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Identification of 104 rapidly-evolving nuclear protein-coding markers for amplification across scaled reptiles using genomic resources


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.

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  • Brito P, Edwards SV (2009) Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135:439–455

    PubMed  Article  Google Scholar 

  • 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

  • Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63:1–19

    PubMed  Article  CAS  Google Scholar 

  • Graybeal A (1994) Evaluating the phylogenetic utility of genes: a search for genes informative about deep divergences among vertebrates. Syst Biol 43:174–193

    Google Scholar 

  • Heled J, Drummond AJ (2008) Bayesian inference of population size history from multiple loci. BMC Evol Biol 8:289

    PubMed  Article  Google Scholar 

  • Hey J (2010) Isolation with migration models for more than two populations. Mol Biol Evol 27:905–920

    PubMed  Article  CAS  Google Scholar 

  • Hey J, Nielsen R (2004) Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D-persimilis. Genetics 167:747–760

    PubMed  Article  CAS  Google Scholar 

  • Jennings WB, Edwards SV (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59:2033–2047

    PubMed  CAS  Google 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

  • Lee JY, Edwards SV (2008) Divergence across Australia’s carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus). Evolution 62:3117–3134

    PubMed  Article  Google Scholar 

  • Portik DM, Bauer AM, Jackman TR (2010) The phylogenetic affinities of Trachylepis sulcata nigra and the intraspecific evolution of coastal melanism in the western rock skink. Afr Zool 45:147–159

    Article  Google Scholar 

  • Portik DM, Bauer AM, Jackman TR (2011) Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa. Mol Ecol 20:1744–1758

    PubMed  Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  CAS  Google Scholar 

  • 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 365–386

    Google Scholar 

  • Sakharkar MK, Kangueane P (2004) Genome SEGE: a database for intronless genes in eukaryotic genomes. BMC Bioinform 5:67

    Article  Google Scholar 

  • Shepelev V, Fedorov A (2006) Advances in the exon-intron database. Brief Bioinform 7:178–185

    PubMed  Article  CAS  Google Scholar 

  • Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A (2009) BioMart—biological queries made easy. BMC Genomics 10:22

    PubMed  Article  Google Scholar 

  • Stanley EL, Bauer AM, Jackman TR, Branch WR, Mouton PLFN (2011) Between a rock and a hard polytomy: rapid radiation in the rupicolous girdled lizards (Squamata: Cordylidae). Mol Phylogen Evol 58:53–70

    Article  Google Scholar 

  • Townsend TM, Alegre RE, Kelley ST, Wiens JJ, Reeder TW (2008) Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: an example from squamate reptiles. Mol Phylogen Evol 47:129–142

    Article  CAS  Google Scholar 

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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.

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Correspondence to Daniel M. Portik.

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Portik, D.M., Wood, P.L., Grismer, J.L. et al. Identification of 104 rapidly-evolving nuclear protein-coding markers for amplification across scaled reptiles using genomic resources. Conservation Genet Resour 4, 1–10 (2012).

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  • Nuclear markers
  • Squamates
  • Primers
  • Marker development
  • Intronless exons