Phylogeographic history of the New Zealand stick insect Niveaphasma annulata (Phasmatodea) estimated from mitochondrial and nuclear loci

Molecular Phylogenetics and Evolution

Volumn 53, Issue 2, 2009, Pages 523-536

  O'Neill, Shay B ^a   Buckley, Thomas R ^b   Jewell, Tony R ^c   Ritchie, Peter A ^a  

^a VICTORIA UNIVERSITY OF WELLINGTON   (New Zealand)

^b LANDCARE RESEARCH   (New Zealand)

^c NONE   (New Zealand)

Author keywords

Mitochondrial DNA; New Zealand biogeography; Nuclear gene; Phasmatodea; Phylogeography; Stick insect

Indexed keywords

MITOCHONDRIAL DNA;

ANIMAL; ARTICLE; CELL NUCLEUS; CLASSIFICATION; DNA SEQUENCE; GENE; GENETICS; GEOGRAPHY; INSECT; MOLECULAR EVOLUTION; NEW ZEALAND; PHYLOGENY; POPULATION GENETICS;

ANIMALS; CELL NUCLEUS; DNA, MITOCHONDRIAL; EVOLUTION, MOLECULAR; GENES, INSECT; GENETICS, POPULATION; GEOGRAPHY; INSECTS; NEW ZEALAND; PHYLOGENY; SEQUENCE ANALYSIS, DNA;

HEXAPODA; PHASMATODEA;

EID: 69249205337     PISSN: 10557903     EISSN: 10959513     Source Type: Journal    
DOI: 10.1016/j.ympev.2009.07.007     Document Type: Article

References (114)

1. Akaike, H., 1973. Information theory as an extension of the Maximum Likelihood principle. In: Petrov, B.N., Csaki, F. (Eds.), Second International Symposium Information Theory, Akademiai Kiado, pp. 267-281.
2. Alloway B.V., Lowe D.J., Barrell D.J.A., et al. Towards a climate event stratigraphy for New Zealand over the past 30 000 years (NZ-INTIMATE project). J. Quat. Sci. 22 (2007) 9-35
3. Apte S., Smith P.J., and Wallis G.P. Mitochondrial phylogeography of New Zealand freshwater crayfishes, Paranephrops spp. Mol. Ecol. 16 (2007) 1897-1908
4. Avise J. Phylogeography: The History and Formation of Species (2000), Harvard Univ. Press, Cambridge, MA
5. Ballard J.W.O., and Rand D.M. The population biology of mitochondrial DNA and its phylogenetic implications. Ann. Rev. Ecol. Evol. Syst. 36 (2005) 621-642
6. Batt G.E., and Braun J. The tectonic evolution of the Southern Alps, New Zealand: insights from thermally coupled dynamical modelling. Geophys. J. Int. 136 (1999) 403-420
7. Bernardi G., Sordino P., and Powers D.A. Concordant mitochondrial and nuclear DNA phylogenies for populations of the Teleost fish Fundulus heteroclitus. Proc. Natl. Acad. Sci. USA 90 (1993) 9271-9274
8. Boyer S.L., Baker J.M., and Giribet G. Deep genetic divergences in Aoraki denticulata (Arachnida, Opiliones, Cyphophthalmi): a widespread 'mite harvestman' defies DNA taxonomy. Mol. Ecol. 16 (2007) 4999-5016
9. Brito P., and Edwards S.V. Multilocus phylogeography and phylogenetics using sequence-based markers. Genetica 135 (2008) 439-455
10. Brower A.V.Z. Rapid morphological radiation and convergence in geographical races of the butterfly, Heliconius erato, inferred from patterns of mitochondrial DNA evolution. Proc. Natl. Acad. Sci. USA 91 (1994) 6491-6495
11. Brower A.V.Z., and DeSalle R. Practical and theoretical considerations for choice of a DNA sequence region in insect molecular systematics, with a short review of published studies using nuclear gene regions. Ann. Entomol. Soc. Am. 87 (1994) 702-716
12. Brown W.M., George Jr. M., and Wilson A.C. Rapid evolution of animal mitochondrial DNA. Proc. Natl. Acad. Sci. USA 76 (1979) 1967-1971
13. Buckley T.R., Simon C., and Chambers G.K. Phylogeography of the New Zealand cicada Maoricicada campbelli based on mitochondrial DNA sequences: ancient clades associated with Cenozoic environmental change. Evolution 55 (2001) 1395-1407
14. Buckley T.R., Cordeiro M., Marshall D.C., and Simon C. Differentiating between hypotheses of lineage sorting and introgression in New Zealand alpine cicadas (Maoricicada Dugdale). Syst. Biol. 55 (2006) 411-425
15. Buckley T.R., and Simon C. Evolutionary radiation of the cicada genus Maoricicada Dugdale (Hemiptera: Cicadoidea) and the origins of the New Zealand alpine biota. Biol. J. Linn. Soc. 91 (2007) 419-435
16. Buckley T.R., Attanayake D., Park D., Ravindran S., Jewell T.R., and Normark B.B. Investigating hybridization in the parthenogenetic New Zealand stick insect Acanthoxyla (Phasmatodea) using single-copy nuclear DNA. Mol. Phylogenet. Evol. 48 (2008) 335-349
17. Buckley T.R., and Young E.C. A revision of the taxonomic status of Sigara potamius and S. limnochares (Hemiptera: Corixidae), water boatmen of braided rivers in New Zealand. New Zeal. Entomol. 31 (2008) 47-57
18. Burridge C.P., Craw D., and Waters J.M. An empirical test of freshwater vicariance via river capture. Mol. Ecol. 16 (2007) 1883-1895
19. Burton R.S., and Lee B.-N. Nuclear and mitochondrial gene genealogies and allozyme polymorphism across a major phylogeographic break in the copepod Tigriopus californicus. Proc. Natl. Acad. Sci. USA 91 (1994) 5197-5201
20. Caccone A., Amato G.D., and Powell J.R. Rates and patterns of scnDNA and mtDNA divergence within the Drosophila melanogaster subgroup. J. Genet. 118 (1988) 671-683
21. Chamberlain C.P., and Poage M.A. Reconstructing the paleotopography of mountain belts from the isotopic composition of authigenic minerals. Geology 28 (2000) 115-118
22. Chapple D.G., Ritchie P.A., and Daugherty C.H. Origin, diversification, and systematics of the New Zealand skink fauna (Reptilia: Scincidae). Mol. Phylogenet. Evol. 52 (2009) 470-487
23. Chinn W.G., and Gemmell N.J. 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 (2004) 1507-1518
24. Clement M., Posada D., and Crandall K.A. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9 (2000) 1657-1660
25. Crosby T.K., Dugdale J.S., and Watt J.C. Area codes for recording specimen localities in the New Zealand subregion. New Zeal. J. Zool. 25 (1998) 175-183
26. Cutten H.N.C. Rappahanock Group: late Cenozoic sedimentation and tectonics contemporaneous with Alpine fault movement. New Zeal. J. Geol. Geophys. 22 (1979) 535-553
27. Drost F., Renwick J., Bhaskaran B., Oliver H., and McGregor J. A simulation of New Zealand's climate during the Last Glacial Maximum. Quat. Sci. Rev. 26 (2007) 2505-2525
28. Drummond A.J., Rambaut A., Shapiro B., and Pybus O.G. Bayesian coalescent inference of past population dynamics from molecular sequences. Mol. Biol. Evol. 22 (2005) 1185-1192
29. Drummond A.J., and Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7 (2007) 214
30. Emerson B.C., and Wallis G.P. Phylogenetic relationships of the Prodontria (Coleoptera; Scarabaeidae; Subfamily Melolonthinae), derived from sequence variation in the mitochondrial cytochrome oxidase II gene. Mol. Phylogenet. Evol. 4 (1995) 433-447
31. Excoffier L., Laval G., and Schneider S. Arlequin version 3.0: an integrated software package for population genetic data analysis. Evol. Biol. Online 1 (2006) 47-50
32. Fay J.C., and Wu C.-I. A human population bottleneck can account for the discordance between patterns of mitochondrial versus nuclear DNA variation. Mol. Biol. Evol. 16 (1999) 1003-1005
33. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39 (1985) 783-791
34. Fischer S.G., and Lerman L.S. DNA fragments differing by single base-pair substitutions are separated in denaturing gradient gels: correspondence with melting theory. Proc. Natl. Acad. Sci. USA 80 (1983) 1579-1583
35. Fischer A., Wiebe V., Pääbo S., and Przeworski M. Evidence for a complex demographic history in Chimpanzees. Mol. Biol. Evol. 21 (2004) 799-808
36. Fitzsimons S.J., and Veit H. Geology and geomorphology of the European Alps and the Southern Alps of New Zealand. Mount. Res. Dev. 21 (2001) 340-349
37. Fleming C.A. The Geological History of New Zealand and its Life (1979), Auckland Univ. Press, Auckland
38. Fouquet, A., Green, D.M., Waldman, B., Bowsher, J.H., McBride, K.P., Gemmell, N.J., in press. Phylogeography of Leiopelma hochstetteri reveals strong genetic structure and suggests new conservation priorities. Conserv. Genet. doi:10.1007/s10592-009-9935-8.
39. Gardner R.C., De Lange P.J., Jeanette Keeling D., Bowala T., Brown H.A., and Wright S.D. A late Quaternary phylogeography for Metrosideros (Myrtaceae) in New Zealand inferred from chloroplast DNA haplotypes. Biol. J. Linn. Soc. 83 (2004) 399-412
40. Garrick R.C., and Sunnucks P. Development and application of three-tiered nuclear genetic markers for basal Hexapods using single-stranded conformation polymorphism coupled with targeted DNA sequencing. BMC Genet. 7 (2006) 11
41. Garrick R.C., Sands C.J., Rowell D.M., Hillis D.M., and Sunnucks P. Catchments catch all: long-term population history of a giant springtail from the southeast Australian highlands - a multigene approach. Mol. Ecol. 16 (2007) 1865-1882
42. Giannasi N., Malhotra A., and Thorpe R.S. Nuclear and mtDNA phylogenies the Trimeresurus complex: implications for the gene versus species tree debate. Mol. Phylogenet. Evol. 19 (2001) 57-66
43. Greaves S.N.J., Chapple G.D., Gleeson D.M., Daugherty C.H., and Ritchie P.A. Phylogeography of the spotted skink (Oligosoma lineoocellatum) and green skink (O. chloronoton) species complex (Lacertilia: Scincidae) in New Zealand reveals pre-Pleistocene divergence. Mol. Phylogenet. Evol. 45 (2007) 729-739
44. Günther K. Über die taxonomische Gliederung und geographische Verbreitung der Insektenordnung der Phasmatodea. Beitr. Entomol. 3 (1953) 541-563
45. Haag-Liautard C., Coffey N., Houle D., Lynch M., Charlesworth B., and Keightley P.D. Direct estimation of the mitochondrial DNA mutation rate in Drosophila melanogaster. PLoS. Biol. 6 (2008) e204
46. Haase M., Marshall B., and Hogg I. Disentangling causes of disjunction on the South Island of New Zealand: the Alpine fault hypothesis of vicariance revisited. Biol. J. Linn. Soc. 91 (2007) 361-374
47. Hare M.P. Prospects for nuclear gene phylogeography. Trends Ecol. Evol. 16 (2001) 700-706
48. Harpending R.C. Signature of ancient population growth in a low-resolution mitochondrial DNA mismatch distribution. Hum. Biol. 66 (1994) 591-600
49. Heads M. Biogeographic disjunction along the Alpine fault, New Zealand. Biol. J. Linn. Soc. 63 (1998) 161-176
50. Hill K.B.R., Simon C., Marshall D.C., and Chambers G.K. Surviving glacial ages within the biotic gap: phylogeography of the New Zealand cicada Maoricicada campbelli. J. Biogeogr. 36 (2009) 675-692
51. Huelsenbeck J.P., and Ronquist F. MrBayes: Bayesian inference of phylogenetic trees. Bioinformatics 17 (2001) 754-755
52. Hutton F.W. The Phasmidae of New Zealand. T. Proc. New Zeal. I. 30 (1898) 160-166
53. Jensen J.L., Bohonak A.J., and Kelley S.T. Isolation by distance, web service. BMC Genet. 6 (2005) 13
54. Jewell T., and Brock P.D. A review of the New Zealand stick insects: new genera and synonymy, keys, and a new catalogue. J. Orthopaed. Res. 11 (2002) 189-197
55. King P.R. Tectonic reconstructions of New Zealand: 40 Ma to the present. New Zeal. J. Geol. Geophys. 43 (1999) 611-638
56. King T.M., Kennedy M., and Wallis G.P. Phylogeographic genetic analysis of the alpine weta, Hemideina maori: evolution of a colour polymorphism and origins of a hybrid zone. J. R. Soc. New Zeal. 33 (2003) 715-729
57. Kliman R.M., Andolfatto P., Coyne J.A., Depaulis F., Kreitman M., Berry A.J., McCarter J., Wakeley J., and Hey J. The population genetics of the origin and divergence of the Drosophila simulans complex species. Genetics 156 (2000) 1913-1931
58. Leschen R.A.B., Buckley T.R., Harman H.M., and Shulmeister J. Determining the origin and age of the Westland Beech (Nothofagus) gap, New Zealand, using fungus beetle genetics. Mol. Ecol. 17 (2008) 1256-1276
59. Liggins L., Chapple D.G., Daugherty C.H., and Ritchie P.A. A SINE of restricted gene flow across the Alpine Fault: phylogeography of the New Zealand common skink (Oligosoma nigriplantare polychroma). Mol. Ecol. 17 (2008) 3668-3683
60. Lloyd B.D. The demographic history of the New Zealand short-tailed bat Mystacina tuberculata inferred from modified control region sequences. Mol. Ecol. 12 (2003) 1895-1911
61. Machado C.A., and Hey J. The causes of phylogenetic conflict in a classic Drosophila species group. Proc. R. Soc. Lond. B Biol. 270 (2003) 1193-1202
62. Marshall D.C., Slon K., Cooley J.R., Hill K.B.R., and Simon C. Steady Plio-Pleistocene diversification and a 2-million-year sympatry threshold in a New Zealand cicada radiation. Mol. Phylogenet. Evol. 48 (2008) 1054-1066
63. Marshall D.C., Hill K.B.R., Buckley T.R., Fontaine K., and Simon C. Glacial refugia in a maritime temperate climate: cicada (Kikihia subalpina) mtDNA phylogeography in New Zealand. Mol. Ecol. 18 (2009) 1995-2009
64. Martin D.P., Williamson C., and Posada D. RDP2: recombination detection and analysis from sequence alignments. Bioinformatics 21 (2005) 260-262
65. McGlone M.S. Plant biogeography and the late Cenozoic history of New Zealand. New Zeal. J. Bot. 23 (1985) 723-749
66. McGlone M.S. New Zealand. In: Huntley B., and Webb III T. (Eds). Vegetation History (1988), Kluwer Academic Publishers 557-599
67. McGlone M.S., Duncan R.P., and Heenan P.B. Endemism, species selection and the origin of the vascular plant flora of New Zealand. J. Biogeogr. 28 (2001) 199-216
68. Morgan-Richards M., and Trewick S.A. Hybrid origin of a parthenogenetic genus?. Mol. Ecol. 14 (2005) 2133-2142
69. Moore W.S. Inferring phylogenies from mtDNA variation: mitochondrial-gene trees versus nuclear-gene trees. Evolution 49 (1995) 718-726
70. Moulton J.K., and Wiegmann B.M. Evolution and phylogenetic utility of CAD (rudimentary) among Mesozoic-aged Eremoneuran Diptera (Insecta). Mol. Phylogenet. Evol. 31 (2004) 363-378
71. Neiman M., and Lively C.M. Pleistocene glaciation is implicated in the phylogeographical structure of Potamopyrgus antipodarum, a New Zealand snail. Mol. Ecol. 13 (2004) 3085-3098
72. Newnham R.M., Lowe D.J., and Williams P.W. Quaternary environmental change in New Zealand: a review. Prog. Phys. Geogr. 23 (1999) 567-610
73. O'Neill S.B., Chapple D.G., Daugherty C.H., and Ritchie P.A. Phylogeography of two New Zealand lizards: McCann's skink (Oligosoma maccanni) and the brown skink (O. zelandicum). Mol. Phylogenet. Evol. 48 (2008) 1168-1177
74. Pamilo P., and Nei M. Relationships between gene trees and species trees. Mol. Biol. Evol. 5 (1988) 568-583
75. Pickrill R.A., Fenner J.M., and McGlone M.S. Late Quaternary evolution of a fjord environment in Preservation Inlet, New Zealand. Quat. Res. 38 (1992) 331-346
76. Pillans B. New Zealand Quaternary stratigraphy: an overview. Quat. Sci. Rev. 10 (1991) 405-418
77. Posada D., and Crandall K.A. Modeltest: testing the model of DNA substitution. Bioinformatics 14 (1998) 817-818
78. Posada D., and Buckley T.R. Model selection and model averaging in phylogenetics: advantages of Akaike Information Criterion and Bayesian approaches over likelihood ratio tests. Syst. Biol. 53 (2004) 793-808
79. Rambaut, A., Drummond, A.J., 2007. Tracer v1.4. Available from: .
80. Ray N., Currat M., and Excoffier L. Intra-deme molecular diversity in spatially expanding populations. Mol. Biol. Evol. 20 (2003) 76-86
81. Rozas J., Sanchez-DelBarrio J.C., Messenguer X., and Rozas R. DNAsp: DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19 (2003) 2496-2497
82. Salmon J.T. The Stick Insects of New Zealand (1991), Reed, Auckland, New Zealand
83. Sambrook J., Fritsch E.F., and Maniatis T. Molecular Cloning: A Laboratory Manual (1989), Cold Springs Harbor Laboratory Press, Cold Springs Harbor, NY
84. Shepherd L.D., Perrie L.R., and Brownsey P.J. Fire and ice: volcanic and glacial impacts on the phylogeography of the New Zealand forest fern Asplenium hookerianum. Mol. Ecol. 16 (2007) 4536-4549
85. Simon C., Frati F., Beckenbach A., Crespi B., Liu H., and Flook P. Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved polymerase chain reaction primers. Ann. Entomol. Soc. Am. 87 (1994) 651-701
86. Simon C., Buckley T.R., Frati F., Stewart J., and Beckenbach A. Incorporating molecular evolution into phylogenetic analysis, and a new compilation of conserved polymerase chain reaction primers for animal mitochondrial DNA. Ann. Rev. Ecol. Evol. Syst. 37 (2006) 545-579
87. Slade R.W., Moritz C., and Heideman A. Multiple nuclear-gene phylogenies: application to pinnipeds and comparison with a mitochondrial DNA gene phylogeny. Mol. Biol. Evol. 11 (1994) 341-356
88. Slatkin M., and Hudson R.R. Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129 (1991) 555-562
89. Smissen R.D., Breitwieser I., Ward J.M., McLenachan P.A., and Lockhart P.J. Use of the ISSR profiles and ITS-sequences to study the biogeography of alpine cushion plants in the genus Raoulia (Asteraceae). Plant Syst. Evol. 239 (2003) 79-94
90. Smith P.J., McVeagh S.M., and Allibone R. Extensive genetic differentiation in Gobiomorphus breviceps from New Zealand. J. Fish Biol. 67 (2005) 627-639
91. Stevens M.I., and Hogg I.D. Population genetic structure of New Zealand's endemic corophiid amphipods: evidence for allopatric speciation. Biol. J. Linn. Soc. 81 (2004) 119-133
92. Suggate R.P., and Almond P.C. The Last Glacial Maximum (LGM) in western South Island, New Zealand: implications for the global LGM and MIS 2. Quat. Sci. Rev. 24 (2005) 1923-1940
93. Sunnucks P., Wilson A.C., Beheregaray L.B., Zenger K., French J., and Taylor A.C. SSCP is not so difficult: the application and utility of single-stranded conformation polymorphism in evolutionary biology and molecular ecology. Mol. Ecol. 9 (2000) 1699-1710
94. Swofford D.L. Paup*. Phylogenetic Analysis using Parsimony (* and other methods). Version 4 (1998), Sinauer Associates, Sunderland, Massachusetts
95. Tajima F. Evolutionary relationship of DNA sequences in finite populations. Genetics 105 (1983) 437-460
96. Tamura, K., Dudley, J., Nei, M., Kumar, S., 2007. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Mol. Biol. Evol. doi: 10.1093/molbev/msm092.
97. Thompson J.D., Higgins D.G., and Gibson T.J. ClustalW: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
98. Trewick S.A., Wallis G.P., and Morgan-Richards M. Phylogeographical pattern correlates with Pliocene mountain building in the alpine scree weta (Orthoptera, Anostostomatidae). Mol. Ecol. 9 (2000) 657-666
99. Trewick S.A., and Wallis G.P. Bridging the "beech-gap": New Zealand invertebrate phylogeography implicates Pleistocene glaciation and Pliocene isolation. Evolution 55 (2001) 2170-2180
100. Trewick S.A. DNA Barcoding is not enough: mismatch of taxonomy and genealogy in New Zealand grasshoppers (Orthoptera: Acrididae). Cladistics 23 (2007) 1-15
101. Vandergoes M.J., and Fitzsimons S.J. The Last Glacial-Interglacial Transition (LGIT) in south Westland, New Zealand: paleoecological insight into mid-latitude Southern Hemisphere climate change. Quat. Sci. Rev. 22 (2003) 1461-1476
102. Vink C.J., and Paterson A.M. Combined molecular and morphological phylogenetic analyses of the New Zealand wolf spider genus Anoteropsis (Araneae: Lycosidae). Mol. Phylogenet. Evol. 28 (2003) 576-587
103. Wagstaff S.J., and Garnock-Jones P.J. Evolution and biogeography of the Hebe complex (Scrophulariaceae) inferred from ITS sequences. New Zeal. J. Bot. 36 (1998) 415-437
104. Wakeley J., and Aliacar N. Gene genealogies in a metapopulation. Genetics 159 (2001) 893-905
105. Walcott R.I. Modes of oblique compression: late Cenozoic tectonics of the South Island of New Zealand. Rev. Geophys. 36 (1998) 1-26
106. Wallis G.P., Judge K.F., Bland J., Waters J.M., and Berra T.M. Genetic diversity in New Zealand Galaxias vulgaris sensu lato (Teleostei: Osmeriformes: Galaxiidae): a test of a biogeographic hypothesis. J. Biogeogr. 28 (2001) 59-67
107. Wardle P. Evolution and distribution of the New Zealand flora, as affected by Quaternary climates. New Zeal. J. Bot. 1 (1963) 3-17
108. Waters J.M., and Wallis G.P. Across the Southern Alps by river capture? Freshwater fish phylogeography in South Island, New Zealand. Mol. Ecol. 9 (2000) 1577-1582
109. Waters J.M., and Wallis G.P. Mitochondrial DNA phylogenetics of the Galaxias vulgaris complex from South Island, New Zealand: rapid radiation of a species flock. J. Fish Biol. 58 (2001) 1166-1180
110. Waters J.M., and Craw D. Evolution and biogeography of New Zealand's longjaw galaxiids (Osmeriformes: Galaxiidae): the genetic effects of glaciation and mountain building. Freshwater Biol. 53 (2008) 521-534
111. Winkworth R.C., Wagstaff S.J., Glenny D., and Lockhart P.J. Evolution of the New Zealand mountain flora: origins, diversification and dispersal. Org. Divers. Evol. 5 (2005) 237-247
112. Wu C.-I. Inferences of species phylogeny in relation to segregation of ancient polymorphisms. Genetics 127 (1991) 429-435
113. Zhang D.X., and Hewitt G.M. Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects. Mol. Ecol. 12 (2003) 563-584
114. Zink R.M., and Barrowclough G.F. Mitochondrial DNA under siege in avian phylogeography. Mol. Ecol. 17 (2008) 2107-2121