title: Genetic diversity and potential responses of New Zealand Rotifera and Antarctic Collembola to environmental changes

authors: Collins, Gemma Elyse

subjects: Mitochondrial DNA

abstract: Environmental changes can impact the diversity and abundance of biotic communities as well as their dispersal among geographic regions. The availability of sensitive molecular techniques has enabled assessments of diversity at levels previously unattainable and allowed investigation of how biota are influenced by their environment. This thesis examines the use of mitochondrial DNA sequence variation in New Zealand freshwater rotifers (Rotifera) and Antarctic springtails (Collembola) to assess diversity and determine responses to environmental changes.
 
Using mitochondrial cytochrome c oxidase subunit I (COI) DNA sequences, I examined the diversity of New Zealand rotifers. The rotifer phylum is comprised of a variety of species and individuals are often abundant in freshwater systems globally. Species are associated with specific trophic states and in New Zealand are routinely monitored as biological indicators of ecosystem health. At present, species’ identification relies on morphological characters which is time consuming and requires appropriate taxonomic expertise. Here, I assessed the use of COI sequences as an alternative for the routine identification of New Zealand rotifers. A total of 177 individuals were sequenced from 45 morphologically-recognised taxa. High intraspecific variation was found among 14 species (3.4 - 39.0% divergence) and based on comparisons with sequences available on GenBank, 18 species were genetically distinct from their global conspecifics (>6.6% divergence). I conclude that these distinct haplotypes are potentially endemic among putatively cosmopolitan species. A better understanding of rotifer diversity in New Zealand will allow the detection and potential control of future non-indigenous species’ incursions. 

In order to assess the effects of environmental temperature changes on the genetic structure of populations, I examined the diversity of COI sequences of Antarctic springtails relative to the environmental conditions during which they were active. The target species, Gomphiocephalus hodgsoni, is known to harbour high genetic (COI) diversity as well as having considerable variation in their ability to tolerate sub-zero temperature – specifically, there appear to be “warm” and “cold” adapted individuals. I sequenced 151 individuals collected in pitfall traps near Spaulding Pond, Taylor Valley and found 19 unique COI haplotypes that separated into two distinct groups (1.6% divergence), with one haplotype group comprising 80% of the sequenced population. During two-hourly sampling, air temperature was the strongest predictor of activity between the two haplotype groups (R2 = 0.56) and when combined with subsurface soil temperature, relative humidity and photosynthetically active radiation, explanatory power increased to R2 = 0.71. Air temperatures are predicted to continue increasing across most of Antarctica which is expected to impact springtails by a detectable amount. Monitoring programmes focussed on the temporal and spatial changes in COI haplotype diversity may provide a sensitive measure of population responses to climate change. 

Collectively, these two studies contribute baseline data of the current genetic diversity and population structure among New Zealand rotifers and Antarctic springtails and provide a platform by which to monitor future environmental changes.

text: Genetic diversity and potential responses of New Zealand Rotifera and Antarctic Collembola to environmental changes Environmental changes can impact the diversity and abundance of biotic communities as well as their dispersal among geographic regions. The availability of sensitive molecular techniques has enabled assessments of diversity at levels previously unattainable and allowed investigation of how biota are influenced by their environment. This thesis examines the use of mitochondrial DNA sequence variation in New Zealand freshwater rotifers (Rotifera) and Antarctic springtails (Collembola) to assess diversity and determine responses to environmental changes.
 
Using mitochondrial cytochrome c oxidase subunit I (COI) DNA sequences, I examined the diversity of New Zealand rotifers. The rotifer phylum is comprised of a variety of species and individuals are often abundant in freshwater systems globally. Species are associated with specific trophic states and in New Zealand are routinely monitored as biological indicators of ecosystem health. At present, species’ identification relies on morphological characters which is time consuming and requires appropriate taxonomic expertise. Here, I assessed the use of COI sequences as an alternative for the routine identification of New Zealand rotifers. A total of 177 individuals were sequenced from 45 morphologically-recognised taxa. High intraspecific variation was found among 14 species (3.4 - 39.0% divergence) and based on comparisons with sequences available on GenBank, 18 species were genetically distinct from their global conspecifics (>6.6% divergence). I conclude that these distinct haplotypes are potentially endemic among putatively cosmopolitan species. A better understanding of rotifer diversity in New Zealand will allow the detection and potential control of future non-indigenous species’ incursions. 

In order to assess the effects of environmental temperature changes on the genetic structure of populations, I examined the diversity of COI sequences of Antarctic springtails relative to the environmental conditions during which they were active. The target species, Gomphiocephalus hodgsoni, is known to harbour high genetic (COI) diversity as well as having considerable variation in their ability to tolerate sub-zero temperature – specifically, there appear to be “warm” and “cold” adapted individuals. I sequenced 151 individuals collected in pitfall traps near Spaulding Pond, Taylor Valley and found 19 unique COI haplotypes that separated into two distinct groups (1.6% divergence), with one haplotype group comprising 80% of the sequenced population. During two-hourly sampling, air temperature was the strongest predictor of activity between the two haplotype groups (R2 = 0.56) and when combined with subsurface soil temperature, relative humidity and photosynthetically active radiation, explanatory power increased to R2 = 0.71. Air temperatures are predicted to continue increasing across most of Antarctica which is expected to impact springtails by a detectable amount. Monitoring programmes focussed on the temporal and spatial changes in COI haplotype diversity may provide a sensitive measure of population responses to climate change. 

Collectively, these two studies contribute baseline data of the current genetic diversity and population structure among New Zealand rotifers and Antarctic springtails and provide a platform by which to monitor future environmental changes.

year: 2015

title: Bandwidth-optimal random shuffling for GPUs

authors: Mitchell, Rory

subjects: computer science

abstract: Linear-time algorithms that are traditionally used to shuffle data on CPUs, such as the method of Fisher-Yates, are not well suited to implementation on GPUs due to inherent sequential dependencies, and existing parallel shuffling algorithms are unsuitable for GPU architectures because they incur a large number of read/write operations to high latency global memory. To address this, we provide a method of generating pseudo-random permutations in parallel by fusing suitable pseudo-random bijective functions with stream compaction operations. Our algorithm, termed “bijective shuffle” trades increased per-thread arithmetic operations for reduced global memory transactions. It is work-efficient, deterministic, and only requires a single global memory read and write per shuffle input, thus maximising use of global memory bandwidth. To empirically demonstrate the correctness of the algorithm, we develop a statistical test for the quality of pseudo-random permutations based on kernel space embeddings. Experimental results show that the bijective shuffle algorithm outperforms competing algorithms on GPUs, showing improvements of between one and two orders of magnitude and approaching peak device bandwidth.

text: Bandwidth-optimal random shuffling for GPUs Linear-time algorithms that are traditionally used to shuffle data on CPUs, such as the method of Fisher-Yates, are not well suited to implementation on GPUs due to inherent sequential dependencies, and existing parallel shuffling algorithms are unsuitable for GPU architectures because they incur a large number of read/write operations to high latency global memory. To address this, we provide a method of generating pseudo-random permutations in parallel by fusing suitable pseudo-random bijective functions with stream compaction operations. Our algorithm, termed “bijective shuffle” trades increased per-thread arithmetic operations for reduced global memory transactions. It is work-efficient, deterministic, and only requires a single global memory read and write per shuffle input, thus maximising use of global memory bandwidth. To empirically demonstrate the correctness of the algorithm, we develop a statistical test for the quality of pseudo-random permutations based on kernel space embeddings. Experimental results show that the bijective shuffle algorithm outperforms competing algorithms on GPUs, showing improvements of between one and two orders of magnitude and approaching peak device bandwidth.

year: 2022

title: Tīaho mai

authors: Maxwell, Te Kahautu

abstract: Waiata ā Ringa (action song). Lyrics composed by Te Kahautu Maxwell. Performed by Ōpōtiki Mai Tawhiti (Kapa Haka group)

text: Tīaho mai Waiata ā Ringa (action song). Lyrics composed by Te Kahautu Maxwell. Performed by Ōpōtiki Mai Tawhiti (Kapa Haka group)

year: 2024