Chemocoding as an identification tool where morphological- and DNA-based methods fall short: Inga as a case study.

The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or 'chemocoding', has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species-level fingerprints, which we define as chemocoding. We evaluated the utility of chemocoding with species that were defined morphologically and subject to next-generation DNA sequencing in the diverse and recently radiated neotropical genus Inga (Leguminosae), both at single study sites and across broad geographic scales. Our results show that chemocoding is a robust method for distinguishing morphologically similar species at a single site and for identifying widespread species across continental-scale ranges. Given that species are the fundamental unit of analysis for conservation and biodiversity research, the development of accurate identification methods is essential. We suggest that chemocoding will be a valuable additional source of data for a quick identification of plants, especially for groups where other methods fall short.

Quantitative and qualitative shifts in defensive metabolites define chemical defense investment during leaf development in Inga, a genus of tropical trees.

Selective pressures imposed by herbivores are often positively correlated with investments that plants make in defense. Research based on the framework of an evolutionary arms race has improved our understanding of why the amount and types of defenses differ between plant species. However, plant species are exposed to different selective pressures during the life of a leaf, such that expanding leaves suffer more damage from herbivores and pathogens than mature leaves. We hypothesize that this differential selective pressure may result in contrasting quantitative and qualitative defense investment in plants exposed to natural selective pressures in the field. To characterize shifts in chemical defenses, we chose six species of Inga, a speciose Neotropical tree genus. Focal species represent diverse chemical, morphological, and developmental defense traits and were collected from a single site in the Amazonian rainforest. Chemical defenses were measured gravimetrically and by characterizing the metabolome of expanding and mature leaves. Quantitative investment in phenolics plus saponins, the major classes of chemical defenses identified in Inga, was greater for expanding than mature leaves (46% and 24% of dry weight, respectively). This supports the theory that, because expanding leaves are under greater selective pressure from herbivores, they rely more upon chemical defense as an antiherbivore strategy than do mature leaves. Qualitatively, mature and expanding leaves were distinct and mature leaves contained more total and unique metabolites. Intraspecific variation was greater for mature leaves than expanding leaves, suggesting that leaf development is canalized. This study provides a snapshot of chemical defense investment in a speciose genus of tropical trees during the short, few-week period of leaf development. Exploring the metabolome through quantitative and qualitative profiling enables a more comprehensive examination of foliar chemical defense investment.

Four species of arboreal folivore show differential tolerance to a secondary metabolite.

The marsupials that eat Eucalyptus in south-eastern Australia provide an example of animals with similar niche requirements occurring sympatrically. They certainly differ in size, ranging from about 1 kg in the greater glider (Petauroides volans) and the closely related common ringtail possum (Pseudocheirus peregrinus), to 4 kg (common brushtail possum, Trichosurus vulpecula) and up to 15 kg in the koala (Phascolarctos cinereus). All species, however, may eat considerable amounts of eucalypt foliage, often favouring the same species, and thus appear to compete for food. In order to better understand the degree of competition for food, we measured feeding by the greater glider in response to increasing concentrations of a specific group of eucalypt plant secondary metabolites (PSM), the sideroxylonals, and then compared it to results published for the other species. The greater glider was more resilient than the other species to increasing concentrations of sideroxylonals. We suggest this allows gliders to feed on leaves from the eucalypt subgenus, Symphyomyrtus, while its small size and gliding ability allow it to feed where koalas cannot, on the young leaves on top of the canopy. In contrast, the common ringtail possum is well adapted to feeding from species of the subgenus Eucalyptus, which do not produce sideroxylonals but contain less available nitrogen (AvailN) than do the symphyomyrtles. These 'nutritional niches' segregate the forest and along with other factors, such as generalist and specialist feeding strategies and differences in body size and requirements for shelter, presumably minimise competition between the marsupial species.

Asymmetric or diffusive co-evolution generates meta-populations in fig-fig wasp mutualisms.

Co-evolutionary theory assumes co-adapted characteristics are a positive response to counter those of another species, whereby co-evolved species reach an evolutionarily stable interaction through bilateral adaptation. However, evidence from the fig-fig wasp mutualistic system implies very different co-evolutionary selection mechanisms, due to the inherent conflict among interacted partners. Fig plants appear to have discriminatively enforced fig wasps to evolve "adaptation characteristics" that provide greater benefit to the fig, and fig wasps appear to have diversified their evolutionary strategies in response to discriminative enforcement by figs and competition among different fig wasp species. In what appears to be an asymmetric interaction, the prosperity of cooperative pollinating wasps should inevitably lead to population increases of parasitic individuals, thus resulting in localized extinctions of pollinating wasps. In response, the sanctioning of parasitic wasps by the fig should lead to a reduction in the parasitic wasp population. The meta-populations created by such asymmetric interactions may result in each population of coevolved species chaotically oscillated, temporally or evolutionarily.

Scent chemicals of the brushtail possum, Trichosurus vulpecula.

The common brushtail possum (Trichosurus vulpecula) is the most widespread browsing marsupial in Australia, where it occupies woodland, agricultural, and urban environments. Following its introduction into New Zealand in the 19th century it has become a major feral pest, threatening native forests. The adaptability of the possum is thought to be due in part to its social organization, in which chemical communication is important. Possums have cloacal glands and exhibit related marking behavior. This study sought to characterize the chemicals involved in scent marking. Swabs were taken of the cloacal region of 15 possums (5 females, 10 males) from north-eastern Tasmania and analyzed by gas chromatography-mass spectrometry. There was a large number of compounds present, including 81 branched and unbranched, and saturated and unsaturated, fatty acids (C(4)-C(15)) and alcohols (C(6)-C(26)); 27 esters of 2,6- and 2,7-dimethyloctanol; 29 esters of formic acid; 39 sulfur compounds including S(8) and a series of dialkyl disulfides, trisulfides, and tetrasulfides (C(4)-C(10)); and several alkylglycerol ethers. Many of these cloacal compounds are new to biology. There was considerable individual variability in the relative amounts of compounds found, and no evident sex differences, although the study was not designed to test this. This pattern suggests that these compounds may be acting collectively as a signature mixture of semiochemicals, carrying information on the individual, its kinship, and physiological and social status. This is the first detailed description of putative semiochemicals in any marsupial species.

A two-phase model for smoothly joining disparate growth phases in the macropodid Thylogale billardierii.

Generally, sigmoid curves are used to describe the growth of animals over their lifetime. However, because growth rates often differ over an animal's lifetime a single curve may not accurately capture the growth. Broken-stick models constrained to pass through a common point have been proposed to describe the different growth phases, but these are often unsatisfactory because essentially there are still two functions that describe the lifetime growth. To provide a single, converged model to age animals with disparate growth phases we developed a smoothly joining two-phase nonlinear function (SJ2P), tailored to provide a more accurate description of lifetime growth of the macropod, the Tasmanian pademelon Thylogale billardierii. The model consists of the Verhulst logistic function, which describes pouch-phase growth--joining smoothly to the Brody function, which describes post-pouch growth. Results from the model demonstrate that male pademelons grew faster and bigger than females. Our approach provides a practical means of ageing wild pademelons for life history studies but given the high variability of the data used to parametrise the second growth phase of the model, the accuracy of ageing of post-weaned animals is low: accuracy might be improved with collection of longitudinal growth data. This study provides a unique, first robust method that can be used to characterise growth over the lifespan of pademelons. The development of this method is relevant to collecting age-specific vital rates from commonly used wildlife management practices to provide crucial insights into the demographic behaviour of animal populations.

Development of tolerance to the dietary plant secondary metabolite 1,8-cineole by the brushtail possum (Trichosurus vulpecula).

The common brushtail possum (Trichosurus vulpecula) is a generalist herbivore whose diet includes Eucalyptus leaves that are well defended by plant secondary metabolites (PSM) such as the terpene 1,8-cineole (cineole). We accustomed possums to a terpene-free diet, then challenged them with the addition of 2% cineole to the diet. Initially, there was a 50% reduction in total overnight food consumption associated with a marked decrease in the mass of the major feeding bout. After nine nights, however, cineole tolerance had developed as total food consumption had returned to the control amount. Compared to the control diet, the cineole diet was eaten in a larger number of smaller bouts, which were also eaten at a slower rate. The experiment was repeated with animals that had been accustomed to day-time feeding to take blood samples during feeding sessions. Feeding variables and blood concentration data for cineole were compared on the first and seventh day of the cineole diet. Although the total food consumed increased 2.5-fold after 7 days of the cineole diet, there was no increase in average blood cineole concentration, measured as the area under the concentration-time curve. This indicates that induction of liver enzymes resulted in greater pre-systemic metabolism of cineole and reduced bioavailability. The maximum tolerated blood concentration of cineole also increased, suggesting some adaptation of the central nervous system to the cineole aversive effects. This appears to be the first report in a vertebrate herbivore that consumption of a dietary PSM leads to metabolism induction and that this contributes to development of tolerance to the PSM. Overall, herbivores adapt to newly encountered dietary PSMs by immediate changes in feeding behavior followed by development of increased metabolism of PSM and probably diminished cellular responsiveness to effects.

Spatial scale of the patchiness of plant poisons: a critical influence on foraging efficiency.

Generalist mammalian browsers and folivores feed on a range of chemically different plant species, which may assist them in diluting toxins and diversifying nutrient consumption. The frequency and order in which their diets are mixed are important determinants of intake. As a result, the degree of plant heterogeneity in an environment, and the spatial scale at which this occurs, should directly influence herbivore foraging decisions. We tested whether altering the Spatial scale of plants, and thus plant secondary metabolites (PSMs), affected foraging efficiency of a generalist folivore, the common brushtail possum (Trichosurus vulpecula). First, we demonstrated that possums were able to consume more from a mixed diet of two chemically different species, Eucalyptus globulus and E. tenuiramis, than when either of these species was offered alone. We then tested whether altering the spatial scale between E. globulus and E. tenuiramis, as small- or large-scale plant heterogeneity "patches," affected possum foraging behavior and, ultimately, their foraging efficiency. Possums increased their foraging efficiency when the spatial scale of plant heterogeneity was small rather than large. We argue that the ability to regularly switch diets, when plant spatial distribution is at a small scale, reduces the negative effects of PSM ingestion. We predict that the heterogeneity of plant patches, in relation to PSM distribution, and the scale at which this occurs across a landscape, are critical factors that influence foraging efficiency and, ultimately, fitness of mammalian herbivores. This research provides a fundamental link between plant chemistry, foraging, and habitat heterogeneity.

Behavioral responses of a generalist mammalian folivore to the physiological constraints of a chemically defended diet.

Mammalian herbivores, particularly browsers and folivores, encounter and consume a range of plant chemical defenses [plant secondary metabolites (PSMs)] on a regular basis. The physiological regulation of PSM ingestion and the resulting behavioral responses of mammalian herbivores directly affect their feeding decisions and the subsequent foraging strategies that they adopt. Generalist mammalian herbivores are hypothesized to consume a generalized diet because of physiological limitations of their detoxification systems. The consumption of a generalized diet is proposed to enable toxin (PSM) dilution through the use of multiple detoxification pathways. We tested the predictions of the detoxification-limitation hypothesis by offering two chemically different plant species, Eucalyptus regnans and E. globulus, to a generalist mammalian folivore, the common brushtail possum (Trichosurus vulpecula), as single- and mixed-species diets. By feeding more efficiently, brushtail possums benefited more, through increased intake, on the mixed-species diet than on either of the single-species diets. We argue that frequently switching between chemically diverse foliage reduces the physiological constraints imposed by a PSM-rich diet and enables more efficient feeding. The behavioral responses of brushtail possums were consistent with the proposed physiological constraints of a chemically defended diet, offering support for predictions of the detoxification-limitation hypothesis. We suggest that feeding behavior of herbivores may be a useful indicator of the physiological constraints imposed by a chemically defended diet.

Sideroxylonal in Eucalyptus foliage influences foraging behaviour of an arboreal folivore.

Plant secondary metabolites (PSMs) offer plants chemical defences against herbivores, and are known to influence intake and diet choice in both insect and mammalian herbivores. However, there is limited knowledge regarding how PSMs influence herbivore foraging decisions. Herbivore foraging decisions, in turn, directly impact on which individual plants, and plant species, are selected for consumption. We took advantage of the natural variation in sideroxylonal concentrations in the foliage of Eucalyptus melliodora (Cunn. ex Schauer) to investigate feeding patterns of a marsupial folivore, the common ringtail possum, Pseudocheirus peregrinus (Boddaert 1785). Foliage, collected from six trees, contained between 0.32 and 12.97 mg g-DM(-1) sideroxylonal. With increasing sideroxylonal concentrations, possums decreased their total intake, rate of intake and intake per feeding bout, and increased their cumulative time spent feeding. Possums did not alter their total feeding time, number of feeding bouts or time per feeding bout in response to increasing sideroxylonal concentrations. Results demonstrate important behavioural changes in foraging patterns in response to sideroxylonal. These behavioural changes have important implications, in relation to altered foraging efficiency and potential predation risk, for herbivores foraging in the field. As a result, the spatial distribution of dietary PSMs across a landscape may directly influence herbivore fitness, and ultimately habitat selection of mammalian herbivores.

Diet switching in a generalist mammalian folivore: fundamental to maximising intake.

Generalist mammalian herbivores exploit a diverse diet. A generalised feeding strategy utilises a mixed diet to obtain a range of nutrients and to reduce the detoxication load of similar groups of plant secondary metabolites (PSMs). There is limited research investigating how mammalian herbivores achieve this dietary mixing in their daily foraging activities. We investigated the patterns of, and behaviours associated with, dietary mixing in a generalist mammalian folivore, the common brushtail possum (Trichosurus vulpecula). Possums were offered foliage of two eucalypt species (Eucalyptus globulus and E. regnans) as either (a) Full choice: both species offered for 8 h; (b) Restricted choice: both species offered for 2x2 h blocks; (c) G-R no choice: E. globulus offered for the first 4 h, E. regnans offered for next 4 h; and (d) R-G no choice: E. regnans offered for first 4 h, E. globulus offered for next 4 h. We hypothesised that possums would maximise intake on the Full choice diet, where time availability was greatest in combination with a choice of foliage. We also hypothesised that diet switching, defined as the frequency of changing between food types while feeding, would play a fundamental role in maximising intake. Possums achieved maximum intake on the Full choice diet and minimum intake on the No choice diets. Although intake was similar between the Restricted choice and No choice diets, possums achieved this intake in half the amount of time when able to switch regularly between foliage on the Restricted choice diet. We conclude that a generalist herbivore's ability to effectively switch diets when foraging is fundamental to maximising intake. Hence, the degree of plant heterogeneity in an environment, and the spatial scale at which it occurs, may affect an herbivore's foraging decisions and, ultimately, influence its foraging efficiency.

Effects of two plant secondary metabolites, cineole and gallic acid, on nightly feeding patterns of the common brushtail possum.

We investigated effects of two plant secondary metabolites (PSMs), cineole and gallic acid, on the nightly feeding behavior of the common brushtail possum (Trichosurus vulpecula), a generalist folivore. We tested whether possums altered their feeding behavior in response to increasing levels of cineole, a dietary terpene. Possums were fed artificial diets containing three levels of cineole: zero (basal diet), medium (6.8% of total dry matter, DM), and high (15.3% DM). In another experiment, we introduced gallic acid, a dietary phenolic, into the diets. Possums were offered a Choice PSM diet (cineole and gallic acid diets simultaneously) or a No-Choice PSM diet (containing either cineole or gallic acid). Detoxification products of cineole and gallic acid were examined in urine to determine that different detoxification pathways were utilized in the elimination of each compound. With increasing cineole levels, possums ate less, had smaller feeding bouts, and had a lower rate of intake, but did not extend their total nightly feeding time. Possums offered the Choice PSM diet, compared with the No-Choice diets, ate more, had larger feeding bouts, and tended to increase their rate of intake. Results from the urinary analysis indicated that gallic acid and cineole were not involved in competing detoxification pathways in brushtail possums. There was also a significant sex effect: females ate more overall, ate more per feeding bout, and ate at a higher rate than males. These results indicate that PSMs not only constrain overall intake, but that possums alter their feeding behavior in response to them. Altered feeding patterns may reduce the negative influence of PSMs on intake.