title: Phylogeography and Ecology of New Zealand Freshwater Amphipoda (Paracalliope, Paraleptamphopus, and Phreatogammarus)

authors: Sutherland, Darin Lee

subjects: Genetics

abstract: This thesis examines phylogenetic patterns in three New Zealand amphipod taxa in relation to current geographic distributions and historical climatic (e.g. glaciation, marine inundation) and geological (e.g. mountain building) events using DNA sequencing and distributional data. It also examines how recognition behaviour can be used to delineate potential species boundaries and to assess the role of sexual selection.
The endemic genus Phreatogammarus has been found in only a limited number of sites and is not very abundant. An analysis of the genetic variation of two species within the genus using allozyme electrophoresis revealed high levels of genetic differentiation among populations but low levels within populations. This suggested that limited dispersal occurred among habitats with one population possibly representing a cryptic species.
The endemic freshwater genus Paraleptamphopus is thought to contain a large number of undescribed species with a number of these existing in small waterbodies such as seepages. Examination of the phylogeographic patterns using both mtDNA (CO1) and nuclear DNA (28S) showed that a number of distinct genetic lineages exist, with CO1 revealing 21 haplotypes with genetic distance of over 20%. Using a molecular clock rate of 2.4%, most haplotypes diverged approximately 8-12 million years ago during the Miocene era, possibly as a result of greater land availability increasing habitat diversity or by allopatric speciation. Morphological and genetic differences were not congruent, with morphologically similar taxa appearing among highly genetically distinct lineages, and some morphologically distinct forms appearing within single lineages.
The distribution and habitat variables of 419 sites were analysed to determine what was affecting the presence or absence of Paraleptamphopus. The presence of native vegetation in catchments had a positive affect on Paraleptamphopus distribution suggesting that large anthropogenic changes in catchment vegetation could have a negative effect on their abundance. I found smaller waterbodies to be more important than larger ones highlighting the need to study such sites as rare taxa may be ignored. A better understanding is needed on the role of small waterbodies in promoting overall species diversity in catchments. 
Examination of Paracalliope fluviatilis phylogenetic patterns using the mtDNA gene CO1 showed that a number of separate clades existed suggesting long term isolation and limited dispersal among catchments. Due to the large genetic divergences among some populations there was the possibility that cryptic species might exist. Species recognition experiments were conducted on seven populations to help determine whether cryptic species were present. For the three most genetically divergent crosses there was bias against inter-population pairings, suggesting that there were between two or three separate species.
Using a combined field and laboratory approach, size assortative mating was examined in Paracalliope fluviatilis. The field study showed positive size assortative mating and that larger females carried more eggs, suggesting they were more fecund. A series of laboratory experiments examining four existing theories explaining the phenomenon found that none adequately explained positive size assortative mating in P. fluviatilis. I therefore presented two new explanations to explain size assortative mating: a combination of female resistance and size-related variation in a male's capacity to amplex larger females or a form of indirect intra-sexual competition.

text: Phylogeography and Ecology of New Zealand Freshwater Amphipoda (Paracalliope, Paraleptamphopus, and Phreatogammarus) This thesis examines phylogenetic patterns in three New Zealand amphipod taxa in relation to current geographic distributions and historical climatic (e.g. glaciation, marine inundation) and geological (e.g. mountain building) events using DNA sequencing and distributional data. It also examines how recognition behaviour can be used to delineate potential species boundaries and to assess the role of sexual selection.
The endemic genus Phreatogammarus has been found in only a limited number of sites and is not very abundant. An analysis of the genetic variation of two species within the genus using allozyme electrophoresis revealed high levels of genetic differentiation among populations but low levels within populations. This suggested that limited dispersal occurred among habitats with one population possibly representing a cryptic species.
The endemic freshwater genus Paraleptamphopus is thought to contain a large number of undescribed species with a number of these existing in small waterbodies such as seepages. Examination of the phylogeographic patterns using both mtDNA (CO1) and nuclear DNA (28S) showed that a number of distinct genetic lineages exist, with CO1 revealing 21 haplotypes with genetic distance of over 20%. Using a molecular clock rate of 2.4%, most haplotypes diverged approximately 8-12 million years ago during the Miocene era, possibly as a result of greater land availability increasing habitat diversity or by allopatric speciation. Morphological and genetic differences were not congruent, with morphologically similar taxa appearing among highly genetically distinct lineages, and some morphologically distinct forms appearing within single lineages.
The distribution and habitat variables of 419 sites were analysed to determine what was affecting the presence or absence of Paraleptamphopus. The presence of native vegetation in catchments had a positive affect on Paraleptamphopus distribution suggesting that large anthropogenic changes in catchment vegetation could have a negative effect on their abundance. I found smaller waterbodies to be more important than larger ones highlighting the need to study such sites as rare taxa may be ignored. A better understanding is needed on the role of small waterbodies in promoting overall species diversity in catchments. 
Examination of Paracalliope fluviatilis phylogenetic patterns using the mtDNA gene CO1 showed that a number of separate clades existed suggesting long term isolation and limited dispersal among catchments. Due to the large genetic divergences among some populations there was the possibility that cryptic species might exist. Species recognition experiments were conducted on seven populations to help determine whether cryptic species were present. For the three most genetically divergent crosses there was bias against inter-population pairings, suggesting that there were between two or three separate species.
Using a combined field and laboratory approach, size assortative mating was examined in Paracalliope fluviatilis. The field study showed positive size assortative mating and that larger females carried more eggs, suggesting they were more fecund. A series of laboratory experiments examining four existing theories explaining the phenomenon found that none adequately explained positive size assortative mating in P. fluviatilis. I therefore presented two new explanations to explain size assortative mating: a combination of female resistance and size-related variation in a male's capacity to amplex larger females or a form of indirect intra-sexual competition.

year: 2006

title: Nearshore and inner shelf sedimentation on the east Coromandel coast, New Zealand

authors: Bradshaw, Barry Edward

abstract: The east Coromandel coastline on the northeast coast of New Zealand has been characterised by localised erosion problems since its commercial subdivision. Increasing pressures have also arisen in recent years for possible use of the adjacent continental shelf as a repository for dredge and mining tailings, and extraction of commercial aggregate and mineral deposits. This has raised the question of dynamic links between the continental shelf and local beach systems I and resulting impacts on the coastline from such activities. The east Coromandel shelf study was therefore undertaken to investigate the modern and past shelf sedimentation processes, and relate these findings to local resource management issues. The results also contribute to the present international understanding of inner shelf sedimentation processes in 'storm-dominated' shelf environments.
Surficial sedimentation patterns have been examined by a variety of methods, including: the use of sea-bed drifters and Aanderaa current meters to determine the shelf hydrodynamics; the collection of 563 samples to determine surface sediment textural patterns; a detailed examination of morphological features on the sea floor through a series of 3 side-scan sonar surveys in which 620 km of sonograph and echosounding trace have been obtained; diver surveys using depth of activity rods to provide information on the mobility of surface sediments under different sea conditions; the collection, of 174 km of continuous sub-bottom seismic profiles which have been used to determine sub-surface stratigraphic patterns; and an examination of the provenance of shelf sediments through a detailed examination of their light and heavy mineralogy.
The east Coromandel coast is located on an active plate margin, resulting in the presence of a steep and rocky coastline fronted by a relatively narrow continental shelf (20 to 30 km wide), and a local geology dominated by Tertiary volcanics covered by a thin veneer of more recent volcanic air fall deposits. It is also located on a lee shelf in a mid-latitude zone of dominant westerly winds, with these prevailing weather patterns disrupted by high speed east to northeasterly winds associated with the infrequent passage of subtropical low pressure systems, occluded fronts, or more infrequent decaying tropical cyclones. This physiographic setting results in spatially and temporally highly variable sedimentation patterns, with sediment transport primarily controlled by the interaction of wave oscillatory and wind-generated currents during storm conditions. However, characteristics of tide-. and oceanic current-dominated conditions also occur in some areas. And conditions generally vary along the coast from being higher energy (current-dominated) on the southern exposed coast, to lower energy (wave- or current-dominated) on the northern embayed coastline. Shelf sedimentation is inferred to occur under three different scale events of fair weather, storm, and extreme storm conditions. The model proposed involves extreme storm conditions transporting large quantities of fine nearshore sands seawards onto the inner shelf surface, where they are slowly reworked along the shelf during annual storm events and back onshore during fair weather conditions. This latter onshore return of fine sands is proposed to result from an enhanced shear stress effect of long-period swell waves over coarse megarippled inner shelf sands.
Shelf sedimentation patterns within the study area are inferred to have been primarily established by processes occurring at about the time sea level stabitised 6500 years B.P. At this stage, transgressive shelf sediments were reworked into equilibrium with the regional oceanographic conditions by the winnowing of fine sand from coarser material during storms, with the fine sands subsequently transported onshore by wave-induced currents during calm periods. Depending on the volume of sediments incorporated into transgressive sand bodies and the local shelf gradients, each embayment then developed into either an integral part of the shelf transport system (usually off large estuary systems), with fine shelf sands moving onshore and forming wide barrier spits, or a closed sedimentary system unaffected by shelf sedimentation patterns (pocket embayments). Shelf equilibrium was evidently attained by the fine sands forming a steep seaward dipping concave-up nearshore profile, and coarse sands developing a flatter inner shelf profile.
An autochthonous mode of shelf sedimentation characterised the east Coromandel coast in early Holocene times, and is still evident under present conditions in most areas by the cyclical reworking of fine sands between the lower nearshore and inner shelf surfaces. Most east Coromandel embayments are, however, presently characterised by varying degrees of an allochthonous mode of shelf sedimentation. This involves the deposition of very fine grained, volcanic glass-enriched terrigenous sands, which are derived from either local catchments or Bay of Plenty river systems. The east Coromandel coast generally differs from most allochthonous shelf environments because the supply of terrigenous sediments has not as yet been sufficient to blanket the lower nearshore and inner shelf surfaces on the open ocean coastlines. Two separate modes of shelf sedimentation occur at present, with a nearshore inner shelf recycling of fine allochthonous shelf sands, and an open exchange of terrestrial autochthonous deposits from the upper nearshore surface to the mid shelf plain.
The results of the study suggest that coastal erosion problems can largely be resolved by establishing stable incipient and frontal dune systems along the coast. and encouraging accretion by renourishment from adjacent infilling harbour deposits. The study has also shown that the dispersion of dredged sediments provides potential benefits to the coast in terms of promoting beach accretion, and that sand and mineral extraction can proceed without adverse coastal erosion effects, provided the extraction does not interfere with the natural shelf sedimentation system.

text: Nearshore and inner shelf sedimentation on the east Coromandel coast, New Zealand The east Coromandel coastline on the northeast coast of New Zealand has been characterised by localised erosion problems since its commercial subdivision. Increasing pressures have also arisen in recent years for possible use of the adjacent continental shelf as a repository for dredge and mining tailings, and extraction of commercial aggregate and mineral deposits. This has raised the question of dynamic links between the continental shelf and local beach systems I and resulting impacts on the coastline from such activities. The east Coromandel shelf study was therefore undertaken to investigate the modern and past shelf sedimentation processes, and relate these findings to local resource management issues. The results also contribute to the present international understanding of inner shelf sedimentation processes in 'storm-dominated' shelf environments.
Surficial sedimentation patterns have been examined by a variety of methods, including: the use of sea-bed drifters and Aanderaa current meters to determine the shelf hydrodynamics; the collection of 563 samples to determine surface sediment textural patterns; a detailed examination of morphological features on the sea floor through a series of 3 side-scan sonar surveys in which 620 km of sonograph and echosounding trace have been obtained; diver surveys using depth of activity rods to provide information on the mobility of surface sediments under different sea conditions; the collection, of 174 km of continuous sub-bottom seismic profiles which have been used to determine sub-surface stratigraphic patterns; and an examination of the provenance of shelf sediments through a detailed examination of their light and heavy mineralogy.
The east Coromandel coast is located on an active plate margin, resulting in the presence of a steep and rocky coastline fronted by a relatively narrow continental shelf (20 to 30 km wide), and a local geology dominated by Tertiary volcanics covered by a thin veneer of more recent volcanic air fall deposits. It is also located on a lee shelf in a mid-latitude zone of dominant westerly winds, with these prevailing weather patterns disrupted by high speed east to northeasterly winds associated with the infrequent passage of subtropical low pressure systems, occluded fronts, or more infrequent decaying tropical cyclones. This physiographic setting results in spatially and temporally highly variable sedimentation patterns, with sediment transport primarily controlled by the interaction of wave oscillatory and wind-generated currents during storm conditions. However, characteristics of tide-. and oceanic current-dominated conditions also occur in some areas. And conditions generally vary along the coast from being higher energy (current-dominated) on the southern exposed coast, to lower energy (wave- or current-dominated) on the northern embayed coastline. Shelf sedimentation is inferred to occur under three different scale events of fair weather, storm, and extreme storm conditions. The model proposed involves extreme storm conditions transporting large quantities of fine nearshore sands seawards onto the inner shelf surface, where they are slowly reworked along the shelf during annual storm events and back onshore during fair weather conditions. This latter onshore return of fine sands is proposed to result from an enhanced shear stress effect of long-period swell waves over coarse megarippled inner shelf sands.
Shelf sedimentation patterns within the study area are inferred to have been primarily established by processes occurring at about the time sea level stabitised 6500 years B.P. At this stage, transgressive shelf sediments were reworked into equilibrium with the regional oceanographic conditions by the winnowing of fine sand from coarser material during storms, with the fine sands subsequently transported onshore by wave-induced currents during calm periods. Depending on the volume of sediments incorporated into transgressive sand bodies and the local shelf gradients, each embayment then developed into either an integral part of the shelf transport system (usually off large estuary systems), with fine shelf sands moving onshore and forming wide barrier spits, or a closed sedimentary system unaffected by shelf sedimentation patterns (pocket embayments). Shelf equilibrium was evidently attained by the fine sands forming a steep seaward dipping concave-up nearshore profile, and coarse sands developing a flatter inner shelf profile.
An autochthonous mode of shelf sedimentation characterised the east Coromandel coast in early Holocene times, and is still evident under present conditions in most areas by the cyclical reworking of fine sands between the lower nearshore and inner shelf surfaces. Most east Coromandel embayments are, however, presently characterised by varying degrees of an allochthonous mode of shelf sedimentation. This involves the deposition of very fine grained, volcanic glass-enriched terrigenous sands, which are derived from either local catchments or Bay of Plenty river systems. The east Coromandel coast generally differs from most allochthonous shelf environments because the supply of terrigenous sediments has not as yet been sufficient to blanket the lower nearshore and inner shelf surfaces on the open ocean coastlines. Two separate modes of shelf sedimentation occur at present, with a nearshore inner shelf recycling of fine allochthonous shelf sands, and an open exchange of terrestrial autochthonous deposits from the upper nearshore surface to the mid shelf plain.
The results of the study suggest that coastal erosion problems can largely be resolved by establishing stable incipient and frontal dune systems along the coast. and encouraging accretion by renourishment from adjacent infilling harbour deposits. The study has also shown that the dispersion of dredged sediments provides potential benefits to the coast in terms of promoting beach accretion, and that sand and mineral extraction can proceed without adverse coastal erosion effects, provided the extraction does not interfere with the natural shelf sedimentation system.

year: 1991

title: Indigenous perspectives and gene editing in Aotearoa New Zealand

authors: Hudson, Maui

subjects: Science & Technology

abstract: Gene editing is arguably the most significant recent addition to the modern biotechnology toolbox, bringing both profoundly challenging and enabling opportunities. From a technical point of view the specificity and relative simplicity of these new tools has broadened the potential applications. However, from an ethical point of view it has re-ignited the debates generated by earlier forms of genetic modification. In New Zealand gene editing is currently considered genetic modification and is subject to approval processes under the Environmental Protection Authority (EPA). This process requires decision makers to take into account Māori perspectives. This article outlines previously articulated Māori perspectives on genetic modification and considers the continuing influence of those cultural and ethical arguments within the new context of gene editing. It also explores the range of ways cultural values might be used to analyse the risks and benefits of gene editing in the Aotearoa New Zealand context. Methods used to obtain these perspectives consisted of (a) review of relevant literature regarding lessons learned from the responses of Maori to genetic modification, (b) interviews of selected ‘key Maori informants’ and (c) surveys of self-selected individuals from groups with interests in either genetics or environmental management. The outcomes of this pilot study identified that while Māori informants were not categorically opposed to new and emerging gene editing technologies a priori, they suggest a dynamic approach to regulation is required where specific uses or types of uses are approved on a case by case basis. This study demonstrates how the cultural cues that Māori referenced in the genetic modification debate continue to be relevant in the context of gene editing but that further work is required to characterize the strength of various positions across the broader community.

text: Indigenous perspectives and gene editing in Aotearoa New Zealand Gene editing is arguably the most significant recent addition to the modern biotechnology toolbox, bringing both profoundly challenging and enabling opportunities. From a technical point of view the specificity and relative simplicity of these new tools has broadened the potential applications. However, from an ethical point of view it has re-ignited the debates generated by earlier forms of genetic modification. In New Zealand gene editing is currently considered genetic modification and is subject to approval processes under the Environmental Protection Authority (EPA). This process requires decision makers to take into account Māori perspectives. This article outlines previously articulated Māori perspectives on genetic modification and considers the continuing influence of those cultural and ethical arguments within the new context of gene editing. It also explores the range of ways cultural values might be used to analyse the risks and benefits of gene editing in the Aotearoa New Zealand context. Methods used to obtain these perspectives consisted of (a) review of relevant literature regarding lessons learned from the responses of Maori to genetic modification, (b) interviews of selected ‘key Maori informants’ and (c) surveys of self-selected individuals from groups with interests in either genetics or environmental management. The outcomes of this pilot study identified that while Māori informants were not categorically opposed to new and emerging gene editing technologies a priori, they suggest a dynamic approach to regulation is required where specific uses or types of uses are approved on a case by case basis. This study demonstrates how the cultural cues that Māori referenced in the genetic modification debate continue to be relevant in the context of gene editing but that further work is required to characterize the strength of various positions across the broader community.

year: 2019