A review of current bioinformatic approaches for analysing target-capture data in plants, with a particular focus on robust phylogenetic inference in the presence of processes that can cause phylogenetic conflict, such as genome duplication, reticulation, deep coalescence and rapid or simultaneous speciation.

This article belongs to the collection: Genomics for Australian plants.

The science of genomics is rapidly revolutionising plant biodiversity science, and many institutions and researchers are ill-equipped to keep up with technical developments. To address this we established a national-scale consortium to build genomics capability and datasets for understanding the Australian flora. We outline the architecture and history of this collaboration and describe the major achievements to date, thereby demonstrating the value of a multi-institutional consortium approach. (Image credit: Glenn Harvey.)

This article belongs to the collection: Genomics for Australian plants.

The genus Melichrus has received very little taxonomic attention and treatments have largely disagreed on species delimitation. We present results from in-depth morphometric and molecular (DArtSeq) analyses designed to test species boundaries. These new lines of evidence form the basis of detailed recommendations for a revised species-level taxonomy of Melichrus including the description of eight new species and one subspecies, recircumscription of previously described species and the correction of a longstanding nomenclatural misapplication. (Photographs by H. T. Kennedy and J. J. Bruhl.)

Australia has a rich seaweed flora with many unique but poorly known species, genera and families. We compare results of an early 1970s anatomical study of one of the families with what modern molecular methods indicate about the same suite of genera. Previously considered to be a closely related group (monophyletic), we conclude that the family is polyphyletic (separate families). The study highlights how new insights from advanced technological applications can improve often intuitive taxonomic classification based on morphological characteristics.

Our study, conducted as part the Genomics for Australian Plants initiative, presents the first phylogenomic study of the very diverse genus Hibbertia using hundreds of nuclear and plastid gene sequences. The subject of significant recent taxonomic work, this study delivers new insights into the evolution and relationships between Hibbertia species. Results identify support for 14 novel clades in the genus and highlight areas of phylogenetic uncertainty, which will be used as a springboard for future systematic studies into the evolution of this remarkable genus. (Photograph by T. A. Hammer.)

This article belongs to the collection: Genomics for Australian plants.

Australian paper daisies have diversified in isolation over the past 20 million years. We studied populations of Coronidium and Leucozoma from across their ranges. Molecular analyses and comparison with morphology recovered both broadly distributed, morphologically variable species and narrow endemics, including four new species. The new insights into biodiversity, ecology, distribution and conservation status will enable conservation and land managers to better protect Australia’s natural heritage, and the broader community to enjoy these remarkable paper daisies. (Photographs by J. J. Bruhl.)

Zieria obcordata, an endangered species from central New South Wales, faces survival threats due to limited occurrence in two small, isolated populations. We show significant genetic divergence, suggesting that the members of each population should be recognised as separate subspecies, each with low genetic diversity. We recommend testing crosses between these populations to assess compatibility and potential fitness improvements to ehnance genetic diversity.

Tribe Chamelaucieae (Myrtaceae), a diverse, spectacular element of the Australian flora, has over 600 species continent-wide. We sequenced more than 300 nuclear genes for over 100 tribal representatives (including all genera), covering geographic and taxonomic diversity. Our understanding of tribal evolutionary relationships and how clades evolved through time and space improved. Tribal diversification correlates with major past climatic events and many lineages are shown to have dispersed from south-west Australia to the arid zone. (Photograph by Kevin R. Thiele.)

This article belongs to the collection: Genomics for Australian plants.

The Swedish Museum of Natural History houses poorly studied Chilean plant fossils that were collected >100 years ago. Among these we found leaf fossils of the Gondwanan Proteaceae family, whose closest relatives are currently found only in Australasian rainforests. These and other fossils from the same ~55-million-year-old assemblage add to evidence that a similar flora was formerly distributed across a vegetated Antarctica, and contradict a long-held view that Chilean forests of that time exclusively comprised Neotropical genera. (Photograph by R. J. Carpenter.)

We demonstrate that the current Gompholobium nitidum comprises three species. Originally described by Robert Brown in 1810 from specimens collected by Banks and Solander from the Endeavour River in 1770, the species was considered highly localised in Far North Queensland but has more recently been deemed a widely distributed plant of extremely variable leaflet form and habit. This work expands our knowledge of the diversity within this group of Gompholobium in north-east Queensland. Photograph by M. T. Mathieson (image 2B5A1345).

This article belongs to the collection: Genomics for Australian plants.

The Nicotiana megalosiphon species complex includes several morphologically cryptic species. We use phylogenetic and population genetic approaches (maximum likelihood, admixture proportions, Bayesian species delimitation and coalescent methods) to assess delimitations of these species and on this basis, describe a new species, N. palssonae M.W.Chase & Christenh. A map of species distributions and key to the species of the N. megalosiphon species complex are also provided.