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Item Novel machine learning-driven comparative analysis of CSP, STFT, and CSP-STFT fusion for EEG data classification across multiple meditation and non-meditation sessions in BCI pipeline.(BioMed Central Ltd, 2025-02-08) Liyanagedera ND; Bareham CA; Kempton H; Guesgen HWThis study focuses on classifying multiple sessions of loving kindness meditation (LKM) and non-meditation electroencephalography (EEG) data. This novel study focuses on using multiple sessions of EEG data from a single individual to train a machine learning pipeline, and then using a new session data from the same individual for the classification. Here, two meditation techniques, LKM-Self and LKM-Others were compared with non-meditation EEG data for 12 participants. Among many tested, three BCI pipelines we built produced promising results, successfully detecting features in meditation/ non-meditation EEG data. While testing different feature extraction algorithms, a common neural network structure was used as the classification algorithm to compare the performance of the feature extraction algorithms. For two of those pipelines, Common Spatial Patterns (CSP) and Short Time Fourier Transform (STFT) were successfully used as feature extraction algorithms where both these algorithms are significantly new for meditation EEG. As a novel concept, the third BCI pipeline used a feature extraction algorithm that fused the features of CSP and STFT, achieving the highest classification accuracies among all tested pipelines. Analyses were conducted using EEG data of 3, 4 or 5 sessions, totaling 3960 tests on the entire dataset. At the end of the study, when considering all the tests, the overall classification accuracy using SCP alone was 67.1%, and it was 67.8% for STFT alone. The algorithm combining the features of CSP and STFT achieved an overall classification accuracy of 72.9% which is more than 5% higher than the other two pipelines. At the same time, the highest mean classification accuracy for the 12 participants was achieved using the pipeline with the combination of CSP STFT algorithm, reaching 75.5% for LKM-Self/ non-meditation for the case of 5 sessions of data. Additionally, the highest individual classification accuracy of 88.9% was obtained by the participant no. 14. Furthermore, the results showed that the classification accuracies for all three pipelines increased with the number of training sessions increased from 2 to 3 and then to 4. The study was successful in classifying a new session of EEG meditation/ non-meditation data after training machine learning algorithms using a different set of session data, and this achievement will be beneficial in the development of algorithms that support meditation.Item Inferring arsenic anomalies indirectly using airborne hyperspectral imaging – Implication for gold prospecting along the Rise and Shine Shear Zone in New Zealand(Elsevier B V, 2024-08-01) Chakraborty R; Kereszturi G; Pullanagari R; Craw D; Durance P; Ashraf SWell-exposed mineral deposits are scarce at a global level and presently potential mineral-rich sites are underlying vegetation cover and topsoil, which are suboptimal for direct remote sensing based exploration techniques. This study aims to implement an indirect approach to arsenic (As) distribution mapping using the surface manifestations of the subsurface geology and link it to the known gold mineralisation in the study area. Rise and Shine Shear Zone (RSSZ) in New Zealand is broadly a part of the Otago schist hosting lower to upper green-schist facies rocks manifesting mesothermal gold mineralisation. The area has several surficial geological imprints separating mineralised and non-mineralised zones, but these are dominated by topographic ruggedness, soil moisture and vegetation (mainly grass/tussock) spectra in the hyperspectral data. Initially, a band selection using Recursive Feature Elimination (RFE) was executed. The bands generated were tallied with the field and geological understanding of the area. The resultant 85 bands were then further put through Orthogonal Total Variation Component Analysis (OTVCA) to concise the information in 10 bands. OTVCA output was then classified using Random Forest classifier to map three levels of As concentration (<20 ppm, between 20 and 100 ppm and >100 ppm). The potentially high As concentration zones are likely to be related to the gold mineralisation. The geology of the area correlates with soil exposure which is captured by the classification in some parts, this increases the accuracy but also makes the classification analysis challenging.Item An investigation of the imputation techniques for missing values in ordinal data enhancing clustering and classification analysis validity(Elsevier Inc, 2023-12) Alam S; Ayub MS; Arora S; Khan MAMissing data can significantly impact dataset integrity and suitability, leading to unreliable statistical results, distortions, and poor decisions. The presence of missing values in data introduces inaccuracies in clustering and classification and compromises the reliability and validity of such analyses. This study investigates multiple imputation techniques specifically designed for handling missing values in ordinal data commonly encountered in surveys and questionnaires. Quantitative approaches are used to evaluate different imputation methods on various datasets with varying missing value percentages. By comparing the performance of imputation techniques using clustering metrics and algorithms (e.g., k-means, Partitioning Around Medoids), the study provides valuable insights for selecting appropriate imputation methods for accurate data analysis. Furthermore, the study examines the impact of imputed values on classification algorithms, including k-Nearest Neighbors (kNN), Naive Bayes (NB), and Multilayer Perceptron (MLP). Results demonstrate that the decision tree method is the most effective approach, closely aligning with the original data and achieving high accuracy. In contrast, random number imputation performs poorly, indicating limited reliability. This study advances the understanding of handling missing values and emphasizes the need to address this issue to enhance data analysis integrity and validity.Item Common spatial pattern for classification of loving kindness meditation EEG for single and multiple sessions(BioMed Central Ltd, Springer Nature, 2023-09-09) Liyanagedera ND; Hussain AA; Singh A; Lal S; Kempton H; Guesgen HWWhile a very few studies have been conducted on classifying loving kindness meditation (LKM) and non-meditation electroencephalography (EEG) data for a single session, there are no such studies conducted for multiple session EEG data. Thus, this study aims at classifying existing raw EEG meditation data on single and multiple sessions to come up with meaningful inferences which will be highly beneficial when developing algorithms that can support medita- tion practices. In this analysis, data have been collected on Pre-Resting (before-meditation), Post-Resting (after- meditation), LKM-Self and LKM-Others for 32 participants and hence allowing us to conduct six pairwise comparisons for the four mind tasks. Common Spatial Patterns (CSP) is a feature extraction method widely used in motor imaginary brain computer interface (BCI), but not in meditation EEG data. Therefore, using CSP in extracting features from medi- tation EEG data and classifying meditation/non-meditation instances, particularly for multiple sessions will create a new path in future meditation EEG research. The classification was done using Linear Discriminant Analysis (LDA) where both meditation techniques (LKM-Self and LKM-Others) were compared with Pre-Resting and Post-Resting instances. The results show that for a single session of 32 participants, around 99.5% accuracy was obtained for clas- sifying meditation/Pre-Resting instances. For the 15 participants when using five sessions of EEG data, around 83.6% accuracy was obtained for classifying meditation/Pre-Resting instances. The results demonstrate the ability to classify meditation/Pre-Resting data. Most importantly, this classification is possible for multiple session data as well. In addi- tion to this, when comparing the classification accuracies of the six mind task pairs; LKM-Self, LKM-Others and Post- Resting produced relatively lower accuracies among them than the accuracies obtained for classifying Pre-Resting with the other three. This indicates that Pre-Resting has some features giving a better classification indicating that it is different from the other three mind tasks.Item Rhododendron taxonomy and diversity of ex situ collections for conservation : (subsection) Maddenia species as a case study : a thesis presented in the partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Agriculture and Horticulture at Massey University (Manawatū campus], Palmerston North, New Zealand(Massey University, 2024-02-01) Hu, LingIn the ‘big genus’ Rhododendron of over 1,000 species, more than half of the species are threatened, at risk, or lacking data for biodiversity conservation. Ex situ collections, especially those from the wild, are crucial for safeguarding the diversity of species. However, lack of knowledge on existing wild diversity in botanic garden collections, and complex taxonomy, are two main problems in species assessments and conservation decision making. This research studied subsection Maddenia, a group of ~65 taxa encountering the two problems but seldom studied, as an exemplar to investigate species taxonomy and ex situ diversity. An ex situ conservation gap analysis was undertaken, using ecogeographical representation as a proxy for genetic representation in current botanic garden collections worldwide. Fifty-five of the total 65 taxa were found in cultivation, with over 86% of the living collections conserved in 66% of global botanic gardens. Half of the 18 threatened taxa, and nine of the 12 Data Deficient taxa require further wild collection to achieve a minimum level of ecogeographical representation in ex situ collections. Occurrence of ex situ collections in countries of origin is limited, and the distribution of ex situ collections worldwide is northern hemisphere centric. The results highlight the necessity of having more ex situ collections in the 10 native countries, and the importance of inter-institutional data sharing and robust documentation of collections. Determination of ploidy level of species was the second study, as the presence of polyploid samples may affect phylogenetic analysis. Ploidy levels were estimated for 263 accessions of 47 taxa (including 135 wild accessions) using flow cytometry. Meiotic chromosomes were counted for representative species of both diploids and polyploids to verify the flow cytometry results. This study showed that all taxa except one were diploid. The exception was that polyploids (2–8x, 12x) occur in the R. maddenii complex, where only seven of the 62 accessions tested were diploid while the rest were polyploid. This high level of polyploidy, combined with (i) the wide geographical distribution of the R. maddenii complex, and (ii) the previous ‘lumping’ of 12 taxa into the two subspecies, suggests the possibility of either some cryptic species or the need to re-evaluate some of the synonymized species. If new species were revealed, some may require conservation action. However, a greater number of wild-collected accessions and of different geographic origins are needed to explore this possibility. Following the ploidy study, molecular phylogeny of 40 taxa, including diploids and polyploids, was analysed using target capture sequencing. Phylogenetic trees from maximum likelihood and Bayesian analyses largely supported the morphological groupings of the Maddenii Series, Ciliicalyx Subseries and Megacalyx Subseries, but not the Ciliatum Subseries as classified by Davidian (1982). Of particular interest was the clustering in one clade of all of the R. maddenii complex, including all polyploid samples. This occurred irrespective of the method of analysis; however, there was no clear pattern of relationships to ploidy levels within the clade. The molecular phylogeny delimited several species and suggested a revision of the boundary of ‘subsection Maddenia’, although further research, to include a wider range of species, is needed to determine whether the new boundaries should be wider or narrower than before. The feasibility of using controlled pollination for safeguarding germplasm of prioritised species in ex situ collections was studied. Fruit set and seed germination identified the self- and cross-incompatibility of R. excellens (Vulnerable), which requires methods other than controlled pollination to conserve the intraspecific diversity in botanic gardens. R. dalhousiae var. dalhousiae (Least Concern), R. dalhousiae var. rhabdotum (Vulnerable), R. lindleyi (Least Concern), and R. nuttallii (Near Threatened) were both self- and cross-compatible, but the compatibility between self and cross pollinations differed from taxon to taxon and from accession to accession. These results suggest the choice of intraspecific pollination should be tested for each species before a programme of propagation is initiated. These aspects studied for subsection Maddenia can be immediately applied to conservation of this group of plants by working with the Global Conservation Consortium for Rhododendron. Meanwhile, the methods used here provide an exemplar for investigating other Rhododendron species or plant groups that encounter similar problems, to guide conservation efforts.Item Spatial patterns in the taxonomic and dietary diversity of New Zealand rocky reef fishes : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biological Sciences at Massey University, Albany, New Zealand(Massey University, 2018) Howarth, Odette RuthLatitudinal gradients of high species richness from the tropics declining towards the poles are well documented for many terrestrial and marine species. However, these broad scale patterns of numbers of species observed don’t inform as to how related these species are, or how they use food resources. By understanding taxonomic relationships between observed species I can predict how resilient these assemblages are and how environmental processes impact their distribution. Dietary diversity between species describes patterns related to mechanisms of food availability and preference of habitats or environmental niches. Marine fishes are speciose and well known taxonomically, and so comprise a useful system for studying broad-scale patterns in biodiversity. Here I examined five indices of diversity—species richness, average taxonomic distinctness, variation in taxonomic distinctness, average diet diversity and variation in diet diversity—using a historical dataset on the presence/absence of rocky reef fishes spanning most of New Zealand. I modelled these indices using boosted regression trees and mapped their distributions to the coastline at a 1km scale resolution. Additionally, I developed a new quantitative methodology to classify coastal, rocky reef fishes into homogenous diet guilds using hierarchical clustering of nine broad food items and SIMPROF multivariate analysis and modelled species richness of three of the diet guilds (herbivore, invertivore and piscivore/benthic invertivores) using boosted regression trees. This research has broadened our understanding of patterns of fish diversity, spatial patterns in diversity of diets in coastal rocky reef fishes in New Zealand. I found the indices of overall species richness, species richness of herbivores and invertivores, and average taxonomic distinctness to be highly correlated with increased wintertime sea-surface temperature indicating a latitudinal gradient to their distributions. Decreased turbidity increased average dietary diversity and species richness of the piscivore/benthic invertivore guild. Average fetch or exposure had a positive relationship with variation in diet diversity and a negative relationship with variation in taxonomic distinctness. Of secondary importance I found the indices of overall species richness, species richness of invertivores, average taxonomic distinctness and variation in diet diversity to be adversely affected by increased turbidity. Variation in taxonomic distinctness and species richness of the herbivore diet guild increased with variable and increasing salinity (respectively) while average diet diversity increased with exposure. Lastly the piscivore/benthic invertivore guild had a positive relationship with increased wintertime sea-surface temperature. Overall I found broad and fine scale environmental processes affected the species richness and taxonomic diversity of NZ reef fishes as did food availability, resource use and habitat preferences.Item Systematics and phylogeography of the large land snail Powelliphanta : a thesis presented in fulfilment of the requirements for the degree of Doctor of Philosophy in Zoology, Massey University, New Zealand(Massey University, 2018) Walker, Kathleen JoyWithout a generally accepted name, a species is less likely to receive conservation effort. For the large, colourful and carnivorous land snails in the New Zealand genus Powelliphanta, doubts about the validity of the existing morphologically-based nomenclature, and the absence of taxonomic assessment for many late-discovered taxa, have been hindering conservation efforts. Powelliphanta have been in decline due to continuing loss of habitat and a suite of predators recently introduced to New Zealand, but scarce conservation resources are targeted to formally described taxa. The aim of this study was to review and if appropriate revise the taxonomy of the genus to remove any taxonomic impediment to conservation action. Like other Pacific Ocean archipelagos, the fauna and flora of New Zealand is characterised by a small number of families with extensive radiations. Understanding of relationships is often hindered by the recency of lineage separations and requires multiple lines of evidence. Allozymes and mitochondrial sequences were used to identify genotypic clusters in Powelliphanta and to assess the relationship with presumed sister taxa Victaphanta. A matrix of morphological characters was assembled for multivariate analysis. These characters included for the first time in Powelliphanta, features of the soft body and Fourier coefficients describing subtle shape differences. Intraspecific variation within one of the species, P. lignaria, received detailed distributional, morphological and genetic evaluation to investigate the use of subspecies in the genus. Powelliphanta fiordlandica was found to be a sister taxon to all other Powelliphanta, with a deep genetic divergence and differences in morphology indicating it should be placed within its own monotypic genus. Allozymes, mtDNA and morphology all identified similar clusters, many of which equated to the already described taxa and to taxa which had been tag-named but remained undescribed. Shell colour, pattern and size, which show environmental plasticity in some molluscs, were found in Powelliphanta to be genetically-based and shape also proved informative. The described subspecies of Powelliphanta lignaria were found to be morphologically diagnosable, largely allopatric, and with gene flow limited to the extent that the integrity of each subspecies has been maintained. A recently discovered and critically threatened species was described as Powelliphanta augusta, and a new classification for the genus comprising 20 species and 59 subspecies (including the existing P. lignaria subspecies) was proposed.Item Molecular systematics of New Zealand skinks of the genus Cyclodina : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Genetics at Massey University, New Zealand(Massey University, 1996) Slack, Kerryn ElizabethThe taxonomic status, relationships and possible origin(s) of eight skinks from the genus Cyclodina were investigated using molecular systematics - one from each of the six recognised and two proposed New Zealand species. DNA sequence data from the mitochondrial 12S ribosomal RNA gene was obtained using the polymerase chain reaction (PCR) and a thermocycling-based sequencing procedure. Phylogenetic analysis was carried out using spectral analysis, which utilizes new and sophisticated algorithms, and the maximum parsimony, minimum evolution and maximum likelihood options of PAUP* Version 4.0, a new test version of PAUP. New Zealand members of the skink genus Leiolopisma and three overseas skinks were also included in analyses. A single resolved tree was not produced, which may indicate that the New Zealand Cyclodina diverged rapidly. The eight Cyclodina taxa form genetically distinct lineages, supporting the separate taxonomic status of each of the recognised and proposed species. The suggestion that the C. aenea population from the Poor Knights Islands is a separate species is well supported, the two C. aenea taxa being separated by and/or pairing with other taxa in most trees. However, the possibility of subspecific status cannot be excluded for C. oliveri from the Mokohinau Islands (the second proposed new species). While the eight Cyclodina taxa form a closely related group, L. fallai pairs with C. alani and L. zelandicum with the Poor Knights C. aenea in many or all of the phylogenies. L. moco and the Mauritian skink L. telfairi also appear to have links with Cyclodina. The level of spectral analysis and bootstrap support is low for most of these relationships; nevertheless a monophyletic origin for Cyclodina with regards to the New Zealand Leiolopisma is not supported under the present taxonomic classification. Longer sequences from additional genes and a larger, more diverse set of skinks are required (in conjunction with other molecular, morphological and ecological information) before the exact relationships of these taxa and the origin(s) and divergence times of the New Zealand Cyclodina can be accurately determined. However, the results of this study do suggest that Cyclodina is older than previously thought, possibly even Gondwanan in origin.Item Evolutionary relationships of the Castle Hill buttercup (Ranunculus crithmifolius subspecies paucifolius) : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Palmerston North, New Zealand(Massey University, 2005) Piripi, Morore MorganThe Castle Hill buttercup (Ranunculus crithmzfolius subsp. paucifolius) is a rare plant found only in a small area of limestone gravel at Castle Hill. Known as Kura Tawhiti in Maori, the region is renowned for an abundance of rare and endangered plants and has historically been an important area of Maori activity. The Castle Hill buttercup has a long conservation history, starting in 1948 and continuing to the present day. Recently the population of Ranunculus crithmifolius subsp. paucifolius has again declined to the point where further conservation effort is needed. Lockhart et al. (2001) found that the Castle Hill buttercup showed ambiguous phylogenetic results when chloroplast and nuclear DNA markers were sequenced. It was theorised that the Castle Hill buttercup was a product of one or more events of diploid hybridisation, which would account for these ambiguous phylogenetic results. The aims of this study were to investigate the Castle Hill buttercup and its closest relatives using phylogenetic methods. Data was gathered from nuclear ribosomal ITS and chloroplast h-\ DNA marker sequencing and the multi-locus fingerprinting (MLF) methods ISSR and AFLP. No evidence was found in this study to support the hypothesis that the Castle Hill buttercup is a diploid hybrid, but both MLF techniques showed a level of genetic distinctiveness between R. crithmifolius subsp. paucifolius and its sister subspecies R. crithmifolius subsp. crithmifolius. Other alpine Ranunculus taxa studied showed genetic groupings related to geography. Most notably, the species R. enysii was divided into two separate genetic groups, one in the Waimakariri basin area, and one located in the southern South Island. This southern group was itself divided into two genetically distinct groups, located in the east and west of the southern South Island. Comparison of the different data gathering methods used in this study showed that MLF has a higher phylogenetic resolution than DNA marker sequencing was able to determine genetic differences between individual accessions. AFLP was found to be superior to ISSR for use in New Zealand alpine Ranunculus due to greater consistency between duplicate reactions.Item Evolution of diversity : analysis of species and speciation in Hemiandrus ground wētā : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Zoology, Massey University, New Zealand(Massey University, 2015) Smith, Briar Leigh TaylorPatterns of biodiversity and endemism in New Zealand are explored, with a focus on the ground weta genus Hemiandrus. I first investigated factors that determined regional levels of endemism using a generalised linear model based on analysis of 2322 species of endemic New Zealand invertebrates. I found that widespread species are uncommon in New Zealand and most invertebrates occupied few regions. Number of endemic species per region was positively correlated with total number of species and size of the region 3 million years ago. Within one clade of Hemiandrus I found that North and South Islands differed in how they were occupied: South Island had many species with small non-overlapping ranges, whereas North Island was largely dominated by a single species. This is likely due to differences in age of different parts of New Zealand, yet this pattern was absent in another clade of ground weta species, showing that properties of species themselves also have a large impact on species ranges and speciation. I applied several strategies to the Hemiandrus maculifrons species complex to test putative species boundaries (chapter 3). I compared morphological methods (Gaps in Continuous Characters across Geography (GCCG)) and genetic methods (Bayesian Species Delimitation, Rosenberg's P(AB), P(Randomly Distinct), P ID(Liberal)). Some of these strategies indicated that all or nearly all mtDNA clades tested represented separate species, while others indicated that no clades were likely to be distinct species. I concluded that H. maculifrons comprises three species (plus an under-sampled microendemic species, chapter 4); a conclusion that is discordant with the results of the “species delimitation” methods but consistent with other genetic, morphological and distributional data. Since the genus Hemiandrus was thought to comprise only nine named species but dozens of alleged species, I tested whether the purported diversity accurately reflected biological diversity in the genus or whether it was exaggerated due to speculative classification (chapter 5). To do this, I applied traditional techniques to search for qualitative or quantitative differences between individuals using a model where species are separately evolving lineages that form separate genotypic clusters with no or few intermediates when in contact (Mallet 1995). Most proposed operational taxonomic units were supported, but some names appear to be synonymies while others appear to encompass more diversity than previously recognised. I concluded that Hemiandrus comprises at least 25 species, but as specimens representing all tag-names1 1 A tag-name is an informal name that indicates an entity that may be a separate species, monophyletic group or separate interbreeding population of uncertain taxonomic rank (Leschen et al. 2009). were not available, additional diversity may exist within Hemiandrus than recognised here. Phylogenetic analysis of mtDNA sequences identified two major clades within New Zealand Hemiandrus. Using nuclear markers and morphological traits I found strong support for these two clades. Derived shared traits were identified that can determine to which clade each species belongs. Concordance between genetic markers (four loci) and morphology resolved evolutionary relationships from which I propose dividing the group into two separate genera.