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This paper outlines current gaps in the Flora of Australia in terms of family-level treatments, and next steps towards completing the Flora, including moving from hard-copy volumes to a more dynamic and collaborative online platform.
Flora writing has traditionally been an important but sporadic part of the taxonomic process. The gap between the completion of Bentham’s Flora australiensis and the commencement of the Flora of Australia project, for example, was 103 years. Floras are generally written by small teams (occasionally by single authors) based in single or coordinated networks of institutions, and function as authoritative, point-in-time syntheses of taxonomic activity during the years preceding their creation. Of course, since taxonomy is a dynamic and (potentially) open-ended science, it is often the case that as soon as a Flora treatment is published, it is rendered superseded by ongoing taxonomy. The traditional taxonomic process can, thus, be modelled as a cyclic alternation of open, unconstrained, more-or-less unmediated taxonomic activity (hypothesis generation) punctuated by short phases of synthesis, constraint and mediation (hypothesis consolidation). The opportunity to move from paper Flora publication to digital management and delivery of eFloras may substantially change this model. Although traditional Floras are understood to be unitary, authoritative, synthetic, sporadic and static, eFloras are expected to be unitary, authoritative, synthetic, continuous and dynamic. There is potential tension between the first three expectations of an eFlora (that it be unitary, authoritative and synthetic) and the last two (that it be continuous and dynamic). Resolving this tension may necessitate a change in the way taxonomy is conducted, mediated and managed; the implications of such change will need to be carefully considered, and the change will need to be carefully managed, to make the most of the opportunities of eFloras, while retaining the values of an open, vigorous taxonomic science.
Present patterns of diversity in the Australian flora have been shaped by increasing seasonality since the Eocene, and by pronounced aridification in the past 3 million years. Arid-zone plants are commonly hypothesised to be the products of radiations of ancestrally temperate or coastal lineages, as in the case of the everlasting paper daisy tribe Gnaphalieae (Asteraceae). However, these inferences are often based on higher-level phylogenies, whereas evolutionary processes in the Australian Gnaphalieae have rarely been studied at the species level. Here, we reconstructed the phylogeny and biogeographic history of the small, but ecologically diverse, paper daisy genus Leucochrysum, to examine recent habitat shifts and character changes, at the same time exploring the feasibility of using amplicon sequencing of low-copy nuclear gene regions to resolve phylogenetic relationships in Australian Gnaphalieae. On the balance of evidence, outgroup comparison and ancestral-area reconstruction support an ancestral range in the arid zone with subsequent diversification towards the south-east, demonstrating a complex evolutionary history with a re-colonisation of temperate areas. Low amplification success rates suggest that methods other than amplicon sequencing of currently available primers will be more promising for molecular phylogenetic work at a larger scale.
Pimelea Banks & Sol. ex Gaertn. is a genus of flowering plants comprising an estimated 90 species in Australia and ∼35 species in New Zealand. The genus is economically important, with the inflorescences of some species having floricultural applications, and the presence of toxic compounds in several species proving poisonous to livestock. Pimelea grows in a variety of habitats ranging from arid to alpine, suggesting a complicated biogeographic history. The relationships within Pimelea remain largely uncertain, despite previous attempts at clarification using molecular phylogenetics. However, it is clear that Pimelea is closely related to Thecanthes Wikstr., with the two genera comprising the subtribe Pimeleinae. We used Bayesian and maximum-likelihood phylogenetic analyses of four plastid markers (matK, rbcL, rps16, trnL–F) and one nuclear ribosomal marker (ITS) to examine the evolutionary relationships within Pimeleinae. We found strong support for the monophyly of Pimeleinae but, similar to previous studies, Pimelea was paraphyletic with respect to Thecanthes. Our results also indicated that P. longiflora R.Br. subsp. longiflora and P. longiflora subsp. eyrei (F.Muell.) Rye are best considered as distinct species. Therefore, we reduce Thecanthes to synonymy with Pimelea, making the necessary new combination Pimelea filifolia (Rye) C.S.P.Foster et M.J.Henwood (previously Thecanthes filifolia Rye), and also reinstate Pimelea eyrei F.Muell.
Several Australian Riccia taxa have been sequenced for the first time, with the majority from the monsoon tropics of the Northern Territory, north of 18° latitude. This allowed testing of several infrageneric groupings within the genus as well as morphological species concepts. Molecular data from one nuclear and four plastid markers support the genus as a monophyletic group. However, the monophyly of the two largest subgenera, subgenus Riccia and subgenus Ricciella, are not supported, with the latter being polyphyletic and well nested within subgenus Riccia. Several currently accepted species such as Riccia inflexa and Riccia lamellosa were also found to be polyphyletic. A second tree reconstruction using only trnL–F sequences allowed comparison to several taxa collected outside of Australia. This showed that some species have a truly cosmopolitan distribution, whereas others have not.
Synostemon trachyspermus (F.Muell.) I.Telford & Pruesapan (Phyllanthaceae, Phyllantheae) is shown, by morphological studies and phylogenetic analysis using nrITS DNA sequence data, to be a heterogeneous species assemblage of four species. Phyllanthus rhytidospermus F.Muell. ex Müll.Arg., with a new combination provided as Synostemon rhytidospermus (F.Muell. ex Müll.Arg.) I.Telford & Pruesapan, and Sauropus hubbardii Airy Shaw, with a new combination as Synostemon hubbardii (Airy Shaw) I.Telford & Pruesapan, are re-instated as species. Phyllanthus arnhemicus S.Moore is lectotypified and placed in synonomy under Synostemon lissocarpus (S.Moore) I.Telford & Pruesapan, which is the new combination provided for Phyllanthus lissocarpus S.Moore (syn. Sauropus lissocarpus (S.Moore) Airy Shaw). Synostemon umbrosus I.Telford & J.J.Bruhl, a rare endemic from the Kimberley, Western Australia, is named as new. The newly described S. hamersleyensis I.Telford & Naaykens, endemic to the Pilbara, Western Australia, and the north-eastern Queensland endemic Sauropus aphyllus J.T.Hunter & J.J.Bruhl are shown to be closely related; the new combination Synostemon aphyllus (J.T.Hunter & J.J.Bruhl) I.Telford & Pruesapan is provided for the latter. Sauropus sp. A of Flora of the Kimberley Region, previously included within S. trachyspermus sens.lat., shows a more distant relationship and is named as Synostemon judithae I.Telford & J.J.Bruhl. Notes on distribution, habitat, phenology, conservation status, photomicrographs of seeds and a key to identification of the species are provided.
Next-generation sequencing (NGS) provides numerous tools for population and systematic studies. These tools are a boon to researchers working with non-model and poorly characterised organisms where little or no genomic resources exist. Several techniques have been developed to subsample the genomes of multiple individuals from related populations and species, so as to discover variable regions. We describe here the use of a modified AFLPseq method that provides a rapid and cost-effective approach to screening variable gene regions (SNPs) for multiple samples. Our method provides an adaptable toolkit for multiple downstream applications, which can be scaled up or down depending on the needs of the research question and budget. Using minor modifications to the protocol, we successfully recovered variable and useful markers that were applied to three case studies examining different scales of biological organisation, namely, from within populations to phylogenetic questions at the genus level and above. The case studies on Acacia and Eucalyptus generated genomic data across multiple taxonomic hierarchies, including demonstrating the detection of Acacia pinguifolia J.M.Black individuals used in restoration and their population origins, regional phylogeography of Acacia pycnantha Benth., and SNP-marker conservatism across some 70 million years of divergence among the Myrtaceae.