title: Development of genetic tools to detect three New Zealand indigenous freshwater mussels in environmental DNA

authors: Hu, Xiaoxue

subjects: digital PCR

abstract: As “ecological engineers”, freshwater mussels are key components in the freshwater ecosystem. However, surveying mussels can be challenging since mussel populations may be difficult to locate. Conventional methods for identifying mussel species are also problematic and require expertise since mussels are often morphologically cryptic. The same problems apply to New Zealand indigenous freshwater mussels. New Zealand had long been considered to have two indigenous species, Echyridella menziesii and Echyridella aucklandica, until a recent revision based on molecular evidence recognised a new species, Echyridella onekaka, which was previously mis-identified as Echyridella menziesii. Results from molecular studies have placed all three freshwater mussel species under a single genus, Echyridella, specific to New Zealand. For conservation and ecosystem management, a fast and reliable method for surveying and identifying New Zealand mussels is required.
This research aims to develop molecular tools that utilise environmental DNA (eDNA) collected from freshwater environments to detect mussel species. These tools target a widely used DNA marker, cytochrome c oxidase subunit I (COI), for species identification. The COI targets in eDNA samples are detected by digital polymerase chain reaction (dPCR) using genus-specific primers and species-specific TaqMan probes. Three species-specific assays were developed, followed by assessment of specificity and sensitivity. Assay for E. aucklandica showed high specificity and tolerance to inhibition from high levels of non-target DNA. A trial of duplexing simultaneously assays detecting E. onekaka and E. aucklandica also showed promising results. With further assessment of assays using in vivo and in situ environmental samples in the future, these techniques hold great promise for being a rapid and cost-effective method for surveying and identifying New Zealand freshwater mussels.
Additionally, to increase detection rate when target concentration in eDNA is extremely low, known mitochondrial sequences for all three species were extended through PCR and de novo sequencing to allow future manufacturing of a customised commercial target DNA enrichment kit (MYbaits). This work is necessary since known mitochondrial genomic sequences for these three species are too short to generate effective MYbaits oligos. Consensus primers were designed based on available complete mitochondrial genomes of closely related mussel species. Most consensus primers successfully amplified in PCR, and about 1700bp have been sequenced so far. Once the sequencing of extended region is completed, a MYbaits kit will be manufactured for future research.

text: Development of genetic tools to detect three New Zealand indigenous freshwater mussels in environmental DNA As “ecological engineers”, freshwater mussels are key components in the freshwater ecosystem. However, surveying mussels can be challenging since mussel populations may be difficult to locate. Conventional methods for identifying mussel species are also problematic and require expertise since mussels are often morphologically cryptic. The same problems apply to New Zealand indigenous freshwater mussels. New Zealand had long been considered to have two indigenous species, Echyridella menziesii and Echyridella aucklandica, until a recent revision based on molecular evidence recognised a new species, Echyridella onekaka, which was previously mis-identified as Echyridella menziesii. Results from molecular studies have placed all three freshwater mussel species under a single genus, Echyridella, specific to New Zealand. For conservation and ecosystem management, a fast and reliable method for surveying and identifying New Zealand mussels is required.
This research aims to develop molecular tools that utilise environmental DNA (eDNA) collected from freshwater environments to detect mussel species. These tools target a widely used DNA marker, cytochrome c oxidase subunit I (COI), for species identification. The COI targets in eDNA samples are detected by digital polymerase chain reaction (dPCR) using genus-specific primers and species-specific TaqMan probes. Three species-specific assays were developed, followed by assessment of specificity and sensitivity. Assay for E. aucklandica showed high specificity and tolerance to inhibition from high levels of non-target DNA. A trial of duplexing simultaneously assays detecting E. onekaka and E. aucklandica also showed promising results. With further assessment of assays using in vivo and in situ environmental samples in the future, these techniques hold great promise for being a rapid and cost-effective method for surveying and identifying New Zealand freshwater mussels.
Additionally, to increase detection rate when target concentration in eDNA is extremely low, known mitochondrial sequences for all three species were extended through PCR and de novo sequencing to allow future manufacturing of a customised commercial target DNA enrichment kit (MYbaits). This work is necessary since known mitochondrial genomic sequences for these three species are too short to generate effective MYbaits oligos. Consensus primers were designed based on available complete mitochondrial genomes of closely related mussel species. Most consensus primers successfully amplified in PCR, and about 1700bp have been sequenced so far. Once the sequencing of extended region is completed, a MYbaits kit will be manufactured for future research.

year: 2017

title: A note on steady flow into a submerged point sink

authors: Hocking, Graeme Charles

subjects: axisymmetric flow

abstract: The steady, axisymmetric flow induced by a point sink (or source) submerged in an unbounded inviscid fluid is computed. The resulting deformation of the free surface is obtained, and a limit of steady solutions is found that is quite different to those obtained in past work. More accurate solutions indicate that the old limiting flow rate was too high and, in fact, the breakdown of steady solutions at a lower flow rate is characterized by the appearance of spurious wavelets at the free surface.

text: A note on steady flow into a submerged point sink The steady, axisymmetric flow induced by a point sink (or source) submerged in an unbounded inviscid fluid is computed. The resulting deformation of the free surface is obtained, and a limit of steady solutions is found that is quite different to those obtained in past work. More accurate solutions indicate that the old limiting flow rate was too high and, in fact, the breakdown of steady solutions at a lower flow rate is characterized by the appearance of spurious wavelets at the free surface.

year: 2014

title: Protecting Māori data: Can a Privacy Code of Practice provide a partial solution?

authors: Watts, David

abstract: This paper explores whether a Māori Data Privacy Code, developed under the Privacy Act 2020, could provide additional protection for classes of information that are regarded by Māori as tapu. The Act already covers the personal information of Māori individuals in the same way it does any other individual. We argue that a MDP Code could offer additional protection for particular classes of sensitive personal information – specifically whakapapa data and data pertaining to deceased Māori. A MDP Code could restrict the purposes for which such information can be collected, used, disclosed, retained, stored and disposed of; put stronger requirements on agencies to demonstrate that their collection and use of this information is justified; require free, prior and informed consent for its use and disclosure; and provide for greater transparency and independent Māori oversight.

text: Protecting Māori data: Can a Privacy Code of Practice provide a partial solution? This paper explores whether a Māori Data Privacy Code, developed under the Privacy Act 2020, could provide additional protection for classes of information that are regarded by Māori as tapu. The Act already covers the personal information of Māori individuals in the same way it does any other individual. We argue that a MDP Code could offer additional protection for particular classes of sensitive personal information – specifically whakapapa data and data pertaining to deceased Māori. A MDP Code could restrict the purposes for which such information can be collected, used, disclosed, retained, stored and disposed of; put stronger requirements on agencies to demonstrate that their collection and use of this information is justified; require free, prior and informed consent for its use and disclosure; and provide for greater transparency and independent Māori oversight.

year: 2025-10