School of Botany - Research Publications
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ItemThe Mitochondrial Genome and Transcriptome of the Basal Dinoflagellate Hematodinium sp.: Character Evolution within the Highly Derived Mitochondrial Genomes of Dinoflagellates(OXFORD UNIV PRESS, 2012)The sister phyla dinoflagellates and apicomplexans inherited a drastically reduced mitochondrial genome (mitochondrial DNA, mtDNA) containing only three protein-coding (cob, cox1, and cox3) genes and two ribosomal RNA (rRNA) genes. In apicomplexans, single copies of these genes are encoded on the smallest known mtDNA chromosome (6 kb). In dinoflagellates, however, the genome has undergone further substantial modifications, including massive genome amplification and recombination resulting in multiple copies of each gene and gene fragments linked in numerous combinations. Furthermore, protein-encoding genes have lost standard stop codons, trans-splicing of messenger RNAs (mRNAs) is required to generate complete cox3 transcripts, and extensive RNA editing recodes most genes. From taxa investigated to date, it is unclear when many of these unusual dinoflagellate mtDNA characters evolved. To address this question, we investigated the mitochondrial genome and transcriptome character states of the deep branching dinoflagellate Hematodinium sp. Genomic data show that like later-branching dinoflagellates Hematodinium sp. also contains an inflated, heavily recombined genome of multicopy genes and gene fragments. Although stop codons are also lacking for cox1 and cob, cox3 still encodes a conventional stop codon. Extensive editing of mRNAs also occurs in Hematodinium sp. The mtDNA of basal dinoflagellate Hematodinium sp. indicates that much of the mtDNA modification in dinoflagellates occurred early in this lineage, including genome amplification and recombination, and decreased use of standard stop codons. Trans-splicing, on the other hand, occurred after Hematodinium sp. diverged. Only RNA editing presents a nonlinear pattern of evolution in dinoflagellates as this process occurs in Hematodinium sp. but is absent in some later-branching taxa indicating that this process was either lost in some lineages or developed more than once during the evolution of the highly unusual dinoflagellate mtDNA.
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ItemNormalizing and Integrating Metabolomics Data(AMER CHEMICAL SOC, 2012-12-18)Metabolomics research often requires the use of multiple analytical platforms, batches of samples, and laboratories, any of which can introduce a component of unwanted variation. In addition, every experiment is subject to within-platform and other experimental variation, which often includes unwanted biological variation. Such variation must be removed in order to focus on the biological information of interest. We present a broadly applicable method for the removal of unwanted variation arising from various sources for the identification of differentially abundant metabolites and, hence, for the systematic integration of data on the same quantities from different sources. We illustrate the versatility and the performance of the approach in four applications, and we show that it has several advantages over the existing normalization methods.
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ItemNew horizons for managing the environment: A review of coupled social-ecological systems modeling(Wiley, 2012)Conventional approaches to natural resource management are increasingly challenged by environmental problems that are embedded in highly complex systems with profound uncertainties. These so‐called social‐ecological systems (SESs) are characterized by strong links between the social and the ecological system and multiple interactions across spatial and temporal scales. New approaches are needed to manage those tightly coupled systems; however, basic understanding of their nonlinear behavior is still missing. Modeling is a traditional tool in natural resource management to study complex, dynamic systems. There is a long tradition of SES modeling, but the approach is now being more widely recognized in other fields, such as ecological and economic modeling, where issues such as nonlinear ecological dynamics and complex human decision making are receiving more attention. SES modeling is maturing as a discipline in its own right, incorporating ideas from other interdisciplinary fields such as resilience or complex systems research. In this paper, we provide an overview of the emergence and state of the art of this cross‐cutting field. Our analysis reveals the substantial potential of SES models to address issues that are of utmost importance for managing complex human‐environment relationships, such as: (i) the implications of ecological and social structure for resource management, (ii) uncertainty in natural and social systems and ways to address it, (iii) the role of coevolutionary processes in the dynamics of SESs, and (iv) the implications of microscale human decision making for sustainable resource management and conservation. The complexity of SESs and the lack of a common analytical framework, however, also pose significant challenges for this emerging field. There are clear research needs with respect to: (i) approaches that go beyond rather simple specifications of human decision making, (ii) development of coping strategies to deal with (irreducible) uncertainties, (iii) more explicit modeling of feedbacks between the social and ecological systems, and (iv) a conceptual and methodological framework for analyzing and modeling SESs. We provide ideas for tackling some of these challenges and indicate potential key focal areas for SES modeling in the future.
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ItemThe Intelligence Game: Assessing Delphi Groups and structured question formats(Edith Cowan University, 2012)
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ItemClassical metapopulation theory as a useful paradigm for the conservation of an endangered amphibian(ELSEVIER SCI LTD, 2012-04)
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