A Taxonomic Investigation into the Red Alga Plocamium within New Zealand

<p>The red alga Plocamium is a cosmopolitan genus, known for its distinct branching pattern and rich chemical composition. Recent studies indicate morphological-based species delimitation approaches have failed to accurately discern diversity, distributions, and evolutionary relationship between species worldwide. Currently there are seven recognized species within New Zealand based on traditional morphological approaches and no molecular based work focused on discerning true diversity of New Zealand species in this genus. This thesis is the first to use molecular-assisted alpha taxonomy to investigate Plocamium within New Zealand. Phylogenetic analyses (Maximum Likelihood and Bayesian Inference) based on COI, rbcL, LSU and combined LSU/COI markers, three molecular species delimitation methods (Automatic Barcode Gap Discovery, General Mixed Yule Coalescent, and Bayesian implementation of the Poisson Tree Processes), and morphometric analyses of various characters (width of main axis (WMA), width of lowest basal ramuli (WLBR), length of lowest basal ramuli (LLBR), number of alternating series of ramuli (NASR), average number of ramuli per alternating series (ANRAS), curvature of basal ramuli (CBR) and serrations present or absent from basal ramuli (SERBR) were used to address this topic. The species delimitation methods revealed at least eleven (A-K) putative genetic species (with some incongruences) within the New Zealand specimens included in the study. Morphometric analyses indicated morphology reflects genetic diversity when multiple measures of multiple characters are used, however this is not the case when considering single characters. Phylogenetic analyses revealed possible monophyly of New Zealand candidate species C-K, and possible relationships to Australian, Chilean, and Taiwanese species. However these backbone relationships were poorly supported. The results of this study indicate that Plocamium diversity within New Zealand has been underestimated and provide the first steps in discovering the true species diversity of Plocamium within New Zealand.</p>

A Taxonomic Investigation into the Red Alga Plocamium within New Zealand

<p>The red alga Plocamium is a cosmopolitan genus, known for its distinct branching pattern and rich chemical composition. Recent studies indicate morphological-based species delimitation approaches have failed to accurately discern diversity, distributions, and evolutionary relationship between species worldwide. Currently there are seven recognized species within New Zealand based on traditional morphological approaches and no molecular based work focused on discerning true diversity of New Zealand species in this genus. This thesis is the first to use molecular-assisted alpha taxonomy to investigate Plocamium within New Zealand. Phylogenetic analyses (Maximum Likelihood and Bayesian Inference) based on COI, rbcL, LSU and combined LSU/COI markers, three molecular species delimitation methods (Automatic Barcode Gap Discovery, General Mixed Yule Coalescent, and Bayesian implementation of the Poisson Tree Processes), and morphometric analyses of various characters (width of main axis (WMA), width of lowest basal ramuli (WLBR), length of lowest basal ramuli (LLBR), number of alternating series of ramuli (NASR), average number of ramuli per alternating series (ANRAS), curvature of basal ramuli (CBR) and serrations present or absent from basal ramuli (SERBR) were used to address this topic. The species delimitation methods revealed at least eleven (A-K) putative genetic species (with some incongruences) within the New Zealand specimens included in the study. Morphometric analyses indicated morphology reflects genetic diversity when multiple measures of multiple characters are used, however this is not the case when considering single characters. Phylogenetic analyses revealed possible monophyly of New Zealand candidate species C-K, and possible relationships to Australian, Chilean, and Taiwanese species. However these backbone relationships were poorly supported. The results of this study indicate that Plocamium diversity within New Zealand has been underestimated and provide the first steps in discovering the true species diversity of Plocamium within New Zealand.</p>

Full Implementation under Ambiguity

This paper introduces the maxmin expected utility framework into the problem of fully implementing a social choice set as ambiguous equilibria. Our model incorporates the Bayesian framework and the Wald-type maxmin preferences as special cases and provides insights beyond the Bayesian implementation literature. We establish necessary and almost sufficient conditions for a social choice set to be fully implementable. Under the Wald-type maxmin preferences, we provide easy-to-check sufficient conditions for implementation. As applications, we implement the set of ambiguous Pareto-efficient and individually rational social choice functions, the maxmin core, the maxmin weak core, and the maxmin value. (JEL D71, D81, D82)

Integrative taxonomy of giant crested Eusirus in the Southern Ocean, including the description of a new species (Crustacea: Amphipoda: Eusiridae)

Among Antarctic amphipods of the genus Eusirus, a highly distinctive clade of giant species is characterized by a dorsal, blade-shaped tooth on pereionites 5–7 and pleonites 1–3. This lineage, herein named ‘crested Eusirus’, includes two potential species complexes, the Eusirus perdentatus and Eusirus giganteus complexes, in addition to the more distinctive Eusirus propeperdentatus. Molecular phylogenies and statistical parsimony networks (COI, CytB and ITS2) of crested Eusirus are herein reconstructed. This study aims to formally revise species diversity within crested Eusirus by applying several species delimitation methods (Bayesian implementation of the Poisson tree processes model, general mixed Yule coalescent, multi-rate Poisson tree processes and automatic barcode gap discovery) on the resulting phylogenies. In addition, results from the DNA-based methods are benchmarked against a detailed morphological analysis of all available specimens of the E. perdentatus complex. Our results indicate that species diversity of crested Eusirus is underestimated. Overall, DNA-based methods suggest that the E. perdentatus complex is composed of three putative species and that the E. giganteus complex includes four or five putative species. The morphological analysis of available specimens from the E. perdentatus complex corroborates molecular results by identifying two differentiable species, the genuine E. perdentatus and a new species, herein described as Eusirus pontomedon sp. nov.

A Hierarchical Bayesian Implementation of the Experience-Weighted Attraction Model

Social and decision-making deficits are often the first symptoms of neuropsychiatric disorders. In recent years, economic games, together with computational models of strategic learning, have been increasingly applied to the characterization of individual differences in social behavior, as well as their changes across time due to disease progression, treatment, or other factors. At the same time, the high dimensionality of these data poses an important challenge to statistical estimation of these models, potentially limiting the adoption of such approaches in patients and special populations. We introduce a hierarchical Bayesian implementation of a class of strategic learning models, experience-weighted attraction (EWA), that is widely used in behavioral game theory. Importantly, this approach provides a unified framework for capturing between- and within-participant variation, including changes associated with disease progression, comorbidity, and treatment status. We show using simulated data that our hierarchical Bayesian approach outperforms representative agent and individual-level estimation methods that are commonly used in extant literature, with respect to parameter estimation and uncertainty quantification. Furthermore, using an empirical dataset, we demonstrate the value of our approach over competing methods with respect to balancing model fit and complexity. Consistent with the success of hierarchical Bayesian approaches in other areas of behavioral science, our hierarchical Bayesian EWA model represents a powerful and flexible tool to apply to a wide range of behavioral paradigms for studying the interplay between complex human behavior and biological factors.

Sparse Logistic Regression: Comparison of Regularization and Bayesian Implementations

In knowledge-based systems, besides obtaining good output prediction accuracy, it is crucial to understand the subset of input variables that have most influence on the output, with the goal of gaining deeper insight into the underlying process. These requirements call for logistic model estimation techniques that provide a sparse solution, i.e., where coefficients associated with non-important variables are set to zero. In this work we compare the performance of two methods: the first one is based on the well known Least Absolute Shrinkage and Selection Operator (LASSO) which involves regularization with an ℓ 1 norm; the second one is the Relevance Vector Machine (RVM) which is based on a Bayesian implementation of the linear logistic model. The two methods are extensively compared in this paper, on real and simulated datasets. Results show that, in general, the two approaches are comparable in terms of prediction performance. RVM outperforms the LASSO both in term of structure recovery (estimation of the correct non-zero model coefficients) and prediction accuracy when the dimensionality of the data tends to increase. However, LASSO shows comparable performance to RVM when the dimensionality of the data is much higher than number of samples that is p > > n .