Utility of the nuclear protein-coding gene, elongation factor-1 gamma (EF-1γ), for spider systematics, emphasizing family level relationships of tarantulas and their kin (Araneae: Mygalomorphae)

Molecular Phylogenetics and Evolution

Volumn 42, Issue 2, 2007, Pages 394-409

  Ayoub, Nadia A ^a   Garb, Jessica E ^a   Hedin, Marshal ^b   Hayashi, Cheryl Y ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

Arthropod; EST; Molecular clock; Nuclear gene; Opisthothelae; Protein coding; Substitution rate

Indexed keywords

ELONGATION FACTOR 1; NUCLEAR PROTEIN;

ANIMAL; ARTICLE; CLASSIFICATION; DNA SEQUENCE; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; SPIDER;

ANIMALS; BASE SEQUENCE; EVOLUTION, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR PROTEINS; PEPTIDE ELONGATION FACTOR 1; PHYLOGENY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SPIDERS;

ANTRODIAETIDAE; ARANEAE; ARANEOMORPHAE; ARTHROPODA; ATYPIDAE; HEXATHELIDAE; MYGALOMORPHAE; NEMESIIDAE; OPISTHOTHELAE; THERAPHOSIDAE;

EID: 33750973950     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2006.07.018     Document Type: Article

References (96)

1. Altschul S.F., Gish W., Miller W., Myers E.W., and Lipman D.J. Basic local alignment tool. J. Mol. Biol. 215 (1990) 403-410
2. Arnedo M.A., Oromi P., and Ribera C. Radiation of the spider genus Dysdera (Araneae, Dysderidae) in the Canary Islands: cladistic assessment based on multiple data sets. Cladistics 17 (2001) 313-353
3. Arnedo M.A., Coddington J., Agnarsson I., and Gillespie R.G. From a comb to a tree: phylogenetic relationships of the comb-footed spiders (Araneae, Theridiidae) inferred from nuclear and mitochondrial genes. Mol. Phylogenet. Evol. 31 (2004) 225-245
4. Averdam A., Markl J., and Burmester T. Subunit sequences of the 4 X 6-mer hemocyanin from the golden orb-web spider, Nephila inaurata. Eur. J. Biochem. 270 (2003) 3432-3439
5. Ayoub N.A., and Riechert S.E. Molecular evidence for Pleistocene glacial cycles driving diversification of a North American desert spider, Agelenopsis aperta. Mol. Ecol. 13 (2004) 3453-3465
6. Ayoub N.A., Riechert S.E., and Small R.L. Speciation history of the North American funnel web spiders, Agelenopsis (Araneae: Agelenidae): Phylogenetic inferences at the population-species interface. Mol. Phylogenet. Evol. 36 (2005) 42-57
7. Baldwin B.G., and Markos S. Phylogenetic utility of the external transcribed spacer (ETS) of 18S-26S rDNA: Congruence of ETS and ITS trees of Calycadenia (Compositae). Mol. Phylogenet. Evol. 10 (1998) 449-463
8. Beuken E., Vink C., and Bruggeman C.A. One step procedure for screening recombinant plasmids by size. Biotechniques 24 (1998) 748-750
9. Bond, J.E. Hedin, M., in press. A total evidence assessment of the phylogeny of North American euctenizine trapdoor spiders (Araneae, Mygalomorphae, Cyrtaucheniidae) using Bayesian inference. Mol. Phylogenet. Evol.
10. Bond J.E., and Opell B.D. Phylogeny and taxonomy of the genera of south-western North American Euctenizinae trapdoor spiders and their relatives (Araneae: Mygalomoprhae, Cyrtaucheniidae). Zool. J. Linn. Soc. -Lond 138 (2002) 487-534
11. Bond J.E., Hedin M.C., Ramirez M.G., and Opell B.D. Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus. Mol. Ecol. 10 (2001) 899-910
12. Bremer K. The limits of amino acid sequence data in angiosperm phylogenetic reconstruction. Evolution 42 (1988) 795-803
13. Burmester T. Molecular evolution of the arthropod hemocyanin superfamily. Mol. Biol. Evol. 18 (2001) 184-195
14. Brower A.V.Z. Rapid morphological radiation and convergence among races of the butterfly Heliconius erato inferred from patterns of mitochondrial DNA evolution. Proc. Natl. Acad. Sci. USA 91 (1994) 6491-6495
15. Chamberlin R.V., and Ivie W. On some nearctic mygalomorph spiders. Ann. Entomol. Soc. Am. 38 (1945) 549-558
16. Coddington J.A. The monophyletic origin of the orb web. In: Shear W.A. (Ed). Spiders. Webs, Behavior, and Evolution (1986), Stanford University Press, Stanford 319-363
17. Coddington J.A., and Levi H.W. Systematics and evolution of spiders (Araneae). Ann. Rev. Ecol. Syst. 22 (1991) 565-592
18. Coddington J.A. Phylogeny and Classification of Spiders. In: Ubick D., Paquin P., Cushing P.E., and Roth V. (Eds). Spiders of North America: an identification manual (2005), American Arachnological Society 18-24
19. Crews S.C., and Hedin M. Studies of morphological and molecular phylogenetic divergence in spiders (Araneae: Homalonychus) from the American southwest, including divergence along the Baja California Peninsula. Mol. Phylogenet. Evol. 38 (2006) 470-487
20. Croucher P.J.P., Oxford G.S., and Searle J.B. Mitochondrial differentiation, introgression, and phylogeny of species in the Tegeneria atrica group (Araneae: Agelenidae). Biol. J. Linn. Soc. 81 (2004) 79-89
21. Danforth B.N., Lin C.-P., and Fang J. How do insect nuclear ribosomal genes compare to protein-coding genes in phylogenetic utility and nucleotide substitution patterns?. Syst. Entom. 30 (2005) 549-562
22. Davila D.S. Higher-level relationships of the spider family Ctenidae (Araneae: Ctenoidea). Bull. Am. Mus. Nat. His. 275 (2003) 1-86
23. Delsuc F., Brinkman H., and Phillipe H. Phylogenomics and the reconstruction of the tree of life. Nat. Rev. Genet. 6 (2005) 361-375
24. DeSalle R., Freeman T., Prager E.M., and Wilson A.C. Tempo and mode of sequence evolution in mitochondrial DNA of Hawaiian Drosophila. J. Mol. Evol. 26 (1987) 157-164
25. Eberhard W.G. Function and phylogeny of spider webs. Annu. Rev. Ecol. Syst. 21 (1990) 341-372
26. Eskov K. A new fossil spider family from the Jurassic of Transbaikalia (Araneae: Chelicerata). N. Jb. Geol. Palaont. Mh. 11 (1984) 645-653
27. Eskov K., and Zonhstein S. First Mesozoic mygalomorph spiders from the Lower Cretaceous of Siberia and Mongolia, with notes on the system and evolution of the infraorder Mygalomorphae (Chelicerate: Araneae). N. Jb. Geol. Palaont. Abh. 178 (1990) 325-368
28. Felsenstein J. Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 39 (1985) 783-791
29. Felsenstein, J., 2004. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle.
30. Gatesy J., Baker R.H., and Hayashi C.Y. Inconsistencies in arguments for the supertree approach: Supermatrices versus supertrees of Crocodylia. Syst. Biol. 53 (2004) 342-355
31. Garb, J.E., 2003. Evolutionary studies of Polynesian crab spiders (Araneae: Thomisidae) and Latrodectus spiders (Araneae: Theridiidae). PhD dissertation. University of California, Berkely, 251 pp.
32. Garb J.E., Gonzalez A., and Gillespie R.G. The black widow spider genus Latrodectus (Araneae: Theridiidae): phylogeny, biogeography, and invasion history. Mol. Phylogenet. Evol. 31 (2004) 1127-1142
33. Gertsch W.J. American spiders (1949), Princeton, Van Nostrand 285 pp.
34. Gillespie R. Community assembly through adaptive radiation in Hawaiian spiders. Science 303 (2004) 356-359
35. Giribet G., Edgecombe G.D., Wheeler W.C., and Babbitt C. Phylogeny and systematic position of Opiliones: a combined analysis of chelicerate relationships using morphological and molecular data. Cladistics 18 (2002) 5-70
36. Giribet G., and Wheeler W.C. On gaps. Mol. Phylogenet. Evol. 13 (1999) 132-143
37. Giribet G., and Edgecombe G.D. Conflict between datasets and phylogeny of centipedes: an analysis based on seven genes and morphology. Proc. R. Soc. B 273 (2006) 531-538
38. Goloboff P.A. Homoplasy and the choice among cladograms. Cladistics 7 (1991) 215-232
39. Goloboff P.A. A reanalysis of mygalomorph spider families (Araneae). Am. Mus. Nov. 3056 (1993) 1-32
40. Griswold C., and Ledford J. A monograph of the migid trap-door spiders of Madagascar, with a phylogeny of world genera (Araneae, Mygalomorphae, Migidae). Occ. Pap. Calif. Acad. Sci. 151 (2001) 1-120
41. Griswold C.E., Coddington J.A., Hormiga G., and Scharff N. Phylogeny of the orb-web building spiders (Araneae, Orbiculariae:Deinopoidea, Araneoidea). Zool. J. Linn. Soc. -Lond. 123 (1998) 1-99
42. Griswold C.E., Coddington J.A., Platnick N.I., and Forster F.F. Towards a phylogeny of entelygyne spiders (Araneae, Entelegynae). J. Arachnol. 27 (1999) 53-63
43. Hausdorf B. Molecular phylogeny of araneomorph spiders. J. Evol. Biol. 12 (1999) 980-985
44. Hedin M.C. Speciational history in a diverse clade of habitat-specialized spiders (Araneae: Nesticidae: Nesticus): inferences from geographic-based sampling. Evolution 51 (1997) 1929-1945
45. Hedin, M., Bond, J.E., in press. Molecular phylogenetics of the spider infraorder Mygalomorphae using nuclear rRNA genes (18S and 28S): Conflict and agreement with the current system of classification. Mol. Phylogenet. Evol.
46. Hedin M.C., and Maddison W.P. Phylogenetic utility and evidence for multiple copies of elongation factor-1 alpha. Mol. Biol. Evol. 18 (2001) 1512-1521
47. Hendrixson B.E., and Bond J.E. Testing species boundaries in the Antrodiaetus unicolor complex (Araneae: Mygalomorphae: Antrodiaetidae): "Paraphyly" and cryptic diversity. Mol. Phylogenet. Evol. 36 (2005) 405-416
48. Higgins D.G., and Sharp P.M. CLUSTAL: a package for performing multiple sequence alignment on a microcomputer. Gene 73 (1988) 237-244
49. Huber K.C., Haider T.S., Muller M.W., Huber B.A., Schweyen R.J., and Barth F.G. DNA sequence data indicates the polyphyly of the family Ctenidae (Araneae). J. Arachnol. 21 (1993) 194-201
50. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference of phylogeny. Bioinformatics 17 (2001) 754-755
51. Hughes J., Longhorn S.J., Papadopoulou A., Theodorides K., de Riva A., Mejia-Chang M., Foster P.G., and Vogler A.P. Dense taxonomic EST sampling and its applications to molecular systematics of the Coleoptera (beetles). Mol. Biol. Evol. 23 (2006) 268-278
52. Hormiga G., Arnedo M., and Gillespie R.G. Speciation on a conveyor belt: Sequential colonization of the Hawaiian islands by Orsonwelles spiders (Araneae, Linyphiidae). Syst. Biol. 52 (2003) 70-88
53. Johnson L.A., and Soltis D.E. Phylogenetic inference in Saxifragaceae sensu stricto and Gilia (Polemoniaceae) using matK sequences. Ann. Mo. Bot. Gard. 82 (1995) 149-175
54. Kullman E.J. The convergent development of orb-webs in cribellate and ecribellate spiders. Am. Zool. 12 (1972) 395-405
55. Lin CP., and Danforth B.N. How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets. Mol. Phylogenet. Evol. 30 (2004) 686-702
56. Maddison W.P., and Hedin M.C. Jumping spider phylogeny (Araneae, Salticidae). Invertebr. Syst. 17 (2003) 529-549
57. Main B.Y. Further studies on the systematics of ctenizid trapdoor spiders: A review of the Australian genera (Araneae: Mygalomorphae: Ctenizidae). Aust. J.Zool. Supp. Ser. 108 (1985) 1-84
58. Masta S.E. Phylogeography of the jumping spider Habronattus pugillis (Araneae: Salticidae): recent vicariance of sky island populations?. Evolution 54 (2000) 1699-1711
59. Monteiro A., and Pierce N.E. Phylogeny of Bicyclus (Lepidoptera: Nypmpalidae) inferred from COI, COII, and EF-1α gene sequences. Mol. Phylogenet. Evol. 18 (2001) 264-281
60. Moriyama E.N., and Powell J.R. Synonymous substitution rates in Drosophila mitochondrial versus nuclear genes. J. Mol. Evol. 45 (1997) 378-391
61. Müller K. SeqState - primer design and sequence statistics for phylogenetic DNA data sets. Appl. Bioinformatics 4 (2005) 65-69
62. Murphy N.P., Framenau V.W., Donnellan S.C., Harvey M.S., Park Y.-C., and Austin A.D. Phylogenetic reconstruction of the wolf spiders (Araneae; Lycosidae) using sequences from the 12S rRNA, 28S rRNA and NADH1 genes: implifications for classification, biogeography, and the evolution of web building behavior. Mol. Phylogenet. Evol. 38 (2006) 583-602
63. Penney D. Spiders in Upper Cretaceous amber from New Jersey (Arthropooda, Araneae). Palaeontology 45 (2002) 709-724
64. Penney D., Wheater C.P., and Selden P.A. Resistance of spiders to Cretaceous-Tertiary extinction events. Evolution 57 (2003) 2599-2607
65. Piel W.H., and Nutt K.J. Kaira is a likely sister group to Metepeira, and Zygiella is an araneid (Araneae: Araneidae): evidence from mitochondrial DNA. J. Arachnol. 25 (1997) 262-268
66. Platnick N.I. The hypochiloid spiders: a cladistic analysis, with notes on the Atypoidea (Arachnida, Araneae). Am. Mus. Nov. 2734 (1977) 1-13
67. Platnick, N.I., 2006. The world spider catalog, version 6.5. American Museum of Natural History, online at .
68. Platnick N.I., and Gertsch W.J. The suborders of spiders: a cladistic analysis (Arachnida, Araneae). Am. Mus. Nov. 2607 (1976) 1-15
69. Platnick N.I., Coddington J.A., Forster R.F., and Griswold C.E. Spinneret evidence and the higher classification of the haplogyne spiders (Araneae, Araneomorphae). Am. Mus. Nov. 3016 (1991) 1-73
70. Pons J., and Gillespie R.G. Evolution of satellite DNAs in a radiation of endemic Hawaiian spiders: does concerted evolution of highly repetitive sequences reflect evolutionary history?. J. Mol. Evol. 59 (2004) 632-641
71. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
72. Prendini L., Crowe T.M., and Wheeler W.C. Systematics and biogeography of the family Scorpionidae (Chelicerata:Scorpiones), with a discussion on phylogenetic methods. Invertebr. Syst. 17 (2003) 185-259
73. Prendini L., Weygoldt P., and Wheeler W.C. Systematics of the Damon variegates group of African whip spiders (Chelicerata: Amplypygi: evidence from behaviour, morphology and DNA. Org. Divers. Evol. 5 (2005) 203-236
74. Raven R.J. The spider infraorder Mygalomorphae (Araneae): cladistics and systematics. Bull. Am. Mus. Nat. Hist. 182 (1985) 1-180
75. Rayner R.J., and Dippenaar-Schoeman A.S. A fossil spider (superfamily Lycosoidea) from the Cretaceous of Botswana. S. Afr. J. Sci. 91 (1995) 98-100
76. Regier J.C., Wilson H.M., and Shultz J.W. Phylogenetic analysis of Myriapoda using three nuclear protein-coding genes. Mol. Phylogenet. Evol. 34 (2005) 147-158
77. Rodriguez F., Oliver J.L., Marin A., and Medina J.R. The general stochastic model of nucleotide substitution. J. Theor. Biol. 142 (1990) 485-501
78. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
79. Sanderson M.J. A nonparametric approach to estimating divergence times in the absence of rate constancy. Mol. Biol. Evol. 14 (1997) 1218-1231
80. Sanderson M.J. Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Mol. Biol. Evol. 19 (2002) 101-109
81. Sanderson M.J. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics 19 (2003) 301-302
82. Sanmartín I., and Ronquist F. Southern hemisphere biogeography inferred by event based models: Plant versus animal patterns. Syst. Biol. 53 (2004) 216-243
83. Selden P.A. Lower Cretaceous spiders from the Sierra de Monsech, north-east Spain. Palaeontology 33 (1990) 257-285
84. Selden P.A., Shear W.A., and Bonamo P.M. A spider and other arachnids from the Devonian of New York, and reinterpretation of Devonian Araneae. Palaeontology 34 (1991) 241-281
85. Selden P.A., and Gall J.-C. A Triassic mygalomorph spider from the northern Vosges, France. Palaeontology 35 (1992) 211-235
86. Senapathy P., Shapiro M.B., and Harris N.L. Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to Genome Project. Meth. Enzymol. 183 (1990) 252-278
87. Shimodaira H., and Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16 (1999) 1114-1116
88. Shultz J.W., and Regier J.C. Phylogenetic analysis of Phalangida (Arachnida, Opiliones) using two nuclear protein-encoding genes supports monophyly of Palpatores. J. Arachnol. 29 (2001) 189-200
89. Simmons M.P., and Ochoterena H. Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol. 49 (2000) 369-381
90. Simon, E., 1892. Histoire naturelle des araignees, Paris, vol. 1. 256 pp.
91. Swofford, D.L., 2002. PAUP*. Phylogenetic Analysis Using Parsimony (* and Other Methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
92. Sorenson, M.D., 1999. TREEROT. Version 2c. Boston University, Boston.
93. Teeling E.C., Springer M.S., Madsen O., Bates P., O'brien S.J., and Murphy W.J. A molecular phylogeny for bats illuminates biogeography and the fossil record. Science 307 (2005) 580-584
94. Thornton S., Anand N., and Purcell D. Not just for housekeeping: protein initiation and elongation factors in cell growth and tumorigenesis. J. Mol. Med. 81 (2003) 536-548
95. Vink C.J., and Paterson A.M. Combined molecular and morphological phylogenetic analyses of the New Zealand wolf spider genus Anoteropsis (Araneae: Lycosidae). Mol. Phylogenet. Evol. 28 (2003) 576-587
96. Zakharov E.V., Caterino M.S., and Sperling F.A. Molecular phylogeny, historical biogeography, and divergence time estimates for swallowtail butterflies of the genus Papilio (Lepidoptera: Papilionidae). Syst. Biol. 53 (2004) 193-215