title: The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest

authors: Featherstone, LA

subjects: Bycatch

abstract: Sequence capture is a genomic technique that selectively enriches target sequences before high throughput next-generation sequencing, to generate specific sequences of interest. Off-target or ‘bycatch’ data are often discarded from capture experiments, but can be leveraged to address evolutionary questions under some circumstances. Here, we investigated the effects of missing data on a variety of evolutionary analyses using bycatch from an exon capture experiment on the global pest moth, Helicoverpa armigera. We added > 200 new samples from across Australia in the form of mitogenomes obtained as bycatch from targeted sequence capture, and combined these into an additional larger dataset to total > 1000 mitochondrial cytochrome c oxidase subunit I (COI) sequences across the species’ global distribution. Using discriminant analysis of principal components and Bayesian coalescent analyses, we showed that mitogenomes assembled from bycatch with up to 75% missing data were able to return evolutionary inferences consistent with higher coverage datasets and the broader literature surrounding H. armigera. For example, low-coverage sequences broadly supported the delineation of two H. armigera subspecies and also provided new insights into the potential for geographic turnover among these subspecies. However, we also identified key effects of dataset coverage and composition on our results. Thus, low-coverage bycatch data can offer valuable information for population genetic and phylodynamic analyses, but caution is required to ensure the reduced information does not introduce confounding factors, such as sampling biases, that drive inference. We encourage more researchers to consider maximizing the potential of the targeted sequence approach by examining evolutionary questions with their off-target bycatch where possible—especially in cases where no previous mitochondrial data exists—but recommend stratifying data at different genome coverage thresholds to separate sampling effects from genuine genomic signals, and to understand their implications for evolutionary research.

text: The effect of missing data on evolutionary analysis of sequence capture bycatch, with application to an agricultural pest Sequence capture is a genomic technique that selectively enriches target sequences before high throughput next-generation sequencing, to generate specific sequences of interest. Off-target or ‘bycatch’ data are often discarded from capture experiments, but can be leveraged to address evolutionary questions under some circumstances. Here, we investigated the effects of missing data on a variety of evolutionary analyses using bycatch from an exon capture experiment on the global pest moth, Helicoverpa armigera. We added > 200 new samples from across Australia in the form of mitogenomes obtained as bycatch from targeted sequence capture, and combined these into an additional larger dataset to total > 1000 mitochondrial cytochrome c oxidase subunit I (COI) sequences across the species’ global distribution. Using discriminant analysis of principal components and Bayesian coalescent analyses, we showed that mitogenomes assembled from bycatch with up to 75% missing data were able to return evolutionary inferences consistent with higher coverage datasets and the broader literature surrounding H. armigera. For example, low-coverage sequences broadly supported the delineation of two H. armigera subspecies and also provided new insights into the potential for geographic turnover among these subspecies. However, we also identified key effects of dataset coverage and composition on our results. Thus, low-coverage bycatch data can offer valuable information for population genetic and phylodynamic analyses, but caution is required to ensure the reduced information does not introduce confounding factors, such as sampling biases, that drive inference. We encourage more researchers to consider maximizing the potential of the targeted sequence approach by examining evolutionary questions with their off-target bycatch where possible—especially in cases where no previous mitochondrial data exists—but recommend stratifying data at different genome coverage thresholds to separate sampling effects from genuine genomic signals, and to understand their implications for evolutionary research.

year: 2024-02-21

title: The Influence of COVID-19 lockdown restrictions on perceived nutrition habits in rugby union players

authors: Roberts, Charlie

subjects: Science & Technology

abstract: The global outbreak of COVID-19 has led to governments and local authorities implementing nationwide lockdowns in an attempt to encourage social distancing and minimize the spread of the virus. Only essential businesses have been able to remain open, with non-essential businesses and activities either closing or restricting services. With no group training sessions allowed, canceled matches, an inability to work and the closure of eating establishments, Rugby Union players have experienced disruption to their daily lives. Two surveys were distributed among Rugby Union athletes to explore (1) the influence of COVID-19 lockdown restrictions on Rugby Union players' nutrition and training habits and (2) how nutrition habits in New Zealand Rugby Union players change after lockdown restrictions were lifted. In total, 258 respondents completed Survey 1 (84.1% male, 26.4% professional/semi-professional). Of the respondents, 58% indicated they lived with family during lockdown. Total food intake was reported to be higher in 36% of respondents. Fruit and vegetable intake was lower (17%) and packaged/convenience food intake higher (26%) in a minority of respondents. In total, 106 respondents completed Survey 2 (84.9% male, 34.0% professional/semi-professional). Of the respondents, 72% prepared and 67% purchased their own food. Less than half of respondents consumed high-protein food more than twice daily either during or following lockdown. Compared to during lockdown, motivation to train and exercise was greater in 58% of respondents following lockdown. Dieticians and nutritionists within clubs provided most of the nutrition knowledge to athletes however other unreliable sources were identified, such as social media and family members. The ongoing pandemic has presented significant challenges for athletes concerning training and nutrition habits and the current study provides some insight into these. Coaches and performance staff should ensure athletes receive appropriate nutritional and training support whilst being aware of the unique demands the individuals' may face.

text: The Influence of COVID-19 lockdown restrictions on perceived nutrition habits in rugby union players The global outbreak of COVID-19 has led to governments and local authorities implementing nationwide lockdowns in an attempt to encourage social distancing and minimize the spread of the virus. Only essential businesses have been able to remain open, with non-essential businesses and activities either closing or restricting services. With no group training sessions allowed, canceled matches, an inability to work and the closure of eating establishments, Rugby Union players have experienced disruption to their daily lives. Two surveys were distributed among Rugby Union athletes to explore (1) the influence of COVID-19 lockdown restrictions on Rugby Union players' nutrition and training habits and (2) how nutrition habits in New Zealand Rugby Union players change after lockdown restrictions were lifted. In total, 258 respondents completed Survey 1 (84.1% male, 26.4% professional/semi-professional). Of the respondents, 58% indicated they lived with family during lockdown. Total food intake was reported to be higher in 36% of respondents. Fruit and vegetable intake was lower (17%) and packaged/convenience food intake higher (26%) in a minority of respondents. In total, 106 respondents completed Survey 2 (84.9% male, 34.0% professional/semi-professional). Of the respondents, 72% prepared and 67% purchased their own food. Less than half of respondents consumed high-protein food more than twice daily either during or following lockdown. Compared to during lockdown, motivation to train and exercise was greater in 58% of respondents following lockdown. Dieticians and nutritionists within clubs provided most of the nutrition knowledge to athletes however other unreliable sources were identified, such as social media and family members. The ongoing pandemic has presented significant challenges for athletes concerning training and nutrition habits and the current study provides some insight into these. Coaches and performance staff should ensure athletes receive appropriate nutritional and training support whilst being aware of the unique demands the individuals' may face.

year: 2020

title: The rhetorical organization of discourse: language revitalisation and the question of authenticity

authors: Crombie, Winifred

subjects: Te reo Māori

abstract: We propose here one approach to unravelling some aspects of authentic discourse construction in a way that may prove useful to teachers and learners of Māori. The approach is illustrated in relation to one text which realises the argument genre in Māori. In terms of text-type, the example provided is an open letter of advice/warning. The approach illustrated here, and the hypotheses emerging from it, are currently being further tested by one of the authors with reference to a corpus of written texts.

text: The rhetorical organization of discourse: language revitalisation and the question of authenticity We propose here one approach to unravelling some aspects of authentic discourse construction in a way that may prove useful to teachers and learners of Māori. The approach is illustrated in relation to one text which realises the argument genre in Māori. In terms of text-type, the example provided is an open letter of advice/warning. The approach illustrated here, and the hypotheses emerging from it, are currently being further tested by one of the authors with reference to a corpus of written texts.

year: 2000-11-24