Otter diet in Sheffield and the Peak District
The main aims of this proposed study:
- identify otter diet and seasonality.
- compare otter diet in different river systems and urban and rural environments.
- study the reliance of the otter on the invasive signal crayfish, that is now common in our local rivers.
- compare the diet of the otter with that of the American mink.
- investigate American mink predation of water vole.
Identifying the drivers of otter movements and how these are linked to prey availability, seasonality or preference is vital to know how to improve habitats and access to food. Identifying otter prey species and mapping their locations will allow us to make efforts to improve prey connectivity with the aim of reducing the risks to otters whilst travelling, such as otter deaths by road traffic.
We intend to investigate the frequency that our local otters feed on the invasive signal crayfish Pacifastacus leniusculus and whether there is any association with the presence of otter and crayfish. Our endangered native white-clawed crayfish Austropotamobius pallipes remains in only a few places in Sheffield and the Peak District due to wide-scale deaths caused by the disease carried by signal crayfish.
The Peak District is one of few remaining regions in the UK, where one of our fastest declining mammals, the water vole Arvicola amphibius can still be regularly seen. Water voles are thought to be predated by the invasive American mink Neovison vison, which is present on most of our local rivers. We therefore also intend to investigate the diet of the American mink and the frequency at which we detect water vole in mink scat.
The work flow
a) Survey the banks of the rivers, lakes and reservoirs surrounding Sheffield and nearby in the Peak District to collect otter droppings (spraint) and mink scats.
b) Extract genomic DNA from the faecal samples using commercial kits.
c) A genetic marker would be used to identify which species produced the dropping. Mink scat and otter spraint can be easily mixed up when collected in the field, as revealed by published DNA-based studies.
d) The diet of local otters and mink will be assessed to detect prey species using a set of mitochondrial DNA markers.
(e) Microscopic analysis will be performed to identity the prey present in 10 spraints. The results will be compared to the list of species list detected by DNA analysis. Microscopic analysis will allow us to estimate the sizes of the prey and whether predated as adults or juveniles. It may also allow us to estimate the minimum numbers of each species of prey items taken and size of the individuals eaten.
(f) For any spraints that were found to contain otter and mink DNA, microscopic analysis of the spraints will be performed to identify if any of the spraints include mink bones (this would suggest otters are eating mink).
To complete this work we plan to collect otter spraint at specific locations along river banks of Sheffield's suburbs and the waterways of the Peak District.
Waterways to be surveyed include:
- Sheffield's rivers: River Don and it's tributaries the Loxley, Rivelin, Porter and Sheaf
- The Sheffield and Tinsley Canal and Sheffield's "Blue Loop"
- Reservoirs in the Peak District and surrounding Sheffield: Rivelin Dams, Redmires, Strines, Dale Dike, Agden, Damflask, Broomhead, Moor Hall, Ladybower, Derwent and Howden Reservoir
- Peak District rivers: River Derwent, Wye and Noe
- The Cromford Canal in Derbyshire
Small Pilot Project - Method Development - Completed
Part 1: DNA analysis of droppings
The diet of local otters was assessed to detect prey species and test the species specificity of the DNA marker. This was done by sequencing the DNA found in 10 otter spraints with a single 12s mitochondrial DNA marker. Additional markers (and samples) will be added in the future, subject to funding.
Examples of the fish species present on the River Don include perch, brown trout, grayling, roach, dace, chub, barbel, gudgeon, minnow, bullhead and brook lamprey (brook lamprey is only found in the River Rivelin). There may also be carp, tench and rudd but these are not resident and will have escaped from adjacent ponds.
The DNA analyses identified nine fish species in total: 6 from the list above, perch, brown trout, grayling, gudgeon, minnow, bullhead and also pike, stickleback and stone loach (Table 1). It was found that many otter spraints included small fish, such as bullhead, minnow and stickleback, suggesting these are a common part of the otters diet on the River Don.
This pilot study revealed that additional genetic markers are required to detect crayfish and amphibian DNA (bones from these species were observed in spraint, see below). Additional markers are also required to distinguish between some species of Cyprinidae fish (common carp, barbel, tench, roach, rudd, chub, dace etc) and to assign songbirds to species level.
Table 1: Prey species detected in droppings by 12s DNA sequencing
|Number of faecal samples analysed||Species producing dropping*||Date samples were collected||Prey taxa found in spraint (number of species)||Species detected in sample by DNA analysis|
Sequenced using a high read depth on a MiSeq Sequencer)
|21st August 2016||Fish (8)
Fish: Perch, Esox (pike), Cottales (bullhead), minnow, Gasterosteales (stickleback), brown trout, gudgeon and Barbatula (stone loach),
|23rd August 2016||Fish (3)
Fish: Bullhead (Cottidae),
|Total of ten otter spraint samples combined||All confirmed otter||20th May 2016 until 23rd October 2016||Fish (9)
|Fish: Bullhead, minnow, stickleback, brown trout, gudgeon, perch, pike, grayling (Thymallus) species and stone loach,
Birds: Moorhen and grey heron
|22nd August 2016||Bird (1)||Bird: Pigeon / wood pigeon|
|13th August 2016||Mammal (1)||Mammal: Short-tailed vole (aka field vole Microtus agrestis)|
|21st August 2016||Mammal (1)||Mammal: Rabbit|
*The identity of the species producing the dropping was revealed by 12s DNA sequencing.
Part 2: Microscopic and visual analysis of prey found in droppings
Microscopic analysis has been performed on three otter spraints (#3, #119 and #137) collected on the River Don in Sheffield and a mink scat from the Peak District (L1).
Species identification was performed using a binocular microscope (Leica MZ125) (#119 and #137) .
Fish species were assigned by comparing the bones to reference images in Conroy et al. 2005 by Barry Soames and by comparison to a reference collection of images and samples held in the Department of Archaeology by Angela Maccarinelli.
Conroy JWH, Watt J, Webb JB, Jones A (2005) A Guide to the Identification of Prey Remains in Otter Spraints. Mammal Society Occasional Publications, London. Illustrated by Ruth Pollitt, Guy Troughton and Anna Jones.
Mammal and amphibian species were assigned by reference to John Rochester's online flickr database of images and collection of bones and teeth. The Rochester reference images used are available here.
We also checked two otter spraints from the River Derwent in the Peak District (samples CG and DJR) for prey items by unaided observation of contents while the spraint was fresh or stored in absolute ethanol.
Microscopic analysis revealed fish, amphibians, birds and crayfish were present in otter spraint (Table 2). Three fish species found in otter spraints using microscopic analysis and the same three species were also found using the DNA analyses (Bullhead, Minnow and Gudgeon). Only one otter spraint sample (#119) was directly compared using both methods.
The results did not conflict but revealed each method had its advantages. The DNA-based analyses allowed us to identify the identities of the fish and birds present to species level resolution, but did not detect the crayfish or amphibian. This revealed that the samples need to be sequenced with additional markers to identify the crayfish or amphibian species present.
Crayfish were present in two of the three otter spraints collected from the River Don in Sheffield and crustacean shell and leg were seen by eye in both spraints collected from the River Derwent in the Peak District. Crayfish were detected in spraint during the months July-October.
It is believed the crustacean parts observed, are remains of the invasive American signal crayfish Pacifastacus leniusculus because white clawed crayfish are not present on the River Don or River Derwent at the location where the spraints were found.
The assignment of skeletal remains, especially fish vertebrae, to specific species requires expert knowledge, and, even then, can prove difficult even when a reference collection is available. Only three fish species were microscopically identified in otter spraint: Bullhead (Cottus gobio), Gudgeon (Gobio gobio), Perch (Perca fluviatilis) or Grayling (Thymallus thymallus).
A frog/toad limb bone and bird beak was seen in one otter spraint but it is not possible to assign the species from these remains. However ages of these prey could be estimated from microscopic analysis, the size of the beak corresponded to an unhatched chick and the frog/toad bone was from an adult.
The size/stage of the prey can't be revealed from DNA analyses but the DNA analyses of the same sample (#119) suggested the beak was that of a moorhen.
Some of the mammals can be identified to species level from microscopic analysis (eg using their teeth for the short-tailed vole) but the DNA analysis will be vital to assign a specific species to many of the prey items present in the spraints, especially the fish and bird species.
The Peak District mink scat contained field vole remains, the fox scat contained rabbit and bird bones, and the pine marten contained vole and amphibian remains, and beetles and fruit stones.
Table 2: Microscopic and Visual Analysis of Otter Spraint and Mink Scat collected in South Yorkshire and Derbyshire
|Sample||Known^ / suspected species of origin*||Location of sample||Date collected||Prey taxa observed (number of species)||Contents identified by microscopic and visible analysis|
|3||Otter^||River Don, Sheffield||20th May 2016||Fish (3)||Fish: Bullhead (multiple bones) [AM]
Cyprinid (multiple bones) [AM]
Gudgeon (Gobio gobio) vertebrae Cyprinidae [AM]
Perch (Perca fluviatilis) or Grayling (Thymallus thymallus) scale [AM]
|94||Otter^||River Don, Sheffield||21st August 2016||Bird (1)||Bird: feathers [JR]
(Little sample remained after DNA extraction. Examined at low magnification.)
|119||Otter^||River Don, Sheffield||23rd August 2016||Crayfish (1)
Crayfish: shell [BS]
|137||Otter^||River Don, Sheffield||9th September 2016||Crayfish (1)
Crayfish: legs [BS]
|CG||Otter*||River Derwent, Peak District||25th July 2017||Crayfish (1)||Crayfish: legs visible on photograph (no samples taken)|
|DJR||Otter*||River Derwent, Peak District||21st October 2017||Crayfish (1)
Fish: fish scales visible on photographs (awaiting microscopic analyses)
|L1||Mink^||River Wye, Peak District||22nd January 2017||Mammal (1)||Mammal: Short-tailed vole (aka Field vole Microtus agrestis) teeth (2 teeth, possibly M1 and M2 lower, adult) [JR],
Rodent (?) jaw [JR],
Mouse/vole hip bone (proximal femur) [JR],
Brown fur [JR]
|B||Fox*||Isle of Skye||20th May 2017||Mammal (1)
Mammal: Rabbit (jaw) [JR]
|C||Pine marten*||Isle of Skye||May 2017||Mammal (1)
Mammal: vole [JR]
|D||Pine marten*||Isle of Skye||May 2017||Invertebrates
Invertebrates: Beetles [BS]
^The identity of the species producing the dropping was confirmed by 12s DNA sequencing.
*The species stated as producing the dropping is based on the appearance and smell of the sample only.
Table 3 Summary of all the species detected in otter spraints, so far..
|Prey Taxa & Family||Prey species identified||Prey DNA detected||Prey seen under microscope||Rivers in which prey was found||Months in which prey was found||Samples containing DNA of stated species
(n=12 tested, samples 3 & 137 not yet assessed)
|Samples examined with microscope
(n=3 tested, all collected on river Don)
|Microscope observation notes|
|94, 119, +10 pooled||3 , 119, 137~|
|94, 119, +10 pooled||137~|
|94, +10 pooled||3|
|Grayling||√||(√)*||Don||May||10 pooled||3||*Grayling/perch, Not possible to distinguish|
|94, +10 pooled||3||*Grayling/perch, Not possible to distinguish|
|Stickleback||√||Don||August||94, +10 pooled|
|Brown trout||√||Don||August||94, 119, +10 pooled|
|Pike||√||Don||August||94, +10 pooled|
|Stone loach||√||Don||August||94, +10 pooled|
|"||Unknown bird species||√||Don||August||119||Small beak, based on size, pre-hatching or nestling. Has a wide bill shape, could be a moorhen.|
|Amphibian||Frog / Toad^||√||Don||August||119||It is not possible to determine if a frog or toad based on any frog / toad skeleton.|
|119, 137||Suspected to be the invasive Signal crayfish.|
*it was not possible to distinguish grayling / perch species using the microscope.
^it was not possible to distinguish between frog and toad bones using the microscope.
~fish bones in samples 3, 137 and 119 were microscopically analysed by AM and BS (sample 137 to be checked by AM for minnow).
In summary, to date, the species we have detected in the diet of our local otters on the river Don surrounding Sheffield includes:
9 fish species, 2 birds (moorhen and grey heron), an amphibian (frog/toad) and a crayfish species
Crayfish was also found in spraints collected on the river Derwent. The crayfish species is likely to be the invasive signal crayfish Pacifastacus leniusculus based on the remains found on the river banks and the distribution of this species on the river Don and river Derwent.
The DNA analysis method was able to assign more fish to species level (n=9) than the microscopic analysis (n=3). However, additional non-fish species were detected by the microscopic analysis which revealed that extra DNA markers are required to detect amphibians and crustaceans. The microscopic analysis also revealed that otters are feeding on either newly hatching chicks or chicks that had not yet hatched (based on the size of the bird beak found).
How to help and get involved
We are appealing for help to find otter spraint and mink scat, particularly in the Peak District. If you know of locations where otters or mink are present or where spraint or scat might be found please contact Dr Deborah Dawson (email@example.com).
Otters are easily disturbed even by the most well-meaning of people and so all information will be kept in confidence and specific details not released to avoid any threat or disturbance to otters.
If you are willing to collect otter spraint or mink scat, we can provide information on recognising spraint/scat, instructions on how to collect samples and provide tubes. We can collect samples from volunteer surveyors or advise on drop-off points.
Several local wildlife groups are surveying for otter spraint (including the Derbyshire Wildlife Trust, the Sorby Natural History Society and the Moors for the Future Partnership). We would be very grateful to receive otter/suspected otter spraint samples for DNA analysis from any groups or individuals (please contact Dr Deborah Dawson (firstname.lastname@example.org).
If you are interested in receiving training and taking part by looking for signs of otters please get in touch.
The Derbyshire Wildlife Trust and the Moors for the Future Partnership provided training sessions in surveying for otters, mink or water voles in 2017 and 2018 and may provide more training in the future.
Collaboration and funding appeal
We are appealing for sponsors and partners to support and collaborate with this work, please contact Dr Deborah Dawson (email@example.com).
Make a donation with Virgin moneygiving
Personnel involved with the pilot project
Dr Deborah Dawson (firstname.lastname@example.org, @ddawson777)
DNA-based diet analyses:
Lucy Knowles (MRes student, 2017-2018)
Dr Sabuj Bhattacharyya (British Commonwealth Fellow, 2016-2017)
Dr Gavin Horsburgh
Dr Helen Hipperson
Microscopic analyses of spraint:
Barry Soames (Otter Project Volunteer)
John Rochester (Head of Anatomy, Academic Unit of Medical Education, UoS)
Angela Maccarinelli (Department of Archaeology, University of Sheffield)
Barry Soames extracted the solid contents from the spraints and scats, and also photographed these and did the initial assessment of the prey species present.
Barry's images of the fish vertebrae and fish bones, crustacean shell, bird beak and a suspected amphibian bone found in otter spraint and also the mammal hair, bones and the two field vole teeth found in a mink scat and the invertebrates in the pine marten scats are available here.
John Rochester also kindly identified the mammal, bird and amphibian species from skeletal remains. John's reference images of bones and teeth as used to assign species are available here.
Angela Maccarinelli identified the fish species present in the otter spraints (sample numbers #3, #119 and #137) based on a comparison to the reference collection held in the Zooarchaelogy Laboratory and a comparison to online images of fish skeletal remains.
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