Conservation Genetics Resources

, Volume 4, Issue 1, pp 1–10 | Cite as

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

  • Daniel M. Portik
  • Perry L. WoodJr.
  • Jesse L. Grismer
  • Edward L. Stanley
  • Todd R. Jackman
Technical Note


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.


Nuclear 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.

Supplementary material

12686_2011_9460_MOESM1_ESM.doc (165 kb)
Supplementary material 1 (DOC 165 kb)


  1. Brito P, Edwards SV (2009) Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135:439–455PubMedCrossRefGoogle Scholar
  2. 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
  3. Edwards SV (2009) Is a new and general theory of molecular systematics emerging? Evolution 63:1–19PubMedCrossRefGoogle Scholar
  4. 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
  5. Heled J, Drummond AJ (2008) Bayesian inference of population size history from multiple loci. BMC Evol Biol 8:289PubMedCrossRefGoogle Scholar
  6. Hey J (2010) Isolation with migration models for more than two populations. Mol Biol Evol 27:905–920PubMedCrossRefGoogle Scholar
  7. 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 167:747–760PubMedCrossRefGoogle Scholar
  8. Jennings WB, Edwards SV (2005) Speciational history of Australian grass finches (Poephila) inferred from thirty gene trees. Evolution 59:2033–2047PubMedGoogle Scholar
  9. Leaché AD, Rannala B (2010) The accuracy of species tree estimation under simulation: a comparison of methods. Syst Biol. doi: 10.1093/sysbio/syq073
  10. Lee JY, Edwards SV (2008) Divergence across Australia’s carpentarian barrier: statistical phylogeography of the red-backed fairy wren (Malurus melanocephalus). Evolution 62:3117–3134PubMedCrossRefGoogle Scholar
  11. 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 45:147–159CrossRefGoogle Scholar
  12. Portik DM, Bauer AM, Jackman TR (2011) Bridging the gap: western rock skinks (Trachylepis sulcata) have a short history in South Africa. Mol Ecol 20:1744–1758PubMedCrossRefGoogle Scholar
  13. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959PubMedGoogle Scholar
  14. 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
  15. Sakharkar MK, Kangueane P (2004) Genome SEGE: a database for intronless genes in eukaryotic genomes. BMC Bioinform 5:67CrossRefGoogle Scholar
  16. Shepelev V, Fedorov A (2006) Advances in the exon-intron database. Brief Bioinform 7:178–185PubMedCrossRefGoogle Scholar
  17. Smedley D, Haider S, Ballester B, Holland R, London D, Thorisson G, Kasprzyk A (2009) BioMart—biological queries made easy. BMC Genomics 10:22PubMedCrossRefGoogle Scholar
  18. 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 58:53–70CrossRefGoogle Scholar
  19. 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 47:129–142CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Daniel M. Portik
    • 1
    • 2
  • Perry L. WoodJr.
    • 1
  • Jesse L. Grismer
    • 1
    • 3
  • Edward L. Stanley
    • 1
    • 4
  • Todd R. Jackman
    • 1
  1. 1.Department of BiologyVillanova UniversityVillanovaUSA
  2. 2.Museum of Vertebrate Zoology and Department of Integrative BiologyUniversity of CaliforniaBerkeleyUSA
  3. 3.Natural History Museum and Biodiversity Research Center and Department of Ecology and Evolutionary BiologyUniversity of KansasLawrenceUSA
  4. 4.Department of HerpetologyAmerican Museum of Natural HistoryNew YorkUSA

Personalised recommendations