Classification and phylogeny of the plant genus Dianella Lam. ex Juss. Karen Mary Muscat 2017 A thesis submitted in total fulfilment of the requirements of the degree of Doctor of Philosophy February 2017 School of BioSciences Faculty of Science The University of Melbourne The beauty and diversity of Dianella flowers, fruit and habitat. Photos by K.M Muscat, P.Y Ladiges, A.J Perkins and B Gray. Produced on archival quality paper ii Abstract The global distribution of Dianella Lam. ex Juss. (flax lilies, Asphodelaceae, Asparagales) extends from south-eastern Africa, Madagascar and India, to south-east Asia (north to Japan), Australia, Pacific Islands from Micronesia to Tahiti, Pitcairn Islands, New Zealand, New Caledonia, Norfolk Island and Hawaii. It occurs throughout Australia (excluding the central arid region), where there is the greatest diversity of 42 taxa (19 species and 23 varieties) (Australian Plant Census 2016). Of those, three taxa also extend to south-east Asia, and a further 17 species occur outside Australia (Australian Plant Census 2016; Kew World Checklist of Selected Families, compiled by Govaerts et al. 2016). Plants are characterised by two leaf forms: basal strap-like leaves and cauline leaves on aerial stems (+/- extravaginal branching units). The showy flowers have a characteristic struma between the anther and filament, while the fruit is a fleshy berry, typically in shades of purple. The name Dianella is attributed to the Greek goddess Diana, the mythical goddess of the hunt. A cpDNA phylogeny by Wurdack & Dorr (2009) found Dianella to be monophyletic and sister to the monotypic genus Eccremis from South America. However, there has been no comprehensive phylogenetic analysis of taxa within Dianella, which has the potential to reveal not only taxonomic relationships but biogeographic patterns and the evolutionary history of the group, including the role of polyploidy. Furthermore, species delimitations, including complexes of varieties, have been based only on morphology from field observation and herbarium samples and require further study. Using three chloroplast markers (trnQUUG–5'rps16, 3'rps16–5'trnK(UUU) and rpl14– rps8–infA–rpl36) and two nuclear markers, (ITS 4, ITS 5, 18SE-ETS and DIAN-ETS) molecular phylogenetic analyses using Bayesian and Maximum Parsimony are presented (Chapters 2, 3, 4 and 5). Accessions include the majority of Australian and extra-Australian Dianella. The related outgroup genera Eccremis, Stypandra, Thelionema and Herpolirion were also included. The cpDNA and nrDNA phylograms were relatively congruent and a combined data set produced the most resolution. The combined results (Chapter 5) differed from those of Wurdack & Dorr (2009) in showing Stypandra with a sister relationship to Herpolirion + Thelionema. Within Dianella, resolved clades largely related to biogeographic regions, such as the iii Hawaiian Islands and New Caledonia, Norfolk Island related to New Zealand and Australian bioregions, revealing for example an early divergence between eastern and Western Australian lineages, congruent with the pattern for other Australian biota. Of the four Australian species complexes described by Rodney Henderson in The Flora of Australia, volume 45, the D. caerulea complex was found to be monophyletic except for two varieties that clustered with other far-north Queensland taxa, and two D. caerulea var. caerulea samples that are morphologically distinct when compared to taxa in the complex. Of the other species complexes, D. revoluta, D. pavopennacea and D. longifolia are each polyphyletic. Their relationships indicate biogeographic patterns, such as for D. longifolia accessions, which were resolved in two separate clades, one clade from the Kimberley and Northern Territory, and one clade from eastern and southern Australia. For extra-Australian Dianella, the widespread D. ensifolia was also polyphyletic occurring in multiple clades with distinct taxonomic units able to be recognised. Chromosome counts available from the literature were plotted on the phylogeny for Dianella and indicated that polyploidy has arisen multiple times, particularly in taxa of some of the Australian species complexes and in D. ensifolia sensu lato. These results indicate the need to recognise new species and to resurrect other taxa for Australian and extra-Australian Dianella. Chapter six is a morphometric, multivariate analysis (using phenetic clustering and ordination methods) of Hawaiian Dianella to determine the number of species on the islands. Field collections were made on Oahu, Maui, Hawaii and Kauai to examine populations in situ, develop species concepts and collect plant material for the dataset. The results indicate that five operational taxonomic units should be recognised including the current taxon D. sandwicensis. Fruit morphology is unique, with distinctive fruit dye colour and fruit surface colour in some taxa. D. lavarum, a narrow endemic that inhabits recent dry lava flows, observed in the Hawaii Volcanoes National Park, is to be resurrected. A review of herbarium specimens confirmed its distributional range extends to Maui, which is in agreement with Otto Degener who originally described the species. The D. caerulea complex was also analysed further in Chapter 7, based on extensive fieldwork in Queensland, New South Wales, Victoria and Western Australia, using iv multivariate analysis of a morphological data set. Morphometric clusters were largely in agreement with Henderson's varieties, but it is recommended that some be raised to species level. D. caerulea var. assera and D. caerulea var. producta, which appear to be sister taxa based on the shared character extravaginal branching, were each found to include morphological variation. It is recommended that these taxa be recognised as species with three subgroups recognised in D. caerulea var. assera, and five subgroups in D. caerulea var. producta; however, further field sampling is required for taxonomic revision. v Declaration and statement of authorship This is to certify that: 1. This thesis comprises only my original work towards the Ph.D. Due acknowledgements have been made in the text and for the use of photographic images, and to all other material used. 2. This thesis is fewer than 100,000 words in length, exclusive of tables, maps, bibliographies and appendices. Karen Mary Muscat vi Acknowledgements I would firstly like to acknowledge the Dianella taxonomists, past and present who provided the stepping stones for the research in this thesis. My supervisors, Dr Mike Bayly and Prof. Pauline Ladiges for their mentorship, expertise, constructive discussions and the review of chapters. Prof. Gary Nelson for his wealth of knowledge and access to his book collection. The staff in the systematics lab, thank you for your support and assistance: Dr Tanja Schuster, Dr Joannne Birch, Dr Gill Brown, Erin Batty and Kathy Vohs. Fellow lab students, Rachel Fowler, Dr Rose Barrett, David Meagher, Dr Daniel Ohlsen, Dr Steph Conway, Cat Clowes, Alice Crowe, Emma Lewis, Dr Todd McLay and Dr Claire Marks. Steve Effedaris, The University of Melbourne Nursery Manager for his care and management of the living Dianella collection. To my family for your patience and assistance with field work, a big thank you. A special thank you to Monty, my little dog. To the numerous Australian botanists who attended field trips, provided information about certain localities, and sent living plant material in the mail, your support and interest in Dianella research was fundamental to the results in this project. Thank you to Dr Andrew Perkins, Dr Paul Forster, Dr Ailsa Holland, Val Stajsic, Neville Walsh, Geoff Carr, Peter Heenan, David Fell, David Cameron, Rober Miller, Colin Gibson Bruce Gray, Gary & Nada Sankowsky, Rod Henderson, Dr John Conran, Bill Molyneux, Ian Menkins, John McCabe, Dr Daniel Ohlsen, Fred & Sue Fetherston. Friends who assisted in the field: Dr Melanie Archer, Karen Lester, Wendy Clark, Ruth Jackson, Jenny Porter and David Shoesmith. Thank you to Geoff Carr who initially introduced me to the diversity and taxonomy of Dianella. Robert Miller and Colin Gibson, thank you for sharing your expertise in Dianella and introducing me to populations in the Blue Mountains region. For extra-Australian plant material used in the phylogeny, thank you to Dr Jenny Reid, Dr Liz James, Prof. Goro Kokubugata, Dr Sarder Uddin, Dr Sook Ngoh Phoon, Dr Barry Conn, Dr Shelley James and Oscar Parraga. Thank you to the Park Rangers at Dorrigo National Park, Moreton Island National Park and Townsville region for assistance with field work. Research on the Hawaiian Islands was supported by numerous colleagues. Thank you to the staff from Bishop Museum and National Tropical Botanical Garden, Kauai for vii your hospitality and assistance, which was fundamental to the success of this project. Thank you to Dr David Lorence, Tim Flynn and Rae Williams for assistance with loans, my collections and for your hospitality whilst on Kauai. Thank you Natalia Tangalin for attending all of the field trips and your skills in collecting Hawaiian Dianella in some difficult localities, and monitoring Dianella fruit on Kauai. Sierra McDaniel, Botanist from Hawaii Volcanoes National Park for providing Dianella flower images. Joel Lau for his invaluable knowledge about Hawaiian Dianella, access to photographs and providing locality information and attending field trips on Oahu. Kenji Suzuki for attending field trips on Oahu; Forest and Kim Starr, and Anna Palomino for access to