Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale)

Systematic Biology

Volumn 55, Issue 3, 2006, Pages 411-425

  Buckley, Thomas R ^a   Cordeiro, Michael ^b   Marshall, David C ^b   Simon, Chris ^b  

^a LANDCARE RESEARCH   (New Zealand)

^b UNIVERSITY OF CONNECTICUT   (United States)

Author keywords

Cicada; Combined data; Hybridization; Introgression, lineage sorting; Reconciled trees

Indexed keywords

CALMODULIN; INSECT PROTEIN; MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; BIOLOGICAL MODEL; CLASSIFICATION; GENETICS; HEMIPTERA; NEW ZEALAND; PHYLOGENY;

ANIMALS; CALMODULIN; DNA, MITOCHONDRIAL; HEMIPTERA; INSECT PROTEINS; MODELS, BIOLOGICAL; NEW ZEALAND; PHYLOGENY;

EID: 33747338447     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1080/10635150600697283     Document Type: Article

References (97)

1. Akaike, H. 1973. Information theory as an extension of the maximum likelihood principle. Pages 267-281 in Second International Symposium on Information Theory (B. N. Petrov and F. Csaki, eds). Akademaia Kiado, Budapest.
2. Arensburger, P., T. R. Buckley, C. Simon, M. Moulds, and K. E. Holsinger. 2004a. Biogeography and phylogeny of the New Zealand cicada genera (Hemiptera: Cicadidae) based on nuclear and mitochondrial DNA data. J. Biogeog. 31:557-569. (Pubitemid 38459055)
3. Arensburger, P. C. Simon, and K. Holsinger. 2004b. Evolution and phylogeny of the New Zealand cicada genus Kikihia (Homoptera: Auchenorrhyncha: Cicadidae) with special reference to the origin of the Kermadec and Norfolk Islands' species. J. Biogeog. 31:1769-1783. (Pubitemid 39408793)
4. Aris-Brosou, S. 2003. How Bayes tests of molecular phylogenies compare with frequentist approaches. Bioinformatics 19:618-624. (Pubitemid 36417056)
5. Arvestad, L., A.-C. Berglund, J. Lagergren, and B. Sennblad. 2003. Bayesian gene/species tree reconciliation and orthology analysis using MCMC. Bioinformatics 19:7-15.
6. Ballard, J. W. O., B. Chernoff, and A. C. James. 2002. Divergence of mitochondrial DNA is not corroborated by nuclear DNA, morphology, or behavior in Drosophila simulans. Evol. 56:527-545. (Pubitemid 34299829)
7. Ballard, J. W. O., and M. Whitlock. 2004. The incomplete natural history of mitochondria. Mol. Ecol. 13:729-744. (Pubitemid 38390584)
8. Barrett, M., M. Donoghue, and E. Sober. 1991. Against consensus. Syst. Zool. 40:486-493.
9. Beamer R. H. 1920. Studies on the biology of Kansas Cicadidae. Univ. Kansas Sci. Bull. 18:155-263.
10. Betrán, M., C. D. Jiggins, V. Bull, M. Linares, J. Mallet, W. O. McMillan, and E. Bermingham. 2002. Phylogenetic discordance at the species boundary: Comparative gene genealogies among rapidly radiating Heliconius butterflies. Mol. Biol. Evol. 19:2176-2190. (Pubitemid 35440452)
11. Besansky, N. J., J. Krzywinski, T. Lehmann, F. Simard, M. Kern, O. Mukabayire, D. Fontenille, Y. Toure, and N. F. Sagnon. 2003. Semipermeable species boundaries between Anopheles gambiae and Anopheles arabiensis: Evidence from multilocus DNA sequence variation. Proc. Nat. Acad. Sci. USA 100:10818-10823. (Pubitemid 37140111)
12. Brandley, M. C, A. Schmitz, and T. W. Reeder. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of scincid lizards. Syst. Biol. 54:373-390. (Pubitemid 41040438)
13. Broughton, R. E., and R. G. Harrison. 2003. Nuclear gene genealogies reveal historical, demographic and selective factors associated with speciation in field crickets. Genetics 163:1389-1401. (Pubitemid 36523390)
14. Buckley, T. R. 2002. Model misspecification and probabilistic tests of topology: Evidence from empirical data sets. Syst. Biol. 51:492-508.
15. Buckley, T. R., P. Arensburger, C. Simon, and G. K. Chambers. 2002. Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera. Syst. Biol. 51:4-18. (Pubitemid 35169404)
16. Buckley, T. R., and C. Simon. Unpublished data. Evolutionary radiation of the cicada genus Maoricicada and the age of the New Zealand alpine biota.
17. Buckley, T. R., C. Simon, and G. K. Chambers. 2001a. Exploring amongsite rate variation models in a maximum likelihood framework using empirical data: Effects of model assumptions on estimates of topology, branch lengths and bootstrap support. Syst. Biol. 50:67-86.
18. Buckley, T. R., C. Simon, and G. K. Chambers. 2001b. Phylogeography of the New Zealand cicada Maoricicada campbelli based on mitochondrial DNA sequences: Ancient clades associated with Cenozoic environmental change. Evol. 55:1395-1407. (Pubitemid 32774056)
19. Buckley, T. R., C. Simon, H. Shimodaira, and G. K. Chambers. 2001c. Evaluating hypotheses on the origin and evolution of the New Zealand alpine cicadas {Maoricicada) using multiple comparison tests of tree topology. Mol. Biol. Evol. 18:223-234. (Pubitemid 32118867)
20. Carstens, B. C, J. D. Degenhardt, A. S. Stevenson, and J. Sullivan. 2005. ccounting for coalescent stochasticity in testing phylogeographic hypotheses: Testing models of Pleistocene population structure in the Idaho giant salamander Dicamptodon aterrimus. Mol. Ecol. 14:255-265. (Pubitemid 40141492)
21. Carstens, B. C, J. Sullivan, L. M. Davalos, P. A. Larsen, and S. C. Pedersen. 2004. Exploring population genetic structure in three species of Lesser Antillean bats. Mol. Ecol. 13:2557-2566. (Pubitemid 39151615)
22. Chinn, W. G., and N. J. Gemmell. 2004. Adaptive radiation within New Zealand endemic species of the cockroach genus Celatoblatta Johns (Blattidae): A response to Plio-Pleistocene mountain building, and climate change. Mol. Ecol. 13:1507-1518. (Pubitemid 38688901)
23. Claridge, M. F. 1985. Acoustic signals in the Homoptera: Behavior, taxonomy, and evolution. Ann. Rev. Entomol. 30:297-317.
24. Cotton, J. A., and R. D. M. Page. 2002. Going nuclear: Gene family evolution and vertebrate phylogeny reconciled. Proc. R. Soc. Lond. B 269:1555-1561.
25. Crosby, T. K., J. S. Dugdale, and J. C. Watt. 1976. Area codes for recording specimen localities in the New Zealand subregion. N. Z. J. Zool. 25:175-183.
26. Cumber, R. A. 1952. Notes on the biology oiMelampsalta cruentata Fabricius (Hemiptera-Homoptera: Cicadidae), with special references to the nymphal stages. Trans. R. Entomol. Soc. Lond. 103:219-237.
27. Davies, N., and E. Bermingham. 2002. The historical biogeography of two Caribbean butterflies (Lepidoptera: Heliconidae) as inferred from genetic variation at multiple loci. Evol. 56:573-589. (Pubitemid 34299833)
28. Degnan, J. H., and L. A. Salter. 2005. Gene tree distributions under the coalescent process. Evolution. 59:24-37. (Pubitemid 40181296)
29. Doyle, J. J. 1992. Gene trees and species trees: Molecular systematics as one-character taxonomy. Syst. Biol. 17:144-163.
30. Dugdale, J. S. 1972. Genera of New Zealand Cicadidae (Homoptera). N. Z. J. Sci. 14:856-882.
31. Dugdale, J. S., and C. A. Fleming. 1978. New Zealand cicadas of the genus Maoricicada (Homoptera: Tibicinidae). N. Z. J. Zool. 5:295-340.
32. Edwards, S. V, and P. Beerli. 2000. Perspective: Gene divergence, population divergence, and the variation in coalescence time in phylogeographic studies. Evolution. 54:1839-1854. (Pubitemid 32113816)
33. Felsenstein, J. 1985. Confidence limits on phytogenies: An approach using the bootstrap. Evol. 39:783-791.
34. Felsenstein, J. 2004. Inferring phylogenies. Sinauer Associates, Sunderland, Massachusetts.
35. Fleming, C. A. 1971. A new species of cicada from rock fans in southern Wellington, with a review of three species with similar songs and habitat. N. Z. J. Sci. 14:443-479.
36. Fleming, C. A. 1975. Acoustic behaviour as a generic character in New Zealand cicadas (Hemiptera: Homoptera). J. R. Soc. N. Z. 5:47-64.
37. Funk, D. J., and K. E. Omland. 2003. Species-level paraphyly and polyphyly: Frequency, causes, and consequences, with insights from animal mitochondrial DNA. Ann. Rev. Ecol. Syst. 34:397-423. (Pubitemid 38171425)
38. Funk, V. A. 1985. Phylogenetic patterns and hybridization. Ann. Missouri Bot. Gard. 72:681-715.
39. Gatesy, J., P. O'Grady, and R. H. Baker. 1999. Corroboration among data sets in simultaneous analysis: Hidden support for phylogenetic relationships among higher level Artiodactyl taxa. Cladistics 15:271-313.
40. Gómez-Zurita, J., and A. P. Vogler. 2003. Incongruent nuclear and mitochondrial phylogeographic patterns in the Timarcha goettingensis species complex (Coleoptera, Chrysomelidae). J. Evol. Biol. 16:833-843. (Pubitemid 37073852)
41. Hare, M. P. 2001. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 16:700-706. (Pubitemid 33082110)
42. Holder, M. T., J. A. Anderson, and A. K. Holloway. 2001. Difficulties in detecting hybridization. Syst. Biol. 50:978-982.
43. Holland, B. R., D. Penny, and M. D. Hendy. 2003. Outgroup misplacement and phylogenetic inaccuracy under a molecular clock - A simulation study. Syst. Biol. 52:229-238. (Pubitemid 36594679)
44. Huelsenbeck, J. P., and B. Rannala. 2004. Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models. Syst. Biol. 53:904-913. (Pubitemid 40141314)
45. Huelsenbeck, J. P., F. Ronquist, R. Nielsen, and J. P. Bollback. 2001. Bayesian inference of phylogeny and its impact on evolutionary biology. Science 294:2310-2314. (Pubitemid 33140548)
46. Hughes, J., and A. P. Vogler. 2004. The phylogeny of acorn weevils (genus Curculio) from mitochondrial and nuclear DNA sequences: The problem of incomplete data. Mol. Phylogenet. Evol. 32:601-615. (Pubitemid 38836858)
47. Jordan, S., C. Simon, and D. Polhemus. 2003. Molecular systematics and adaptive radiation of Hawaii's endemic damselfly genus Megalagrion. Syst. Biol. 52:89-109. (Pubitemid 36300062)
48. Jukes, T. H., and C. R. Cantor. 1969. Evolution of protein molecules. Pages 21-123 in Mammalian protein metabolism (N. H. Munro, ed). Academic Press, New York.
49. Kimura, M. 1981. Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl. Acad. Sci. USA 78:454-458. (Pubitemid 11129426)
50. Kliman, R. M., P. Andolfatto, J. A. Coyne, F. Depaulis, M. Kreitman, A. J. Berry, J. McCarter, J. Wakeley, and J. Hey. 2000. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156:1913-1931. (Pubitemid 32001252)
51. Knowles, L.L. 2004. The burgeoning field of statistical phylogeography. J. Evol. Biol. 17:1-10. (Pubitemid 38162174)
52. Knowles, L. L., and W. P. Maddison. 2002. Statistical phylogeography. Mol. Ecol. 11:2623-2635. (Pubitemid 35436682)
53. Lane, D. H. 1995. The recognition concept of species applied in an analysis of putative hybridization in New Zealand cicadas of the genus Kikihia (Insecta: Hemiptera: Tibicinidae). Pages 367-421 in Speciation and the recognition concept: Theory and applications (D. M. Lambert, and H. G. Spencer, eds.). The John Hopkins University Press, Baltimore.
54. Lewis, P. O., M. T. Holder, and K. E. Holsinger. 2005. Polytomies and Bayesian phylogenetic inference. Syst. Biol. 54:241-253. (Pubitemid 40707806)
55. Lin, C.-P., and B. N. Danforth. 2004. How do insect nuclear and mitochondrial gene substitution patterns differ? Insights from Bayesian analyses of combined datasets. Mol. Phylogenet. Evol. 30:686-702. (Pubitemid 38265489)
56. Machado, C. A., and J. Hey. 2003. The causes of phylogenetic conflict in a classic Drosophila species group. Proc. R. Soc. Lond. B 270:1193-1202. (Pubitemid 36683465)
57. Maddison, W. P. 1997. Gene trees in species trees. Syst. Biol. 46:523-536.
58. Maddison, W. P., and D. R. Maddison. 2004. Mesquite: A modular system for evolutionary analysis. Version 1.04. http://mesquiteproject.org.
59. Marshall, D. C, J. R. Cooley, K. Hill, and C. Simon. Unpublished data a. Phylogenetic utility of acoustic sexual signals in New Zealand cicadas.
60. Marshall, D. C, J. R. Cooley, K. Hill, and C. Simon. Unpublished data b. Phylogeography of the New Zealand grass cicadas of the Kikihia muta complex: Song and mtDNA concordance in a parapatric radiation.
61. Miller, R. E., T. R. Buckley, and P. S. Manos. 2002. An examination of the monophyly of morning glory taxa using Bayesian phylogenetic inference. Syst. Biol. 51:740-753. (Pubitemid 35294806)
62. Neilsen, R., and J. Wakeley. 2001. Distinguishing migration from isolation: A Markov chain Monte Carlo approach. Genetics 158:885-896. (Pubitemid 32552323)
63. Nichols, R. 2001. Gene trees and species trees are not the same. Trends Ecol. Evol. 16:358-364. (Pubitemid 32525776)
64. Nylander, J. A. A., F. Ronquist, J. P. Huelsenbeck, and J. L. Nievea-Aldrey. 2004. Bayesian phylogenetic analysis of combined data. Syst. Biol. 53:47-67. (Pubitemid 38370420)
65. Page, R. D. M. 1994. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol. 43:58-77. (Pubitemid 24979624)
66. Page, R. D. M. 1998. GeneTree: Comparing gene and species trees using reconciled trees. Bioinformatics 14:819-820. (Pubitemid 28552117)
67. Page, R. D. M., and M. A. Charleston. 1997. From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Mol. Phylogenet. Evol. 7:231-240. (Pubitemid 127345887)
68. Pamilo, P., and M. Nei. 1988. Relationships between gene trees and species trees. Mol. Biol. Evol. 5:568-583.
69. Posada, D., and T. R. Buckley. 2004. Model selection and model averaging in phylogenetics: Advantages of Akaike information criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793-808. (Pubitemid 39568279)
70. Posada, D., and K. A. Crandall. 1998. ModelTest: Testing the model of DNA substitution. Bioinformatics 14:817-818. (Pubitemid 28552116)
71. Ragge, D. R., and W. J. Reynolds. 1998. The songs of the grasshoppers and crickets of Western Europe. Harley Books, Colchester, Essex.
72. Ronquist, F. 1995. Reconstructing the history of host-parasite associations using generalised parsimony. Cladistics 11:73-89.
73. Ronquist, F., and J. P. Huelsenbeck. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinfomatics 19:1572-1574. (Pubitemid 37038874)
74. Rosenberg, N. A. 2002. The probability of topological concordance of gene trees and species trees. Theor. Pop. Biol. 61:225-247. (Pubitemid 38042804)
75. Sang, T., and Y. Zhong. 2000. Testing hybridization hypotheses based on incongruent gene trees. Syst. Biol. 49:422-434.
76. Seehausen, 0.2004. Hybridization and adaptive radiation. Trends Ecol. Evol. 19:198-207.
77. Seo, T.-K., H. Kishino, and J.L. Thorne. 2005. Incorporating gene-specific variation when inferring and evaluating optimal evolutionary tree topologies from multilocus sequence data. Proc. Nat. Acad. Sci. USA 102:4436-4441. (Pubitemid 40397130)
78. Shaw, K. L. 2002. Conflict between nuclear and mitochondrial DNA phylogenies of a recent species radiation: What mtDNA reveals and conceals about modes of speciation in Hawaiian crickets. Proc. Nat. Acad. Sci. USA 99:16122-16127. (Pubitemid 35462759)
79. Shimodaira, H. 2001. Multiple comparisons of log-likelihoods and combining nonnested models with applications to phylogenetic tree selection. Comm. Stat. Theory Meth. 30:1751-1772. (Pubitemid 33767653)
80. Shimodaira, H., and M. Hasegawa. 1999. Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol. Biol. Evol. 16:1114-1116. (Pubitemid 29368141)
81. Simon, C, F. Frati, B. Crespi, H. Liu, and P. K. Flook. 1994. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved PCR primers. Ann. Entomol. Soc. Am. 87:651-701.
82. Slowinski, J. B., and R. D. M. Page. 1999. How should species phylogenies be inferred from sequence data? Syst. Biol. 48:814-825. (Pubitemid 129490565)
83. Sota, T., and A. P. Vogler. 2001. Incongruence of mitochondrial and nuclear gene trees in the carabid beetles Ohomopterus. Syst. Biol. 50:39-59.
84. Swofford, D.L. 1998. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Version 4. Sinauer Associates, Sunderland, Massachusetts.
85. Tateno, T., M. Nei, and F. Tajima. 1982. Accuracy of estimated phylogenetic trees from molecular data. J. Mol. Evol. 18:387-404. (Pubitemid 13244591)
86. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. (Pubitemid 24354800)
87. Waddell, P. J., H. Kishino, and R. Ota. 2001. A phylogenetic foundation for comparative mammalian genomics. Genome Inform. Series 12:141-154.
88. Walker, T. J. 1964. Cryptic species among sound-producing Ensiferan Orthoptera (Gryllidae and Tettigoniidae). Quart. Rev. Biol. 39:345-355.
89. Warren, D.L., J. Wilgenbusch, and D.L. Swofford. 2003. Converge: A program for implementing MCMC convergence diagnostics. Available from the authors at danwarren@ucdavis.edu.
90. Wells, M. M., and C. S. Henry. 1998. Songs, reproductive isolation and speciation in cryptic species of insects: A case study using green lacewings. Pages 217-233 in Endless forms: Species and speciation (D. Howard and S. Berlocher, eds.). Oxford University Press, New York.
91. Wilder, J.A., and H. Hollocher. 2003. Recent radiation of endemic Caribbean Drosophila of the dunni subgroup inferred from multilocus DNA sequence variation. Evolution. 57:2566-2579. (Pubitemid 37502559)
92. Wu, C.-I.1991. Inference of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127:429-435.
93. Yang, Z. 1996. Maximum likelihood models for combined analyses of multiple sequence data. J. Mol. Evol. 42:587-596. (Pubitemid 26197149)
94. Yang, Z. 1997. PAML: A program package for phylogenetic analysis by maximum likelihood. Comp. Appl. Biosci. 13:555-556. (Pubitemid 27480216)
95. Yang, Z. 1998. Likelihood ratio tests for detecting positive selection and application to primate lyzosyme evolution. Mol. Biol. Evol. 15:568-573. (Pubitemid 28194621)
96. Yang, Z., R. Nielsen, N. Goldman, and A.-M. Krabbe Pederson. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449. (Pubitemid 30257141)
97. Zhang, D.-X., and G. M. Hewitt. 2003. Nuclear DNA analyses in genetic studies of populations: Practice, problems and prospects. Mol. Ecol. 12:563-584. (Pubitemid 36380417)