Phylogenomics resolves a spider backbone phylogeny and rejects a prevailing paradigm for orb web evolution

Current Biology

Volumn 24, Issue 15, 2014, Pages 1765-1771

  Bond, Jason E ^a   Garrison, Nicole L ^a   Hamilton, Chris A ^a   Godwin, Rebecca L ^a   Hedin, Marshal ^b   Agnarsson, Ingi ^c  

^a AUBURN UNIVERSITY   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

^c UNIVERSITY OF VERMONT   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARANEAE; ARANEIDAE; ARANEOIDEA; ARTHROPODA; DEINOPOIDEA;

ARTHROPOD PROTEIN;

ANIMAL; CLASSIFICATION; DNA SEQUENCE; EVOLUTION; GENETICS; MOLECULAR GENETICS; PHYLOGENY; PHYSIOLOGY; PREDATION; SPIDER;

ANIMALS; ARTHROPOD PROTEINS; BIOLOGICAL EVOLUTION; MOLECULAR SEQUENCE DATA; PHYLOGENY; PREDATORY BEHAVIOR; SEQUENCE ANALYSIS, DNA; SPIDERS;

EID: 84905657657     PISSN: 09609822     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cub.2014.06.034     Document Type: Article

References (37)

1. I. Agnarsson, J.A. Coddington, and M. Kuntner Systematics: progress in the study of spider diversity and evolution D. Penney, Spider Research in the 21st Century 2013 Siri Scientific Press Manchester 58 111
2. Platnick, N.I. (2014). The World Spider Catalog v 14.5. The World Spider Catalog. http://research.amnh.org/iz/spiders/catalog/INTRO1.html.
3. I. Agnarsson, M. Kuntner, and T.A. Blackledge Bioprospecting finds the toughest biological material: extraordinary silk from a giant riverine orb spider PLoS ONE 5 2010 e11234
4. C.Y. Hayashi, T.A. Blackledge, and R.V. Lewis Molecular and mechanical characterization of aciniform silk: uniformity of iterated sequence modules in a novel member of the spider silk fibroin gene family Mol. Biol. Evol. 21 2004 1950 1959
5. J. Gui, B. Liu, G. Cao, A.M. Lipchik, M. Perez, Z. Dekan, M. Mobli, N.L. Daly, P.F. Alewood, and L.L. Parker et al. A tarantula-venom peptide antagonizes the TRPA1 nociceptor ion channel by binding to the S1-S4 gating domain Curr. Biol. 24 2014 473 483
6. G.F. King, and M.C. Hardy Spider-venom peptides: structure, pharmacology, and potential for control of insect pests Annu. Rev. Entomol. 58 2013 475 496
7. J.A. Coddington Phylogeny and classification of spiders D. Ubick, P. Paquin, P.E. Cushing, V. Roth, Spiders of North America an Identification Manual 2005 American Arachnological Society Poughkeepsie 18 24
8. C.E. Griswold, M.J. Ramirez, J.A. Coddington, and N.I. Platnick Atlas of phylogenetic data for entelegyne spiders (Araneae: Araneomorphae: Entelegynae) with comments on their phylogeny Proc. Cal. Acad. Sci. 56 Suppl 2 2005 1 324
9. B. Roure, D. Baurain, and H. Philippe Impact of missing data on phylogenies inferred from empirical phylogenomic data sets Mol. Biol. Evol. 30 2013 197 214
10. A.R. Lemmon, J.M. Brown, K. Stanger-Hall, and E.M. Lemmon The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and Bayesian inference Syst. Biol. 58 2009 130 145
11. K.M. Kocot, J.T. Cannon, C. Todt, M.R. Citarella, A.B. Kohn, A. Meyer, S.R. Santos, C. Schander, L.L. Moroz, B. Lieb, and K.M. Halanych Phylogenomics reveals deep molluscan relationships Nature 477 2011 452 456
12. J.E. Bond, B.E. Hendrixson, C.A. Hamilton, and M. Hedin A reconsideration of the classification of the spider infraorder Mygalomorphae (Arachnida: Araneae) based on three nuclear genes and morphology PLoS ONE 7 2012 e38753
13. R.J. Raven The spider infraorder mygalomorphae (Araneae): cladistics and systematics Bull. Am. Mus. Nat. Hist. 182 1985 1 180
14. J.E. Bond, and B.D. Opell Testing adaptive radiation and key innovation hypotheses in spiders Evolution 52 1998 403 414
15. T.A. Blackledge, N. Scharff, J.A. Coddington, T. Szüts, J.W. Wenzel, C.Y. Hayashi, and I. Agnarsson Reconstructing web evolution and spider diversification in the molecular era Proc. Natl. Acad. Sci. USA 106 2009 5229 5234
16. G. Hormiga, and C.E. Griswold Systematics, phylogeny, and evolution of orb-weaving spiders Annu. Rev. Entomol. 59 2014 487 512
17. B. Hausdorf Molecular phylogeny of araneomorph spiders J. Evol. Biol. 12 1999 980 985
18. N.A. Ayoub, J.E. Garb, M. Hedin, and C.Y. Hayashi Utility of the nuclear protein-coding gene, elongation factor-1 gamma (EF-1gamma), for spider systematics, emphasizing family level relationships of tarantulas and their kin (Araneae: Mygalomorphae) Mol. Phylogenet. Evol. 42 2007 394 409
19. D. Dimitrov, L. Lopardo, G. Giribet, M.A. Arnedo, F. Alvarez-Padilla, and G. Hormiga Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling Proc. Biol. Sci. 279 2012 1341 1350
20. J. Starrett, M. Hedin, N. Ayoub, and C.Y. Hayashi Hemocyanin gene family evolution in spiders (Araneae), with implications for phylogenetic relationships and divergence times in the infraorder Mygalomorphae Gene 524 2013 175 186
21. R.M. Fernández, G. Hormiga, and G. Giribet Phylogenomic analysis of spiders reveals nonmonophyly of orb weavers Curr. Biol. 2014 10.1016/j.cub.2014.06.035 Published online July 17, 2014
22. P.A. Selden, C. Shih, and D. Ren A giant spider from the Jurassic of China reveals greater diversity of the orbicularian stem group Naturwissenschaften 100 2013 1171 1181
23. M.G. Grabherr, B.J. Haas, M. Yassour, J.Z. Levin, D.A. Thompson, I. Amit, X. Adiconis, L. Fan, R. Raychowdhury, and Q. Zeng et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome Nat. Biotechnol. 29 2011 644 652
24. I. Ebersberger, S. Strauss, and A. von Haeseler HaMStR: profile hidden markov model based search for orthologs in ESTs BMC Evol. Biol. 9 2009 157
25. K. Katoh, K. Misawa, K.I. Kuma, and T. Miyata MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform Nucleic Acids Res. 30 2002 3059 3066
26. B. Roure, N. Rodriguez-Ezpeleta, and H. Philippe SCaFoS: a tool for selection, concatenation and fusion of sequences for phylogenomics BMC Evol. Biol. 7 Suppl 1 2007 S2
27. J. Castresana Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis Mol. Biol. Evol. 17 2000 540 552
28. P. Kück, K. Meusemann, J. Dambach, B. Thormann, B.M. von Reumont, J.W. Wägele, and B. Misof Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees Front. Zool. 7 2010 10
29. P. Kück, and K. Meusemann FASconCAT: Convenient handling of data matrices Mol. Phylogenet. Evol. 56 2010 1115 1118
30. M.S. Brewer, and J.E. Bond Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses PLoS ONE 8 2013 e79935
31. L. Liu, L. Yu, D.K. Pearl, and S.V. Edwards Estimating species phylogenies using coalescence times among sequences Syst. Biol. 58 2009 468 477
32. L. Liu, L. Yu, and S.V. Edwards A maximum pseudo-likelihood approach for estimating species trees under the coalescent model BMC Evol. Biol. 10 2010 302
33. L. Liu, and L. Yu Estimating species trees from unrooted gene trees Syst. Biol. 60 2011 661 667
34. A. Stamatakis RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies Bioinformatics 30 2014 1312 1313
35. P.A. Goloboff, J.S. Farris, and K.C. Nixon TNT, a free program for phylogenetic analysis Cladistics 24 2008 774 786
36. H. Shimodaira, and M. Hasegawa CONSEL: for assessing the confidence of phylogenetic tree selection Bioinformatics 17 2001 1246 1247
37. K. Tamura, F.U. Battistuzzi, P. Billing-Ross, O. Murillo, A. Filipski, and S. Kumar Estimating divergence times in large molecular phylogenies Proc. Natl. Acad. Sci. USA 109 2012 19333 19338