Abstract
Species identification is essential for non-invasive studies of elusive and rare animals, and for detecting illegal harvest or trade of wildlife species. However, most molecular tests identify only a limited number of species or require multiple laboratory steps to distinguish many taxa. Additionally, most protocols use mitochondrial DNA being, therefore, especially prone to problems such as nuclear insert copies, high intraspecific diversity or heteroplasmy. Here, we developed a molecular test based on the polymorphisms detected on a small nuclear gene fragment (221 bp of the IRBP -Interphotoreceptor Retinoid-Binding Protein- exon 1). This fragment revealed 51 variable sites (including 12 non-synonymous and 19 species-specific sites), which enabled the successful distinction of all 16 carnivore species native to South-western Europe. A SSCP (Single-Strand Conformational Polymorphism) gel electrophoresis technique was also optimized to allow the simple and inexpensive application of this molecular test. Sequences and SSCP profiles were consistent in identifying a total of 387 samples, including faeces (172) and hairs (17) collected non-invasively in the field. Due to its low cost, simplicity, and wide range of identifiable species, this test shows great promise to facilitate studies in molecular ecology, conservation genetics, and forensic analysis, as well as DNA bar-coding projects.
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Acknowledgments
We thank N. Ferrand and R. Faria for comments on earlier versions of this manuscript. We are grateful to Portuguese National Tissues Bank/National Institute for Nature and Biodiversity Conservation (BTVS/ICN-B), P. Monterroso, F. Alvares, B. Gomez-Moliner, C. Gortazar, J. Searle, F. Suchentrunk, E. Randi, J. Godoy, P. Ferreras, A. Ruiz-González, C. Ferreira, J. Vicente, Z. Boratynski, T. Perez and J. Paupério for providing samples. This work was partially financed by the research project PTDC/CVT/71683/2006, from FCT (Fundação para a Ciência e a Tecnologia). R. Oliveira and R. Godinho worked under PhD (SFRH/BD/24361/2005) and Post-Doc (SFRH/BPD/36021/2007) grants, respectively, both financed by FCT. D. Castro was supported by a CIBIO grant and G. Luikart was supported by the Portuguese-American Foundation for Development, CIBIO and UP.
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Oliveira, R., Castro, D., Godinho, R. et al. Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe. Conserv Genet 11, 1023–1032 (2010). https://doi.org/10.1007/s10592-009-9947-4
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DOI: https://doi.org/10.1007/s10592-009-9947-4