Climate change may shift metapopulations towards unstable source-sink dynamics in a fire-killed, serotinous shrub.

Climate change, with warming and drying weather conditions, is reducing the growth, seed production, and survival of fire-adapted plants in fire-prone regions such as Mediterranean-type ecosystems. These effects of climate change on local plant demographics have recently been shown to reduce the persistence time of local populations of the fire-killed shrub Banksia hookeriana dramatically. In principle, extinctions of local populations may be partly compensated by recolonization events through long-distance dispersal mechanisms of seeds, such as post-fire wind and bird-mediated dispersal, facilitating persistence in spatially structured metapopulations. However, to what degree and under which assumptions metapopulation dynamics might compensate for the drastically increased local extinction risk remains to be explored. Given the long timespans involved and the complexity of interwoven local and regional processes, mechanistic, process-based models are one of the most suitable approaches to systematically explore the potential role of metapopulation dynamics and its underlying ecological assumptions for fire-prone ecosystems. Here we extend a recent mechanistic, process-based, spatially implicit population model for the well-studied fire-killed and serotinous shrub species B. hookeriana to a spatially explicit metapopulation model. We systematically tested the effects of different ecological processes and assumptions on metapopulation dynamics under past (1988-2002) and current (2003-2017) climatic conditions, including (i) effects of different spatio-temporal fires, (ii) effects of (likely) reduced intraspecific plant competition under current conditions and (iii) effects of variation in plant performance among and within patches. In general, metapopulation dynamics had the potential to increase the overall regional persistence of B. hookeriana. However, increased population persistence only occurred under specific optimistic assumptions. In both climate scenarios, the highest persistence occurred with larger fires and intermediate to long inter-fire intervals. The assumption of lower intraspecific plant competition caused by lower densities under current conditions alone was not sufficient to increase persistence significantly. To achieve long-term persistence (defined as >400 years) it was necessary to additionally consider empirically observed variation in plant performance among and within patches, that is, improved habitat quality in some large habitat patches (≥7) that could function as source patches and a higher survival rate and seed production for a subset of plants, specifically the top 25% of flower producers based on current climate conditions monitoring data. Our model results demonstrate that the impacts of ongoing climate change on plant demographics are so severe that even under optimistic assumptions, the existing metapopulation dynamics shift to an unstable source-sink dynamic state. Based on our findings, we recommend increased research efforts to understand the consequences of intraspecific trait variation on plant demographics, emphasizing the variation of individual traits both among and within populations. From a conservation perspective, we encourage fire and land managers to revise their prescribed fire plans, which are typically short interval, small fires, as they conflict with the ecologically appropriate spatio-temporal fire regime for B. hookeriana, and likely as well for many other fire-killed species.

Experimental seed sowing reveals seedling recruitment vulnerability to unseasonal fire.

Unseasonal fire occurrence is increasing globally, driven by climate change and other human activity. Changed timing of fire can inhibit postfire seedling recruitment through interactions with plant phenology (the timing of key processes, e.g., flower initiation, seed production, dispersal, germination), and therefore threaten the persistence of many plant species. Although empirical evidence from winter-rainfall ecosystems shows that optimal seedling recruitment is expected following summer and autumn (dry season) fires, we sought experimental evidence isolating the mechanisms of poor recruitment following unseasonal (wet season) fire. We implemented a seed-sowing experiment using nine species native to fire-prone, Mediterranean-climate woodlands in southwestern Australia to emulate the timing of postfire recruitment and test key mechanisms of fire seasonality effects. For seeds sown during months when fire is unseasonal (i.e., August-September: end of the wet winter season), seedling recruitment was reduced by up to 99% relative to seeds sown during seasonal fire months (i.e., May-June: end of the dry summer season) because of varying seed persistence, seedling emergence, and seedling survival. We found that up to 70 times more seedlings emerged when seeds were sown during seasonal fire months compared to when seeds were sown during unseasonal fire months. The few seedlings that emerged from unseasonal sowings all died with the onset of the dry season. Of the seeds that failed to germinate from unseasonal sowings, only 2% survived exposure on the soil surface over the ensuing hot and dry summer. Our experimental results demonstrate the potential for unseasonal fire to inhibit seedling recruitment via impacts on pregermination seed persistence and seedling establishment. As ongoing climate change lengthens fire seasons (i.e., unseasonal wildfires become more common) and managed fires are implemented further outside historically typical fire seasons, postfire seedling recruitment may become more vulnerable to failure, causing shifts in plant community composition towards those with fewer species solely dependent on seeds for regeneration.

Mechanisms of Fire Seasonality Effects on Plant Populations.

Altered fire regimes resulting from climate change and human activity threaten many terrestrial ecosystems. However, we lack a holistic and detailed understanding of the effects of altering one key fire regime component - season of fire. Altered fire seasonality can strongly affect post-fire recovery of plant populations through interactions with plant phenology. We identify seven key mechanisms of fire seasonality effects under a conceptual demographic framework and review evidence for these. We reveal negative impacts of altered fire seasonality and identify research gaps for mechanisms and climate types for future analyses of fire seasonality effects within the identified demographic framework. This framework and these mechanisms can inform critical decisions for conservation, land management, and fire management policy development globally.

Soil fungal responses to experimental warming and drying in a Mediterranean shrubland.

Implications of a drying and warming climate have been investigated for aboveground vegetation across a range of biomes yet below-ground effects on microorganisms have received considerably less attention, especially in Mediterranean Type Ecosystems (MTE) that are predicted to be negatively impacted by climate change. We experimentally reduced rainfall and increased temperature across two contrasting study sites (deep sand dune vs shallow sand swale) to test how projected future climate conditions may impact soil fungal composition, richness and diversity. We also assessed fungal OTU warming responses and putative functions of 100 most abundant OTUs and 120 OTUs that either increased or decreased based on their presence/absence across treatments. We found a significant effect of study site, treatment and canopy species on fungal composition. Soil fungal diversity increased under warming treatment in swale plots as compared to control plots indicating a positive effect of warming on fungal diversity. In dunes, significantly more OTUs responded to drought than warming treatment. Among the most abundant soil fungal putative functional groups were endophytes, ericoid mycorrhizas, yeasts and ectomycorrhizas consistent with previous studies. Plant pathogens were found to increase across dunes and swales, while ericoid mycorrhizae decreased. In summary, our study revealed that it is critical to understand belowground microbial patterns as a result of climate change treatments for our ability to better predict how ecosystems may respond to global environmental changes in the future.

Environmental drivers and genomic architecture of trait differentiation in fire-adapted Banksia attenuata ecotypes.

Trait divergence between populations is considered an adaptive response to different environments, but to what extent this response is accompanied by genetic differentiation is less clear since it may be phenotypic plasticity. In this study, we analyzed phenotypic variation between two Banksia attenuata growth forms, lignotuberous (shrub) and epicormic resprouting (tree), in fire-prone environments to identify the environmental factors that have driven this phenotypic divergence. We linked genotype with phenotype and traced candidate genes using differential gene expression analysis. Fire intervals determined the phenotypic divergence between growth forms in B. attenuata. A genome-wide association study identified 69 single nucleotide polymorphisms, putatively associated with growth form, whereas no growth form- or phenotype-specific genotypes were identified. Genomic differentiation between the two growth forms was low (Fst = 0.024). Differential gene expression analysis identified 37 genes/transcripts that were differentially expressed in the two growth forms. A small heat-shock protein gene, associated with lignotuber presence, was differentially expressed in the two forms. We conclude that different fire regimes induce phenotypic polymorphism in B. attenuata, whereas phenotypic trait divergence involves the differential expression of a small fraction of genes that interact strongly with the disturbance regime. Thus, phenotypic plasticity among resprouters is the general strategy for surviving varying fire regimes.

Subcontinental heat wave triggers terrestrial and marine, multi-taxa responses.

Heat waves have profoundly impacted biota globally over the past decade, especially where their ecological impacts are rapid, diverse, and broad-scale. Although usually considered in isolation for either terrestrial or marine ecosystems, heat waves can straddle ecosystems of both types at subcontinental scales, potentially impacting larger areas and taxonomic breadth than previously envisioned. Using climatic and multi-species demographic data collected in Western Australia, we show that a massive heat wave event straddling terrestrial and maritime ecosystems triggered abrupt, synchronous, and multi-trophic ecological disruptions, including mortality, demographic shifts and altered species distributions. Tree die-off and coral bleaching occurred concurrently in response to the heat wave, and were accompanied by terrestrial plant mortality, seagrass and kelp loss, population crash of an endangered terrestrial bird species, plummeting breeding success in marine penguins, and outbreaks of terrestrial wood-boring insects. These multiple taxa and trophic-level impacts spanned >300,000 km2-comparable to the size of California-encompassing one terrestrial Global Biodiversity Hotspot and two marine World Heritage Areas. The subcontinental multi-taxa context documented here reveals that terrestrial and marine biotic responses to heat waves do not occur in isolation, implying that the extent of ecological vulnerability to projected increases in heat waves is underestimated.

Characterization of Leaf Transcriptome in Banksia hookeriana.

Banksia is a significant element in vegetation of southwestern Australia, a biodiversity hotspot with global significance. In particular, Banksia hookeriana represents a species with significant economic and ecological importance in the region. For better conservation and management, we reported an overview of transcriptome of B. hookeriana using RNA-seq and de novo assembly. We have generated a total of 202.7 million reads (18.91 billion of nucleotides) from four leaf samples in four plants of B. hookeriana, and assembled 59,063 unigenes (average size=1098bp) through de novotranscriptome assembly. Among them, 39,686 unigenes were annotated against the Swiss-Prot, Clusters of Orthologous Groups (COG), and NCBI non-redundant (NR) protein databases. We showed that there was approximately one single nucleotide polymorphism (SNP) per 5.6-7.1kb in the transcriptome, and the ratio of transitional to transversional polymorphisms was approximately 1.82. We compared unigenes of B. hookeriana to those of Arabidopsis thaliana and Nelumbo nucifera through sequence homology, Gene Ontology (GO) annotation, and KEGG pathway analyses. The comparative analysis revealed that unigenes of B. hookeriana were closely related to those of N. nucifera. B. hookeriana, N. nucifera, and A. thaliana shared similar GO annotations but different distributions in KEGG pathways, indicating that B. hookeriana has adapted to dry-Mediterranean type shrublands via regulating expression of specific genes. In total 1927 potential simple sequence repeat (SSR) markers were discovered, which could be used in the genotype and genetic diversity studies of the Banksia genus. Our results provide valuable sequence resource for further study in Banksia.

Evolutionary potential and adaptation of Banksia attenuata (Proteaceae) to climate and fire regime in southwestern Australia, a global biodiversity hotspot.

Substantial climate changes are evident across Australia, with declining rainfall and rising temperature in conjunction with frequent fires. Considerable species loss and range contractions have been predicted; however, our understanding of how genetic variation may promote adaptation in response to climate change remains uncertain. Here we characterized candidate genes associated with rainfall gradients, temperatures, and fire intervals through environmental association analysis. We found that overall population adaptive genetic variation was significantly affected by shortened fire intervals, whereas declining rainfall and rising temperature did not have a detectable influence. Candidate SNPs associated with rainfall and high temperature were diverse, whereas SNPs associated with specific fire intervals were mainly fixed in one allele. Gene annotation further revealed four genes with functions in stress tolerance, the regulation of stomatal opening and closure, energy use, and morphogenesis with adaptation to climate and fire intervals. B. attenuata may tolerate further changes in rainfall and temperature through evolutionary adaptations based on their adaptive genetic variation. However, the capacity to survive future climate change may be compromised by changes in the fire regime.

Soil-vegetation relationships on a banded ironstone 'island', Carajás Plateau, Brazilian Eastern Amazonia.

Vegetation and soil properties of an iron-rich canga (laterite) island on the largest outcrop of banded-iron formation in Serra de Carajás (eastern Amazonia, Brazil) were studied along a topographic gradient (738-762 m asl), and analyzed to test the hypothesis that soil chemical and physical attributes play a key role in the structure and floristic composition of these plant communities. Soil and vegetation were sampled in eight replicate plots within each of the four vegetation types. Surface (0-10 cm) soil samples from each plot were analyzed for basic cations, N, P and plant species density for all species was recorded. CCA ordination analysis showed a strong separation between forest and non-forest sites on the first axis, and between herbaceous and shrubby campo rupestre on the second axis. The four vegetation types shared few plant species, which was attributed to their distinctive soil environments and filtering of their constituent species by chemical, physical and hydrological constraints. Thus, we can infer that Edaphic (pedological) factors are crucial in explaining the types and distributions of campo rupestre vegetation associated with ferruginous ironstone uplands (Canga) in Carajás, eastern Amazonia, therefore the soil properties are the main drivers of vegetation composition and structure on these ironstone islands.

A synthesis of postfire recovery traits of woody plants in Australian ecosystems.

Postfire resprouting and recruitment from seed are key plant life-history traits that influence population dynamics, community composition and ecosystem function. Species can have one or both of these mechanisms. They confer resilience, which may determine community composition through differential species persistence after fire. To predict ecosystem level responses to changes in climate and fire conditions, we examined the proportions of these plant fire-adaptive traits among woody growth forms of 2880 taxa, in eight fire-prone ecosystems comprising ~87% of Australia's land area. Shrubs comprised 64% of the taxa. More tree (>84%) than shrub (~50%) taxa resprouted. Basal, epicormic and apical resprouting occurred in 71%, 22% and 3% of the taxa, respectively. Most rainforest taxa (91%) were basal resprouters. Many trees (59%) in frequently-burnt eucalypt forest and savanna resprouted epicormically. Although crown fire killed many mallee (62%) and heathland (48%) taxa, fire-cued seeding was common in these systems. Postfire seeding was uncommon in rainforest and in arid Acacia communities that burnt infrequently at low intensity. Resprouting was positively associated with ecosystem productivity, but resprouting type (e.g. basal or epicormic) was associated with local scale fire activity, especially fire frequency. Although rainforest trees can resprout they cannot recruit after intense fires and may decline under future fires. Semi-arid Acacia communities would be susceptible to increasing fire frequencies because they contain few postfire seeders. Ecosystems dominated by obligate seeders (mallee, heath) are also susceptible because predicted shorter inter-fire intervals will prevent seed bank accumulation. Savanna may be resilient to future fires because of the adaptive advantage of epicormic resprouting among the eucalypts. The substantial non-resprouting shrub component of shrublands may decline, but resilient Eucalyptus spp. will continue to dominate under future fire regimes. These patterns of resprouting and postfire seeding provide new insights to ecosystem assembly, resilience and vulnerability to changing fire regimes on this fire-prone continent.

Microsatellite markers from the Ion Torrent: a multi-species contrast to 454 shotgun sequencing.

The development and screening of microsatellite markers have been accelerated by next-generation sequencing (NGS) technology and in particular GS-FLX pyro-sequencing (454). More recent platforms such as the PGM semiconductor sequencer (Ion Torrent) offer potential benefits such as dramatic reductions in cost, but to date have not been well utilized. Here, we critically compare the advantages and disadvantages of microsatellite development using PGM semiconductor sequencing and GS-FLX pyro-sequencing for two gymnosperm (a conifer and a cycad) and one angiosperm species. We show that these NGS platforms differ in the quantity of returned sequence data, unique microsatellite data and primer design opportunities, mostly consistent with the differences in read length. The strength of the PGM lies in the large amount of data generated at a comparatively lower cost and time. The strength of GS-FLX lies in the return of longer average length sequences and therefore greater flexibility in producing markers with variable product length, due to longer flanking regions, which is ideal for capillary multiplexing. These differences need to be considered when choosing a NGS method for microsatellite discovery. However, the ongoing improvement in read lengths of the NGS platforms will reduce the disadvantage of the current short read lengths, particularly for the PGM platform, allowing greater flexibility in primer design coupled with the power of a larger number of sequences.

Species-specific traits plus stabilizing processes best explain coexistence in biodiverse fire-prone plant communities.

Coexistence in fire-prone Mediterranean-type shrublands has been explored in the past using both neutral and niche-based models. However, distinct differences between plant functional types (PFTs), such as fire-killed vs resprouting responses to fire, and the relative similarity of species within a PFT, suggest that coexistence models might benefit from combining both neutral and niche-based (stabilizing) approaches. We developed a multispecies metacommunity model where species are grouped into two PFTs (fire-killed vs resprouting) to investigate the roles of neutral and stabilizing processes on species richness and rank-abundance distributions. Our results show that species richness can be maintained in two ways: i) strictly neutral species within each PFT, or ii) species within PFTs differing in key demographic properties, provided that additional stabilizing processes, such as negative density regulation, also operate. However, only simulations including stabilizing processes resulted in structurally realistic rank-abundance distributions over plausible time scales. This result underscores the importance of including both key species traits and stabilizing (niche) processes in explaining species coexistence and community structure.

Low rate of between-population seed dispersal restricts genetic connectivity and metapopulation dynamics in a clonal shrub.

Clonal species normally have low seed production, low recruitment rates and long lifespans, and it is expected that the rates of long-distance dispersal (LDD) of seeds will be low as well. Banksia candolleana is a clonal shrub in Mediterranean-type, fire-prone sclerophyll shrublands of southwestern Australia, whose reproductive biology and population dynamics contrast with those of co-occurring nonclonal congeneric species, all of which are restricted to a mosaic of sand dunes set within a matrix of inhospitable swales. Using microsatellite markers, we genotyped 499 plants in all 15 populations of B. candolleana within a 12-km(2) area, assessed population genetic differentiation, and quantified the effective rate of interpopulation seed dispersal through genetic assignment of individuals to populations. We measured life history, reproductive and demographic attributes, and compared these with two co-occurring Banksia species, a non-clonal resprouter and a nonsprouter. B. candolleana has much higher levels of population genetic differentiation, and one-third the rate of interpopulation seed migration, as the other two species (2.2% vs 5.5-6.8% of genotyped plants inferred to be immigrants), though distances reached by LDD are comparable (0.3-2.3 km). The low rate of interpopulation dispersal was supported by an analysis of the age structure of three populations that suggests a mean interdune migration rate of <800 m in 200 years, and 60% of suitable dunes remain uninhabited. Thus, B. candolleana has poor properties for promoting long-distance dispersal. It is unclear if these are idiosyncratic to this species or whether such properties are to be expected of clonal species in general where LDD is less critical for species survival.

Genetic connectivity and inter-population seed dispersal of Banksia hookeriana at the landscape scale.

BACKGROUND AND AIMS: Landscape genetics combines approaches from population genetics and landscape ecology, increasing the scope for conceptual advances in biology. Banksia hookeriana comprises clusters of individuals located on dune crests (geographical populations) physically separated by uninhabitable swales, with local extinctions common through frequent fire and/or severe drought. METHODS: A landscape genetics approach was used to explore landscape-scale genetic connectivity and structure among geographical populations of B. hookeriana on 18 physically separated dunes located within a heterogeneous landscape of 3 x 5 km. These geographical populations were separated by approx. 0.1 to >1 km of unsuitable intervening swale habitat. Using 11 highly variable microsatellite loci, we utilized a Bayesian approach to identify genetic discontinuities within and between these geographical populations. Population allocation tests were then used to detect inter-dune seed dispersal inferred from assignment of individuals to a source population other than that from which they were collected. KEY RESULTS: For the modal number of genetically distinct clusters (n = 17 genetic populations), two coincided with the geographical (dune) populations, eight spanned two to four geographical populations, and the remaining seven were spread among various parts of the sampled dunes, so that most geographical populations were spatially defined mosaics of individuals (subpopulations) belonging to two or more genetic populations. We inferred 25 inter-dune immigrants among the 582 individuals assessed, with an average distance between sink and source dunes of 1.1 km, and a maximum of 3.3 km. CONCLUSIONS: The results show that genetic structure in an apparently strongly spatially structured landscape is not solely dependent on landscape structure, and that many physically defined geographical populations were genetic mosaics. More strikingly, there were physically separated individuals and groups of individuals that were part of the same genetically defined populations. We attribute this mismatch between spatially and genetically defined population structure to the varying closeness of the dunes and the ability of seeds to disperse long distances.

Ants cannot account for interpopulation dispersal of the arillate pea Daviesia triflora.

Estimating distances and rates of seed dispersal, especially long-distance dispersal (LDD), is critical for understanding the dynamics of patchily distributed populations and species' range shifts in response to environmental change. Daviesia triflora (Papilionaceae) is an ant-dispersed shrub. The ant Rhytidoponera violacea was recorded dispersing its seeds to a maximum distance of 4.7 m, and in more intensive trials seeds of a related species from the study area, to a maximum of 8.1 m. Microsatellite DNA markers and population assignment tests identified interpopulation immigrants among 764 plants on 23 adjacent dunes bearing D. triflora, and 13 interpopulation seed dispersal (LDD) events (1.7%) were inferred. The distance between source and sink populations ranged from 410 m to 2350 m (mean 1260 m). These distances exceed ant dispersal distances by two to three orders of magnitude but are comparable with previous measurements of LDD for two co-occurring wing-seeded (wind-dispersed) species from the same system. The observed distances of seed dispersal in this arillate species demonstrate the significance of nonstandard dispersal mechanisms in LDD and the independence of these from primary dispersal syndromes. The likely role of emus in dispersal of the many 'ant-dispersed' species in Australia is discussed.

Late Quaternary climate change and spatial genetic structure in the shrub Banksia hookeriana.

Spatial genetic variation within species is influenced by both contemporary and historical factors. We attempted to assess the impact of increased aridity and lower temperatures associated with the last glacial maximum on possible refugia and the structuring of genetic variation in Banksia hookeriana, a shrub species restricted to deep sands on the Eneabba sandplain and adjacent Gingin Scarp/Dandaragan Plateau, centred 300 km north of Perth, Western Australia. We used optically stimulated luminescence (OSL) dating to estimate the last time these sands were mobile, as well as amplified fragment length polymorphisms (AFLP) to infer spatial patterns and the phylogeographical history of genetic variation among 15 populations of B. hookeriana. While genetic variation at the species level was high, with 96.6% of 238 AFLP markers polymorphic, average within population gene diversity was low (H(pop) = 0.16). Of the total genetic variation, an analysis of molecular variance (amova) partitioned 70% within populations, 24% among populations within substrate and 6% between substrates. There was an isolation-by-distance effect among populations within the same substrate, but not across substrates, and ordination highlighted genetic differentiation between the sandplain and scarp/plateau populations. A neighbour-joining tree identified the sandplain populations as a distinct clade, with the exception of the most northern sandplain population, which clustered with two northern and eastern plateau populations. The most southern plateau populations formed a clade sister to the sandplain clade. OSL dating of sand at six extant populations suggested that dunes were last mobile 15,000-35,000 years ago, with no clear difference in the ages of sandplain and plateau dunes. These data are consistent with a historical scenario of (re)colonization from isolated refugia of smaller populations either within the patchily vegetated sandplain and/or refugia at the northern, eastern and southern sandplain/scarp margins following postglacial climate amelioration and dune stabilization. Historic interpretations were confounded by the possible effects of long-distance dispersal, natural selection by substrate, and weak and/or ancient introgression with the sister species, Banksia prionotes.

Long-distance seed dispersal in a metapopulation of Banksia hookeriana inferred from a population allocation analysis of amplified fragment length polymorphism data.

There is currently a poor understanding of the nature and extent of long-distance seed dispersal, largely due to the inherent difficulty of detection. New statistical approaches and molecular markers offer the potential to accurately address this issue. A log-likelihood population allocation test (AFLPOP) was applied to a plant metapopulation to characterize interpopulation seed dispersal. Banksia hookeriana is a fire-killed shrub, restricted to sandy dune crests in fire-prone shrublands of the Eneabba sandplain, southwest Australia. Population genetic variation was assessed for 221 individuals sampled from 21 adjacent dune-crest populations of B. hookeriana using amplified fragment length polymorphism. Genetic diversity was high, with 175 of 183 (96%) amplified fragment length polymorphism markers polymorphic. Of the total genetic diversity, 8% was partitioned among populations by amova and FST. There was no relationship between genetic diversity within populations and population demographic parameters such as population size and sample size. A population allocation test on these data unambiguously assigned 177 of 221 (80.1%) individuals to a single population. Of these, 171 (77.4% of total) were assigned to the population from which they were sampled and 6 (2.7% of total) were assigned to a known population other than the one from which they were sampled. A further 9 (4.1% of total) were assigned to outside the sampled metapopulation area, and 35 individuals (15.8%) could not be assigned unambiguously to any particular population. These results suggest that both the extent [15 of 221 (6.8%) individuals originating from a population other than the one in which they occur] and distance (1.6 to > 2.5 km), of seed dispersal between dune-crest populations is greater than expected from previous studies. The extent of long-distance interpopulation seed dispersal observed provides a basis for explaining the survival of populations of the fire-killed B. hookeriana in a landscape experiencing frequent fire, where local extinctions and recolonizations may be a regular occurrence.