title: An analysis of U-Value as a measure of variability

authors: Kong, Xiuyuan

subjects: Behavioral variability

abstract: The variability in behavior has frequently been assessed using a measure known as the U-value. Of concern in this article were the limits and constraints on U-value as a measure of variability. The relation between the U-value and aspects of variability was examined using three sets of simulated data. Our analysis demonstrates that the U-value as a measure of variability on its own fails to capture repetitive patterns in the sequence of responding. The U-value was shown to reflect the evenness of the distributions of responses across the categories/options used; however, when the number of categories actually used by the participant differed from the total number available, the relation between U-values and the number of categories allocated with responses was shown to be nonlinear. It was also shown that the same value of U can represent different levels of evenness in response distributions over categories, depending on the number of categories/options actually used. These constraints and limitations are discussed in relation to how researchers might report on behavioral variability.

text: An analysis of U-Value as a measure of variability The variability in behavior has frequently been assessed using a measure known as the U-value. Of concern in this article were the limits and constraints on U-value as a measure of variability. The relation between the U-value and aspects of variability was examined using three sets of simulated data. Our analysis demonstrates that the U-value as a measure of variability on its own fails to capture repetitive patterns in the sequence of responding. The U-value was shown to reflect the evenness of the distributions of responses across the categories/options used; however, when the number of categories actually used by the participant differed from the total number available, the relation between U-values and the number of categories allocated with responses was shown to be nonlinear. It was also shown that the same value of U can represent different levels of evenness in response distributions over categories, depending on the number of categories/options actually used. These constraints and limitations are discussed in relation to how researchers might report on behavioral variability.

year: 2017

title: Fungal biodiversity in extreme environments and wood degradation potential

authors: Jurgens, Joel Allan

subjects: fungi

abstract: This doctoral thesis reports results from a multidisciplinary investigation of fungi from extreme locations, focusing on one of the driest and thermally broad regions of the world, the Taklimakan Desert, with comparisons to polar region deserts. Additionally, the capability of select fungal isolates to decay lignocellulosic substrates and produce degradative related enzymes at various temperatures was demonstrated.  

The Taklimakan Desert is located in the western portion of the People's Republic of China, a region of extremes dominated by both limited precipitation, less than 25 mm of rain annually and tremendous temperature variation. The organisms that inhabit this region are required to function in conditions that preclude most forms of life. Fungi are particularly interesting organisms for consideration of life in extreme environments since they absorb nutrients from their surroundings with diffusion taking place through the cell wall and plasma membrane requiring free water.  The regions near the poles are another example of areas with extreme environmental conditions, with the north and south polar regions having similarities and differences to each other and to the Taklimakan Desert. All three regions experiences extreme cold but only the Taklimakan Desert has exceedingly warm temperatures. The Taklimakan Desert is diurnal and the polar regions have long periods of light and dark in summer and winter months, respectively. The annual precipitation in the specific polar sites is between 100-200 mm, 5-20 fold more than the Taklimakan Desert.

From soil, rock and wood collected in the Taklimakan Desert, 194 independent fungal isolates were generated and identified based on extracted DNA and analysis of the internal transcribed spacer (ITS) region of the rDNA. Dominant taxa were from closely related Thielavia, Embellisia and Alternaria genera. Total DNA extracted directly from environmental samples and subjected to molecular fingerprinting identified 51 consensus sequences almost entirely of taxa not represented by culturing, with the dominant taxa in the Penicillium and Colletotrichum genera.  
 
The sequence data from the Taklimakan Desert cultured fungi were phylogenetically investigated by means of neighbor-joining analysis and compared to fungal sequences derived from various substrates collected at sites in Antarctica and the Arctic with wood as the common substrate from which isolates were obtained among all three locations. Based on comparisons of consensus sequences to the polar fungi and fungal databases, 72 isolates appear to represent novel taxa that may be endemic to the Taklimakan Desert and warrant further investigation. 

Selected fungal isolates from the Taklimakan Desert, Arctic and Antarctic research were investigated to determine and compare their ability to degrade two types of lignocellulose substrates, Pinus resinosa and Populus tremuloides, the latter being a genera of tree identified in some locations of the Taklimakan Desert and the former as a model softwood example. Fungi from all regions were able to degrade these substrates to varying degrees though minimal weight loss was common. These isolates did not produce cellulase or lignin peroxidase concurrent to the temperatures prevalent in the regions from which they were collected, posing interesting possibilities for their wood degradation pathways.

text: Fungal biodiversity in extreme environments and wood degradation potential This doctoral thesis reports results from a multidisciplinary investigation of fungi from extreme locations, focusing on one of the driest and thermally broad regions of the world, the Taklimakan Desert, with comparisons to polar region deserts. Additionally, the capability of select fungal isolates to decay lignocellulosic substrates and produce degradative related enzymes at various temperatures was demonstrated.  

The Taklimakan Desert is located in the western portion of the People's Republic of China, a region of extremes dominated by both limited precipitation, less than 25 mm of rain annually and tremendous temperature variation. The organisms that inhabit this region are required to function in conditions that preclude most forms of life. Fungi are particularly interesting organisms for consideration of life in extreme environments since they absorb nutrients from their surroundings with diffusion taking place through the cell wall and plasma membrane requiring free water.  The regions near the poles are another example of areas with extreme environmental conditions, with the north and south polar regions having similarities and differences to each other and to the Taklimakan Desert. All three regions experiences extreme cold but only the Taklimakan Desert has exceedingly warm temperatures. The Taklimakan Desert is diurnal and the polar regions have long periods of light and dark in summer and winter months, respectively. The annual precipitation in the specific polar sites is between 100-200 mm, 5-20 fold more than the Taklimakan Desert.

From soil, rock and wood collected in the Taklimakan Desert, 194 independent fungal isolates were generated and identified based on extracted DNA and analysis of the internal transcribed spacer (ITS) region of the rDNA. Dominant taxa were from closely related Thielavia, Embellisia and Alternaria genera. Total DNA extracted directly from environmental samples and subjected to molecular fingerprinting identified 51 consensus sequences almost entirely of taxa not represented by culturing, with the dominant taxa in the Penicillium and Colletotrichum genera.  
 
The sequence data from the Taklimakan Desert cultured fungi were phylogenetically investigated by means of neighbor-joining analysis and compared to fungal sequences derived from various substrates collected at sites in Antarctica and the Arctic with wood as the common substrate from which isolates were obtained among all three locations. Based on comparisons of consensus sequences to the polar fungi and fungal databases, 72 isolates appear to represent novel taxa that may be endemic to the Taklimakan Desert and warrant further investigation. 

Selected fungal isolates from the Taklimakan Desert, Arctic and Antarctic research were investigated to determine and compare their ability to degrade two types of lignocellulose substrates, Pinus resinosa and Populus tremuloides, the latter being a genera of tree identified in some locations of the Taklimakan Desert and the former as a model softwood example. Fungi from all regions were able to degrade these substrates to varying degrees though minimal weight loss was common. These isolates did not produce cellulase or lignin peroxidase concurrent to the temperatures prevalent in the regions from which they were collected, posing interesting possibilities for their wood degradation pathways.

year: 2010

title: Quantifying relationships between kōura  (Paranephrops planifrons) abundance and micro-habitat features in Waikato hill-country streams

authors: Parata, Riki Neihana

subjects: kōura

abstract: Kōura (Paranephrops planifrons) is considered a taonga species by Māori and was once an abundant traditional fishery harvested throughout New Zealand. Kōura populations are under pressure in Waikato hill-country streams due to a range of factors including habitat loss and water quality degradation. Now that stakeholders have been engaging in collaborative decision-making and practices to restore/enhance biodiversity and ecosystem health within the Waikato catchment, there is opportunity to implement measures specifically targeted at kōura. Information on kōura habitat requirements to assist with the development of habitat enhancement work is therefore timely.
This research comprised two discrete studies which, in combination, provide important insights into daytime habitat use by kōura in Waikato hill-country streams. The first study was a field survey that examined in-stream habitat characteristics affecting kōura density and size, with a focus on juveniles ≤ 8 mm orbital carapace length (OCL), across a range of scales ranging from habitat patches to streams with contrasting catchment and riparian vegetation treatments – pasture, early or late riparian planting, and native forest. Micro-habitat variables related to kōura density included water depth and velocity, substrate size, and the area of bank undercuts and organic cover types, with root mat area significantly and positively related to juvenile densities across all scales. Although there was no significant effect of treatment type, there were strong associations between kōura and ponga logs, root systems, and coarse particulate organic matter (CPOM) across scales within and between streams.
The second study was a habitat manipulation experiment conducted to investigate whether kōura abundances, in particular juveniles, could be enhanced by additions of organic habitat consisting of 0.5 m² coconut fibre matting to simulate ponga (Cyathea dealbata) root systems that occur on the stream bank, and 1 m² ponga frond bundles to simulate the natural habitat structures formed in native forested areas. These two artificial habitats were compared with natural in-stream cobble habitats. Kōura and toi toi (Gobiomorphus spp.), both showed a preference for ponga frond habitats which were predicted to provide submerged habitat for more than 200 days. Although the coconut fibre matting was predicted to outlast ponga frond bundles by up to 107 days, it was more susceptible to sedimentation and did not provide adequate habitat for kōura due to its dense structure.
This study highlighted the influence of riparian treatments, hydrological processes, and inorganic and organic habitats on kōura populations. Information from this study can provide restoration managers with guidance on how to enhance in-stream and stream edge habitat suitability for kōura and can be used with existing mātauranga Māori, and western and community science, to determine suitable vegetation for riparian planting, assess what factors and drivers contribute to in-stream habitat availability and sustainability, and identify important habitat features that relate to kōura when conducting habitat restoration.

text: Quantifying relationships between kōura  (Paranephrops planifrons) abundance and micro-habitat features in Waikato hill-country streams Kōura (Paranephrops planifrons) is considered a taonga species by Māori and was once an abundant traditional fishery harvested throughout New Zealand. Kōura populations are under pressure in Waikato hill-country streams due to a range of factors including habitat loss and water quality degradation. Now that stakeholders have been engaging in collaborative decision-making and practices to restore/enhance biodiversity and ecosystem health within the Waikato catchment, there is opportunity to implement measures specifically targeted at kōura. Information on kōura habitat requirements to assist with the development of habitat enhancement work is therefore timely.
This research comprised two discrete studies which, in combination, provide important insights into daytime habitat use by kōura in Waikato hill-country streams. The first study was a field survey that examined in-stream habitat characteristics affecting kōura density and size, with a focus on juveniles ≤ 8 mm orbital carapace length (OCL), across a range of scales ranging from habitat patches to streams with contrasting catchment and riparian vegetation treatments – pasture, early or late riparian planting, and native forest. Micro-habitat variables related to kōura density included water depth and velocity, substrate size, and the area of bank undercuts and organic cover types, with root mat area significantly and positively related to juvenile densities across all scales. Although there was no significant effect of treatment type, there were strong associations between kōura and ponga logs, root systems, and coarse particulate organic matter (CPOM) across scales within and between streams.
The second study was a habitat manipulation experiment conducted to investigate whether kōura abundances, in particular juveniles, could be enhanced by additions of organic habitat consisting of 0.5 m² coconut fibre matting to simulate ponga (Cyathea dealbata) root systems that occur on the stream bank, and 1 m² ponga frond bundles to simulate the natural habitat structures formed in native forested areas. These two artificial habitats were compared with natural in-stream cobble habitats. Kōura and toi toi (Gobiomorphus spp.), both showed a preference for ponga frond habitats which were predicted to provide submerged habitat for more than 200 days. Although the coconut fibre matting was predicted to outlast ponga frond bundles by up to 107 days, it was more susceptible to sedimentation and did not provide adequate habitat for kōura due to its dense structure.
This study highlighted the influence of riparian treatments, hydrological processes, and inorganic and organic habitats on kōura populations. Information from this study can provide restoration managers with guidance on how to enhance in-stream and stream edge habitat suitability for kōura and can be used with existing mātauranga Māori, and western and community science, to determine suitable vegetation for riparian planting, assess what factors and drivers contribute to in-stream habitat availability and sustainability, and identify important habitat features that relate to kōura when conducting habitat restoration.

year: 2019