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Open Access Research article

The genomic distribution of intraspecific and interspecific sequence divergence of human segmental duplications relative to human/chimpanzee chromosomal rearrangements

Tomàs Marques-Bonet12, Ze Cheng2, Xinwei She2, Evan E Eichler2 and Arcadi Navarro134*

Author Affiliations

1 Unitat de Biologia Evolutiva Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, Barcelona, Catalonia, Spain

2 Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA

3 Institucio Catalana de Recerca i Estudis Avancats (ICREA) and Universitat Pompeu Fabra, Barcelona, Catalonia, Spain

4 Population Genomics Node (GNV8), National Institute for Bioinformatics (INB) Universitat Pompeu Fabra, Spain

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BMC Genomics 2008, 9:384  doi:10.1186/1471-2164-9-384

Published: 12 August 2008

Abstract

Background

It has been suggested that chromosomal rearrangements harbor the molecular footprint of the biological phenomena which they induce, in the form, for instance, of changes in the sequence divergence rates of linked genes. So far, all the studies of these potential associations have focused on the relationship between structural changes and the rates of evolution of single-copy DNA and have tried to exclude segmental duplications (SDs). This is paradoxical, since SDs are one of the primary forces driving the evolution of structure and function in our genomes and have been linked not only with novel genes acquiring new functions, but also with overall higher DNA sequence divergence and major chromosomal rearrangements.

Results

Here we take the opposite view and focus on SDs. We analyze several of the features of SDs, including the rates of intraspecific divergence between paralogous copies of human SDs and of interspecific divergence between human SDs and chimpanzee DNA. We study how divergence measures relate to chromosomal rearrangements, while considering other factors that affect evolutionary rates in single copy DNA.

Conclusion

We find that interspecific SD divergence behaves similarly to divergence of single-copy DNA. In contrast, old and recent paralogous copies of SDs do present different patterns of intraspecific divergence. Also, we show that some relatively recent SDs accumulate in regions that carry inversions in sister lineages.