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Item Comparing methods of identifying plants visited by pollinators through morphological and genetic techniques : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Zoology, School of Food Technology and Natural Sciences, Massey University, Palmerston North, New Zealand(Massey University, 2025) Hobbs, JasperInterest in bumblebee pollination is increasing as honeybee populations appear insufficient to meet agricultural pollination demand. Effective use of non-honeybee pollinators like bumblebees will also save farmers money, compared to managing commercial honeybees. Potentially, bumblebee populations can be increased by providing supplementary sources of nutrients (plants that blossom outside of crop flowering) on farms. To identify the most beneficial plant species, three methods were proposed that had been used to answer similar questions previously: (1) Using morphology of intentionally and unintentionally collected external pollen from the bumblebees to identify the plants they visited. (2) Using amplicon DNA sequencing (metabarcoding) on DNA extracted from pollen from bees to identify the plants they visited by comparing sequences against reference databases. (3) Using the same amplicon DNA sequencing method on the DNA extracted from bee stomach contents to identify the plants they visited. These methods were compared using five bumblebees (Bombus terrestris), two native bees (Leioproctus monticola) and one honeybee (Apis mellifera). For method-1. 3627 individual pollen granules were counted and identified to 10 plant genera. For method-2 & 3 the target amplification region used for was the choloroplast gene trnL. 2,631,048 reads were obtained from seven pollen samples and for method-3. 916,868 reads were obtained from eight stomach DNA samples. 732 unique cpDNA sequences were recorded, however many of these referenced to the same genera, or to non-viridiplantae genera or did not reliably match at all (low match and coverage). After the bioinformatics, 35 New Zealand plant genera were identified although 13 represented pollen and stomach exclusive genera, which contained only one genus with >1% which was 1.7%. These findings resulted in the claim that the plant genera visited for pollen does match the plant genera visited for nectar. The main outcome of this study is that pollen DNA amplicon method was the most effective in terms of time and quality, and can be trusted to be representative of the species bumblebees feed on, as the third main finding showed using pollen did not exclude any significant genera only found in the stomach, or include significant genera that bumblebees do not consume. However, the failure of the metabarcoding approach to detect wild radish pollen suggests this approach is not perfect.Item Studies of the life history of school sharks (Galeorhinus galeus) : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Ecology at Massey University, Albany, New Zealand(Massey University, 2025-09-26) Burton, Alex J. C.The school shark (Galeorhinus galeus) is a globally distributed, migratory species that was recently reclassified, globally, as Critically Endangered due to all but the New Zealand population having collapsed due to overfishing. Effective management and recovery of these populations is currently limited by a lack of accurate biological information, which is increasingly difficult to obtain due to the scarcity of school sharks throughout their range. By studying the last stable school shark population, located in New Zealand, the aim of this thesis is to provide accurate information on the biology of school sharks to better inform their management worldwide. Specifically, this thesis examines allometric relationships, inter-population variation in life-history stage transitions, intra-population variation in juvenile growth rates, extent of the transfer of elements from mother to pups, and the spatio-temporal connectivity of habitats important to life-history. To enable better standardisation of length data when combining datasets, the optimal model for converting between different length measurements of school sharks was first identified. After standardising length and life-history stage data, a novel Bayesian generative classifier model suggested that length at life-history stage transitions varied among several, globally distributed, school shark populations. A study of juvenile school shark growth across several regions in New Zealand (i.e., Kaipara Harbour, Tasman and Golden Bays, and the Canterbury Bight) revealed that somatic (increase in body length with age) and hepatosomatic (increase of energy stores in the liver with age) growth was consistent among regions, but body condition was generally greater in the Canterbury Bight compared to other two regions. Tracking the year-long, three-dimensional movements of large female school sharks tagged in the Kaipara Harbour with satellite tags showed these sharks dispersed to several potentially important reproductive and feeding habitats around New Zealand. Finally, nutrients and essential and non-essential elements maternally provided to developing young were likely sourced from those assimilated from the mother’s diet during vitellogenesis. This thesis has national and international implications for school sharks and other elasmobranch species, as it provides information and techniques crucial to better understanding the biology of species that is needed to inform more effective management and recovery efforts.Item Who goes there? : an analysis of North Island brown kiwi (Apteryx mantelli) vocal anatomy, vocalisations, and associated behaviours : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Zoology at Massey University, Manawatū, New Zealand(Massey University, 2025) Urquhart, LiamThis thesis explores individual variations in the vocal tract, vocalisations, and calling behaviour of the North Island brown kiwi (Apteryx mantelli). Kiwi are cryptic, nocturnal birds and are commonly monitored using acoustic methods – either manual call counts, or automated field recordings. Kiwi are loud callers with males and females producing very different calls. The number of times an individual bird calls per night varies, therefore turning call rates into estimates of population abundance is challenging and thus call counts fall short of estimating population numbers. This thesis aims to improve the knowledge we have of kiwi vocal behaviour using two approaches: (i) examining and describing for the first time the complete vocal tract of kiwi looking for differences between the sexes that could explain the different sounds they produce, and (ii) attempting to identify individuals through call variables obtained through multiple manual and automated call recordings. I also utilised calls shared between multiple recorders in an area to triangulate their location and identify a trend in call location selection. I investigated this to link calling behaviour to calling purpose, as the close proximity of kiwi nests on Ponui Island may influence calling for nest defence. Anatomical analysis of six brown kiwi (male = 3, female = 3) revealed a considerable difference in lateral labium area between the sexes (male = 2.43 mm2 ± 1.1, female = 1.19 mm2 ± 0.95), though this was not statistically significant (Mann-Whitney U test: n = 6; p = 0.3827), likely influenced by a small sample size. The syrinx was of the tracheobronchial type, which was larger in females (length = 8.98mm ± 2.78; width = 9.24mm ± 0.96), than in males (length = 6.13mm ± 0.8; width = 8.51mm ± 0.47). The tongue was spoon-like with a cartilaginous tip, and the oropharyngeal cavity contained two pairs of pharyngeal folds posterior to the glottis and choana. Call recordings, collected passively from 29 recorders near nine nests on Ponui Island and manually from six males, were analysed using k-means clustering to assess individual call distinctiveness. Results indicated that individual calls could not be reliably classified (percentage of correct identifications = 9%) using the selected call variables. Choice of calling location was examined using a three-tiered call quality ranking system. I evaluated call quality based on the number of harmonics visible in the call recording, which correlates with distance between calling bird and the recorder. Using a negative binomial GLM I found that altitude was not a predictive factor in site selection; however, high elevation sites functioned as good listening vantage points for the acoustic recorders, with higher ranked calls significantly correlated with increasing altitude. These findings highlight important considerations for future research. The differences in the sound generation source between the sexes highlights a potential source of the brown kiwi's sexually dimorphic calls, however, the degree of neuromuscular control of call production must be investigated. Additionally, utilising syllable (a distinct segment of harmonics in a bird’s call) variables for individual identification is paramount as they seem to be more informative than using call (the full vocalisation) variables alone, thus potentially providing more evidence for vocal individuality in kiwi. More time is needed for both studies to provide informative results to account for limitations in sample sizes and to account for seasonal variability of kiwi calls. Addressing these challenges could improve passive acoustic monitoring techniques for kiwi and other cryptic nocturnal species.Item Population dynamics and anthropogenic threats to New Zealand fur seal (Arctocephalus forsteri) in New Zealand : a thesis submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Veterinary Science at Massey University, Palmerston North, Aotearoa New Zealand(Massey University, 2025) Hall, AlasdairNew Zealand fur seals (Arctocephalus forsteri; ‘NZFS’) are New Zealand’s most encountered pinniped. However, substantial gaps exist in the knowledge of their abundance and distribution. This study provides NZFS abundance and distribution data for Kaikōura and Banks Peninsula and investigates anthropogenic risks in both locations. Additionally, the thesis undertakes the first nationwide NZFS abundance estimate in ca. 50 years. The Kaikōura population study was the first since the 2016 earthquake. Kaikōura’s NZFS population has grown and spread post-earthquake, with an upper population estimate of 21,560 – 28,327 NZFS in the 2022/23 breeding season. However, pup production at Ōhau Point, the most impacted colony, has not grown, and breeding distribution has changed significantly. Following earthquake damage, State Highway 1 (SH1), which runs close to NZFS colonies, was reconstructed. This study detected an almost fivefold increase in the annual number of NZFS recorded on SH1 from 2012 – 2022, compared to 1996 – 2005. Ten statistically significant NZFS incident clusters were located, representing 89% of the incidents. Cluster location shifted following post-earthquake road reconstruction. Monthly NZFS incident numbers were significantly positively associated with traffic and windspeed, and significantly negatively associated with temperature and rainfall. Road-abutting NZFS breeding explained most of the spatial variation in NZFS incidents. An abundance estimate of 13,147 – 17,675 NZFS was calculated for Banks Peninsula in 2023/24, and 25 previously unrecorded colonies were assessed. This study considered response strategies for an oil spill impacting Banks Peninsula’s NZFS, as the region is classified as ‘high risk’ for such incidents. Priority response strategies include preventing oil from reaching colonies, and hazing individuals away from waterborne slicks. From the most recently available count data, a minimum nationwide population estimate of 131,338 – 168,269 NZFS was calculated. Using recent counts and stage-structured population modelling, a more reliable estimate of 181,646 – 239,473 NZFS was calculated, a substantial increase on the most cited nationwide abundance figure, 100,000 NZFS. This thesis’ population findings provide useful baselines and highlight the need for improved NZFS population monitoring. This is particularly important due to the changing human-NZFS relationship, evidenced by the Kaikōura road reconstruction and the risk of oil spills in Banks Peninsula.Item Food plants and chemical ecology of sympatric species of endemic New Zealand alpine grasshoppers : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University, Palmerston North, New Zealand(Massey University, 2023-12-20) Nakano, MariIn some habitats, multiple related species coexist without competitive exclusion. This is possibly because sympatric species have adapted to use different resources in their habitat, such as shelter and food. Sympatric species may also have sophisticated mate recognition to avoid hybridization and maximises reproductive fitness. Therefore, exploring resources, feeding and sensory structures and sexual communication systems would allow us to understand how species coexist and maintain diversity. In central South Island, three endemic species of New Zealand alpine grasshoppers Brachaspis nivalis, Sigaus australis and Paprides nitidus (Orthoptera: Acrididae) occur in sympatry at high elevation (>1200 m above sea level). Past studies showed that these species are closely related and each have a preference for a particular vegetation type (rock/scree or vegetated), but their communication systems have never been explored. Insects rely on chemical cues to locate and recognize their food and mates but the majority of chemical communication systems in acridid grasshoppers are focused on economically important species (locusts). Thus, this is the first study to explore chemoreception in the New Zealand endemic grasshopper radiation. In this thesis, I first reviewed current knowledge of chemical ecology and olfaction in acridid grasshoppers to understand the tools and techniques used to investigate chemoreception and chemical ecology in insects (Chapter 2). Then, I investigated mechanisms of the coexistence of B. nivalis, S. australis and P. nitidus by examining their diet, mandible morphology (Chapter 3), antennal sensory organs i.e., sensilla (Chapter 4), olfactory perception of plant volatiles (Chapter 5) and chemical profiles (Chapter 6). The three grasshopper species were found to have broadly similar diets, sensory organs and olfactory responses to plants. Microhistological epidermal and DNA analyses (Chapter 3) showed the three species had similar food plants in their gut, with shrubs and herbs detected more often than grasses. Despite significant differences in mandible morphology, males and females eat similar plant species. Females of all species had larger mandibles than males, suggesting that they may be adapted to eating thicker plant tissues than males, and S. australis mandibles of both sexes were more heavily melanized than the other species indicating adaption to eating tougher plant tissues. Five morphological types of sensilla (one taste and four olfactory receptors) were observed on the grasshopper antennae, but none were specific to a particular species or sex (Chapter 4). Brachaspis nivalis, however, had the fewest taste sensilla but the most olfactory sensilla compared to the other two species and showed olfactory responses to plant-derived smells even at the lowest concentration. This may be related to their rock/scree habitat where the food resources are scattered and thus require higher olfactory sensitivity (long-distance cues) than taste reception (short-distance cues) compared to more vegetated habitats of S. australis and P. nitidus. Olfactory response recordings to plant volatiles (Chapter 5) showed all three species responded more strongly to green leaf volatiles than to terpenoids, which could indicate sensitivity to plant damage rather than to plant-specific smells. A higher abundance of olfactory sensilla was observed in male S. australis compared to conspecific females but no sex differences were observed in B. nivalis or P. nitidus (Chapter 4). However, female-specific compounds (oleamide and octadecanamide) were detected in cuticular hydrocarbons (CHCs) of all three species and some compounds were more abundant in particular species than in others (Chapter 6). This shows CHC composition has potential information for mate recognition in these grasshoppers. Altogether, males and females of three New Zealand alpine grasshopper species showed similarity in their food plants, sensory organs and sensitivity to plant smells, but sexual and species differences in mandible morphology and CHC composition allow one to infer specific adaptation to food plants and sophisticated mate recognition system that explain how these three alpine grasshoppers can co-occur.Item Investigating physiological markers of heat stress in response to water temperature in kākahi (Echyridella menziesii) to provide insight into their vulnerability to anthropogenic climate change : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Physiology, Massey University, Palmerston North, New Zealand(Massey University, 2022) Parkinson, EllaAnthropogenic climate change (ACC) is expected to increase the water temperatures of aquatic ecosystems, which can cause heat stress in aquatic animals. Kākahi (Echyridella menziesii) are a species of freshwater mussel that are endemic to Aotearoa New Zealand. Kākahi are an ecological and cultural keystone species in Aotearoa New Zealand’s aquatic ecosystems. Little is known about the thermal physiology of this species and, therefore, their vulnerability to increasing water temperatures under ACC. Increasing our knowledge of kākahi thermal physiology and their vulnerability to projected future water temperatures is important for the conservation of the species and the ongoing health of the ecosystems of which they are part. For bivalve species (Class: Bivalvia), measuring the concentrations of heat stress biomarkers in the circulatory fluid is a common method of assessing vulnerability to elevated water temperatures. This has not been attempted in kākahi, leaving a gap in our understanding of how different water temperatures affect their metabolism and physiological performance. In this thesis, I measured the concentrations of three known physiological markers of heat stress (lactate dehydrogenase, alanine aminotransferase, and aspartate aminotransferase) in the haemolymph of kākahi exposed to different water temperatures. This method was used in separate field and laboratory studies to measure potential heat stress at current (2022) summer water temperatures (field) and at projected water temperatures under different warming scenarios (laboratory). In the field study, I found that current summer water temperatures in 2022 did not cause an increase in heat stress biomarker concentrations in kākahi haemolymph. In the lab study, I found no significant increases in heat stress biomarker concentrations in kākahi exposed to 26˚C or 32˚C for seven days. The results suggest that kākahi may be resilient to increasing water temperatures under ACC. Additionally, I extracted DNA from kākahi gill tissue and used primers designed from the consensus sequences of other molluscs to attempt to amplify the heat shock protein 70 (HSP70) gene. This additional piece of research aimed to provide important baseline information to enable future studies to measure changes in HSP70 expression in response to elevated water temperature. The designed primers were unfortunately unsuccessful at targeting the desired gene. However, this work provided important knowledge that will help refine the process for future attempts in identifying the HSP70 gene in kākahi.Item Eco-evolutionary mechanisms shaping aggregation and ‘piggy-backing’ of the endemic Kermadec Islands giant limpet, Scutellastra kermadecensis : 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, 2022) Kim, Julia (Ji Hyun)The Kermadec giant limpet, Scutellastra kermadecensis, is a broadcast-spawning, protandrous hermaphrodite that is endemic to Rangitāhua, Kermadec archipelago, New Zealand. This limpet is the most abundant intertidal/shallow-subtidal grazer on these islands and lives at very high density, covering most of the available rocky substrate. Nonetheless, the species is extremely range-restricted and therefore vulnerable to extinction. My thesis investigated the socioecology of the Kermadec giant limpet, using surveys as well as genetic analysis of relatedness and spatial structure to better understand the population dynamics of this species. In Chapter 2, I focused on the “piggy-backing” habit of these limpets, whereby small limpets (piggies), predominantly male, piggy-back on the shells of larger, predominantly female, limpets. I investigated whether the ontogenetic habitat shift between piggy-backing and being rock-attached was determined by rock space availability, as a mechanism to avoid bulldozing by larger limpets, to access grazing opportunities on limpet shells, and/or to monopolize breeding with rock-attached females. I found that available rock space did not influence the transitional size from being a piggy to rock-attached, suggesting that social environment motivated piggy-backing behaviour rather than space constraints. As spatial proximity often determines fertilization success in broadcast spawning marine invertebrates, in Chapter 3, I investigated the genetic relationships of piggy-host pairs, and among neighbouring limpets. I sought to understand whether the species had mechanisms to promote genetic diversity, such as kin-avoidance in piggy-host pairings, or among piggies on the same host, or whether there was evidence for limpets moving away from relatives when transitioning from piggy-backing to being rock-attached. I found that paired and neighbouring limpets were no more related to each other than to any other sampled limpet in the subpopulation. However, there was spatial genetic structure among sampled sites and locations, and evidence for adaptive genetic divergence over very small scales (<1 metre). Furthermore, estimated levels of inbreeding were very high (FIS = 1.37-1.43), but in keeping with estimates for other marine invertebrates. Unveiling these eco-evolutionary drivers of piggy-backing behaviour helps us to understand how Kermadec giant limpets have persisted despite their isolation and provides insight into how to conserve them.Item Resource allocations of Ephestia kuehniella Zeller (Lepidoptera: Pyralidae) in response to socio-sexual environment during immature and adult stages : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Entomology at Massey University, Palmerston North, New Zealand(Massey University, 2023) Liu, JunyanAnimals adjust their investment in different life history traits according to their surroundings to maximise their fitness. Using a polygamous insect, the Mediterranean flour moth Ephestia kuehniella Zeller, which produces fertile eupyrene and infertile apyrene sperm, I investigated resource allocation strategies employed by males in response to socio-sexual cues during the adult and juvenile stages. I demonstrate that adult males raised their lifetime production and ejaculation of both eupyrenes and apyrenes after detecting either acoustic or chemical cues from adult rivals with combined cues strengthening such response, and that rival-experienced males could remember the sperm competition risk for most of their reproductive life. I manipulated juvenile socio-sexual settings and then examined their sperm production and ejaculation as well as survival, body and testis size, and mating behaviour. I provided the first evidence that juvenile social cues from conspecific larvae, pupae or adults had lasting impacts on lifetime sperm production and allocation. Adults from group-reared larvae, regardless of sex ratio, had smaller testes but produced more eupyrenes at emergence than from singly reared ones, and that body size and apyrene numbers remained the same across treatments. Male pupae had similar testis size but increased production of both eupyrenes and apyrenes at emergence in response to cues from conspecific pupae irrespective of sex. Late instar male larvae were able to detect cues from adult rivals and subsequently produced more sperm of both types at emergence, but adult cues had no effect on body and testis size. Juvenile socio-sexual environment had significant effects on sperm production and ejaculation during adult stage. My study indicates that after their late instar larvae were exposed to juvenile or adult rivals, adults produced and ejaculated more eupyrenes and apyrenes in their lifetime and had shorter mating latency. However, rival exposure had no effect on males’ mating frequency and longevity. Knowledge generated here enhances our understanding of how males of a polygamous insect calibrate their resource investment in response to dynamic social environment.Item Spatio-temporal change in species and morphological diversity of reef fishes in the South Pacific Ocean : a thesis presented in partial fulfilment of the requirements for the degree of Master of Biological Sciences at Massey University, New Zealand(Massey University, 2020) Kilduff, LiamThe geography of the South Pacific, with its numerous oceanic islands, offers a unique opportunity to examine prevailing theories on the accumulation and maintenance of biodiversity. It is well recognised that for most taxonomic groups, species richness declines poleward from the equator and eastward across the South Pacific. However, as ocean temperatures warm and oceanographic barriers move with climate change, shifts in the ranges of tropical species towards higher latitudes may lead to changes in community structure and resilience in subtropical locations. Here, I examine the existing biodiversity gradients of reef fishes across the South Pacific Ocean, and identify potentially climate-induced temporal shifts of tropical species into the high latitude and isolated Rangitāhua archipelago. Furthermore, I examine morphological changes across latitude and longitude to identify traits associated with species colonisation ability and function within the often species depauperate communities in more isolated and southerly regions of the South Pacific. Additionally, I examine how morphological changes over time might impact the morphological space of the fish community at Rangitāhua. I assessed morphological change in 12 standard measurements for 948 fish species, from nine families found on the reefs surrounding 19 of the major island groups of the South Pacific Ocean. I found that while species richness followed the predicted decline towards the east and south, morphological diversity showed the opposite trend, increasing east and south. Furthermore, similar morphological changes were evident with body size and pre-orbit length increasing in response to both latitude and longitude, although more significantly with longitude. Despite this, analysis of individual families revealed unique patterns of morphological change within the South Pacific Ocean, may be indicative of the differing strategies of each family to colonise and persist in more southerly and easterly locations. Within Rangitāhua, using a list of 149 shallow Teleost fishes including the dates of their first sighting, I identified a temporal shift in the biogeographic affinities of the fish assemblage with an increasing contribution from tropical regions over time. Newly discovered, more tropical species, only occurred in low numbers, possibly because they are still in the early colonising stage or because the islands environment is still more temperate than these fish require to increase in abundance significantly. Despite also finding that the morphological diversity of the fish assemblage changed through time, morphological change was not directional, indicating that although new species are arriving, their morphology is similar to longer-established, more temperate fishes. Therefore, although the frequency of species with tropical biogeographic affinities is increasing over time at Rangitāhua, this is not strongly impacting the community’s morphological variation. My results for Rangitāhua support the global pattern of tropical species re-distributing towards higher latitude region over time. Overall, my thesis examining both species and morphological change in reef fishes across large-scale geographic gradients within the South Pacific Ocean provides insight into potential future biodiversity changes and may allow us to predict which species are likely, or capable of extending their ranges towards the poles.Item The molecular ecology of an understudied endemic marine isopod - Isocladus armatus : a thesis presented in partial fulfilment of the requirements for the degree of Master of Natural Science at Massey University, Albany, New Zealand(Massey University, 2019) Pearman, William SamuelThe study of populations and the adaptive significance of traits is a major theme in molecular ecology literature. In this thesis I present three lines of research that contribute to the understanding the molecular ecology of a species of New Zealand endemic marine isopod - Isocladus armatus (family: Sphaeromatidae). The goal of this thesis is to develop and utilize a framework to better understand the genomics of marine isopods from a range of genomic perspectives. The first primary chapter aims to assess two ways of enriching mitochondrial DNA from whole genome DNA, and to assemble this species mitochondrial genome. My research indicates that an atypical mitochondrial genome structure, widespread across Isopoda - but previously thought absent within Sphaeromatidae, is present within I. armatus suggesting that this trait has been maintained for an order of magnitude longer than previous estimates. The second primary chapter aims to describe and understand the genetic structure of populations for 8 locations around New Zealand, to understand connectivity and dispersal for I. armatus. Using a panel of 8,020 loci, I find high gene flow on a small spatial scale, while populations on a larger spatial scale exhibit a pattern of Isolation-By-Distance. Additionally, gene flow over one well known biogeographic barrier was much higher than between any other populations on a similar spatial scale, suggesting this barrier may not exhibit a strong effect on this species. Thus, my research indicates a need to revisit and study the way biogeographic barriers affect species with different life histories. The final primary chapter aims to understand the genetic basis for colour polymorphism in I. armatus, with the intention of understanding the adaptive significance and selective mechanism behind this trait. I use genome wide association approaches with a panel of 20,000 loci to answer these questions. I found that loci associated with Colour Polymorphism exhibited signatures of disruptive selection, contrary to initial hypothesis where I expected balancing selection to main colour polymorphism. I propose that substrate heterogeneity in Isocladus armatus’ habitat results in microhabitats, each of which imposes a selective pressure benefiting a specific morph type. The size of these microhabitats is so small that high levels of interbreeding between these microhabitats, and thus between morphs, results in the maintenance of polymorphism across the population.