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On the comparison of population-level estimates of haplotype and nucleotide diversity: a case study using the gene cox1 in animals

Advances in molecular biology have resulted in a widespread use of DNA sequencing to evaluate the genetic diversity of species. The mitochondrion gene cytochrome c oxidase subunit I (cox1, COI) is commonly sequenced to measure diversity within and between animal populations, particularly in invertebrate species. Comparisons of population-level diversity are especially important when genetic information is intended to aid conservation and management programmes. Unfortunately, such comparisons are not straightforward due to methodological differences between studies and the absence of a general summary of cox1 diversity levels. Furthermore, comparisons are complicated by a lack of standardisation in defining what represents ‘low’ or ‘high’ genetic diversity.

BAS researchers addressed this issue by collating large numbers of population-level cox1 DNA datasets from public archives and reanalyzing them using a single consistent method. This generated standardised reference values against which further cox1 diversity studies can be compared and will allow a better assessment of whether genetic diversity values within a particular species or population are low or high. The researchers also developed a new method of assessing diversity, which uses two different measures of the genetic variation - haplotype diversity and nucleotide diversity. The method gives even greater resolution on where diversity within populations is different from expected, which could be invaluable in identifying the need for conservation measures at an early stage. Through collating the data, the researchers found that public archives were less complete and accurate than widely assumed. Therefore, recommendations on data archiving methodologies were made to ensure that future records contain only data of sufficient quality to carry out valid diversity comparisons. There are multiple challenges associated with measuring genetic diversity and standardized methods are of great benefit to studies of biodiversity worldwide. The present study will not only help researchers interested in understanding the biology of particular species but will also assist in producing more informed guidelines for future conservation and management programmes.

Link to the full paper in the NERC Open Research Archive


William P. Goodall-Copestake, Geraint A. Tarling, Eugene J. Murphy


Heredity 109: 50-56