While many studies have considered the ability of eDNA to assess animal communities in lacustrine settings, fewer have considered riverine systems, particularly those spanning the environmental ...gradients present in large river basins. Such dynamic systems are challenging for eDNA biomonitoring due to differing eDNA transport distances in rivers and the effects of river chemistry. To address this challenge, we focused on the Thames River system, UK, which has exceptional historical fish records providing a baseline to test the accuracy of eDNA metabarcoding in recovering fish community structure across both fresh and tidal zones. Two primer sets targeting 12S and CO1 regions were used to capture fish communities across the Thames catchment, from the upper freshwaters to the mid estuary. eDNA was collected at 35 sites, 14 of which were simultaneously paired with traditional fish surveys for direct comparison. We demonstrated that eDNA metabarcoding consistently detected more freshwater species than traditional methods, despite extensive sampling effort using the latter. In contrast, metabarcoding did not perform as well as traditional approaches in estuarine waters, although results included the novel detection of the protected sea lamprey. We further demonstrated that minor variations in the recovery of all approaches would not impact on the assessment of simple ecological models of community structure and, thus, some variability between approaches should not be viewed as a serious hindrance to uptake. Rather, our findings support a growing consensus that eDNA can reliably detect fish communities across dynamic freshwater habitats.
In this study, we compare eDNA metabarcoding using two genetic markers, with traditional fishing surveys in the River Thames, UK, spanning the environmental gradient from freshwater to mid estuary. We directly compare eDNA with simultaneous surveys employing traditional capture methods, and also compare eDNA with survey data over the previous 5 years. In addition, we investigate the seasonal variability of eDNA detections in a subset of sites, and investigate if the impact of variations in detections by different survey methods affects the results of a simple ecological model (elements of metacommunity structure).
Ongoing anthropogenic change is altering the planet at an unprecedented rate, threatening biodiversity, and ecosystem functioning. Species are responding to abiotic pressures at both individual and ...population levels, with changes affecting trophic interactions through consumptive pathways. Collectively, these impacts alter the goods and services that natural ecosystems will provide to society, as well as the persistence of all species. Here, we describe the physiological and behavioral responses of species to global changes on individual and population levels that result in detectable changes in diet across terrestrial and marine ecosystems. We illustrate shifts in the dynamics of food webs with implications for animal communities. Additionally, we highlight the myriad of tools available for researchers to investigate the dynamics of consumption patterns and trophic interactions, arguing that diet data are a crucial component of ecological studies on global change. We suggest that a holistic approach integrating the complexities of diet choice and trophic interactions with environmental drivers may be more robust at resolving trends in biodiversity, predicting food web responses, and potentially identifying early warning signs of diversity loss. Ultimately, despite the growing body of long-term ecological datasets, there remains a dearth of diet ecology studies across temporal scales, a shortcoming that must be resolved to elucidate vulnerabilities to changing biophysical conditions.
The analysis of environmental DNA (DNA shed by organisms into the environment, hereafter eDNA) has rapidly become adopted as a biomonitoring tool, particularly in aquatic ecosystems. However, this ...technique requires performance evaluations, comparisons with conventional surveys and data, and a greater understanding of the temporal variability of eDNA in order to provide robust interpretations of detections in lotic systems. This thesis applies eDNA metabarcoding to the fish communities of the River Thames in Southern England; a well-documented study site against which eDNA detections can be compared with traditional fishing surveys and historic data collected by the UK Environment Agency (EA). This work represents the first attempt at utilizing eDNA metabarcoding to investigate fish diversity in the Thames catchment, and builds on the rich history of previous monitoring work conducted by the EA. In Chapter 2, long term trends in fish diversity and abundance in the freshwater and tidal Thames are explored using GLM models. Declines in diversity are shown in the freshwater reaches of the Thames, and multivariate analyses are used to identify the species responsible for these trends. In Chapter 3, a wide ranging eDNA sampling campaign is conducted across the Thames. Detections are validated against traditional surveys by pairing eDNA collections with concurrent EA surveys, as well as historic records of diversity. Chapter 4 conducts two year-long sampling campaigns in the Thames catchment to investigate temporal changes in eDNA detections, using variation partitioning to identify environmental factors contributing to community change, and verifies detections against previous ecological studies. This thesis ground-proofs eDNA metabarcoding, and provides greater insight into the interpretation of detections, with these findings supporting the use of eDNA as an accurate and non-invasive tool for biomonitoring in lotic environments in the hope of benefiting the field and influencing current management decisions.
The accuracy and reliability of DNA metabarcoding analyses depend on the breadth and quality of the reference libraries that underpin them. However, there are limited options available to obtain and ...curate the huge volumes of sequence data that are available on public repositories such as NCBI and BOLD. Here, we provide a pipeline to download, clean and annotate mitochondrial DNA sequence data for a given list of fish species. Features of this pipeline include (a) support for multiple metabarcode markers; (b) searches on species synonyms and taxonomic name validation; (c) phylogeny assisted quality control for identification and removal of misannotated sequences; (d) automatically generated coverage reports for each new GenBank release update; and (e) citable, versioned DOIs. As an example we provide a ready‐to‐use curated reference library for the marine and freshwater fishes of the U.K. To augment this reference library for environmental DNA metabarcoding specifically, we generated 241 new MiFish‐12S sequences for 88 U.K. marine species, and make available new primer sets useful for sequencing these. This brings the coverage of common U.K. species for the MiFish‐12S fragment to 93%, opening new avenues for scaling up fish metabarcoding across wide spatial gradients. The Meta‐Fish‐Lib reference library and pipeline is hosted at https://github.com/genner-lab/meta-fish-lib.
Long‐term monitoring is critical to measure the response of biodiversity patterns and processes to human‐mediated environmental pressures. This is particularly pertinent in freshwaters, where recent ...estimates indicated a third of all fish species are threatened with extinction, making ongoing biomonitoring essential for conservation management. High frequency annual monitoring is critical for identifying temporal changes in fish community composition; however, traditional survey methods are typically less practical over such timeframes. While environmental (e)DNA measurement represents a potentially powerful tool for monitoring temporal community dynamics, studies are lacking. To address this deficit, we generated a high frequency time‐series dataset of entire fish communities using eDNA metabarcoding, to directly assess the repeatability and sensitivity of this method for detecting annual population trends. We targeted two differing environments (freshwater vs. intertidal) within the Thames catchment, UK, where detailed historical records from traditional monitoring were available for comparison. To test how robust eDNA data is for inferring the known community, we applied a hierarchical, nested design encompassing short and longer‐term variation in eDNA data. Our analyses showed that irrespective of environment, eDNA metabarcoding represented known seasonal shifts in fish communities, where increased relative read abundance of eDNA coincided with known migratory and spawning events, including those of the critically endangered native species Anguilla anguilla (European eel). eDNA species detections across a single year included over 75% of species recorded in a ca. 30‐year historical dataset, highlighting the power of eDNA for species detection. Our findings provide greater insight into the utility of eDNA metabarcoding for recovering temporal trends in fish communities from dynamic freshwater systems and insight into the potential best sampling strategy for future eDNA surveys.
We generated a high frequency time‐series dataset of entire fish communities from the River Thames using eDNA metabarcoding, to directly assess the repeatability and sensitivity of this method for detecting annual population trends. Our analyses showed that eDNA metabarcoding represented known seasonal shifts in fish communities, where increased relative read abundance of eDNA coincided with known migratory and spawning events, including those of the critically endangered native species Anguilla anguilla (European eel).
•Invasive crayfish may spread to new habitats by walking over land.•Both signal and red swamp crayfish leave the water to a similar degree.•The terrestrial walking speed of both signal and red swamp ...crayfish was similar.
To disperse between isolated waterbodies, freshwater organisms must often cross terrestrial barriers and many freshwater animals that are incapable of flight must rely on transport via flooding events, other animals or anthropogenic activity. Decapods such as crayfish, on the other hand, can disperse to nearby waterbodies by walking on land, a behaviour that has facilitated the spread of invasive species. Overland movement could play a key role in the management of non-native crayfish, though to what extent terrestrial emigration occurs in different species is poorly understood. Here, we directly compared the terrestrial emigration tendency of two non-native crayfish species in Great Britain; red swamp (Procambarus clarkii) and signal (Pacifastacus leniusculus) crayfish. We found that both species emigrated from the water and that there was no significant difference in terms of their terrestrial emigration tendency, suggesting that there is a risk both of these species will migrate overland and disperse to new habitats. This study shows that terrestrial emigration is an important behavioural trait to consider when preventing the escape of crayfish from aquaculture and further spread of invasive species.
Atrial fibrillation (AF) affects 1.5–2% of the population and is associated with a five-fold increased lifetime risk of stroke 1. The left atrial appendage (LAA) is the source of embolic strokes in ...up to 90% of patients with non-valvular AF with clots in the left atrium 2.
We reviewed the clinical notes and echocardiographic findings of 20 patients who underwent open cardiac surgery in which concurrent AtriClip (Atricure Inc, Westchester, OH, USA) device insertion was attempted at our institution from July 2013 to February 2015. This was to examine the safety and efficacy of LAA exclusion with clip devices during open cardiac surgery. Indications for LAA exclusion included a history or suspicion of atrial arrhythmia, left ventricular dilatation, or a history of transient ischaemic attacks.
All 20 of the 20 participants had successful placement of the clip device (100% success rate). There were no adverse events related to the device and no perioperative mortality. There were three late deaths due to chronic obstructive pulmonary disease (COPD), leukaemia, and refractory congestive cardiac failure. No late device related complications were found on follow-up imaging in the remaining patients.
The results of our study demonstrate the LAA exclusion during open cardiac surgery with the AtriClip device is safe, has a 100% success rate, and appears to be stable over time.
This paper provides an assessment of the excavation of an apparently ordinary space in Bristol (UK) in 2009. Although the space appears unremarkable to most passers-by, it is unusual in being a place ...used routinely by many of the city's street-drinking and homeless community. Homeless people were 'colleagues', involved in excavation, finds processing and interpretation. The collaborative nature of this project goes further than merely attempting to represent social groups who have traditionally been excluded from heritage practice and interpretation - it lays methodological foundations for praxis.
Turbo Island, Bristol: fouiller un lieu contemporain pour les sans abris
Cet article traite des données relatives à la fouille archéologique, menée en 2009 à Bristol (GB), d'un lieu apparemment ordinaire. Bien que l'espace semble quelconque pour la plupart des passants, sa fréquentation par de nombreux sans-abris et par des ivrognes en font un lieu peu commun. Au cours de cette fouille, les sans-abris sont devenus des «collègues», impliqués dans le dégagement, le traitement des découvertes et leur interprétation. La nature collaborative de ce projet va plus loin qu'une simple tentative de représenter les groupes sociaux qui ont traditionnellement été exclus de la pratique et de l'interprétation du patrimoine, cette étude permet en effet de poser des bases méthodologiques pour la praxis.
Turbo Insel, Bristol: Ausgrabungen eines Platzes für gegenwärtig Heimatlose
Dieser Artikel untersucht die Ausgrabungen eines scheinbar gewöhnlichen Platzes in Bristol (UK) in 2009. Obwohl der Platz Vorübergehenden nicht weiter bemerkenswert erscheint, ist er ungewöhnlich, weil er routinemäßig von vielen städtischen Straßentrinkern und Heimatlosen genutzt wird. Heimatlose wurden zu "Kollegen", denn sie halfen bei den Ausgrabungen, bei der Säuberung und Einordnung der Funde und Interpretation. Die Zusammenarbeit in diesem Projekt führte weiter als nur eine soziale Gruppe einzubeziehen, die traditionellerweise aus dem Prozess des Kulturerbes und dessen Interpretation ausgeschlossen ist - es legte methodologische Fundamente für die Praxis.
Turbo Island, Bristol: scavo di un luogo per senza tetto di epoca contemporanea
Questo saggio fornisce una valutazione sullo scavo di uno spazio apparentemente ordinario a Bristol (UK) effettuato nel 2009. Sebbene questo spazio sembri anonimo alla maggior parte dei passanti, è insolito per essere un luogo utilizzato abitualmente da una parte della comunità cittadina dei senza fissa dimora e dalle persone che bevono in strada. I senza-tetto sono stati coinvolti come "colleghi" nello scavo e nelle fasi di studio e interpretazione dei reperti. La natura collaborativa di questo progetto va oltre il mero tentativo di rappresentare gruppi sociali che sono stati tradizionalmente esclusi dall'interpretazione e dalla valorizzazione del patrimonio, gettando le basi metodologiche per una prassi.
Isla de Turbo, Bristol: excavación de un lugar desahuciado contemporáneo
Este artículo presenta los resultados de la excavación de un espacio aparentemente ordinario en Bristol (Reino Unido) en 2009. Aunque el espacio aparenta ser normal para la mayoría de los transeúntes, el lugar es utilizado habitualmente por muchos de los habitantes de la ciudad que se dedican a beber en las calles y también por vagabundos. Muchos de ellos participaron en la excavación, en el procesado de los hallazgos y ene la interpretación. La naturaleza colaborativa de este proyecto va más allá de intentar simplemente representar a los grupos sociales que tradicionalmente han sido excluidos de la interpretación y de la práctica de patrimonio, ya que establece bases metodológicas para su praxis.
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