1 |
Bonfield, J. K., Smith, K. F. & Staden, R. 1995. A new DNA sequence assembly program. Nucleic Acids Res. 23:4992-4999.
DOI
|
2 |
Buchanan, J. & Zuccarello, G. C. 2012. Decoupling of shortand long-distance dispersal pathways in the endemic New Zealand seaweed Carpophyllum maschalocarpum (Phaeophyceae, Fucales). J. Phycol. 48:518-529.
DOI
|
3 |
Bunce, M., Worthy, T. H., Phillips, M. J., Holdaway, R. N., Willerslev, E., Haile, J., Shapiro, B., Scofield, R. P., Drummond, A., Kamp, P. J. J. & Cooper, A. 2009. The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography. Proc. Natl. Acad. Sci. U. S. A. 106:20646-20651.
DOI
|
4 |
Chiswell, S. M. 2000. The Wairarapa Coastal Current. N. Z. J. Mar. Freshw. Res. 34:303-315.
DOI
|
5 |
Clement, M., Posada, D. & Crandall, K. A. 2000. TCS: a computer program to estimate gene genealogies. Mol. Ecol. 9:1657-1659.
DOI
|
6 |
Department of Conservation, Ministry of Fisheries. 2008. Marine protected areas: classification, protection standard and implementation guidelines. Department of Conservation, Ministry of Fisheries, Wellington, 54 pp.
|
7 |
Department of Conservation, Ministry of Fisheries. 2011. Coastal marine habitats and marine protected areas in New Zealand Territorial Sea: a broad scale gap analysis. Vol. 1. Ministry of Fisheries, Wellington, 50 pp.
|
8 |
Ewing, B. & Green, P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186-194.
DOI
|
9 |
Felsenstein, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783-791.
DOI
|
10 |
Fleming, C. A. 1979. The geological history of New Zealand and its life. Auckland University Press, Auckland, 141 pp.
|
11 |
Fraser, C. I., Nikula, R., Spencer, H. G. & Waters, J. M. 2009. Kelp genes reveal effects of subantarctic sea ice during the Last Glacial Maximum. Proc. Natl. Acad. Sci. U. S. A. 106:3249-3253.
DOI
|
12 |
Goldstien, S. J., Schiel, D. R. & Gemmell, N. J. 2006. Comparative phylogeography of coastal limpets across a marine disjunction in New Zealand. Mol. Ecol. 15:3259-3268.
DOI
|
13 |
González, A., Beltrán, J., Hiriart-Bertrand, L., Flores, V., de Reviers, B., Correa, J. A. & Santelices, B. 2012. Identification of cryptic species in Lessonia nigrescens complex (Phaeophyceae, Laminariales). J. Phycol. 48:1153-1165.
DOI
|
14 |
Guillemin, M. -L., Valero, M., Tellier, F., Macaya, E. C., Destombe, C. & Faugeron, S. 2016. Phylogeography of seaweeds in the South East Pacific: complex evolutionary processes along a latitudinal gradient. In Hu, Z. -M. & Fraser, C. (Eds.) Seaweed Phylogeography: Adaptation and Evolution of Seaweeds under Environment Changes. Springer Science, Dordrecht, pp. 251-277.
|
15 |
Hall, T. A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41:95-98.
|
16 |
Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R., Thompson, J. D., Gibson, T. J. & Higgins, D. G. 2007. ClustalW and ClustalX version 2. Bioinformatics 23:2947-2948.
DOI
|
17 |
Macaya, E. C. & Zuccarello, G. C. 2010. DNA barcoding and genetic divergence in the giant kelp Macrocystis (Laminariales). J. Phycol. 46:736-742.
DOI
|
18 |
Martin, P. & Zuccarello, G. C. 2012. Molecular phylogeny and timing of radiation in Lessonia (Phaeophyceae, Laminariales). Phycol. Res. 60:276-287.
DOI
|
19 |
Muangmai, N., Fraser, C. I. & Zuccarello, G. C. 2015. Contrasting patterns of population structure and demographic history in cryptic species of Bostrychia intricata (Rhodomelaceae, Rhodophyta) from New Zealand. J. Phycol. 51:574-585.
DOI
|
20 |
Nelson, W. A. 2013. New Zealand seaweeds: an illustrated guide. Te Papa Press, Wellington, 328 pp.
|
21 |
Posada, D. & Crandall, K. A. 1998. Modeltest: testing the model of DNA substitution. Bioinformatics 14:817-818.
DOI
|
22 |
Posada, D. & Crandall, K. A. 2001. Selecting the best-fit model of nucleotide substitution. Syst. Biol. 50:580-601.
DOI
|
23 |
Rambaut, A. & Drummond, A. J. 2009. Tracer v1.5. Available from: http://beast.bio.ed.ac.uk/tracer. Accessed Mar 1, 2015.
|
24 |
Ronquist, F., Teslenko, M., van der Mark, P., Ayres, D. L., Darling, A., Höhna, S., Larget, B., Liu, L., Suchard, M. A. & Huelsenbeck, J. P. 2012. MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst. Biol. 61:539-542.
DOI
|
25 |
Ross, P. M., Hogg, I. D., Pilditch, C. A. & Lundquist, C. J. 2009. Phylogeography of New Zealand’s coastal benthos. N. Z. J. Mar. Freshw. Res. 43:1009-1027.
DOI
|
26 |
Shears, N. T., Smith, F., Babcock, R. C., Duffy, C. A. J. & Villouta, E. 2008. Evaluation of biogeographic classification schemes for conservation planning: application to New Zealand’s coastal marine environment. Conserv. Biol. 22:467-481.
DOI
|
27 |
Staden, R., Judge, D. P. & Bonfield, J. K. 2001. Sequence assembly and finishing methods. Methods Biochem. Anal. 43:303-322.
DOI
|
28 |
Stamatakis, A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
DOI
|
29 |
Avise, J. C. 2006. Evolutionary pathways in nature: a phylogenetic approach. Cambridge University Press, Cambridge, 298 pp.
|
30 |
Apte, S. & Gardner, J. P. A. 2002. Population genetic subdivision in the New Zealand greenshell mussel (Perna canaliculus) inferred from single-strand conformation polymorphism analysis of mitochondrial DNA. Mol. Ecol. 11:1617-1628.
DOI
|
31 |
Ayers, K. L. & Waters, J. M. 2005. Marine biogeographic disjunction in central New Zealand. Mar. Biol. 147:1045-1052.
DOI
|
32 |
Bassam, B. J., Caetano-Anollés, G. & Gresshoff, P. M. 1991. Fast and sensitive silver staining of DNA in polyacrylamide gels. Anal. Biochem. 196:80-83.
DOI
|
33 |
Tellier, F., Meynard, A. P., Correa, J. A., Faugeron, S. & Valero, M. 2009. Phylogeographic analyses of the 30°S southeast Pacific biogeographic transition zone establish the occurrence of a sharp genetic discontinuity in the kelp Lessonia nigrescens: vicariance or parapatry? Mol. Phyloget. Evol. 53:679-693.
DOI
|
34 |
Stanton, B. R., Sutton, P. J. H. & Chiswell, S. M. 1997. The East Auckland Current, 1994-95. N. Z. J. Mar. Freshw. Res. 31:537-549.
DOI
|
35 |
Stevens, M. I. & Hogg, I. D. 2004. Population genetic structure of New Zealand’s endemic corophiid amphipods: evidence for allopatric speciation. Biol. J. Linn. Soc. 81:119-133.
DOI
|
36 |
Tellier, F., Faugeron, S. & Valero, M. 2011a. Possible role of a mitochondrial genome rearrangement in maintaining the spatial segregation of two cryptic species of the Lessonia nigrescens species complex. Cah. Biol. Mar. 52:371-383.
|
37 |
Tellier, F., Tapia, J., Faugeron, S., Destombe, C. & Valero, M. 2011b. The Lessonia nigrescens species complex (Laminariales, Phaeophyceae) shows strict parapatry and complete reproductive isolation in a secondary contact zone. J. Phycol. 47:894-903.
DOI
|
38 |
Trewick, S. A. & Bland, K. J. 2012. Fire and slice: palaeogeography for biogeography at New Zealand’s North Island/South Island juncture. J. R. Soc. N. Z. 42:153-183.
DOI
|
39 |
Waters, J. M. & Roy, M. S. 2004a. Out of Africa: the slow train to Australasia. Syst. Biol. 53:18-24.
DOI
|
40 |
Waters, J. M. & Roy, M. S. 2004b. Phylogeography of a high-dispersal New Zealand sea-star: does upwelling block gene-flow? Mol. Ecol. 13:2797-2806.
DOI
|
41 |
Zuccarello, G. C., West, J. A., Kamiya, M. & King, R. J. 1999. A rapid method to score plastid haplotypes in red seaweeds and its use in determining parental inheritance of plastids in the red alga Bostrychia (Ceramiales). Hydrobiologia 401:207-214.
DOI
|
42 |
Zuccarello, G. C. & Lokhorst, G. M. 2005. Molecular phylogeny of the genus Tribonema (Xanthophyceae) using rbcL gene sequence data: monophyly of morphologically simple algal species. Phycologia 44:384-392.
DOI
|