Characterisation of the Mitochondrial Genome and the Phylogeographic Structure of Blue Cod (Parapercis colias)

<p>This thesis primarily addresses the genetic population structure of blue cod (Parapercis colias) in the New Zealand Exclusive Economic Zone, within which approximately 2800 Tonnes of the endemic fish are harvested annually. Several regions with traditionally healthy blue cod stocks have recently experienced localised depletion due to over-exploitation. This highlights the importance for a clearer understanding of the genetic structure of the species in order to maximise the potential for the fishery to be managed sustainably. Also covered within this thesis are characteristics of the blue cod's mitochondrial genome, and development of a set of genetic tools that can improve the level of understanding for several important fisheries species in New Zealand waters. Chapter two focuses on the characterisation of the blue cod mitochondrial genome, with the use of second-generation sequencing providing the first fully documented sequence for this species. The blue cod mitochondrial genome is identical in organisation to several other documented fish species' mitochondrial genomes, with no unexpected results. Also dealt with in Chapter two is the development and implementation of a set of generic control region primers, designed primarily for use on commercially important inshore New Zealand fish species. Nine of the eleven species which the primer was tested on had the targeted region successfully amplified, though heteroplasmy may be present in at least four species. Chapter three reports the bulk of this research, with the phylogeographic structure of blue cod investigated. Samples were taken from the pectoral and pelvic fins of blue cod from 14 sites around New Zealand. A total of 475 sequences were taken from the hypervariable 5' end of the control region, with each sequence 491 bp in length. The null hypothesis of genetic homogeneity throughout their distribution was rejected, with significant differentiation observed between mainland New Zealand and Chatham Island samples. While pairwise differences between mainland New Zealand sampling sites was limited, a significant trend of isolation by distance was observed. A demographic population expansion occurred more steeply and more recently in mainland populations, with a slower growth curve in Chatham Island populations. With a trend of isolation by distance present between mainland sampling sites, it is suggested that further investigations are made, utilising genetic markers capable of resolving deeper patterns of genetic structure within the population (e.g. microsatellites, SNP's). Finally, Chapter four summarises and contextualises the results from the research components of this thesis, discussing management implications and potential threats to both the commercial and recreational blue cod fishery. A key area of focus for this section is the genetic and demographic risk that the population may face with continued targeting of larger individuals, given the biological trait of protogynous hermaphroditism in the species.</p>

Characterisation of the Mitochondrial Genome and the Phylogeographic Structure of Blue Cod (Parapercis colias)

<p>This thesis primarily addresses the genetic population structure of blue cod (Parapercis colias) in the New Zealand Exclusive Economic Zone, within which approximately 2800 Tonnes of the endemic fish are harvested annually. Several regions with traditionally healthy blue cod stocks have recently experienced localised depletion due to over-exploitation. This highlights the importance for a clearer understanding of the genetic structure of the species in order to maximise the potential for the fishery to be managed sustainably. Also covered within this thesis are characteristics of the blue cod's mitochondrial genome, and development of a set of genetic tools that can improve the level of understanding for several important fisheries species in New Zealand waters. Chapter two focuses on the characterisation of the blue cod mitochondrial genome, with the use of second-generation sequencing providing the first fully documented sequence for this species. The blue cod mitochondrial genome is identical in organisation to several other documented fish species' mitochondrial genomes, with no unexpected results. Also dealt with in Chapter two is the development and implementation of a set of generic control region primers, designed primarily for use on commercially important inshore New Zealand fish species. Nine of the eleven species which the primer was tested on had the targeted region successfully amplified, though heteroplasmy may be present in at least four species. Chapter three reports the bulk of this research, with the phylogeographic structure of blue cod investigated. Samples were taken from the pectoral and pelvic fins of blue cod from 14 sites around New Zealand. A total of 475 sequences were taken from the hypervariable 5' end of the control region, with each sequence 491 bp in length. The null hypothesis of genetic homogeneity throughout their distribution was rejected, with significant differentiation observed between mainland New Zealand and Chatham Island samples. While pairwise differences between mainland New Zealand sampling sites was limited, a significant trend of isolation by distance was observed. A demographic population expansion occurred more steeply and more recently in mainland populations, with a slower growth curve in Chatham Island populations. With a trend of isolation by distance present between mainland sampling sites, it is suggested that further investigations are made, utilising genetic markers capable of resolving deeper patterns of genetic structure within the population (e.g. microsatellites, SNP's). Finally, Chapter four summarises and contextualises the results from the research components of this thesis, discussing management implications and potential threats to both the commercial and recreational blue cod fishery. A key area of focus for this section is the genetic and demographic risk that the population may face with continued targeting of larger individuals, given the biological trait of protogynous hermaphroditism in the species.</p>

Human Identification with their VOC Distribution Through CMS – SEN Model

Smell printing or odor printing is a novel morphological characteristic that an object can be defined by its odor. Human body odor is one such biological trait that yields less error rate of 15% among other biometrics. The human odor printing or smell printing possesses significance against the world towards screening of security checkpoint, searching for survivals under rubbles, investigating criminals, and many more. Cogno-monitoring system (CMS) is a specific prototype to furnish two essential processes -odor analysis and odor encoding through the Sensing-Encoding-Notifying (SEN) model to give the sensitivity and specificity score among the individuals. Human body odor can be interpreted as the alliance of various volatile organic compounds (VOCs) and they are recognized, classified in the encoding process. This article exhibits a detailed analysis of the traditional detection methods including bioanalysis concerning the human body human body odor experimented with 6 people. By applying principal component analysis along with random forest classifier, the VOCs distribution of the individuals is measured. This work calculates that 18.7% of VOCs are having a match with all the individuals which become the plinth for the identification of humans.

Integrative Modelling of Gene Expression and Digital Phenotypes to Describe Senescence in Wheat

Senescence is the final stage of leaf development and is critical for plants’ fitness as nutrient relocation from leaves to reproductive organs takes place. Although senescence is key in nutrient relocation and yield determination in cereal grain production, there is limited understanding of the genetic and molecular mechanisms that control it in major staple crops such as wheat. Senescence is a highly orchestrated continuum of interacting pathways throughout the lifecycle of a plant. Levels of gene expression, morphogenesis, and phenotypic development all play key roles. Yet, most studies focus on a short window immediately after anthesis. This approach clearly leaves out key components controlling the activation, development, and modulation of the senescence pathway before anthesis, as well as during the later developmental stages, during which grain development continues. Here, a computational multiscale modelling approach integrates multi-omics developmental data to attempt to simulate senescence at the molecular and plant level. To recreate the senescence process in wheat, core principles were borrowed from Arabidopsis Thaliana, a more widely researched plant model. The resulted model describes temporal gene regulatory networks and their effect on plant morphology leading to senescence. Digital phenotypes generated from images using a phenomics platform were used to capture the dynamics of plant development. This work provides the basis for the application of computational modelling to advance understanding of the complex biological trait senescence. This supports the development of a predictive framework enabling its prediction in changing or extreme environmental conditions, with a view to targeted selection for optimal lifecycle duration for improving resilience to climate change.

Functional Pattern of Benthic Epifauna in the Chukchi Borderland, Arctic Deep Sea

Assessment of Arctic deep-sea ecosystem functioning is currently an urgent task considering that ongoing sea-ice reduction opens opportunities for resource exploitation of yet understudied deep-sea regions. We used Biological Trait Analysis to evaluate ecosystem functioning and test if common paradigms for deep-sea fauna apply to benthic epifauna of the deep-sea Arctic Chukchi Borderland (CBL). We also investigated the influence of environmental factors on the functional structure of the epifauna. The analysis was performed for 106 taxa collected with a beam trawl and a Remotely Operated Vehicle from 486 to 2610 m depth. The most common trait modalities were small-medium size, mobile, benthic direct and lecithotrophic larval development, and predatory feeding, which mostly supports the current view of epifauna in the global deep sea. Functional composition of epifauna differed between two depth strata (486–1059 m and 1882–2610 m), with depth and sediment carbon content explaining most of the functional variability. Proportional abundances of the modalities free-living, swimming, suspension feeders, opportunists/scavengers, internal fertilization and globulose were higher at deep stations. Functional redundancy (FR) was also higher there compared to the mid-depth stations, suggesting adaptation of fauna to the more homogeneous deep environment by fewer and shared traits. Mid-depth stations represented higher functional variability in terms of both trait modality composition and functional diversity, indicating more variable resource use in the more heterogeneous habitat. Food input correlated positively with the proportional abundance of the modalities tube-dwelling, sessile and deposit feeding. Areas with drop stones were associated with higher proportional abundance of the modalities attached, upright, and predators. Comparatively low FR may render the heterogeneous mid-depth area of the CBL vulnerable to disturbance through the risk of loss of functions. Across the study area, high occurrence of taxa with low dispersal ability among adult and larval life stages may prevent rapid adaptation to changes, reduce ability to recolonize and escape perturbation.

Bivariate Genomic Prediction of Phenotypes by Selecting Epistatic Interactions Across Years Based on Haplotype Blocks and Pruned Sets of SNPs

The importance of accurate genomic prediction of phenotypes in plant breeding is undeniable, as higher prediction accuracy can increase selection responses. In this study, we investigated the ability of three models to improve prediction accuracy by including phenotypic information from the last growing season. This was done by considering a single biological trait in two growing seasons (2017 and 2018) as separate traits in a multi-trait model. Thus, bivariate variants of the Genomic Best Linear Unbiased Prediction (GBLUP) as an additive model, Epistatic Random Regression BLUP (ERRBLUP) and selective Epistatic Random Regression BLUP (sERRBLUP) as epistasis models were compared with respect to their prediction accuracies for the second year. The results indicate that bivariate ERRBLUP is almost identical to bivariate GBLUP in prediction accuracy, while bivariate sERRBLUP has the highest prediction accuracy in most cases. The obtained prediction accuracies were similar when utilizing pruned sets of SNPs and haplotype blocks, while utilizing haplotype blocks reduces the computational load significantly compared to utilizing pruned sets of SNPs. The prediction accuracies of bivariate GBLUP, ERRBLUP and sERRBLUP have been assessed across eight phenotypic traits and studied datasets from 471/402 doubled haploid lines in the European maize landrace Kemater Landmais Gelb/Petkuser Ferdinand Rot. We further investigated the genomic correlation, phenotypic correlation and trait heritability as factors affecting the bivariate models’ prediction accuracy, with genetic correlation between growing seasons being the most important one. For all three considered model architectures results were far worse when using a univariate version of the model.