Taxonomic status of Melaleuca argentea "Ashburton biotype" and identification and evaluation of exon capture loci for Myrtaceae

Abstract

Melaleuca sensu lato is the second biggest genus (ca. 380 spp.) that is mainly distributed in Australia, but some species are found in Southeast Asia, Papua New Guinea and New Caledonia. Melaleuca occupy a range of habitats and are found in all biomes, which makes this hyper-diverse genus an excellent group to carry out evolutionary studies.

The taxonomy of Melaleuca sensu lato (tribe Melaleuceae) has been controversial. The tribe originally included eight other genera: Beaufortia, Calothamnus, Conothamnus, Eremaea, Lamarchea, Petraeomyrtus, Phymatocarpus, and Regelia. However, with taxonomic changes all of the genera in the tribe were transferred to Melaleuca. To date, the phylogenetic studies based on molecular data have shown that Melaleuca is paraphyletic with respect to the other genera in the tribe. However, the taxonomic boundary of Melaleuca is still debated. Existing molecular phylogenies of Melelauceae have used only a few genetic markers, and the relationships within the genus remain unresolved with large polytomies.

Taxonomy of eucalypts has been problematic. Eucalypts include the following seven genera (Eucalyptus, Corymbia, Angophora, Arillastrum, Allosyncarpia, Stockwellia, Eucalyptosis). They are mainly Australian but some genera/species extend outside Australia. The taxonomic relationship of Corymbia, and Angophora is still debated. Some molecular phylogenies have shown monophyly of Corymbia and Angophora while Corymbia was paraphyletic with respect to Angophora in other studies.

In Chapter 2, the genetic diversity of Melaleuca argentea (M. leucadendra complex) was explored. Previous research suggested that populations in the Pilbara region of Western Australia had some genetic distinctions. The Pilbara populations were recorded as M. argentea “Ashburton biotype” (AB) in older literature, but no further information was available. Morphological characters and molecular data to assess the taxonomic status of the Pilbara population were used. We found that AB is more similar and closely related to M. leucadendra than to M. argentea. The results did not have conclusive evidence to support that AB is a distinct species from M. leucadendra. In order to test the taxonomic status, presence of gene flow between AB and M. leucadendra need to be further tested.

With the ultimate aim of estimating a comprephensive phylogeny of Melaleuca and eucalypts using more samples and many more loci compared to previous studies, we developed genetic markers for exon capture in Chapter 3. A workflow to locate orthologous and low copy number nuclear loci is introduced along with the method that was employed to identify the chloroplast markers. 209 chloroplast and nuclear loci that might be useful for Myrtaceae were identified by and 43 Myrtaceae taxa were successfully sequenced.

In Chapter 4, a gene tree approach for each individual locus was undertaken to remove potentially paralogous loci. We have found 144 loci that might be useful for Melaleuca and 174 loci for eucalypts. The present study contributes towards more robust estimations of phylogenetic relationships in the genus Melaleuca, eucalypts as well as other genera in Myrtaceae. Further work is required to verify the markers and to study phylogenetic relationships of the taxa at different taxonomic levels using the loci. Show more