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All Outputs (47)

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., …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.

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. (in press). 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, Article e56087. 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.

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.

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., …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., …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., …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., …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., …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.

The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding (2018)
Journal Article
Li, J., Lawson Handley, L. J., Read, D. S., & Hänfling, B. (2018). The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding. Molecular Ecology Resources, 18(5), 1102-1114. https://doi.org/10.1111/1755-0998.12899

© 2018 John Wiley & Sons Ltd. Environmental DNA (eDNA) is a promising tool for rapid and noninvasive biodiversity monitoring. eDNA density is low in environmental samples, and a capture method, such as filtration, is often required to concentrate e... Read More about The effect of filtration method on the efficiency of environmental DNA capture and quantification via metabarcoding.

Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus) (2018)
Journal Article
Harper, L. R., Lawson Handley, L., Hahn, C., Boonham, N., Rees, H. C., Gough, K. C., …Hänfling, B. (2018). Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus). Ecology and Evolution, 8(12), 6330-6341. https://doi.org/10.1002/ece3.4013

Environmental DNA (eDNA) analysis is a rapid, cost‐effective, non‐invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species‐specific survey tool for rar... Read More about Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus).

Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive (2018)
Journal Article
Hering, D., Borja, A., Jones, J. I., Pont, D., Boets, P., Bouchez, A., …Kelly, M. (2018). Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive. Water Research, 138, 192-205. https://doi.org/10.1016/j.watres.2018.03.003

Assessment of ecological status for the European Water Framework Directive (WFD) is based on “Biological Quality Elements” (BQEs), namely phytoplankton, benthic flora, benthic invertebrates and fish. Morphological identification of these organisms is... Read More about Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive.

A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations (2017)
Journal Article
Sellers, G. S., Griffin, L. R., Hänfling, B., & Gómez, A. (2017). A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations. PeerJ, 2017(5), Article e3228. https://doi.org/10.7717/peerj.3228

© 2017 Sellers et al. The tadpole shrimp, Triops cancriformis, is a freshwater crustacean listed as endangered in the UK and Europe living in ephemeral pools. Populations are threatened by habitat destruction due to land development for agriculture a... Read More about A new molecular diagnostic tool for surveying and monitoring Triops cancriformis populations.

Detection of a new non-native freshwater species by DNA metabarcoding of environmental samples — first record of Gammarus fossarum in the UK (2017)
Journal Article
Blackman, R. C., Constable, D., Hahn, C., Sheard, A. M., Durkota, J., Hänfling, B., & Handley, L. L. (2017). Detection of a new non-native freshwater species by DNA metabarcoding of environmental samples — first record of Gammarus fossarum in the UK. Aquatic Invasions, 12(2), 177-189. https://doi.org/10.3391/ai.2017.12.2.06

© 2017 The Author(s). and 2017 REABIC. We report the discovery of a non-native gammarid, Gammarus fossarum (Koch, 1836) (Crustacea, Amphipoda), in UK rivers. Gammarus fossarum is a common freshwater gammarid in many parts of mainland Europe, but was... Read More about Detection of a new non-native freshwater species by DNA metabarcoding of environmental samples — first record of Gammarus fossarum in the UK.

Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England (2017)
Journal Article
Jeffries, D. L., Copp, G. H., Maes, G. E., Lawson Handley, L., Sayer, C. D., & Hänfling, B. (2017). Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England. Ecology and Evolution, 7(9), 2871-2882. https://doi.org/10.1002/ece3.2831

© 2017 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd. A fundamental consideration for the conservation of a species is the extent of its native range, that is, regions naturally colonized. However, both natural processes and... Read More about Genetic evidence challenges the native status of a threatened freshwater fish (Carassius carassius) in England.

Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods (2016)
Journal Article
Hänfling, B., Lawson Handley, L., Read, D. S., Hahn, C., Li, J., Nichols, P., …Winfield, I. J. (2016). Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Molecular ecology, 25(13), 3101-3119. https://doi.org/10.1111/mec.13660

Organisms continuously release DNA into their environments via shed cells, excreta, gametes and decaying material. Analysis of this ‘environmental DNA’ (eDNA) is revolutionizing biodiversity monitoring. eDNA outperforms many established survey method... Read More about Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods.

Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L. (2016)
Journal Article
Jeffries, D. L., Copp, G. H., Lawson Handley, L., Olsén, K. H., Sayer, C. D., & Hänfling, B. (2016). Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L. Molecular ecology, 25(13), 2997-3018. https://doi.org/10.1111/mec.13613

The conservation of threatened species must be underpinned by phylogeographic knowledge. This need is epitomized by the freshwater fish Carassius carassius, which is in decline across much of its European range. Restriction site-associated DNA sequen... Read More about Comparing RADseq and microsatellites to infer complex phylogeographic patterns, an empirical perspective in the Crucian carp, Carassius carassius, L..