3affed0d-fe6f-4916-89e3-e672639191e5
English
ISO/IEC 8859-1 (also known as Latin 1)
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NERC EDS Environmental Information Data Centre
Lancaster Environment Centre, Library Avenue, Bailrigg
Lancaster
LA1 4AP
UK
info@eidc.ac.uk
https://eidc.ac.uk/
EIDC website
The Environmental Information Data Centre (EIDC) is the UK's national data centre for terrestrial and freshwater sciences.
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2024-03-01T11:27:28
UK GEMINI
2.3
WGS 84
Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia
2018-08-08
publication
https://catalogue.ceh.ac.uk/id/3affed0d-fe6f-4916-89e3-e672639191e5
10.5285/3affed0d-fe6f-4916-89e3-e672639191e5
doi:
Drinkwater, R., Schnell, I.D., Bohmann, K., Bernard, H., Veron, G., Clare, E., Gilbert, T.P., Rossiter, S.J. (2018). Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia. NERC Environmental Information Data Centre 10.5285/3affed0d-fe6f-4916-89e3-e672639191e5
This dataset contains the results from a metabarcoding study of terrestrial leech blood meals to detect differences in the diets of two leech species, Haemadipsa picta and Haemadipsa sumatrana. Mammal taxa were identified using metabarcoding of 16s rRNA and comparisons of operational taxonomic units (OTUs) to a curated reference database from NCBI (National Center for Biotechnology Information) GenBank. All leeches were collected from the Stability of Altered Forest Ecosystems project (SAFE; www.SAFEproject.net) as part of the NERC Human Modified tropical Forest Programme and the LOMBOK consortia (Land-use Options for Maintaining BiOdiversity & eKosystem functions). Leech samples were collected at different sites across a habitat gradient, to assess these invertebrates as molecular sampling tools for mammals. Individuals were pooled before amplicon sequencing with Illumina MiSeq 150-200bp x2. The resultant raw sequences were filtered and clustered at 97%, curated and then assigned to the reference database using BLAST and MEGAN programmes. Full details about this dataset can be found at https://doi.org/10.5285/3affed0d-fe6f-4916-89e3-e672639191e5
Rosie Drinkwater
Queen Mary University of London
enquiries@ceh.ac.uk
pointOfContact
Drinkwater, R.
Queen Mary University of London
enquiries@ceh.ac.uk
https://orcid.org/0000-0001-6892-1664
ORCID record
ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.
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author
Schnell, I.D.
Natural History Museum of Denmark
enquiries@ceh.ac.uk
https://orcid.org/0000-0002-0436-785X
ORCID record
ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.
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author
Bohmann, K.
Natural History Museum of Denmark
enquiries@ceh.ac.uk
https://orcid.org/0000-0001-7907-064X
ORCID record
ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.
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author
Bernard, H.
Universiti of Malaysia Sabah
enquiries@ceh.ac.uk
author
Veron, G.
Muséum national d'Histoire naturelle
enquiries@ceh.ac.uk
https://orcid.org/0000-0003-4247-3976
ORCID record
ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.
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author
Clare, E.
Queen Mary University of London
enquiries@ceh.ac.uk
https://orcid.org/0000-0002-6563-3365
ORCID record
ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.
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author
Gilbert, T.P.
Natural History Museum of Denmark
enquiries@ceh.ac.uk
https://orcid.org/0000-0002-5805-7195
ORCID record
ORCID is an open, non-profit, community-driven effort to create and maintain a registry of unique researcher identifiers and a transparent method of linking research activities and outputs to these identifiers.
information
author
Rossiter, S.J.
Queen Mary University of London
enquiries@ceh.ac.uk
author
NERC EDS Environmental Information Data Centre
enquiries@ceh.ac.uk
custodian
NERC Environmental Information Data Centre
enquiries@ceh.ac.uk
publisher
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no limitations
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This resource is made available under the terms of the Open Government Licence
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If you reuse this data, you should cite: Drinkwater, R., Schnell, I.D., Bohmann, K., Bernard, H., Veron, G., Clare, E., Gilbert, T.P., Rossiter, S.J. (2018). Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia. NERC Environmental Information Data Centre https://doi.org/10.5285/3affed0d-fe6f-4916-89e3-e672639191e5
textTable
150
English
utf8
biota
2015-02-01
2015-06-30
113.75
119.353
4.182
7.111
Comma-separated values (CSV)
NERC EDS Environmental Information Data Centre
info@eidc.ac.uk
distributor
https://data-package.ceh.ac.uk/data/3affed0d-fe6f-4916-89e3-e672639191e5
Download the data
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https://data-package.ceh.ac.uk/sd/3affed0d-fe6f-4916-89e3-e672639191e5.zip
Supporting information
Supporting information available to assist in re-use of this dataset
information
dataset
dataset
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
2010-12-08
Individuals of both species were collected at 25m2 vegetation plots in the forest blocks (A-F, LFE, LF1-3 & VJR) at the SAFE project Sabah (corresponding to second order points). Plots are approximately 173m apart and all plots were sampled 4 times between February 2015 and June 2015. Sampling consists of searching the leaf litter and undergrowth for leeches for a fixed time of 20 minutes. Individuals are kept in RNALater to stabilise DNA until extraction. DNA extraction of pools of ten individual leeches was undertaken using a digestion buffer with modified QiaQuick (Qiagen) protocol and dual tagged PCR in triplicate reactions (details in Drinkwater et al. in review). After screening samples for successful PCR amplification, a total of 41 samples of pooled Haemadipsa sumatrana and 49 pooled Haemadipsa picta from six sites remained for sequencing (B, F, D, LF, LFE, VJR). Amplicons were pooled for library build following Carøe et al, 2017) and sequencing with Illumina MiSeq 150-200bp x2. Sumaclust was used for OTU clustering (Mercier et al., 2013) and LULU was used for post-clustering filtering (Frøslev et al., 2017). This resulted in the final contingency table comparing mammal detections with leech pool. Carøe, C., Gopalakrishnan, S., Vinner, L., Mak, S. S. T., Sinding, M. H. S., Samaniego, J. A., Wales, N., Sicheritz-Ponten, M., Gilbert, M. T. P. (2017). Single-tube library preparation for degraded DNA. Methods in Ecology and Evolution, 9(2), 410-419. https://doi.org/10.1111/2041-210X.12871 Frøslev, T. G., Kjøller, R., Bruun, H. H., Ejrnæs, R., Brunbjerg, A. K., Pietroni, C., & Hansen, A. J. (2017). Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates. Nature Communications, 8(1), 1188. https://doi.org/10.1038/s41467-017-01312-x Mercier, C., Boyer, F., Bonin, A., & Coissac, E. (2013). SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. In Programs and Abstracts of the SeqBio workshop (pp. 27-29).