Rapid development of multiple nuclear loci for phylogenetic analysis using genomic resources: An example from squamate reptiles

Molecular Phylogenetics and Evolution

Volumn 47, Issue 1, 2008, Pages 129-142

  Townsend, Ted M ^a   Alegre, R Eric ^a   Kelley, Scott T ^a   Wiens, John J ^b   Reeder, Tod W ^a  

^a SAN DIEGO STATE UNIVERSITY   (United States)

^b STONY BROOK UNIVERSITY   (United States)

Author keywords

Genes; Genomics; Phylogenetics; Primers; Reptiles; Vertebrates

Indexed keywords

PRIMER DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; CLASSIFICATION; EXON; GENETICS; GENOMICS; HUMAN; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; REPTILE; SEQUENCE HOMOLOGY;

ANIMALS; BASE SEQUENCE; CELL NUCLEUS; DNA PRIMERS; EXONS; GENOMICS; HUMANS; MOLECULAR SEQUENCE DATA; PHYLOGENY; REPTILES; SEQUENCE HOMOLOGY, NUCLEIC ACID;

AMPHIBIA; REPTILIA; VERTEBRATA;

EID: 41049084425     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2008.01.008     Document Type: Article

References (67)

1. Arnason U., Adegoke J.A., Bodin K., Born E.W., Esa Y.B., Gullberg A., Nilsson M., Short R.V., Xu X.F., and Janke A. Mammalian mitogenomic relationships and the root of the eutherian tree. Proc. Natl. Acad. Sci. USA 99 (2002) 8151-8156
2. Ast J.C. Mitochondrial DNA evidence and evolution in Varanoidea (Squamata). Cladistics 17 (2001) 211-226
3. Avise J.C. Mitochondrial-DNA and the evolutionary genetics of higher animals. Phil. Trans. R. Soc. Lond. B 312 (1986) 325-342
4. Ballard J.W.O., and Rand D.M. The population biology of mitochondrial DNA and its phylogenetic implications. Annu. Rev. Ecol. Evol. Syst. 36 (2005) 621-642
5. Bardeleben C., Moore R.L., and Wayne R.K. A molecular phylogeny of the Canidae based on six nuclear loci. Mol. Phylogenet. Evol. 37 (2005) 815-831
6. Benton M.J., and Donoghue P.C.J. Paleontological evidence to date the tree of life. Mol. Biol. Evol. 24 (2007) 26-53
7. Birks S.M., and Edwards S.V. A phylogeny of the megapodes (Aves: Megapodiidae) based on nuclear and mitochondrial DNA sequences. Mol. Phylogenet. Evol. 23 (2002) 408-421
8. Blouin M.S., Yowell C.A., Courtney C.H., and Dame J.B. Substitution bias, rapid saturation, and the use of mtDNA for nematode systematics. Mol. Biol. Evol. 15 (1998) 1719-1727
9. Boekhorst J., and Snel B. Identification of homologs in insignificant blast hits by exploiting extrinsic gene properties. BMC Bioinform. 8 (2007) 7
10. Brinkmann H., Venkatesh B., Brenner S., and Meyer A. Nuclear protein-coding genes support lungfish and not the coelacanth as the closest living relatives of land vertebrates. Proc. Natl. Acad. Sci. USA 101 (2004) 4900-4905
11. Brown W.M. The mitochondrial genome of animals. In: MacIntyre R.J. (Ed). Molecular Evolutionary Genetics (1985), Plenum, NY 95-130
12. Burns K.J. Molecular systematics of tanagers (Thraupinae): evolution and biogeography of a diverse radiation of neotropical birds. Mol. Phylogenet. Evol. 8 (1997) 334-348
13. Dolman G., and Phillips B. Single copy nuclear DNA markers characterized for comparative phylogeography in Australian wet tropics rainforest skinks. Mol. Ecol. Notes 4 (2004) 185-187
14. Douglas D.A., Janke A., and Arnason U. A mitogenomic study on the phylogenetic position of snakes. Zool. Scr. 35 (2006) 545-558
15. Downie D.A., and Gullan P.J. Phylogenetic analysis of mealybugs (Hemiptera: Coccoidea: Pseudococcidae) based on DNA sequences from three nuclear genes, and a review of the higher classification. Syst. Entomol. 29 (2004) 238-259
16. Estes R., de Queiroz K., and Gauthier J.A. Phylogenetic relationships within Squamata. In: Estes R., and Pregill G. (Eds). Phylogenetic Relationships of the Lizard Families (1988), Stanford University Press, Stanford 119-281
17. Frost, D.R., Etheridge, R., 1989. A phylogenetic analysis and taxonomy of iguanian lizards (Reptilia: Squamata). The University of Kansas Museum of Natural History, Miscellaneous Publications, pp. 1-65.
18. Funk D.J., and Omland K.E. Species-level paraphyly and polyphyly: frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 34 (2003) 397-423
19. Gaines C.A., Hare M.P., Beck S.E., and Rosenbaum H.C. Nuclear markers confirm taxonomic status and relationships among highly endangered and closely related right whale species. Proc. R. Soc. Lond. B 272 (2005) 533-542
20. Groth J.G., and Barrowclough G.F. Basal divergences in birds and the phylogenetic utility of the nuclear RAG-1 gene. Mol. Phylogenet. Evol. 12 (1999) 115-123
21. Harrison R.G. Animal mitochondrial-DNA as a genetic marker in population and evolutionary biology. Trends Ecol. Evol. 4 (1989) 6-11
22. Heise P.J., Maxson L.R., Dowling H.G., and Hedges S.B. Higher-level snake phylogeny inferred from mitochondrial-DNA sequences of 12S ribosomal-RNA and 16S ribosomal-RNA genes. Mol. Biol. Evol. 12 (1995) 259-265
23. Hillier L.W., Miller W., Birney E., Warren W., Hardison R.C., Ponting C.P., Bork P., Burt D.W., Groenen M.A.M., Delany M.E., Dodgson J.B., Chinwalla A.T., Cliften P.F., Clifton S.W., Delehaunty K.D., Fronick C., Fulton R.S., Graves T.A., Kremitzki C., Layman D., Magrini V., McPherson J.D., Miner T.L., Minx P., Nash W.E., Nhan M.N., Nelson J.O., Oddy L.G., Pohl C.S., Randall-Maher J., Smith S.M., Wallis J.W., Yang S.P., Romanov M.N., Rondelli C.M., Paton B., Smith J., Morrice D., Daniels L., Tempest H.G., Robertson L., Masabanda J.S., Griffin D.K., Vignal A., Fillon V., Jacobbson L., Kerje S., Andersson L., Crooijmans R.P.M., Aerts J., van der Poel J.J., Ellegren H., Caldwell R.B., Hubbard S.J., Grafham D.V., Kierzek A.M., McLaren S.R., Overton I.M., Arakawa H., Beattie K.J., Bezzubov Y., Boardman P.E., Bonfield J.K., Croning M.D.R., Davies R.M., Francis M.D., Humphray S.J., Scott C.E., Taylor R.G., Tickle C., Brown W.R.A., Rogers J., Buerstedde J.M., Wilson S.A., Stubbs L., Ovcharenko I., Gordon L., Lucas S., Miller M.M., Inoko H., Shiina T., Kaufman J., Salomonsen J., Skjoedt K., Wong G.K.S., Wang J., Liu B., Wang J., Yu J., Yang H.M., Nefedov M., Koriabine M., deJong P.J., Goodstadt L., Webber C., Dickens N.J., Letunic I., Suyama M., Torrents D., von Mering C., Zdobnov E.M., Makova K., Nekrutenko A., Elnitski L., Eswara P., King D.C., Yang S., Tyekucheva S., Radakrishnan A., Harris R.S., Chiaromonte F., Taylor J., He J.B., Rijnkels M., Griffiths-Jones S., Ureta-Vidal A., Hoffman M.M., Severin J., Searle S.M.J., Law A.S., Speed D., Waddington D., Cheng Z., Tuzun E., Eichler E., Bao Z.R., Flicek P., Shteynberg D.D., Brent M.R., Bye J.M., Huckle E.J., Chatterji S., Dewey C., Pachter L., Kouranov A., Mourelatos Z., Hatzigeorgiou A.G., Paterson A.H., Ivarie R., Brandstrom M., Axelsson E., Backstrom N., Berlin S., Webster M.T., Pourquie O., Reymond A., Ucla C., Antonarakis S.E., Long M.Y., Emerson J.J., Betran E., Dupanloup I., Kaessmann H., Hinrichs A.S., Bejerano G., Furey T.S., Harte R.A., Raney B., Siepel A., Kent W.J., Haussler D., Eyras E., Castelo R., Abril J.F., Castellano S., Camara F., Parra G., Guigo R., Bourque G., Tesler G., Pevzner P.A., Smit A., Fulton L.A., Mardis E.R., and Wilson R.K. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432 (2004) 695-716
24. In: Hillis D.M., Moritz C., and Mable B.K. (Eds). Molecular Systematics (1996), Sinauer Associates, Sunderland, MA
25. Honeycutt R.L., and Adkins R.M. Higher-level systematics of eutherian mammals-an assessment of molecular characters and phylogenetic hypotheses. Annu. Rev. Ecol. Syst. 24 (1993) 279-305
26. Hugall A.F., Foster R., and Lee M.S.Y. Calibration choice, rate smoothing, and the pattern of tetrapod diversification according to the long nuclear gene RAG-1. Syst. Biol. 56 (2007) 543-563
27. Hyman I.T., Ho S.Y.W., and Jermiin L.S. Molecular phylogeny of Australian Helicarionidae, Euconulidae and related groups (Gastropoda: Pulmonata: Stylommatophora) based on mitochondrial DNA. Mol. Phylogenet. Evol. 45 (2007) 792-812
28. Jesus J., Brehm A., and Harris D.J. Relationships of Tarentola (Reptilia: Gekkonidae) from the Cape Verde Islands estimated from DNA sequence data. Amphibia-Reptilia 23 (2002) 47-54
29. Klicka J., Burns K., and Spellman G.M. Defining a monophyletic Cardinalini: a molecular perspective. Mol. Phylogenet. Evol. 45 (2007) 1014-1032
30. Leache A.D., and McGuire J.A. Phylogenetic relationships of horned lizards (Phrynosoma) based on nuclear and mitochondrial data: evidence for a misleading mitochondrial gene tree. Mol. Phylogenet. Evol. 39 (2006) 628-644
31. Lemmon E.M., Lemmon A.R., Collins J.T., Lee-Yaw J.A., and Cannatella D.C. Phylogeny-based delimitation of species boundaries and contact zones in the trilling chorus frogs (Pseudacris). Mol. Phylogenet. Evol. 44 (2007) 1068-1082
32. Li C., Ortí G., Zhang G., and Lu G. A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinipterygii) as a case study. BMC Evol. Biol. 7 (2007)
33. Lyons L.A., Laughlin T.F., Copeland N.G., Jenkins N.A., Womack J.E., and Obrien S.J. Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nat. Genet. 15 (1997) 47-56
34. Macey J.R., Schulte J.A., Larson A., Ananjeva N.B., Wang Y.Z., Pethiyagoda R., Rastegar-Pouyani N., and Papenfuss T.J. Evaluating trans-tethys migration: an example using acrodont lizard phylogenetics. Syst. Biol. 49 (2000) 233-256
35. Maddison W.P. Gene trees in species trees. Syst. Biol. 46 (1997) 523-536
36. Matthee C.A., Burzlaff J.D., Taylor J.F., and Davis S.K. Mining the mammalian genome for artiodactyl systematics. Syst. Biol. 50 (2001) 367-390
37. Mitchell A., and Wen J. Phylogenetic utility and evidence for multiple copies of Granule-Bound Starch Synthase I (GBSSI) in Araliaceae. Taxon 53 (2004) 29-41
38. Murphy W.J., Eizirik E., Johnson W.E., Zhang Y.P., Ryderk O.A., and O'Brien S.J. Molecular phylogenetics and the origins of placental mammals. Nature 409 (2001) 614-618
39. Murphy W.J., Eizirik E., O'Brien S.J., Madsen O., Scally M., Douady C.J., Teeling E., Ryder O.A., Stanhope M.J., de Jong W.W., and Springer M.S. Resolution of the early placental mammal radiation using Bayesian phylogenetics. Science 294 (2001) 2348-2351
40. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
41. Ritchie P.A., Lavoue S., and Lecointre G. Molecular phylogenetics and the evolution of Antarctic notothenioid fishes. Comp. Biochem. Physiol., A: Mol. Integr. Physiol. 118 (1997) 1009-1025
42. Roelants K., and Bossuyt F. Archaeobatrachian paraphyly and Pangaean diversification of crown-group frogs. Syst. Biol. 54 (2005) 111-126
43. Roelants K., Gower D.J., Wilkinson M., Loader S.P., Biju S.D., Guillaume K., Moriau L., and Bossuyt F. Global patterns of diversification in the history of modern amphibians. Proc. Natl. Acad. Sci. USA 104 (2007) 887-892
44. San Mauro D., Vences M., Alcobendas M., Zardoya R., and Meyer A. Initial diversification of living amphibians predated the breakup of Pangaea. Am. Nat. 165 (2005) 590-599
45. Sasakawa K., and Kubota K. Phylogeny and genital evolution of carabid beetles in the genus Pterostichus and its allied genera (Coleoptera: Carabidae) inferred from two nuclear gene sequences. Ann. Entomol. Soc. Am. 100 (2007) 100-109
46. Schulte J.A., Valladares J.P., and Larson A. Phylogenetic relationships within Iguanidae inferred using molecular and morphological data and a phylogenetic taxonomy of Iguanian lizards. Herpetologica 59 (2003) 399-419
47. Sequeira F., Ferrand N., and Harris D.J. Assessing the phylogenetic signal of the nuclear beta-fibrinogen intron 7 in salamandrids (Amphibia: Salamandridae). Amphibia-Reptilia 27 (2006) 409-418
48. Simon C., Buckley T.R., Frati F., Stewart J.B., and Beckenbach A.T. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Annu. Rev. Ecol. Evol. Syst. 37 (2006) 545-579
49. Smith S.A., Arif S., de Oca A.N.M., and Wiens J.J. A phylogenetic hot spot for evolutionary novelty in middle American treefrogs. Evolution 61 (2007) 2075-2085
50. Sota T., and Ishikawa R. Phylogeny and life-history evolution in Carabus (subtribe Carabina: Coleoptera, Carabidae) based on sequences of two nuclear genes. Biol. J. Linn. Soc. 81 (2004) 135-149
51. Sota T., Takami Y., Monteith G.B., and Moore B.P. Phylogeny and character evolution of endemic Australian carabid beetles of the genus Pamborus based on mitochondrial and nuclear gene sequences. Mol. Phylogenet. Evol. 36 (2005) 391-404
52. Sotoadames F.N., Robertson H.M., and Berlocher S.H. Phylogenetic utility of partial DNA sequences of G6PDH at different taxonomic levels in Hexapoda with emphasis on Diptera. Ann. Entomol. Soc. Am. 87 (1994) 723-736
53. *and other methods), version 4.0b10. Sinauer Associates, Sunderland, MA.
54. Sword G.A., Senior L.B., Gaskin J.F., and Joern A. Double trouble for grasshopper molecular systematics: intra-individual heterogeneity of both mitochondrial 12S-valine-16S and nuclear internal transcribed spacer ribosomal DNA sequences in Hesperotettix viridis (Orthoptera: Acrididae). Syst. Entomol. 32 (2007) 420-428
55. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura R.M. (Ed). Some Mathematical Questions in Biology-DNA Sequence Analysis (1986), American Mathematical Society, Providence 57-86
56. Thompson J.D., Higgins D.G., and Gibson T.J. Clustal-W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
57. Townsend T.M., Larson A., Louis E., and Macey J.R. Molecular phylogenetics of Squamata: the position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Syst. Biol. 53 (2004) 735-757
58. Vidal N., and Hedges S.B. Molecular evidence for a terrestrial origin of snakes. Proc. R. Soc. Lond. B 271 (2004) S226-S229
59. Vidal N., and Hedges S.B. The phylogeny of squamate reptiles (lizards, snakes, and amphisbaenians) inferred from nine nuclear protein-coding genes. C. R. Biol. 328 (2005) 1000-1008
60. Waddell P.J., and Shelley S. Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models. Mol. Phylogenet. Evol. 28 (2003) 197-224
61. Weibel A.C., and Moore W.S. A test of a mitochondrial gene-based phylogeny of woodpeckers (genus Picoides) using an independent nuclear gene, beta-fibrinogen intron 7. Mol. Phylogenet. Evol. 22 (2002) 247-257
62. Weisrock D.W., Harmon L.J., and Larson A. Resolving deep phylogenetic relationships in salamanders: analyses of mitochondrial and nuclear genomic data. Syst. Biol. 54 (2005) 758-777
63. Wiens J.J., Bonett R.M., and Chippindale P.T. Ontogeny discombobulates phylogeny: paedomorphosis and higher-level salamander relationships. Syst. Biol. 54 (2005) 91-110
64. Wiens J.J., and Hollingsworth B.D. War of the iguanas: conflicting molecular and morphological phylogenies and long-branch attraction in iguanid lizards. Syst. Biol. 49 (2000) 143-159
65. Willows-Munro S., Robinson T.J., and Matthee C.A. Utility of nuclear DNA intron markers at lower taxonomic levels: phylogenetic resolution among nine Tragelaphus spp. Mol. Phylogenet. Evol. 35 (2005) 624-636
66. Zhou K.Y., Li H.D., Han D.M., Bauer A.M., and Feng J.Y. The complete mitochondrial genome of Gekko gecko (Reptilia: Gekkonidae) and support for the monophyly of Sauria including Amphisbaenia. Mol. Phylogenet. Evol. 40 (2006) 887-892
67. Zwickl, D.J., 2006. Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion. Ph.D. dissertation, The University of Texas at Austin. Available from: ().