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.

Recruitment dynamics of invasive species in rainforest habitats following Cyclone Larry

In tropical forests, natural disturbance creates opportunities for species to claim previously utilized space and resources and is considered an important mechanism in the maintenance of species diversity. However, ecologists have long recognized that disturbance also promotes exotic plant invasions. Cyclones cause extensive defoliation, loss of major branches and multiple tree falls, resulting in a significantly more open canopy and increased light and heat levels in the understorey. The widespread and massive disturbance caused by cyclones provides ideal conditions for rapid recruitment and spread of invasive species. The ecological roles of invasive species in rainforest habitats following such a severe disturbance are poorly understood. Severe category 4 Cyclone Larry crossed the North Queensland coast in March 2006 causing massive disturbance to rainforest habitats from Tully to Cairns and west to the Atherton Tablelands. We established 10 plots in an area extensively damaged by this cyclone near El Arish in North Queensland. On each plot nine 2 × 2 m quadrats were established with three quadrats per plot in each of the following treatments: (i) complete debris removal down to the soil layer, (ii) removal of coarse woody debris only, and (iii) uncleared. We monitored recruitment, growth and mortality of all native and invasive species in the 90 quadrats every 3 months since the cyclone. Here we present the recruitment dynamics of invasive species across the study area in relation to the level of disturbance, the type of quadrat treatment, and the diversity and abundance of the native recruiting flora over the first 12 months post-cyclone. Our results suggest that invasive species will mostly comprise a transient component of the flora in the early stages of the successional response. However, some species may have longer-term effects on the successional trajectory of the rainforest and future forest composition and structure.

Effects of an invasive species on refuge-site selection by native fauna : the impact of cane toads on native frogs in the Australian tropics

Invasive species can induce shifts in habitat use by native taxa: either by modifying habitat availability, or by repelling or attracting native species to the vicinity of the invader. The ongoing invasion of cane toads (Rhinella marina) through tropical Australia might affect native frogs by affecting refuge-site availability, because both frogs and toads frequently shelter by day in burrows. Our laboratory and field studies in the wet-dry tropics show that native frogs of at least three species (Litoria tornieri, Litoria nasuta and Litoria dahlii) preferentially aggregate with conspecifics, and with (some) other species of native frogs. However, the frogs rarely aggregated with cane toads either in outdoor arenas or in standardized experimental burrows that we monitored in the field. The native frogs that we tested either avoided burrows containing cane toads (or cane toad scent) or else ignored the stimulus (i.e. treated such a burrow in the same way as they did an empty burrow). Native frogs selected a highly non-random suite of burrows as diurnal retreat sites, whereas cane toads were less selective. Hence, even in the absence of toads, frogs do not use many of the burrows that are suitable for toads. The invasion of cane toads through tropical Australia is unlikely to have had a major impact on retreat-site availability for native frogs.

Historical demography of Lantana camara L. reveals clues about the influence of land use and weather in the management of this widespread invasive species

Weather is a general stochastic influence on the life history of weeds. In contrast, anthropogenic disturbance (e.g. land use) is an important deterministic influence on weed demography. Our aim with this study was to investigate the relative contributions of land use and weather on the demography of Lantana camara (lantana), a weed of agricultural and natural habitats, based on the intensive monitoring of lantana populations under three land uses (viz. farm[pasture], and burnt and grazed forests) in subtropical Australia. Lantana populations were growing vigorously across all land uses (asymptotic population growth rate, lambda > 3). Examination of historical demography using retrospective perturbation analyses showed that weather was a strong influence on lantana demography with the transition from an El Nino (2008-09) to a La Nina (2009-10) year having a strong positive effect on population growth rate. This effect was most marked at the grazed site, and to a lesser extent at the burnt site, with seedling-to-juvenile and juvenile-to-adult transitions contributing most to these effects. This is likely the result of burning and grazing having eliminated/reduced interspecific competition at these sites. Prospective perturbation analyses revealed that lambda was most sensitive to proportionate changes in growth transitions, followed by fecundity and survival transitions. Examination of context-specific patterns in elasticity revealed that growth and fecundity transitions are likely to be the more critical vital rates to reduce lambda in wet years at the burnt and grazed forest sites, compared to the farm/pasture site. Management of lantana may need to limit the transition of juveniles into the adult stages, especially in sites where lantana is free from competition (e.g. in the presence of fire or grazing), and this particularly needs to be achieved in wet years. Collectively, these results shed light on aspects of spatial and temporal variation in the demography of lantana, and offer insights on its context-specific management.

Historical demography of Lantana camara L. reveals clues about the influence of land use and weather in the management of this widespread invasive species

Weather is a general stochastic influence on the life history of weeds. In contrast, anthropogenic disturbance (e.g. land use) is an important deterministic influence on weed demography. Our aim with this study was to investigate the relative contributions of land use and weather on the demography of Lantana camara (lantana), a weed of agricultural and natural habitats, based on the intensive monitoring of lantana populations under three land uses (viz. farm[pasture], and burnt and grazed forests) in subtropical Australia. Lantana populations were growing vigorously across all land uses (asymptotic population growth rate, λ > 3). Examination of historical demography using retrospective perturbation analyses showed that weather was a strong influence on lantana demography with the transition from an El Niño (2008–09) to a La Niña (2009–10) year having a strong positive effect on population growth rate. This effect was most marked at the grazed site, and to a lesser extent at the burnt site, with seedling-to-juvenile and juvenile-to-adult transitions contributing most to these effects. This is likely the result of burning and grazing having eliminated/reduced interspecific competition at these sites. Prospective perturbation analyses revealed that λ was most sensitive to proportionate changes in growth transitions, followed by fecundity and survival transitions. Examination of context-specific patterns in elasticity revealed that growth and fecundity transitions are likely to be the more critical vital rates to reduce λ in wet years at the burnt and grazed forest sites, compared to the farm/pasture site. Management of lantana may need to limit the transition of juveniles into the adult stages, especially in sites where lantana is free from competition (e.g. in the presence of fire or grazing), and this particularly needs to be achieved in wet years. Collectively, these results shed light on aspects of spatial and temporal variation in the demography of lantana, and offer insights on its context-specific management.

Maternal effects on offspring size and packaging constraints in the whelk

Life-history theory predicts an optimal offspring size, irrespective of reproductive effort; however, in some species offspring size correlates positively with maternal size. We examine hypotheses for why this latter situation should occur in the whelk Buccinum undatum. The trade-offs between aspects of reproduction in whelks are complicated due to the provision of protective egg capsules. Many eggs are placed within each capsule but c. 99% of these eggs are consumed by the remaining developing young. Large maternal size results in more eggs, larger eggs, more eggs consumed per hatchling, more capsules, larger capsules, more eggs per capsule, a larger number of hatchlings per capsule and larger hatchlings. Increased intra-capsule and post-hatch sibling competition may decrease the marginal value for additional young and select for larger young, however, our data do not support this explanation. Instead, packaging constraints within each capsule limit the size of hatchlings but this constraint is relaxed for medium to large females because they produce large capsules. Small females appear to produce young below optimum size because of the space constraint thus explaining the correlation between maternal size and offspring size.

Existing and emerging high impact invasive species are characterized by higher functional responses than natives

Predicting ecological impacts of invasive species and identifying potentially damaging future invaders are research priorities. Since damage by invaders is characterized by their depletion of resources, comparisons of the ‘functional response’ (FR; resource uptake rate as a function of resource density) of invaders and natives might predict invader impact. We tested this by comparing FRs of the ecologically damaging ‘world's worst’ invasive fish, the largemouth bass (Micropterus salmoides), with a native equivalent, the Cape kurper (Sandelia capensis), and an emerging invader, the sharptooth catfish (Clarias gariepinus), with the native river goby (Glossogobius callidus), in South Africa, a global invasion hotspot. Using tadpoles (Hyperolius marmoratus) as prey, we found that the invaders consumed significantly more than natives. Attack rates at low prey densities within invader/native comparisons reflected similarities in predatory strategies; however, both invasive species displayed significantly higher Type II FRs than the native comparators. This was driven by significantly lower prey handling times by invaders, resulting in significantly higher maximum feeding rates. The higher FRs of these invaders are thus congruent with, and can predict, their impacts on native communities. Comparative FRs may be a rapid and reliable method for predicting ecological impacts of emerging and future invasive species.

Maternal effects in the Zebra Finch : a model mother reviewed

Birds are a particularly good group with which to examine the importance of maternal effects, as parental contributions can be relatively easily quantified compared with other groups. There have undoubtedly been more studies on maternal effects in the Zebra Finch than any other single bird species. Studies of this species have examined the importance of maternal effects mediated through sex allocation, size, nutrients and hormones of of eggs, incubation behaviour and provisioning levels. A synthesis of all of this work illustrates some contrasting results (e.g. many high-profile results have failed to be replicated), some very common patterns (e.g. investment shifts through the laying sequence), and potentially interesting and complex interactions between traits (e.g. between sex of offspring and hormonal profiles of eggs). This extensive collection of work on the Zebra Finch provides useful general insight into the patterns of maternal investment in birds and the effects on offspring phenotype. However, we caution that the literature is probably littered with studies that have overemphasised the importance of some maternal effects and recent studies have highlighted analytical and logical flaws that have probably led to misplaced confidence in some of the findings reported to date. Finally, it is worth considering that the bulk of the literature is based on studies of captive domesticated birds and ecological and physiological data from individuals in the wild is currently lacking. The biological relevance of maternal effects documented in this model species is therefore unclear.

Detecting the impact of invasive species on native fauna: Cane toads (Bufo marinus), frillneck lizards (Chlamydosaurus kingii) and the importance of spatial replication

An understanding of which native species are severely impacted by an anthropogenic change (such as the arrival of an invasive species) and which are not is critical to prioritizing conservation efforts. However, it is difficult to detect such impacts if the native taxa exhibit strong stochastic variations in abundance; a ‘natural’ population decline might be wrongly interpreted as an impact of the invader. Frillneck lizards (Chlamydosaurus kingii) are large iconic Australian agamids, and have been reported to decline following the invasion of toxic cane toads. We monitored three populations of the species in the savanna woodland of tropical Australia over a 7-year period bracketing toad arrival. One population crashed, one remained stable and one increased. Hence, studies on any single population might have inferred that cane toads have negative, negligible or positive effects on frillneck lizards. With the benefit of spatial replication, and in combination with observations of prey choice by captive lizards, our data suggest that invasive cane toads have had little or no effect on frillneck abundance.

Mechanisms of species divergence through visual adaptation and sexual selection: Perspectives from a cichlid model system

The theory of ecological speciation suggests that assortative mating evolves most easily when mating preferences are;directly linked to ecological traits that are subject to divergent selection. Sensory adaptation can play a major role in this process,;because selective mating is often mediated by sexual signals: bright colours, complex song, pheromone blends and so on. When;divergent sensory adaptation affects the perception of such signals, mating patterns may change as an immediate consequence.;Alternatively, mating preferences can diverge as a result of indirect effects: assortative mating may be promoted by selection;against intermediate phenotypes that are maladapted to their (sensory) environment. For Lake Victoria cichlids, the visual environment;constitutes an important selective force that is heterogeneous across geographical and water depth gradients. We investigate;the direct and indirect effects of this heterogeneity on the evolution of female preferences for alternative male nuptial colours;(red and blue) in the genus Pundamilia. Here, we review the current evidence for divergent sensory drive in this system, extract;general principles, and discuss future perspectives

Antipredator defences of young are independently determined by genetic inheritance, maternal effects and own early experience in mouthbrooding cichlids.

1. Predation is a prime force of natural selection. Vulnerability to predation is typically highest early in life, hence effective antipredator defences should work already shortly after birth. Such early defences may be innate, transmitted through non-genetic parental effects or acquired by own early experience. 2. To understand potential joint effects of these sources of antipredator defences on pheno- typic expression, they should be manipulated within the same experiment. We investigated innate, parental and individual experience effects within a single experiment. Females of the African cichlid Simochromis pleurospilus were exposed to the offspring predator Ctenochromis horei or a benign species until spawning. Eggs and larvae were hand-reared, and larvae were then exposed to odour cues signalling the presence or absence of predators in a split-brood design. 3. Shortly after independence of maternal care, S. pleurospilus undergo a habitat shift from a deeper, adult habitat to a shallow juvenile habitat, a phase where young are thought to be par- ticularly exposed to predation risk. Thus, maternal effects induced by offspring predators pres- ent in the adult habitat should take effect mainly shortly after independence, whereas own experience and innate antipredator responses should shape behaviour and life history of S. pleurospilus during the later juvenile period. 4. We found that the manipulated environmental components independently affected different offspring traits. (i) Offspring of predator-exposed mothers grew faster during the first month of life and were thus larger at termination of maternal care, when the young migrate from the adult to the juvenile habitat. (ii) The offspring’s own experience shortly after hatching exerted lasting effects on predator avoidance behaviour. (iii) Finally, our results suggest that S. pleuro- spilus possess a genetically inherited ability to distinguish dangerous from benign species. 5. In S. pleurospilus, maternal effects were limited to a short but critical time window, when young undergo a niche shift. Instead, own environmental sampling of predation risk combined with an innate predisposition to correctly identify predators appears to prepare the young best for the environment, in which they grow up as juveniles.

A conceptual ecological model to facilitate understanding the role of invasive species in large-scale ecosystem restoration

We developed a conceptual ecological model (CEM) for invasive species to help understand the role invasive exotics have in ecosystem ecology and their impacts on restoration activities. Our model, which can be applied to any invasive species, grew from the eco-regional conceptual models developed for Everglades restoration. These models identify ecological drivers, stressors, effects and attributes; we integrated the unique aspects of exotic species invasions and effects into this conceptual hierarchy. We used the model to help identify important aspects of invasion in the development of an invasive exotic plant ecological indicator, which is described a companion paper in this special issue journal. A key aspect of the CEM is that it is a general ecological model that can be tailored to specific cases and species, as the details of any invasion are unique to that invasive species. Our model encompasses the temporal and spatial changes that characterize invasion, identifying the general conditions that allow a species to become invasive in a de novo environment; it then enumerates the possible effects exotic species may have collectively and individually at varying scales and for different ecosystem properties, once a species becomes invasive. The model provides suites of characteristics and processes, as well as hypothesized causal relationships to consider when thinking about the effects or potential effects of an invasive exotic and how restoration efforts will affect these characteristics and processes. In order to illustrate how to use the model as a blueprint for applying a similar approach to other invasive species and ecosystems, we give two examples of using this conceptual model to evaluate the status of two south Florida invasive exotic plant species (melaleuca and Old World climbing fern) and consider potential impacts of these invasive species on restoration.

Is Rapid Adaptation to New Environments Fueled by Old Mutations? A Case Study of Copper Tolerance on Mimulus guttatus

Rapid adaptation and tolerance is a phenomenon experienced by a variety of organisms typically because of new and harsh environments. Mimulus guttatus, a plant commonly seen on the west coast of the United States, is a prime example as it has rapidly evolved to soil contamination by copper due to mining in California in the last 150 years. There have been two hypotheses posed by researchers as to the genetic basis of how organisms have evolved so quickly which I set out to study: 1) There is a low frequency of tolerant genotypes in the ancestral population otherwise known as standing variation or 2) new mutations occurred once exposed to a new environment. In the past, researchers found it difficult to distinguish between the two because they lacked the technology we have today for DNA analysis. I used four different populations of M. guttatus from varying locations in order to address which hypothesis was valid. I conducted both survival assays of these populations and DNA analysis of known tolerant and non-tolerant lines using a copper oxidase gene. I found that there was at least some degree of tolerance in all populations in the survival assays, supporting the hypothesis of standing variation. I also found patterns within DNA analysis suggesting the copper oxidase gene would be useful for further study to verify the standing variation hypothesis. The results from this experiment helps in understanding rapid evolution not just in the context of soil contamination by metals but also ties back to why an alarming number of species are not able to adapt to our constantly changing world.

Allelopathic assessment of selected invasive species of Pakistan

All rights reserved.Invader species are a great threat to local flora. Eight invader species of Pakistan were screened for their allelopathic activity through sandwich method. Toxic (inhibitory) and non-toxic (stimulatory) effects were assessed by recording their effect on germination and growth of lettuce. Radicle and plumule growth of lettuce were recorded at 5, 10 and 50 mg leaves concentrations of each species. Among all species the growth activity was found to be concentration dependent. Except Eutcalyptus glabra all species resulted in inhibitory effects at 5, 10 and 50 mg leaves concentrations. Xanthium strumarium and Cannabis sativa showed strong inhibitory effects on radicle and plumule growth of lettuce. Maximum inhibition was recorded at highest concentration; even growth of lettuce was stopped with 50 mg leaves concentration of C. sativa.

Info-gap theory and robust design of surveillance for invasive species : the case study of Barrow Island

Surveillance for invasive non-indigenous species (NIS) is an integral part of a quarantine system. Estimating the efficiency of a surveillance strategy relies on many uncertain parameters estimated by experts, such as the efficiency of its components in face of the specific NIS, the ability of the NIS to inhabit different environments, and so on. Due to the importance of detecting an invasive NIS within a critical period of time, it is crucial that these uncertainties be accounted for in the design of the surveillance system. We formulate a detection model that takes into account, in addition to structured sampling for incursive NIS, incidental detection by untrained workers. We use info-gap theory for satisficing (not minimizing) the probability of detection, while at the same time maximizing the robustness to uncertainty. We demonstrate the trade-off between robustness to uncertainty, and an increase in the required probability of detection. An empirical example based on the detection of Pheidole megacephala on Barrow Island demonstrates the use of info-gap analysis to select a surveillance strategy.