Inferring Ecological Processes from Taxonomic, Phylogenetic and Functional Trait β-Diversity

Understanding the influences of dispersal limitation and environmental filtering on the structure of ecological communities is a major challenge in ecology. Insight may be gained by combining phylogenetic, functional and taxonomic data to characterize spatial turnover in community structure (β-diversity). We develop a framework that allows rigorous inference of the strengths of dispersal limitation and environmental filtering by combining these three types of β-diversity. Our framework provides model-generated expectations for patterns of taxonomic, phylogenetic and functional β-diversity across biologically relevant combinations of dispersal limitation and environmental filtering. After developing the framework we compared the model-generated expectations to the commonly used “intuitive” expectation that the variance explained by the environment or by space will, respectively, increase monotonically with the strength of environmental filtering or dispersal limitation. The model-generated expectations strongly departed from these intuitive expectations: the variance explained by the environment or by space was often a unimodal function of the strength of environmental filtering or dispersal limitation, respectively. Therefore, although it is commonly done in the literature, one cannot assume that the strength of an underlying process is a monotonic function of explained variance. To infer the strength of underlying processes, one must instead compare explained variances to model-generated expectations. Our framework provides these expectations. We show that by combining the three types of β-diversity with model-generated expectations our framework is able to provide rigorous inferences of the relative and absolute strengths of dispersal limitation and environmental filtering. Phylogenetic, functional and taxonomic β-diversity can therefore be used simultaneously to infer processes by comparing their empirical patterns to the expectations generated by frameworks similar to the one developed here

The use of taxonomic relationships among species in applied ecological research: Baseline, steps forward and future challenges

Taxonomy is more than a mere exercise of nomenclature and classification of biological diversity: it profiles the identity of species by investigating their biological and ecological traits. Taxonomy is intimately related to ecology which, in turn, cannot be a mere exercise in describing ecological patterns, but instead requires deep knowledge of species’ biological structures, roles, interactions and functions. Thus, the study of taxonomic and phylogenetic relatedness of species is of paramount importance in ecological research, enabling insights into potential evolutionary patterns and processes, allowing a more comprehensive view of biodiversity, and providing opportunities to improve the assessment and monitoring of ecological changes in time and space. The work of K. Robert (‘Bob’) Clarke forged new pathways in this direction, providing new ideas and statistical tools to include and exploit taxonomic relationships in applied marine ecological studies and beyond, also inspiring the next generation of ecologists. In this short review, we synthesise the application and development of these tools and concepts in marine biodiversity research over the last three decades and suggest future pathways in this evolving field

Improved annotation of the insect vector of citrus greening disease: Biocuration by a diverse genomics community

The Asian citrus psyllid (Diaphorina citri Kuwayama) is the insect vector of the bacterium Candidatus Liberibacter asiaticus (CLas), the pathogen associated with citrus Huanglongbing (HLB, citrus greening). HLB threatens citrus production worldwide. Suppression or reduction of the insect vector using chemical insecticides has been the primary method to inhibit the spread of citrus greening disease. Accurate structural and functional annotation of the Asian citrus psyllid genome, as well as a clear understanding of the interactions between the insect and CLas, are required for development of new molecular-based HLB control methods. A draft assembly of the D. citri genome has been generated and annotated with automated pipelines. However, knowledge transfer from well-curated reference genomes such as that of Drosophila melanogaster to newly sequenced ones is challenging due to the complexity and diversity of insect genomes. To identify and improve gene models as potential targets for pest control, we manually curated several gene families with a focus on genes that have key functional roles in D. citri biology and CLas interactions. This community effort produced 530 manually curated gene models across developmental, physiological, RNAi regulatory and immunity-related pathways. As previously shown in the pea aphid, RNAi machinery genes putatively involved in the microRNA pathway have been specifically duplicated. A comprehensive transcriptome enabled us to identify a number of gene families that are either missing or misassembled in the draft genome. In order to develop biocuration as a training experience, we included undergraduate and graduate students from multiple institutions, as well as experienced annotators from the insect genomics research community. The resulting gene set (OGS v1.0) combines both automatically predicted and manually curated gene models.Peer reviewedBiochemistry and Molecular BiologyEntomology and Plant Patholog

Cooperative games with bounded dependency degree

Cooperative games provide a framework to study cooperation among self-interested agents. They offer a number of solution concepts describing how the outcome of the cooperation should be shared among the players. Unfortunately, computational problems associated with many of these solution concepts tend to be intractable---NP-hard or worse. In this paper, we incorporate complexity measures recently proposed by Feige and Izsak (2013), called dependency degree and supermodular degree, into the complexity analysis of coopera- tive games. We show that many computational problems for cooperative games become tractable for games whose dependency degree or supermodular degree are bounded. In particular, we prove that simple games admit efficient algorithms for various solution concepts when the supermodular degree is small; further, we show that computing the Shapley value is always in FPT with respect to the dependency degree. Finally, we observe that, while determining the dependency among players is computationally hard, there are efficient algorithms for special classes of games

Partitioning, iterating when teaching, and learning fraction addition on number lines. In E. Silver and P. Kenney (Editors) Chapter 17:

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Pancreatitis in association with hypercalcemia in patients receiving total parenteral nutrition

Six patients receiving total parenteral nutrition (TPN) developed hypercalcemia and acute pancreatitis. Four were long-term home TPN patients, and two were short-term hospital TPN patients. Causes of pancreatitis other than hypercalcemia were not found. The etiology of the hypercalcemia remained unclear and in particular was not due to calcium infusion or hyperparathyroidism. In 4 patients in whom it was measured, the plasma parathyroid hormone was normal (in 2) or nondetectable (in 2). Hypercalcemia and pancreatitis subsided with discontinuation of TPN. Thus, some patients receiving TPN develop hypercalcemia, and in some of these pancreatitis ensues

Pulping catalysts in trees

"December 1999.""Submitted to Journal of Wood Chemistry and Technology.