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Resolving reticulate evolutionary histories of polyploid species of Azorella (Apiaceae) endemic to New Zealand
(Elsevier Inc, USA, 2026-01) Ning W; Meudt HM; Nicolas AN; Plunkett GM; Heenan PB; Lee WG; Tate JA
Genera with species of multiple ploidy levels provide models to understand successive rounds of whole genome duplication leading to intricate reticulate relationships of polyploid plant species. Here, we studied 17 polyploid taxa (species, subspecies, or varieties) in Azorella (Apiaceae) sections Schizeilema and Stilbocarpa that are mostly endemic to New Zealand. Using phylogenomic approaches, our goals were to resolve species relationships, determine the origins of the higher-level polyploids (6x and 10x), and assess the biogeography of the New Zealand Azorella species. Phylogenomic analysis of Anigosperms353 baits-captured Hyb-Seq data, together with comparison of phylogenies reconstructed using genome-skimming retrieved nrDNA and plastome sequences, showed that species diversification within New Zealand may relate to multiple origins from South America, which has been further shaped by additional rounds of polyploidy as well as hybridization or introgression. The two Azorella sections in New Zealand likely resulted from different biogeographic events from South America − one to the subantarctic islands (section Stilbocarpa) and a second to the South Island (section Schizeilema). In addition, within section Schizeilema, species have dispersed from the South Island (New Zealand) to Australia, the subantarctic islands, and the North Island (New Zealand). Our combined approach of phylogenomic analyses of plastome and nuclear locus-based data, together with SNP-based network approaches allowed us to determine the origins of some higher-level polyploids in New Zealand Azorella and revealed a more complex picture of historical and ongoing polyploidy and hybridization within these lineages.
Forget-me-not phylogenomics: Improving the resolution and taxonomy of a rapid island and mountain radiation in Aotearoa New Zealand (Myosotis; Boraginaceae)
(Elsevier Inc., 2024-11-22) Meudt HM; Pearson S; Ning W; Prebble JM; Tate JA
Island and mountain systems represent natural laboratories for studies of species radiations, but they often present several challenges for phylogenetic inference and species delimitation. The southern hemisphere forget-me-nots (Myosotis, Boraginaceae) comprise a geologically recent radiation centred in New Zealand, a mountainous archipelago, with about 50 species that are morphologically and ecologically divergent but lack genetic variation sufficient to resolve phylogenetic relationships and species boundaries using standard DNA Sanger sequencing markers, AFLPs, or microsatellites. Many of these Myosotis species are geographically restricted in alpine areas, uncommon or threatened, have polyploid and dysploid genomes, and are of high taxonomic and conservation priority. Here we present phylogenomic analyses using target-capture of Angiosperms353 baits, and genome skimming of whole plastomes and nrDNA, to improve resolution of the radiation, explore biogeographic and morphological patterns within it, and address specific taxonomic questions for each species. Our comprehensive sampling includes over 300 individuals representing nearly all species from Aotearoa New Zealand and Australia, which is ∼ 2-3 × more taxon sampling and ∼ 80-120 × more molecular data than previously published for Myosotis. Exploration of different data filtering, curation and analyses (coalescent vs. concatenation) improved the resolution of the Angiosperms353 tree, which despite short backbone branches with low support values, showed taxonomic and geographic patterns, including multiple switches between ebracteate and bracteate inflorescences and multiple expansions within New Zealand from Te Waipounamu South Island to Te Ika-a-Māui North Island, Rakiura Stewart Island, subantarctic islands, and Australia. Some of these patterns were also seen in the genome skimming datasets, and comparison of the three datasets was useful for improving our understanding of the taxonomy and resolution of this radiation. Although this phylogenomic study does not fully overcome all of the challenges regarding species delimitation of this rapid island and mountain species radiation, it nevertheless makes an important contribution to an integrative taxonomic revision of the southern hemisphere species of Myosotis.
Island biogeography : a study of habitat islands of mountain beech forest (Nothofagus solandri, var. cliffortioides) in Tongariro National Park : a thesis presented in partial fulfilment of the requirement for the degree of Master of Science in Zoology at Massey University
(Massey University, 1982) Seden, Moyra
MacArthur and Wilson's (1967) model for island biogeography is examined, particularly with regard to the proposed species-area relationship. The first chapter includes a consideration of the theoretical background. Nine habitat islands and corresponding mainland regions of similar area were selected. All the sites possess a canopy of mountain beech trees, (Nothofagus solandri var. cliffortioides), and are located in the western segment of Tongariro National Park. Plants and litter animals were sampled from within these sites to determine the possible relationship between species and area. Forest plant species numbers as well as proportions, assessed using a modification of the Point-centred quarter method, revealed a statistically significant species-area relationship. Litter Crustacea collected in one thousandth of a square metre core samples, and removed from cores by wet extraction, show a gradation in habitat preference, hence a species-area relationship cannot be determined. A wide range of animals collected in pitfall traps appear also not to produce a significant species-area relationship. Possible reasons for the obscurity of such a relationship are considered. An overall assessment of the information gathered in the light of island biogeographic theory is presented, and some more recent thought on the causal explanations for the species-area relationship are discussed.
The biogeography and origin of New Zealand Sophora (Leguminosae) : a thesis presented in partial fulfillment of the requirements for the degree of Master of Science in Plant Molecular Genetics at Massey University, New Zealand
(Massey University, 1996) Hurr, Kathryn Ann
The application of DNA sequencing to studies of the biogeography and origin of New Zealand plant groups is illustrated by evolutionary relationships of kowhai (Sophora spp.; sect. Edwardsia; Sophoreae: Papilionoideae: Leguminosae). DNA sequences from an intergene region of the chloroplast atpB-rbcL were determined for l2 species by the use of the polymerase chain reaction. Signals in the molecular data were evaluated using phylogenetic algorithms to reconstruct the evolutionary history of the species. The extremely high genetic similarity between Edwardsia Sophora resulted in an inability to fully resolve the phylogenetic tree. Three hypotheses are presented to account for the patterns of sequence differences between the New Zealand Edwardsia. One proposes a recent origin of Sophora section Edwardsia in New Zealand (4-10 million years ago), with subsequent dispersal of buoyant Sophora microphylla seeds to offshore and oceanic islands, where they might occasionally colonise. A second hypothesis suggests a recent radiation of Sophora microphylla and Sophora prostrata populations during the Pleistocene (0.1 - 1.6 million years ago), but is not well supported by the available sequence data. A third hypothesis proposes that the Lord Howe Island and New Zealand Sophora are derived from a Miocene (5-16 million years ago) oceanic migration of a Chilean ancestor of Sophora section Edwardsia. Predictions of the three hypotheses and strategies to test them are discussed. Some of the conclusions derived from analyses of the chloroplast DNA sequences conflict with those obtained from morphological and chemotaxonomical studies. Analyses of all data sets indicates that the variations in morphology and secondary metabolitic constituents between Sophora prostrata and Sophora microphylla obscures a small amount of genetic diversity. The question of hybrid origins for Sophora microphylla is not supported by tree reconstructions from the molecular data set, and further genetic and ecological studies are required to investigate this.
Population genetics, biogeography and ecological interactions of the New Zealand bellbird (Anthornis melanura) and their avian malaria parasites : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy (Ph.D.) in Zoology at Massey University, Albany, New Zealand
(Massey University, 2011) Baillie, Shauna Maureen
Habitat loss and redistribution of species has lead to population declines and loss of genetic diversity with serious implications to species survival on ecological and evolutionary scales. While there is no doubt that rapidly dwindling endangered populations require our immediate attention, studies on common species are equally important. The purpose of this thesis is to investigate the genetic connectivity, biogeographical relationships and host-parasite interactions of a common and widely distributed bird species, mainly because we want common species to remain common. Furthermore, I illustrate how studies such as this provide invaluable comparisons for sympatric endangered species. In this thesis, patterns of genetic variation of the New Zealand bellbird (Anthornis melanura) are delineated to assess their re-colonization potential among fragmented landscapes. Using a phylogeographic perspective I show how dispersal ability and secondary contact among isolated population fragments shape the evolutionary trajectory of a species. I also determine the biogeographical relationships between the bellbird host and its malaria parasites with key emphasis on host-parasite specificity. Finally, immunological trade-offs are investigated in disease epidemiology by examining host factors that influence malaria prevalence. I show that an immense capacity for dispersal has prevented divergence and shaped the high levels of genetic diversity and connectivity in bellbirds today. However, substantial genetic differentiation among subpopulations reflects recent habitat fragmentation. Based on these findings I conclude that continued habitat loss can lead to further reductions in gene flow, despite dispersal. Though restricted to northern populations, I provide evidence that the most abundant avian malaria lineage infecting bellbirds is likely an endemic Plasmodium (Novyella). This parasite exhibits bimodal seasonality and male-biased infections, but these relationships vary among subpopulations. Malaria prevalence appears to be governed by food availability and territory stability, thus habitat disturbance has repercussions to immune phenotype. With this thesis I advocate a re-thinking of conservation strategies toward spatial planning that enables ‘natural’ secondary contact among habitat fragments. Translocation is not necessary for all species. In addition to being the first study on seasonal and host factors affecting malaria patterns in the Southern Hemisphere, this thesis makes major contributions to science by elucidating some ecological relationships that underpin the evolution of immunity.
Origins and evolution of the New Zealand forest flora : a molecular phylogenetic approach : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Plant Biology at Massey University, Palmerston North, New Zealand
(Massey University, 2001) Stöckler, Karen
The origins and evolution of the New Zealand flora have puzzled the imagination of botanists world-wide. Competing hypotheses have sought to explain the floristic relationships between New Zealand and other Southern Hemisphere landmasses. Scientific approaches have involved geology, plant morphology, palynology and palaeobotany in investigations of the distribution patterns of these floras. Analyses presented in the current thesis use molecular data to investigate phylogenetic relationships of plant lineages native to the New Zealand forest flora. In the present thesis, molecular work included amplification and sequencing of standard DNA markers such as nuclear ribosomal DNA, ndhF and rbcL gene sequence. These data were obtained for New Zealand and overseas species of Myrsinaceae, Nothofagaceae and genus Agathis (Araucariaceae). Analyses of these data have been presented alongside results and re-analyses of genetic data for Podocarpaceae, Proteaceae, Winteraceae and genus Metrosideros (Myrtaceae). These analyses aimed to synthesise recent work and provide a framework for further molecular investigations into the origins of the New Zealand woody forest flora. Amplified fragment length polymorphism (AFLP) was used to locate polymorphic genome regions that were converted into sequence specific DNA markers. Information from AFLP and AFLP derived markers was used to elucidate evolutionary processes as well as interspecific and intraspecific relationships between closely related taxa of Myrsine and Nothofagus. DNA analyses showed that the New Zealand forest hosts plants with very different origins and evolutionary histories. Results presented in the current thesis support hypotheses of vicariance and long-distance dispersal across Southern Hemisphere lands. Molecular data are consistent with a continuous presence of Agathis (Araucariaceae), Dacrydium (Podocarpaceae) and Pseudowintera (Winteraceae) on the New Zealand archipelago since the break-up of the Gondwanan supercontinent. It is proposed that extant species of these lineages have evolved from ancestors that arrived on the New Zealand landmass during the Cretaceous. In contrast, divergence time estimates on Nothofagus suggest that relationships between extant Fuscaspora and Lophozonia beeches date back to the Mid Tertiary and are not explained by vicariance and continental drift. Phylogenetic analyses substantiate fossil evidence of a Tertiary arrival of Metrosideros (Myrtaceae), Myrsine (Myrsinaceae). Knightia and Toronia (both Proteaceae). Similarly, dispersal from New Zealand to other southern lands has been inferred for Metrosideros and Myrsine. These findings and those reported earlier for alpine plant groups suggest that trans-oceanic dispersal is likely to be an important explanation of floristic relationships between New Zealand and other distant landmasses. Molecular studies on New Zealand Myrsine suggest recent speciation events, geographic differentiation and ongoing hybridisation between some morphologically and ecologically distinct species Intraspecific analyses on Myrsine divaricata and Nothofagus menziesii show that extant distribution patterns within New Zealand are relatively recent and may have developed during the Quaternary. Although both lineages have an ancient history on the New Zealand archipelago, it is concluded that species and their distributions - including that of the monotypic genera Elingamita - are of recent origin.
Patterns and processes in animal evolution : molecular phylogenetics of Southern Hemisphere fauna : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Genetics
(Massey University, 2008) Pratt, Renae
Three kinds of processes are known to modify the geographical spatial arrangement of organisms: dispersal, extinction and vicariance. The Southern Hemisphere has an intriguing and complicated geological history that provides an ideal backdrop to study these processes. This thesis focuses on three historical events that illustrate these processes: the proposed marine inundation of New Zealand in the Oligocene, the asteroid impact at the K – Pg boundary, and the continental breakup of Gondwana. It investigates what impact these events had on species diversification by studying the phylogenetic relationships of two groups of taxa – the family Anostostomatidae (insects), and Neoaves (birds). Anostostomatidae were studied in relation to the Oligocene drowning and the break up of Gondwana as they have a wide southern distribution, found on all “Gondwanan” fragments with the exception of Antarctica, and are thought represent an ancient lineage that predates the Gondwanan breakup. Birds, in particular Neoaves, were studied in relation to the asteroid impact at the K – Pg boundary. Although birds are mobile and many circumnavigate the globe between seasons, they are suggested to have originated in the Southern Hemisphere in Gondwanan times, and subsequently undergone range expansion and diversification around the world. In order to address the relationship (if any) between modern biotic diversity and historical geological events, phylogenetic relationships were determined and where possible, molecular clock analysis carried out. Timing information provided by molecular clock analysis is important as it enables distinction between opposing hypotheses such as vicariance and dispersal. In Chapter Two, the phylogenetic relationships within the family Anostostomatidae are investigated. One of the most controversial times in New Zealand’s geological history is during the Oligocene. Some suggest that the lack of fossils and evidence for recent dispersal of numerous taxa support the notion that all modern biota reached the region during the last 25 million years. Anostostomatidae were chosen as they represent a group of insects that are thought to be ancient and there is little published data in the literature. Previous studies focused on the relationships within Hemideina and Deinacrida suggesting that these groups diversified in the early Miocene. The data presented here are from mitochondrial (COI and 12S) and nuclear (18S and 28S) sequences. Molecular dating using a relaxed clock as implemented in BEAST suggest that in fact some lineages were present at or shortly after continental breakup and could have survived throughout this turbulent time. As there were no definitive fossils to use for calibration points, geological events were used as calibration points for the molecular clock. Mutation rates obtained from the different analyses were compared to those published for other insects in an attempt to identify the most likely model. Both maximum likelihood and Bayesian analyses support the presence of three distinct ecological groups in New Zealand; Hemiandrus (ground weta), Anisoura/Motuweta (tusked weta) and Hemideina–Deinacrida (tree–giant weta). With regards to their Australasian relatives (taxa from Australia and New Caledonia) it appears that the family is divided with the most northern New Zealand taxa (tusked weta) more closely related to New Caledonian taxa while all other New Zealand taxa are more closely related to Australian taxa. There does not appear to be any link between the Australian and New Caledonian taxa studied here. Results should be viewed with caution however as an increased mutation rate was observed in the New Caledonian-tusked weta lineage, something future studies will have to address. Chapter Three presents new sequence data and phylogenetic analyses that go towards resolving the apparent basal polytomy of neoavian birds. This chapter includes analyses carried out on previously published data with the addition of nine new mitochondrial genomes. My contribution to this larger project was to perform the phylogenetic analysis and to sequence three of the nine mitochondrial genomes. The genomes I sequenced were the Southern Hemisphere species: dollar bird (Eurystomus orientalis), Owlet nightjar (Aegotheles cristatus cristatus) and great potoo (Nyctibius grandis). The inclusion of these nine new genomes allows assessment and comparison of the six hypothesised groups reported in Cracraft (2001). First an improved conditional down-weighting technique is described reducing noise relative to signal, which is important for resolving deeper divergences. Second, a formula is presented for calculating probabilities of finding predefined groupings in the optimal tree. Maximum likelihood and Bayesian based phylogenetic analyses were carried out and in addition, dating using a relaxed molecular clock was performed in BEAST. Results suggested that the six groups suggested by Cracraft (2001) represent robust lineages. The results suggested that one group, the owls, are more closely related to other raptors, particularly accipitrids (buzzards/eagles) and the osprey rather than the Caprimulgiformes, which could indicate morphological convergent evolution. In addition, a group termed shorebirds appears to be distinct from the large group referred to as ‘Conglomerati’ to which previous publications have suggested they belong. The ‘Conglomerati’ is the least well studied group and may actually comprise of at least three subgroups (as suggested by Cracraft). Within the three suggested groups, Cracraft grouped shorebirds with pigeons and sandgrouse, neither of which (pigeons or sandgrouse) were analysed here. So although the shorebirds are at least close to the ‘Conglomerati’ and may be within that group, their exact position is still not clear. The molecular dating reported here utilised two fossil calibrations (Vegavis and Waimanu), for which there is relatively little dispute as to age or the lineage to which they belong. Calibrations resulting from BEAST analyses suggest that at least 12 distinct lineages were present prior to the K – Pg boundary, a finding supported by previous studies. Robust phylogenies will allow future studies to investigate not only the relationships within Neoaves, but look more closely at the biological and ecological evolution of the group. Chapter Four for the first time investigates whether the phylogenetic relationships within the family Anostostomatidae follow the conventionally accepted order and timing of Gondwanan breakup. Following the initial restults for taxa studied in Australasia (Chapter Two) an attempt to resolve family relationships in a wider spatial (geographic) context was carried out to determine if Australasian taxa are monophyletic when other members of the family are included. Again both maximum likelihood and Bayesian phylogenetic analyses were carried out on both mitochondrial (COI and 12S) and nuclear (18S and 28S) sequences. In this chapter, datasets included samples from across the geographic range of Anostostomatidae (South Africa, Madagascar, South America, Australia, New Caledonia and New Zealand), and two clades were observed, congruent with earlier findings. Sequence divergence within geographic regions was found to be relatively high in the mitochondrial genes (COI and 12S) while low in the nuclear ribosomal RNA genes (18S and 28S) as expected given their relative mutation rates. Under the vicariance paradigm, phylogenetic relationships should follow the order of continental breakup, but this was not found. Further, if dispersal and colonisation were continuous, no geographic substructure is expected, however distinct geographic substructure within clades was consistently observed. This interesting phylogenetic pattern may be a case of convergent evolution or paraphyletic sampling which highlights taxonomic issues of the group. Future studies need to include not only molecular data but information on morphology, ecology and behaviour along with the implementation of biogeographic programs that can test alternative hypotheses (such as dispersal and vicariance) directly. Also, the inclusion of the recently reported fossil from the subfamily Euclydesinae (Martins-Neto 2007) should allow for more accurate date estimates within the family. Taken as a whole the results presented in this thesis suggest that microevolutionary processes are sufficient to explain modern diversity without the need to invoke abiotic events. The three cases investigated here - marine inundation, asteroid impact and continental drift - all appear to have had only a limited effect on the diversity of taxa studied. To reach even stronger conclusions future studies should incorporate different data (for instance nuclear genes, intron position, and genome structure) and use biogeographic software capable of including ecological, morphological and habitat information.

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