All Outputs (55)

The genome sequence of the Eurasian minnow, Phoxinus phoxinus (Linnaeus, 1758) (2024)
Journal Article
Nunn, A., Moccetti, P., & Hanfling, B. (online). The genome sequence of the Eurasian minnow, Phoxinus phoxinus (Linnaeus, 1758). Wellcome Open Research, 9, Article 504. https://doi.org/10.12688/wellcomeopenres.22867.1

We present a genome assembly from an individual female Phoxinus phoxinus (the Eurasian minnow; Chordata; Actinopteri; Cypriniformes; Leuciscidae). The genome sequence spans 950.50 megabases. Most of the assembly is scaffolded into 25 chromosomal pseu... Read More about The genome sequence of the Eurasian minnow, Phoxinus phoxinus (Linnaeus, 1758).

Towards the conservation of the crucian carp in Europe: Prolific hybridization but no evidence for introgression between native and non-native taxa (2024)
Journal Article
Jeffries, D., Lawson-Handley, L., Lamatsch, D., Olsén, K. H., Sayer, C. D., & Hänfling, B. (2024). Towards the conservation of the crucian carp in Europe: Prolific hybridization but no evidence for introgression between native and non-native taxa. Molecular ecology, 33(19), Article e17515. https://doi.org/10.1111/mec.17515

Hybridization plays a pivotal role in evolution, influencing local adaptation and speciation. However, it can also reduce biodiversity, which is especially damaging when native and non-native species meet. Hybridization can threaten native species vi... Read More about Towards the conservation of the crucian carp in Europe: Prolific hybridization but no evidence for introgression between native and non-native taxa.

Optimising species detection probability and sampling effort in lake fish eDNA surveys (2024)
Journal Article
Sellers, G. S., Jerde, C. L., Harper, L. R., Benucci, M., Muri, C. D., Li, J., Peirson, G., Walsh, K., Hatton-Ellis, T., Duncan, W., Duguid, A., Ottewell, D., Willby, N., Law, A., Bean, C. W., Winfield, I. J., Read, D. S., Handley, L. L., & Hänfling, B. (2024). Optimising species detection probability and sampling effort in lake fish eDNA surveys. Metabarcoding and Metagenomics, 8, 121–143. https://doi.org/10.3897/mbmg.8.104655

Environmental DNA (eDNA) metabarcoding is transforming biodiversity monitoring in aquatic environments. Such an approach has been developed and deployed for monitoring lake fish communities in Great Britain, where the method has repeatedly shown a co... Read More about Optimising species detection probability and sampling effort in lake fish eDNA surveys.

Improving environmental DNA (eDNA) methods for the detection and monitoring of invasive Dreissenid mussels (2024)
Thesis
Peixoto, S. P. F. Improving environmental DNA (eDNA) methods for the detection and monitoring of invasive Dreissenid mussels. (Thesis). University of Hull. https://hull-repository.worktribe.com/output/4706368

Dreissenid bivalves, zebra mussel (Dreissena polymorpha, Pallas, 1771) and quagga mussel (Dreissena rostriformis bugensis, Andrusov, 1897), are small freshwater molluscs native to the Ponto-Caspian region in Eastern Europe. Increasing globalization h... Read More about Improving environmental DNA (eDNA) methods for the detection and monitoring of invasive Dreissenid mussels.

The genome sequence of the stone loach, Barbatula barbatula (Linnaeus, 1758) (2023)
Journal Article
Hänfling, B., Nunn, A. D., Moccetti, P., & Darwin Tree of Life Consortium. (2023). The genome sequence of the stone loach, Barbatula barbatula (Linnaeus, 1758). Wellcome Open Research, 8, Article 518. https://doi.org/10.12688/wellcomeopenres.20293.1

We present a genome assembly from an individual female Barbatula barbatula (the stone loach; Chordata; Actinopteri; Cypriniformes; Nemacheilidae). The genome sequence is 617.6 megabases in span. Most of the assembly is scaffolded into 25 chromosomal... Read More about The genome sequence of the stone loach, Barbatula barbatula (Linnaeus, 1758).

Integrating environmental DNA monitoring to inform eel (Anguilla anguilla) status in freshwaters at their easternmost range—A case study in Cyprus (2023)
Journal Article
Griffiths, N. P., Wright, R. M., Hänfling, B., Bolland, J. D., Drakou, K., Sellers, G. S., Zogaris, S., Tziortzis, I., Dörflinger, G., & Vasquez, M. I. (2023). Integrating environmental DNA monitoring to inform eel (Anguilla anguilla) status in freshwaters at their easternmost range—A case study in Cyprus. Ecology and Evolution, 13(2), Article e9800. https://doi.org/10.1002/ece3.9800

Despite significant population declines and targeted European Union regulations aimed at Anguilla anguilla conservation, little attention has been given to their status at their easternmost range. This study applies wide-scale integrated monitoring t... Read More about Integrating environmental DNA monitoring to inform eel (Anguilla anguilla) status in freshwaters at their easternmost range—A case study in Cyprus.

What is an otter's favourite food? - a molecular investigation into the dietary preferences of the Eurasian otter (Lutra lutra) across the River Hull Catchment (2022)
Thesis
Macarthur, J. A. What is an otter's favourite food? - a molecular investigation into the dietary preferences of the Eurasian otter (Lutra lutra) across the River Hull Catchment. (Thesis). University of Hull. https://hull-repository.worktribe.com/output/4297795

Knowledge of top predator diets is fundamental to designing appropriate management strategies which ensure the protection of both predator and prey populations. The Eurasian otter (Lutra lutra) has traditionally been described as... Read More about What is an otter's favourite food? - a molecular investigation into the dietary preferences of the Eurasian otter (Lutra lutra) across the River Hull Catchment.

Spatio-temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding (2022)
Journal Article
Di Muri, C., Lawson Handley, L., Bean, C. W., Benucci, M., Harper, L. R., James, B., Li, J., Winfield, I. J., & Hänfling, B. (2023). Spatio-temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding. Environmental DNA, 5(5), 849-860. https://doi.org/10.1002/edn3.343

Determining the timing and location of fish reproductive events is crucial for the implementation of correct management and conservation schemes. Conventional methods used to monitor these events are often unable to assess the spawning activity direc... Read More about Spatio-temporal monitoring of lake fish spawning activity using environmental DNA metabarcoding.

Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison) (2020)
Journal Article
Harper, L. R., Watson, H. V., Donnelly, R., Hampshire, R., Sayer, C. D., Breithaupt, T., & Hänfling, B. (2020). Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison). Metabarcoding and Metagenomics, 4, 113-133. https://doi.org/10.3897/MBMG.4.56087

In the UK, the native European otter (Lutra lutra) and invasive American mink (Neovison vison) have experienced concurrent declines and expansions. Currently, the otter is recovering from persecution and waterway pollution, whereas the mink is in dec... Read More about Using DNA metabarcoding to investigate diet and niche partitioning in the native European otter (Lutra lutra) and invasive American mink (Neovison vison).

Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water (2020)
Journal Article
Blackman, R. C., Ling, K. K. S., Harper, L. R., Shum, P., Hänfling, B., & Lawson-Handley, L. (2020). Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water. Ecology and Evolution, https://doi.org/10.1002/ece3.6921

The early detection of invasive non-native species (INNS) is important for informing management actions. Established monitoring methods require the collection or observation of specimens, which is unlikely at the beginning of an invasion when densiti... Read More about Targeted and passive environmental DNA approaches outperform established methods for detection of quagga mussels, Dreissena rostriformis bugensis in flowing water.

Environmental DNA metabarcoding provides enhanced detection of the European eel Anguilla anguilla and fish community structure in pumped river catchments (2020)
Journal Article
Griffiths, N. P., Bolland, J. D., Wright, R. M., Murphy, L. A., Donnelly, R. K., Watson, H. V., & Hänfling, B. (2020). Environmental DNA metabarcoding provides enhanced detection of the European eel Anguilla anguilla and fish community structure in pumped river catchments. Journal of fish biology, 97, 1375-1384. https://doi.org/10.1111/jfb.14497

© 2020 Fisheries Society of the British Isles The European eel Anguilla anguilla (eel hereafter) is critically endangered and has a catadromous life cycle, which means adult eels that live in pumped catchments must pass through pumps during their dow... Read More about Environmental DNA metabarcoding provides enhanced detection of the European eel Anguilla anguilla and fish community structure in pumped river catchments.

Fishing for mammals: Landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from riverine systems (2020)
Journal Article
Sales, N. G., McKenzie, M. B., Drake, J., Harper, L. R., Browett, S. S., Coscia, I., Wangensteen, O. S., Baillie, C., Bryce, E., Dawson, D. A., Ochu, E., Hänfling, B., Lawson Handley, L., Mariani, S., Lambin, X., Sutherland, C., & McDevitt, A. D. (2020). Fishing for mammals: Landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from riverine systems. The journal of applied ecology, 57(4), 707-716. https://doi.org/10.1111/1365-2664.13592

© 2020 British Ecological Society Environmental DNA (eDNA) metabarcoding has revolutionized biomonitoring in both marine and freshwater ecosystems. However, for semi-aquatic and terrestrial animals, the application of this technique remains relativel... Read More about Fishing for mammals: Landscape-level monitoring of terrestrial and semi-aquatic communities using eDNA from riverine systems.

Simple, sensitive and species-specific assays for detecting quagga and zebra mussels (Dreissena rostriformis bugensis and D. polymorpha) using environmental DNA (2020)
Journal Article
Blackman, R. C., Benucci, M., Donnelly, R., Hänfling, B., Harper, L. R., Sellers, G. S., & Lawson-Handley, L. (2020). Simple, sensitive and species-specific assays for detecting quagga and zebra mussels (Dreissena rostriformis bugensis and D. polymorpha) using environmental DNA. Management of Biological Invasions, 11(2), 218-236. https://doi.org/10.3391/mbi.2020.11.2.04

Early detection is paramount for attempts to remove invasive non-native species (INNS). Traditional methods rely on physical sampling and morphological identification, which can be problematic when species are in low densities and/or are cryptic. The... Read More about Simple, sensitive and species-specific assays for detecting quagga and zebra mussels (Dreissena rostriformis bugensis and D. polymorpha) using environmental DNA.

Monitoring methods for assessing inshore fish communities. Natural England Commissioned Report NECR269 (2020)
Report
Franco, A., Nunn, A., Smyth, K., Hanfling, B., & Mazik, K. (2020). Monitoring methods for assessing inshore fish communities. Natural England Commissioned Report NECR269. Natural England

Executive Summary

This report provides a review of the monitoring techniques that can be used to assess inshore fish communities. This is the first part of a study aimed at developing a regional pilot monitoring programme for inshore fish communit... Read More about Monitoring methods for assessing inshore fish communities. Natural England Commissioned Report NECR269.

Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian (2019)
Journal Article
Harper, L. R., Lawson Handley, L., Hahn, C., Boonham, N., Rees, H. C., Lewis, E., Adams, I. P., Brotherton, P., Phillips, S., & Hänfling, B. (2020). Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian. Environmental DNA, 2(2), 184-199. https://doi.org/10.1002/edn3.57

Background: Environmental DNA (eDNA) metabarcoding is revolutionizing biodiversity monitoring, but has unrealized potential for ecological hypothesis generation and testing. Aims: Here, we validate this potential in a large-scale analysis of vertebra... Read More about Generating and testing ecological hypotheses at the pondscape with environmental DNA metabarcoding: A case study on a threatened amphibian.

Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals (2019)
Journal Article
Ghazali, M., Harper, L. R., Lawson Handley, L., Carpenter, A. I., Murray-Dickson, G., Di Muri, C., Macgregor, C. J., Logan, T. W., Law, A., Breithaupt, T., Read, D. S., McDevitt, A. D., & Hänfling, B. (2019). Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals. Biological Conservation, 238(October 2019), Article 108225. https://doi.org/10.1016/j.biocon.2019.108225

© 2019 Elsevier Ltd Environmental DNA (eDNA) metabarcoding can identify terrestrial taxa utilising aquatic habitats alongside aquatic communities, but terrestrial species' eDNA dynamics are understudied. We evaluated eDNA metabarcoding for monitoring... Read More about Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals.

Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding (2019)
Journal Article
Li, J., Lawson Handley, L. J., Harper, L. R., Brys, R., Watson, H. V., Di Muri, C., Zhang, X., & Hänfling, B. (2019). Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding. Environmental DNA, 1(3), 238-250. https://doi.org/10.1002/edn3.24

Background: Environmental DNA (eDNA) metabarcoding is a promising tool for rapid, non-invasive biodiversity monitoring. Aims: In this study, eDNA metabarcoding is applied to explore the spatial and temporal distribution of fish communities in two aqu... Read More about Limited dispersion and quick degradation of environmental DNA in fish ponds inferred by metabarcoding.

Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake (2019)
Journal Article
Lawson Handley, L., Read, D. S., Winfield, I. J., Kimbell, H., Johnson, H., Li, J., Hahn, C., Blackman, R., Wilcox, R., Donnelly, R., Szitenberg, A., & Hänfling, B. (2019). Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake. Environmental DNA, 1(1), 26-39. https://doi.org/10.1002/edn3.5

Environmental DNA offers great potential as a biodiversity monitoring tool. Previous work has demonstrated that eDNA metabarcoding provides reliable information for lake fish monitoring, but important questions remain about temporal and spatial repea... Read More about Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake.

Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds (2018)
Journal Article
Harper, L. R., Buxton, A. S., Rees, H. C., Bruce, K., Brys, R., Halfmaerten, D., Read, D. S., Watson, H. V., Sayer, C. D., Jones, E. P., Priestley, V., Mächler, E., Múrria, C., Garcés-Pastor, S., Medupin, C., Burgess, K., Benson, G., Boonham, N., Griffiths, R. A., Lawson Handley, L., & Hänfling, B. (2019). Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds. Hydrobiologia, 826(1), 25-41. https://doi.org/10.1007/s10750-018-3750-5

© 2018, The Author(s). Environmental DNA (eDNA) analysis is a rapid, non-invasive, cost-efficient biodiversity monitoring tool with enormous potential to inform aquatic conservation and management. Development is ongoing, with strong commercial inter... Read More about Prospects and challenges of environmental DNA (eDNA) monitoring in freshwater ponds.

Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types (2018)
Journal Article
Sellers, G. S., Di Muri, C., Gómez, A., & Hänfling, B. (2018). Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types. Metabarcoding and Metagenomics, 2, e24556. https://doi.org/10.3897/mbmg.2.24556

Efficient DNA extraction is fundamental to molecular studies. However, commercial kits are expensive when a large number of samples need to be processed. Here we present a simple, modular and adaptable DNA extraction ‘toolkit’ for the isolation of hi... Read More about Mu-DNA: a modular universal DNA extraction method adaptable for a wide range of sample types.