title: Biases in the metabarcoding of plant pathogens using rust fungi as a model system

authors: Makiola, Andreas

subjects: Cloning

abstract: Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost‐effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next‐generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large‐scale detection and quantification of rust fungi, but not for confirming the absence of species.

text: Biases in the metabarcoding of plant pathogens using rust fungi as a model system Plant pathogens such as rust fungi (Pucciniales) are of global economic and ecological importance. This means there is a critical need to reliably and cost‐effectively detect, identify, and monitor these fungi at large scales. We investigated and analyzed the causes of differences between next‐generation sequencing (NGS) metabarcoding approaches and traditional DNA cloning in the detection and quantification of recognized species of rust fungi from environmental samples. We found significant differences between observed and expected numbers of shared rust fungal operational taxonomic units (OTUs) among different methods. However, there was no significant difference in relative abundance of OTUs that all methods were capable of detecting. Differences among the methods were mainly driven by the method's ability to detect specific OTUs, likely caused by mismatches with the NGS metabarcoding primers to some Puccinia species. Furthermore, detection ability did not seem to be influenced by differences in sequence lengths among methods, the most appropriate bioinformatic pipeline used for each method, or the ability to detect rare species. Our findings are important to future metabarcoding studies, because they highlight the main sources of difference among methods, and rule out several mechanisms that could drive these differences. Furthermore, strong congruity among three fundamentally different and independent methods demonstrates the promising potential of NGS metabarcoding for tracking important taxa such as rust fungi from within larger NGS metabarcoding communities. Our results support the use of NGS metabarcoding for the large‐scale detection and quantification of rust fungi, but not for confirming the absence of species.

year: 2018

title: Country institutional report: New Zealand

authors: Michelle, Carolyn

subjects: women’s studies

abstract: Waikato University pioneered the development of Women’s Studies as an academic discipline in New Zealand, with the first paper on this subject being offered in 1974. By 1982, a programme of papers was offered within five departments and the subject could be taken as a second supporting subject. A Centre for Women’s Studies was established in 1986, and, by 1988, was offering five taught core undergraduate papers and six electives, all of which could be taken towards a first or second support. A supporting BSocSci major in Women’s Studies became available in 1988, along with a Diploma in Women’s Studies. The full major became available in 1990. At this time, the major comprised a limited selection of core Women’s Studies papers complemented by a wider range of elective papers offered by other departments. This structure ensured that the programme had strong interdisciplinary, and in some cases inter-faculty linkages, along with wide support across the university through a network of elective teachers. These linkages appear to have facilitated strong growth in student numbers during the late 1980s and early 1990s.

text: Country institutional report: New Zealand Waikato University pioneered the development of Women’s Studies as an academic discipline in New Zealand, with the first paper on this subject being offered in 1974. By 1982, a programme of papers was offered within five departments and the subject could be taken as a second supporting subject. A Centre for Women’s Studies was established in 1986, and, by 1988, was offering five taught core undergraduate papers and six electives, all of which could be taken towards a first or second support. A supporting BSocSci major in Women’s Studies became available in 1988, along with a Diploma in Women’s Studies. The full major became available in 1990. At this time, the major comprised a limited selection of core Women’s Studies papers complemented by a wider range of elective papers offered by other departments. This structure ensured that the programme had strong interdisciplinary, and in some cases inter-faculty linkages, along with wide support across the university through a network of elective teachers. These linkages appear to have facilitated strong growth in student numbers during the late 1980s and early 1990s.

year: 2004

title: "He taketake, he hurumanu te moana i rōhia ai": Mā te Māori ngā toronga o te motu ki whenua kē e taurima?

authors: Dewes, Kaneihana

subjects: Iwi taketake

abstract: Kai te tino ia o te tuhinga rangahau nei, he whakatōmene i te āhua kaiārahi o te Māori i ngā tūāhua hono ki ahurea kē. Mā konei e whakatau ai, e whakatūwherahia rānei ngā āhuatanga e mea ana mā te Māori ngā toronga o te motu ki whenua kē e taurima. He momo tēnei nā te Māori, i takea mai i ngā mahi pokai moana, me ngā waka i whakaterea i ngā rohenga moana o Te Moana-nui-a-Kiwa, ā, puta noa. Waihoki, he taonga tonu wā tātau kai ngā tauira o ngā tūhononga ahurea o ngā iwi taketake o te ao; he taonga anō kai waenganui i a tātau ngā whenua maha i pakanga ki rāwāhi, he tohu nui nā te ‘price of citizenship’. He momo nā te Māori te tātaki i ngā mahi whakarauora reo, waihoki, he rite tonu te noho tahi ki whenua kē i roto i te kōingo ki te whakatipu i te reo o te whenua. Mā konei, ka marohi ai te hiranga o Te Reo Māori me ngā Tikanga Māori, tēnei hiranga e tohu ana i te hua o ngā hononga ahurea ki ngā iwi taketake huri noa, kia whai hua mō Niu Tireni i ngā toronga ki whenua kē.

text: "He taketake, he hurumanu te moana i rōhia ai": Mā te Māori ngā toronga o te motu ki whenua kē e taurima? Kai te tino ia o te tuhinga rangahau nei, he whakatōmene i te āhua kaiārahi o te Māori i ngā tūāhua hono ki ahurea kē. Mā konei e whakatau ai, e whakatūwherahia rānei ngā āhuatanga e mea ana mā te Māori ngā toronga o te motu ki whenua kē e taurima. He momo tēnei nā te Māori, i takea mai i ngā mahi pokai moana, me ngā waka i whakaterea i ngā rohenga moana o Te Moana-nui-a-Kiwa, ā, puta noa. Waihoki, he taonga tonu wā tātau kai ngā tauira o ngā tūhononga ahurea o ngā iwi taketake o te ao; he taonga anō kai waenganui i a tātau ngā whenua maha i pakanga ki rāwāhi, he tohu nui nā te ‘price of citizenship’. He momo nā te Māori te tātaki i ngā mahi whakarauora reo, waihoki, he rite tonu te noho tahi ki whenua kē i roto i te kōingo ki te whakatipu i te reo o te whenua. Mā konei, ka marohi ai te hiranga o Te Reo Māori me ngā Tikanga Māori, tēnei hiranga e tohu ana i te hua o ngā hononga ahurea ki ngā iwi taketake huri noa, kia whai hua mō Niu Tireni i ngā toronga ki whenua kē.

year: 2022