Identification of 104 rapidly-evolving nuclear protein-coding markers for amplification across scaled reptiles using genomic resources
- 339 Downloads
As the fields of molecular systematics and phylogeography are advancing, it is necessary to incorporate multiple loci in both population and species-level inference. Here, we present primer sets for 104 intronless orthologus exons designed for amplification in all squamates. When comparing the Anolis genome to the Gallus genome, all the markers have less than 67.2% DNA sequence identity, the percent identity of the first third of the commonly used nuclear marker RAG-1. The rate of evolution in these markers is therefore greater than nuclear markers commonly used, and we demonstrate their usefulness for both phylogeographic and phylogenetic studies.
KeywordsNuclear markers Squamates Primers Marker development Intronless exons
We would like to thank Nicole Rocha, Andrew Feiter, Arianna Kuhn, Maria Tempera, Lauren Adderly, and Stuart Love Nielsen for contributions in laboratory work. We thank Aaron Bauer for providing many tissue samples used in this study. Funding for this project was provided by a National Science Foundation grant (DEB 0515909) and by the Department of Biology at Villanova University.
- Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Duran C, Field M, Heled J, Kearse M, Markowitz S, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2011) Geneious v5.4. Available from http://www.geneious.com/
- Graybeal A (1994) Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Syst Biol 43:174–193Google Scholar
- Leaché AD, Rannala B (2010) The accuracy of species tree estimation under simulation: a comparison of methods. Syst Biol. doi: 10.1093/sysbio/syq073
- Rozen S, Skaletsky J (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols: methods in molecular biology. Humana Press, Totowa, pp 365–386Google Scholar