title: Assessing the Diversity of Antarctic and New Zealand Arthropods through DNA Barcoding

authors: Beet, Clare Rose

subjects: DNA Barcoding

abstract: Diversity is the foundation of all biological and ecological studies. Globally however, biodiversity is under threat from the varied and cumulative impacts of humans on the environment. It is thus necessary to continually develop tools that are able to assess diversity at the scales now required. DNA barcoding has become an increasingly common approach for species identification as it is efficient and can facilitate high throughput analyses without the routine need of taxonomic experts. This thesis examines the genetic diversity of invertebrate groups from Antarctica and New Zealand to gain an understanding of current baseline levels of variability and to facilitate their use as indicators of environmental change.
The juvenile stages of Ephemeroptera (mayflies), Plecoptera (stoneflies) and Trichoptera (caddisflies) (EPT taxa) are key components of aquatic food webs and are frequently used as bioindicators of water quality. However, challenges in identifying juveniles to species levels are one factor limiting their more routine use. New Zealand has over 244 caddisfly species 106 species of stonefly and 50 mayfly species all of which are endemic. Here, my primary aim was to obtain COI sequence coverage for the New Zealand EPT taxa using expertly identified collections of adult specimens. A second aim was to examine levels of sequence diversity within taxa and to test the endemicity of the New Zealand fauna through comparison with international records. Thus far, 225 caddisfly BINs, 48 stonefly and 37 mayfly BINs have been generated. Average intraspecific divergences were between 1.2-1.4% for all three orders while average interspecific distances ranged from 24-32%. The designation of all New Zealand EPT species as endemic was supported with interspecific divergences generally above 13%. These data can facilitate the rapid and accurate assessment of larval specimens and can furthermore be used to facilitate research into the phylogenetic and phylogeographic patterns that have shaped the EPT fauna worldwide.
I also examined mitochondrial DNA (COI) sequences for three Antarctic springtail (Collembola) species collected from sites in the vicinity, and to the north of, the Mackay Glacier (77oS) within the Ross Sea region. This area represents a transitional zone between two biogeographic regions (North and South Victoria Land). Here, I assessed levels of genetic variability within and among populations of the three putative springtail species. Each of the three recognised species had multiple highly divergent intraspecific populations (5-11.3% sequence divergence). Based on molecular clock estimates, these divergent lineages were likely to have been isolated for 3-5 million years, a time when the Western Antarctic Ice Sheet (WAIS) was thought to have completely collapsed. Given the current isolation of these genetically distinct populations, any future changes in species’ distributions can be easily tracked through the DNA barcoding of individual springtails across the Mackay Glacier ecotone. 
Collectively these two studies have established baseline levels of COI diversity for New Zealand and Antarctic invertebrates. Furthermore, they have revealed hidden (cryptic) diversity in both regions and presented opportunities to incorporate DNA barcoding into future studies of New Zealand aquatic and terrestrial Antarctic ecosystems.

text: Assessing the Diversity of Antarctic and New Zealand Arthropods through DNA Barcoding Diversity is the foundation of all biological and ecological studies. Globally however, biodiversity is under threat from the varied and cumulative impacts of humans on the environment. It is thus necessary to continually develop tools that are able to assess diversity at the scales now required. DNA barcoding has become an increasingly common approach for species identification as it is efficient and can facilitate high throughput analyses without the routine need of taxonomic experts. This thesis examines the genetic diversity of invertebrate groups from Antarctica and New Zealand to gain an understanding of current baseline levels of variability and to facilitate their use as indicators of environmental change.
The juvenile stages of Ephemeroptera (mayflies), Plecoptera (stoneflies) and Trichoptera (caddisflies) (EPT taxa) are key components of aquatic food webs and are frequently used as bioindicators of water quality. However, challenges in identifying juveniles to species levels are one factor limiting their more routine use. New Zealand has over 244 caddisfly species 106 species of stonefly and 50 mayfly species all of which are endemic. Here, my primary aim was to obtain COI sequence coverage for the New Zealand EPT taxa using expertly identified collections of adult specimens. A second aim was to examine levels of sequence diversity within taxa and to test the endemicity of the New Zealand fauna through comparison with international records. Thus far, 225 caddisfly BINs, 48 stonefly and 37 mayfly BINs have been generated. Average intraspecific divergences were between 1.2-1.4% for all three orders while average interspecific distances ranged from 24-32%. The designation of all New Zealand EPT species as endemic was supported with interspecific divergences generally above 13%. These data can facilitate the rapid and accurate assessment of larval specimens and can furthermore be used to facilitate research into the phylogenetic and phylogeographic patterns that have shaped the EPT fauna worldwide.
I also examined mitochondrial DNA (COI) sequences for three Antarctic springtail (Collembola) species collected from sites in the vicinity, and to the north of, the Mackay Glacier (77oS) within the Ross Sea region. This area represents a transitional zone between two biogeographic regions (North and South Victoria Land). Here, I assessed levels of genetic variability within and among populations of the three putative springtail species. Each of the three recognised species had multiple highly divergent intraspecific populations (5-11.3% sequence divergence). Based on molecular clock estimates, these divergent lineages were likely to have been isolated for 3-5 million years, a time when the Western Antarctic Ice Sheet (WAIS) was thought to have completely collapsed. Given the current isolation of these genetically distinct populations, any future changes in species’ distributions can be easily tracked through the DNA barcoding of individual springtails across the Mackay Glacier ecotone. 
Collectively these two studies have established baseline levels of COI diversity for New Zealand and Antarctic invertebrates. Furthermore, they have revealed hidden (cryptic) diversity in both regions and presented opportunities to incorporate DNA barcoding into future studies of New Zealand aquatic and terrestrial Antarctic ecosystems.

year: 2016

title: Nearshore sediment dynamics in a mixed sand/mud environment

authors: Beamsley, Brett James

abstract: Poverty Bay, on the New Zealand's northeast coastline, is a high-energy coastal embayment that receives significant quantities of fine, fluvial sediment from two river systems. Examining seabed geomechanical characteristics, sediment fluxes and morphological features in northern Poverty Bay provided the opportunity to study interactive processes, including sediment entrainment rates over the cohesively bound mixed sand/mud seabeds, and the dispersion of a turbid river plume. Three field experiments and an extensive seabed-sampling programme were undertaken, and a 2-cell numerical model was developed and validated against infilling rates of the port of Gisborne navigation channel. The implications for existing and future operations at the port of Gisborne, including the suitability of capital and maintenance dredged material for use in reclamation, have been evaluated. 

Within the study site, near-bed wave orbital velocities and fluvial inputs control the spatial variability in the seabed sediment textural characteristics, with the seabed grain size decreasing with depth and distance from the mouth of the Turanganui River. A hand-held shear vane was used to quantify the in-situ shear strength of the cohesively bonded mud/sand surficial sediment, and the in-situ shear strength has been correlated (R² = 0.83) with the cumulative effect of several of the sediment textural and environmental parameters. 

Near-bed sediment diffusion and entrainment was examined using an array of micro-scale inline pumps. The effect that cohesive bonding of the mixed sand/mud seabed has on retarding the entrainment rate was examined by considering both the textural and geomechanical characteristics of the seabed. No correlation was found between the ratios of estimated to predicted near bed reference concentration (ζ) and either the median grain size (d₅₀) or the ratio of percent sand to mud of the seabed. However, a good correlation was found between ζ and the normalised in-situ shear strength (𝑥) of the seabed (adjusted R² = 0.99), with the relationship of the form, 

𝑙n(ζ) = -0.51-1.30 𝑥³ 

The conversion of the downward flux from sediment traps to a time-averaged suspended sediment concentration (SSC), and near bed reference concentration (C₀) was found to be critically dependant on the fall velocity statistic (w∫) of the grain size distribution. Due to flocculation of the near-bed suspended sediment, the dispersed equivalent w∫ distribution and median w∫ of the distribution resulted in poor predictions of C₀. Instead, an in-situ ‘effective’ w∫ distribution of the suspended sediment was developed using the measured 𝑙ₛ from individual dispersed grain size bins within the SSC profile and the predicted sediment diffusivity (εₛ). C₀ predicted using the effective w∫ distribution agreed with pumped samples and theory predicted C₀, and provided a robust method of determining the time-averaged SSC of mixed sand/mud sediment using sediment traps. 

The diffusion of sediment within the near-bed SSC profile varied as a function of w∫, with relatively finer sediment exhibiting less diffusion. The mixing length (𝑙ₛ) profile was well approximated by a linear profile, with 𝑙ₛ varying as a function of elevation (z) and the von Karman constant (κ), i.e. 𝑙ₛ = κ𝚣. Within 4-8 cm of the bed 𝑙ₛ is constant and equal to 0.06 m.

β is defined as the ratio of sediment diffusivity (εₛ) to eddy viscosity (ε∫), and is commonly used as a correction factor for predictive SSC profile equations. By examining the diffusion of sediment within the near-bed SSC profile a new equation for β was obtained,

 	𝑙n( β ) = -0. 95 - 0.4ψ / 𝑙n(ψ) 

The horizontal diffusion of sediment within the Turanganui River plume was found to be a function of the distance (x) from the mouth of the Turanganui River and a decay rate factor (Dₓ), where

 	Cₓ = Cₒbe ⁽⁻ ͯ/ᴰͯ ⁾

The form of the equation is similar to the Nielsen time-averaged gradient diffusion equation. Dₓ was correlated (R² = 0.92) with river discharge (φᵣᵢᵥₑᵣ), and found to exponentially decrease with increasing φᵣᵢᵥₑᵣ, where 

	Dₓ = 591+2850 exp(⁻ᵠʳⁱᵛᵉʳ/2.1)

The relationship suggests that the effective w∫ of the suspended sediment within the plume increases with increasing SSC, presumably due to increased flocculated particle size. Based on the developed empirical formulae the Turanganui River is predicted to discharge 7.6x10⁷ kg of fluvial derived sediment into Poverty Bay on an annual basis. 

The developed relationships and formulae that describe the hydrodynamical processes within northern Poverty Bay have been implemented in a 2-cell numerical model that considers both downward and horizontal sediment fluxes. The port of Gisborne shipping channel infilling rate, as determined from hydrographic surveys and dredging records, was used to validate the model. The 2-cell numerical model accurately predicts channel infilling rates, and provides an insight into the governing hydrodynamical processes in northern Poverty Bay. The developed model represents an alternative to the implementation of a full 3-dimensional hydrodynamic model. 

Hydrographic surveys and dredging records show the channel area passes through the beach nearshore zone, and during the monitoring period maintenance dredging only maintained the channel design depth along the channel leads, while significant infilling occurred near the channel edges (Δh = -1 m). Extrapolation of the results suggests an annual channel infilling rate of 171,400 m³ per year, corresponding to a maintenance dredging cost of approximately $857,000 to $1,200,000 per annum. Wave and river discharge conditions during the monitoring period were smaller than average, and more infilling is expected during stormy years. 

Relocating the channel and port entrance to a site in deeper water, further from the mouth of the Turanganui River, with relatively strong seabed in-situ shear strength is identified as a means of reducing dredging costs. The material dredged from the shipping channel is suitable for use in land-based reclamation, particularly if the soil structure is improved by addition of a coarser material such as of the underlying mudstone unit. The bearing capacity of the reclamation can be improved by mixing the mud/sand with concrete to create mudcrete.

text: Nearshore sediment dynamics in a mixed sand/mud environment Poverty Bay, on the New Zealand's northeast coastline, is a high-energy coastal embayment that receives significant quantities of fine, fluvial sediment from two river systems. Examining seabed geomechanical characteristics, sediment fluxes and morphological features in northern Poverty Bay provided the opportunity to study interactive processes, including sediment entrainment rates over the cohesively bound mixed sand/mud seabeds, and the dispersion of a turbid river plume. Three field experiments and an extensive seabed-sampling programme were undertaken, and a 2-cell numerical model was developed and validated against infilling rates of the port of Gisborne navigation channel. The implications for existing and future operations at the port of Gisborne, including the suitability of capital and maintenance dredged material for use in reclamation, have been evaluated. 

Within the study site, near-bed wave orbital velocities and fluvial inputs control the spatial variability in the seabed sediment textural characteristics, with the seabed grain size decreasing with depth and distance from the mouth of the Turanganui River. A hand-held shear vane was used to quantify the in-situ shear strength of the cohesively bonded mud/sand surficial sediment, and the in-situ shear strength has been correlated (R² = 0.83) with the cumulative effect of several of the sediment textural and environmental parameters. 

Near-bed sediment diffusion and entrainment was examined using an array of micro-scale inline pumps. The effect that cohesive bonding of the mixed sand/mud seabed has on retarding the entrainment rate was examined by considering both the textural and geomechanical characteristics of the seabed. No correlation was found between the ratios of estimated to predicted near bed reference concentration (ζ) and either the median grain size (d₅₀) or the ratio of percent sand to mud of the seabed. However, a good correlation was found between ζ and the normalised in-situ shear strength (𝑥) of the seabed (adjusted R² = 0.99), with the relationship of the form, 

𝑙n(ζ) = -0.51-1.30 𝑥³ 

The conversion of the downward flux from sediment traps to a time-averaged suspended sediment concentration (SSC), and near bed reference concentration (C₀) was found to be critically dependant on the fall velocity statistic (w∫) of the grain size distribution. Due to flocculation of the near-bed suspended sediment, the dispersed equivalent w∫ distribution and median w∫ of the distribution resulted in poor predictions of C₀. Instead, an in-situ ‘effective’ w∫ distribution of the suspended sediment was developed using the measured 𝑙ₛ from individual dispersed grain size bins within the SSC profile and the predicted sediment diffusivity (εₛ). C₀ predicted using the effective w∫ distribution agreed with pumped samples and theory predicted C₀, and provided a robust method of determining the time-averaged SSC of mixed sand/mud sediment using sediment traps. 

The diffusion of sediment within the near-bed SSC profile varied as a function of w∫, with relatively finer sediment exhibiting less diffusion. The mixing length (𝑙ₛ) profile was well approximated by a linear profile, with 𝑙ₛ varying as a function of elevation (z) and the von Karman constant (κ), i.e. 𝑙ₛ = κ𝚣. Within 4-8 cm of the bed 𝑙ₛ is constant and equal to 0.06 m.

β is defined as the ratio of sediment diffusivity (εₛ) to eddy viscosity (ε∫), and is commonly used as a correction factor for predictive SSC profile equations. By examining the diffusion of sediment within the near-bed SSC profile a new equation for β was obtained,

 	𝑙n( β ) = -0. 95 - 0.4ψ / 𝑙n(ψ) 

The horizontal diffusion of sediment within the Turanganui River plume was found to be a function of the distance (x) from the mouth of the Turanganui River and a decay rate factor (Dₓ), where

 	Cₓ = Cₒbe ⁽⁻ ͯ/ᴰͯ ⁾

The form of the equation is similar to the Nielsen time-averaged gradient diffusion equation. Dₓ was correlated (R² = 0.92) with river discharge (φᵣᵢᵥₑᵣ), and found to exponentially decrease with increasing φᵣᵢᵥₑᵣ, where 

	Dₓ = 591+2850 exp(⁻ᵠʳⁱᵛᵉʳ/2.1)

The relationship suggests that the effective w∫ of the suspended sediment within the plume increases with increasing SSC, presumably due to increased flocculated particle size. Based on the developed empirical formulae the Turanganui River is predicted to discharge 7.6x10⁷ kg of fluvial derived sediment into Poverty Bay on an annual basis. 

The developed relationships and formulae that describe the hydrodynamical processes within northern Poverty Bay have been implemented in a 2-cell numerical model that considers both downward and horizontal sediment fluxes. The port of Gisborne shipping channel infilling rate, as determined from hydrographic surveys and dredging records, was used to validate the model. The 2-cell numerical model accurately predicts channel infilling rates, and provides an insight into the governing hydrodynamical processes in northern Poverty Bay. The developed model represents an alternative to the implementation of a full 3-dimensional hydrodynamic model. 

Hydrographic surveys and dredging records show the channel area passes through the beach nearshore zone, and during the monitoring period maintenance dredging only maintained the channel design depth along the channel leads, while significant infilling occurred near the channel edges (Δh = -1 m). Extrapolation of the results suggests an annual channel infilling rate of 171,400 m³ per year, corresponding to a maintenance dredging cost of approximately $857,000 to $1,200,000 per annum. Wave and river discharge conditions during the monitoring period were smaller than average, and more infilling is expected during stormy years. 

Relocating the channel and port entrance to a site in deeper water, further from the mouth of the Turanganui River, with relatively strong seabed in-situ shear strength is identified as a means of reducing dredging costs. The material dredged from the shipping channel is suitable for use in land-based reclamation, particularly if the soil structure is improved by addition of a coarser material such as of the underlying mudstone unit. The bearing capacity of the reclamation can be improved by mixing the mud/sand with concrete to create mudcrete.

year: 2003

title: Māori leaders wellbeing: A self-determination perspective

authors: Roche, Maree A.

subjects: Positive psychology

abstract: This research draws on interviews with 18 Māori leaders from various leadership positions within business, community, political and marae organisations, to garner an understanding of how their leadership roles interact with their own well-being. Analysis of interviews revealed that crosscultural developments in self-determination theory could be gained by incorporating Māori tikanga and values into a model of well-being for Māori leaders. Largely, the principles of tino rangatiratanga (autonomy and self-determination), mana (respect and influence), whānau (extended family), whakapapa (shared history) and whanaungatanga (kin relations, consultation and engagement), were united into a model of leader well-being. This ensured that mātauranga Māori (Māori knowledge) informed our model of Māori leader well-being, while also drawing on the burgeoning Western research in the area of well-being, specifically self-determination theory. Overall, we find that similarities exist with self-determination theory and Māori tikanga and values. However, in contrast to self-determination theory, autonomy and competence are developed within relationships, which means that ‘others’ underpin Māori leaders’ well-being. From this perspective, we present a view of the psychological and well-being resources that Māori leaders draw on to guide them through complex times.

text: Māori leaders wellbeing: A self-determination perspective This research draws on interviews with 18 Māori leaders from various leadership positions within business, community, political and marae organisations, to garner an understanding of how their leadership roles interact with their own well-being. Analysis of interviews revealed that crosscultural developments in self-determination theory could be gained by incorporating Māori tikanga and values into a model of well-being for Māori leaders. Largely, the principles of tino rangatiratanga (autonomy and self-determination), mana (respect and influence), whānau (extended family), whakapapa (shared history) and whanaungatanga (kin relations, consultation and engagement), were united into a model of leader well-being. This ensured that mātauranga Māori (Māori knowledge) informed our model of Māori leader well-being, while also drawing on the burgeoning Western research in the area of well-being, specifically self-determination theory. Overall, we find that similarities exist with self-determination theory and Māori tikanga and values. However, in contrast to self-determination theory, autonomy and competence are developed within relationships, which means that ‘others’ underpin Māori leaders’ well-being. From this perspective, we present a view of the psychological and well-being resources that Māori leaders draw on to guide them through complex times.

year: 2015