Phylogeny and classification of the trapdoor spider genus Myrmekiaphila: An integrative approach to evaluating taxonomic hypotheses

PLoS ONE

Volumn 5, Issue 9, 2010, Pages 1-15

  Bailey, Ashley L ^a   Brewer, Michael S ^a   Hendrixson, Brent E ^b   Bond, Jason E ^a  

^a EAST CAROLINA UNIVERSITY   (United States)

^b MILLSAPS COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID TRANSFER RNA LIGASE; CELL NUCLEUS DNA; MITOCHONDRIAL DNA; RIBOSOME RNA; RNA 12S; RNA 16S; TRANSFER RNA; RNA, RIBOSOMAL, 12S;

ANIMAL TISSUE; ARTICLE; BAYES THEOREM; CLASSIFICATION; CONTROLLED STUDY; DNA BARCODING; GENETIC IDENTIFICATION; GENOME ANALYSIS; MALE; MITOCHONDRIAL GENOME; MOLECULAR TYPING; MYRMEKIAPHILA; MYRMEKIAPHILA COREYI; MYRMEKIAPHILA HOWELLI; MYRMEKIAPHILA MILLERAE; MYRMEKIAPHILA TORREYA; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; SPECIES DIFFERENCE; SPECIES IDENTIFICATION; SPIDER; ANIMAL; GENETIC PROCEDURES; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS;

NEMESIIDAE; TORREYA;

ANIMALS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENETIC TECHNIQUES; MALE; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 16S; SPIDERS;

EID: 77958580700     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0012744     Document Type: Article

References (78)

1. Will K, Rubinoff D (2004) Myth of the molecule: DNA barcodes for species cannot replace morphology for identification and classification. Cladistics 20: 47–55.
2. Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003) Biological identifications through DNA barcodes. Proceedings of the Royal Society of London Series B-Biological Sciences 270: 313-321.
3. Hebert PDN, Gregory TR (2005) The promise of DNA barcoding for taxonomy. Systematic Biology 54: 852-859.
4. Valentini A, Pompanon F, Taberlet P (2009) DNA barcoding for ecologists. Trends in Ecology & Evolution 24: 110-117.
5. Pons J, Barraclough TG, Gomez-Zurita J, Cardoso A, Duran DP, et al. (2006) Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biol 55: 595-609.
6. O'Meara BC (2010) New Heuristic Methods for Joint Species Delimitation and Species Tree Inference. Systematic Biololgy 59: 59-73.
7. Hurst GDD, Jiggins FM (2005) Problems with mitochondrial DNA as a marker in population, phylogeographic and phylogenetic studies: the effects of inherited symbionts. Proceedings of the Royal Society B-Biological Sciences 272: 1525-1534.
8. Ballard JWO, Rand DM (2005) The population biology of mitochondrial DNA and its phylogenetic implications. Annual Review of Ecology Evolution and Systematics 36: 621-642.
9. Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Molecular Ecology 13: 729-744.
10. Wares JP (2010) Natural Distributions of Mitochondrial Sequence Diversity Support New Null Hypotheses. Evolution 64: 1136-1142.
11. Funk DJ, Omland KE (2003) Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Annual Review of Ecology Evolution and Systematics 34: 397-423.
12. Bickford D, Lohman DJ, Sodhi NS, Ng PKL, Meier R, et al. (2007) Cryptic species as a window on diversity and conservation. Trends in Ecology & Evolution 22: 148-155.
13. Bond JE, Sierwald P (2002) Cryptic speciation in the Anadenobolus excisus millipede species complex on the Island of Jamaica. Evolution 56: 1123-1135.
14. Bond JE, Stockman AK (2008) An Integrative Method for Delimiting Cohesion Species: Finding the Population-Species Interface in a Group of Californian Trapdoor Spiders with Extreme Genetic Divergence and Geographic Structuring. Systematic Biology 57: 628-646.
15. Ross KG, Gotzek D, Ascunce MS, Shoemaker DD (2010) Species Delimitation: A Case Study in a Problematic Ant Taxon. Systematic Biology 59: 162-184.
16. Agnarsson I, Kuntner M (2007) Taxonomy in a changing world: Seeking solutions for a science in crisis. Systematic Biology 56: 531-539.
17. Wheeler Q (2004) Taxonomic triage and the poverty of phylogeny. Philosophical Transactions Of The Royal Society Of London Series BBiological Sciences 359: 571-583.
18. Korf R (2005) Reinventing taxonomy: a curmudgeon's view of 250 years of fungal taxonomy, the crisis in biodiversity, and the pitfalls of the phylogenetic age. Mycotaxon 93: 407-415.
19. Rodman J, Cody J (2003) The taxonomic impediment overcome: NSF's partnerships for enhancing expertise in taxonomy (PEET) as a model. Systematic Biology 52: 428-435.
20. Paquin P, Hedin M (2004) The power and perils of 'molecular taxonomy': a case study of eyeless and endangered Cicurina (Araneae: Dictynidae) from Texas caves. Molecular Ecology 13: 3239-3255.
21. Bond J, Hedin M, Ramirez M, Opell B (2001) Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus. Molecular Ecology 10: 899-910.
22. Robinson EA, Blagoev GA, Hebert PDN, Adamowicz SJ (2009) Prospects for using DNA barcoding to identify spiders in species-rich genera. Zookeys. pp 27-46.
23. Wiens JJ, Penkrot TA (2002) Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Systematic Biology 51: 69-91.
24. Bond JE (2004) Systematics of the Californian euctenizine spider genus Apomastus (Araneae: Mygalomorphae: Cyrtaucheniidae): the relationship between molecular and morphological taxonomy. Invertebrate Systematics 18: 361-376.
25. Bond JE (2004) Systematics of the Californian euctenizine spider genus Apomastus (Araneae: Mygalomorphae: Cyrtaucheniidae): the relationship between molecular and morphological taxonomy. Invertebrate Systematics 18: 361-376.
26. Atkinson GF (1886) Descriptions of some New Trap-Door Spiders; Their Notes and Food habits. Entomologica Americana 2: 109-117.
27. Hedin M, Bond JE (2006) Molecular phylogenetics of the spider infraorder Mygalomorphae using nuclear rRNA genes (18S and 28S): Conflict and agreement with the current system of classification. Molecular Phylogenetics and Evolution 41: 454-471.
28. Bond JE, Platnick NI (2007) A taxonomic review of the trapdoor spider genus Myrmekiaphila (Araneae, Mygalomorphae, Cyrtaucheniidae). American Museum Novitates. pp 1-30.
29. de Queiroz K (1998) The general lineage concept of species, species criteria, and the process of speciation. In: Howard DJ, Berlocher SH, eds. Endless Forms: Species and Speciation. Oxford, UK: Oxford University Press. pp 57-75.
30. de Queiroz K (1999) The general lineage concept of species and the defining properties of the species category. In: Wilson RA, ed. Species, New Interdisciplinary Essays. Cambridge, Massachusetts: MIT Press. pp 49-90.
31. Swofford DL (2002) PAUP*. Phylogenetic Analysis Using Parsimony (and Other Methods), Version 4.0b8a. 4.0b8a ed. Sunderland, Massachusetts: Sinauer Associates.
32. Bond JE, Hedin M (2006) A total evidence assessment of the phylogeny of North American euctenizine trapdoor spiders (Araneae, Mygalomorphae, Cyrtaucheniidae) using Bayesian inference. Molecular Phylogenetics and Evolution 41: 70-85.
33. Bond JE, Opell BD (2002) Phylogeny and taxonomy of the genera of southwestern North American Euctenizinae trapdoor spiders and their relatives (Araneae: Mygalomorphae, Cyrtaucheniidae). Zoological Journal of the Linnean Society 136: 487-539.
34. Huber B (2004) The significance of copulatory structures in spider systematics. In: Shult J, ed. Biosemiotik Praktische Anwendung und Konsequenzen für die Einzelwissenschaften Berlin: VWB-Verlag. pp 89-100.
35. Astrin JJ, Huber BA, Bernhard M, Kluetsch CFC (2006) Molecular taxonomy in pholcid spiders (Pholcidae, Araneae): evaluation of species identification methods using CO1 and 16S rRNA. Zoologica Scripta 35: 441-457.
36. Bond JE, Beamer DA, Hedin MC, Sierwald P (2003) Gradual evolution of male genitalia in a sibling species complex of millipedes (Diplopoda: Spirobolida: Rhinocricidae: Anadenobolus). Invertebrate Systematics 17: 711-717.
37. Eberhard WG (1985) Sexual Selection and Animal Genitalia. Cambridge, Massachusetts: Harvard University Press.
38. Eberhard WG (1987) Runaway Sexual Selection - Why Do Taxonomists Spend So Much Time Studying Genitalia. Natural History 96: 4-&.
39. Butlin R (1987) Species, speciation, and reinforcement. American Naturalist 130: 461-464.
40. Butlin R (1995) Reinforcement: an idea evolving. Trends in Ecology & Evolution 10: 432-434.
41. Dobzhansky T (1940) Speciation as a stage in evolutionary divergence. American Naturalist 74: 312-321.
42. Rice W, Hostert E (1993) Laboratory experiments on speciation: what have we learned in 40 years? Evolution 47: 1637-1653.
43. Rundle H, Schluter D (1998) Reinforcement of stickleback mate preferences: sympatry breeds contempt. Evolution 52: 200-208.
44. Servedio M, Noor M (2003) The role of reinforcement in speciation: Theory and data. Annual Review of Ecology and Systematics 34: 339-364.
45. Kameda Y, Kawakita A, Kato M (2009) Reproductive Character Displacement in Genital Morphology in Satsuma Land Snails. American Naturalist 173: 689-697.
46. Tanabe T, Sota T (2008) Complex copulatory behavior and the proximate effect of genital and body size differences on mechanical reproductive isolation in the millipede genus Parafontaria. American Naturalist 171: 692-699.
47. Collin R, Miglietta MP (2008) Reversing opinions on Dollo's Law. Trends in Ecology & Evolution 23: 602-609.
48. Goldberg EE, Igic B (2008) On Phylogenetic Tests of Irrereversible Evolution. Evolution 62: 2727-2741.
49. Song HJ, Bucheli SR (2010) Comparison of phylogenetic signal between male genitalia and non-genital characters in insect systematics. Cladistics 26: 23-35.
50. Hendrixson BE, Bond JE (2005) Testing species boundaries in the Antrodiaetus unicolor complex (Araneae: Mygalomorphae: Antrodiaetidae): "Paraphyly" and cryptic diversity. Molecular Phylogenetics and Evolution 36: 405-416.
51. Metzger GA, Kraus F, Allison A, Parkinson CL (2010) Uncovering cryptic diversity in Aspidomorphus (Serpentes: Elapidae): Evidence from mitochondrial and nuclear markers. Molecular Phylogenetics and Evolution 54: 405-416.
52. Albert EM, Fernandez A (2009) Evidence of cryptic speciation in a fossorial reptile: description of a new species of Blanus (Squamata: Amphisbaenia: Blanidae) from the Iberian Peninsula. Zootaxa. pp 56-68.
53. Hedin M, Thomas SM (2010) Molecular systematics of eastern North American Phalangodidae (Arachnida: Opiliones: Laniatores), demonstrating convergent morphological evolution in caves. Molecular Phylogenetics and Evolution 54: 107-121.
54. Starrett J, Hedin M (2007) Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae). Molecular Ecology 16: 583-604.
55. Bond J, Beamer D, Lamb T, Hedin M (2006) Combining genetic and geospatial analyses to infer population extinction in mygalomorph spiders endemic to the Los Angeles region. Anim Conserv 9: 145-157.
56. Stockman AK, Bond JE (2007) Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability. Molecular Ecology 16: 3374-3392.
57. Stockman AK, Bond JE (2008) A taxonomic review of the trapdoor spider genus Promyrmekiaphila Schenkel (Araneae, Mygalomorphae, Cyrtaucheniidae, Euctenizinae). Zootaxa. pp 25-41.
58. Huang D, Meier R, Todd PA, Chou LM (2009) More evidence for pervasive paraphyly in scleractinian corals: Systematic study of Southeast Asian Faviidae (Cnidaria; Scleractinia) based on molecular and morphological data. Molecular Phylogenetics and Evolution 50: 102-116.
59. Meier R, Zhang GY, Ali F (2008) The Use of Mean Instead of Smallest Interspecific Distances Exaggerates the Size of the "Barcoding Gap" and Leads to Misidentification. Systematic Biology 57: 809-813.
60. Regier JC, Shultz JW, Ganley ARD, Hussey A, Shi D, et al. (2008) Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein- Coding Nuclear Gene Sequence. Systematic Biology 57: 920-938.
61. Tan DSH, Ang Y, Lim GS, Bin Ismail MR, Meier R (2010) From 'cryptic species' to integrative taxonomy: an iterative process involving DNA sequences, morphology, and behaviour leads to the resurrection of Sepsis pyrrhosoma (Sepsidae: Diptera). Zoologica Scripta 39: 51-61.
62. Will KW, Mishler BD, Wheeler QD (2005) The perils of DNA barcoding and the need for integrative taxonomy. Systematic Biology 54: 844-851.
63. Meier R (2008) DNA Sequences in Taxonomy: Opportunities and Challenges. In: Wheeler Q, ed. The New Taxonomy. Boca Raton, Florida: CRC Press, Taylor Francis Group. pp 95-127.
64. Maddison DR, Maddison WP (2000) MACCLADE 4: Analysis of Phylogeny and Character Evolution, Version 4.0. Sunderland, MA: Sinauer Associates.
65. Lou M, Golding GB (2007) FINGERPRINT: visual depiction of variation in multiple sequence alignments. Molecular Ecology Notes 7: 908-914.
66. Hendrixson BE, Bond JE (2007) Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus). Molecular Phylogenetics and Evolution 42: 738-755.
67. Simon C, Frati F, Beckenbach A, Crespi B, Liu H, et al. (1994) Evolution, Weighting, and Phylogenetic Utility of Mitochondrial Gene-Sequences and a Compilation of Conserved Polymerase Chain-Reaction Primers. Annals of the Entomological Society of America 87: 651-701.
68. Regier JC, Shultz JW, Ganley ARD, Hussey A, Shi D, et al. (2008) Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein- Coding Nuclear Gene Sequence. Syst Biol 57: 920-938.
69. Edgar RC (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity. Bmc Bioinformatics 5: 1-19.
70. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-1797.
71. Maddison WP, Maddison DR (2009) Mesquite: a modular system for evolutionary analysis. Version 2.7 ed.
72. Tanabe AS (2007) KAKUSAN: a computer program to automate the selection of a nucleotide substitution model and the configuration of a mixed model on multilocus data. Molecular Ecology Notes 7: 962-964.
73. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
74. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17: 754-755.
75. Rambaut A, Drummond A (2009) Tracer MCMC Trace Analysis Package. 1.5 ed.
76. Kass RE, Raftery AE (1995) Bayes Factors. Journal of the American Statistical Association 90: 773-795.
77. Lewis PO (2001) A likelihood approach to estimating phylogeny from discrete morphological character data. Systematic Biology 50: 913-925.
78. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology 53: 47-67.