title: Biotic interactions are an unexpected yet critical control on the complexity of an abiotically driven polar ecosystem.

authors: Lee, Charles Kai-Wu

abstract: Abiotic and biotic factors control ecosystem biodiversity, but their relative contributions remain unclear. The ultraoligotrophic ecosystem of the Antarctic Dry Valleys, a simple yet highly heterogeneous ecosystem, is a natural laboratory well-suited for resolving the abiotic and biotic controls of community structure. We undertook a multidisciplinary investigation to capture ecologically relevant biotic and abiotic attributes of more than 500 sites in the Dry Valleys, encompassing observed landscape heterogeneities across more than 200 km². Using richness of autotrophic and heterotrophic taxa as a proxy for functional complexity, we linked measured variables in a parsimonious yet comprehensive structural equation model that explained significant variations in biological complexity and identified landscape-scale and fine-scale abiotic factors as the primary drivers of diversity. However, the inclusion of linkages among functional groups was essential for constructing the best-fitting model. Our findings support the notion that biotic interactions make crucial contributions even in an extremely simple ecosystem.

text: Biotic interactions are an unexpected yet critical control on the complexity of an abiotically driven polar ecosystem. Abiotic and biotic factors control ecosystem biodiversity, but their relative contributions remain unclear. The ultraoligotrophic ecosystem of the Antarctic Dry Valleys, a simple yet highly heterogeneous ecosystem, is a natural laboratory well-suited for resolving the abiotic and biotic controls of community structure. We undertook a multidisciplinary investigation to capture ecologically relevant biotic and abiotic attributes of more than 500 sites in the Dry Valleys, encompassing observed landscape heterogeneities across more than 200 km². Using richness of autotrophic and heterotrophic taxa as a proxy for functional complexity, we linked measured variables in a parsimonious yet comprehensive structural equation model that explained significant variations in biological complexity and identified landscape-scale and fine-scale abiotic factors as the primary drivers of diversity. However, the inclusion of linkages among functional groups was essential for constructing the best-fitting model. Our findings support the notion that biotic interactions make crucial contributions even in an extremely simple ecosystem.

year: 2019

title: Revisiting deep hybrid models for out-of-distribution detection

authors: Schlumbom, Paul-Ruben

subjects: computer science

abstract: Deep hybrid models (DHMs) for out-of-distribution (OOD) detection, jointly training a deep feature extractor with a classification head and a density estimation head based on a normalising flow, provide a conceptually appealing approach to visual OOD detection. The paper that introduced this approach reported 100% AuROC in experiments on two standard benchmarks, including one based on the CIFAR-10 data. As there are no implementations available, we set out to reproduce the approach by carefully filling in gaps in the description of the algorithm. Although we were unable to attain 100% OOD detection rates, and our results indicate that such performance is impossible on the CIFAR-10 benchmark, we achieved good OOD performance. We provide a detailed analysis of when the architecture fails and argue that it introduces an adversarial relationship between the classification component and the density estimator, rendering it highly sensitive to the balance of these two components and yielding a collapsed feature space without careful fine-tuning. Our implementation of DHMs is publicly available.

text: Revisiting deep hybrid models for out-of-distribution detection Deep hybrid models (DHMs) for out-of-distribution (OOD) detection, jointly training a deep feature extractor with a classification head and a density estimation head based on a normalising flow, provide a conceptually appealing approach to visual OOD detection. The paper that introduced this approach reported 100% AuROC in experiments on two standard benchmarks, including one based on the CIFAR-10 data. As there are no implementations available, we set out to reproduce the approach by carefully filling in gaps in the description of the algorithm. Although we were unable to attain 100% OOD detection rates, and our results indicate that such performance is impossible on the CIFAR-10 benchmark, we achieved good OOD performance. We provide a detailed analysis of when the architecture fails and argue that it introduces an adversarial relationship between the classification component and the density estimator, rendering it highly sensitive to the balance of these two components and yielding a collapsed feature space without careful fine-tuning. Our implementation of DHMs is publicly available.

year: 2025

title: Lake Rotokakahi: The kakahi (Hyridella menziesi) in a general framework of lake health

authors: Butterworth, Joseph

subjects: Rotokakahi

abstract: Lake Rotokakahi is a mesotrophic lake located within the Rotorua Lakes District, North Island, New Zealand. Under the legal guardianship of the Tuhourangi and Ngati Tumatawera tribes of Te Arawa it has remained closed to the public since 1948. 

Lake Rotokakahi was last monitored regularly in 1996 under the Environment Bay of Plenty (EBOP) water quality monitoring programme with only the lake outlet (Te Wairoa Stream) being monitored since that time. Water quality data collected up to 1996 suggests that there may be degradation of water quality in the lake, as indicated by declining levels of dissolved oxygen in the bottom waters.

 Lake Rotokakahi steeped in historical significance, as well as having major cultural and recreational values was well known for its abundant resources and as the name suggests, particularly for its massive supply of the freshwater mussel or kakahi (Hyridella menziesi). Freshwater mussel species worldwide are in decline however little is known on factors controlling kakahi abundance and distribution. 

The overarching objective of this thesis is update water quality data last monitored in Lake Rotokakahi in 1996 while also identifying key environmental variables thought to influence kakahi populations.  This objective is underpinned by a number of aims that include:
 	Establishment of a 12-13 month water quality programme within Lake Rotokakahi so that data is obtained for comparisons with previous water quality data (pre-1997) to allow assessment of whether there have been water quality changes in the lake.
 	Conduct a population survey of the resident kakahi population examining possible environmental factors influencing their populations.
 	Present an oral history of Lake Rotokakahi focusing on its historical significance, water quality, and collection of kairoto (food collected form lakes).

from the 18 September 2006 to 14 September 2007 monthly water sampling was carried out at a mid lake station, the lake outflow and inflow for measures of nutrients, phytoplankton, zooplankton and chlorophyll a. Vertical profiles of temperature dissolved oxygen and chlorophyll fluorescence were also taken on various part of Lake Rotokakahi.

A lengthened period of anoxia in the bottom waters during thermal stratification was recorded with increased levels of chlorophyll a in winter and reduced secchi disk depth indicating an increase in phytoplankton biomass. Nutrient concentrations remain moderate relative to historical data. On going water quality monitoring on Lake Rotokakahi is recommended to further evaluate the extent of which water quality change is occurring. This will provide a better understanding of how Lake Rotokakahi can be best managed to further preserve the lake.

On 1 March and 20 April kakahi were sampled at five sites. Large kakahi densities were distributed predominantly in depths above the hypolimnion. Chlorophyll a fluorescence and dissolved oxygen were found to be the best correlates for kakahi density and biomass respectively. Low dissolved oxygen concentrations in the hypolimnion are thought to restrict kakahi distributions to above the thermocline in periods of hypolimnetic anoxia.

text: Lake Rotokakahi: The kakahi (Hyridella menziesi) in a general framework of lake health Lake Rotokakahi is a mesotrophic lake located within the Rotorua Lakes District, North Island, New Zealand. Under the legal guardianship of the Tuhourangi and Ngati Tumatawera tribes of Te Arawa it has remained closed to the public since 1948. 

Lake Rotokakahi was last monitored regularly in 1996 under the Environment Bay of Plenty (EBOP) water quality monitoring programme with only the lake outlet (Te Wairoa Stream) being monitored since that time. Water quality data collected up to 1996 suggests that there may be degradation of water quality in the lake, as indicated by declining levels of dissolved oxygen in the bottom waters.

 Lake Rotokakahi steeped in historical significance, as well as having major cultural and recreational values was well known for its abundant resources and as the name suggests, particularly for its massive supply of the freshwater mussel or kakahi (Hyridella menziesi). Freshwater mussel species worldwide are in decline however little is known on factors controlling kakahi abundance and distribution. 

The overarching objective of this thesis is update water quality data last monitored in Lake Rotokakahi in 1996 while also identifying key environmental variables thought to influence kakahi populations.  This objective is underpinned by a number of aims that include:
 	Establishment of a 12-13 month water quality programme within Lake Rotokakahi so that data is obtained for comparisons with previous water quality data (pre-1997) to allow assessment of whether there have been water quality changes in the lake.
 	Conduct a population survey of the resident kakahi population examining possible environmental factors influencing their populations.
 	Present an oral history of Lake Rotokakahi focusing on its historical significance, water quality, and collection of kairoto (food collected form lakes).

from the 18 September 2006 to 14 September 2007 monthly water sampling was carried out at a mid lake station, the lake outflow and inflow for measures of nutrients, phytoplankton, zooplankton and chlorophyll a. Vertical profiles of temperature dissolved oxygen and chlorophyll fluorescence were also taken on various part of Lake Rotokakahi.

A lengthened period of anoxia in the bottom waters during thermal stratification was recorded with increased levels of chlorophyll a in winter and reduced secchi disk depth indicating an increase in phytoplankton biomass. Nutrient concentrations remain moderate relative to historical data. On going water quality monitoring on Lake Rotokakahi is recommended to further evaluate the extent of which water quality change is occurring. This will provide a better understanding of how Lake Rotokakahi can be best managed to further preserve the lake.

On 1 March and 20 April kakahi were sampled at five sites. Large kakahi densities were distributed predominantly in depths above the hypolimnion. Chlorophyll a fluorescence and dissolved oxygen were found to be the best correlates for kakahi density and biomass respectively. Low dissolved oxygen concentrations in the hypolimnion are thought to restrict kakahi distributions to above the thermocline in periods of hypolimnetic anoxia.

year: 2008