Improved Wood Species Identification Based On Multi-View Imagery of The Three Anatomical Planes

Background: The identification of tropical African wood species based on microscopic imagery is a challenging problem due to the heterogeneous nature of the composition of wood combined with the vast number of candidate species. Image classification methods that rely on machine learning can facilitate this identification, provided that sufficient training material is available. Despite the fact that the three main anatomical sections contain information that is relevant for species identification, current methods only rely on the transversal section. Additionally, commonly used procedures for evaluating the performance of these methods neglect the fact that multiple images often originate from the same tree, leading to an overly optimistic estimate of the performance. Results: We introduce a new image dataset containing microscopic images of the three main anatomical sections of 77 Congolese wood species. A dedicated multiview image classification method is developed and obtains an accuracy (computed using the naive but common approach) of 95%, outperforming the singleview methods by a large margin. An in-depth analysis shows that naive accuracy estimates can lead to a dramatic over-prediction, of up to 60%, of the accuracy. Conclusions: Additional images from the non-transversal sections can boost the performance of machine-learning-based wood species identification methods. Additionally, care should be taken when evaluating the performance of machine-learningbased wood species identification methods to avoid an overestimation of the performance.

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>

A review on the potential of filamentous fungi for microbial self-healing of concrete

Concrete is the most used construction material worldwide due to its abundant availability and inherent ease of manufacturing and application. However, the material bears several drawbacks such as the high susceptibility for crack formation, leading to reinforcement corrosion and structural degradation. Extensive research has therefore been performed on the use of microorganisms for biologically mediated self-healing of concrete by means of CaCO3 precipitation. Recently, filamentous fungi have been recognized as high-potential microorganisms for this application as their hyphae grow in an interwoven three-dimensional network which serves as nucleation site for CaCO3 precipitation to heal the crack. This potential is corroborated by the current state of the art on fungi-mediated self-healing concrete, which is not yet extensive but valuable to direct further research. In this review, we aim to broaden the perspectives on the use of fungi for concrete self-healing applications by first summarizing the major progress made in the field of microbial self-healing of concrete and then discussing pioneering work that has been done with fungi. Starting from insights and hypotheses on the types and principles of biomineralization that occur during microbial self-healing, novel potentially promising candidate species are proposed based on their abilities to promote CaCO3 formation or to survive in extreme conditions that are relevant for concrete. Additionally, an overview will be provided on the challenges, knowledge gaps and future perspectives in the field of fungi-mediated self-healing concrete.

An Evaluation of Prior Residency and Habitat Effects on the Persistence of Settling Reef Fishes

<p>Both habitat complexity and competitive interactions can shape patterns of distribution and abundance of species. I evaluated the separate and joint effects of competitive interactions and habitat complexity on the survival of young fishes (Family Labridae) on coral reefs. First, I developed (in Chapter 2) a quantitative approach to evaluate potential resource (i.e., niche) overlap among groups of co-occurring species. Using appropriate transformations and probability models, I show that different types of data (e.g., categorical, continuous, count or binary data, as well as electivity scores) give rise to a standard measure of niche overlap, with the overlap statistic between two species defined as the overlapping area between the distributions for each species. Measurements derived from different types of data can be combined into a single multivariate analysis of niche overlap by averaging over multiple axes. I then describe null model permutation tests that differentiate between species occupying similar and different niches within my unified indices. I then implemented this approach (in Chapter 3) to evaluate potential habitat overlap among eight species of wrasse (Gomphosus varius, Halichoeres hortulanus, H. trimaculatus, Pseudocheilinus hexataenia, Scarus sordidus, Stethojulis bandanensis, Thalassoma hardwicke and T. quinquevittatum), and used these results to inform my subsequent field experiments. In a field assay, I identified the presence of T. quinquevittatum as having the greatest negative effect on survival of transplanted T. hardwicke from a suite of three candidate species which were most similar in habitat use to T. hardwicke (the other two candidate species were G. varius and P. hexataenia). In a subsequent field experiment, I tested how competition with T. quinquevittatum and structural refuge interact to influence the postsettlement survival of T. hardwicke. Competition with T. quinquevittatum and structural refuge both altered the survival of T. hardwicke, although their effects were not interactive, indicating that structural complexity did not mitigate the negative effects of competition. Survival of T. hardwicke was 2.3 times greater in treatments without T. quinquevittatum relative to those with T. quinquevittatum, and 2.8 times greater in treatments with structural refuge relative to treatments without structural refuge. Thalassoma hardwicke and T. quinquevittatum often enter reef communities asynchronously, resulting in competitive pressures faced by earlyarriving individuals that potentially differ from those experienced by late-arriving individuals. In a series of field experiments, I investigated whether the strength of intra-cohort competitive interactions between recent T. hardwicke and T. quinquevittatum settlers were dependent upon the sequence and temporal separation of their arrival into communities. Survival rates for both species were greatest in the absence of competitors, but when competitors were present, survival rates were maximized when competitors arrived simultaneously. Survival rates declined as each species entered the community progressively later than its competitor. Further, reversals in the sequence of arrival reversed competitive outcomes. Results provide empirical evidence for competitive lotteries in the maintenance of species diversity in demographically open marine systems, while also highlighting the importance of temporal variation in the direction and magnitude of interaction strengths. To further our understanding of how timing of arrival influences interaction strengths, I tested whether increasing the availability of complex habitat attenuates or enhances timing-of-arrival effects. Results from this field experiment indicated that aggression by early-arriving individuals towards late-arriving individuals increased as arrival times diverged. When aggression was weak, subordinate individuals were not displaced from complex habitat. Experimental increases in the availability of complex habitat resulted in increased survival of subordinates, presumably by disrupting predation pressure. However, when aggression was intense, competitive subordinates were displaced from complex habitat (regardless of the amount of complex habitat available), and this likely increased their exposure to predators. Overall, the experimental and observational components of this thesis emphasise heterogeneity in competitive environments experienced by recently settled reef fishes. These results highlight the important role that priority effects and habitat complexity play in determining the persistence of reef fish settlers, and illustrate how ecological contexts can add considerable variation to realised interaction strengths.</p>

An Evaluation of Prior Residency and Habitat Effects on the Persistence of Settling Reef Fishes

<p>Both habitat complexity and competitive interactions can shape patterns of distribution and abundance of species. I evaluated the separate and joint effects of competitive interactions and habitat complexity on the survival of young fishes (Family Labridae) on coral reefs. First, I developed (in Chapter 2) a quantitative approach to evaluate potential resource (i.e., niche) overlap among groups of co-occurring species. Using appropriate transformations and probability models, I show that different types of data (e.g., categorical, continuous, count or binary data, as well as electivity scores) give rise to a standard measure of niche overlap, with the overlap statistic between two species defined as the overlapping area between the distributions for each species. Measurements derived from different types of data can be combined into a single multivariate analysis of niche overlap by averaging over multiple axes. I then describe null model permutation tests that differentiate between species occupying similar and different niches within my unified indices. I then implemented this approach (in Chapter 3) to evaluate potential habitat overlap among eight species of wrasse (Gomphosus varius, Halichoeres hortulanus, H. trimaculatus, Pseudocheilinus hexataenia, Scarus sordidus, Stethojulis bandanensis, Thalassoma hardwicke and T. quinquevittatum), and used these results to inform my subsequent field experiments. In a field assay, I identified the presence of T. quinquevittatum as having the greatest negative effect on survival of transplanted T. hardwicke from a suite of three candidate species which were most similar in habitat use to T. hardwicke (the other two candidate species were G. varius and P. hexataenia). In a subsequent field experiment, I tested how competition with T. quinquevittatum and structural refuge interact to influence the postsettlement survival of T. hardwicke. Competition with T. quinquevittatum and structural refuge both altered the survival of T. hardwicke, although their effects were not interactive, indicating that structural complexity did not mitigate the negative effects of competition. Survival of T. hardwicke was 2.3 times greater in treatments without T. quinquevittatum relative to those with T. quinquevittatum, and 2.8 times greater in treatments with structural refuge relative to treatments without structural refuge. Thalassoma hardwicke and T. quinquevittatum often enter reef communities asynchronously, resulting in competitive pressures faced by earlyarriving individuals that potentially differ from those experienced by late-arriving individuals. In a series of field experiments, I investigated whether the strength of intra-cohort competitive interactions between recent T. hardwicke and T. quinquevittatum settlers were dependent upon the sequence and temporal separation of their arrival into communities. Survival rates for both species were greatest in the absence of competitors, but when competitors were present, survival rates were maximized when competitors arrived simultaneously. Survival rates declined as each species entered the community progressively later than its competitor. Further, reversals in the sequence of arrival reversed competitive outcomes. Results provide empirical evidence for competitive lotteries in the maintenance of species diversity in demographically open marine systems, while also highlighting the importance of temporal variation in the direction and magnitude of interaction strengths. To further our understanding of how timing of arrival influences interaction strengths, I tested whether increasing the availability of complex habitat attenuates or enhances timing-of-arrival effects. Results from this field experiment indicated that aggression by early-arriving individuals towards late-arriving individuals increased as arrival times diverged. When aggression was weak, subordinate individuals were not displaced from complex habitat. Experimental increases in the availability of complex habitat resulted in increased survival of subordinates, presumably by disrupting predation pressure. However, when aggression was intense, competitive subordinates were displaced from complex habitat (regardless of the amount of complex habitat available), and this likely increased their exposure to predators. Overall, the experimental and observational components of this thesis emphasise heterogeneity in competitive environments experienced by recently settled reef fishes. These results highlight the important role that priority effects and habitat complexity play in determining the persistence of reef fish settlers, and illustrate how ecological contexts can add considerable variation to realised interaction strengths.</p>

Discovery of nondiazotrophic Trichodesmium species abundant and widespread in the open ocean

Filamentous and colony-forming cells within the cyanobacterial genus Trichodesmium might account for nearly half of nitrogen fixation in the sunlit ocean, a critical mechanism that sustains plankton’s primary productivity. Trichodesmium has long been portrayed as a diazotrophic genus. By means of genome-resolved metagenomics, here we reveal that nondiazotrophic Trichodesmium species not only exist but also are abundant and widespread in the open ocean, benefiting from a previously overlooked functional lifestyle to expand the biogeography of this prominent marine genus. Near-complete environmental genomes for those closely related candidate species reproducibly shared functional features including a lack of genes related to nitrogen fixation, hydrogen recycling, and hopanoid lipid production concomitant with the enrichment of nitrogen assimilation genes. Our results elucidate fieldwork observations of Trichodesmium cells fixing carbon but not nitrogen. The Black Queen hypothesis and burden of low-oxygen concentration requirements provide a rationale to explain gene loss linked to nitrogen fixation among Trichodesmium species. Disconnecting taxonomic signal for this genus from a microbial community’s ability to fix nitrogen will help refine our understanding of the marine nitrogen balance. Finally, we are reminded that established links between taxonomic lineages and functional traits do not always hold true.

Molecular species delimitation refines the taxonomy of native and nonnative physinine snails in North America

Being able to associate an organism with a scientific name is fundamental to our understanding of its conservation status, ecology, and evolutionary history. Gastropods in the subfamily Physinae have been especially troublesome to identify because morphological variation can be unrelated to interspecific differences and there have been widespread introductions of an unknown number of species, which has led to a speculative taxonomy. To resolve uncertainty about species diversity in North America, we targeted an array of single-locus species delimitation methods at publically available specimens and new specimens collected from the Snake River basin, USA to generate species hypotheses, corroborated using nuclear analyses of the newly collected specimens. A total-evidence approach delineated 18 candidate species, revealing cryptic diversity within recognized taxa and a lack of support for other named taxa. Hypotheses regarding certain local endemics were confirmed, as were widespread introductions, including of an undescribed taxon likely belonging to a separate genus in southeastern Idaho for which the closest relatives are in southeast Asia. Overall, single-locus species delimitation was an effective first step toward understanding the diversity and distribution of species in Physinae and to guiding future investigation sampling and analyses of species hypotheses.

Towards a Cardoon (Cynara cardunculus var. altilis)-Based Biorefinery: A Case Study of Improved Cell Cultures via Genetic Modulation of the Phenylpropanoid Pathway

Cultivated cardoon (Cynara cardunculus var. altilis L.) is a promising candidate species for the development of plant cell cultures suitable for large-scale biomass production and recovery of nutraceuticals. We set up a protocol for Agrobacterium tumefaciens-mediated transformation, which can be used for the improvement of cardoon cell cultures in a frame of biorefinery. As high lignin content determines lower saccharification yields for the biomass, we opted for a biotechnological approach, with the purpose of reducing lignin content; we generated transgenic lines overexpressing the Arabidopsis thaliana MYB4 transcription factor, a known repressor of lignin/flavonoid biosynthesis. Here, we report a comprehensive characterization, including metabolic and transcriptomic analyses of AtMYB4 overexpression cardoon lines, in comparison to wild type, underlining favorable traits for their use in biorefinery. Among these, the improved accessibility of the lignocellulosic biomass to degrading enzymes due to depletion of lignin content, the unexpected increased growth rates, and the valuable nutraceutical profiles, in particular for hydroxycinnamic/caffeoylquinic and fatty acids profiles.

COMPARATIVE PHARMACOGNOSTIC EVALUATION OF MARKET SAMPLES OF PRSNIPARNI WITH GENUINE SOURCE OF URARIA PICTA (JACQ) DESV EX DC

The medicinal plants and its active principles are playing a dominant role in the maintenance of human health since ancient times. The degree of threat to natural population of medicinal plants has increased, because more than 90% of medicinal plant raw material for herbal industries in India draw from natural habitat In ayurvedic medicine Dasamula plants are top traded group and their annual demand is more than1000 Metric tons, Prsniparni moola is one among the Dasamula, The degree of threat to natural population of medicinal plants has increased, because more than 90% of medicinal plant raw material for herbal industries in India draws from natural habitat, this demand is not often met with supply of original raw drugs alone and is topped up with other species of plants that are substitutes or adulterants. This directly affects the quality and efficacy of the herbal products and the same has reflected in case of Uraria picta. Over usage, destructive harvesting and lack of cultivation have reduced the availability of Uraria picta. Inorder to characterize and compare the raw drugs used as prsniparni in market, the candidate species traded under the name Prsniparni were subjected to macroscopic and organoleptic evaluation, microscopic study, Physical and Phytochemical evaluation.