1. Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
2. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
3. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

Correspondence to: David Reich^1,3 Correspondence and requests for materials should be addressed to D.R. (Email: reich@genetics.med.harvard.edu).
To obtain sequencing reads from the NCBI trace archive (Email: http://www.ncbi.nlm.nih.gov/Traces), use the following queries:
(1) Gorilla data (Gorilla gorilla):
CENTER_NAME ='WIBR' and CENTER_PROJECT ='G611'
CENTER_NAME = 'WIBR' and CENTER_PROJECT = 'G612'
CENTER_NAME = 'WIBR' and CENTER_PROJECT = 'G618'
CENTER_NAME = 'WIBR' and CENTER_PROJECT = 'G619'
CENTER_NAME = 'WIBR' and CENTER_PROJECT = 'G744';
(2) New world monkey data (Ateles geoffroyi):
CENTER_NAME = 'WIBR' and CENTER_PROJECT = 'G820'.

Abstract

The genetic divergence time between two species varies substantially across the genome, conveying important information about the timing and process of speciation. Here we develop a framework for studying this variation and apply it to about 20 million base pairs of aligned sequence from humans, chimpanzees, gorillas and more distantly related primates. Human–chimpanzee genetic divergence varies from less than 84% to more than 147% of the average, a range of more than 4 million years. Our analysis also shows that human–chimpanzee speciation occurred less than 6.3 million years ago and probably more recently, conflicting with some interpretations of ancient fossils. Most strikingly, chromosome X shows an extremely young genetic divergence time, close to the genome minimum along nearly its entire length. These unexpected features would be explained if the human and chimpanzee lineages initially diverged, then later exchanged genes before separating permanently.

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