Recent range expansion in Australian hummock grasses (Triodia) inferred using genotyping-by-sequencing.

The Australian arid zone (AAZ) has undergone aridification and the formation of vast sandy deserts since the mid-Miocene. Studies on AAZ organisms, particularly animals, have shown patterns of mesic ancestry, persistence in rocky refugia and range expansions in arid lineages. There has been limited molecular investigation of plants in the AAZ, particularly of taxa that arrived in Australia after the onset of aridification. Here we investigate populations of the widespread AAZ grass Triodia basedowii to determine whether there is evidence for a recent range expansion, and if so, its source and direction. We also undertake a dating analysis for the species complex to which T. basedowii belongs, in order to place its diversification in relation to changes in AAZ climate and landscapes. We analyse a genomic single nucleotide polymorphism data set from 17 populations of T. basedowii in a recently developed approach for detecting the signal and likely origin of a range expansion. We also use alignments from existing and newly sequenced plastomes from across Poaceae for analysis in BEAST to construct fossil-calibrated phylogenies. Across a range of sampling parameters and outgroups, we detected a consistent signal of westward expansion for T. basedowii, originating in central or eastern Australia. Divergence time estimation indicates that Triodia began to diversify in the late Miocene (crown 7.0-8.8 million years (Ma)), and the T. basedowii complex began to radiate during the Pleistocene (crown 1.4-2.0 Ma). This evidence for range expansion in an arid-adapted plant is consistent with similar patterns in AAZ animals and likely reflects a general response to the opening of new habitat during aridification. Radiation of the T. basedowii complex through the Pleistocene has been associated with preferences for different substrates, providing an explanation why only one lineage is widespread across sandy deserts.

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions.

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae. Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae. Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 28.7 Mbases of sequence data. Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses. Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment. All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci. The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results. Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP). Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees. Analyses of newly sequenced plastomes were in agreement with current classifications. Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies. Alternative topologies were recovered in trees from partitions that included alignment gaps. This suggests that ambiguities in aligning these uncertain regions might introduce a false signal. Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 99.9% of grass diversity.

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.

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.

Morphological diversity and evolution of Centrolepidaceae (Poales), a species-poor clade with diverse body plans and developmental patterns.

UNLABELLED: • PREMISE OF THE STUDY: The small primarily Australian commelinid monocot family Centrolepidaceae displays remarkably high structural diversity that has been hitherto relatively poorly explored. Data on Centrolepidaceae are important for comparison with other Poales, including grasses and sedges.• METHODS: We examined vegetative and reproductive morphology in a global survey of Centrolepidaceae based on light and scanning electron microscopy of 18 species, representing all three genera. We used these data to perform a cladistic analysis to assess character evolution.• KEY RESULTS: Each of the three genera is monophyletic; Centrolepis is sister to Aphelia. Some Centrolepidaceae show a change from spiral to distichous phyllotaxy on inflorescence transition. In Aphelia and most species of Centrolepis, several morphologically distinct leaf types develop along the primary shoot axis and flowers are confined to dorsiventral lateral spikelets. Centrolepis racemosa displays secondary unification of programs of leaf development, absence of the leaf hyperphyll and loss of shoot dimorphism. Presence or absence of a leaf ligule and features of inflorescence and flower morphology are useful as phylogenetic characters in Centrolepidaceae.• CONCLUSIONS: Ontogenetic changes in phyllotaxy differ fundamentally between some Centrolepidaceae and many grasses. Inferred evolutionary transformations of phyllotaxy in Centrolepidaceae inflorescences also differ from those in grasses. In contrast with grasses, some Centrolepidaceae possess ligulate leaves where the ligule represents the boundary between the bifacial hypophyll and unifacial hyperphyll. All the highly unusual features of the morphological-misfit species Centrolepis racemosa could result from the same saltational event. Centrolepidaceae offer good perspectives for studies of evolutionary developmental biology.

Effectiveness of a tailored neck training program on neck strength, movement, and fatigue in under-19 male rugby players: a randomized controlled pilot study.

PURPOSE: To investigate the effect of a tailored neck muscle conditioning program on neck muscle strength, neck muscle fatigue, and range of neck movement in 16-18-year-old male rugby players. MATERIALS AND METHODS: Thirty-four male rugby players were divided into forward and back playing positions and randomized within these groups. Seventeen players were randomly assigned to each group. The test group was given a tailored 6-week exercise regime based on their baseline measurements to be performed three times a week in addition to their normal training and playing. The control group trained and played as normal. The outcome measures used were cervical spine range of movement, neck strength, and neck muscle fatigability. RESULTS: There were no clinically relevant statistically significant differences between the two groups. Trends identified between the two groups suggest that a tailored neck exercise program increases neck strength, particularly neck extension, and increases resistance to fatigue, as well as influencing right- and left-sided neck muscle balance. A reduction in range of movement was also demonstrated in the test group. There was a great deal of variability in range of movement and strength within this age group. No previously undiagnosed neck conditions were detected, and there were no adverse events reported. CONCLUSION: This study has shown that neck strength, range of movement, and susceptibility of the neck muscles to fatigue can be influenced using a focused neck training regime. It forms an important basis for a larger, multicenter study to ensure the neck is given due attention in rugby training and receives the same focus of conditioning as other parts of the body.

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

BACKGROUND: The 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. RESULTS: We 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. CONCLUSIONS: A 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.

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.