Testing avian, squamate, and mammalian nuclear markers for cross amplification in turtles

Conservation Genetics Resources

Volumn 2, Issue 1, 2010, Pages 127-129

  Spinks, Phillip Q ^a   Thomson, Robert C ^a   Barley, Anthony J ^a,b   Newman, Catherine E ^a   Bradley Shaffer, H ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF KANSAS   (United States)

Author keywords

Intron; Nuclear loci; Primers; Testudines

Indexed keywords

ACTINEMYS MARMORATA; AVES; CLEMMYS MARMORATA; MAMMALIA; PELUSIOS CASTANEUS; SQUAMATA; TESTUDINES; VERTEBRATA;

EID: 84859946368     PISSN: 18777252     EISSN: 18777260     Source Type: Journal    
DOI: 10.1007/s12686-010-9184-7     Document Type: Article

References (21)

1. Armstrong MH, Braun EL, Kimball RT (2001) Phylogenetic utility of avian ovomucoid intron G: a comparison of nuclear and mitochondrial phylogenies in Galliformes. Auk 118:799-804
2. Backström N, Fagerberg S, Ellegren H (2008) Genomics of natural bird populations: a gene-based set of reference markers evenly spread across the avian genome. Mol Ecol 17:964-980
3. Barley AJ, Spinks PQ, Thomson RC, Shaffer HB (in press) Fourteen nuclear genes provide phylogenetic resolution for difficult nodes in the turtle tree of life. Mol Phylogen Evol. doi:10.1016/j.ympev.2009.11.005
4. Berlin S, Quintela M, Höglund J (2008) Amultilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus). BMC Genetics 9:89
5. Chubb AL (2004) New nuclear evidence for the oldest divergence among neognath birds: the phylogenetic utility of ZENK. Mol Phylogen Evol 30:140-151
6. Dolman G, Phillips B (2004) Single copy nuclear DNA markers characterized for comparative phylogeography in Australian wet tropics rainforest skinks. Mol Ecol Notes 4:185-187
7. Friesen VL, Congdon BC, Kidd MG, Birt TP (1999) Polymerase chain reaction (PCR) primers for the amplification of five nuclear introns in vertebrates. Mol Ecol Notes 8:2141-2152
8. Handley LJL, Ceplitis H, Ellegren H (2004) Evolutionary strata on the chicken Z chromosome: implications for sex chromosome evolution. Genetics 167:367-376
9. Kimball RT, Braun EL, Barker FK et al (2009) A well-tested set of primers to amplify regions spread across the avian genome. Mol Phylogen Evol 30:654-660
10. Li C, Ortí G, Zhang G, Lu G (2007) A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study. BMC Evol Biol 7:44
11. Lyons LA, Laughlin TF, Copeland NG et al (1997) Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nat Genet 15:47-56
12. Murphy WJ, Eizirik E, Johnson WE et al (2001) Molecular phylogenetics and the origins of placental mammals. Nature 409:614-618
13. Noonan BP, Chippindale PT (2006) Vicariant origin of Malagasy reptiles supports late cretaceous Antarctic land bridge. Am Nat 168:730-741
14. Primmer CR, Borge T, Lindell J, Saetre GP (2002) Single-nucleotide polymorphism characterization in species with limited available sequence information: high nucleotide diversity revealed in the avian genome. Mol Ecol 11:603-611
15. Prychitko TM, Moore WS (1997) The utility of DNA sequences of an intron from the b-fibrinogen gene in phylogenetic analysis of woodpeckers (Aves: Picidae). Mol Phylogen Evol 8:193-204
16. Sehgal RNM, Lovette IJ (2003) Molecular evolution of three avian neurotrophin genes: implications for proregion functional constraints. J Mol Evol 57:335-342
17. Spinks PQ, Shaffer HB (2007) Conservation phylogenetics of the Asian box turtles (Geoemydidae, Cuora): mitochondrial introgression, numts, and inferences from multiple loci. Cons Genet 8:641-657
18. Spinks PQ, Shaffer HB (2009) Conflicting mitochondrial and nuclear phylogenies for the widely disjunct Emys (Testudines: Emydidae) species complex, and what they tell us about biogeography and hybridization. Syst Biol 58:1-20
19. Spinks PQ, Thomson RC, Lovely GA, Shaffer HB (2009) Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles. BMC Evol Biol 9:56
20. Thomson RC, Shedlock AM, Edwards SV, Shaffer HB (2008) Developing markers for multilocus phylogenetics in non-model organisms: a test case with turtles. Mol Phylogen Evol 49:514-525
21. Townsend TM, Alegre RE, Kelley ST, Weins 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