Drinkwater, R. et al

Mammal occurrence identified from metabarcoding of two leech species from Sabah, Malaysia

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.

Publication date: 2018-08-08

Get the data

This dataset is made available under the terms of the Open Government Licence

Format of the dataset : Comma-separated values (CSV)

You must 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

 

This dataset is part of the following

Where/When

Study area
Temporal extent
2015-02-01    to    2015-06-30

Supplemental information

Other useful information regarding this dataset:

Provenance & quality

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).

Correspondence/contact details

Rosie Drinkwater
Queen Mary University of London
Mile End Road
London
E1 4NS
UK
r.drinkwater@qmul.ac.uk

Authors

Drinkwater, R.
Queen Mary University of London
Schnell, I.D.
Natural History Museum of Denmark
Bohmann, K.
Natural History Museum of Denmark
Bernard, H.
Universiti Malaysia Sabah
Clare, E.
Queen Mary University of London
Gilbert, T.P.
Natural History Museum of Denmark
Rossiter, S.J.
Queen Mary University of London

Other contacts

Custodian
Environmental Information Data Centre
eidc@ceh.ac.uk
Publisher
NERC Environmental Information Data Centre
eidc@ceh.ac.uk

Spatial

Spatial representation type
Tabular (text)
Spatial reference system
WGS 84

Tags

Topic categories
Biota
Keywords
Biodiversity Borneo Haemadipsa picta Haemadipsa sumatrana,  Sabah