General models for resource use or other compositional count data using the Dirichlet-multinomial distribution.

Many ecological studies investigate how organisms use resources, such as habitats or foods, in relation to availability or other variables. Related statistical problems include analysis of proportions of species or genotypes in a community or population. These require statistical modeling of compositional count data: data on relative proportions of each category collected as counts. Common methods for analyzing compositional count data lack one or more important considerations. Some methods lack explicit accommodation of count data, dealing instead with proportions. Others do not handle between-sample heterogeneity for overdispersed data. Yet others do not allow general types of relationships between explanatory variables and resource use. All three components have been combined in a Bayesian framework, but for frequentist hypothesis tests and AIC model selection, maximum-likelihood estimation is needed. Here we propose the Dirichlet-multinomial distribution to accommodate overdispersed compositional count data. This approach can be used flexibly in combination with explanatory models, but the only correlations among compositional proportions that it can accommodate are the negative correlations due to the fact that proportions must sum to 1. Many existing models can be generalized to use the Dirichlet-multinomial distribution for residual variation, and the flexibility of the approach allows new hypotheses that have often not been considered in resource preference analysis, including that availability has no relation to use. We also highlight a new design for resource use studies, with multiple individual-use data sets from each of multiple sites, with different explanatory data for each site. We illustrate the approach with three examples. For two previously published habitat use data sets, we support the original conclusions and show that use is not unrelated to availability. For a data set of pollen collected by multiple bees from each of two sites, pollen use differs between the sites. Using bootstrap goodness-of-fit tests, we illustrate that the Dirichlet-multinomial is acceptable for two of the examples but unsuitable for one of the habitat use examples.

Assessing the speed and predictability of local adaptation in invasive California poppies (Eschscholzia californica).

Insight into the speed and predictability of local adaptation can be gained by studying organisms, such as invasive species, that have recently expanded their geographical ranges. Common garden studies were designed to address these issues with the California poppy, Eschscholzia californica, collected from a wide range of environments in both its native (California) and invasive (Chile) ranges. We found similar patterns of plant trait variation along similar abiotic gradients in plants collected from both areas. Multivariate analysis demonstrated that coastal plants from both areas tended to be shorter, smaller plants with smaller seeds and flowers that germinate and flower later than plants collected from inland locations. In addition, size and fecundity traits in both native and invasive poppies were correlated with average rainfall totals; the plants that grew the largest and were the most fecund during the first year of growth originated from the driest areas. This parallel variation suggests that these traits are adaptive and that these patterns have evolved in Chile during the 110-150 years since introduction.

EcFLO, a FLORICAULA-like gene from Eschscholzia californica is expressed during organogenesis at the vegetative shoot apex.

FLORICAULA/ LEAFY-like genes were initially characterized as flower meristem identity genes. In a range of angiosperms, expression occurs also in vegetative shoot apices and developing leaves, and in some species with dissected leaves expression is perpetuated during organogenesis at the leaf marginal blastozone. The evolution of these expression patterns and associated functions is not well understood. We have isolated and characterized a FLORICAULA-like gene from California Poppy, Eschscholzia californica Cham. (Papaveraceae), a species belonging to the basal eudicot clade Ranunculales. EcFLO encodes a putative 416-amino-acid protein with highest similarity to homologous genes from Trochodendron and Platanus. We show that EcFLO mRNA is expressed during the vegetative phase of the shoot apical meristem and in developing dissected leaves in a characteristic manner. This pattern is compared to that of other eudicots and discussed in terms of evolution of FLORICAULA expression and function.