Reich, complex speciation

Reich, complex speciation - 2006 Nature Publishing Group...

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Unformatted text preview: 2006 Nature Publishing Group Genetic evidence for complex speciation of humans and chimpanzees Nick Patterson 1 , Daniel J. Richter 1 , Sante Gnerre 1 , Eric S. Lander 1,2 & David Reich 1,3 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. Humanchimpanzee 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 humanchimpanzee 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. The genetic divergence between two species (the proportion of nucleotides differing between representative individuals of the two species) can be converted into a divergence time in terms of millions of years, provided that differences between genomes have accumu- lated at a constant rate as a result of new mutations 1,2 . The average genetic divergence, t genome , is sometimes used to estimate the speciation time, t species . However, t ( x ), the genetic divergence at any position x , fluctuates across the genome and is everywhere larger 3 than t species (Fig. 1a, and Supplementary Note 1). Thus, its average t genome necessarily exceeds t species . Inferring ancient speciation from genetic data With the availability of large-scale sequencing, enough data can now be obtained to study not only the average t genome but the distribution t ( x ). This should allow direct inferences about t species , which must be less than the minimum time divergence, and about variability in t ( x ), which conveys information about the speciation process. Several issues must be considered in studying t ( x ) for any pair of modern species. First, the genetic divergence should be corrected for local variation in the neutral mutation rates across the genome. This can be done by dividing the local divergence between two species by the divergence of one from an outgroup, for example macaque for the humanchimpanzee comparison. Second, any estimate, ^ t x , of local genetic divergence should be corrected for the effects of recurrent mutation; we do this using two independent methods. Third, variability of ^ t x should be assessed by studying large enough subsets of the genome for the resulting estimates to be reliable....
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This note was uploaded on 03/20/2010 for the course BIOCHEM 410 taught by Professor Whien during the Winter '10 term at Ohio State.

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Reich, complex speciation - 2006 Nature Publishing Group...

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