Molecular phylogenetic relationships reveal taxonomic and biogeographic clades in Dianella (flax lilies; Asphodelaceae, Hemerocallidoideae)

References

• Angiosperm Phylogeny Group. (2016). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG IV. Botanical Journal of the Linnean Society, 181, 1–20.
   Web of Science ®Google Scholar
• Asker, S. E., & Jerling, L. (1992). Apomixis in Plants. Boca Raton: CRC Press.
   Google Scholar
• Australian Plant Census. (2016). Centre for Australian National Biodiversity Research. Council of Heads of Australasian Herbaria. Retrieved from http://www.chah.gov.au/apc/index.html (accessed 15 December 2016).
   Google Scholar
• Australasian Virtual Herbarium. (2016). Council of Heads of Australasian Herbaria. Retrieved from http://avh.chah.org.au (accessed 21 June 2016).
   Google Scholar
• Baldwin, B. G., & Markos, S. (1998). Phylogenetic utility of the external transcribed spacer (ETS) of 18S–26S rDNA: Congruence of ETS and ITS trees of Calycadenia (Compositae). Molecular Phylogenetics and Evolution, 10, 449–463.
   PubMed Web of Science ®Google Scholar
• Barlow, B. A. (1981). The Australian flora: Its origin and evolution. In A. S. George (Ed.), Flora of Australia (Vol. 1, pp. 25–75). Canberra: Australian Government Publishing Service.
   Google Scholar
• Bayly, M. J., Holmes, G. D., Forster, P. I., Cantrill, D. J., & Ladiges, P. Y. (2013). Major clades of Australasian Rutoideae (Rutaceae) based on rbcL and atpB sequences. Public Library of Science. One, 8, e72493.
   Google Scholar
• Bentham, G. (1878). Liliaceae. In Flora Australiensis (Vol. 7, pp. 3–16). London: Reeve & Co.
   Google Scholar
• Bicknell, R. A., & Koltunow, A. M. (2004). Understanding apomixis: Recent advances and remaining conundrums. The Plant Cell, 16, S228–S245.
   PubMed Web of Science ®Google Scholar
• Birch, J. L., & Keeley, S. C. (2013). Dispersal pathways across the Pacific: The historical biogeography of Astelia s.l. (Asteliaceae, Asparagales). Journal of Biogeography, 40, 1914–1927.
   Web of Science ®Google Scholar
• Bowman, D. M. J. S., Brown, G. K., Braby, M. F., Brown, J. R., Cook, L. G., Crisp, M. D., … Ladiges, P. Y. (2010). Biogeography of the Australian monsoon tropics. Journal of Biogeography, 37, 201–216.
   Web of Science ®Google Scholar
• Bremer, K., & Janssen, T. (2006). Gondwanan origin of major monocot groups inferred from dispersal-vicariance analysis. Aliso, 22, 22–27.
   Google Scholar
• Brown, R. (1810). Prodromus Florae Novae Hollandiae et Insulae Van Diemen. London: Taylor.
   Google Scholar
• Brown, G. K., Udovicic, F., & Ladiges, P. Y. (2001). Molecular phylogeny and biogeography of Melaleuca, Callistemon and related genera (Myrtaceae.). Australian Systematic Botany, 14, 565–585.
   Web of Science ®Google Scholar
• Burbidge, N. (1960). The phytogeography of the Australian Region. Australian Journal of Botany, 8, 75–211.
   Google Scholar
• Cañellas-Boltà, N., Rull, V., Sáez, A., Prebble, M., & Margalef, O. (2014). First records and potential paleoecological significance of Dianella (Xanthorrhoeaceae), an extinct representative of the native flora of Rapa Nui (Easter Island). Vegetation History and Archaeobotany, 23, 331–338.
   Web of Science ®Google Scholar
• Carlquist, S. (1967). The biota of long-distance dispersal versus plant dispersal to Pacific Islands. Bulletin of the Torrey Botanical Club, 94, 129–162.
   Web of Science ®Google Scholar
• Carr, G. D. (1978). Chromosome numbers of Hawaiian flowering plants and the significance of cytology in selected taxa. American Journal of Botany, 65, 236–242.
   Web of Science ®Google Scholar
• Carr, G. W. (2006). Dianella tenuissima (Hemerocallidaceae), a remarkable new species from the Blue Mountains, New South Wales, Australia. Telopea, 11, 300–306.
   Google Scholar
• Carr, G. W. (2007a). Taxonomy of Dianella and implications for conservation. Australasian Plant Conservation: Journal of the Australian Network for Plant Conservation, 16, 11–13.
   Google Scholar
• Carr, G. W. (2007b). Collection and curation of material of Dianella Lam. ex Juss. and Rhuacophila Blume (Hemerocallidaceae) for herbarium and living collections. Australian Systematic Botany Society Newsletter, 133, 30–35.
   Google Scholar
• Carr, G. W., & Horsfall, P. F. (1995). Studies in Phormiaceae (Liliaceae) 1: New species and combintations in Dianella Lam. ex Juss. Muelleria, 8, 365–378.
   Google Scholar
• Chuang, T., Chao, C. Y., Wilma, W. L. H., & Kwan, S. C. (1962). Chromosome numbers of the vascular plants of Taiwan I. Taiwania, 8, 51–66.
   Google Scholar
• Clifford, H. T., Henderson, R. J. F., & Conran, J. G. (1998). Hemerocallidaceae. In K. Kubitzki, H. Huber, P. J. Rudall, P. S. Stevens, & T. Stutzel (Eds.), The families and genera of vascular plants III, Flowering plants: Monocotyledons Lilianae (except Orchidaceae) (pp. 245–253). Berlin: Springer-Verlag.
   Google Scholar
• Conran, J. G., Christophel, D. C., & Cunningham, L. (2003). An Eocene monocotyledon from Nelly Creek, Central Australia, with affinities to Hemerocallidaceae (Lilianae: Asparagales). Alcheringa, 27, 107–115.
   Web of Science ®Google Scholar
• Crayn, D. M., Costion, C., & Harrington, M. G. (2015). The Sahul-Sunda floristic exchange: Dated molecular phylogenies document Cenozoic intercontinental dispersal dynamics. Journal of Biogeography, 42, 11–24.
   Web of Science ®Google Scholar
• Crisp, M. D., & Cook, L. G. (2007). A congruent molecular signature of vicariance across multiple plant lineages. Molecular Phylogenetics and Evolution, 43, 1106–1117.
   PubMed Web of Science ®Google Scholar
• Crisp, M. D., West, J. G., & Linder, H. P. (1999). Biogeography of the terrestrial flora. In A. E. Orchard (Ed.), Flora of Australia (Vol. 1, 2nd ed., pp. 321–67). Melbourne: ABRS/CSIRO.
   Google Scholar
• Crisp, M. D., Hardy, N. B., & Cook, L. G. (2014). Clock model makes a large difference to age estimates of long-stemmed clades with no internal calibration: A test using Australian grasstrees. BioMed Central Evolutionary Biology, 14, 263.
   PubMed Web of Science ®Google Scholar
• Curtis, W. M. (1952). Variation in certain Tasmanian plants. New Phytologist, 51, 398–414.
   Web of Science ®Google Scholar
• de Lange, P. J., Gardner, R. O., Sykes, W. R., Crowcroft, G. M., Cameron, E. K., Stalker, F., … Braggins, J. E. (2005). Vascular flora of Norfolk Island: Some additions and taxonomic notes. New Zealand Journal of Botany, 43, 563–596.
   Web of Science ®Google Scholar
• de Lange, P. J., & Murray, B. G. (2002). Contributions to a chromosome atlas of the New Zealand flora – 37. Miscellaneous families. New Zealand Journal of Botany, 40, 1–23.
   Web of Science ®Google Scholar
• de Lange, P. J., & Murray, B. G. (2003). Chromosome numbers of Norfolk Island endemic plants. Australian Journal of Botany, 51, 211–215.
   Web of Science ®Google Scholar
• Debjatyoti, P., White, W. M., & Blichert-Toft, J. (2005). Geochemistry of Mauritius and the origin of rejuvenescent volcanism on oceanic island volcanoes. Geochemistry Geophysics Geosystems, 6, 1525–2027.
   Web of Science ®Google Scholar
• Degener, O. (1932). Dianella sandwicensis, Dianella lavarum, Dianella multipedicellata. In Flora Hawaiiensis: The New Illustrated Flora of the Hawaiian Islands. Honolulu: O. Degener.
   Google Scholar
• Devey, D., Leitch, I., Rudall, P. J., Pires, C., Pillon, Y., & Chase, M. (2006). Systematics of Xanthorrhoeaceae sensu lato, with an emphasis on Bulbine. Aliso, 22, 345–351.
   Google Scholar
• Donnon, M. J. (2009). Molecular systematics of the Lomandra Labill. complex (Asparagales: Laxmanniaceae) [Unpublished PhD thesis]. The University of Adelaide, Adelaide, Australia.
   Google Scholar
• Fosberg, F. R., & Corwin, G. (1958). A fossil flora from Pagan, Mariana Islands. Pacific Science, 12, 3–16.
   Google Scholar
• Fox, M. D. (1999). Present environmental influences on the Australian flora. In A. E. Orchard (Ed.), Flora of Australia (Vol. 1, 2nd ed., pp. 205–241). Melbourne: ABRS/CSIRO.
   Google Scholar
• Gibbs, A. K., Udovicic, F. B., Drinnan, A. N., & Ladiges, P. Y. (2009). Phylogeny and classification of Eucalyptus subgenus Eudesmia (Myrtaceae) based on nuclear ribosomal DNA, chloroplast DNA and morphology. Australian Systematic Botany, 22, 158–179.
   Web of Science ®Google Scholar
• Govaerts, R., & Newton, L. (2016). World Checklist of Dianella. Facilitated by the Royal Botanic Gardens, Kew. Retrieved from http://apps.kew.org/wcsp/ (accessed 11 June 2019).
   Google Scholar
• Green, P. S. (1994). Liliaceae. In A. J. G. Wilson (Ed.), Flora of Australia (Vol. 49, pp. 505–506). Canberra: Australian Government Publishing Service.
   Google Scholar
• Grigg, R. (2012). In the beginning Archipelago. The origin and discovery of the Hawaiian Islands. Hawaii: Island Heritage Publishing.
   Google Scholar
• Heads, M. (2014). Biogeography of Australasia. A molecular analysis. New York: Cambridge University Press.
   Google Scholar
• Heads, M. (2017). Biogeography and evolution in New Zealand. New York: CRC Press.
   Google Scholar
• Heenan, P. B., & de Lange, P. J. (2007). Two new species of Dianella (Hemerocallidaceae) from New Zealand. New Zealand Journal of Botany, 45, 269–285.
   Web of Science ®Google Scholar
• Henderson, R. J. F. (1985). Thelionema, a new genus of the Phormiaceae from Australia. Austrobaileya, 2, 109–111.
   Google Scholar
• Henderson, R. J. F. (1987a). Dianella. In. A. S. George (Ed.), Flora of Australia (Vol. 45, pp. 194–225). Canberra: Australian Government Publishing Service.
   Google Scholar
• Henderson, R. J. F. (1987b). Stypandra. In. A.S. George (Ed.), Flora of Australia (Vol. 45, pp. 225–228). Canberra: Australian Government Publishing Service.
   Google Scholar
• Henderson, R. J. F. (1987c). Thelionema. In. A.S. George (Ed.), Flora of Australia (Vol. 45, pp. 228–230). Canberra: Australian Government Publishing Service.
   Google Scholar
• Henderson, R. J. F. (1988). Nomenclatural studies in Dianella Lam. ex Juss. (Phormiaceae) 1. Austrobaileya, 2, 419–426.
   Google Scholar
• Henderson, R. J. F. (1991). Studies in Dianella Lam. Ex Juss. (Phormiaceae) 2. Austrobaileya, 3, 473–480.
   Google Scholar
• Herendeen, P. S., & Crane, P. R. (1995). The fossil history of the monocotyledons. In P. J. Rudall, P. J. Cribb, D. F. Cutler, & C. J. Humphries (Eds.), Monocotyledons: Systematics and evolution (pp. 1–21). Kew: Royal Botanic Gardens.
   Google Scholar
• Hewson, H. J. (1987). Herpolirion. In A.S. George (Ed.), Flora of Australia (Vol. 45, p. 242). Canberra: Australian Government Publishing Service.
   Google Scholar
• Hill, R. S. (1998). Fossil evidence for the onset of xeromorphy and scleromorphy in Australian Proteaceae. Australian Systematic Botany, 11, 391–400.
   Web of Science ®Google Scholar
• Hill, R. S. (2004). Origins of the south-eastern Australian Vegetation. Philosophical Transactions. Biological Sciences of the Royal Society of London, 359, 1537–1549.
   PubMed Web of Science ®Google Scholar
• Hooker, J. D. (1860). Botany of the Antarctic Voyage of H.M Discovery ships Erebus and Terror in the years. 1839–1843. Monocotyledons and Dicotyledons. London: Lovell Reeve.
   Google Scholar
• Hopper, S. D., & Gioia, P. (2004). The southwest Australian floristic region: Evolution and conservation of a global hot spot of biodiversity. Annual Review of Ecology, Evolution, and Systematics, 35, 623–650.
   Web of Science ®Google Scholar
• Jessop, J. P. (1979). Dianella. In C. G. G. J. Van Steenis (Ed.), Flora Malesiana (ser. 1, 9, pp. 206–209). Boston: The Hague.
   Google Scholar
• Johnson, L. A., & Soltis, D. E. (1998). Assessing congruence: Empirical examples from molecular Data. In Molecular systematics of plants II DNA sequencing (pp. 297–348). New York: Springer Science.
   Google Scholar
• Kearse, M., Moir, R., Wilson, A., Stones-Havas, S., Cheung, M., Sturrock, S., … Drummond, A. (2012). Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics (Oxford, England), 28, 1647–1649.
   PubMed Web of Science ®Google Scholar
• Kokubugata, G., Nakamura, K., Forster, P. I., Hirayama, Y., & Yokota, M. (2012). Antitropical distribution of Lobelia species (Campanulaceae) between Ryukyu Archipelago of Japan and Oceania as indicated by molecular data. Australian Journal of Botany, 60, 417. 428
   Web of Science ®Google Scholar
• Ladiges, P. Y., & Cantrill, D. (2007). New Caledonia-Australian connections: Biogeographic patterns and geology. Australian Systematic Botany, 20, 383–389.
   Web of Science ®Google Scholar
• Ladiges, P. Y., Parra-O, C., Gibbs, A., Udovicic, F., Nelson, G., & Bayly, M. (2010). Historical biogeographic patterns in continental Australia: Congruence among areas of endemism of two major clades of eucalypts. Cladistics, 26, 1–13.
   Google Scholar
• Ladiges, P. Y., Bayly, M. J., & Nelson, G. (2012). Searching for ancestral areas and artifactual centres of origin in biogeography: With comment on east-west patterns across southern Australia. Systematic Biology, 61, 703–708.
   PubMed Web of Science ®Google Scholar
• Lee, D. E., Lee, W. G., & Mortimer, N. (2001). Where and why have all the flowers gone? Depletion and turnover in the New Zealand Cenozoic angiosperm flora in relation to palaeogeography and climate. Australian Journal of Botany, 49, 341–356.
   Web of Science ®Google Scholar
• Lee, D. E., Conran, J. G., Lindqvis, J. K., Bannister, J. M., & Mildenhall, D. C. (2012). New Zealand Eocene and Miocene macrofossil and pollen records and modern plant distributions in southern hemisphere. The Botanical Review, 78, 235–260.
   Web of Science ®Google Scholar
• Liu, B., Le, C. T., Barrett, R. L., Nickrent, D. L., Chen, Z., Lu, L., & Vidal-Russell, R. (2018). Historical biogeography of Loranthaceae (Santalales): Diversification agrees with emergence of tropical forests and radiation of songbirds. Molecular Phylogenetics and Evolution, 124, 199–212.
   PubMed Web of Science ®Google Scholar
• McDougall, I., & Chamalaun, F. H. (1969). Isotopic dating and geomagnetic polarity studies on volcanic rocks from Mauritius, Indian Ocean. Geological Society of America Bulletin, 80, 1419–1442.
   Web of Science ®Google Scholar
• McDougall, I., Embleton, B. J. J., & Stone, D. B. (1981). Origin and evolution of Lord Howe Island, Southwest Pacific Ocean. Journal of the Geological Society of Australia, 28, 155–176.
   Web of Science ®Google Scholar
• McLoughlin, S. (2001). The breakup history of Gondwana and its impact on pre-Cenozoic floristic provincialism. Australian Journal of Botany, 49, 271–300.
   Web of Science ®Google Scholar
• McLay, T. G. B., & Bayly, M. J. (2016). A new family placement for Australian blue squill, Chamaescilla: Xanthorrhoeaceae (Hemerocallidoideae), not Asparagaceae. Phytotaxa, 275, 97–111. doi:10.11646/phytotaxa.275.2.2
   Web of Science ®Google Scholar
• Mole, B. J., Udovicic, F., Ladiges, P. Y., & Duretto, M. F. (2004). Molecular phylogeny of Phebalium (Rutaceae: Boronieae) and related genera based on ITS 1 + 2 regions of rDNA. Plant Systematics and Evolution, 249, 197–212.
   Web of Science ®Google Scholar
• Moore, L. B., & Edgar, E. (1970). Herpolirion. In Flora of New Zealand Vol. II. Indigenous Tracheophyta: Monocotyledons except Gramineae. New Zealand: Government Printer.
   Google Scholar
• Mueller, F. (1868). Fragmenta Phytographiae Australiae (Vol. 6, pp. 121–123). Melbourne: Government Printer.
   Google Scholar
• Müller, K. (2005). SeqState: Primer design and sequence statistics for phylogenetic DNA data sets. Applied Bioinformatics, 4, 65–69.
   PubMedGoogle Scholar
• Muscat, K. M. M. (2009). A morphometric study of Dianella tasmanica Hook.f. [Honours thesis]. La Trobe University, Australia.
   Google Scholar
• Muscat, K. M. M. (2017). Classification and phylogeny of the plant genus Dianella Lam. ex Juss [PhD thesis]. The University of Melbourne, Melbourne, Australia.
   Google Scholar
• Nakamura, K. O. H., Denda, T., Kokubugata, G., Forster, P. I., Wilson, G., Peng, C.-I., & Yokota, M. (2012). Molecular phylogeography reveals an antitropical distribution and local diversification of Solenogyne (Asteraceae) in the Ryukyu Archipelago of Japan and Australia. Biological Journal of the Linnean Society, 105, 197–217.
   Web of Science ®Google Scholar
• Nandi, S. (1974). Chromosome characteristics and their correlation with phenotypic and ecological variants in Chlorophytum, Ophiopogon and Dianella. Bulletin of the Botanical Society of Bengal, 28, 117–122.
   Google Scholar
• Noguchi, J., & De-Yuan, H. (2004). Multiple origins of the Japanese nocturnal Hemerocallis citrina var. vespertina (Asparagales: Hemerocallidaceae): Evidence from noncoding chloroplast DNA sequences and morphology. International Journal of Plant Science, 165, 219–230.
   Web of Science ®Google Scholar
• Noguchi, J., Hong, D. Y., & Grant, W. F. (2004). The historical evolutionary development of Hemerocallis middendorfii (Hemerocallidaceae) revealed by non-coding regions in chloroplast DNA. Plant Systematics Evolution, 247, 1–22.
   Web of Science ®Google Scholar
• Oh, S., & Potter, D. (2005). Molecular phylogenetic systematics and biogeography of tribe Neillieae (Rosaceae) using DNA sequences of CPDNA, RDNA, and LEAFY. American Journal of Botany, 92, 179–192.
   PubMed Web of Science ®Google Scholar
• Pamilo, P., & Nei, M. (1988). Relationships between gene trees and species trees. Molecular Biology and Evolution, 5, 568–583.
   PubMed Web of Science ®Google Scholar
• Rambaut, A., Drummond, A. J., Xie, D., Baele, G., & Suchard, M. A. (2018). Posterior summarisation in Bayesian phylogenetics using Tracer 1.7. Systematic Biology, 67, 901–904.
   PubMed Web of Science ®Google Scholar
• Redouté, P. J. (1802). Les Liliacées 1. Paris: Chez l'Auteur.
   Google Scholar
• Ronquist, F., & Huelsenbeck, J. P. (2003). MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics, 19, 1572–1574.
   PubMed Web of Science ®Google Scholar
• Schlittler, J. (1940). Monographie der Lilaceengattung Dianella Lam. Mitt. Botanical Museum University of Zürich, 163, 1–283.
   Google Scholar
• Seelanan, T., Schnabel, H., & Wendel, J. F. (1997). Congruence and consensus in the cotton tribe. Systematic Botany, 22, 259–290.
   Web of Science ®Google Scholar
• Sharma, A. K., & Chatterji, A. K. (1958). Chromosome studies as a means of detecting the method of speciation in some members of Liliaceae. Genetica Iberica, 10, 149–178.
   Google Scholar
• Shaw, J., Lickey, E. B., Schilling, E. E., & Small, R. L. (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, 275–288.
   PubMed Web of Science ®Google Scholar
• Shepherd, D. L., & McLay, T. B. (2011). Two micro-scale protocols for the isolation of DNA from polysaccharide-rich plant tissue. Journal of Plant Research, 124, 311–314.
   PubMed Web of Science ®Google Scholar
• Simmons, M. P., & Ochoterena, H. (2000). Gaps as characters as sequenced-based phylogenetic analyses. Systematic Biology, 49, 369–381.
   PubMed Web of Science ®Google Scholar
• Sirisena, U. M. (2010). Systematic studies on Thysanothus R.Br (Asparagales:Laxmanniaceae) [Ph.D. dissertation, Unpublished PhD thesis]. The University of Adelaide, Adelaide, Australia.
   Google Scholar
• Stevens, P. F. (2001, onwards). Angiosperm Phylogeny Website. Version 14, July 2017. Retrieved from http://www.mobot.org/MOBOT/research/APweb/ (accessed 11 June 2019).
   Google Scholar
• Swofford, D. (2001). PAUP*. Phylogenetic Analysis Using Parsimony, version 4.0b10. Champaign, Illinois: Illinois Natural History Survey, Smithsonian Institution.
   Google Scholar
• Turner, H., Hovenkamp, P., & van Welzen, P. C. (2001). Biogeography of southeast Asia and the west Pacific. Journal of Biogeography, 28, 217–230.
   Web of Science ®Google Scholar
• Wagner, W. L., Herbst, D. R., & Sohmer, S. H. (1990). Manual of the Flowering Plants of Hawai'i. Honolulu: University of Hawaii Press, Bishop Museum Press.
   Google Scholar
• Walsh, N. G., & Stajsic, V. (2007). A Census of the Vascular Plants of Victoria (8th ed.). Melbourne: National Herbarium of Victoria.
   Google Scholar
• White, T. J., Bruns, T., Lee, S., & Taylor, J. (1990). Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In M. A. Innis, D. H. Gelfand, J. J. Sninsky, & T. J. White (Eds.), PCR Protocols: A Guide to Methods and Applications. (pp. 315–322). San Diego: Academic Press.
   Google Scholar
• Wild, H. (1953). Dianella ensifolia: A new generic record for continental Africa. Kew Bulletin, 8, 251–252.
   Google Scholar
• Wilson, K. L. (1993). Phormiaceae. In G. W. Harden (Ed.), Flora of New South Wales (Vol. 4, pp. 73–80). Victoria: New South Wales University Press.
   Google Scholar
• Wurdack, K. J., & Dorr, L. J. (2009). The South American genera of Hemerocallidaceae (Eccremis and Pasithea): two introductions to the New World. TAXON, 58, 1122–1132. doi:10.1002/tax.584006
   Web of Science ®Google Scholar
• Yatabe, R. (1803). New or little known plants of Japan. The Botanical Magazine, 7, 435–437.
   Google Scholar