Determining the origin and age of the Westland beech (Nothofagus) gap, New Zealand, using fungus beetle genetics

Molecular Ecology

Volumn 17, Issue 5, 2008, Pages 1256-1276

  Leschen, Richard A B ^a   Buckley, Thomas R ^a   Harman, Helen M ^a   Shulmeister, James ^b  

^a LANDCARE RESEARCH   (New Zealand)

^b UNIVERSITY OF CANTERBURY   (New Zealand)

Author keywords

Coalescence dating; Coalescent analysis; Nested clade analysis; New Zealand biogeography; Nothofagus gap; Pleistocene; Refugia

Indexed keywords

DNA;

ANIMAL; ARTICLE; BAYES THEOREM; BEECH; BEETLE; CHI SQUARE DISTRIBUTION; GENE; GENETIC VARIABILITY; GENETICS; GEOGRAPHY; HAPLOTYPE; HISTORY; NEW ZEALAND; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSIOLOGY; POPULATION DYNAMICS; STATISTICAL MODEL;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; BEETLES; CHI-SQUARE DISTRIBUTION; DNA; FAGUS; GENES, INSECT; GEOGRAPHY; HAPLOTYPES; HISTORY, ANCIENT; LIKELIHOOD FUNCTIONS; NEW ZEALAND; PHYLOGENY; POPULATION DYNAMICS; VARIATION (GENETICS);

COLEOPTERA; FAGUS; FUNGI; LEPTOSPERMUM; LEPTOSPERMUM SCOPARIUM; NITIDULIDAE; NOTHOFAGUS; SCUTELLARIS; STAPHYLINIDAE;

EID: 39749084637     PISSN: 09621083     EISSN: 1365294X     Source Type: Journal    
DOI: 10.1111/j.1365-294X.2007.03630.x     Document Type: Article

References (81)

1. Anonymous [Herbarium PDD] (2007) NZFUNGI Database of New Zealand Fungi. Landcare Research, New Zealand. http://nzfungi.landcareresearch.co.nz/.
2. Akaike H (1973) Information theory and an extension of the maximum likelihood principle. In : Second International Symposium on Information Theory, pp. 267 281. Akademiai Kiado, Budapest.
3. Apte S, Smith PJ, Wallis GP (2007) Mitochondrial phylogeography of New Zealand freshwater crayfishes, Paranephrops spp. Molecular Ecology, 16, 1897 1908.
4. Bridle JR, Vines TH (2006) Limits to evolution at range margins: when and why does adaptation fail? Trends in Ecology & Evolution, 22, 140 147.
5. Brower AVZ (1994) Rapid morphological radiation and convergence in geographical races of the butterfly, Heliconius erato, inferred from patterns of mitochondrial DNA evolution. Proceedings of the National Academy of Sciences, 91, 6491 6495.
6. Buckley TR, Simon C (2007) Evolutionary radiation of the cicada genus Maoricicada Dugdale (Hemiptera: Cicadoidea) and the origins of the New Zealand alpine biota. Biological Journal of the Linnaean Society, 91, 419 435.
7. Buckley TR, Simon C, Chambers GK (2001a) Phylogeography of the New Zealand cicada Maoricicada campbelli based on mitochondrial DNA sequences: ancient clades associated with Cenozoic environmental change. Evolution, 55, 1395 1407.
8. Buckley TR, Simon C, Chambers GK (2001b) Exploring among-site rate variation models in a maximum likelihood framework using empirical data: effects of model assumptions on estimates of topology, branch lengths and bootstrap support. Systematic Biology, 50, 67 86.
9. Burge PI, Shulmeister J (2007a) An OIS 5a to OIS 4 (or early OIS 3) environmental and climatic reconstruction from the northwest, South Island, New Zealand, using beetle fossils. Journal of Quaternary Science, 22, 501 516.
10. Burge PI, Shulmeister J (2007b) Re-envisioning the structure of New Zealand vegetation during the last glaciation using beetle fossils. Quaternary Research, 68, 121 132.
11. Burrows JC (1965) Some discontinuous distributions of plants within New Zealand and their ecological significance. II. Disjunctions between Otago-Southland and Nelson Marlborough and related distribution patterns. Tuatara, 13, 9 29.
12. Carlton CE, Leschen RAB (2007) Descriptions of Soronia complex (Nitidulidae: Nitiduline) larvae of New Zealand with comments on life history and taxonomy. New Zealand Entomologist, 30, 41 51.
13. Carter RM (2005) A New Zealand climatic template back to c. 3.9 Ma: ODP Site 1119, Canterbury Bight, south-west Pacific Ocean, and its relationship to onland successions. Journal of the Royal Society of New Zealand, 35, 9 42.
14. Clement M, Posada D, Crandall KA (2000) tcs: a computer program to estimate gene genealogies. Molecular Ecology, 9, 1657 1660.
15. Cockayne L (1926) Monograph on the New Zealand beech forests. Part I. The ecology of the forests and taxonomy of the beeches. Bulletin of the New Zealand State Forest Service 4, Wellington.
16. Cockayne L (1928) The Vegetation of New Zealand, 2nd edn. Engelmann Press, Leipzig.
17. Colhoun E, Shulmeister J (2007) Glaciation of the South West Pacific. In : Encyclopaedia of Quaternary Science (ed. Elias S pp. 1066 1075. Elsevier, London.
18. Crandall KA, Templeton AR (1993) Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction. Genetics, 134, 959 969.
19. Drummond AJ, Rambaut A (2006) beast version 1.4, Available from http://beast.bio.ed.ac.uk/.
20. Drummond AJ, Nicholls GK, Rodrigo AG, Solomon W (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics, 161, 1307 1320.
21. Drummond AJ, Rambaut A, Shapiro B, Pybus OG (2005) Bayesian coalescent inference of past population dynamics from molecular sequences. Molecular Biology and Evolution, 22, 1185 1192.
22. Drummond AJ, Ho SYW, Philips MJ, Rambaut A (2006) Relaxed phylogenetics and dating with confidence. Public Library of Science, Biology, 4, e88.
23. Edwards SV, Beerli B (2000) Perspective: gene divergence, population divergence, and the variation in coalescence time in phylogeographic studies. Evolution, 54, 1839 1854.
24. Gu X, Fu YX, Li WH (1995) Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Molecular Biology and Evolution, 12, 546 557.
25. Haase P (1990) Environmental and floristic gradients in Westland, New Zealand, and the discontinuous distribution of Nothofagus. New Zealand Journal of Botany, 28, 25 40.
26. Hall GMJ, McGlone MS (2006) Potential forest cover of New Zealand as determined by an ecosystem process model. New Zealand Journal of Botany, 44, 211 232.
27. Hasegawa M, Kishino H, Yano T (1985) Dating the human-ape split by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, 22, 160 174.
28. Huelsenbeck JP, Imennov NS (2002) Geographic origin of human mitochondrial DNA: accommodating phylogenetic uncertainty and model comparison. Systematic Biology, 51, 155 165.
29. Hughes SJ (1976) Sooty moulds. Mycologia, 68, 693 820.
30. Jesus FF, Wilkins JF, Solferini VN, Wakeley J (2006) Expected coalescent times and segregating sites in a model of glacial cycles. Genetics and Molecular Research, 5, 466 474.
31. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In : Mammalian Protein Metabolism (ed. Munro NH pp. 21 123. Academic Press, New York.
32. Kass RE, Raftery AE (1995) Bayes factors. Journal of the American Statistical Association, 90, 773 795.
33. Kirejtshuk AG (2003) Four new genera of the Soronia complex (Coleoptera: Nitidulidae) from Australia, New Zealand, Fiji and tropical America with notes on composition of the complex and description of new species from Southern Hemisphere. Russian Entomological Journal, 12, 239 256.
34. Kishino H, Thorne JL, Bruno WJ (2001) Performance of a divergence time estimation method under a probabilistic model of rate evolution. Molecular Biology and Evolution, 18, 352 361.
35. Kuhner MK, Yamato J, Felsestein J (1998) Maximum likelihood estimation of population growth rates based on coalescent. Genetics, 149, 429 434.
36. Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. Journal of Molecular Evolution, 20, 86 93.
37. Leathwick JR (1998) Are New Zealand's Nothofagus species in equilibrium with their environment? Journal of Vegetation Science, 9, 719 732.
38. Leathwick JR, Morgan F, Wilson G, Rutledge D, McLeod M, Johnston K (2003) Land Environments of New Zealand Technical Guide. David Bateman, Auckland.
39. Leschen RAB, Löbl I (2005) Phylogeny and classification of Scaphisomatini (Staphylinidae: Scaphidiinae) with notes on mycophagy, termitophily, and functional morphology. Coleopterists Society Monographs, 3, 1 63.
40. Leschen RAB, Michaux B (2005) Phylogeny and evolution of New Zealand Priasilphidae (Coleoptera). New Zealand Journal of Entomology, 28, 55 64.
41. Löbl I, Leschen RAB (2003a) Scaphidiinae (Insecta: Coleoptera: Staphylinidae). Fauna of New Zealand Number 48. Manaaki Whenua Press, Lincoln, New Zealand.
42. Löbl I, Leschen RAB (2003b) Redescription and new species of Alexidia (Staphylinidae: Scaphidiinae). Revue Suisse de Zoologie, 110, 315 324.
43. Marra MJ, Shulmeister J, Smith ECG (2006) Reconstructing temperature during the Last Glacial Maximum from Lyndon Stream, South Island, New Zealand using beetle fossils and maximum likelihood envelopes. Quaternary Science Reviews, 25, 1841 1849.
44. McDowall RM (1997) Indigenous vegetation type and the distribution of short-jawed kokopu, Galaxia postvectic (Teleosti: Galaxiidae), in New Zealand. New Zealand Journal of Zoology, 24, 243 255.
45. McDowall RM (2005) Historical biogeography of the New Zealand freshwater crayfishes (Parastacidae, Paranephrops spp.): restoration of a refugial survivor? New Zealand Journal of Zoology, 32, 55 77.
46. McGlone MS (1985) Plant biogeography and the late Cenozoic history of New Zealand. New Zealand Journal of Botany, 23, 723 749.
47. McGlone MS, Mildenhall DC, Pole MS (1996) The history and paleoecology of New Zealand Nothofagus forests. In : Nothofagus: Ecology and Evolution (eds Veblen TT Hill RS Read J pp. 83 130. Yale University Press, New Haven, Connecticut.
48. Mortimer N, Sutherland R, Nathan S (2001) Torlesse greywacke and Haast Schist source for Pliocene conglomerates near Reefton, New Zealand. New Zealand Journal of Geology and Geophysics, 44, 105 111.
49. Neilsen R, Wakeley J (2001) Distinguishing migration from isolation: a Markov chain Monte Carlo approach. Genetics, 158, 885 896.
50. Newton MA, Raftery AE (1994) Approximate Bayesian inference with the weighted likelihood bootstrap (with discussion). Journal of the Royal Statistical Society (Series B), 56, 3 48.
51. Nylander JAA, Ronquist F, Huelsenbeck JP, Nievea-Aldrey JL (2004) Bayesian phylogenetic analysis of combined data. Systematic Biology, 53, 47 67.
52. Posada D, Buckley TR (2004) Model selection and model averaging in phylogenetics: advantages of the AIC and Bayesian approaches over likelihood ratio tests. Systematic Biology, 53, 793 808.
53. Posada D, Crandall KA (1998) modeltest: testing the model of DNA substitution. Bioinformatics, 14, 817 818.
54. Posada D, Crandall KA, Templeton AR (2000) geodis: a program for the cladistic nested analysis of the geographical distribution of genetic haplotypes. Molecular Ecology, 9, 487 488.
55. Pybus OG, Rambaut A, Harvey PH (2000) An integrated framework for the inference of viral population history from reconstructed genealogies. Genetics, 155, 1429 1437.
56. Quek S-P, Davies SJ, Itino T, Pierce NE (2004) Codiversification in an ant-plant mutualism: stem texture and the evolution of host use in Crematogaster (Formicidae: Myrmicinae) inhabitants of Macaranga (Euphorbiaceae). Evolution, 58, 554 570.
57. Remington CL (1968) Suture-zones of hybrid interaction between recently joined biotas. In : Evolutionary Biology (eds Dobzhansky T, Hetch MK, Steere WC pp. 321 428. Plenum, New York.
58. Rother H (2006) Late Pleistocene glacial geology of the Waiau-Hope Valley system in North Canterbury, New Zealand. Unpublished PhD Thesis, University of Canterbury, Christchurch, New Zealand.
59. Rozas J, Sánchez-DelBarrio JC, Messeguer X, Rozas R (2003) dnasp, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics, 19, 2496 2497.
60. Shulmeister J (2005) The nature and timing of mountain glaciation in Australasia between c. 130 and 10 ka. Geological Society of America Annual Meeting, 15-19 October 2005, Salt Lake City, Utah.
61. Simon C, Frati F, Crespi B, Liu H, Flook PK (1994) Evolution, weighting, and phylogenetic utility of mitochondrial gene sequences and a compilation of conserved PCR primers. Annals of the Entomological Society of America, 87, 651 701.
62. Suggate RP (1990) Late Pliocene and Quaternary glaciations of New Zealand. Quaternary Science Reviews, 9, 175 197.
63. Suggate RP, Almond PC (2005) The Last Glacial Maximum (LGM) in western South Island, New Zealand: implications for the global LGM and MIS 2. Quaternary Science Reviews, 24, 1923 1940.
64. Swenson NG, Howard DJ (2005) Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. American Naturalist, 166, 581 591.
65. Swofford DL (1998) paup*. Phylogenetic Analysis Using Parsimony (*and Other Methods), Version 4. Sinauer Associates, Sunderland, Massachusetts.
66. Tajima (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585 595.
67. Templeton AR (1998) Nested clade analyses of phylogeographic data: testing hypotheses about gene flow and population history. Molecular Ecology, 7, 381 397.
68. Templeton AR, Sing CF (1993) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. IV. Nested analyses with cladogram uncertainty and recombination. Genetics, 134, 659 669.
69. Templeton AR, Boerwinkle E, Sing CF (1987) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping. I. Basic theory and an analysis of alcohol dehydrogenase activity in Drosophila. Genetics, 117, 343 351.
70. Templeton AR, Crandall KA, Sing CF (1992) A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics, 132, 619 633.
71. Templeton AR, Routman E, Phillips CA (1995) Separating population structure from population history: a cladistic analysis of the geographical distribution of mitochondrial DNA haplotypes in the tiger salamander, Ambystoma tigrinum. Genetics, 140, 767 782.
72. Thompson JD, Higgins DG, Gibson TJ (1994) clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Research, 22, 4673 4680.
73. Thorne JL, Kishino H (2002) Divergence time and evolutionary rate estimation with multilocus data. Systematic Biology, 51, 689 702.
74. Wakeley J (2000) The effects of subdivision on the genetic divergence of populations and species. Evolution, 54, 1092 1101.
75. Wardle P (1963) Evolution and distribution of the New Zealand flora, as affected by Quaternary climates. New Zealand Journal of Botany, 1, 3 17.
76. Wardle P (1964) Facets of the distribution of the forest vegetation in New Zealand. New Zealand Journal of Botany, 2, 352 366.
77. Wardle P (1980) Ecology and distribution of silver beech (Nothofagus menziesii) in the Paringa district, South Westland, New Zealand. New Zealand Journal of Ecology, 3, 23 34.
78. Wardle P, Harris W, Buxton RP (1988) Effects of glacial climates on floristic distributions in New Zealand. 2. The role of long-distance hybridization in disjunct distributions. New Zealand Journal of Botany, 26, 557 564.
79. Woodward CA, Shulmeister J (2007) Chironomid-based reconstructions of air temperature and phytoplankton productivity (chlorophyll a) from lake deposits in Lyndon Stream, New Zealand. Implications for environmental conditions during the New Zealand Last Glacial Maximum (LGM). Quaternary Science Reviews, 27, 142 154.
80. Yang Z (1994) Estimating the pattern of nucleotide substitution. Journal of Molecular Evolution, 39, 105 111.
81. Yang Z, Rannala B (2005) Branch-length prior influences Bayesian posterior probability of phylogeny. Systematic Biology, 54, 455 470.