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: Quaternary environmental change in New Zealand: a review

authors: Newnham, Rewi M.

subjects: climate change

abstract: The discovery that orbital variations are the driving force behind Quaternary climate change provides an impetus to set local and regional records of environmental change into the global context, a principle that has been strongly embraced by Quaternary scientists working in New Zealand. Their major achievements and significant current initiatives are reviewed here. The importance of the New Zealand Quaternary stems from its geographical context: a climatically sensitive, remote oceanic, southern location spanning 17 degrees of the mid-latitudes; an obliquely convergent plate boundary setting resulting in a high mountain range athwart the prevailing westerlies, active volcanism, a youthful and dynamic landscape, and mountains high enough to maintain glaciers today; and a remarkably short prehistory. The resultant records show marked environmental changes due not only to climatic oscillations but also to vigorous, active tectonism and volcanism. The Taupo Volcanic Zone, containing the world's strongest concentration of youthful rhyolitic volcanoes, has produced at least 10 000 km3 of magma in the last 2 Ma. Climatic interpretations of records from marine sediments in the New Zealand region, together with several long sequences of alternating marine and terrestrial sediments, indicate broad synchrony with Northern Hemisphere events (within limitations of dating), although there are differences in detail for shorter-term climatic events. It is not yet certain that glacial advances coincided precisely with those in the Northern Hemisphere or were of similar duration. Late Cainozoic glaciation commenced c. 2.6-2.4 Ma but the record of glacial deposits is fragmentary and poorly dated except for the most recent events. The Last (Otira) Glaciation, from c. 100-10 ka, was characterized by at least five glacial advances including during the Last Glacial Maximum from 25 to 15 ka, when snowlines fell by 600-800 m. New Zealand evidence for cooling during the Younger Dryas stade is equivocal whilst isotopic records from speleothems, and other data, indicate warmer and wetter conditions from 10-7 ka, broadly conforming with records from mid-latitude Northern Hemisphere locations. Future advances will require sampling at shorter timescales, improvements in the accuracy and precision of existing dating methods and the development of new ones, extension of palaeoecological techniques to cover the full potential of New Zealand's diverse biota, and a stronger emphasis on quantification of palaeoclimatic parameters.

text: Quaternary environmental change in New Zealand: a review The discovery that orbital variations are the driving force behind Quaternary climate change provides an impetus to set local and regional records of environmental change into the global context, a principle that has been strongly embraced by Quaternary scientists working in New Zealand. Their major achievements and significant current initiatives are reviewed here. The importance of the New Zealand Quaternary stems from its geographical context: a climatically sensitive, remote oceanic, southern location spanning 17 degrees of the mid-latitudes; an obliquely convergent plate boundary setting resulting in a high mountain range athwart the prevailing westerlies, active volcanism, a youthful and dynamic landscape, and mountains high enough to maintain glaciers today; and a remarkably short prehistory. The resultant records show marked environmental changes due not only to climatic oscillations but also to vigorous, active tectonism and volcanism. The Taupo Volcanic Zone, containing the world's strongest concentration of youthful rhyolitic volcanoes, has produced at least 10 000 km3 of magma in the last 2 Ma. Climatic interpretations of records from marine sediments in the New Zealand region, together with several long sequences of alternating marine and terrestrial sediments, indicate broad synchrony with Northern Hemisphere events (within limitations of dating), although there are differences in detail for shorter-term climatic events. It is not yet certain that glacial advances coincided precisely with those in the Northern Hemisphere or were of similar duration. Late Cainozoic glaciation commenced c. 2.6-2.4 Ma but the record of glacial deposits is fragmentary and poorly dated except for the most recent events. The Last (Otira) Glaciation, from c. 100-10 ka, was characterized by at least five glacial advances including during the Last Glacial Maximum from 25 to 15 ka, when snowlines fell by 600-800 m. New Zealand evidence for cooling during the Younger Dryas stade is equivocal whilst isotopic records from speleothems, and other data, indicate warmer and wetter conditions from 10-7 ka, broadly conforming with records from mid-latitude Northern Hemisphere locations. Future advances will require sampling at shorter timescales, improvements in the accuracy and precision of existing dating methods and the development of new ones, extension of palaeoecological techniques to cover the full potential of New Zealand's diverse biota, and a stronger emphasis on quantification of palaeoclimatic parameters.

year: 1999

title: Anhedonia: He kohinga whiti mai i te tirohanga o ngā wahanga e rima o te pōuri / A collection of poetry themed around loss presented through the lens of the five stages of grief

authors: Nicholls, Rawiri Rangihouhiri Terrence

subjects: Grief

abstract: Anhedonia is a collection of personal experiences centred around loss examined through the lens of the five stages of grief (denial, anger, bargaining, depression, and acceptance) and framed within a personal confessional postmodernism style. It was also influenced by the collected works of Federico Garcia Lorca, Sylvia Plath, Cassandra Barnett (Ngāti Huri, Raukawa), Kirsty Dunn (Te Aupōuri, Te Rarawa), and Ngahuia Te Awekotuku (Te Arawa, Tūhoe).

While loss and grief are intrinsically linked to death, within this collection, I further explore other forms of loss and grief. I touch on my loss of cultural identity, mind, and self. As a student, I have been diving deeper into my cultural identity of being Māori and what that means to me. I have lost many things throughout my life at the hands of abuse, depression, grief, and mental health. The poetry within this collection will continue to serve as a blunt reminder of the experiences (both positive and negative) that I have endured or witnessed over the last couple of decades.

I have seen a multitude of losses (in its many variations) as I continue the dance to discover what the mortality of not only myself but those around me means to me. While everyone will experience feelings of grief and loss, I have framed my own experiences in my interpretation of our collective mortality.

text: Anhedonia: He kohinga whiti mai i te tirohanga o ngā wahanga e rima o te pōuri / A collection of poetry themed around loss presented through the lens of the five stages of grief Anhedonia is a collection of personal experiences centred around loss examined through the lens of the five stages of grief (denial, anger, bargaining, depression, and acceptance) and framed within a personal confessional postmodernism style. It was also influenced by the collected works of Federico Garcia Lorca, Sylvia Plath, Cassandra Barnett (Ngāti Huri, Raukawa), Kirsty Dunn (Te Aupōuri, Te Rarawa), and Ngahuia Te Awekotuku (Te Arawa, Tūhoe).

While loss and grief are intrinsically linked to death, within this collection, I further explore other forms of loss and grief. I touch on my loss of cultural identity, mind, and self. As a student, I have been diving deeper into my cultural identity of being Māori and what that means to me. I have lost many things throughout my life at the hands of abuse, depression, grief, and mental health. The poetry within this collection will continue to serve as a blunt reminder of the experiences (both positive and negative) that I have endured or witnessed over the last couple of decades.

I have seen a multitude of losses (in its many variations) as I continue the dance to discover what the mortality of not only myself but those around me means to me. While everyone will experience feelings of grief and loss, I have framed my own experiences in my interpretation of our collective mortality.

year: 2024