Wild rodent trapping, tracking and sampling for genetics and gut microbiome, Silwood Park, Berkshire, November 2014 to November 2015

This data set is a combination of trapping data, tracking data and data on the genetic relatedness and gut microbiome composition of wild rodents caught in 2.3 ha study site in Nash’s Copse, Silwood Park, from November 2014 to November 2015. As part of a longer-term capture-mark-recapture study, three species of rodents were trapped with Sherman live-traps fortnightly for 12 months: wood mouse (Apodemus sylvaticus), yellow-necked mouse (Apodemus flavicollis) and bank vole (Myodes glaerolus). Upon capture, they were measured, weighted, sexed, aged and a tissue sample and a faecal sample were collected from all mouse individuals for genetic and microbiome analyses. All rodents were released to their location of capture. First time each individual was captured, they were injected with a permanent subcutaneous identification Radio-Frequency Identification(RFID)-tag (Passive Integrated Transponde-tag). The tagged rodents were subsequently tracked with a set of custom-made tracking devices (loggers). Loggers produced dense time-stamped occurrence data suitable for inferring spatio-temporal activity patterns of rodents, such as temporal niches, home ranges and social networks. Tissue samples were used to genotype the wood mouse population and bacterial DNA extracted from faecal samples were used to profile their gut microbiome composition.

This work was funded by a NERC independent Research Fellowship to Sarah Knowles (NE/L011867/1)

Full details about this dataset can be found at https://doi.org/10.5285/c67fde7f-a1c8-4cb4-a76e-0c6d21c82222

Identification info

Metadata Language: English (en)

Character set: utf8

Dataset Reference Date (): 2022-11-25

Identifier: https://catalogue.ceh.ac.uk/id/c67fde7f-a1c8-4cb4-a76e-0c6d21c82222

Identifier: doi: / 10.5285/c67fde7f-a1c8-4cb4-a76e-0c6d21c82222

Other citation details: Raulo, A., Allen, B.E., Troitsky, T., Husby, A., Firth, J., Coulson, T., Knowles, S.C.L. (2022). Wild rodent trapping, tracking and sampling for genetics and gut microbiome, Silwood Park, Berkshire, November 2014 to November 2015. NERC EDS Environmental Information Data Centre 10.5285/c67fde7f-a1c8-4cb4-a76e-0c6d21c82222

University of Oxford - Raulo, A.

University of Liverpool - Allen, B.E.

University of Helsinki - Troitsky, T.

Uppsala University - Husby, A.

University of Oxford - Firth, J.

University of Oxford - Coulson, T.

University of Oxford - Knowles, S.C.L.

University of Oxford - Raulo, A.

NERC EDS Environmental Information Data Centre

Imperial College London

GEMET - INSPIRE themes, version 1.0 ()

Environmental Monitoring Facilities

Keywords

Microbiome
microbiota
gut microbiome
trapping
Sherman
wild mouse
wild
mouse
wood mouse
bank vole
yellow-necked mouse
Apodemus
Myodes
RFID-tracking
social network analysis
home range analysis
microsatellites
kinship
pedigree

Limitations on Public Access: otherRestrictions

Other constraints: no limitations

Use constraints: otherRestrictions

Other constraints: This resource is available under the terms of the Open Government Licence

Use constraints: otherRestrictions

Other constraints: If you reuse this data, you should cite: Raulo, A., Allen, B.E., Troitsky, T., Husby, A., Firth, J., Coulson, T., Knowles, S.C.L. (2022). Wild rodent trapping, tracking and sampling for genetics and gut microbiome, Silwood Park, Berkshire, November 2014 to November 2015. NERC EDS Environmental Information Data Centre https://doi.org/10.5285/c67fde7f-a1c8-4cb4-a76e-0c6d21c82222

Spatial representation type: textTable

Topic category

Biota

Begin date: 2014-11-01

End date: 2015-11-30

Code: OSGB 1936 / British National Grid

Distribution Information

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Resource Locator: Supporting information
Supporting information available to assist in re-use of this dataset

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Resource Locator: Supporting information
Supporting information available to assist in re-use of this dataset

Quality Scope: dataset

Other: dataset

Report

Dataset Reference Date (): 2010-12-08

Statement: Wild rodents were trapped fortnightly, tagged and continuously monitored with tracking technology for one year. This is a natural rodent population and no experimental manipulations were made. Upon capture, faecal samples were collected from the rodents and a piece of ear tissue was collected upon first capture of each individual. Tissue samples were stored in ethanol in -20 C and faecal samples were stored without buffer in -80 C for 3 years. In 2017 DNA was extracted from the faecal samples of wood mice and their gut microbiome was characterised from this by amplification and sequencing of the V3 region of bacterial 16S rRNA marker gene. In 2018 the wood mouse population was genotyped and their pedigree reconstructed from ear tissue samples using 11 microsatellite markers. Details of the data and the cleaning process can be found from the supporting documentation.

Metadata

File identifier: c67fde7f-a1c8-4cb4-a76e-0c6d21c82222 XML

Metadata Language: English (en)

Character set: ISO/IEC 8859-1 (also known as Latin 1)

Resource type: dataset

Hierarchy level name: dataset

Metadata Date: 2023-02-09T11:08:57

Metadata standard name: UK GEMINI

Metadata standard version: 2.3

Environmental Information Data Centre

Lancaster Environment Centre, Library Avenue, Bailrigg , Lancaster , LA1 4AP , UK

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