Matthew D. Barrett

Reconstructing the age and historical biogeography of the ancient flowering-plant family Hydatellaceae (Nymphaeales).

BackgroundThe aquatic flowering-plant family Hydatellaceae has a classic Gondwanan distribution, as it is found in Australia, India and New Zealand. To shed light on the biogeographic history of this apparently ancient branch of angiosperm phylogeny, we dated the family in the context of other seed-plant divergences, and evaluated its biogeography using parsimony and likelihood methods. We also explicitly tested the effect of different extinction rates on biogeographic inferences.ResultsWe infer that the stem lineage of Hydatellaceae originated in the Lower Cretaceous; in contrast, its crown originated much more recently, in the early Miocene, with the bulk of its diversification after the onset of the Pliocene. Biogeographic reconstructions predict a mix of dispersal and vicariance events, but considerations of geological history preclude most vicariance events, besides a split at the root of the family between southern and northern clades. High extinction rates are plausible in the family, and when these are taken into account there is greater uncertainty in biogeographic inferences.ConclusionsA stem origin for Hydatellaceae in the Lower Cretaceous is consistent with the initial appearance of fossils attributed to its sister clade, the water lilies. In contrast, the crown clade is young, indicating that vicariant explanations for species outside Australia are improbable. Although long-distance dispersal is likely the primary driver of biogeographic distribution in Hydatellaceae, we infer that the recent drying out of central Australia divided the family into tropical vs. subtropical/temperate clades around the beginning of the Miocene.

Pollen morphology of the Myrtaceae. Part 3: Tribes Chamelaucieae, Leptospermeae and Lindsayomyrteae

The pollen morphology of 36 genera and 147 species from the Myrtaceae tribes Chamelaucieae, Leptospermeae and Lindsayomyrteae was surveyed using scanning electron microscopy (SEM) and light microscopy (LM). Syncolpate pollen were observed in all genera of Leptospermeae and some genera of Chamelaucieae. Genera of tribe Chamelaucieae displayed five distinct colpal morphologies, which makes it the tribe with the most diverse pollen in Myrtaceae. Six genera of Chamelaucieae, including Actinodium, Chamelaucium, Darwinia, Homoranthus, Pileanthus and Verticordia, produce large acolpate pollen not observed in any other Myrtaceae. Two of these genera produce distinct pollen; Actinodium is the only genus to have prolate-spheroidal shaped pollen, and Pileanthus pollen is large and dicolporate. A number of anomalous aperture types occurred in species of Chamelaucieae, including monocolporate (Homoranthus thomasii), pentacolporate (Calytrix oldfieldii) and hexacolporate (Sannantha tozerensis). Pollen of Lindsayomyrteae appeared similar to those of Leptospermeae and Chamelaucieae, and on the basis of pollen features, could be related to these two tribes.

Untangling a species complex of arid zone grasses (Triodia) reveals patterns congruent with co-occurring animals.

The vast Australian arid zone formed over the last 15million years, and gradual aridification as well as more extreme Pliocene and Pleistocene climate shifts have impacted the evolution of its biota. Understanding the evolutionary history of groups of organisms or regional biotas such as the Australian arid biota requires clear delimitation of the units of biodiversity (taxa). Here we integrate evidence from nuclear (ETS and ITS) and chloroplast (rps16-trnK spacer) regions and morphology to clarify taxonomic boundaries in a species complex of Australian hummock grasses (Triodia) to better understand the evolution of Australian arid zone plants and to evaluate congruence in distribution patterns with co-occurring organisms. We find evidence for multiple new taxa in the T. basedowii species complex, but also incongruence between data sets and indications of hybridization that complicate delimitation. We find that the T. basedowii complex has high lineage diversity and endemism in the biologically important Pilbara region of Western Australia, consistent with the region acting as a refugium. Taxa show strong geographic structure in the Pilbara, congruent with recent work on co-occurring animals and suggesting common evolutionary drivers across the biota. Our findings confirm recognition of the Pilbara as an important centre of biodiversity in the Australian arid zone, and provide a basis for future taxonomic revision of the T. basedowii complex and more detailed study of its evolutionary history and that of arid Australia.

Molecular phylogeny and global diversity of the remarkable genus Bondarzewia (Basidiomycota, Russulales)

Bondarzewia is a remarkable polypore genus due to its relatively large poroid basidiocarps and belongs to order Russulales according to recent phylogenetic analyses. Two species, B. berkeleyi and B. mesenterica, are commonly reported in North America and Europe but the genus is poorly known elsewhere. We explored the phylogeny and species diversity of Bondarzewia based on a larger number of samples covering a wider geographic range, including eastern Asia, Europe, North America, Oceania and South America. Sequences were generated from the nuc rDNA region encompassing the internal transcribed spacers 1 and 2, along with the 5.8S rDNA (ITS) and nuc 28S rDNA D1-D2 domains (28S), and the final dataset included 28 samples of which 21 ITS and 28S sequences were newly generated. As a result of phylogenetic analyses and comparison of morphological features we propose a new classification of the genus recognizing 10 species. Most of the novel taxonomic concepts are geographically restricted in contrast to the past broad species concepts, especially of B. berkeleyi. In addition, a degree of host specificity is observed with B. mesenterica, B. occidentalis, B. podocarpi, B. propria and B. submesenterica apparently restricted to gymnosperms and all others on angiosperm hosts where known. Three new species, B. kirkii, B. occidentalis and B. submesenterica, are described and illustrated. Three new combinations (B. dickinsii, B. propria, B. retipora) are revived from synonymy under B. berkeleyi. A key to known species of Bondarzewia is provided.

Characterization and cross application of novel microsatellite markers for a rare sedge, Lepidosperma gibsonii (Cyperaceae).

PREMISE OF THE STUDY Ten polymorphic microsatellite loci for the rare sword sedge Lepidosperma gibsonii (Cyperaceae) were characterized for the future study of population structure, hybridization, and clonality. METHODS AND RESULTS Twenty samples from each of three populations were screened with the markers to assess genetic variation. Observed population heterozygosities ranged from 0.35 to 1.00, and number of alleles observed per locus ranged from eight to 23. No departures from Hardy-Weinberg equilibrium were detected for any locus in any population. Single samples from 14 species were screened to examine the transferability of the microsatellites to other species of Lepidosperma. At least eight out of 10 loci amplified in all species tested. CONCLUSIONS These loci will be useful for studying genetic variation, hybridization, dispersal, and breeding systems in Lepidosperma, a ubiquitous element of the flora of southern Australia.

Eriocortex eriocauli, gen. et sp. nov. (Ustilaginomycetes) from Australia

A new genus, Eriocortex is proposed to accommodate a peculiar, new smut fungus, E. eriocauli, collected in Australia on Eriocaulon scullionii.

Phylogenetic revision of Backhousieae (Myrtaceae): Neogene divergence, a revised circumscription of Backhousia and two new species

Abstract. Backhousieae is a small tribe of Myrtaceae composed of two genera (Backhousia and Choricarpia) endemic to Australia. Phylogenetic analyses (parsimony, maximum likelihood and Bayesian) were performed on a combined chloroplast (matK, trnH–psbA, trnC–psbM, trnL–F, rps16) and nuclear (internal transcribed spacers) dataset for all nine species of Backhousia, two species of Choricarpia and two undescribed species. Backhousieae is monophyletic; however, Choricarpia is embedded within Backhousia. In all analyses there were four strongly supported clades containing two to four taxa, with no support for relationships among clades, and the relationships of B. bancroftii and B. citriodora remain unresolved. Bayesian relaxed-clock molecular dating indicated that the Backhousieae has been potentially present in rainforest across Australia for more than 50 million years. The current distribution of Backhousia is inferred to be largely due to the contraction of Australian rainforest in the Neogene. New combinations in Backhousia are made for the two species of Choricarpia, and B. gundarara and B. tetraptera are described as new species. B. gundarara is known only from the Kimberley region of Western Australia, widely disjunct from the remaining Backhousia in eastern Queensland and New South Wales, and appears to be a lineage isolated by increasing aridity during the Miocene.

Novel chloroplast markers for the study of intraspecific variation and hybridisation in the Lepidosperma costale species complex (Cyperaceae)

To investigate intraspecific variation and hybridisation in the Lepidosperma costale species complex, forty-one primers to amplify regions containing chloroplast microsatellites and insertions/deletions were designed using de novo sequencing. Twenty-six loci were polymorphic within three diploid populations, with 2 to 9 alleles per locus. A further 15 loci exhibited fixed size differences between the diploid individuals and a population of putative allopolyploid origin. These markers will assist studies of genetic diversity and hybridisation in Lepidosperma, help inform the conservation of taxa in the Lepidosperma costale species complex, and may have utility across the Cyperaceae.

Genotyping-by-Sequencing in a Species Complex of Australian Hummock Grasses (Triodia): Methodological Insights and Phylogenetic Resolution

Next-generation sequencing is becoming increasingly accessible to researchers asking biosystematic questions, but current best practice in both choosing a specific approach and effectively analysing the resulting data set is still being explored. We present a case study for the use of genotyping-by-sequencing (GBS) to resolve relationships in a species complex of Australian arid and semi-arid grasses (Triodia R.Br.), highlighting our solutions to methodological challenges in the use of GBS data. We merged overlapping paired-end reads then optimised locus assembly in the program PyRAD to generate GBS data sets for phylogenetic and distance-based analyses. In addition to traditional concatenation analyses in RAxML, we also demonstrate the novel use of summary species tree analyses (taking gene trees as input) with GBS loci. We found that while species tree analyses were relatively robust to variation in PyRAD assembly parameters, our RAxML analyses resulted in well-supported but conflicting topologies under different assembly settings. Despite this conflict, multiple clades in the complex were consistently supported as distinct across analyses. Our GBS data assembly and analyses improve the resolution of taxa and phylogenetic relationships in the Triodia basedowii complex compared to our previous study based on Sanger sequencing of nuclear (ITS/ETS) and chloroplast (rps16-trnK spacer) markers. The genomic results also partly support previous evidence for hybridization between species in the complex. Our methodological insights for analysing GBS data will assist researchers using similar data to resolve phylogenetic relationships within species complexes.

DNA ploidy variation and distribution in the Lepidosperma costale complex (Cyperaceae): implications for conservation and restoration in a biodiversity hotspot

Intraspecific ploidy variation is an important component of angiosperm biodiversity; however, this variation is rarely considered in conservation programs. This is of particular concern when conservation activities include augmentation, reintroduction or ecological restoration because there are potentially negative consequences when ploidy variants are unintentionally mixed within populations. We surveyed regional ploidy variation in the Lepidosperma costale Nees species complex (Schoeneae: Cyperaceae) in the South West Australian Floristic Region, an international biodiversity hotspot. Several L. costale sensu lato populations are threatened by iron-ore extraction, including the rare L. gibsonii R.L.Barrett, and these populations are the subject of ecological restoration programs. The DNA ploidy of 2384 individuals from 28 populations across the range of the species complex was determined and four DNA ploidy levels were discovered, namely, diploid, triploid, tetraploid and pentaploid. Diploids and tetraploids were the most common cytotypes and were largely geographically segregated, even at an exhaustively studied contact zone. Triploids were found at a low frequency in two populations. The rarity of triploids suggests substantial interploidy sterility, and that mixing of ploidy variants should, therefore, be avoided when restoring L. costale s.l. populations. These data provide a guide for L. costale s.l. germplasm collection and suggest that polyploidy may be an important driver of diversification in these sedges.