Identification

Title

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

Abstract

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

Resource type

dataset

Resource locator

https://data-package.ceh.ac.uk/data/c67fde7f-a1c8-4cb4-a76e-0c6d21c82222

name: Download the data

description: Download a copy of this data

function: download

https://data-package.ceh.ac.uk/sd/c67fde7f-a1c8-4cb4-a76e-0c6d21c82222.zip

name: Supporting information

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

function: information

Unique resource identifier

code

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

codeSpace

doi:

Dataset language

eng

Spatial reference system

code identifying the spatial reference system

Classification of spatial data and services

Topic category

biota

Keywords

Keyword set

keyword value

Environmental Monitoring Facilities

originating controlled vocabulary

title

GEMET - INSPIRE themes, version 1.0

reference date

date type

publication

effective date

2008-06-01

Keyword set

keyword value

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

Geographic location

West bounding longitude

-0.66

East bounding longitude

-0.633

North bounding latitude

51.422

South bounding latitude

51.398

Temporal reference

Temporal extent

Begin position

2014-11-01

End position

2015-11-30

Dataset reference date

date type

publication

effective date

2022-11-25

Frequency of update

Quality and validity

Lineage

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.

Conformity

Conformity report

specification

title

Commission Regulation (EU) No 1089/2010 of 23 November 2010 implementing Directive 2007/2/EC of the European Parliament and of the Council as regards interoperability of spatial data sets and services

owner

Metadata on metadata

Metadata point of contact

organisation name

Environmental Information Data Centre

full postal address

Lancaster Environment Centre, Library Avenue, Bailrigg

Lancaster

LA1 4AP

email address

info@eidc.ac.uk

responsible party role

pointOfContact

Metadata date

2023-02-09T11:08:57

Metadata language

eng