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

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Nguyen, Binh, Spillner, Andreas, Emerson, Brent C. and Moulton, Vincent ORCID: https://orcid.org/0000-0001-9371-6435 (2010) Distinguishing between hot-spots and melting-pots of genetic diversity using haplotype connectivity. Algorithms for Molecular Biology, 5. ISSN 1748-7188

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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.

Item Type:	Article
Faculty \ School:	Faculty of Science > School of Biological Sciences Faculty of Science > School of Computing Sciences
UEA Research Groups:	Faculty of Science > Research Groups > Computational Biology > Computational biology of RNA (former - to 2018) Faculty of Science > Research Groups > Computational Biology > Phylogenetics (former - to 2018) Faculty of Science > Research Groups > Organisms and the Environment Faculty of Science > Research Groups > Computational Biology Faculty of Science > Research Groups > Norwich Epidemiology Centre Faculty of Medicine and Health Sciences > Research Groups > Norwich Epidemiology Centre
Related URLs:	http://www.almob.org/content/5/1/19
Depositing User:	Vishal Gautam
Date Deposited:	10 Mar 2011 11:40
Last Modified:	15 Jun 2023 23:47
URI:	https://ueaeprints.uea.ac.uk/id/eprint/22032
DOI:	10.1186/1748-7188-5-19

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