title: Investigating bioinformatic pipelines for De novo variant identification in New Zealand dairy cattle

authors: Erika, Duerre

subjects: Bioinformatic pipelines

abstract: New Zealand is the biggest single entity for milk and milk product export in the world and being the country’s main industry, keeping track of bovine mutations allows influence of the national herd’s health and the ability to breed cattle better suited to the current farming and climate needs. With advances in next-generation sequencing of whole genomes, research understanding and tracking germline de novo mutations (DNMs) is attainable. However, current techniques being used to identify and study candidate DNMs are unvetted and experimental. Some of these techniques include bioinformatic software packages such as DenovoCNN, DenovoGear, PedFilter, and RUFUS.
This thesis aimed to investigate and test two of these identification pipelines, DenovoGear and PedFilter using next-generation sequencing data from bovine trios. Output data was generated by writing scripts and extracting data from six trios into Excel workbooks or manual IGV validation of selected candidate DNMs. Of the total 714,393 candidates identified across PedFilter and DenovoGear, only 161 of them were identified by both programs. After Integrative Genomic Viewer validation, 50% of these candidates were deemed to be true positives while only 12% were deemed false positives. Data analysis shows neither technique is 100% accurate and they both should be used with secondary filtering and confirmation of the identified DNM candidates. It was also apparent that the different techniques would be better suited to different study situations. For example, (1) For smaller studies (e.g., 3–15 trios), with limited data available to them, using DenovoGear with a secondary software program for filtering would be best (2) If sufficient samples are available to provide a simulated population data set, PedFilter has higher accuracy than DenovoGear on its own (3) For fast analysis without requiring heavy filtering of the output data use a combination of both PedFilter and DenovoGear. 
Lastly, it is clear that further developments and more testing is required in this area of research before a set standard of practice or guidelines can be recommended and implemented. It is suggested to testing DenovoCNN and Rufus or branching out to other packages to trial like SynthDNM, DNMFilter_INDELs or HAPDeNovo.

text: Investigating bioinformatic pipelines for De novo variant identification in New Zealand dairy cattle New Zealand is the biggest single entity for milk and milk product export in the world and being the country’s main industry, keeping track of bovine mutations allows influence of the national herd’s health and the ability to breed cattle better suited to the current farming and climate needs. With advances in next-generation sequencing of whole genomes, research understanding and tracking germline de novo mutations (DNMs) is attainable. However, current techniques being used to identify and study candidate DNMs are unvetted and experimental. Some of these techniques include bioinformatic software packages such as DenovoCNN, DenovoGear, PedFilter, and RUFUS.
This thesis aimed to investigate and test two of these identification pipelines, DenovoGear and PedFilter using next-generation sequencing data from bovine trios. Output data was generated by writing scripts and extracting data from six trios into Excel workbooks or manual IGV validation of selected candidate DNMs. Of the total 714,393 candidates identified across PedFilter and DenovoGear, only 161 of them were identified by both programs. After Integrative Genomic Viewer validation, 50% of these candidates were deemed to be true positives while only 12% were deemed false positives. Data analysis shows neither technique is 100% accurate and they both should be used with secondary filtering and confirmation of the identified DNM candidates. It was also apparent that the different techniques would be better suited to different study situations. For example, (1) For smaller studies (e.g., 3–15 trios), with limited data available to them, using DenovoGear with a secondary software program for filtering would be best (2) If sufficient samples are available to provide a simulated population data set, PedFilter has higher accuracy than DenovoGear on its own (3) For fast analysis without requiring heavy filtering of the output data use a combination of both PedFilter and DenovoGear. 
Lastly, it is clear that further developments and more testing is required in this area of research before a set standard of practice or guidelines can be recommended and implemented. It is suggested to testing DenovoCNN and Rufus or branching out to other packages to trial like SynthDNM, DNMFilter_INDELs or HAPDeNovo.

year: 2023

title: Assessing dissolved organic carbon export from Kopuatai bog, New Zealand

authors: Sturgeon, Catherine

subjects: peatland

abstract: Peatlands sequester carbon (C) through CO₂ uptake and, ultimately, storage as peat. Carbon is lost from peatlands though gaseous pathways (as CO₂ and CH₄) and water pathways as dissolved organic C (DOC), dissolved inorganic C (DIC), particulate organic C (POC) or dissolved CO₂ and CH₄. Many studies have shown that the loss of C through DOC export is an important component of the annual C budget, but there are very few published studies where atmospheric fluxes of CO₂ and CH₄ and waterborne fluxes of DOC are measured at the same time. Also, little is known about the spatial variations in DOC concentration within peatlands and the processes leading to the delivery of DOC into rivers.
The research described in this thesis focuses on understanding the ways in which vegetation, temperature, peat quality and hydrology interact to determine variability in DOC concentrations and export, both seasonally and spatially, at Kopuatai bog. DOC concentrations were measured at 14 sites across the bog for a year. At each site peat pore water was sampled from three different depths and represented three different vegetation types dominated by Empodisma robustum (jointed wire rush), Leptospermum scoparium (manuka) and Sporadanthus ferrugineus. There were no strong seasonal trends in DOC concentration, possibly due to the small seasonal range in temperatures. DOC concentrations varied spatially, with highest concentrations found under L. scoparium vegetation, likely due to differing chemical properties of plant materials leading to higher decomposition rates. DOC concentration did not vary significantly with depth.
DOC export was estimated using a water balance based approach where evaporation (E), precipitation (P) and change in storage were measured to determine water discharge (Q) from the eddy covariance (EC) footprint. Discharge was then multiplied by average DOC concentrations within the EC footprint to derive DOC export. This method had not been directly applied in the literature. It was estimated that 11.7 ± 0.82 g C m⁻² of DOC was exported from the EC footprint from the year 1 February 2012 to 1 February 2013, which is at the lower end of the range when compared to literature values. DOC export had strong seasonal variation with highest export during the winter due to high rainfall and lowest in summer due to low rainfall. A simple method to estimate DOC export was proposed using the strong correlations between DOC export and monthly P and P–E.
When annual DOC export was compared to annual net ecosystem exchange (NEE) at Kopuatai, DOC export was equivalent to only 6% of CO₂ sequestered in a year. This is in contrast to the literature where, on average, DOC export is often equal to around 25% of NEE. Preliminary analyses shows that NEE values are significantly higher at Kopuatai than NEE published for Northern Hemisphere peatlands and this is likely an effect of the dominance by vascular plants and the year-round growing conditions at Kopuatai.

text: Assessing dissolved organic carbon export from Kopuatai bog, New Zealand Peatlands sequester carbon (C) through CO₂ uptake and, ultimately, storage as peat. Carbon is lost from peatlands though gaseous pathways (as CO₂ and CH₄) and water pathways as dissolved organic C (DOC), dissolved inorganic C (DIC), particulate organic C (POC) or dissolved CO₂ and CH₄. Many studies have shown that the loss of C through DOC export is an important component of the annual C budget, but there are very few published studies where atmospheric fluxes of CO₂ and CH₄ and waterborne fluxes of DOC are measured at the same time. Also, little is known about the spatial variations in DOC concentration within peatlands and the processes leading to the delivery of DOC into rivers.
The research described in this thesis focuses on understanding the ways in which vegetation, temperature, peat quality and hydrology interact to determine variability in DOC concentrations and export, both seasonally and spatially, at Kopuatai bog. DOC concentrations were measured at 14 sites across the bog for a year. At each site peat pore water was sampled from three different depths and represented three different vegetation types dominated by Empodisma robustum (jointed wire rush), Leptospermum scoparium (manuka) and Sporadanthus ferrugineus. There were no strong seasonal trends in DOC concentration, possibly due to the small seasonal range in temperatures. DOC concentrations varied spatially, with highest concentrations found under L. scoparium vegetation, likely due to differing chemical properties of plant materials leading to higher decomposition rates. DOC concentration did not vary significantly with depth.
DOC export was estimated using a water balance based approach where evaporation (E), precipitation (P) and change in storage were measured to determine water discharge (Q) from the eddy covariance (EC) footprint. Discharge was then multiplied by average DOC concentrations within the EC footprint to derive DOC export. This method had not been directly applied in the literature. It was estimated that 11.7 ± 0.82 g C m⁻² of DOC was exported from the EC footprint from the year 1 February 2012 to 1 February 2013, which is at the lower end of the range when compared to literature values. DOC export had strong seasonal variation with highest export during the winter due to high rainfall and lowest in summer due to low rainfall. A simple method to estimate DOC export was proposed using the strong correlations between DOC export and monthly P and P–E.
When annual DOC export was compared to annual net ecosystem exchange (NEE) at Kopuatai, DOC export was equivalent to only 6% of CO₂ sequestered in a year. This is in contrast to the literature where, on average, DOC export is often equal to around 25% of NEE. Preliminary analyses shows that NEE values are significantly higher at Kopuatai than NEE published for Northern Hemisphere peatlands and this is likely an effect of the dominance by vascular plants and the year-round growing conditions at Kopuatai.

year: 2013

title: He huringa āhuarangi, he huringa ao: A changing climate, a changing world

authors: Awatere, S

subjects: climate change adaptation

abstract: Iwi/hapū (tribe/subtribe) governance institutions are increasingly asserting their rangatiratanga (autonomy) to manage climate change risks and meet the well-being of whānau (family)/ hapū/iwi. Howevere, there is a shortange of specific guidance for whānau/hapū/iwi with respect to climate change adaptation and mitigation. We provide a commentary about risk and uncertainty, knowledge gaps, and options for climate change mitigation and adaptation for whānau/hapū/iwi.

text: He huringa āhuarangi, he huringa ao: A changing climate, a changing world Iwi/hapū (tribe/subtribe) governance institutions are increasingly asserting their rangatiratanga (autonomy) to manage climate change risks and meet the well-being of whānau (family)/ hapū/iwi. Howevere, there is a shortange of specific guidance for whānau/hapū/iwi with respect to climate change adaptation and mitigation. We provide a commentary about risk and uncertainty, knowledge gaps, and options for climate change mitigation and adaptation for whānau/hapū/iwi.

year: 2021-10