Schoolyard Biodiversity Determines Short-Term Recovery of Disturbed Skin Microbiota in Children.

Creating biodiverse urban habitat has been proposed, with growing empirical support, as an intervention for increasing human microbial diversity and reducing associated diseases. However, ecological understanding of urban biodiversity interventions on human skin microbiota remains limited. Here, we experimentally test the hypotheses that disturbed skin microbiota recover better in outdoor schoolyard environments and that greater biodiversity provides a greater response. Repeating the experiment three times, we disturbed skin microbiota of fifty-seven healthy 10-to-11-year-old students with a skin swab (i.e., cleaning), then exposed them to one school environment-either a 'classroom' (n = 20), 'sports field' (n = 14), or biodiverse 'forest' (n = 23)-for 45 min. Another skin swab followed the exposure to compare 'before' and 'after' microbial communities. After 45 min, the disturbance immediately followed by outdoor exposure, especially the 'forest', had an enriching and diversifying effect on skin microbiota, while 'classroom' exposure homogenised inter-personal variability. Each effect compounded over consecutive days indicating longer-term exposure outcomes. The experimental disturbance also reduced the core skin microbiota, and only outdoor environments were able to replenish lost species richness to core membership (n species > 50% prevalent). Overall, we find that environmental setting, especially including biodiversity, is important in human microbiota recovery periods and that the outdoors provide resilience to skin communities. This work also has implications for the inclusion of short periods of outside or forest exposure in school scheduling. Future investigations of the health impacts of permanent urban biodiversity interventions are needed.

Components of leaf-trait variation along environmental gradients.

Leaf area (LA), mass per area (LMA), nitrogen per unit area (Narea ) and the leaf-internal to ambient CO2 ratio (χ) are fundamental traits for plant functional ecology and vegetation modelling. Here we aimed to assess how their variation, within and between species, tracks environmental gradients. Measurements were made on 705 species from 116 sites within a broad north-south transect from tropical to temperate Australia. Trait responses to environment were quantified using multiple regression; within- and between-species responses were compared using analysis of covariance and trait-gradient analysis. Leaf area, the leaf economics spectrum (indexed by LMA and Narea ) and χ (from stable carbon isotope ratios) varied almost independently among species. Across sites, however, χ and LA increased with mean growing-season temperature (mGDD0 ) and decreased with vapour pressure deficit (mVPD0 ) and soil pH. LMA and Narea showed the reverse pattern. Climate responses agreed with expectations based on optimality principles. Within-species variability contributed < 10% to geographical variation in LA but > 90% for χ, with LMA and Narea intermediate. These findings support the hypothesis that acclimation within individuals, adaptation within species and selection among species combine to create predictable relationships between traits and environment. However, the contribution of acclimation/adaptation vs species selection differs among traits.

Bacterial natural product biosynthetic domain composition in soil correlates with changes in latitude on a continent-wide scale.

Although bacterial bioactive metabolites have been one of the most prolific sources of lead structures for the development of small-molecule therapeutics, very little is known about the environmental factors associated with changes in secondary metabolism across natural environments. Large-scale sequencing of environmental microbiomes has the potential to shed light on the richness of bacterial biosynthetic diversity hidden in the environment, how it varies from one environment to the next, and what environmental factors correlate with changes in biosynthetic diversity. In this study, the sequencing of PCR amplicons generated using primers targeting either ketosynthase domains from polyketide biosynthesis or adenylation domains from nonribosomal peptide biosynthesis was used to assess biosynthetic domain composition and richness in soils collected across the Australian continent. Using environmental variables collected at each soil site, we looked for environmental factors that correlated with either high overall domain richness or changes in the domain composition. Among the environmental variables we measured, changes in biosynthetic domain composition correlate most closely with changes in latitude and to a lesser extent changes in pH. Although it is unclear at this time the exact mix of factors that may drive the relationship between biosynthetic domain composition and latitude, from a practical perspective the identification of a latitudinal basis for differences in soil metagenome biosynthetic domain compositions should help guide future natural product discovery efforts.

Landscape biodiversity correlates with respiratory health in Australia.

Megatrends of urbanisation and reducing contact with natural environments may pose a largely unappreciated risk to human health, particularly in children, through declining normal (healthy) immunomodulatory environmental exposures. On the other hand, building knowledge of connections between environments, biodiversity and human health may offer new integrated ways of addressing global challenges of rising population health costs and declining biodiversity. In this study we are motivated to build insight and provide context and priority for emerging research into potential protective (e.g. immunomodulatory) environmental exposures. We use respiratory health as a test case to explore whether some types and qualities of environment may be more beneficial than others, and how such exposures may compare to known respiratory health influences, via a cross-sectional ecological epidemiology study for the continent of Australia. Using Lasso penalized regression (to interpret key predictors from many candidate variables) and 10-fold cross-validation modelling (to indicate reproducibility and uncertainty), within different socio-geographic settings, our results show surrogate measures of landscape biodiversity correlate with respiratory health, and rank amongst known predictors. A range of possible drivers for this relationship are discussed. Perhaps most novel and interesting of these is the possibility of protective immunomodulatory influence from microbial diversity (suggested by the understudied 'biodiversity hypothesis') and other bioactive agents associated with biodiverse environments. If beneficial influences can be demonstrated from biodiverse environments on immunomodulation and human health, there may be potential to design new cost-effective nature-based health intervention programs to reduce the risk of immune-related disease at a population level. Our approach and findings are also likely to have use in the evaluation of environment and health associations elsewhere.

Revegetation rewilds the soil bacterial microbiome of an old field.

Ecological restoration is a globally important and well-financed management intervention used to combat biodiversity declines and land degradation. Most restoration aims to increase biodiversity towards a reference state, but there are concerns that intended outcomes are not reached due to unsuccessful interventions and land-use legacy issues. Monitoring biodiversity recovery is essential to measure success; however, most projects remain insufficiently monitored. Current field-based methods are hard to standardize and are limited in their ability to assess important components of ecosystems, such as bacteria. High-throughput amplicon sequencing of environmental DNA (metabarcoding of eDNA) has been proposed as a cost-effective, scalable and uniform ecological monitoring solution, but its application in restoration remains largely untested. Here we show that metabarcoding of soil eDNA is effective at demonstrating the return of the native bacterial community in an old field following native plant revegetation. Bacterial composition shifted significantly after 8 years of revegetation, where younger sites were more similar to cleared sites and older sites were more similar to remnant stands. Revegetation of the native plant community strongly impacted on the belowground bacterial community, despite the revegetated sites having a long and dramatically altered land-use history (i.e. >100 years grazing). We demonstrate that metabarcoding of eDNA provides an effective way of monitoring changes in bacterial communities that would otherwise go unchecked with conventional monitoring of restoration projects. With further development, awareness of microbial diversity in restoration has significant scope for improving the efficacy of restoration interventions more broadly.

Finding needles in a genomic haystack: targeted capture identifies clear signatures of selection in a nonmodel plant species.

Teasing apart neutral and adaptive genomic processes and identifying loci that are targets of selection can be difficult, particularly for nonmodel species that lack a reference genome. However, identifying such loci and the factors driving selection have the potential to greatly assist conservation and restoration practices, especially for the management of species in the face of contemporary and future climate change. Here, we focus on assessing adaptive genomic variation within a nonmodel plant species, the narrow-leaf hopbush (Dodonaea viscosa ssp. angustissima), commonly used for restoration in Australia. We used a hybrid-capture target enrichment approach to selectively sequence 970 genes across 17 populations along a latitudinal gradient from 30°S to 36°S. We analysed 8462 single-nucleotide polymorphisms (SNPs) for FST outliers as well as associations with environmental variables. Using three different methods, we found 55 SNPs with significant correlations to temperature and water availability, and 38 SNPs to elevation. Genes containing SNPs identified as under environmental selection were diverse, including aquaporin and abscisic acid genes, as well as genes with ontologies relating to responses to environmental stressors such as water deprivation and salt stress. Redundancy analysis demonstrated that only a small proportion of the total genetic variance was explained by environmental variables. We demonstrate that selection has led to clines in allele frequencies in a number of functional genes, including those linked to leaf shape and stomatal variation, which have been previously observed to vary along the sampled environmental cline. Using our approach, gene regions subject to environmental selection can be readily identified for nonmodel organisms.

Transcriptome sequencing, annotation and polymorphism detection in the hop bush, Dodonaea viscosa.

BACKGROUND: The hop bush, Dodonaea viscosa, is a trans-oceanic species distributed oversix continents. It evolved in Australia where it is found over a wide range of habitat types and is an ecologically important species. Limited genomic resources are currently available for this species, thus our understanding of its evolutionary history and ecological adaptation is restricted. Here, we present a comprehensive transcriptome dataset for future genomic studies into this species. METHODS: We performed Illumina sequencing of cDNA prepared from leaf tissue collected from seven populations of D. viscosa ssp. angustissima and spatulata distributed along an environmental gradient in South Australia. Sequenced reads were assembled to provide a transcriptome resource. Contiguous sequences (contigs) were annotated using BLAST searches against the NCBI non-redundant database and gene ontology definitions were assigned. Single nucleotide polymorphisms were detected for the establishment of a genetic marker set. A comparison between the two subspecies was also carried out. RESULTS: Illumina sequencing returned 268,672,818 sequence reads, which were de novoassembled into 105,125 contigs. Contigs with significant BLAST alignments (E value < 1e(-5))numbered at 44,191, with 38,311 of these having their most significant hits to sequences from land plant species. Gene Ontology terms were assigned to 28,440 contigs and KEGG analysis identified 146 pathways that the gene products from 5,070 contigs are potentially involved in. The subspecies comparison identified 8,494 fixed SNP differences across 3,979 contiguous sequences, indicating a level of genetic differentiation between them. Across all samples, 248,235 SNPs were detected. CONCLUSIONS: We have established a significant genomic data resource for D. viscosa,providing a comprehensive transcriptomic reference. Genetic differences among morphologically distinct subspecies were found. A wide range of putative gene regions were identified along with a large set of variable SNP markers, providing a basis for studies into the evolution and ecological adaptation of D. viscosa.

Contrasting levels of connectivity and localised persistence characterise the latitudinal distribution of a wind-dispersed rainforest canopy tree.

Contrasting signals of genetic divergence due to historic and contemporary gene flow were inferred for Coachwood, Ceratopetalum apetalum (Cunoniaceae), a wind-dispersed canopy tree endemic to eastern Australian warm temperate rainforest. Analysis of nine nuclear microsatellites across 22 localities revealed two clusters between northern and southern regions and with vicariance centred on the wide Hunter River Valley. Within populations diversity was high indicating a relatively high level of pollen dispersal among populations. Genetic variation was correlated to differences in regional biogeography and ecology corresponding to IBRA regions, primary factors being soil type and rainfall. Eleven haplotypes were identified by chloroplast microsatellite analysis from the same 22 localities. A lack of chloroplast diversity within sites demonstrates limited gene flow via seed dispersal. Network representation indicated regional sharing of haplotypes indicative of multiple Pleistocene refugia as well as deep divergences between regional elements of present populations. Chloroplast differentiation between sites in the upper and lower sections of the northern population is reflective of historic vicariance at the Clarence River Corridor. There was no simple vicariance explanation for the distribution of the divergent southern chlorotype, but its distribution may be explained by the effects of drift from a larger initial gene pool. Both the Hunter and Clarence River Valleys represent significant dry breaks within the species range, consistent with this species being rainfall dependent rather than cold-adapted.

Systematic monitoring of heathy woodlands in a Mediterranean climate--a practical assessment of methods.

Practical and useful vegetation monitoring methods are needed, and data compatibility and validation of remotely sensed data are desirable. Methods have not been adequately tested for heathy woodlands. We tested the feasibility of detecting species composition shifts in remnant woodland in South Australia, comparing historical (1986) plot data with temporal replicates (2010). We compared the uniformity of species composition among spatially scattered versus spatially clustered plots. At two sites, we compared visual and point-intercept estimation of cover and species diversity. Species composition (presence/absence) shifted between 1986 and 2010. Species that significantly shifted in frequency had low cover. Observations of decreasing species were consistent with predictions from temperature response curves (generalised additive models) for climate change over the period. However, long-term trends could not be distinguished from medium-term dynamics or short-term changes in visibility from this dataset. Difficulties were highlighted in assessing compositional change using historical baselines established for a different purpose in terms of spatial sampling and accuracy of replicate plots, differences in standard plot methods and verification of species identifications. Spatially clustered replicate plots were more similar in species composition than spatially scattered plots, improving change detection potential but decreasing area of inference. Visual surveys detected more species than point-intercepts. Visual cover estimates differed little from point-intercepts although underestimating cover in some instances relative to intercepts. Point-intercepts provide more precise cover estimates of dominant species but took longer and were difficult in steep, heathy terrain. A decision tree based on costs and benefits is presented assessing monitoring options based on data presented. The appropriate method is a function of available resources, the need for precise cover estimates versus adequate species detection, replication and practical considerations such as access and terrain.

Shifts in reproductive assurance strategies and inbreeding costs associated with habitat fragmentation in Central American mahogany.

The influence of habitat fragmentation on mating patterns and progeny fitness in trees is critical for understanding the long-term impact of contemporary landscape change on the sustainability of biodiversity. We examined the relationship between mating patterns, using microsatellites, and fitness of progeny, in a common garden trial, for the insect-pollinated big-leaf mahogany, Swietenia macrophylla King, sourced from forests and isolated trees in 16 populations across Central America. As expected, isolated trees had disrupted mating patterns and reduced fitness. However, for dry provenances, fitness was negatively related to correlated paternity, while for mesic provenances, fitness was correlated positively with outcrossing rate and negatively with correlated paternity. Poorer performance of mesic provenances is likely because of reduced effective pollen donor density due to poorer environmental suitability and greater disturbance history. Our results demonstrate a differential shift in reproductive assurance and inbreeding costs in mahogany, driven by exploitation history and contemporary landscape context.

Leaf evolution in Southern Hemisphere conifers tracks the angiosperm ecological radiation.

The angiosperm radiation has been linked to sharp declines in gymnosperm diversity and the virtual elimination of conifers from the tropics. The conifer family Podocarpaceae stands as an exception with highest species diversity in wet equatorial forests. It has been hypothesized that efficient light harvesting by the highly flattened leaves of several podocarp genera facilitates persistence with canopy-forming angiosperms, and the angiosperm ecological radiation may have preferentially favoured the diversification of these lineages. To test these ideas, we develop a molecular phylogeny for Podocarpaceae using Bayesian-relaxed clock methods incorporating fossil time constraints. We find several independent origins of flattened foliage types, and that these lineages have diversified predominantly through the Cenozoic and therefore among canopy-forming angiosperms. The onset of sustained foliage flattening podocarp diversification is coincident with a declining diversification rate of scale/needle-leaved lineages and also with ecological and climatic transformations linked to angiosperm foliar evolution. We demonstrate that climatic range evolution is contingent on the underlying state for leaf morphology. Taken together, our findings imply that as angiosperms came to dominate most terrestrial ecosystems, competitive interactions at the foliar level have profoundly shaped podocarp geography and as a consequence, rates of lineage diversification.

Pollen diversity matters: revealing the neglected effect of pollen diversity on fitness in fragmented landscapes.

Few studies have documented the impacts of habitat fragmentation on plant mating patterns together with fitness. Yet, these processes require urgent attention to better understand the impact of contemporary landscape change on biodiversity and for guiding native plant genetic resource management. We examined these relationships using the predominantly insect-pollinated Eucalyptus socialis. Progeny were collected from trees located in three increasingly disturbed landscapes in southern Australia and were planted out in common garden experiments. We show that individual mating patterns were increasingly impacted by lower conspecific density caused by habitat fragmentation. We determined that reduced pollen diversity probably has effects over and above those of inbreeding on progeny fitness. This provides an alternative mechanistic explanation for the indirect density dependence often inferred between conspecific density and offspring fitness.

Anthropogenic landscape change promotes asymmetric dispersal and limits regional patch occupancy in a spatially structured bird population.

1. Local extinctions in habitat patches and asymmetric dispersal between patches are key processes structuring animal populations in heterogeneous environments. Effective landscape conservation requires an understanding of how habitat loss and fragmentation influence demographic processes within populations and movement between populations. 2. We used patch occupancy surveys and molecular data for a rainforest bird, the logrunner (Orthonyx temminckii), to determine (i) the effects of landscape change and patch structure on local extinction; (ii) the asymmetry of emigration and immigration rates; (iii) the relative influence of local and between-population landscapes on asymmetric emigration and immigration; and (iv) the relative contributions of habitat loss and habitat fragmentation to asymmetric emigration and immigration. 3. Whether or not a patch was occupied by logrunners was primarily determined by the isolation of that patch. After controlling for patch isolation, patch occupancy declined in landscapes experiencing high levels of rainforest loss over the last 100 years. Habitat loss and fragmentation over the last century was more important than the current pattern of patch isolation alone, which suggested that immigration from neighbouring patches was unable to prevent local extinction in highly modified landscapes. 4. We discovered that dispersal between logrunner populations is highly asymmetric. Emigration rates were 39% lower when local landscapes were fragmented, but emigration was not limited by the structure of the between-population landscapes. In contrast, immigration was 37% greater when local landscapes were fragmented and was lower when the between-population landscapes were fragmented. Rainforest fragmentation influenced asymmetric dispersal to a greater extent than did rainforest loss, and a 60% reduction in mean patch area was capable of switching a population from being a net exporter to a net importer of dispersing logrunners. 5. The synergistic effects of landscape change on species occurrence and asymmetric dispersal have important implications for conservation. Conservation measures that maintain large patch sizes in the landscape may promote asymmetric dispersal from intact to fragmented landscapes and allow rainforest bird populations to persist in fragmented and degraded landscapes. These sink populations could form the kernel of source populations given sufficient habitat restoration. However, the success of this rescue effect will depend on the quality of the between-population landscapes.

Leaf morphology shift linked to climate change.

Climate change is driving adaptive shifts within species, but research on plants has been focused on phenology. Leaf morphology has demonstrated links with climate and varies within species along climate gradients. We predicted that, given within-species variation along a climate gradient, a morphological shift should have occurred over time due to climate change. We tested this prediction, taking advantage of latitudinal and altitudinal variations within the Adelaide Geosyncline region, South Australia, historical herbarium specimens (n = 255) and field sampling (n = 274). Leaf width in the study taxon, Dodonaea viscosa subsp. angustissima, was negatively correlated with latitude regionally, and leaf area was negatively correlated with altitude locally. Analysis of herbarium specimens revealed a 2 mm decrease in leaf width (total range 1-9 mm) over 127 years across the region. The results are consistent with a morphological response to contemporary climate change. We conclude that leaf width is linked to maximum temperature regionally (latitude gradient) and leaf area to minimum temperature locally (altitude gradient). These data indicate a morphological shift consistent with a direct response to climate change and could inform provenance selection for restoration with further investigation of the genetic basis and adaptive significance of observed variation.

Shifts in floristic composition and structure in Australian rangelands.

Monitoring shifts in vegetation composition over time is essential for tracking biodiversity changes and for designing ecosystem management strategies. In Australia, the Terrestrial Ecosystem Research Network (TERN) provides a continent-wide network of monitoring sites (AusPlots) that can be used to assess the shifts in vegetation composition and structure of Australian Major Vegetation Groups (MVGs). Here we use time-series site data to quantify the extent and rate of MVG shifts between repeat visits and to recommend the most appropriate sampling frequency for specific MVGs. The research area spans a ~1,500 km latitudinal gradient within south/central Australia from arid rangelands in the north to Mediterranean vegetation in the south. The standardized AusPlots protocol was employed to repeatedly survey 103 one-hectare plots, assessed between 2011 and 2019. Floristic and growth form dissimilarities between visits were calculated with distance metrics and then regressed against survey interval. Multivariate ordination was used to explore temporal floristic shifts. Rank-dominance curves were used to display variations in species' importance. Between repeated visits, sites exhibited high variability for all vegetation parameters and trajectories. However, several trends emerged: (a) Species composition moved away from baseline linearly with intervals between surveys. (b) The rate of species turnover was approximately double in communities that are herbaceous versus woody-dominated. (c) Species abundances and growth forms shift at different speeds. All floristic and structural metrics shifted between re-visits, with varying magnitude and speed, but herbaceous-dominated plots showed higher floristic dynamism. Although the expanse, logistics, and the short time between visits constrained our analysis and interpretation, our results suggest that shorter revisit intervals may be appropriate for herbaceous compared to woody systems to track change most efficiently.

Assessing candidate DNA barcodes for Chinese and internationally traded timber species.

Accurate identification of species from timber is an essential step to help control illegal logging and forest loss. However, current approaches to timber identification based on morphological and anatomical characteristics have limited species resolution. DNA barcoding is a proven tool for plant species identification, but there is a need to build reliable reference data across broad taxonomic and spatial scales. Here, we construct a species barcoding library consisting of 1550 taxonomically diverse timber species from 656 genera and 124 families, representing a comprehensive genetic reference data set for Chinese timber species and international commercial traded timber species, using four barcodes (rbcL, matK, trnH-psbA, and ITS2). The ITS2 fragment was found to be the most efficient locus for Chinese timber species identification among the four barcodes tested, both at the species and genus level, despite its low recovery rate. Nevertheless, the barcode combination matK+trnH-psbA+ITS2 was required as a complementary barcode to distinguish closely related species in complex data sets involving internationally traded timber species. Comparative analyses of family-level discrimination and species/genus ratios indicated that the inclusion of closely related species is an important factor affecting the resolution ability of barcodes for timber species verification. Our study indicates that although nuclear ITS2 is the most efficient single barcode for timber species authentication in China, complementary combinations like matK+trnH-psbA+ITS2 are required to provide broader discrimination power. These newly-generated sequences enrich the existing publicly available databases, especially for tropical and subtropical evergreen timber trees and this current timber species barcode reference library can serve as an important genetic resource for forestry monitoring, illegal logging prosecution and biodiversity projects.

Rare genera differentiate urban green space soil bacterial communities in three cities across the world.

Vegetation complexity is potentially important for urban green space designs aimed at fostering microbial biodiversity to benefit human health. Exposure to urban microbial biodiversity may influence human health outcomes via immune training and regulation. In this context, improving human exposure to microbiota via biodiversity-centric urban green space designs is an underused opportunity. There is currently little knowledge on the association between vegetation complexity (i.e. diversity and structure) and soil microbiota of urban green spaces. Here, we investigated the association between vegetation complexity and soil bacteria in urban green spaces in Bournemouth, UK; Haikou, China; and the City of Playford, Australia by sequencing the 16S rRNA V4 gene region of soil samples and assessing bacterial diversity. We characterized these green spaces as having 'low' or 'high' vegetation complexity and explored whether these two broad categories contained similar bacterial community compositions and diversity around the world. Within cities, we observed significantly different alpha and beta diversities between vegetation complexities; however, these results varied between cities. Rare genera (<1% relative abundance individually, on average 35% relative abundance when pooled) were most likely to be significantly different in sequence abundance between vegetation complexities and therefore explained much of the differences in microbial communities observed. Overall, general associations exist between soil bacterial communities and vegetation complexity, although these are not consistent between cities. Therefore, more in-depth work is required to be done locally to derive practical actions to assist the conservation and restoration of microbial communities in urban areas.

Genomic, Habitat, and Leaf Shape Analyses Reveal a Possible Cryptic Species and Vulnerability to Climate Change in a Threatened Daisy.

Olearia pannosa is a plant species listed as vulnerable in Australia. Two subspecies are currently recognised (O. pannosa subsp. pannosa (silver daisy) and O. pannosa subsp. cardiophylla (velvet daisy)), which have overlapping ranges but distinct leaf shape. Remnant populations face threats from habitat fragmentation and climate change. We analysed range-wide genomic data and leaf shape variation to assess population diversity and divergence and to inform conservation management strategies. We detected three distinct genetic groupings and a likely cryptic species. Samples identified as O. pannosa subsp. cardiophylla from the Flinders Ranges in South Australia were genetically distinct from all other samples and likely form a separate, range-restricted species. Remaining samples formed two genetic clusters, which aligned with leaf shape differences but not fully with current subspecies classifications. Levels of genetic diversity and inbreeding differed between the three genetic groups, suggesting each requires a separate management strategy. Additionally, we tested for associations between genetic and environmental variation and carried out habitat suitability modelling for O. pannosa subsp. pannosa populations. We found mean annual maximum temperature explained a significant proportion of genomic variance. Habitat suitability modelling identified mean summer maximum temperature, precipitation seasonality and mean annual rainfall as constraints on the distribution of O. pannosa subsp. pannosa, highlighting increasing aridity as a threat for populations located near suitability thresholds. Our results suggest maximum temperature is an important agent of selection on O. pannosa subsp. pannosa and should be considered in conservation strategies. We recommend taxonomic revision of O. pannosa and provide conservation management recommendations.

Massively parallel sequencing and analysis of expressed sequence tags in a successful invasive plant.

BACKGROUND: Invasive species pose a significant threat to global economies, agriculture and biodiversity. Despite progress towards understanding the ecological factors associated with plant invasions, limited genomic resources have made it difficult to elucidate the evolutionary and genetic factors responsible for invasiveness. This study presents the first expressed sequence tag (EST) collection for Senecio madagascariensis, a globally invasive plant species. METHODS: We used pyrosequencing of one normalized and two subtractive libraries, derived from one native and one invasive population, to generate an EST collection. ESTs were assembled into contigs, annotated by BLAST comparison with the NCBI non-redundant protein database and assigned gene ontology (GO) terms from the Plant GO Slim ontologies. KEY RESULTS: Assembly of the 221,746 sequence reads resulted in 12,442 contigs. Over 50 % (6183) of 12,442 contigs showed significant homology to proteins in the NCBI database, representing approx. 4800 independent transcripts. The molecular transducer GO term was significantly over-represented in the native (South African) subtractive library compared with the invasive (Australian) library. Based on NCBI BLAST hits and literature searches, 40 % of the molecular transducer genes identified in the South African subtractive library are likely to be involved in response to biotic stimuli, such as fungal, bacterial and viral pathogens. CONCLUSIONS: This EST collection is the first representation of the S. madagascariensis transcriptome and provides an important resource for the discovery of candidate genes associated with plant invasiveness. The over-representation of molecular transducer genes associated with defence responses in the native subtractive library provides preliminary support for aspects of the enemy release and evolution of increased competitive ability hypotheses in this successful invasive. This study highlights the contribution of next-generation sequencing to better understanding the molecular mechanisms underlying ecological hypotheses that are important in successful plant invasions.