title: The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life

authors: Zhou, Xin

subjects: Science & Technology

abstract: DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.

This article is part of the themed issue ‘From DNA barcodes to biomes’.

text: The Trichoptera barcode initiative: a strategy for generating a species-level Tree of Life DNA barcoding was intended as a means to provide species-level identifications through associating DNA sequences from unknown specimens to those from curated reference specimens. Although barcodes were not designed for phylogenetics, they can be beneficial to the completion of the Tree of Life. The barcode database for Trichoptera is relatively comprehensive, with data from every family, approximately two-thirds of the genera, and one-third of the described species. Most Trichoptera, as with most of life's species, have never been subjected to any formal phylogenetic analysis. Here, we present a phylogeny with over 16 000 unique haplotypes as a working hypothesis that can be updated as our estimates improve. We suggest a strategy of implementing constrained tree searches, which allow larger datasets to dictate the backbone phylogeny, while the barcode data fill out the tips of the tree. We also discuss how this phylogeny could be used to focus taxonomic attention on ambiguous species boundaries and hidden biodiversity. We suggest that systematists continue to differentiate between ‘Barcode Index Numbers’ (BINs) and ‘species’ that have been formally described. Each has utility, but they are not synonyms. We highlight examples of integrative taxonomy, using both barcodes and morphology for species description.

This article is part of the themed issue ‘From DNA barcodes to biomes’.

year: 2016

title: Gut structure and diet adaptability of yellowbelly flounder: A step towards integrating Rhombosolea leporina into New Zealand aquaculture

authors: Thomson, Caitlin

subjects: gut structure

abstract: Aquaculture is a rapidly expanding industry as wild fish stocks decline due to overfishing, climate change, and increased seafood consumption. Flatfish, being highly prized, have faced significant declines in the wild, but several species are now being cultivated in land-based recirculating aquaculture systems to meet market demand. Flatfish are low-trophic feeders and thrive in relatively simple farming setups, making them viable candidates for sustainable aquaculture.
In New Zealand, the yellowbelly flounder (Rhombosolea leporina), or pātiki, is a sought-after species in commercial and recreational fisheries. Introducing this species into aquaculture could support the local seafood market and aid in replenishing wild stocks. However, limited research exists on yellowbelly flounder compared to other flatfish, particularly regarding its digestive system and dietary needs. Feed costs are a significant challenge in aquaculture, especially when striving to reduce reliance on unsustainable ingredients like fishmeal and oil while maintaining low feed conversion ratios. Understanding the digestive tract structure and function of the yellowbelly flounder is critical for developing sustainable, species-specific diets.
This study examined the gut structure and function of wild-caught adult and juvenile yellowbelly flounder, as well as juveniles fed a mussel-based diet, a fishmeal-based pellet diet, or subjected to starvation. The histological analysis examined the muscularis externa, mucosal folds, and goblet cell distribution throughout the alimentary canal, while qPCR assessed the expression of the cholecystokinin hormone paralogs (ccka and cckb).
Unexpectedly, findings suggested that yellowbelly flounder may be agastric, differing from other flatfish. Consistent gut tissue patterns, goblet cell presence, and ccka and cckb expression throughout the canal supported this conclusion. The pellet diet did cause higher ccka expression compared to the mussel diet, but overall, the results suggested the yellowbelly flounder is adaptable to varying feeds. While limited by a small-scale study, these results provided a basis for further exploration of yellowbelly flounder digestive capabilities in hopes of facilitating this species into the New Zealand aquaculture industry.

text: Gut structure and diet adaptability of yellowbelly flounder: A step towards integrating Rhombosolea leporina into New Zealand aquaculture Aquaculture is a rapidly expanding industry as wild fish stocks decline due to overfishing, climate change, and increased seafood consumption. Flatfish, being highly prized, have faced significant declines in the wild, but several species are now being cultivated in land-based recirculating aquaculture systems to meet market demand. Flatfish are low-trophic feeders and thrive in relatively simple farming setups, making them viable candidates for sustainable aquaculture.
In New Zealand, the yellowbelly flounder (Rhombosolea leporina), or pātiki, is a sought-after species in commercial and recreational fisheries. Introducing this species into aquaculture could support the local seafood market and aid in replenishing wild stocks. However, limited research exists on yellowbelly flounder compared to other flatfish, particularly regarding its digestive system and dietary needs. Feed costs are a significant challenge in aquaculture, especially when striving to reduce reliance on unsustainable ingredients like fishmeal and oil while maintaining low feed conversion ratios. Understanding the digestive tract structure and function of the yellowbelly flounder is critical for developing sustainable, species-specific diets.
This study examined the gut structure and function of wild-caught adult and juvenile yellowbelly flounder, as well as juveniles fed a mussel-based diet, a fishmeal-based pellet diet, or subjected to starvation. The histological analysis examined the muscularis externa, mucosal folds, and goblet cell distribution throughout the alimentary canal, while qPCR assessed the expression of the cholecystokinin hormone paralogs (ccka and cckb).
Unexpectedly, findings suggested that yellowbelly flounder may be agastric, differing from other flatfish. Consistent gut tissue patterns, goblet cell presence, and ccka and cckb expression throughout the canal supported this conclusion. The pellet diet did cause higher ccka expression compared to the mussel diet, but overall, the results suggested the yellowbelly flounder is adaptable to varying feeds. While limited by a small-scale study, these results provided a basis for further exploration of yellowbelly flounder digestive capabilities in hopes of facilitating this species into the New Zealand aquaculture industry.

year: 2025

title: Observations by and conversations with health workers and hospital personnel involved in transferring Maori patients and whānau to Waikato Hospital in Aotearoa New Zealand

authors: Masters-Awatere, Bridgette

subjects: Science & Technology

abstract: The predominant focus of Aotearoa New Zealand’s public health system on biomedical models of health has left little room for meaningful engagement with holistic indigenous approaches. Culturally appropriate provision and support are recognized for their relevance and importance during hospital transferals. Hospital staff involved in transfers to one of New Zealand’s trauma centers share their observations of whānau Māori engagement during an admission away from their home base. Sixteen key informants share their experiences, which are presented as strategies and challenges to whānau engagement. Three main themes highlight challenges within the health system that make it difficult for hospital staff to engage whānau in the desired ways and as often as both parties would like. Key informants described services and practices that are not designed with patients and their whānau in mind; instead they are designed by clinicians around the needs of administrative systems. As employees within the public health system, key informants felt powerless to challenge dominant settings. Nevertheless, employees managed to circumnavigate processes. Our findings highlight the need for continued decolonization and anti-racism work within public health settings.

text: Observations by and conversations with health workers and hospital personnel involved in transferring Maori patients and whānau to Waikato Hospital in Aotearoa New Zealand The predominant focus of Aotearoa New Zealand’s public health system on biomedical models of health has left little room for meaningful engagement with holistic indigenous approaches. Culturally appropriate provision and support are recognized for their relevance and importance during hospital transferals. Hospital staff involved in transfers to one of New Zealand’s trauma centers share their observations of whānau Māori engagement during an admission away from their home base. Sixteen key informants share their experiences, which are presented as strategies and challenges to whānau engagement. Three main themes highlight challenges within the health system that make it difficult for hospital staff to engage whānau in the desired ways and as often as both parties would like. Key informants described services and practices that are not designed with patients and their whānau in mind; instead they are designed by clinicians around the needs of administrative systems. As employees within the public health system, key informants felt powerless to challenge dominant settings. Nevertheless, employees managed to circumnavigate processes. Our findings highlight the need for continued decolonization and anti-racism work within public health settings.

year: 2020