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Subject: search.filters.subject.310410 Phylogeny and comparative analysis

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    Phylogenetic analysis and population structure of the New Zealand Huntaway and heading dog : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Animal Science at Massey University, Al Rae Centre, Hamilton, New Zealand
    (Massey University, 2025) Henry, Millicent Frances
    The New Zealand Huntaway and Heading Dog are vital to the success of New Zealand’s livestock farming industry. This study presents one of the first large-scale genomic analyses of these two unique working breeds. Utilising phylogenetic and population structure methodology, the primary objectives of this research were to investigate the genetic relationships of the New Zealand Huntaway and Heading Dog with international dog breeds, formalise the major historical breed contributions that have shaped their development, and assess their population structure and diversity. This study utilised a dataset of 1,735 individuals, representing 129 dog breeds and three wild canid species, and included 211 Huntaways and 246 Heading Dog genomic datasets generated as part of this project. Genomic analyses revealed that both breeds can be traced back to ancestral UK rural working dog populations, occupying positions within the UK rural subclade on the domestic canine phylogeny. Baseline inbreeding scores suggest that neither the New Zealand Huntaway or Heading Dog populations express significantly high inbreeding levels, and the scores obtained are similar to those seen in other formally recognised dog breeds. A list of genes under putative positive selection in both populations is presented and could be used for future genetic selection in these dog populations. This study highlights the Huntaway and Heading Dog as genetically distinct breeds adapted to the unique demands of New Zealand’s pastoral farming systems. These results not only contribute to the current understanding of breed development in geographically isolated environments such as New Zealand but also highlights the opportunity of integrating genomics into working dog management and breeding practices. The genetic resources generated through this study will serve as a valuable reference for future research in the “Right Dog for the Job” project, aimed at preserving the health, diversity and functionality of the New Zealand Huntaway and Heading Dog.
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    Population genetics and genomics of a marsupial species : analysis of native and invasive brushtail possum populations (Trichosurus vulpecula) : a dissertation presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Conservation Biology, Massey University, Manawatū Campus, New Zealand
    (Masey University, 2024-04-15) Pattabiraman, Nimeshika
    One of the leading causes of global biodiversity decline is the introduction of invasive pest species that destroy native flora and compete with native fauna for food and other resources. Aotearoa New Zealand is one of the foremost countries in the world that has focussed on eradicating pest species and in particular exotic mammals from the archipelago, which lacks native, terrestrial mammals. The New Zealand Government recently set in train the ambitious task of removing all mustelids, rats, and possums from the terrestrial landscape by the year 2050. Brushtail possums (Trichosurus vulpecula) were introduced to Aotearoa New Zealand from Australia in the mid-1800s, after which they were translocated across the country and have become widespread, destroying indigenous habitat, eating native birds and invertebrates, and spreading bovine TB. Control efforts have seen possum numbers decline in the last two decades from close to 75 million in 2002 to 40 million in 2020. There is, however, a gap in the scientific understanding of possum populations with respect to their genetic composition and population structure across the country, and this knowledge could help us develop effective and dynamic management strategies to eradicate possums on a nationwide scale. In this thesis, I focus on three aspects of population structure and diversity of brushtail possums. First, I investigated a small geographical study area - The Kenepuru Peninsula - where I sought evidence of genetic correlations with geography, time and fur colour. I used two types of genetic markers that target the nuclear and mitochondrial regions of possum DNA with large population samples. In every case, it was determined that the possums comprised one freely interbreeding population at this scale. In particular I demonstrated that colour morphs associated with distinct subspecies in Australia, freely interbreed in New Zealand. I then increased the scale of sampling to include representation of populations across New Zealand and Australia, with the same genetic markers. This threw light on the heterogenous nature of possum diversity in New Zealand, and showed that even after ~110 generations, possums retained genetic separation among spatial groups. Additionally, the data showed evidence of multiple possum lineages across New Zealand that are derived from several Australian populations. High haplotype diversity in New Zealand suggests that the rapidly expanding population has retained novel haplotypes and the data thus far indicated a non-homogenous (metapopulation) distribution of possums without geographical concordance. As the project progressed, I was able to apply high-throughput genotyping-by-sequencing to generate a large genomic dataset. This dataset provided much more detail of the genotypic distribution of possums in Australia and among invasive metapopulations in New Zealand, as well as informing us of the relationship between them. This large, robust database of possum population structure and genetic diversity throughout Aotearoa New Zealand will support future studies in providing informed management decisions to eradicate brushtail possums.
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    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, Ling
    In 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.
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    Morphology of the feeding apparatus in shorebirds (Charadriiformes) : a comparative analysis : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Zoology at Massey University, Palmerston North, New Zealand
    (Massey University, 2022) Lin, Chieh-Ting
    Shorebirds (Charadriiformes) have developed diverse foraging strategies to feed in different niches. These foraging strategies are associated with morphological variation in their feeding apparatus. This variation among species is complex, with different morphological features reflecting different aspects of foraging ecology. These traits are also presumed to relate to the evolutionary history of the species. Here I attempt to untangle the mystery of the development of diverse feeding apparatus in shorebirds through a series of morphological and phylogenetic comparative analyses using 20 species. First, I used landmark-based geometric morphometrics to compare skull shapes between species. The results showed that the major variation was the bill length, and there were also other variations. The results suggest that bill and cranial shapes vary phylogenetically, but do not suggest that visual foragers have larger eyes than tactile foragers. Second, I compare the interspecific variation of bill forms, including the length and curvature of bills, and the bony sensory pit under the rhamphotheca. Individuals of the family Scolopacidae (sandpipers and allies) possess various bill-tip organs with large numbers of concentrated sensory pits. The variety of bill shapes and sensory pits is suggested to relate to different foraging behaviours. Moreover, I test the relationship between distal rhynchokinesis (the ability of some species to bend the tip of the upper mandible) and bill forms. The results suggest that rhynchokinesis may enhance the grabbing capability of some species with bill-tip organs. Third, I documented and compared the morphology of tongues and palates, including the gross anatomy of oropharyngeal cavities and scanning electron microscopy of micro tongue tip spines. Tongue lengths generally increased with mandible lengths, though there were some exceptions. The spines were significantly associated with small size (light weight) and with a short distance between the tongue tip and the mandible tip. The variety of the forms of tongue tip spines may relate to different foraging behaviours and diets. Finally, I used the taxonomic distribution of three traits (sensory pits, micro tongue tip spines and distal rhynchokinesis) to test for a role of phylogeny on the evolution of these traits. Different evolutionary models were tested with the traits, and the phylogenetic signal was measured to determine which model best fit the partial phylogeny of charadriiform shorebirds. The results suggest that sensory pits were present in the common ancestor of all shorebirds, but that the number of pits has rapidly accumulated during the evolution of the Scolopacidae. Micro tongue tip spines were suggested to be absent at the root and to have independently evolved twice across the partial phylogeny. Distal rhynchokinesis was present in some species throughout the phylogeny, and it was suggested to be lost more rapidly than it was gained. Together, these results provide new insights into how the fundamental structures of the feeding apparatus have been modified during the diversification of the shorebirds.
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    Historical biogeography of marine ray-finned fishes (Actinopterygii) of the Southwest Pacific : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Marine Evolutionary Ecology at Massey University, Auckland, New Zealand
    (Massey University, 2023) Samayoa, André Philippe
    Current environmental and anthropogenic pressures are driving significant biodiversity loss and range shifts in marine environments. Understanding how biodiversity is generated and how it responded to past environmental changes is fundamental to inform future management strategies for marine resources. As the largest ubiquitous taxonomic group among marine vertebrates, ray-finned fishes (Actinopterygii) represent the best model to understand the generation of biodiversity and the processes that shaped contemporary geographic patterns in the sea. In this sense, centers of marine endemism are of evolutionary value as they translate evolutionary and ecological mechanisms that drive biodiversity dynamics. In the Pacific Ocean, endemism centers for marine fishes are mainly located in remote oceanic islands at the periphery of the tropical West Pacific which harbors the highest levels of biodiversity. Biogeographic research suggests that marine fish endemism in the oceanic islands of the Central Pacific originated via multiple independent jump-dispersal colonization events, and that the islands have acted as sources of new unique biodiversity. However, as the evolutionary setting starts to be revealed for marine fish endemism in the Pacific, processes that generate and maintain biodiversity in other peripheral islands remain unknown. My thesis aims to fill this gap by studying the origin, evolution, and processes that have shaped endemism and biodiversity of marine fishes in the Southwest Pacific. I examined the historical biogeography of the region´s marine fish fauna using open-access molecular data to infer evolutionary histories, and geographic distribution information to assess spatial patterns of endemism and biodiversity. Data were analyzed across three research projects based on time-calibrated phylogenies, probabilistic biogeographic modeling, and statistical analysis of phylogenetic measures of endemism and biodiversity. My results confirm the role of the subtropical islands of the Southwest Pacific as sources of new unique biodiversity, identify mainland Australia as the major source of endemic lineages, highlight the significance of jump-dispersal and vicariance in shaping endemism patterns, and reveal that the processes shaping patterns of endemism and biodiversity differ at local scales. My thesis contributes to the understanding of unique contemporary biogeographic patterns in the marine fish fauna of the Southwest Pacific.
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    Convergent evolution of flightlessness in rails (Aves: Rallidae) : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Evolutionary Ecology at Massey University, Manawatū, New Zealand
    (Massey University, 2022) Gaspar, Julien
    Different species can independently evolve similar phenotypic traits in response to the same environmental challenges. The resulting convergence of traits shows how environmental circumstances that apply selective pressure on the genomes of different lineages can result in analogous adaptations. A remarkable example of this evolutionary process is the secondary loss of flight in birds which repeatedly occurs in avian diversification. Flightlessness in bird species have been encountered on many oceanic islands and is interpreted as an effect of the insular condition that often provides a habitat with few or no predators, reduced competition for resources, and the opportunity to forage without flying. The rails or Rallidae are an exceptional avian family to study the evolution of flightlessness as among the 130 extant species, 30 have independently lost the ability to fly. In this research, genomic and morphological data were integrated to compare traits of volant and flightless species in a phylogenetic context and to investigate the evolutionary processes involved in the loss of flight. First, morphological and phylogenetic data were used to compare species with and without the ability to fly in order to determine whether major phenotypic effects of the transition from volant to flightless are shared among lineages. Second, genome assemblies were generated for representatives of four rails: two volant and two flightless species. Then, a genome-wide comparison of coding regions from volant and flightless rails was performed to detect genetic regions associated with the flightless trait. The newly assembled and annotated genomes showed differences in heterozygosity between flightless and volant species with lower heterozygosity in flightless species that probably reflects their relatively small populations. I found statistical support for similar morphological responses among unrelated flightless lineages, characterised by a shift in energy allocation from the forelimbs to the hindlimbs. Flightless birds exhibited smaller sterna and wings than volant taxa in the same family along with wider pelves and more robust femora. Phylogenetic signal tests showed that those differences were independent of phylogeny and instead demonstrated convergent morphological adaptation associated with a walking ecology. Evidence of different selective pressures between species with and without the ability to fly was detected in hundreds of genes. This included relaxed, intensified, and positive selection in flightless species as well as evolutionary rate differences of genes in volant and flightless taxa and proteins carrying function-altering amino acid changes in the flightless rails. Genes associated with flightlessness were enriched in biological functions that aligned well with the ability to fly such as muscle, bone, limb, and heart development. However, other enriched functions were not directly linked to flying and may result from the ecological consequences of flightlessness; these included the immune system, renal functions, lipid metabolic system, cognition, and the sensory system. Finally, many genes under selective pressures in flightless species were involved in gene regulation and post-translational modification. This suggests that genetic adaptations to flightlessness are not only found in important developmental genes but also in patterns of gene expression and protein modifications. This study presents reliable methods to generate genomic data and to use it to assess the selective pressures involved in a convergent phenotype.
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    Comparative analyses of complete oomycete mitochondrial genome sequences : insights into structural evolution : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biological Sciences at Massey University, Manawatū, New Zealand
    (Massey University, 2022) Neal, Grace
    The oomycetes, or “water molds”, are fungi-like in appearance but more closely related to algae and diatoms. This large, widespread group of pathogens infects a wide range of plant and animal hosts across habitats ranging from marine, to freshwater and terestrial. Previous studies of oomycete mitogenomes suggest that large invert repeats are common as are structural rearrangements. However, sampling has been heavily biased towards Peronosporaceae with only limited representation of the other families. This study presents comparative and phylogenetic analyses of 135 mitogenomes, including 74 newly assembled sequences, from representatives of six families in the oomycete crown group. Gene content is strongly conserved across the sampled genomes, but synteny is only weakly conserved. The present analyses identified 68 distinct synteny types and within these 26 synteny blocks ranging in size from one to 23 genes. Patterns of diversity differed between the two major crown clades, one containing Saprolegniaceae and the other the remaining families. Several types of structural change appear to have occurred with the frequency of change varying across individual genomes (e.g., conserved and variable regions). Combined with the well resolved and supported phylogenetic tree recovered from analyses of the concatenated 32 mitochondrial gene matrix these results provide insights into the structural evolution of oomycete mitocohondrial genomes. In particular, suggesting associations between the loss of the large inverted repeat and duplications of tRNA-Met and between the compactness of these genome and the relative importance of different types of structural change in specific groups (e.g., early and late diverging Peronosporaceae).
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    Investigating relationships in the New Zealand alpine Ranunculus using RNA sequencing : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Plant Biology at Massey University, Manawatū, New Zealand
    (Massey University, 2021) Henry, John Curteis
    Whether the alpine flora of New Zealand is resilient enough to withstand the effects of climate change is an important and unanswered question. Conspicuous amongst the alpine flora are the species of Ranunculus in section Pseudadonis. This monophyletic group of species is hypothesised to have rapidly diversified into distinct mountain habitats, with some species convergently evolving into similar habitats. Investigating how cryptic physiologies have convergently evolved in some Ranunculus species may provide insight into the adaptive potential of this group of plants. It has been argued that hybridisation is an important evolutionary process explaining the morphological and ecological variation of New Zealand alpine Ranunculus species. Hybridisation, and in particular introgression, has also been hypothesised elsewhere as an effective means for closely-related species to share genetic material and undergo rapid adaptation through selection of standing genetic variation. This research aimed to use RNA sequencing technology to address questions of physiology and phylogeny amongst four taxa of the alpine Ranunculus group. Habitat characterisation was carried out before plants were sampled and grown under standardised conditions in a common garden experiment. Bioinformatic approaches were used to analyse high-throughput sequencing data of RNA extracted from these laboratory-grown plants. This research illustrates the potential of RNA sequencing for studying non-model plant species. However, the conservative analytical approaches adopted, and noise within the data, limited inferences of physiological traits and evolutionary relationships. Analyses of heterozygosity and issues with de novo transcriptome assembly suggested greater numbers of gene variants than expected for these small, isolated populations of alpine plants. These gene variants likely occur because of the polyploid genomes of the New Zealand alpine Ranunculus. Further work is needed, however, to confirm this genetic diversity. Overall, this work reinforces the difficulties in studying non-model polyploid systems. Yet, it does hint at a genetic richness within the alpine Ranunculus that might aid survival of this clade during a rapidly changing future.
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    The shape of penguins in four dimensions : assessing macroevolutionary shifts in a constructional morphology framework : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Zoology at Massey University, Albany Campus, New Zealand
    (Massey University, 2022) Giovanardi, Simone
    Describing the morphology of a clade through deep time provides rich insight into the drivers that shaped modern diversity. It is in this context that Adolph Seilacher developed the constructional morphology concept, in order to describe which are the major pressures acting on an organism's morphological appearance. The three components or apices of constructional morphology are the evolutionary history of the organism, the constraints placed on the structure, and the opportunity provided by adaptation. The structure of this thesis is based on the constructional morphology concept with each chapter focusing on the impact of each of the three components of constructional morphology with the scope to provide a novel approach to quantify morphological macroevolution. After introducing concepts of constructional morphology, geometric morphometrics and Bayesian statistics in Chapter 1, Chapter 2 presents an analysis to estimate the historical apex: a phylogenetic analysis based on the synthesis of previous published matrices, as well as a description of the giant fossil penguin Kairuku waewaeroa. The resulting phylogenetic tree indicates that the penguin evolutionary history was characterised by many monophyletic large groups that challenges previous results and indicate that the body plan of extinct penguins could be more diverse than previously thought. Chapter 3 focused on the structural apex, aiming to provide a generalisable Bayesian approach to estimate the size of extinct giant penguins in the context. By measuring the total volume of the femur and the humeral articular facet of the coracoid it was possible to generate two sets of models that together provided novel evidence in favour of reduced body mass estimates for giant penguins when compared with prior published estimates. Moreover, although the two sets of estimates are derived from two distinct features, the body mass estimates from the two models tend to converge, providing confidence in the accuracy of the Bayesian-informed method. Chapter 4 presents and investigation into the impact of adaptation on two separate locomotory modules, the humerus and the tarsometatarsus, using 3D geometric morphometric techniques. Comparing morphological rates of change reveals a steady rate decrease in the humerus and more heterogeneous rates for the tarsometatarsus. Similar results are obtained by estimating the morphospaces for humeri and tarsometatarsi from hypothetical ancestors using a penalized likelihood approach. The synthesis that this constructional morphology framework approach provides highlights the important relationship between shape and size, showing how size can be a driver of morphological innovation. More importantly, the results of this thesis highlight the relevance that constructional morphology still has today, and how it can be integrated into palaeontology and evolutionary biology studies through the use of advanced statistical techniques. A constructional morphology approach is not solely applicable to penguins and may be extended to a broad range of groups of organisms, contributing thus to better understand the underlying forces that shaped the origins of modern biota.