exactly what linguistics needs," says April Mc Mahon, who studies the history of languages at the University of Sheffield, UK.
The work was funded by the Howard Hughes Medical Institute. A family tree of Indo-European languages suggests they began to spread and split about 9,000 years ago.