title: Population genetic structure of Antarctic springtails (Collembola) and New Zealand damselflies (Odonata)

authors: Nolan, Liam

subjects: Antarctic

abstract: Since Darwin (Darwin, 1859), the process of speciation and maintenance of biological diversity has caused intensive debate in the scientific and non-scientific communities alike. The ability to analyze differences in the molecular structure of enzymes and DNA sequences has provided an extremely sensitive tool for investigating gene flow within and among populations, a key facet of the genetic divergence required for speciation to occur.
Using such techniques, we are now able to gain a snapshot of the genetic structure of a population and its geographical distribution (Hewitt, 2001) In this way, the phylogeography of species from many environments around the globe have now been studied in fine detail. It has also been possible to generate hypotheses proposing restricted distribution in 'refugia' and subsequent recolonisation after climatic events such as glaciation have occurred. Refugia appear to be particularly important in shaping high latitude biodiversity (Willis & Whittaker, 2000). On such occasions the distribution of different populations may ultimately overlap again at a contact zone, and the species geographical subdivision may provide enough evidence to suggest speciation or the creation of a hybrid zone (Hewitt, 2001 ).
In addition, the DNA sequences may yield important information on the evolutionary history, dispersal and taxonomy of various species. Morphologically indistinguishable organisms may be discovered as 'cryptic species', and vice versa, taxa considered to be very different based on observable characteristics can be found to be genetically similar and not reproductively isolated (e.g. Trewick, 2000; Witt & Hebert, 2000).
In this way, the genetic diversity within and among closely related species may be determined to a high degree of resolution. In today's climate of human interference and relatively rapid environmental change, it is vital that we appreciate and make full use of the detailed population information available to us. In this way, we may be able to predict and potentially mitigate the consequences of environmental change for organisms by analyzing their evolutionary past.
This thesis contains an analysis of molecular data (mtDNA and allozymes) on two arthropod taxa. The thesis consists of two chapters. Chapter I describes the distribution of mitochondrial (mt) DNA haplotypes for the Antarctic springtail Gomphiocephalus hodgsoni (Collembola) in Taylor Valley, southern Victoria Land. The observed distribution was congruent with a hypothesis of multiple refugia during the Pleistocene glaciations and a barrier to gene flow by a glacial lake. Chapter II assesses the genetic variability of the New Zealand damselfly genera (Odonata) from sites throughout the North, South and Chatham islands using both allozyme and mtDNA analyses. All morphologically recognized species were clearly discernible on the basis of both mtDNA and allozymes. However, variability within and among sites was limited for all species, and may have implications from a conservation perspective.
The thesis ends with a brief summary section highlighting the main findings contained in the thesis and outlining potential future research directions.

text: Population genetic structure of Antarctic springtails (Collembola) and New Zealand damselflies (Odonata) Since Darwin (Darwin, 1859), the process of speciation and maintenance of biological diversity has caused intensive debate in the scientific and non-scientific communities alike. The ability to analyze differences in the molecular structure of enzymes and DNA sequences has provided an extremely sensitive tool for investigating gene flow within and among populations, a key facet of the genetic divergence required for speciation to occur.
Using such techniques, we are now able to gain a snapshot of the genetic structure of a population and its geographical distribution (Hewitt, 2001) In this way, the phylogeography of species from many environments around the globe have now been studied in fine detail. It has also been possible to generate hypotheses proposing restricted distribution in 'refugia' and subsequent recolonisation after climatic events such as glaciation have occurred. Refugia appear to be particularly important in shaping high latitude biodiversity (Willis & Whittaker, 2000). On such occasions the distribution of different populations may ultimately overlap again at a contact zone, and the species geographical subdivision may provide enough evidence to suggest speciation or the creation of a hybrid zone (Hewitt, 2001 ).
In addition, the DNA sequences may yield important information on the evolutionary history, dispersal and taxonomy of various species. Morphologically indistinguishable organisms may be discovered as 'cryptic species', and vice versa, taxa considered to be very different based on observable characteristics can be found to be genetically similar and not reproductively isolated (e.g. Trewick, 2000; Witt & Hebert, 2000).
In this way, the genetic diversity within and among closely related species may be determined to a high degree of resolution. In today's climate of human interference and relatively rapid environmental change, it is vital that we appreciate and make full use of the detailed population information available to us. In this way, we may be able to predict and potentially mitigate the consequences of environmental change for organisms by analyzing their evolutionary past.
This thesis contains an analysis of molecular data (mtDNA and allozymes) on two arthropod taxa. The thesis consists of two chapters. Chapter I describes the distribution of mitochondrial (mt) DNA haplotypes for the Antarctic springtail Gomphiocephalus hodgsoni (Collembola) in Taylor Valley, southern Victoria Land. The observed distribution was congruent with a hypothesis of multiple refugia during the Pleistocene glaciations and a barrier to gene flow by a glacial lake. Chapter II assesses the genetic variability of the New Zealand damselfly genera (Odonata) from sites throughout the North, South and Chatham islands using both allozyme and mtDNA analyses. All morphologically recognized species were clearly discernible on the basis of both mtDNA and allozymes. However, variability within and among sites was limited for all species, and may have implications from a conservation perspective.
The thesis ends with a brief summary section highlighting the main findings contained in the thesis and outlining potential future research directions.

year: 2006

title: Applying machine learning to agricultural data

authors: McQueen, Robert J.

subjects: computer science

abstract: Many techniques have been developed for abstracting, or "learning," rules and relationships from diverse data sets, in the hope that machines can help in the often tedious and error-prone process of acquiring knowledge from empirical data. While these techniques are plausible, theoretically well-founded, and perform well on more or less artificial test data sets, they stand or fall on their ability to make sense of real-world data. This paper describes a project that is applying a range of learning strategies to problems in primary industry, in particular agriculture and horticulture. We briefly survey some of the more readily applicable techniques that are emerging from the machine learning research community, describe a software workbench that allows users to experiment with a variety of techniques on real-world data sets, and detail the problems encountered and solutions developed in a case study of dairy herd management in which culling rules were inferred from a medium-sized database of herd information.

text: Applying machine learning to agricultural data Many techniques have been developed for abstracting, or "learning," rules and relationships from diverse data sets, in the hope that machines can help in the often tedious and error-prone process of acquiring knowledge from empirical data. While these techniques are plausible, theoretically well-founded, and perform well on more or less artificial test data sets, they stand or fall on their ability to make sense of real-world data. This paper describes a project that is applying a range of learning strategies to problems in primary industry, in particular agriculture and horticulture. We briefly survey some of the more readily applicable techniques that are emerging from the machine learning research community, describe a software workbench that allows users to experiment with a variety of techniques on real-world data sets, and detail the problems encountered and solutions developed in a case study of dairy herd management in which culling rules were inferred from a medium-sized database of herd information.

year: 1994-07

title: Toitu Te Moananui a Toi – The Effects of the MV Rena on the Water Quality, Chemistry and Zooplankton of Otaiti (Astrolabe Reef)

authors: Dempsey, Te Puea Toni

subjects: metal contamination

abstract: Humans have had a profound effect on the world’s oceans, particularly through pollution. Marine pollution incidents are particularly important and increasingly involve both petrochemical and metal contamination. The effects of complex high level, point source pollution events such as ship wrecks on larval recruitment to reef environments is not well understood. Larval settlement is heavily influenced by chemical cues, hence pollution events could have a long term influence on reef ecology, and the likelihood that planktonic zooplankton can entrain contaminants into the reef food web is also of concern.
This thesis aims to address concerns from local Tangata Whenua, government, researchers, stakeholders and the public about the long term recovery of Otaiti following the MV Rena shipwreck and subsequent reef contamination. The incident is a complex one involving metallic container debris contamination along with oil. Research focussed on assessing the effects of water borne contamination surrounding the wreck site in order to examine acute and chronic responses of planktonic invertebrates: (1) the influence of Rena and associated debris to the chemistry and quality of water in the benthic zone around the wreck, (2) the toxicity of contaminants to survivorship of zooplankton, and (3) the influence on contaminant plumes to zooplankton recruitment behaviour of Otaiti.
There is a clear effect from the Rena and its associated debris field on the water quality and chemistry of Otaiti. Aluminium and copper for example, were consistently elevated in dissolved and total metal concentrations around the debris field. Laboratory based exposure of zooplankton to realistic concentration gradients of Rena contaminated sediments resulted in increased mortality with increased contaminant concentrations. Behavioural responses of pelagic and settling invertebrates to Rena pollution influenced sediment highlighted sensitivity to associated contaminant plumes. This could have significant ecological implications to the recruitment behaviour of other planktonic organisms that rely on reef conspecifics and chemical cues to initiate settlement.
Ecological concepts such as ecosystem function and biodiversity dynamics (including recruitment) relate the life force and longevity of a system. Key concerns within the scope of this research were highlighted that may have implications to Tangata Whenua decision making in assessing the Mauri of Otaiti. It can be implied that the Rena continues to impact the Mauri of Otaiti due to the presence of contaminants within the debris field.

text: Toitu Te Moananui a Toi – The Effects of the MV Rena on the Water Quality, Chemistry and Zooplankton of Otaiti (Astrolabe Reef) Humans have had a profound effect on the world’s oceans, particularly through pollution. Marine pollution incidents are particularly important and increasingly involve both petrochemical and metal contamination. The effects of complex high level, point source pollution events such as ship wrecks on larval recruitment to reef environments is not well understood. Larval settlement is heavily influenced by chemical cues, hence pollution events could have a long term influence on reef ecology, and the likelihood that planktonic zooplankton can entrain contaminants into the reef food web is also of concern.
This thesis aims to address concerns from local Tangata Whenua, government, researchers, stakeholders and the public about the long term recovery of Otaiti following the MV Rena shipwreck and subsequent reef contamination. The incident is a complex one involving metallic container debris contamination along with oil. Research focussed on assessing the effects of water borne contamination surrounding the wreck site in order to examine acute and chronic responses of planktonic invertebrates: (1) the influence of Rena and associated debris to the chemistry and quality of water in the benthic zone around the wreck, (2) the toxicity of contaminants to survivorship of zooplankton, and (3) the influence on contaminant plumes to zooplankton recruitment behaviour of Otaiti.
There is a clear effect from the Rena and its associated debris field on the water quality and chemistry of Otaiti. Aluminium and copper for example, were consistently elevated in dissolved and total metal concentrations around the debris field. Laboratory based exposure of zooplankton to realistic concentration gradients of Rena contaminated sediments resulted in increased mortality with increased contaminant concentrations. Behavioural responses of pelagic and settling invertebrates to Rena pollution influenced sediment highlighted sensitivity to associated contaminant plumes. This could have significant ecological implications to the recruitment behaviour of other planktonic organisms that rely on reef conspecifics and chemical cues to initiate settlement.
Ecological concepts such as ecosystem function and biodiversity dynamics (including recruitment) relate the life force and longevity of a system. Key concerns within the scope of this research were highlighted that may have implications to Tangata Whenua decision making in assessing the Mauri of Otaiti. It can be implied that the Rena continues to impact the Mauri of Otaiti due to the presence of contaminants within the debris field.

year: 2015