Developments from analysis of variance through to generalized linear models and beyond

The collaborations between statisticians and biologists during the 100 years since AAB was founded have led to a very impressive list of statistical techniques, whose use now goes well beyond agriculture and biology. One example is the maximum likelihood methodology for probit analysis, arising from the collaboration between Sir Ronald Fisher and Chester Bliss. Others include analysis of variance, design of experiments, generalized linear models and the residual, or restricted, maximum likelihood (REML) algorithm for fitting unbalanced linear mixed models.     

CONVERGENT AND CORRELATED EVOLUTION OF MAJOR LIFE‐HISTORY TRAITS IN THE ANGIOSPERM GENUS LEUCADENDRON (PROTEACEAE)

Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life‐history traits. Here, we quantify the extent of convergence of five key life‐history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed‐dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire‐prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse genus that involves more taxa and molecular markers than previously. This reconstruction identifies new clades that were not detected by previous molecular study and morphological classifications. Using this new phylogeny and robust methods that account for phylogenetic uncertainty, we show that the five life‐history traits studied were labile during the evolutionary history of the genus. This diversity allowed us to tackle major questions about the correlated evolution of life‐history strategies. We found that species with longer seed‐dispersal distances tended to evolve lower pollen‐dispersal distance, that insect‐pollinated species evolved decreased sexual dimorphism, and that species with a persistent soil seed‐bank evolved toward reduced fire‐survival ability of adults.     

Inference of the Properties of the Recombination Process from Whole Bacterial Genomes

Patterns of linkage disequilibrium, homoplasy, and incompatibility are difficult to interpret because they depend on several factors, including the recombination process and the population structure. Here we introduce a novel model-based framework to infer recombination properties from such summary statistics in bacterial genomes. The underlying model is sequentially Markovian so that data can be simulated very efficiently, and we use approximate Bayesian computation techniques to infer parameters. As this does not require us to calculate the likelihood function, the model can be easily extended to investigate less probed aspects of recombination. In particular, we extend our model to account for the bias in the recombination process whereby closely related bacteria recombine more often with one another. We show that this model provides a good fit to a data set of Bacillus cereus genomes and estimate several recombination properties, including the rate of bias in recombination. All the methods described in this article are implemented in a software package that is freely available for download at http://code.google.com/p/clonalorigin/.     

Host plant‐related variation in thermal tolerance of Eldana saccharina

Understanding tolerance of thermal extremes by pest insects is essential for developing integrated management strategies, as tolerance traits can provide insights into constraints on activity and survival. A major question in thermal biology is whether thermal limits vary systematically with microclimate variation, or whether other biotic or abiotic factors can influence these limits in a predictable manner. Here, we report the results of experiments determining thermal limits to activity and survival at extreme temperatures in the stalk borer Eldana saccharina Walker (Lepidoptera: Pyralidae), collected from either Saccharum spp. hybrids (sugarcane) (Poaceae) or Cyperus papyrus L. (Cyperaceae) and then reared under standard conditions in the laboratory for 1–2 generations. Chill‐coma temperature (CT_min), critical thermal maximum (CT_max), lower lethal temperatures (LLT), and freezing temperature between E. saccharina collected from the two host plants were compared. CT_min and CT_max of E. saccharina moths collected from sugarcane were significantly lower than those from C. papyrus (CT_min = 2.8 ± 0.4 vs. 3.9 ± 0.4 °C; CT_max = 44.6 ± 0.1 vs. 44.9 ± 0.2 °C). By contrast, LLT of moths and freezing temperatures of pupae did not vary with host plant [LLT for 50% (LT₅₀) of the moth population, when collected from sugarcane: ?3.2 ± 0.5 °C, from C. papyrus: ?3.9 ± 0.8 °C]. Freezing temperatures of pupae collected from C. papyrus were ?18.0 ± 1.0 °C and of those from sugarcane ?17.5 ± 1.8 °C. The E. saccharina which experienced the lowest minimum temperature (in C. papyrus) did not have the lowest CT_min, although the highest estimate of CT_max was found in E. saccharina collected from C. papyrus and this was also the microsite which reported the highest maximum temperatures. These results therefore suggest that host plant may strongly mediate lower critical thermal limits, but not necessarily LLT or freezing temperatures. These results have significant implications for ongoing pest management and thermal biology of these and other insects.     

The Interplay of Habitat and Seed Type on Scatterhoarding Behavior in a Fragmented Afromontane Forest Landscape

Scatterhoarding by rodents, whereby seeds are collected and stored for later consumption, can result in seed dispersal. Seeds may be covered in litter on the forest floor (cached) or buried. This is particularly so in the Neotropics for large, nutritious seeds, and where primary dispersers are rare or missing. In African forests, contemporary anthropogenic pressures such as hunting, forest degradation, and fragmentation are contributing toward major declines in large frugivores, yet the potential for scatterhoarding to mitigate this loss is largely unknown. In this study, we used thread‐marked seed to explore the balance between seed predation and dispersal by rodents in Afromontane forest. We studied two tree species in three habitats: (1) continuous forest; (2) continuous forest edge, and (3) small, degraded riparian forest patches. We found that seed removal rates were high and almost the same in all three habitats for both tree species, but that the predation/dispersal balance differed among habitats. In continuous forest, more seeds of each species were scatterhoarded than depredated, and rates of scatterhoarding differed between the two species. In all habitats, burying seeds up to 2 cm belowground was more common than caching. Distances seeds were moved was approximately five times greater in continuous forest than in forest edge or riparian patches. We found strong evidence to suggest that the African pouched rat, Cricetomys sp. nov was responsible for the scatterhoarding.     

Asymmetrical Dependence Between a Neotropical Mistletoe and its Avian Seed Disperser

The degree of interdependence among interacting species has major implications for our understanding of the coevolutionary process and biodiversity maintenance. However, the mutualism strength among fruiting plants and their seed dispersers remains poorly understood in tropical ecosystems. We evaluated simultaneously the effectiveness of the avian seed dispersers of the mistletoe Struthanthus flexicaulis (Loranthaceae) and the contribution of its fruits to their diets in a highland rocky savanna in southeastern Brazil. The mistletoe fruits are small lipid‐rich pseudoberries available throughout the year. Four passerine birds fed on fruits, but Elaenia cristata (Tyrannidae) was the most effective disperser, responsible for more than 96 percent of the dispersed seeds. This bird swallowed fruits whole, expelling and depositing undamaged seeds by regurgitation and bill wiping on perches. From 646 dispersed seeds, 56 percent were deposited on safe sites, thin live twigs of 38 susceptible host species. Elaenia cristata were predominantly frugivorous, feeding on typically ornithocoric fruits of at least 12 species, but also on arthropods. Although fruits represented 75 percent of the feeding bouts along the year, S. flexicaulis fruits represented only 34 percent of the E. cristata diet. Our results highlight the asymmetrical nature of this mutualistic interaction, with the mistletoe life cycle locally linked to one highly effective seed disperser that is more weakly dependent on mistletoes fruits as a food source. We suggest that merging the seed dispersal effectiveness framework with diet assessment of seed dispersers is needed to clarify the asymmetries in mutualistic pairwise interactions involving plants and their animal partners.     

Fruit and seed heteromorphism in the cold desert annual ephemeral Diptychocarpus strictus (Brassicaceae) and possible adaptive significance

Background and Aims

Diptychocarpus strictus is an annual ephemeral in the cold desert of northwest China that produces heteromorphic fruits and seeds. The primary aims of this study were to characterize the morphology and anatomy of fruits and seeds of this species and compare the role of fruit and seed hetermorphism in dispersal and germination.

Methods

Shape, size, mass and dispersal of siliques and seeds and the thickness of the mucilage layer on seeds were measured, and the anatomy of siliques and seeds, the role of seed mucilage in water absorption/dehydration, germination and adherence of seeds to soil particles, the role of pericarp of lower siliques in seed dormancy and seed after-ripening and germination phenology were studied using standard procedures.

Key Results

Plants produce dehiscent upper siliques with a thin pericarp containing seeds with large wings and a thick mucilage layer and indehiscent lower siliques with a thick pericarp containing nearly wingless seeds with a thin mucilage layer. The dispersal ability of seeds from the upper siliques was much greater than that of intact lower siliques. Mucilage increased the amount of water absorbed by seeds and decreased the rate of dehydration. Seeds with a thick mucilage layer adhered to soil particles much better than those with a thin mucilage layer or those from which mucilage had been removed. Fresh seeds were physiologically dormant and after-ripened during summer. Non-dormant seeds germinated to high percentages in light and in darkness. Germination of seeds from upper siliques is delayed until spring primarily by drought in summer and autumn, whereas the thick, indehiscent pericarp prevents germination for >1 year of seeds retained in lower siliques.

Conclusions

The life cycle of D. strictus is morphologically and physiologically adapted to the cold desert environment in time and space via a combination of characters associated with fruit and seed heteromorphism.     

Prior hydration of Brassica tournefortii seeds reduces the stimulatory effect of karrikinolide on germination and increases seed sensitivity to abscisic acid

Background and Aims

The smoke-derived compound karrikinolide (KAR₁) shows significant potential as a trigger for the synchronous germination of seeds in a variety of plant-management contexts, from weed seeds in paddocks, to native seeds when restoring degraded lands. Understanding how KAR₁ interacts with seed physiology is a necessary precursor to the development of the compound as an efficient and effective management tool. This study tested the ability of KAR₁ to stimulate germination of seeds of the global agronomic weed Brassica tournefortii, at different hydration states, to gain insight into how the timing of KAR₁ applications in the field should be managed relative to rain events.

Methods

Seeds of B. tournefortii were brought to five different hydration states [equilibrated at 15 % relative humidity (RH), 47 % RH, 96 % RH, fully imbibed, or re-dried to 15 % RH following maximum imbibition] then exposed to 1 nm or 1 µm KAR₁ for one of five durations (3 min, 1 h, 24 h, 14 d or no exposure).

Key Results

Dry seeds with no history of imbibition were the most sensitive to KAR₁; sensitivity was lower in seeds that were fully imbibed or fully imbibed then re-dried. In addition, reduced sensitivity to KAR₁ was associated with an increased sensitivity to exogenously applied abscisic acid (ABA).

Conclusions

Seed water content and history of imbibition were found to significantly influence whether seeds germinate in response to KAR₁. To optimize the germination response of seeds, KAR₁ should be applied to dry seeds, when sensitivity to ABA is minimized.     

A new type of specialized morphophysiological dormancy and seed storage behaviour in Hydatellaceae, an early-divergent angiosperm family

Background and Aims

Recent phylogenetic analysis has placed the aquatic family Hydatellaceae as an early-divergent angiosperm. Understanding seed dormancy, germination and desiccation tolerance of Hydatellaceae will facilitate ex situ conservation and advance hypotheses regarding angiosperm evolution.

Methods

Seed germination experiments were completed on three species of south-west Australian Hydatellaceae, Trithuria austinensis, T. bibracteata and T. submersa, to test the effects of temperature, light, germination stimulant and storage. Seeds were sectioned to examine embryo growth during germination in T. austinensis and T. submersa.

Key Results

Some embryo growth and cell division in T. austinensis and T. submersa occurred prior to the emergence of an undifferentiated embryo from the seed coat (‘germination’). Embryo differentiation occurred later, following further growth and a 3- to 4-fold increase in the number of cells. The time taken to achieve 50 % of maximum germination for seeds on water agar was 50, 35 and 37 d for T. austinensis, T bibracteata and T. submersa, respectively.

Conclusions

Seeds of Hydatellaceae have a new kind of specialized morphophysiological dormancy in which neither root nor shoot differentiates until after the embryo emerges from the seed coat. Seed biology is discussed in relation to early angiosperm evolution, together with ex situ conservation of this phylogenetically significant group.