Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity

Springer Science and Business Media LLC - Tập 5 Số 1 - 2010
Binh Thanh Nguyen1, Andreas Spillner2, Brent C. Emerson3, Vincent Moulton1
1School of Computing Sciences, University of East Anglia, Norwich NR4 7TJ, UK
2Department of Mathematics and Computer Science, University of Greifswald, 17489, Greifswald, Germany
3School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, UK

Tóm tắt

Abstract We introduce a method to help identify how the genetic diversity of a species within a geographic region might have arisen. This problem appears, for example, in the context of identifying refugia in phylogeography, and in the conservation of biodiversity where it is a factor in nature reserve selection. Complementing current methods for measuring genetic diversity, we analyze pairwise distances between the haplotypes of a species found in a geographic region and derive a quantity, called haplotype connectivity, that aims to capture how divergent the haplotypes are relative to one another. We propose using haplotype connectivity to indicate whether, for geographic regions that harbor a highly diverse collection of haplotypes, diversity evolved inside a region over a long period of time (a "hot-spot") or is the result of a more recent mixture (a "melting-pot"). We describe how the haplotype connectivity for a collection of haplotypes can be computed efficiently and briefly discuss some related optimization problems that arise in this context. We illustrate the applicability of our method using two previously published data sets of a species of beetle from the genus Brachyderes and a species of tree from the genus Pinus.

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