title: Diversity of New Zealand Deep-sea Amphipoda

authors: Knox, Matthew Andrew

subjects: Challenger Plateau

abstract: Biodiversity and the ecological and evolutionary processes which influence faunal distributions are poorly understood in deep-sea habitats. This thesis assesses diversity of deep-sea amphipod crustaceans at three taxonomic levels (family, species, genetic) on continental margins of New Zealand relative to environmental variables. Sampling was undertaken at 20 stations located on Chatham Rise and Challenger Plateau, two major geomorphic features with contrasting environmental conditions.

In Chapter 1, total diversity of the >12,500 amphipods assessed at the family-level revealed high abundance (range: 44 – 2074 individuals 1000 m⁻²) and taxonomic richness (27 families). Amphipod assemblages at all stations were largely dominated by the same families. Chatham Rise stations were mostly similar in family composition to one another and to the two closest Challenger Plateau stations. Overall, amphipod community composition correlated most strongly with surface chlorophyll a, suggesting strong benthic-pelagic coupling.

In Chapter 2, I used molecular methods (COI DNA sequence thresholds of 6%) to estimate species diversity in the dominant amphipod family identified from Chapter 1 - the Phoxocephalidae. Analyses revealed 49 putative species-level taxa, which greatly exceeds the current number (n=17) of formally described New Zealand phoxocephalid species. A cluster of stations with highly similar taxa was identified, broadly distributed over the crest of the Chatham Rise, in association with elevated food availability. Similar to the family-level analyses of Chapter 1 multivariate analysis of phoxocephalid assemblages and environmental parameters revealed a strong correlation with measures of food supply. Analyses of inter-station assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions on eastern and western continental margins.

Chapter 3 examined genetic connectivity among deep-sea habitats. A phylogenetic analyses of three relatively abundant and widespread taxa; cf. Ampelisca chiltoni, cf. Oediceroides apicalis and Phoxocephalidae sp., was combined with available genetic data from a further 61 taxa collected from the same stations, to examine mean levels of inter-station genetic divergences. Nearly identical levels of genetic divergence were found between eastern and western regions for all three taxa. Furthermore, inter-station analysis of the wider amphipod community revealed similar patterns of genetic structure in most taxa. Based on molecular clock estimates, genetic divergences most likely corresponded to isolation following landmass changes during the Pleistocene.

This thesis research has revealed a biodiversity hotspot on New Zealand continental margins. I conclude that Cook Strait and the subtropical front are important structures responsible for shaping benthic communities on New Zealand continental margins and that vicariance is likely to have played an important role in the evolutionary radiation of the New Zealand deep-sea fauna.

text: Diversity of New Zealand Deep-sea Amphipoda Biodiversity and the ecological and evolutionary processes which influence faunal distributions are poorly understood in deep-sea habitats. This thesis assesses diversity of deep-sea amphipod crustaceans at three taxonomic levels (family, species, genetic) on continental margins of New Zealand relative to environmental variables. Sampling was undertaken at 20 stations located on Chatham Rise and Challenger Plateau, two major geomorphic features with contrasting environmental conditions.

In Chapter 1, total diversity of the >12,500 amphipods assessed at the family-level revealed high abundance (range: 44 – 2074 individuals 1000 m⁻²) and taxonomic richness (27 families). Amphipod assemblages at all stations were largely dominated by the same families. Chatham Rise stations were mostly similar in family composition to one another and to the two closest Challenger Plateau stations. Overall, amphipod community composition correlated most strongly with surface chlorophyll a, suggesting strong benthic-pelagic coupling.

In Chapter 2, I used molecular methods (COI DNA sequence thresholds of 6%) to estimate species diversity in the dominant amphipod family identified from Chapter 1 - the Phoxocephalidae. Analyses revealed 49 putative species-level taxa, which greatly exceeds the current number (n=17) of formally described New Zealand phoxocephalid species. A cluster of stations with highly similar taxa was identified, broadly distributed over the crest of the Chatham Rise, in association with elevated food availability. Similar to the family-level analyses of Chapter 1 multivariate analysis of phoxocephalid assemblages and environmental parameters revealed a strong correlation with measures of food supply. Analyses of inter-station assemblages revealed a major split between regions, indicating minimal overlap in taxon distributions on eastern and western continental margins.

Chapter 3 examined genetic connectivity among deep-sea habitats. A phylogenetic analyses of three relatively abundant and widespread taxa; cf. Ampelisca chiltoni, cf. Oediceroides apicalis and Phoxocephalidae sp., was combined with available genetic data from a further 61 taxa collected from the same stations, to examine mean levels of inter-station genetic divergences. Nearly identical levels of genetic divergence were found between eastern and western regions for all three taxa. Furthermore, inter-station analysis of the wider amphipod community revealed similar patterns of genetic structure in most taxa. Based on molecular clock estimates, genetic divergences most likely corresponded to isolation following landmass changes during the Pleistocene.

This thesis research has revealed a biodiversity hotspot on New Zealand continental margins. I conclude that Cook Strait and the subtropical front are important structures responsible for shaping benthic communities on New Zealand continental margins and that vicariance is likely to have played an important role in the evolutionary radiation of the New Zealand deep-sea fauna.

year: 2012

title: Logistic regression and boosting for labeled bags of instances

authors: Xu, Xin

subjects: computer science

abstract: In this paper we upgrade linear logistic regression and boosting to multi-instance data, where each example consists of a labeled bag of instances. This is done by connecting predictions for individual instances to a bag-level probability estimate by simple averaging and maximizing the likelihood at the bag level—in other words, by assuming that all instances contribute equally and independently to a bags label. We present empirical results for artificial data generated according to the underlying generative model that we assume, and also show that the two algorithms produce competitive results on the Musk benchmark datasets.

text: Logistic regression and boosting for labeled bags of instances In this paper we upgrade linear logistic regression and boosting to multi-instance data, where each example consists of a labeled bag of instances. This is done by connecting predictions for individual instances to a bag-level probability estimate by simple averaging and maximizing the likelihood at the bag level—in other words, by assuming that all instances contribute equally and independently to a bags label. We present empirical results for artificial data generated according to the underlying generative model that we assume, and also show that the two algorithms produce competitive results on the Musk benchmark datasets.

year: 2004

title: A step into the light: developing a culturally appropriate research prcoess to study Maori Rangatahi perspectives of leisure in one setting.

authors: Harvey, Geraldine

subjects: research -- methodology

abstract: There is little knowledge of Maori peoples' leisure understandings, experiences and participation. This article reports on the development of a culturally appropriate research process that investigated the leisure participation, perspectives, and experiences of five Rotorua Maori Rangatahi in one research setting'. Within this exploration there is a focus on the need to conduct leisure research with Maori people in culturally appropriate ways. This research approach incorporates focus group methodology within a Kaupapa Maori research framework which addresses issues of research for Maori. The research process revealed that focus group methodology can be adapted into a Kaupapa Maori research framework and that this research approach could be an important tool when conducting research with Maori Rangatahi, including in educational contexts.

text: A step into the light: developing a culturally appropriate research prcoess to study Maori Rangatahi perspectives of leisure in one setting. There is little knowledge of Maori peoples' leisure understandings, experiences and participation. This article reports on the development of a culturally appropriate research process that investigated the leisure participation, perspectives, and experiences of five Rotorua Maori Rangatahi in one research setting'. Within this exploration there is a focus on the need to conduct leisure research with Maori people in culturally appropriate ways. This research approach incorporates focus group methodology within a Kaupapa Maori research framework which addresses issues of research for Maori. The research process revealed that focus group methodology can be adapted into a Kaupapa Maori research framework and that this research approach could be an important tool when conducting research with Maori Rangatahi, including in educational contexts.

year: 2002