The secret hidden in dust: Assessing the potential to use biological and chemical properties of the airborne fraction of soil for provenance assignment and forensic casework.

The airborne fraction of soil (dust) is both ubiquitous in nature and contains localised biological and chemical signatures, making it a potential medium for forensic intelligence. Metabarcoding of dust can yield biological communities unique to the site of interest, similarly, geochemical analyses can uncover elements and minerals within dust that can be matched to a geographic location. Combining these analyses presents multiple lines of evidence as to the origin of dust collected from items of interest. In this work, we investigated whether bacterial and fungal communities in dust change through time and whether they are comparable to soil samples of the same site. We integrated dust metabarcoding into a framework amenable to forensic casework, (i.e., using calibrated log-likelihood ratios) to predict the origin of dust samples using models constructed from both dust samples and soil samples from the same site. Furthermore, we tested whether both metabarcoding and geochemical/mineralogical analyses could be conducted on a single swabbed sample, for situations where sampling is limited. We found both analyses could generate results from a single swabbed sample and found biological and chemical signatures unique to sites. However, we did find significant variation within sites, where this did not always correlate with time but was a random effect of sampling. This variation within sites was not greater than between sites and so did not influence site discrimination. When modelling bacterial and fungal diversity using calibrated log-likelihood ratios, we found samples were correctly predicted using dust 67% and 56% of the time and using soil 56% and 22% of the time for bacteria and fungi communities respectively. Incorrect predictions were related to within site variability, highlighting limitations to assigning dust provenance using metabarcoding of soil.

Historic and contemporary biogeographic perspectives on range-wide spatial genetic structure in a widespread seagrass.

Historical and contemporary processes drive spatial patterns of genetic diversity. These include climate-driven range shifts and gene flow mediated by biogeographical influences on dispersal. Assessments that integrate these drivers are uncommon, but critical for testing biogeographic hypotheses. Here, we characterize intraspecific genetic diversity and spatial structure across the entire distribution of a temperate seagrass to test marine biogeographic concepts for southern Australia. Predictive modeling was used to contrast the current Posidonia australis distribution to its historical distribution during the Last Glacial Maximum (LGM). Spatial genetic structure was estimated for 44 sampled meadows from across the geographical range of the species using nine microsatellite loci. Historical and contemporary distributions were similar, with the exception of the Bass Strait. Genetic clustering was consistent with the three currently recognized biogeographic provinces and largely consistent with the finer-scale IMCRA bioregions. Discrepancies were found within the Flindersian province and southwest IMCRA bioregion, while two regions of admixture coincided with transitional IMCRA bioregions. Clonal diversity was highly variable but positively associated with latitude. Genetic differentiation among meadows was significantly associated with oceanographic distance. Our approach suggests how shared seascape drivers have influenced the capacity of P. australis to effectively track sea level changes associated with natural climate cycles over millennia, and in particular, the recolonization of meadows across the Continental Shelf following the LGM. Genetic structure associated with IMCRA bioregions reflects the presence of stable biogeographic barriers, such as oceanic upwellings. This study highlights the importance of biogeography to infer the role of historical drivers in shaping extant diversity and structure.

Population decline in a Pleistocene refugium: Stepwise, drought-related dieback of a South Australian eucalypt.

Refugia can facilitate the persistence of species under long-term environmental change, but it is not clear if Pleistocene refugia will remain functional as anthropogenic climate change progresses. Dieback in populations restricted to refugia therefore raises concerns about their long-term persistence. Using repeat field surveys, we investigate dieback in an isolated population of Eucalyptus macrorhyncha during two droughts and discuss prospects for its continued persistence in a Pleistocene refugium. We first confirm that the Clare Valley in South Australia has constituted a long-term refugium for the species, with the population being genetically highly distinct from other conspecific populations. However, the population lost >40 % of individuals and biomass through the droughts, with mortality being just below 20 % after the Millennium Drought (2000-2009) and almost 25 % after the Big Dry (2017-2019). The best predictors of mortality differed after each drought. While north-facing aspect of a sampling location was significant positive predictor after both droughts, biomass density and slope were significant negative predictors only after the Millennium Drought, and distance to the north-west corner of the population, which intercepts hot, dry winds, was a significant positive predictor after the Big Dry only. This suggests that more marginal sites with low biomass and sites located on flat plateaus were more vulnerable initially, but that heat-stress was an important driver of dieback during the Big Dry. Therefore, the causative drivers of dieback may change during population decline. Regeneration occurred predominantly on southern and eastern aspects, which would receive the least solar radiation. While this refugial population is experiencing severe decline, some gullies with lower solar radiation appear to support relatively healthy, regenerating stands of red stringybark, providing hope for persistence in small pockets. Monitoring and managing these pockets during future droughts will be essential to ensure the persistence of this isolated and genetically unique population.

The utility of dust for forensic intelligence: Exploring collection methods and detection limits for environmental DNA, elemental and mineralogical analyses of dust samples.

Environmental DNA (eDNA), elemental and mineralogical analyses of soil have been shown to be specific to their source material, prompting consideration of using the airborne fraction of soil (dust) for forensic intelligence work. Dust is ubiquitous in the environment and is easily transferred to items belonging to a person of interest, making dust analysis an ideal tool in forensic casework. The advent of Massive Parallel Sequencing technologies means metabarcoding of eDNA can uncover bacterial, fungal, and even plant genetic fingerprints in dust particles. Combining this with elemental and mineralogical compositions offers multiple, complementary lines of evidence for tracing the origin of an unknown dust sample. This is particularly pertinent when recovering dust from a person of interest to ascertain where they may have travelled. Prior to proposing dust as a forensic trace material, however, the optimum sampling protocols and detection limits need to be established to place parameters around its utility in this context. We tested several approaches to collecting dust from different materials and determined the lowest quantity of dust that could be analysed for eDNA, elemental composition and mineralogy, whilst still yielding results capable of distinguishing between sites. We found that fungal eDNA profiles could be obtained from multiple sample types and that tape lifts were the optimum collection method for discriminating between sites. We successfully recovered both fungal and bacterial eDNA profiles down to 3 mg of dust (the lowest tested quantity) and recovered elemental and mineralogical compositions for all tested sample quantities. We show that dust can be reliably recovered from different sample types, using different sampling techniques, and that fungi and bacteria, as well as elemental and mineralogical profiles, can be generated from small sample quantities, highlighting the utility of dust for forensic intelligence.

A targeted capture approach to generating reference sequence databases for chloroplast gene regions.

Metabarcoding has improved the way we understand plants within our environment, from their ecology and conservation to invasive species management. The notion of identifying plant taxa within environmental samples relies on the ability to match unknown sequences to known reference libraries. Without comprehensive reference databases, species can go undetected or be incorrectly assigned, leading to false-positive and false-negative detections. To improve our ability to generate reference sequence databases, we developed a targeted capture approach using the OZBaits_CP V1.0 set, designed to capture chloroplast gene regions across the entirety of flowering plant diversity. We focused on generating a reference database for coastal temperate plant species given the lack of reference sequences for these taxa. Our approach was successful across all specimens with a target gene recovery rate of 92%, which was achieved in a single assay (i.e., samples were pooled), thus making this approach much faster and more efficient than standard barcoding. Further testing of this database highlighted 80% of all samples could be discriminated to family level across all gene regions with some genes achieving greater resolution than others-which was also dependent on the taxon of interest. Thus, we demonstrate the importance of generating reference sequences across multiple chloroplast gene regions as no single loci are sufficient to discriminate across all plant groups. The targeted capture approach outlined in this study provides a way forward to achieve this.

Phylogenomics and continental biogeographic disjunctions: insight from the Australian starflowers (Calytrix).

PREMISE: Continental-scale disjunctions and associated drivers are core research interests in biogeographic studies. Here, we selected a species-rich Australian plant genus (Calytrix; Myrtaceae) as a case study to investigate these patterns. Species of this endemic Australian starflower genus have a disjunct distribution across the mesic fringes of the continent and are largely absent from the arid center. METHODS: We used high-throughput sequencing to generate unprecedented resolution and near complete species-level nuclear and plastid phylogenies for Calytrix. BioGeoBEARS and biogeographic stochastic mapping were used to infer ancestral areas, the relative contributions of vicariance and dispersal events, and directionality of dispersal. RESULTS: Present-day disjunctions in Calytrix are explained by a combination of scenarios: (1) retreat of multiple lineages from the continental center to the more mesic fringes as Australia became progressively more arid, with subsequent extinction in the center as well as (2) origination of ancestral lineages in southwestern Australia (SWA) for species-rich clades. The SWA biodiversity hotspot is a major diversification center and the most common source area of dispersals, with multiple lineages originating in SWA and subsequently spreading to the adjacent arid Eremaean region. CONCLUSIONS: Our results suggest that major extinction, as a result of cooling and drying of the Australian continent in the Eocene-Miocene, shaped the present-day biogeography of Calytrix. We hypothesize that this peripheral vicariance pattern, which is similar to the African Rand flora, may explain the disjunctions of many other Australian plant groups. Further studies with densely sampled phylogenies are required to test this hypothesis.

Historical biogeography of Pomaderris (Rhamnaceae): Continental vicariance in Australia and repeated independent dispersals to New Zealand.

AIM: Gondwanan biogeographic patterns include a combination of old vicariance events following the breakup of the supercontinent, and more recent long-distance dispersals across the southern landmasses. Floristic relationships between Australia and New Zealand have mostly been attributed to recent dispersal events rather than vicariance. We assessed the biogeographic history of Pomaderris (Rhamnaceae), which occurs in both Australia and New Zealand, by constructing a time-calibrated molecular phylogeny to infer (1) phylogenetic relationships and (2) the relative contributions of vicariance and dispersal events in the biogeographic history of the genus. LOCATION: Australia and New Zealand. METHODS: Using hybrid capture and high throughput sequencing, we generated nuclear and plastid data sets to estimate phylogenetic relationships and fossil calibrated divergence time estimates for Pomaderris. BioGeoBEARS and biogeographical stochastic mapping (BSM) were used to assess the ancestral area of the genus and the relative contributions of vicariance vs dispersal, and the directionality of dispersal events. RESULTS: Our analyses indicate that Pomaderris originated in the Oligocene and had a widespread Australian distribution. Vicariance of western and eastern Australian clades coincides with the uplift of the Nullarbor Plain c. 14 Ma, followed by subsequent in-situ and within-biome diversification with little exchange across regions. A rapid radiation of southeastern Australian taxa beginning c. 10 Ma was the source for at least six independent long-distance dispersal events to New Zealand during the Pliocene-Pleistocene. MAIN CONCLUSIONS: Our study demonstrates the importance of dispersal in explaining not only the current cross-Tasman distributions of Pomaderris, but for the New Zealand flora more broadly. The pattern of multiple independent long-distance dispersal events for Pomaderris, without significant radiation within New Zealand, is congruent with other lowland plant groups, suggesting that this biome has a different evolutionary history compared with the younger alpine flora of New Zealand, which exhibits extensive radiations often following single long distance dispersal events.

Extinction pulse at Eocene-Oligocene boundary drives diversification dynamics of two Australian temperate floras.

The diversification dynamics of the Australian temperate flora remains poorly understood. Here, we investigate whether differences in plant richness in the southwest Australian (SWA) biodiversity hotspot and southeast Australian (SEA) regions of the Australian continent can be attributed to higher net diversification, more time for species accumulation, or both. We assembled dated molecular phylogenies for the 21 most species-rich flowering plant families found across mesic temperate Australia, encompassing both SWA and SEA regions, and applied a series of diversification models to investigate responses across different groups and timescales. We show that the high richness in SWA can be attributed to a higher net rate of lineage diversification and more time for species accumulation. Different pulses of diversification were retrieved in each region. A decrease in diversification rate across major flowering plant lineages at the Eocene-Oligocene boundary (ca 34 Ma) was witnessed in SEA but not in SWA. Our study demonstrates the importance of historical diversification pulses and differential responses to global events as drivers of present-day diversity. More broadly, we show that diversity within the SWA biodiversity hotspot is not only the result of recent radiations, but also reflects older events over the history of this planet.

Can bacterial indicators of a grassy woodland restoration inform ecosystem assessment and microbiota-mediated human health?

Understanding how microbial communities change with environmental degradation and restoration may offer new insights into the understudied ecology that connects humans, microbiota, and the natural world. Immunomodulatory microbial diversity and 'Old Friends' are thought to be supplemented from biodiverse natural environments, yet deficient in anthropogenically disturbed or degraded environments. However, few studies have compared the microbiomes of natural vs. human-altered environments and there is little knowledge of which microbial taxa are representative of ecological restoration-i.e. the assisted recovery of degraded ecosystems typically towards a more natural, biodiverse state. Here we use novel bootstrap-style resampling of site-level soil bacterial 16S rRNA gene environmental DNA data to identify genus-level indicators of restoration from a 10-year grassy eucalypt woodland restoration chronosequence at Mt Bold, South Australia. We found two key indicator groups emerged: 'opportunistic taxa' that decreased in relative abundance with restoration and more stable and specialist, 'niche-adapted taxa' that increased. We validated these results, finding seven of the top ten opportunists and eight of the top ten niche-adapted taxa displayed consistent differential abundance patterns between human-altered vs. natural samples elsewhere across Australia. Extending this, we propose a two-dimensional mapping for ecosystem condition based on the proportions of these divergent indicator groups. We also show that restoring a more biodiverse ecosystem at Mt Bold has increased the potentially immune-boosting environmental microbial diversity. Furthermore, environmental opportunists including the pathogen-containing genera Bacillus, Clostridium, Enterobacter, Legionella and Pseudomonas associated with disturbed ecosystems. Our approach is generalizable with potential to inform DNA-based methods for ecosystem assessment and help target environmental interventions that may promote microbiota-mediated human health gains.

Range-wide population genetic structure of the Caribbean marine angiosperm Thalassia testudinum.

Many marine species have widespread geographic ranges derived from their evolutionary and ecological history particularly their modes of dispersal. Seagrass (marine angiosperm) species have ranges that are unusually widespread, which is not unexpected following recent reviews of reproductive strategies demonstrating the potential for long-distance dispersal combined with longevity through clonality. An exemplar of these dual biological features is turtle grass (Thalassia testudinum) which is an ecologically important species throughout the tropical Atlantic region. Turtle grass has been documented to have long-distance dispersal via floating fruits and also extreme clonality and longevity. We hypothesize that across its range, Thalassia testudinum will have very limited regional population structure due to these characteristics and under typical models of population structure would expect to detect high levels of genetic connectivity. There are very few studies of range-wide genetic connectivity documented for seagrasses or other sessile marine species. This study presents a population genetic dataset that represents a geographic area exceeding 14,000 km2. Population genetic diversity was evaluated from 32 Thalassia testudinum populations sampled across the Caribbean and Gulf of Mexico. Genotypes were based on nine microsatellites, and haplotypes were based on chloroplast DNA sequences. Very limited phylogeographic signal from cpDNA reduced the potential comparative analyses possible. Multiple analytical clustering approaches on population genetic data revealed two significant genetic partitions: (a) the Caribbean and (b) the Gulf of Mexico. Genetic diversity was high (H E = 0.641), and isolation by distance was significant; gene flow and migration estimates across the entire range were however modest, we suggest that the frequency of successful recruitment across the range is uncommon. Thalassia testudinum maintains genetic diversity across its entire distribution range. The genetic split may be explained by genetic drift during recolonization from refugia following relatively recent reduction in available habitat such as the last glacial maxima.

Population structure and gene flow of the tropical seagrass, Syringodium filiforme, in the Florida Keys and subtropical Atlantic region.

Evaluating genetic diversity of seagrasses provides insight into reproductive mode and adaptation potential, and is therefore integral to broader conservation strategies for coastal ecosystems. In this study, we assessed genetic diversity, population structure and gene flow in an opportunistic seagrass, Syringodium filiforme, in the Florida Keys and subtropical Atlantic region. We used microsatellite markers to analyze 20 populations throughout the Florida Keys, South Florida, Bermuda and the Bahamas primarily to understand how genetic diversity of S. filiforme partitions across the Florida Keys archipelago. We found low allelic diversity within populations, detecting 35-106 alleles across all populations, and in some instances moderately high clonal diversity (R = 0.04-0.62). There was significant genetic differentiation between Atlantic and Gulf of Mexico (Gulf) populations (FST = 0.109 ± 0.027, p-value = 0.001) and evidence of population structure based on cluster assignment, dividing the region into two major genetic demes. We observed asymmetric patterns in gene flow, with a few instances in which there was higher than expected gene flow from Atlantic to Gulf populations. In South Florida, clustering into Gulf and Atlantic groups indicate dispersal in S. filiforme may be limited by historical or contemporary geographic and hydrologic barriers, though genetic admixture between populations suggests exchange may occur between narrow channels in the Florida Keys, or has occurred through other mechanisms in recent evolutionary history, maintaining regional connectivity. The variable genotypic diversity, low genetic diversity and evidence of population structure observed in populations of S. filiforme resemble the population genetics expected for a colonizer species.

Mega Clonality in an Aquatic Plant-A Potential Survival Strategy in a Changing Environment.

Many ecosystems are experiencing rapid transformations due to global environmental change. Understanding how ecological shifts affect species persistence is critical to modern management strategies. The edge of a species range is often where physiological tolerances are in conflict with ability to persist. Extreme examples of clonality over large spatial and temporal scales can occur where the life history of a species allows for it. We examine extreme clonality in an aquatic plant species at the edge if its range. Here we describe an ancient seagrass clone of unprecedented size inhabiting a 47 km stretch of a central Florida estuary, the Indian River Lagoon (IRL). Amongst the largest clones on earth detected, this Thalassia testudinum (turtlegrass) genet had ramets dispersed across 47 km of this water body. Indeed among 382 samples collections along the length of the IRL, 89% were a single shared multilocus genotype. Furthermore, this clone was the only genet detected at 63% of sample sites. The presence of such a large clone demonstrates they can form and persist over long periods. In addition, we must challenge the paradigm that fragmentation is not possible in this species. Reliance on clonality is an expected component of a classic 'bet-hedging' strategy enabling persistence on timescales typically not considered, including millennia. At locations near ocean inlets we did find a few other individuals of T. testudinum supporting the concept that recruitment is dispersal limited. These additional clones indicate there is the potential, albeit limited, for seeds based recruitment to occur when environmental conditions are favorable during a "window of opportunity." Extreme clonality represents a potential strategy for survival such that in the extreme, clonal populations of a species would be the first to decline or disappear if conditions extend beyond the adaptability of the local genotype. This disappearance possibility makes the species a potential sentinel of system decline.

Predicting the cumulative effect of multiple disturbances on seagrass connectivity.

The rate of exchange, or connectivity, among populations effects their ability to recover after disturbance events. However, there is limited information on the extent to which populations are connected or how multiple disturbances affect connectivity, especially in coastal and marine ecosystems. We used network analysis and the outputs of a biophysical model to measure potential functional connectivity and predict the impact of multiple disturbances on seagrasses in the central Great Barrier Reef World Heritage Area (GBRWHA), Australia. The seagrass networks were densely connected, indicating that seagrasses are resilient to the random loss of meadows. Our analysis identified discrete meadows that are important sources of seagrass propagules and that serve as stepping stones connecting various different parts of the network. Several of these meadows were close to urban areas or ports and likely to be at risk from coastal development. Deep water meadows were highly connected to coastal meadows and may function as a refuge, but only for non-foundation species. We evaluated changes to the structure and functioning of the seagrass networks when one or more discrete meadows were removed due to multiple disturbance events. The scale of disturbance required to disconnect the seagrass networks into two or more components was on average >245 km, about half the length of the metapopulation. The densely connected seagrass meadows of the central GBRWHA are not limited by the supply of propagules; therefore, management should focus on improving environmental conditions that support natural seagrass recruitment and recovery processes. Our study provides a new framework for assessing the impact of global change on the connectivity and persistence of coastal and marine ecosystems. Without this knowledge, management actions, including coastal restoration, may prove unnecessary and be unsuccessful.

Ambient soil cation exchange capacity inversely associates with infectious and parasitic disease risk in regional Australia.

Human contact with soil may be important for building and maintaining normal healthy immune defence mechanisms, however this idea remains untested at the population-level. In this continent-wide, cross-sectional study we examine the possible public health benefit of ambient exposures to soil of high cation exchange capacity (CEC), a surrogate for potential immunomodulatory soil microbial diversity. We compare distributions of normalized mean 2011/12-2012/13 age-standardized public hospital admission rates (cumulative incidence) for infectious and parasitic diseases across regional Australia (representing an average of 29,516 patients/year in 228 local government areas), within tertiles of socioeconomic status and soil exposure. To test the significance of soil CEC, we use probabilistic individual-level environmental exposure data (with or without soil), and group-level variables, in robust non-parametric multilevel modelling to predict disease rates in unseen groups. Our results show that in socioeconomically-deprived areas with high CEC soils, rates of infectious and parasitic disease are significantly lower than areas with low CEC soils. Also, health inequality (relative risk) due to socioeconomic status is significantly lower in areas with high CEC soils compared to low CEC soils (Δ relative risk = 0.47; 95% CI: 0.13, 0.82). Including soil exposure when modelling rates of infectious and parasitic disease significantly improves prediction performance, explaining an additional 7.5% (Δ r2 = 0.075; 95% CI: 0.05, 0.10) of variation in disease risk, in local government areas that were not used for model building. Our findings suggest that exposure to high CEC soils (typically high soil biodiversity) associates with reduced risk of infectious and parasitic diseases, particularly in lower socioeconomic areas.

Seagrass ecosystem trajectory depends on the relative timescales of resistance, recovery and disturbance.

Seagrass ecosystems are inherently dynamic, responding to environmental change across a range of scales. Habitat requirements of seagrass are well defined, but less is known about their ability to resist disturbance. Specific means of recovery after loss are particularly difficult to quantify. Here we assess the resistance and recovery capacity of 12 seagrass genera. We document four classic trajectories of degradation and recovery for seagrass ecosystems, illustrated with examples from around the world. Recovery can be rapid once conditions improve, but seagrass absence at landscape scales may persist for many decades, perpetuated by feedbacks and/or lack of seed or plant propagules to initiate recovery. It can be difficult to distinguish between slow recovery, recalcitrant degradation, and the need for a window of opportunity to trigger recovery. We propose a framework synthesizing how the spatial and temporal scales of both disturbance and seagrass response affect ecosystem trajectory and hence resilience.

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.

Disturbance Is an Important Driver of Clonal Richness in Tropical Seagrasses.

Clonality is common in many aquatic plant species, including seagrasses, where populations are maintained through a combination of asexual and sexual reproduction. One common measure used to describe the clonal structure of populations is clonal richness. Clonal richness is strongly dependent on the biological characteristics of the species, and how these interact with the environment but can also reflect evolutionary scale processes especially at the edge of species ranges. However, little is known about the spatial patterns and drivers of clonal richness in tropical seagrasses. This study assessed the spatial patterns of clonal richness in meadows of three tropical seagrass species, Thalassia hemprichii, Halodule uninervis, and Halophila ovalis, spanning a range of life-history strategies and spatial scales (2.5-4,711 km) in Indonesia and NW Australia. We further investigated the drivers of clonal richness using general additive mixed models for two of the species, H. uninervis and H. ovalis, over 8° latitude. No significant patterns were observed in clonal richness with latitude, yet disturbance combined with sea surface temperature strongly predicted spatial patterns of clonal richness. Sites with a high probability of cyclone disturbance had low clonal richness, whereas an intermediate probability of cyclone disturbance and the presence of dugong grazing combined with higher sea surface temperatures resulted in higher levels of clonal richness. We propose potential mechanisms for these patterns related to the recruitment and mortality rates of individuals as well as reproductive effort. Under a changing climate, increased severity of tropical cyclones and the decline in populations of mega-grazers have the potential to reduce clonal richness leading to less genetically diverse populations.

Identifying knowledge gaps in seagrass research and management: An Australian perspective.

Seagrass species form important marine and estuarine habitats providing valuable ecosystem services and functions. Coastal zones that are increasingly impacted by anthropogenic development have experienced substantial declines in seagrass abundance around the world. Australia, which has some of the world's largest seagrass meadows and is home to over half of the known species, is not immune to these losses. In 1999 a review of seagrass ecosystems knowledge was conducted in Australia and strategic research priorities were developed to provide research direction for future studies and management. Subsequent rapid evolution of seagrass research and scientific methods has led to more than 70% of peer reviewed seagrass literature being produced since that time. A workshop was held as part of the Australian Marine Sciences Association conference in July 2015 in Geelong, Victoria, to update and redefine strategic priorities in seagrass research. Participants identified 40 research questions from 10 research fields (taxonomy and systematics, physiology, population biology, sediment biogeochemistry and microbiology, ecosystem function, faunal habitats, threats, rehabilitation and restoration, mapping and monitoring, management tools) as priorities for future research on Australian seagrasses. Progress in research will rely on advances in areas such as remote sensing, genomic tools, microsensors, computer modeling, and statistical analyses. A more interdisciplinary approach will be needed to facilitate greater understanding of the complex interactions among seagrasses and their environment.

Molecular phylogenetics and the morphology of the Lycopodiaceae subfamily Huperzioideae supports three genera: Huperzia, Phlegmariurus and Phylloglossum.

The generic classification of huperzioid Lycopodiaceae was tested using Bayesian inference and Maximum likelihood phylogenetic analyses of DNA sequences from four chloroplast loci for 119 taxa and optimisation of 29 morphological characteristics onto the phylogeny. Consistent with previous studies, the subfamilies Lycopodioideae and Huperzioideae are monophyletic and diagnosable by synapomorphies that correlate with differences in their life-histories. Within the Huperzioideae, the monophyly of the widely adopted genus Huperzia (excl. Phylloglossum) is poorly supported. Three clades of huperzioid Lycopodiaceae were recovered in all analyses of molecular data: Phylloglossum drummondii, Huperzia sensu stricto and Phlegmariurus sensu lato. These clades are strongly supported by morphological characters, including differences in spores, gametophytes, sporophyte macro-morphology, as well as growth habit and life-histories. Our findings indicate that either a one-genus (Huperzia s.l.) or a three-genus (Phylloglossum, Huperzia s.s. and Phlegmariurus s.l.) classification of huperzioid Lycopods are equally supported by molecular evidence, but a two-genus system (Huperzia s.l.+Phylloglossum) is not. We recommend recognising three genera in the huperzioid Lycopodiaceae, as this classification best reflects evolutionary, ecological, and morphological divergence within the lineage.

A framework for the resilience of seagrass ecosystems.

Seagrass ecosystems represent a global marine resource that is declining across its range. To halt degradation and promote recovery over large scales, management requires a radical change in emphasis and application that seeks to enhance seagrass ecosystem resilience. In this review we examine how the resilience of seagrass ecosystems is becoming compromised by a range of local to global stressors, resulting in ecological regime shifts that undermine the long-term viability of these productive ecosystems. To examine regime shifts and the management actions that can influence this phenomenon we present a conceptual model of resilience in seagrass ecosystems. The model is founded on a series of features and modifiers that act as interacting influences upon seagrass ecosystem resilience. Improved understanding and appreciation of the factors and modifiers that govern resilience in seagrass ecosystems can be utilised to support much needed evidence based management of a vital natural resource.