title: Fatty acid biomarkers reveal landscape influences on linkages between aquatic and terrestrial food webs

authors: Burdon, Frank

subjects: fatty acids

abstract: Stream and riparian habitats are meta-ecosystems that can be strongly connected via the emergence of aquatic insects, which form an important prey subsidy for terrestrial consumers. Anthropogenic perturbations that impact these habitats may indirectly propagate across traditional ecosystem boundaries, thus weakening aquatic-terrestrial food web linkages. We investigated how algal production, aquatic invertebrates, and terrestrial spiders influence cross-ecosystem connectivity in temperate streams across four European catchments with varying levels of human disturbance. We used fatty acid biomarkers to measure putative aquatic linkages to riparian spiders. Variation-partitioning analysis indicated that aquatic insect dispersal traits explained a relatively large proportion of variability in the fatty acid profile of spiders. Trophic connectivity, as measured by the proportion of the polyunsaturated fatty acid eicosapentaenoic acid (EPA) and the ratio of EPA to its chemical precursor, alpha-linolenic acid (ALA), was positively associated with abundances of “aerial active” dispersing aquatic insects. However, this positive influence was also associated with changes in environmental context and arachnid beta diversity. Structural equation modeling disentangled how aquatic insect communities influence trophic connectivity with riparian predators after accounting for biological and environmental contingencies. Our results show how subsidies of stream insects are a putative source of essential fatty acids for adjacent terrestrial food webs. Catchment-wide impacts indirectly propagated to the local scale through impacts on aquatic invertebrate communities, thus affecting stream-riparian food webs. Increased riparian tree cover enhanced stream insect subsidies via dispersal traits despite reducing aquatic primary production through shading. Consequently, ecosystem properties such as woody riparian buffers that increase aquatic-terrestrial trophic connectivity have the potential to affect a wide range of consumers in modified landscapes.

text: Fatty acid biomarkers reveal landscape influences on linkages between aquatic and terrestrial food webs Stream and riparian habitats are meta-ecosystems that can be strongly connected via the emergence of aquatic insects, which form an important prey subsidy for terrestrial consumers. Anthropogenic perturbations that impact these habitats may indirectly propagate across traditional ecosystem boundaries, thus weakening aquatic-terrestrial food web linkages. We investigated how algal production, aquatic invertebrates, and terrestrial spiders influence cross-ecosystem connectivity in temperate streams across four European catchments with varying levels of human disturbance. We used fatty acid biomarkers to measure putative aquatic linkages to riparian spiders. Variation-partitioning analysis indicated that aquatic insect dispersal traits explained a relatively large proportion of variability in the fatty acid profile of spiders. Trophic connectivity, as measured by the proportion of the polyunsaturated fatty acid eicosapentaenoic acid (EPA) and the ratio of EPA to its chemical precursor, alpha-linolenic acid (ALA), was positively associated with abundances of “aerial active” dispersing aquatic insects. However, this positive influence was also associated with changes in environmental context and arachnid beta diversity. Structural equation modeling disentangled how aquatic insect communities influence trophic connectivity with riparian predators after accounting for biological and environmental contingencies. Our results show how subsidies of stream insects are a putative source of essential fatty acids for adjacent terrestrial food webs. Catchment-wide impacts indirectly propagated to the local scale through impacts on aquatic invertebrate communities, thus affecting stream-riparian food webs. Increased riparian tree cover enhanced stream insect subsidies via dispersal traits despite reducing aquatic primary production through shading. Consequently, ecosystem properties such as woody riparian buffers that increase aquatic-terrestrial trophic connectivity have the potential to affect a wide range of consumers in modified landscapes.

year: 2025

title: A study of hierarchical and flat classification of proteins

authors: Zimek, Arthur

subjects: computer science

abstract: Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be exploited to improve classification performance. In this article we investigate empirically whether this is the case for two such hierarchies. We compare multi-class classification techniques that exploit the information in those class hierarchies and those that do not, using logistic regression, decision trees, bagged decision trees, and support vector machines as the underlying base learners. In particular, we compare hierarchical and flat variants of ensembles of nested dichotomies. The latter have been shown to deliver strong classification performance in multi-class settings. We present experimental results for synthetic, fold recognition, enzyme classification, and remote homology detection data. Our results show that exploiting the class hierarchy improves performance on the synthetic data, but not in the case of the protein classification problems. Based on this we recommend that strong flat multi-class methods be used as a baseline to establish the benefit of exploiting class hierarchies in this area.

text: A study of hierarchical and flat classification of proteins Automatic classification of proteins using machine learning is an important problem that has received significant attention in the literature. One feature of this problem is that expert-defined hierarchies of protein classes exist and can potentially be exploited to improve classification performance. In this article we investigate empirically whether this is the case for two such hierarchies. We compare multi-class classification techniques that exploit the information in those class hierarchies and those that do not, using logistic regression, decision trees, bagged decision trees, and support vector machines as the underlying base learners. In particular, we compare hierarchical and flat variants of ensembles of nested dichotomies. The latter have been shown to deliver strong classification performance in multi-class settings. We present experimental results for synthetic, fold recognition, enzyme classification, and remote homology detection data. Our results show that exploiting the class hierarchy improves performance on the synthetic data, but not in the case of the protein classification problems. Based on this we recommend that strong flat multi-class methods be used as a baseline to establish the benefit of exploiting class hierarchies in this area.

year: 2008

title: He whare mātātuhi Tūhoe:  A Tūhoe re-visioning of English language literary texts

authors: Salsano, Marama

subjects: Māori writers

abstract: This thesis urges more Māori to undertake iwi-based readings of English language literary texts. I have chosen to privilege my father’s iwi, Ngāi Tūhoe, and to examine what Tūhoetana means to me and how it might thus enrich my reading of texts. In our ancestral tongue, Ngāi Tūhoe have a rich and pronounced history of storytelling, literary composition, analysis and critique. Unfortunately, this richness is woefully underappreciated within the English language literary landscape. Yet, as the ranks of Māori writers swell, along with the diversity of literary forms that Māori create, so too must Māori – and more specifically iwi – literary scholarship flourish, for if we do not critique the texts that are written about, of, and on behalf of us, who will? Throughout this thesis, I use the terms ‘iwi literary scholars’ and ‘iwi literary scholarship’ to consciously and repeatedly remind the reader of the rich, literary legacies residing within iwi archives; I also hope to highlight the exciting and endless possiblitites for the English language literary landscape to be enriched by readings that are founded within these archives – including the histories, everyday experiences and understandings from our tīpuna. 

Structurally, this thesis is divided into three broad strands. Chapters 1-3 focus on whakawhanaunatana and background information to my research. Because this thesis also represents the singular piece of writing that I wish I had read prior to enrolling in the thesis paper for this Master’s degree, my academic hīkoi – frustrations and all – is a necessary component and is covered in chapter 2. Chapters 4-6 then examine three different types of literary texts created by wāhine. These texts include the short story “Birth Rights” by Ngāi Tahu science fiction and fantasy writer, J.C. Hart (2010), the Instagram post Te Kuharere tapes by Ngāti Kahungungu and Ngāti Tuwharetoa songwriter and storyteller @tekahureremoa (2019) – also known as the performer Ladyfruit – and the young adult novel Dark Souls by Ngāti Wai, Ngāti Manuhiri, and Ngāti Whatua writer, Paula Morris (2011). While 21st century texts published on platforms such as Instagram may not sit easily within a traditional English literary curriculum, and indeed the novelty of these specific forms may well prove fleeting, the ‘everydayness’ of online texts yields rewarding analysis opportunities and is currently amiss within mainstream English literary studies. Each of these analysis chapters contains a focused introduction and conclusion, since chapter 7, the concluding chapter of this thesis, is a letter to future iwi literary scholars. 

Woven throughout this rangahau is a call for iwi scholars to consciously: engage with the literary traditions of their own iwi; identify the colonial thoughts and motives that they bring to the reading of literary texts; bring their tīpuna to the reading, but let the text itself breathe life into the critique and; consider the genres and types of texts that they critique. Ultimately, this thesis considers how engaging with the literary legacies of our tīpuna might broaden the English language literary landscape and thus enhance the body of iwi literary scholarship in Oceania and beyond.

text: He whare mātātuhi Tūhoe:  A Tūhoe re-visioning of English language literary texts This thesis urges more Māori to undertake iwi-based readings of English language literary texts. I have chosen to privilege my father’s iwi, Ngāi Tūhoe, and to examine what Tūhoetana means to me and how it might thus enrich my reading of texts. In our ancestral tongue, Ngāi Tūhoe have a rich and pronounced history of storytelling, literary composition, analysis and critique. Unfortunately, this richness is woefully underappreciated within the English language literary landscape. Yet, as the ranks of Māori writers swell, along with the diversity of literary forms that Māori create, so too must Māori – and more specifically iwi – literary scholarship flourish, for if we do not critique the texts that are written about, of, and on behalf of us, who will? Throughout this thesis, I use the terms ‘iwi literary scholars’ and ‘iwi literary scholarship’ to consciously and repeatedly remind the reader of the rich, literary legacies residing within iwi archives; I also hope to highlight the exciting and endless possiblitites for the English language literary landscape to be enriched by readings that are founded within these archives – including the histories, everyday experiences and understandings from our tīpuna. 

Structurally, this thesis is divided into three broad strands. Chapters 1-3 focus on whakawhanaunatana and background information to my research. Because this thesis also represents the singular piece of writing that I wish I had read prior to enrolling in the thesis paper for this Master’s degree, my academic hīkoi – frustrations and all – is a necessary component and is covered in chapter 2. Chapters 4-6 then examine three different types of literary texts created by wāhine. These texts include the short story “Birth Rights” by Ngāi Tahu science fiction and fantasy writer, J.C. Hart (2010), the Instagram post Te Kuharere tapes by Ngāti Kahungungu and Ngāti Tuwharetoa songwriter and storyteller @tekahureremoa (2019) – also known as the performer Ladyfruit – and the young adult novel Dark Souls by Ngāti Wai, Ngāti Manuhiri, and Ngāti Whatua writer, Paula Morris (2011). While 21st century texts published on platforms such as Instagram may not sit easily within a traditional English literary curriculum, and indeed the novelty of these specific forms may well prove fleeting, the ‘everydayness’ of online texts yields rewarding analysis opportunities and is currently amiss within mainstream English literary studies. Each of these analysis chapters contains a focused introduction and conclusion, since chapter 7, the concluding chapter of this thesis, is a letter to future iwi literary scholars. 

Woven throughout this rangahau is a call for iwi scholars to consciously: engage with the literary traditions of their own iwi; identify the colonial thoughts and motives that they bring to the reading of literary texts; bring their tīpuna to the reading, but let the text itself breathe life into the critique and; consider the genres and types of texts that they critique. Ultimately, this thesis considers how engaging with the literary legacies of our tīpuna might broaden the English language literary landscape and thus enhance the body of iwi literary scholarship in Oceania and beyond.

year: 2021