Multilocus species delimitation in a complex of morphologically conserved trapdoor spiders (mygalomorphae, antrodiaetidae, Aliatypus)

Systematic Biology

Volumn 62, Issue 6, 2013, Pages 805-823

  Satler, Jordan D ^a   Carstens, Bryan C ^a   Hedin, Marshal ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b UNIVERSITY OF SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTOCHROME C OXIDASE; ELONGATION FACTOR 1; MICROTUBULE PROTEIN; RIBOSOME DNA;

ANIMAL; ARTICLE; CLASSIFICATION; GENETICS; HISTOLOGY; PHYLOGENY; REPRODUCIBILITY; SPECIES DIFFERENCE; SPIDER; UNITED STATES;

ANIMALS; CALIFORNIA; DNA, RIBOSOMAL; ELECTRON TRANSPORT COMPLEX IV; MICROTUBULE PROTEINS; PEPTIDE ELONGATION FACTOR 1; PHYLOGENY; REPRODUCIBILITY OF RESULTS; SPECIES SPECIFICITY; SPIDERS;

EID: 84885964273     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/syt041     Document Type: Article

References (98)

1. Arnedo M. A., Ferrandez M. 2007. Mitochondrial markers reveal deep population subdivision in the European protected spider Macrothele calpeiana (Walckenaer, 1805) (Araneae, Hexathelidae). Conserv. Genet. 8:1147-1162.
2. Bailey T. H., Jahns R. H. 1954. Geology of the Transverse Range province, southern California. California Div. Mines and Geology Bull. 170:83-106.
3. Barrett C. F., Freudenstein J. V. 2011. An integrative approach to delimiting species in a rare but widespread mycoheterotrophic orchid. Mol. Ecol. 20:2771-2786.
4. Beerli P., Felsenstein J. 1999. Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach. Genetics. 152:763-773.
5. Beerli P., Felsenstein J. 2001. Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach. Proc. Natl. Acad. Sci. USA. 98:4563-4568.
6. Bickford D., Lohman D. J., Sodhi N. S., Ng P. K. L., Meier R., Winker K., Ingram K. K., Das I. 2007. Cryptic species as a window on diversity and conservation. Trends Ecol. Evol. 22:148-155.
7. Bond J. E. 2012. Phylogenetic treatment and taxonomic revision of the trapdoor spider genus Aptostichus Simon (Araneae: Mygalomorphae: Euctenizidae). Zookeys. 252:1-209.
8. Bond J. E., Beamer D. A., Lamb T., Hedin M. 2006. Combining genetic and geospatial analyses to infer population extinction in mygalomorph spiders endemic to the Los Angeles region. Animal Conservation. 9:145-157.
9. Bond J. E., Hedin M. C., Ramirez M. G., Opell B. D. 2001. Deep molecular divergence in the absence of morphological and ecological change in the Californian coastal dune endemic trapdoor spider Aptostichus simus. Mol. Ecol. 10:899-910.
10. Bond J. E., Hendrixson B. E., Hamilton C. A., Hedin M. 2012. A reconsideration of the classification of the spider infraorder mygalomorphae (Arachnida: Araneae) based on three nuclear genes and morphology. PLoS ONE. 7(6):e38753.
11. Bond J. E., Stockman A. K. 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. Syst. Biol. 57:628-646.
12. Brito P. H., Edwards S. V. 2009. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica. 135:439-455.
13. Burnham K. P., Anderson D. A. 2002. Model selection and multimodel inference: a practical information-theoretic approach. 2nd ed. New York: Springer. p. 488.
14. Buwalda J. P. 1954. Geology of the Tehachapi Mountains, California. California Div. Mines and Geology Bull. 170:131-142.
15. Calsbeek R., Thompson J. N., Richardson J. E. 2003. Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province. Mol. Ecol. 12:1021-1029.
16. Camargo A., Morando M., Avila L. J., Sites J. W. 2012. Species delimitation with ABC and other coalescent-based methods: a test of accuracy with simulations and an empirical example with lizards of the Liolaemus darwinii complex (Squamata: Liolaemidae). Evolution. 66:2834-2849.
17. Carstens B. C., Dewey T. A. 2010. Species delimitation using a combined coalescent and information-theoretic approach: an example from North American Myotis bats. Syst. Biol. 59:400-414.
18. Carstens B. C., Satler J. D. 2013. The carnivorous plant described as Sarracenia alata contains two cryptic species. Biol. J. Linn. Soc. doi: 10.1111/bij.12093.
19. Castresana J. 2000. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol. Biol. Evol. 17:540-552.
20. Chatzimanolis S., Caterino M. S. 2007. Toward a better understanding of the "transverse range break": lineage diversification in southern California. Evolution. 61:2127-2141.
21. Coyle F. A. 1974. Systematics of the trapdoor spider genus Aliatypus (Araneae: Antrodiaetidae). Psyche. 81:431-500.
22. Coyle F. 1983. Aerial dispersal by mygalomorph spiderlings (Araneae, Mygalomorphae). J. Arachnology. 11:283-286.
23. Coyle F. A. 1994. Cladistic analysis of the species of the trapdoor spider genus Aliatypus (Araneae, Antrodiaetidae). J. Arachnology. 22:218-224.
24. Coyle F. A., Icenogle W. R. 1994. Natural history of the Californian trapdoor spider genus Aliatypus (Araneae, Antrodiaetidae). J. Arachnology. 22: 224-255.
25. Davis E. B., Koo M. S., Conroy C., Patton J. L., Moritz C. 2008. The California hotspots project: identifying regions of rapid diversification of mammals. Mol. Ecol. 17:120-138.
26. de Queiroz K. 2007. Species concepts and species delimitation. Syst. Biol. 56:879-886.
27. Drummond A. J., Ashton B., Buxton S., Cheung M., Cooper A., Duran C., Field M., Heled J., Kearse M., Markowitz S., Moir R., Stones-Havas S., Sturrock S., Thierer T., Wilson A. 2011. Geneious v5.4, Available from: http://www.geneious.com (last accessed November 15, 2012).
28. Drummond A. J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
29. Dyer R. J. 2009. Genetic Studio: a suite of programs for spatial analysis of genetic-marker data. Mol. Ecol. Resour. 9:110-113.
30. Earl D. A., von Holdt B. M. 2011. STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv. Genet. Resour. 4:359-361.
31. Edwards S. V. 2009. Is a new and general theory of molecular systematics emerging? Evolution. 63:1-19.
32. Ence D. D., Carstens B. C. 2011. Spede STEM: a rapid and accurate method for species delimitation. Mol. Ecol. Resour. 11:473-480.
33. Evanno G., Regnaut S., Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol. Ecol. 14:2611-2620.
34. Excoffier L., Smouse P. E., Quattro J. M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application tohumanmitochondrial DNA restriction data. Genetics. 131:479-491.
35. Fujita M. K., Leaché A. D. 2011. A coalescent perspective on delimiting and naming species: a reply to Bauer et al. Proc. Royal Society B. 278:493-495.
36. Fujita M. K., Leaché A. D., Burbrink F. T., McGuire J. A., Moritz C. 2012. Coalescent-based species delimitation in an integrative taxonomy. Trends Ecol. Evol. 27:480-488.
37. Guindon S., Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
38. Hall C. A. J. 2002. Nearshore marine paleoclimate regions, increasing zoogeographic provinciality, molluscan extinctions, and paleoshorelines, California: late Oligocene (27 Ma) to late Pliocene (2.5 Ma). Geol. Soc. Am., Special Paper, 357: v-489.
39. Hamilton C. A., Formanowicz D. R., Bond J. E. 2011. Species delimitation and phylogeography of Aphonopelma hentzi (Araneae, Mygalomorphae, Theraphosidae): cryptic diversity in North American tarantulas. PLoS ONE. 6(10):e26207.
40. Hedin M., Bond J. E. 2006. 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. 41:454-471.
41. Hedin M., Carlson D. 2011. A new trapdoor spider species from the southern Coast Ranges of California (Mygalomorphae, Antrodiaetidae, Aliatypus coylei, sp. nov,), including consideration of mitochondrial phylogeographic structuring. Zootaxa. 2963: 55-68.
42. Hedin M, Starrett J, Hayashi C. 2013. Crossing the uncrossable: novel trans-valley biogeographic patterns revealed in the genetic history of low-dispersal mygalomorph spiders (Antrodiaetidae, Antrodiaetus) from California. Mol. Ecol. 22:508-526.
43. Heled J., Drummond A. J. 2010. Bayesian inference of species trees from multilocus data. Mol. Biol. Evol. 27:570-580.
44. Hendrixson B. E., Bond J. E. 2005. Testing species boundaries in the Antrodiaetus unicolor complex (Araneae: Mygalomorphae: Antrodiaetidae): "paraphyly" and cryptic diversity. Mol. Phylogenet. Evol. 36:405-416.
45. Hendrixson B. E., Bond J. E. 2007. Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus). Mol. Phylogenet. Evol. 42:738-755.
46. Hendrixson B. E., De Russy B. M., Hamilton C. A., Bond J. E. 2013. An exploration of species boundaries in turret-building tarantulas of the Mojave Desert (Araneae, Mygalomorphae, Theraphosidae, Aphonopelma). Mol. Phylogenet. Evol. 66:327-340.
47. Hill, M. L., Dibblee T. W. 1953. San Andreas, Garlock, and Big Pine faults, California: a study of the character, history, and tectonic significance of their displacements. Geological Soc. America Bulletin. 64:443-458.
48. Hudson R. R. 1991. Gene genealogies and the coalescent process. In: Futuyma D., Antonovics J., editors. Oxford surveys in evolutionary biology. New York: Oxford University Press. p. 1-44.
49. Irwin D. E. 2002. Phylogeographic breaks without geographic barriers to gene flow. Evolution. 56:2383-2394.
50. Jackman T. R., Wake D. B. 1994. Evolutionary and historical analysis of protein variation in the blotched forms of salamanders of the Ensatina complex (Amphibia: Plethodontidae). Evolution. 48: 876-897.
51. Jackson N. D., Austin C. C. 2010. The combined effects of rivers and refugia generate extreme cryptic fragmentation within the common ground skink (Scincella lateralis). Evolution. 64:409-428.
52. Jakobsson M., Rosenberg N. A. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 23:1801-1806.
53. Jockusch E. L., Martínez-Solano I., Hansen R. W., Wake D. B. 2012. Morphological and molecular diversification of slender salamanders (Caudata: Plethodontidae: Batrachoseps) in the southern Sierra Nevada of California with descriptions of two new species. Zootaxa. 3190:1-30.
54. Jockusch E. L., Wake D. B. 2002. Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West. Biol. J. Linn. Soc. 76:361-391.
55. Katoh K., Kuma K., Toh H., Miyata T. 2005. MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33: 511-518.
56. Keith R., Hedin M. 2012. Extreme mitochondrial population subdivision in southern Appalachian paleoendemic spiders (Araneae: Hypochilidae: Hypochilus), with implications for species delimitation. J. Arachnology. 40:167-181.
57. Kingman J. F. C. 1982. The coalescent. Stochastic Processes and their Applications. 13: 235-248.
58. Knowles L. L., Carstens B. C. 2007. Delimiting species without monophyletic gene trees. Syst. Biol. 56:887-895.
59. Kubatko L. S., Carstens B. C., Knowles L. L. 2009. STEM: species tree estimation using maximum likelihood for gene trees under coalescence. Bioinformatics. 25:971-973.
60. Kubatko L., Gibbs H., Bloomquist E. 2011. Inferring species-level phylogenies and taxonomic distinctiveness using multilocus data in Sistrurus rattlesnakes. Syst. Biol. 60:393-409.
61. Leaché A. D., Fujita M. K. 2010. Bayesian species delimitation in West African forest geckos (Hemidactylus fasciatus). Proc. Royal Soc. B. 277:3071-3077.
62. Lohse K. 2009. Can mtDNA barcodes be used to delimit species? A response to Pons et al. (2006). Syst. Biol. 58:439-442.
63. Maddison D. R., Maddison W. P. 2005. MacClade 4: Analysis of phylogeny and character evolution. Version 4.08a. Available from: http://macclade. org.
64. McGuire G., Wright G., Prentice M. J. 1997. A graphical method for detecting recombination in phylogenetic data sets. Mol. Biol. Evol. 14:1125-1131.
65. Milne I., Lindner D., Bayer M., Husmeier D., McGuire G., Marshall D. F., Wright F. 2009. TOPA Li v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics. 25:126-127.
66. Milne I., Wright F., Rowe G., Marshall D. F., Husmeier D., McGuire G. 2004. TOPA Li: software for automatic identification of recombinant sequences within DNA multiple alignments. Bioinformatics. 20:1806-1807.
67. Myers N., Mittermeier R. A., Mittermeier C. G., da Fonseca G. A. B., Kent J. 2000. Biodiversity hotspots for conservation priorities. Nature. 403:853-858.
68. Niemiller M. L., Near T. J., Fitzpatrick B. M. 2012. Delimiting species using multilocus data: diagnosing cryptic diversity in the southern cavefish, Typhlichthys subterraneus (Teleostei: Amblyopsidae). Evolution. 66:846-866.
69. O'Meara B. C. 2010. New heuristic methods for joint species delimitation and species tree inference. Syst. Biol. 59:59-73.
70. Papadopoulou A., Bergsten J., Fujisawa T., Monaghan M. T., Barraclough T. G., Vogler A. P. 2008. Speciation and DNA barcodes: testing the effects of dispersal on the formation of discrete sequence clusters. Phil. Trans. R. Soc. B. 363:2987-2996.
71. Parham J. F., Papenfuss T. J. 2009. High genetic diversity among fossorial lizard populations (Anniella pulchra) in a rapidly developing landscape (Central California). Conserv. Genet. 10:169-176.
72. Polihronakis M., Caterino M. S. 2010. Contrasting patterns of phylogeographic relationships in sympatric sister species of ironclad beetles (Zopheridae: Phloeodes spp.) in California's Transverse Ranges. BMC Evol. Biol. 10:195.
73. Pons J., Barraclough T. G., Gomez-Zurita J., Cardoso A., Duran D. P., Hazell S., Kamoun S., Sumlin W. D., Vogler A. P. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Syst. Biol. 55:595-609.
74. Pons J., Fujisawa T., Claridge E. M., Savill R. A., Barraclough T. G., Vogler A. P. 2011. Deep mtDNA subdivision within Linnean species in an endemic radiation of tiger beetles from New Zealand (genus Neocicindela). Mol. Phylogenet. Evol. 59:251-262.
75. Posada D. 2008. Jmodel Test: Phylogenetic Model Averaging. Mol. Biol. Evol. 25:1253-1256.
76. Pritchard J. K., Stephens M., Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155:945-959.
77. Pritchard J. K., Wen X., Falush D. 2010. Documentation for structure software: Version 2.3. Available from: http://pritch.bsd.uchicago.edu/structure. html. 1-38 (last accessed October 8, 2012).
78. Rannala B., Yang Z. 2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164:1645-1656.
79. Raven R. J. 1985. The spider infraorder Mygalomorphae (Araneae): cladistics and systematics. Bull. Am. Mus. Nat. Hist. 182:1-175.
80. Reid N. M., Carstens B. C. 2012. Phylogenetic estimation error can decrease the accuracy of species delimitation: a Bayesian implementation of the general mixed Yule-coalescent model. BMC Evol. Biol. 12:196.
81. Rittmeyer E. N., Austin C. C. 2012. The effects of sampling on delimiting species from multi-locus sequence data. Mol. Phylogenet. Evol. 65:451-463.
82. Rosenberg N. A. 2004. Distruct: a program for the graphical display of population structure. Mol. Ecol. Notes. 4:137-138.
83. Rosenberg N. A. 2007. Statistical tests for taxonomic distinctiveness from observations of monophyly. Evolution. 61:317-323.
84. Sáez A. G., Lozano E. 2009. Body doubles. Nature. 433:111.
85. Satler J. D. 2011. Species trees and species delimitation in the California trapdoor spider genus Aliatypus (Mygalomorphae, Antrodiaetidae). Master's thesis, San Diego State University.
86. Satler J. D., Starrett J., Hayashi C. Y., Hedin M. 2011. Inferring species trees from gene trees in a radiation of California trapdoor spiders (Araneae, Antrodiaetidae, Aliatypus). PLoS ONE. 6(9): e25355.
87. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 22:2688-2690.
88. Stamatakis A., Hoover P., Rougemont J. 2008. A rapid bootstrap algorithm for the RAxML Web Servers. Syst. Biol. 57:758-771.
89. Starrett J., Hedin M. 2007. Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae). Mol. Ecol. 16:583-604.
90. Stephens M., Donnelly P. 2003. A comparison of Bayesian methods for haplotype reconstruction from population genotype data. Am. J. Hum. Genet. 73:1162-1169.
91. Stephens M., Smith N., Donnelly P. 2001. A new statistical method for haplotype reconstruction frompopulation data. Am. J. Hum. Genet. 68:978-989.
92. Stockman A. K., Bond J. E. 2007. Delimiting cohesion species: extreme population structuring and the role of ecological interchangeability. Mol. Ecol. 16:3374-3392.
93. Swofford D. L. 2002. PAUP: Phylogenetic analysis using parsimony (and Other Methods). Version 4. Sunderland (MA): Sinauer Associates.
94. Wakabayashi J., Sawyer T. L. 2001. Stream incision, tectonics, uplift, and evolution of topography of the Sierra Nevada, California. J. Geology. 109: 539-562.
95. Weisrock D. W., Rasoloarison R. M., Fiorentino I., Ralison J. M., Goodman S. M., Kappeler P. M., Yoder A. D. 2010. Delimiting species without nuclear monophyly in Madagascar's mouse lemurs. PLoS ONE. 5(3):e9883.
96. Wiens J. J. 2007. Species delimitation: new approaches for discovering diversity. Syst. Biol. 56:875-878.
97. Yang Z., Rannala B. 2010. Bayesian species delimitation using multilocus sequence data. Proc. Natl. Acad. Sci. USA. 107: 9264-9269.
98. Zhang C., Zhang D. X., Zhu T., Yang Z. 2011. Evaluation of a Bayesian coalescent method of species delimitation. Syst. Biol. 60: 747-761.