Baba, Yumiko (2013) Evolution, systematics and taxonomy of Elaeocarpus (Elaeocarpaceae) in Australasia. PhD thesis, James Cook University.

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Abstract

An important role of taxonomy is to document the biological world by discovering and determining the relationships of, and formally describing, organisms. This not only enhances our knowledge of biodiversity, but also provides fundamental information for other disciplines. The aim was to increase the understanding of the hierarchical relationships within the rainforest tree genus Elaeocarpus as the basis for a better understanding of the evolutionary processes that have given rise to the extant diversity. An hierarchical approach using different methods and datasets for different taxonomic questions was employed: phylogenetics, population genetics, morphometrics and traditional descriptive taxonomy.

The phylogenetic relationships of Elaeocarpaceae were investigated using nucleotide sequences of two plastid intergenic spacers, trnL-trnF and trnV-ndhC, and the nuclear encoded Internal Transcribed Spacer region. Maximum parsimony and Bayesian analyses of the combined plastid and nuclear data with enhanced taxon sampling produced a more detailed estimate of relationships within Elaeocarpaceae than previous studies. Monophyly of all the genera of Elaeocarpaceae except Elaeocarpus, Aceratium and Sericolea was confirmed. Elaeocarpus, Aceratium and Sericolea formed a strongly supported clade in the multigene tree in the Bayesian analysis but the determination of taxonomic rank for each group requires further investigation.

Some morphological groups such as Group V Subgroup A, Group VI Subgroup B and part of Group XI subgroup B proposed by Coode (1984) were each strongly supported as monophyletic based on the separate marker data sets as well as the combined data set. Additionally, samples of the Elaeocarpus obovatus species complex (Group V D + E. coorangooloo) formed a monophyletic group strongly supported in most analyses. Some clades showed correlation with geography. These areas are New Caledonia-Pacific and Asia.

The phylogenetic study provided an evolutionary framework within which to place the undescribed taxa in Australia. The undescribed taxa sampled for this study now have their positions in their respective groups confirmed: E. sp. Mt Misery was nested in Group VI B; E. Mt. Windsor Tableland was placed in Group XI Subgroup B. Further investigation of these entities was beyond the scope of this study, partly because insufficient material was available for a thorough analysis.

With the aim to solve long-standing problems of taxonomic delimitation within the E. obovatus species complex (Group V D + E. coorangooloo), genetic variation, diversity and relatedness were assessed using a population genetics approach with established microsatellite markers. While there needs a validation from other data source to confirm microsatellite profiles suggested that E. arnhemicus and E. obovatus may be tetraploids. Because the appropriate methodology for analysing polyploid and diploid species together in population genetics is yet to be standardised, a synthesis of three different approaches was utilised in this study: similarity based analysis (PCoA), model based analysis (STRUCTURE), hypothesis testing (Analysis of Molecular Variance (AMOVA) using Φ(PT) and Multigroup Discriminant Function Analysis (MDFA)).

Elaeocarpus arnhemicus was supported as an entity distinct from the other two groups by the cluster analyses, AMOVA (Φ(PT)= 0.43) and MDFA. All of the E. obovatus populations are weakly supported as a single entity by the majority of the clustering methods, and this group is strongly supported as distinct from E. sp. Mt Bellenden Ker based on AMOVA (Φ(PT)= 0.31) and MDFA. Although some differentiation was found between E. obovatus North and South populations in the STRUCTURE analysis, it was decided that as a working hypothesis E. obovatus should be regarded as a single genetic entity because there exists a large sampling gap between them. STRUCTURE analysis detected some genetic admixture between E. arnhemicus and E. obovatus, E. sp. Mt Bellenden Ker and E. coorangooloo, and between E. obovatus and E. sp. Mt. Bellenden Ker. AMOVA indicated only up to 23 % of the variation was shared between each pair, with the likely explanation being retained ancestral polymorphism in both cases. Taken together the results suggest that there are three distinct genetic groups corresponding to E. arnhemicus, E. obovatus, and E. sp. Mt. Bellenden Ker.

Morphological variation within the E. obovatus complex was evaluated against the working hypothesis (the existence of three entities) that resulted from the population genetic study. The results of PCA, PCoA, Cluster analysis, Multigroup Discriminant Function Analysis and Classification Tree analysis revealed that E. obovatus, E. arnhemicus, and E. sp. Mt. Bellenden Ker are morphologically discrete on the basis of fruit and vegetative characters. Taken together, the results of both the genetic and morphological analyses indicate that recognition of E. sp. Bellenden Ker at species rank is justified. Hence the two named species, E. obovatus and E. arnhemicus, are maintained and E. sp. Mt. Bellenden Ker is newly described as E. biracemosus Y.Baba & Crayn. A dichotomous key to all entities and fully revised accounts of E. arnhemicus, E. coorangooloo and E. obovatus are provided.

A detailed investigation of the long-standing putatively recognised taxon E. sp. Mossman Bluff (D.G.Fell 1666) was undertaken and resulted in the description of a new species from the Australian Wet Tropics. The taxon was formally named E. hylobroma Y.Baba & Crayn and a full description and a line drawing of the species was produced. The position of this species as sister to the morphologically distinct Group V was strongly supported by Bayesian analysis of the combined sequence data plus indel data. Since the broader relationships of this clade are unclear, the species was tentatively assigned to Group V with the subgroup assignment suspended until more evidence becomes available.

Item ID:	38321
Item Type:	Thesis (PhD)
Keywords:	Australia; classification; Elaeocarpaceae; Elaeocarpus; evolution; morphology; phylogenetics; plant genetics; systematics; taxonomy
Date Deposited:	05 Aug 2015 22:37
FoR Codes:	06 BIOLOGICAL SCIENCES > 0603 Evolutionary Biology > 060310 Plant Systematics and Taxonomy @ 50% 06 BIOLOGICAL SCIENCES > 0604 Genetics > 060411 Population, Ecological and Evolutionary Genetics @ 50%
SEO Codes:	96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960805 Flora, Fauna and Biodiversity at Regional or Larger Scales @ 50% 96 ENVIRONMENT > 9608 Flora, Fauna and Biodiversity > 960806 Forest and Woodlands Flora, Fauna and Biodiversity @ 50%
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