Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae)

Molecular Ecology

Volumn 16, Issue 3, 2007, Pages 583-604

  Starrett, James ^a,b   Hedin, Marshal ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b SAN DIEGO STATE UNIVERSITY   (United States)

Author keywords

California biogeography; Genealogical congruence; Parapatry; Phylogeography; Population subdivision; Speciation

Indexed keywords

CYTOCHROME C OXIDASE; MITOCHONDRIAL DNA; RIBOSOME DNA; RIBOSOME RNA; RNA 28S; RNA, RIBOSOMAL, 12S; UNCLASSIFIED DRUG;

ANIMAL; ARTICLE; BIODIVERSITY; CLASSIFICATION; EVOLUTION; GENETICS; GEOGRAPHY; PHYLOGENY; SPIDER; UNITED STATES;

ANIMALS; BIODIVERSITY; CALIFORNIA; DNA, MITOCHONDRIAL; DNA, RIBOSOMAL; ELECTRON TRANSPORT COMPLEX IV; EVOLUTION; GEOGRAPHY; PHYLOGENY; RNA, RIBOSOMAL; RNA, RIBOSOMAL, 28S; SPIDERS;

ANTRODIAETIDAE; ANTRODIAETUS; ARANEAE; MYGALOMORPHAE;

EID: 33846483825     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2006.03164.x     Document Type: Article

References (69)

1. Avise JC (2000) Phylogeography: the History and Formation of Species. Harvard University Press, Cambridge, Massachusetts.
2. Avise J, Ball M (1990) Principles of genealogical concordance in species concepts and biological taxonomy. Oxford Surveys in Evolutionary Biology, 7, 45-67.
3. Ballard JWO, Whitlock MC (2004) The incomplete natural history of mitochondria. Molecular Ecology, 13, 729-743.
4. Baum DA, Shaw KL (1995) Genealogical perspectives on the species problem. In: Experimental and Molecular Approaches to Plant Biosystematics (eds Hoch PC, Stephenson AG), pp. 289-303. Missouri Botanical Gardern, St Louis, Missouri.
5. 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.
6. Bond JE, Beamer DA, 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.
7. Bond JE, Hedin MC, Ramirez MG, Opell BD (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.
8. Brandley MC, Schmitz A, Reeder TW (2005) Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Systematic Biology, 54, 373-390.
9. Broughton RE, Harrison RG (2003) Nuclear gene genealogies reveal historical, demographic and selection factors associated with speciation in field crickets. Genetics, 163, 1389-1401.
10. Calsbeek R, Thompson JN, Richardson JE (2003) Patterns of molecular evolution and diversification in a biodiversity hotspot: the California Floristic Province. Molecular Ecology, 12, 1021-1029.
11. Coyle F (1968) The mygalomorph spider genus Atypoides (Araneae: Antrodiaetidae). Psyche, 75, 157-193.
12. Coyle FA (1971) Systematics and natural history of the mygalomorph spider genus Antrodiaetus and related genera (Araneae: Antrodiaetidae). Bulletin Museum Comparative Zoology, Harvard, 141, 269-402.
13. De Queiroz K (1998) The general lineage concept of species, species criteria, and the process of speciation: a conceptual unification and terminological recommendations. In: Endless Form: Species and Speciation (eds Howard DJ, Berlocher SH), pp. 57-75. Oxford University Press, Oxford, UK
14. Dettman JR, Jacobson DJ, Taylor JW (2003) A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution, 57, 2703-2720.
15. Eskov K, Zonshtein S (1990) First Mesozoic mygalomorph spiders from the Lower Cretaceous of Siberia and Mongolia, with notes on the system and evolution of the infraorder Mygalomorphae (Chelicerata: Araneae). Neues Jahrbuch Fur Geologie und Paläontologie Monatschefte, 178, 325-368.
16. Feldman CR, Spicer GS (2006) Comparative phylogeography of woodland reptiles in California: repeated patterns of cladogenesis and population expansion. Molecular Ecology, 15, 2201-2222.
17. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39, 783-791.
18. Furlong KP, Schwartz SY (2004) Influence of the Mendocino triple junction on the tectonics of coastal California. Annual Review of Earth and Planetary Sciences, 32, 403-433.
19. Harden DR (1997) California Geology. Prentice Hall, Upper Saddle River, New Jersey.
20. 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.
21. Hedin MC, Maddison WP (2001) A combined molecular approach to phylogeny of the jumping spider subfamily Dendryphantinae (Araneae, Salticidae). Molecular Phylogenetics and Evolution, 18, 386-403.
22. 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.
23. Hendrixson BE, Bond JE (2006) Molecular phylogeny and biogeography of an ancient Holarctic lineage of mygalomorph spiders (Araneae: Antrodiaetidae: Antrodiaetus). Molecular Phylogenetics and Evolution. In press.
24. Hickson RE, Simon C, Cooper A, Spicer GS, Sullivan J, Penny D (1996) Conserved sequence motifs, alignment, and secondary structure for the third domain of animal 12S rRNA. Molecular Biology and Evolution, 13, 150-169.
25. Hillis DM, Dixon MT (1991) Ribosomal DNA: molecular evolution and phylogenetic inference. Quarterly Review of Biology, 66, 411-453.
26. Huelsenbeck JP, Ronquist F (2001) MRBAYES: Bayesian inference of phylogeny. Bioinformatics, 17, 754-755.
27. Jacobs DK, Haney TA, Louie KD (2004) Genes, diversity, and geologic process on the Pacific Coast. Annual Review Earth and Planetary Sciences, 32, 601-652.
28. Jockusch EL, Wake DB (2002) Falling apart and merging: diversification of slender salamanders (Plethodontidae: Batrachoseps) in the American West. Biological Journal of the Linnean Society, 76, 361-391.
29. Jockusch EL, Yanev KP, Wake DB (2001) Molecular phylogenetic analysis of slender salamanders, genus Batrachoseps (Amphibia: Plethodontidae), from central coastal California with descriptions of four new species. Herpetological Monographs, 15, 54-99.
30. Kimura M (1980) A simple method for estimating evolutionary rate of base substitution through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111-120.
31. Kuo C-H, Avise JC (2005) Phylogeographic breaks in low-dispersal species: the emergence of concordance across gene trees. Genetica, 124, 179-186.
32. Lapointe FJ, Rissler LJ (2005) Congruence, consensus, and the comparative phylogeography of codistributed species in California. American Naturalist, 166, 290-299.
33. Larson A, Wake DB, Yanev KP (1984) Measuring gene flow among populations having high levels of genetic fragmentation. Genetics, 106, 293-308.
34. Law JH, Crespi BJ (2002) The evolution of geographic parthenogenesis in Timema walking-sticks. Molecular Ecology, 11, 1417-1489.
35. Leech RE (1972) A revision of the Nearctic Amaurobiidae (Arachnida: Araneida). Memoirs of the Entomological Society of Canada, 84, 1-182.
36. Macey JR, Strasburg JL, Brisson JA, Vredenburg VT, Jennings M, Larson A (2001) Molecular phylogenetics of western North American frogs of the Rana boylii species group. Molecular Phylogenetics and Evolution, 19, 131-143.
37. Maddison DR, Maddison WP (2000) MACCLADE 4: Analysis of Phylogeny and Character Evolution, Version 4.0. Sinauer Associates, Sunderland, MA, USA.
38. Mallatt JM, Garey JR, Schultz JW (2004) Ecdysozoan phylogeny and Bayesian inference: First use of nearly complete 28S and 18S rRNA gene sequences to classify the arthropods and their kin. Molecular Phylogenetics and Evolution, 31, 178-191.
39. Miller J, Coyle F (1996) Cladistic analysis of the Atypoides plus Antrodiaetus lineage of mygalomorph spiders (Araneae, Antrodiaetidae). Journal of Arachnology, 24, 201-213.
40. Monaghan MT, Balke M, Gregory TR, Vogler AP (2005) DNA-based species delineation in tropical beetles using mitochondrial and nuclear markers. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences, 360, 1925-1933.
41. Moritz C, Schneider CJ, Wake DB (1992) Evolutionary relationships within the Ensatina eschscholtzii complex confirm the ring species interpretation. Systematic Biology, 41, 273-291.
42. Nylander JAA, Ronquist F, Huelsenbeck JP, Nieves-Aldrey JL (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology, 53, 47-67.
43. Penney D, Wheater CP, Selden PA (2003) Resistance of spiders to Cretaceous-Tertiary extinction events. Evolution, 57, 2599-2607.
44. Platnick NI, Ubick D (2001) A revision of the North America spiders of the new genus Socalchemmis (Araneae, Tengellidae). American Museum Novitates, 3339, 1-25.
45. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of Akaike information criterion and Bayesian approaches over likelihood ratio rests. Systematic Biology, 53, 793-808.
46. Posada D, Crandall KA (1998) MODELTEST: testing the model of DNA substitution. Bioinformatics, 14, 817-818.
47. Ramirez M, Chi B (2004) Cryptic speciation, genetic diversity and gene flow in the California turret spider Antrodiaetus riversi (Araneae: Antrodiaetidae). Biological Journal of the Linnean Society, 82, 27-37.
48. Rissler LJ, Hijmans RJ, Graham CH, Moritz C, Wake DB (2006) Phylogeographic lineages and species comparisons in conservation analyses: a case study of California herpetofauna. American Naturalist, 167, 655-666.
49. Ronquist F, Huelsenbeck JP (2003) MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572-1574.
50. Ronquist F, Huelsenbeck JP, van der Mark P (2005) MRBAYES 3.1 manual, draft 5/26/2005, online at http://mrbayes.csit.fsu.edu/manual.php (accessed 20 January, 2006).
51. Rubinoff D, Holland BS (2005) Between two extremes: mitochondrial DNA is neither the panacea nor the nemesis of phylogenetic and taxonomic inference. Systematic Biology, 54, 952-961.
52. Rutschmann F (2006) Molecular dating of phylogenetic trees: a brief review of current methods that estimate divergence times. Diversity and Distributions, 12, 35-48.
53. Sanderson MJ (2002) Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. Molecular Biology and Evolution, 19, 101-109.
54. Sanderson MJ (2003) r8s: inferring absolute rates of molecular evolution and divergences times in the absence of a molecular clock. Bioinformatics, 19, 301-302.
55. Segraves KA, Pellmyr O (2001) Phylogeography of the yucca moth Tegiticula maculata: the role of historical biogeography in reconciling high genetic structure with limited speciation. Molecular Ecology, 10, 1247-1253.
56. Shaffer HB, Fellers GM, Voss SR, Oliver JC, Pauly GB (2004) Species boundaries, phylogeography and conservation genetics of the red-legged frog (Rana aurora/draytonii) complex. Molecular Ecology, 13, 2667-2677.
57. Shahjahan RM, Hughes KJ, Leopold RA, DeVault JD (1995) Lower incubation temperature increases yield of insect genomic DNA isolated by the CTAB method. BioTechniques, 19, 333-334.
58. Simon C, Frati F, Beckenbach A, Crespi B, Liu H, Flook P (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Annals Entomological Society America, 87, 651-701.
59. Sites JW Jr, Marshall JC (2004) Operational criteria for delimiting species. Annual Review of Ecology, Evolution and Systematics, 35, 199-227.
60. Swofford DL (2002) PAUP*: Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, Massachusetts.
61. Thompson J, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTALX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25, 4876-4882.
62. Thorne JL, Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology, 51, 689-702.
63. Ubick D, Briggs TS (1989) The harvestmen family Phalangodidae. I. The new genus Calicina, with notes on Sitalcina (Opiliones, Laniatores). Proceedings of the California Academy of Sciences, 46, 95-136.
64. Vincent LS (1993) The natural history of the California turret spider Atypoides riversi (Araneae, Antrodiaetidae): demographics, growth rates, survivorship, and longevity. Journal of Arachnology, 21, 29-39.
65. Wakabayashi J, Sawyer TL (2001) Stream incision, tectonics, uplift, and evolution of topography of the Sierra Nevada, California. Journal of Geology, 109, 539-562.
66. Wake D (1997) Incipient species formation in salamanders of the Ensatina complex. Proceedings of the National Academy of Sciences, USA, 94, 7761-7767.
67. Yang Z, Yoder AD (2003) Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse lemur species. Systematic Biology, 52, 705-716.
68. Zhang D, Hewitt GM (2003) Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Molecular Ecology, 12, 563-584.
69. Zhang AB, Kubota K, Takami Y, Kim JL, Kim JK, Sota T (2005) Species status and phylogeography of two closely related Coptolabrus species (Coleoptera: Carabidae) in South Korea inferred from mitochondrial and nuclear gene sequences. Molecular Ecology, 14, 3823-3841.