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Start date: 2022Subject: search.filters.subject.Evolution

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    Reciprocally formed Tragopogon allopolyploids and their diploid parents : a comparative study : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology, School of Natural Sciences, Massey University, Palmerston North. EMBARGOED to 14 March 2027.
    (Massey University , 2025-02-28) Mukhtar, Usama
    Allopolyploidy has been a significant evolutionary force across the eukaryotic tree of life, particularly in plants. Newly formed polyploids inherit traits from their progenitors but may also show transgressive characters that allow them to inhabit different areas and/or outcompete their parents in similar habitats. In this thesis, multiple approaches were used to study differences between reciprocally formed allopolyploids (Tragopogon miscellus) and their diploid parents (T. dubius and T. pratensis) in the genus Tragopogon. This system was chosen because the parentage of the allopolyploids is known and the polyploids were recently (within the last 100 years) formed. These four species were analysed for: growth parameters under variable temperature and water conditions; physiology and cellular characteristics; and variations in plastid genomes. Both reciprocally formed polyploids were found to have different growth profiles from each other, with short-liguled Tragopogon miscellus being potentially more robust. Leaf physiology revealed T. dubius had low water use efficiency, but a higher transpiration capacity than the other diploid T. pratensis and the polyploids. Comparison of whole plastid genomes revealed variations in both DNA sequence and base modifications, including methylation patterns, among the four species. Collectively, these results help further our understanding of phenotypic and genotypic evolution in young allopolyploids.
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    Global warming responses within the New Zealand alpine radiation of acridid grasshoppers : a thesis submitted in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Ecology at Massey University, Manawatu, New Zealand
    (Massey University, 2024-07-20) Meza-Joya, Fabio Leonardo
    We are living in the Anthropocene, where humans are directly and indirectly altering climatic regimes, leading to warmer conditions with multifarious effects on the biosphere. Well-documented ecological responses to planetary heating include distributional, phenological, and/or phenotypical shifts. Anthropogenic global warming is predicted to significantly impact alpine ecosystems, yet our current understanding of alpine species responses to both ongoing and future global warming is limited. My thesis bridges this gap by investigating the influence of past and future climates on New Zealand’s endemic alpine short-horn grasshoppers (Orthoptera: Acrididae), as representatives of New Zealand’s alpine fauna. As one of the most ubiquitous herbivores in alpine areas worldwide, grasshoppers provide a marvellous lens to examine responses of native systems to increasing temperatures and explore the mechanisms behind such responses. For this, I used an integrative approach combining phylogeographic tools, demographic statistics, phenotypic data (size and shape), niche models and niche metrics, and genotype–phenotype–environment associations. My findings indicate that (1) distinct climatic, biological, and geophysical factors controlled population structuring of grasshopper species during the Pleistocene with a legacy of spatially separate intraspecific lineages; (2) departures from current climatic conditions are projected to vary with geography, and so species exposure and vulnerability to climate change will vary; (3) habitat loss predicted over the next 50 years of warming will lead to smaller and more-fragmented populations with reduced adaptive potential; (4) differences in niche features between diverging intraspecific lineages may lead to lineage-specific responses; (5) distinct climatic factors influence body size clines, and this might strongly influence potential phenotypic responses. An unexpected and important result is that closely related species are predicted to respond in different ways to climate change, suggesting such responses are more evolutionarily labile than conserved. Collectively, this body of research offers valuable insights into the eco-evolutionary responses of alpine organisms to global warming with broad implications for alpine biota everywhere in the world. The thermal environment is a powerful abiotic driver of evolution, and as we face unparalleled rates of warming, understanding how temperature hinder or foster evolution is critical for assisting management decisions that embrace evolutionary resilience.
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    Phylogenomics and evolution of polyploid Azorella (Apiaceae) in New Zealand : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Manawatū, New Zealand
    (Massey University, 2023) Ning, Weixuan
    Polyploid plants have more than the usual two sets of chromosomes in every cell. Analysing the macroevolutionary patterns of polyploid plants can provide further insight into the mechanisms of polyploidization or whole genome duplication (WGD) in driving species diversification. The polyploid-rich lineage, Azorella, in New Zealand (NZ) has two sections, Schizeilema and Stilbocarpa, with a total of 17 described polyploid taxa (species, subspecies, or varieties) in three known ploidy levels (4x, 6x and 10x). The divergent leaf morphologies and distinct distribution range of polyploid taxa in NZ Azorella makes this lineage an ideal system to investigate the macroevolutionary outcomes of WGD in a polyploid-rich lineage. This thesis aimed to 1) resolve the origins and species relationships of NZ Azorella using phylogenetic inference, and 2) compare the polyploidy-associated genomic, morphological, and ecological traits to understand the post-WGD diversification of Azorella polyploids. In this thesis (Chapter 1), I first reviewed the current phylogenomic approaches for resolving species relationships in groups that have complex evolutionary histories, including polyploidization and reticulation. To resolve the NZ Azorella phylogenetic relationships (Chapter 2), I applied Hyb-Seq of the Angiosperms353 bait set via Illumina sequencing to amplify 353 target-enriched single copy nuclear genes. Additionally, nrDNA and whole chloroplast DNA were recovered via genome-skimming reads to represent high copy genes/regions that are traditionally used in phylogenetics. Hyb-Seq of Angiosperms353 loci was combined with a PacBio sequencing run to improve homeologous gene extraction (Chapter 3). Finally, NZ Azorella post-polyploidization diversification patterns (Chapter 3) were assessed using the variation in genome sizes (via flow cytometry), stomatal guard cell length (using scanning electron microscopy), and ecological niches (using the R package ENMTools). Overall, from biogeographical analyses, I found two independent dispersal events of species in New Zealand Azorella sections Stilbocarpa and Schizeilema, respectively. Using the concordance factors among gene trees and single nucleotide polymorphisms from Hyb-Seq data, as well as the topological incongruence between single copy and high copy gene trees, the results indicated hybrid origins of several hexaploid (6x) species, reticulate relationships among tetraploids, and an allopolyploid origin of the 10x species A. colensoi. Furthermore, different post-polyploidization diversification patterns were compared among Azorella taxa in different ploidy levels, which showed that phylogenetic relationships (i.e., genome content), reticulate evolutionary histories, genomic modification processes (i.e., expansion or contraction), niche shifts, and the age of the polyploid species are all important factors to predict the macroevolutionary patterns of polyploid species.
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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.