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Summary1. Ecological invasions are often associated with persistent changes to underlying ecological processes. Restoration of invaded communities is dependent on manipulation of these processes to favour the target species composition and impart resistance to further invasion. We applied these principles to extensively degraded grassy woodlands in temperate agricultural regions of Australia, where widespread invasion by mediterranean annuals is related to altered ecological processes such as soil nutrient cycling. 2. We investigated carbon supplementation and spring burns, in association with reestablishment of native perennial grasses, as potential management tools for manipulating nitrogen cycling, soil seed banks and establishment conditions in degraded woodland understoreys. Through these mechanisms we aimed to enhance native cover and increase resistance to invasion by exotic annuals. 3. In two contrasting degraded remnants, repeated sucrose applications temporarily reduced soil nitrate to inferred pre-European levels, which dramatically reduced growth of exotic annuals and enhanced native perennial abundance. Repeated spring burns did not reduce soil nitrate but reduced exotic annual grasses through effects on soil seed banks and/or establishment conditions. 4. Spring burns and carbon supplements both significantly enhanced establishment of Themeda australis , a dominant tussock grass prior to European settlement. Combinations of T. australis seed addition and either spring burning or carbon supplements enhanced native plant abundance more effectively than treatments without seed addition. 5. Within 18 months of their establishment, T. australis seedlings significantly reduced soil nitrate in some treatments, providing a preliminary indication that re-establishment of a dense sward of this species may restore ecosystem function to a low-nitrate state that favours native perennials over exotic annuals. 6. Synthesis and applications . Ecological restoration can be viewed as targeted intervention in species-environment interactions, whereby ecological conditions are manipulated to enhance establishment or vigour of key species, and these species in turn help restore ecological processes that favour the target species composition. In grassy ecosystems re-establishing a perennial sward of appropriate native tussock grasses may be critical for restoring pre-disturbance nitrogen cycles and improving resistance to invasion by exotic annuals. Carbon supplements and spring burns facilitate this process through complementary mechanisms.

Temperate grassy woodlands were once the dominant vegetation across many agricultural regions of south-eastern Australia, but most of these are now highly degraded and fragmented. Adequate conservation of these woodlands is dependent on successful ecological restoration; however, ecological barriers often limit ecosystem recovery once degrading processes are removed. To help identify these barriers, we used a state and transition framework to compare topsoils of little-disturbed (reference) and variously degraded remnants of grassy Eucalyptus albens Benth. and E. melliodora Cunn. ex Schauer woodlands. Topsoils of degraded remnants showed a repeated pattern, with the most compacted, most acidic and most depleted topsoils occurring in remnants dominated by Aristida ramosa R.Br. or Austrodanthonia H.P.Linder and Austrostipa scabra (Lindl.) S.W.L.Jacobs & J.Everett; the least compacted and most nutrient rich topsoils in remnants dominated by annual exotics; and generally intermediate topsoils in remnants dominated by Bothriochloa macra (Steud.) S.T.Blake or Austrostipa bigeniculata (Hughes) S.W.L.Jacobs & J.Everett. Surprisingly, topsoils beneath trees in reference sites (supporting Poa sieberiana Spreng.) were similar to topsoils supporting annual exotics for most soil properties. Chemical properties of topsoils from open areas of reference sites [supporting Themeda australis (R.Br.) Stapf] were usually intermediate and similar to Bothriochloa macra and Austrostipa bigeniculata topsoils. The most striking exception to these trends was for soil nitrate, which was extremely low in all reference topsoils and showed a high correlation with annual exotic abundance. We discuss the potential for positive feedbacks between soil nitrogen cycling and understorey composition and the need for intervention to assist possible nitrate-dependent transitions between annual and perennial understorey states. Dominant grasses, trees and annual weed abundance may be useful indicators of soil conditions and could inform selection of target sites, species and techniques for restoration projects.

Before European settlement, grassy white box woodlands were the dominant vegetation in the east of the wheat-sheep belt of south-eastern Australia. Tree clearing, cultivation and pasture improvement have led to fragmentation of this once relatively continuous ecosystem, leaving a series of remnants which themselves have been modified by livestock grazing. Little-modified remnants are extremely rare. We examined and compared the effects of fragmentation and disturbance on the understorey flora of woodland remnants, through a survey of remnants of varying size, grazing history and tree clearing. In accordance with fragmentation theory, species richness generally increased with remnant size, and, for little-grazed remnants, smaller remnants were more vulnerable to weed invasion. Similarly, tree clearing and grazing encouraged weed invasion and reduced native species richness. Evidence for increased total species richness at intermediate grazing levels, as predicted by the intermediate disturbance hypothesis, was equivocal. Remnant quality was more severely affected by grazing than by remnant size. All little-grazed remnants had lower exotic species abundance and similar or higher native species richness than grazed remnants, despite their extremely small sizes (< 6 ha). Further, small, littlegrazed remnants maintained the general character of the pre-European woodland understorey, while grazing caused changes to the dominant species. Although generally small, the little-grazed remnants are the best representatives of the pre-European woodland understorey, and should be central to any conservation plan for the woodlands. Selected larger remnants are needed to complement these, however, to increase the total area of woodland conserved, and, because most little-grazed remnants are cleared, to represent the ecosystem in its original structural form. For the maintenance of native plant diversity and composition in little-grazed remnants, it is critical that livestock grazing continues to be excluded. For grazed remnants, maintenance of a site in its current state would allow continuation of past management, while restoration to a pre-European condition would require management directed towards weed removal, and could take advantage of the difference noted in the predominant life-cycle of native (perennial) versus exotic (annual or biennial) species.

Abstract— Data scored for cladistic analyses may be quantitative or qualitative, continuous or discrete, and show overlapping or non‐overlapping values between taxa. Quantitative and qualitative are modes of expression of data, while continuous or discrete refer to properties of the set of numbers that express the data; both these pairs of terms have been confused with overlapping and non‐overlapping. The degree of overlap of values between taxa is often used to filter characters in cladistic analyses: if a minimum amount of overlap is exceeded, or a minimum amount of disjunction not reached, characters are rejected as “not cladistic". However, this rests on a confusion between features of taxa and features of individual organisms (attributes). Cladistic characters are features of taxa, and comprise frequency distributions of attribute values over individuals of a taxon. Cladistic characters logically cannot overlap, although taxa may have overlapping attribute values. Thus, a priori rejection of characters that have overlapping attribute values is non‐sensical. Such data may still be rejected from consideration for cladistic analysis if it could be demonstrated that they contain little recoverable phylogenetic signal. Few published analyses have empirically tested this. An analysis of overlapping morphometric data from three series of Banksia suggests that, at least in these cases, they map phylogeny almost as accurately as more conventional, qualitative morphological data. While more such tests are required, morphometric data should not be rejected a priori from cladistic analyses.

BackgroundHerbaria are valuable sources of extensive curated plant material that are now accessible to genetic studies because of advances in high-throughput, next-generation sequencing methods. As an applied assessment of large-scale recovery of plastid and ribosomal genome sequences from herbarium material for plant identification and phylogenomics, we sequenced 672 samples covering 21 families, 142 genera and 530 named and proposed named species. We explored the impact of parameters such as sample age, DNA concentration and quality, read depth and fragment length on plastid assembly error. We also tested the efficacy of DNA sequence information for identifying plant samples using 45 specimens recently collected in the Pilbara.ResultsGenome skimming was effective at producing genomic information at large scale. Substantial sequence information on the chloroplast genome was obtained from 96.1% of samples, and complete or near-complete sequences of the nuclear ribosomal RNA gene repeat were obtained from 93.3% of samples. We were able to extract sequences for the core DNA barcode regions rbcL and matK from 96 to 93.3% of samples, respectively. Read quality and DNA fragment length had significant effects on sequencing outcomes and error correction of reads proved essential. Assembly problems were specific to certain taxa with low GC and high repeat content (Goodenia, Scaevola, Cyperus, Bulbostylis, Fimbristylis) suggesting biological rather than technical explanations. The structure of related genomes was needed to guide the assembly of repeats that exceeded the read length. DNA-based matching proved highly effective and showed that the efficacy for species identification declined in the order cpDNA >> rDNA > matK >> rbcL.ConclusionsWe showed that a large-scale approach to genome sequencing using herbarium specimens produces high-quality complete cpDNA and rDNA sequences as a source of data for DNA barcoding and phylogenomics.

Temperate grassy woodlands were once widespread and dominant in many agricultural regions of south-eastern Australia. Most are now highly degraded and fragmented and exist within a context of broadscale landscape degradation. Greater understanding of natural processes in these woodlands is needed to benchmark management and restoration efforts that are now critical for their ongoing survival. We studied physical and chemical properties of topsoils from rare, little-grazed remnants of grassy Eucalyptus albens Benth. and E. melliodora Cunn. ex Schauer woodlands in central New South Wales and examined natural patterns in topsoil properties and understorey flora in relation to trees and canopy gaps. Topsoils were generally low in available macronutrients (nitrogen, phosphorus and sulfur), but were favourable for plant growth in most other measured characteristics. Topsoils beneath trees were notably more fertile than in open areas, particularly in total carbon, total nitrogen, available phosphorus, available potassium and salinity. Higher nutrient concentrations, particularly of available phosphorus, may have contributed to patterns in understorey dominants, with Themeda australis (R.Br.) Stapf predominating in open areas and Poa sieberiana Spreng. beneath trees. Trees were also associated with a higher native-plant richness, possibly resulting from their influence on the competitive dynamics of the dominant grasses. We discuss the implications of these interactions for the use of burning, grazing and slashing in woodland management and re-establishment of native grasses and trees in restoration efforts.