More data, fewer shifts: Molecular insights into the evolution of the spinning apparatus in non-orb-weaving spiders

Molecular Phylogenetics and Evolution

Volumn 46, Issue 1, 2008, Pages 347-368

  Spagna, Joseph C ^a   Gillespie, Rosemary G ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Agelenidae; Bayesian inference; Cribellum; POY; RTA clade; Systematics

Indexed keywords

INSECT PROTEIN;

ANIMAL; ARTICLE; BAYES THEOREM; BIOSYNTHESIS; CLASSIFICATION; EVOLUTION; GENETICS; MOLECULAR EVOLUTION; PHYSIOLOGY; SILK; SPECIES DIFFERENTIATION; SPIDER;

ANIMALS; BAYES THEOREM; EVOLUTION; EVOLUTION, MOLECULAR; GENETIC SPECIATION; INSECT PROTEINS; SILK; SPIDERS;

AGELENIDAE; ARANEAE; ARANEIDAE; LYCOSIDAE; PLOCEINAE; RTA CLADE; SALTICIDAE;

EID: 37249087372     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2007.08.008     Document Type: Article

References (99)

1. Aagesen L., Petersen G., and Seberg O. Sequence length variation, indel costs, and congruence in sensitivity analysis. Cladistics 21 (2005) 15-30
2. Arnedo M.A., Coddington J.A., 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
3. Berenbaum M.R., Favret C., and Schular M.A. On defining "key innovations" in an adaptive radiation: cytochrome P450s and Papilionidae. Am. Nat. 148 (1996) S139-S155
4. Bell M.A., Orti G., Walker J.A., and Koenings J.P. Evolution of pelvic reduction in threespine stickleback fish: a test of competing hypotheses. Evolution 47 (1993) 906-914
5. Bergsten J. A review of long-branch attraction. Cladistics 21 (2005) 163-193
6. Blest A.D., and Taylor P.W. Cambridgea quadromaculata n. sp. (Araneae: Stiphidiidae): a large New Zealand spider from wet, shaded habitats. NZ J Zool 22 (1995) 351-356
7. Bond J.E., and Opell B.D. Testing adaptive radiation and key innovation hypotheses in spiders. Evolution 52 (1998) 403-414
8. Brandley M.C., Shmitz A., and Reeder T.W. Partitioned Bayesian analyses, partition choice, and the phylogeny of scincid lizards. Syst. Biol. 54 (2005) 373-390
9. Bristowe W.S. The classification of spiders. Proc. Zool. Soc. Lond. B 108 (1938) 285-322
10. Camin J.H., and Sokal R.R. A method for deducing branching sequences in phylogeny. Evolution 19 (1965) 311-326
11. Chenna R., Sugawara H., Koike T., Lopez R., Gibson T.J., Higgins D.G., and Thompson J.D. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res. 31 (2003) 3497-3500
12. Clements K.D., Gray R.D., and Choat J.H. Rapid evolutionary divergences in reef fishes of the family Acanthuridae (Perciformes: Teleostei). Mol. Phylogenet. Evol. 26 (2003) 190-201
13. Coddington J. The monophyletic origin of the orb web. In: Shear W.A. (Ed). Spiders: Webs, Behavior, and Evolution (1986), Stanford University Press, Stanford, CA 319-363
14. Coddington J.A., Giribet G., Harvey M.S., Prendini L., and Walter D.E. Arachnida. In: Cracraft J., and Donoghue M. (Eds). Assembling the Tree of Life (2004), Oxford University Press, New York 296-318
15. Coddington J.A., and Levi H.W. Systematics and evolution of spiders (Araneae). Ann. Rev. Ecol. Syst. 22 (1991) 565-592
16. Colgan D., McLauchlan A., Wilson G., and Livingston S. Histone H3 and U2 snRNA DNA sequences and arthropod molecular evolution. Aust. J. Zool. 46 (1998) 419-437
17. Croucher P.J.P., Oxford G.S., and Searle J.B. Mitochondrial differentiation, introgression and phylogeny of species in the Tegenaria atrica group (Araneae: Agelenidae). Biol. J. Linn. Soc. 81 (2004) 79-89
18. Day W.H.E. Optimal algorithms for comparing trees with labeled leaves. J. Classification 1 (1985) 7-28
19. de Blauwe R. Révision de la famille des Agelenidae (Araneae) de la région meditteranéenne. Bull. Institut. Roy. Sci. Nat. Belg. 49 (1973) 1-111
20. Domes K., Norton R.A., Maraun M., and Scheu S. Reevolution of sexuality breaks Dollo's law. Proc. Nat. Acad. Sci. USA 104 (2007) 7139-7144
21. Erwin D.H. A preliminary classification of evolutionary radiations. Historical Biol. 6 (1992) 133-147
22. Felsenstein J. Cases in which parsimony or compatibility methods will be positively misleading. Syst. Zool. 27 (1978) 401-410
23. Forster R.R., and Wilton C.L. The spiders of New Zealand. Part IV. Otago Mus. Bull. 4 (1973) 1-309
24. Giribet G., Carranza S., Baguña N., Riutort M., and Ribera C. First molecular evidence for the existence of a Tardigrada + Arthropoda clade. Mol. Biol. Evol. 13 (1996) 76-84
25. Giribet G., and Wheeler W.C. Some unusual small-subunit ribosomal DNA sequences of metazoans. Am. Mus. Novitat. 3337 (2001) 1-14
26. Goloboff P. Analyzing large data sets in reasonable times: solutions for composite optima. Cladistics 15 (1999) 415-428
27. Gray M.R., and Smith H.M. The "striped" group of stiphidiid spiders: two new genera from northeastern New South Wales, Australia (Araneae: Stiphidiidae: Amaurobioidea). Records Aust. Mus. 56 (2004) 123-128
28. Graybeal A. Is it better to add taxa or characters to a difficult phylogenetic problem?. Syst. Biol. 47 (1998) 9-17
29. Griswold C.E. Investigations into the phylogeny of the lycosid spiders and their kin (Arachnida: Araneae: Lycosoidea). Smithsonian Contrib. Zool. 539 (1993) 1-39
30. Griswold C.E., Coddington J., Hormiga G., and Scharff N. Phylogeny of the orb-web building spiders (Araneae, Orbiculariae: Deinopoidea, Araneoidea). Zool. J. Linn. Soc. 123 (1998) 1-99
31. Griswold C.E., Coddington J.A., Platnick N.I., and Forster R.R. Towards a phylogeny of entelegyne spiders (Araneae, araneomorphae, entelegynae). J. Arach. 27 (1999) 53-63
32. Griswold C.E., Ramirez M.J., Coddington J.A., and Platnick N.I. Atlas of phylogenetic data for entelegyne spiders. Proc. Cal. Acad. Sci. 56 (2005) 1-324
33. Hawthorn A.C., and Opell B.D. Evolution of adhesive mechanisms in cribellar spider prey capture thread: evidence for van der Waals and hygroscopic forces. Biol. J. Linn. Soc. 77 (2002) 1-8
34. Hedin M.C., and Bond J.E. 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. 41 (2006) 454-471
35. Hedin M.C., and Maddison W.P. A combined molecular approach to phylogeny of the jumping spider subfamily Dendryphantinae (Araneae: Salticidae). Mol. Phylogenet. Evol. 18 (2001) 386-403
36. Hendy M.D., and Penny D. A framework for the quantitative study of evolutionary trees. Syst. Zool. 38 (1989) 297-309
37. Hillis D.M., Huelsenbeck J.P., and Swofford D.L. Hobgoblin of phylogenetics?. Nature 369 (1994) 363-364
38. Homann H. Die Augen der Araneae: Anatomie, Ontogenese und Bedeutung fur die Systematik (Chelicerata, Arachnida). Zeitsch. Morph. Tiere 69 (1971) 201-272
39. Hunter J.P. Key innovations and the ecology of macroevolution. Trends Ecol. Evol. 13 (1998) 31-36
40. Ke-Ran B., and Kai-Ya Z. Phylogenetic position of the spider subfamily Coelotinae (Araneae) inferred from nuclear rDNA gene sequences. Acta Zool. Sin. 51 (2005) 521-525
41. Kennedy M., Paterson A.M., Morales J.C., Parsons S., Winnington A.P., and Spencer H.G. The long and short of it: branch lengths and the problem of placing the New Zealand short-tailed bats, Mystacina. Mol. Phylogenet. Evol. 13 (1999) 405-416
42. Kjer K.M. Aligned 18S and insect phylogeny. Syst. Biol. 53 (2004) 506-514
43. Lande R. Evolutionary mechanisms of limb-loss in tetrapods. Evolution 32 (1978) 73-92
44. Lanyon S.M. Detecting internal inconsistencies in distance data. Syst. Zool. 34 (1985) 397-403
45. Lehtinen P. Classification of the cribellate spiders and some allied families. Ann. Zool. Fenn. 5 (1967) 199-468
46. Lunt D.H., Zhang D.-X., Szymura J.M., and Hewitt G.M. The insect cytchrome oxidase I gene: evolutionary patterns and conserved primers for phylogenetic studies. Insect Mol. Biol. 5 (1996) 153-165
47. Maddison W.P., Donoghue M.J., and Maddison D.R. Outgroup analysis and parsimony. Syst. Zool. 33 (1984) 83-103
48. Maddison W.P., and Hedin M.C. Jumping spider phylogeny (Araneae: Salticidae). Invert. Syst. 17 (2003) 529-549
49. Maddison, W.P., Maddison, D.R., 2005. MacClade: Analysis of Phylogenetic and Character Evolution. Sinauer and Associates.
50. Mallatt J.M., Garey J.R., and Shultz J.W. Ecdysozoan phylogeny and Bayesian inference first use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Mol. Phylogenet. Evol. 31 (2004) 178-191
51. Miller A.H. Some ecologic and morphologic considerations in the evolution of higher taxonomic categories. In: Mayr E., and Schuz E. (Eds). Ornithologie als Biologische Wissenschaft (1949), Carl Winter 84-88
52. Nardi F., Spinsanti G., Boore J.L., Carapelli A., Dallai R., and Frati F. Hexapod origins: monophyletic or paraphyletic?. Science 299 (2003) 1887-1889
53. Nixon K. The parsimony ratchet, a new method for rapid parsimony analysis. Cladistics 15 (1999) 407-414
54. Nylander, J.A.A., 2004. MrModeltest. version 2.2, .
55. Ogden T.H., and Rosenberg M. Alignment and topological accuracy of the direct optimization approach via POY and traditional phylogenetics via Clustal W + Paup. Syst. Biol. 56 (2007) 182-193
56. Opell B.D. A comparison of capture thread and architectural features of deinopoid and araneoid orb-webs. J. Arach. 25 (1997) 295-306
57. Page, R.D.M., 1993. Component. Natural History Museum of London, London.
58. Palmer J.D., Soltis D.E., and Chase M.W. The plant tree of life: an overview and some points of view. Am. J. Bot. 91 (2004) 1437-1445
59. Platnick N.I. The hypochiloid spiders: a cladistic analysis, with notes on the Atypoidea (Arachnida, Araneae). Am. Mus. Novitat 2627 (1977) 1-23
60. Platnick, N.I., 2007. The World Spider Catalog Version 7.5. American Museum of Natural History, .
61. Platnick N.I., Coddington J.A., Forster R.R., and Griswold C.E. Spinneret evidence and the higher classification of the haplogyne spiders. Am. Mus. Novitat. 3016 (1991) 1-73
62. Platnick N.I., and Gertsch W. The suborders of spiders : a cladistic analysis (Arachnida, Araneae). Am. Mus. Novitat. 2607 (1976) 1-15
63. Pons J., and Vogler A.P. Size, frequency, and phylogenetic signal of multiple-residue indels in sequence alignment of introns. Cladistics 22 (2006) 144-156
64. Posada D., and Crandall K.A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
65. Reeder T.W. A phylogeny of the Australian Sphenomorphus group (Scincidae: Squamata) and the phylogenetic placement of the crocodile skinks (Tribolonotus): Bayesian approaches to assessing congruence and obtaining confidence in maximum likelihood inferred relationships. Mol. Phylogenet. Evol. 27 (2003) 384-397
66. Rohde K. Robust phylogenies and adaptive radiations: a critical examination of methods used to identify key innovations. Am. Nat. 148 (1996) 481-500
67. Ronquist F., and Huelsenbeck J.P. MrBayes 3: Phylogenetic inference under mixed models. Bioinformatics 19 (2003) 1572-1574
68. Roth V.D., and Brame P.L. Nearctic genera of the spider family Agelenidae (Arachnida, Araneida). Am. Mus. Novitat. 2505 (1972) 1-52
69. Sanger F., Nicklen S., and Coulson A.R. DNA sequencing with chain-terminating inhibitors. Proc. Nat. Acad. Sci. USA 74 (1977) 5463-5467
70. Selden P.A. Missing links between Argyroneta and Cybaeidae revealed by fossil spiders. J. Arach. 30 (2002) 189-200
71. Siddall M.E. Another monophyly index: revisiting the jackknife. Cladistics 11 (1995) 33-56
72. Silva Davila D. Higher-level relationships of the spider family Ctenidae (Araneae: Ctenoidea). Bull. Am. Mus. Nat. Hist. 274 (2003) 1-86
73. Simon, E., 1892. Histoire naturelle des araignees, Paris.
74. Swofford D., Waddell P.J., Huelsenbeck J.P., Foster P.G., Lewis P.O., and Rogers J.S. Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods. Syst. Biol. 50 (2001) 525-539
75. Szymura J.M., Lunt D.H., and Hewitt G.M. The sequence and structure of the meadow grasshopper (Chorthippus parallelus) mitochondrial srRNA, ND2, COI, COII, ATPase8 and 9 tRNA genes. Insect Mol. Biol. 5 (1996) 127-139
76. Tanaka M., Hale L.A., Amores A., Yan Y.-L., Cresko W.A., Suzuki T., and Postlethwait J.H. Developmental genetic basis for the evolution of pelvic fin loss in the pufferfish Takifugu rubripes. Dev. Biol. 281 (2005) 227-239
77. Terry M.D., and Whiting M.F. Comparison of two alignment techniques within a single complex data set: POY versus Clustal. Cladistics 21 (2005) 272-281
78. Thompson J.D., Gibson T.J., Plewniak F., Jeanmougin F., and Higgins D.G. The Clustal_X windows interface: flexible strategies for multiple sequence alignment aided by quality alignment tools. Nucleic Acids Res. 25 (1997) 4876-4882
79. Tourasse N.J., and Gouy M. Accounting for evolutionary rate variation among sequence sites consistently changes universal phylogenies deduced from rRNA and protein-coding genes. Mol. Phylogenet. Evol. 31 (1999) 159-168
80. van Valen L.M. Adaptive zones and the orders of mammals. Evolution 25 (1971) 420-428
81. Vandergast A.G., Gillespie R.G., and Roderick G.K. Influence of volcanic activity on the population genetic structure of Hawaiian Tetragnatha spiders: fragmentation, rapid population growth and the potential for accelerated evolution. Mol. Ecol. 13 (2004) 1729-1743
82. Wang X.P. A generic-level revision of the spider subfamily Coelotinae (Araneae: Amaurobiidae). Bull. Am. Mus. Nat. Hist. 269 (2002) 1-150
83. Wang X.P. Species revision of the coelotine spider genera Bifidocoelotes, Coronilla, Draconarius, Femoracoelotes, Leptocoelotes, Longicoelotes, Platocoelotes, Spiricoelotes, Tegecoelotes, and Tonsilla (Araneae, Amaurobiidae). Proc. Cal. Acad. Sci. 54 (2003) 499-662
84. Wang, X.P., 2007. Online Coelotinae, version 2.0., .
85. Wenzel J.W., and Siddall M.E. Noise. Cladistics 15 (1998) 51-64
86. Wheeler W.C. Sequence alignment, parameter sensitivity, and the phylogenetic analysis of molecular data. Syst. Biol. 44 (1995) 321-331
87. Wheeler W.C. Optimization alignment: the end of multiple sequence alignment in phylogenetics?. Cladistics 12 (1996) 1-9
88. Wheeler W.C., Aagesen L., Arango C.P., Grant T., Janies D., Varon A., Faivovich J., D'Haese C.A., Smith W.L., and Giribet G. Dynamic homology and phylogenetic systematics: A unified approach using POY (2006), American Museum of Natural History, New York
89. Wheeler, W.C., Gladstein, D.S., De Laet, J. 1996-2003. POY. Version 3.0 ftp.amnh.org/pub/molecular/POY [current version 3.0.11]. Documentation by Daniel Janies and Ward Wheeler. Command line documentation by Daniel Janies and Ward Wheeler.
90. Wheeler W.C., and Hayashi C.Y. The phylogeny of the extant chelicerate orders. Cladistics 14 (1998) 173-192
91. Whitfield J.B., and Lockhart P.J. Deciphering ancient rapid radiations. Trends Ecol. Evol. 22 (2007) 258-265
92. Whiting M.F., Bradler S., and Maxwell T. Loss and recovery of wings in stick insects. Nature 421 (2003) 264-267
93. Wiens J.J. Missing data, incomplete taxa, and phylogenetic accuracy. Syst. Biol. 52 (2003) 528-538
94. Wiens J.J. Can incomplete taxa rescue phylogenetic analyses from long-branch attraction?. Syst. Biol. 54 (2005) 731-742
95. Wilgenbusch J.C., Warren D.L., Swofford D.L., 2004. AWTY: a system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference, .
96. Wunderlich J. Spinnenfauna gestern und heute: Fossile Spinnen in Bernstein und ihre heute lebenden Verwandten (1986), Quelle and Meyer, Wiesbaden
97. Wunderlich, J., 1995. Beschreibung einer bisher unbekannten Art der Gattung Cryphoeca Thorell 1870 aus der Türkei (Arachnida: Araneae: Dictynoidea: ?Dictynidae). Beiträge zur Araneologie 4, 719-721.
98. Wunderlich J. Fossil spiders (Araneae) of the family Dictynidae s. l., including Cryphoecinae and Hahniinae in Baltic and Dominican amber and copal from Madagascar, and on selected extant Holarctic taxa, with new descriptions and diagnoses. Beitrage zur Araneologie 3 (2004) 1380-1482
99. Yang Z., and Rannala B. Bayesian phylogenetic inference using DNA sequences: a Markov chain Monte Carlo method. Mol. Biol. Evol. 14 (1997) 717-724