608
Views
2
CrossRef citations to date
0
Altmetric
Research Articles

Phylogeography of the endemic New Zealand tree Entelea arborescens (whau; Malvaceae)

ORCID Icon, ORCID Icon, ORCID Icon & ORCID Icon
Pages 154-168 | Received 09 Nov 2018, Accepted 28 Jan 2019, Published online: 26 Feb 2019

References

  • Allan HH. 1961. Flora of New Zealand. Vol. 1. Wellington: Government Printer.
  • Andersen JC. 1923. An introduction to Māori music. Transactions of the Royal Society of New Zealand. 54:743–762.
  • Armstrong TTJ, de Lange PJ. 2005. Conservation genetics of Hebe speciosa (Plantaginaceae) an endangered New Zealand shrub. Botanical Journal of the Linnean Society. 149:229–239. doi: 10.1111/j.1095-8339.2005.00437.x
  • Atherton RA, Lockhart PJ, McLenachan PA, de Lange PJ, Wagstaff SJ, Shepherd LD. 2015. Molecular investigation into the origin and relationships of karaka/kopi (Corynocarpus laevigatus) in New Zealand. Journal of the Royal Society of New Zealand. 45:212–220. doi: 10.1080/03036758.2015.1093006
  • Bandelt H-J, Forster P, Röhl A. 1999. Median-joining networks for inferring intraspecific phylogenies. Molecular Biology and Evolution. 16:37–48. doi: 10.1093/oxfordjournals.molbev.a026036
  • Benor S. 2018. Molecular phylogeny of the genus Corchorus (Grewioideae, Malvaceae s.l.) based on nuclear rDNA ITS sequences. The Crop Journal. 6(5):552–563. doi: 10.1016/j.cj.2018.03.007
  • Best E. 1925. The Maori Canoe. An account of various types of vessel used by the Maori of New Zealand in former times, with some description of these isles of the Pacific, and a brief account of the peopling of New Zealand. Wellington: AR Shearer.
  • Bouckaert R, Heled J, Kühnert D, Vaughan T, Wu CH, Xie D, Suchard MA, Rambaut A, Drummond AJ, Prlic A. 2014. BEAST 2: a software platform for Bayesian evolutionary analysis. PLoS Computational Biology. 10(4):e1003537. doi: 10.1371/journal.pcbi.1003537
  • Brunken U, Muellner AN. 2012. A new tribal classification of Grewioideae (Malvaceae) based on morphological and molecular phylogenetic evidence. Systematic Botany. 37:699–711. doi: 10.1600/036364412X648670
  • Buckley TR, Leschen RAB. 2013. Comparative phylogenetic analysis reveals long-term isolation of lineages on the Three Kings Islands, New Zealand. Biological Journal of the Linnean Society. 108:361–377. doi: 10.1111/j.1095-8312.2012.02009.x
  • Bulgarella M, Biggs PJ, de Lange PJ, Shepherd LD. 2017. Isolation and characterization of microsatellite loci from Arthropodium cirratum (Asparagaceae). Applications in Plant Sciences. 5(8):1700041. doi: 10.3732/apps.1700041
  • Butterfield BG. 2003. Wood anatomy in relation to wood quality. In: Barnett JR, Jeronimidis G, editors. Wood quality and its biological basis. Carlton, Australia: Blackwell Publishing Ltd; p. 30–52.
  • Carvalho MR, Herrera FA, Jaramillo CA, Wing SL, Callejas R. 2011. Paleocene Malvaceae from Northern South America and their biogeographical implications. American Journal of Botany. 98:1337–1355. doi: 10.3732/ajb.1000539
  • Clarkson BD. 1991. Coastal plants inland. In: Clarkson BD, Smale MC, Ecroyd CE, editors. Botany of Rotorua. Rotorua: Forest Research Institute; p. 93–96.
  • Colenso W. 1869. On the geographic and economic botany of the North Island of New Zealand. Transactions of the New Zealand Institute. 1:1–58.
  • Dawson J, Lucas R. 2011. New Zealand’s native trees. Nelson: Craig Potton Publishing. p. 576.
  • de Lange PJ. 2018. Entelea arborescens Fact Sheet (content continuously updated). New Zealand Plant Conservation Network; [accessed 2018 Oct 15]. http://www.nzpcn.org.nz/flora_details.aspx?ID=1377.
  • de Lange WP, de Lange PJ. 1994. An appraisal of factors controlling the latitudinal distribution of mangrove (Avicennia marina var. resinifera) in New Zealand. Journal of Coastal Research. 10:539–548.
  • Dellicour S, Mardulyn P. 2014. SPADS 1.0: a toolbox to perform spatial analyses on DNA sequence data sets. Molecular Ecology Resources. 14(3):647–651. doi: 10.1111/1755-0998.12200
  • Drummond AJ, Ho SYW, Rawlence N, Rambaut A. 2007. A rough guide to BEAST 1.4; [accessed 2018 Oct 2]. http://www.molecularevolution.org/molevolfiles/beast/BEAST14_MANUAL-7-6-07.pdf.
  • Dupanloup I, Schneider S, Excoffier L. 2002. A simulated annealing approach to define the genetic structure of populations. Molecular Ecology. 11:2571–2581. doi: 10.1046/j.1365-294X.2002.01650.x
  • Earl DA, vonHoldt BM. 2012. Structure harvester: a website and program for visualizing structure output and implementing the Evanno method. Conservation Genetics Resources. 4(2):359–361. doi: 10.1007/s12686-011-9548-7
  • Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the soft ware structure: a simulation study. Molecular Ecology. 14(8):2611–2620. doi: 10.1111/j.1365-294X.2005.02553.x
  • Falush D, Stephens M, Pritchard JK. 2007. Inference of population structure using multilocus genotype data: dominant markers and null alleles. Molecular Ecology Notes. 7(4):574–578. doi: 10.1111/j.1471-8286.2007.01758.x
  • Fleming CA. 1975. The geological history of New Zealand and its biota. In: Kuschel G, editor. Biogeography and ecology in New Zealand. The Hague: Dr W Junk b.v. Publishers; p. 1–86.
  • Gardner RC, de Lange PJ, Keeling J, Bowala T, Brown HA, Wright SD. 2004. A late Quaternary phylogeography for Metrosideros (Myrtaceae) in New Zealand inferred from chloroplast DNA haplotypes. Biological Journal of the Linnean Society. 83:399–412. doi: 10.1111/j.1095-8312.2004.00398.x
  • Hare KM, Daugherty CH, Chapple DG. 2008. Comparative phylogeography of three skink species (Oligosoma moco, O. smithi, O.suteri; Reptilia: Scincidae) in Northeastern New Zealand. Molecular Phylogenetics and Evolution. 46:303–315. doi: 10.1016/j.ympev.2007.08.012
  • Heine EM. 1938. Observations on the pollination of New Zealand flowering plants. Transactions of the Royal Society of New Zealand. 67:134–148.
  • Isaac M, Herzer R, Brook F, Hayward B. 1994. Cretaceous and Cenozoic sedimentary basins of Northland, New Zealand. Institute of Geological & Nuclear Sciences 8. Wellington, New Zealand: IGNS.
  • Jakobsson M, Rosenberg NA. 2007. CLUMPP: a cluster matching and permutation program for dealing with label switching and multimodality in analysis of population structure. Bioinformatics. 23(14):1801–1806. doi: 10.1093/bioinformatics/btm233
  • Kay K, Whittall J, Hodges S. 2006. A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evolutionary Biology. 6:1471–2148. doi: 10.1186/1471-2148-6-36
  • Leach H, Stowe C. 2005. Oceanic arboriculture at the margins – the case of the karaka (Corynocarpus laevigatus) in Aotearoa. Journal of Polynesian Society. 114(1):7–27.
  • Leberg PL. 2002. Estimating allelic richness: effects of sample size and bottlenecks. Molecular Ecology. 11(11):2445–2449. doi: 10.1046/j.1365-294X.2002.01612.x
  • Leigh JW, Bryant D. 2015. PopART: full-feature software for haplotype network construction. Methods in Ecology and Evolution. 6(9):1110–1116. doi: 10.1111/2041-210X.12410
  • Li DC, Liu M, Luo R, Sadakane K, Lam TW. 2015. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 31:1674–1676.
  • Martins WS, Lucas DCS, Neves KFS, Bertioli DJ. 2009. WebSat - a web software for microsatellite marker development. Bioinformation. 3:282–283. doi: 10.6026/97320630003282
  • McGlone MS. 1985. Plant biogeography and the late Cenozoic history of New Zealand. New Zealand Journal of Botany. 23:723–749. doi: 10.1080/0028825X.1985.10434240
  • McGlone MS, Duncan RP, Heenan PB. 2001. Endemism, species selection and the origin and distribution of the vascular plant flora of New Zealand. Journal of Biogeography. 28:199–216. doi: 10.1046/j.1365-2699.2001.00525.x
  • Millener LH. 1946. A study of Entelea arborescens. Part 1. Ecology. Transactions of the Royal Society of New Zealand. 76(3):267–288.
  • Miller MP, Knaus BJ, Mullins TD, Haig SM. 2013. SSR_pipeline - Computer software for the identification of microsatellite sequences from paired-end Illumina High-Throughput DNA sequence data (ver. 1.1, 2014 Feb). USGS Data Series 778.
  • Morgan-Richards M, Trewick SA, Wallis GP. 2001. Chromosome races with Pliocene origins: evidence from mtDNA. Heredity. 86:303–312. doi: 10.1046/j.1365-2540.2001.00828.x
  • Myers SS, Holwell GI, Buckley TR. 2017. Genetic and morphometric data demonstrate alternative consequences of secondary contact in Clitarchus stick insects. Journal of Biogeography. 44:2069–2081. doi: 10.1111/jbi.13004
  • Neall VE, Trewick SA. 2008. The age and origin of the Pacific islands: a geological overview. Philosophical Transactions of the Royal Society B: Biological Sciences. 363:3293–3308. doi: 10.1098/rstb.2008.0119
  • Newnham R, McGlone M, Moar N, Wilmshurst J, Vandergoes M. 2013. The vegetation cover of New Zealand at the last glacial maximum. Quaternary Science Reviews. 74:202–214. doi: 10.1016/j.quascirev.2012.08.022
  • Peakall R, Smouse PE. 2012. Genalex 6.5: genetic analysis in excel. Population genetic software for teaching and research—An update. Bioinformatics. 28(19):2537–2539. doi: 10.1093/bioinformatics/bts460
  • Pons O, Petit RJ. 1996. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics. 144(3):1237–1245.
  • Posada D. 2008. Jmodeltest: phylogenetic model averaging. Molecular Biology and Evolution. 25:1253–1256. doi: 10.1093/molbev/msn083
  • Pritchard JC, Stephens M, Donnelly P. 2000. Inference of population structure using multilocus genotype data. Genetics. 155(2):945–959.
  • Pruett CL, Winker K. 2008. The effects of sample size on population genetic diversity estimates in Song Sparrows Melospiza melodia. Journal of Avian Biology. 39(2):252–256. doi: 10.1111/j.0908-8857.2008.04094.x
  • Ramasamy RK, Ramasamy S, Bindroo BB, Naik VG. 2014. Structure plot: a program for drawing elegant structure bar plots in user friendly interface. SpringerPlus. 3(431).
  • Rambaut A, Suchard MA, Xie W, Drummond AJ. 2013. Tracer v1.6. http://tree.bio.ed.ac.uk/software/tracer.
  • Reid I, Sawyer J, Rolfe J. 2009. Introduction to the plant life in New Zealand: plant conservation training module 1. The New Zealand Plant Conservation Network; [accessed 2018 Oct 1]. http://nzpcn.org.nz/publications/Module_1_full_document.pdf.
  • Richardson JE, Whitlock BA, Meerow AW, Madriñán S. 2015. The age of chocolate: a diversification history of Theobroma and Malvaceae. Frontiers in Ecology and Evolution. 3(120).
  • Riley M. 1994. Māori healing and Herbal. Paraparaumu: Viking Sevenseas N.Z. Ltd. p. 528.
  • Ross PM, Hogg ID, Pilditch CA, Lundquist CJ. 2009. Phylogeography of New Zealand’s coastal benthos. New Zealand Journal of Marine and Freshwater Research. 43(5):1009–1027. doi: 10.1080/00288330.2009.9626525
  • Shaw J, Lickey EB, Schilling EE, Small RL. 2007. Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. American Journal of Botany. 94(3):275–288. doi: 10.3732/ajb.94.3.275
  • Shepherd LD, Bulgarella M, de Lange PJ, Chiang T-Y. 2018. Genetic structuring of the coastal herb Arthropodium cirratum (Asparagaceae) is shaped by low gene flow, hybridization and prehistoric translocation. PLOS ONE. 13(10):e0204943. doi: 10.1371/journal.pone.0204943
  • Shepherd LD, de Lange PJ, Cox S, McLenachan PA, Roskruge NR, Lockhart PJ, Kolokotronis S-O. 2016. Evidence of a string domestication bottleneck in the recent cultivated New Zealand endemic root crop, Arthropodium cirratum (Asparagaceae). PLOS ONE. 11(3):e0152455. doi: 10.1371/journal.pone.0152455
  • Shepherd LD, de Lange PJ, Perrie LR, Heenan PB. 2017. Chloroplast phylogeography of New Zealand Sophora trees (Fabaceae): extensive hybridization and widespread last glacial maximum survival. Journal of Biogeography. 44:1640–1651. doi: 10.1111/jbi.12963
  • Shepherd LD, McLay TGB. 2011. Two micro-scale protocols for the isolation of DNA from polysaccharide-rich plant tissue. Journal of Plant Research. 124(2):311–314. doi: 10.1007/s10265-010-0379-5
  • Soltis DE, Morris AB, McLachlan JS, Manos PS, Soltis PS. 2006. Comparative phylogeography of unglaciated eastern North America. Molecular Ecology. 15:4261–4293. doi: 10.1111/j.1365-294X.2006.03061.x
  • Spencer HG, Brook FJ, Kennedy M. 2006. Phylogeography of Kauri Snails and their allies from Northland, New Zealand (Mollusca: Gastropoda: Rhytididae: Paraphantinae). Molecular Phylogenetics and Evolution. 38:835–842. doi: 10.1016/j.ympev.2005.10.015
  • Taylor R. 1855. Te Ika a Maui: New Zealand and its inhabitants. London: Wertheim and MacIntosh.
  • Tennyson A, Martinson P. 2006. Extinct brids of New Zealand. Wellington: Te Papa Press. p. 180.
  • Thorsen MJ, Dickinson KJM, Seddon PJ. 2009. Seed dispersal systems in the New Zealand flora. Perspectives in Plant Ecology, Evolution and Systematics. 11:285–309. doi: 10.1016/j.ppees.2009.06.001
  • Walsh RS. 1967. Nectar and pollen sources of New Zealand. Wellington: National Beekeepers Association of New Zealand (Inc).
  • Wardle P. 1963. Evolution and distribution of the New Zealand flora, as affected by Quaternary climates. New Zealand Journal of Botany. 1:3–17. doi: 10.1080/0028825X.1963.10429318
  • White T, Bruns T, Lee S, Taylor J. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M, Gelfand D, Shinsky J, White T, editors. PCR protocols: a guide to methods and applications. San Diego: Academic Press; p. 315–322.
  • Worthy TH, Holdaway RN 2002. Prehistoric life of New Zealand – the lost world of the moa. Indiana: Indiana University Press. p. 718.
  • Zhou W, Li D-Z, Wang H. 2012. Coexistence of delayed autonomous self-pollination and deceptive pollination in Arthropodium cirratum (Asparagaceae). Plant Diversity and Resources. 34:187–191. doi: 10.3724/SP.J.1143.2012.11169

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.