Leech blood-meal iDNA reveals differences in Bornean mammal diversity across habitats

Description:

This data set includes the data used in Drinkwater et al. (2020) Leech blood-meal iDNA reveals differences in Bornean mammal diversity across habitats, submitted to Molecular Ecology. There are three sets of data based on the biomonitoring of mammals using iDNA extracted from leeches collected across the SAFE project (and DVCA) in 2016. At each site in the SAFE landscape 20 minute handsearches took place within the boundaries of fixed 25m2 vegetation plots. For these analyses we only used Haemadipsa picta individuals, as previous studies have revealed species differences between H. picta and H. zeylanica in the SAFE area. With metabarcoding techniques, first we extracted and amplified the 16S rRNA region of mammal DNA, from site-matched pools of leeches using PCR and specific mammal primers. NGS sequencing was used and the short fragments were then identified using in silico PCR with ecoPCR and OBITOOLS (metabarcoding packages) to assign taxonomy to the unknown sequences. We then analysed diversity in different habitats across the landscape and included microclimate data, from LiDAR scans of the landscape as variables which could impact the detection of mammals.

Project: This dataset was collected as part of the following SAFE research project: The effects of rainforest fragmentation on mammal community assemblages using leech blood-meal analysis

Funding: These data were collected as part of research funded by:

• NERC (Standard grant , NE/K016148/1)
• NERC (Independent research grant, NE/S01537X/1)

This dataset is released under the CC-BY 4.0 licence, requiring that you cite the dataset in any outputs, but has the additional condition that you acknowledge the contribution of these funders in any outputs.

Permits: These data were collected under permit from the following authorities:

• Sabah Biodiversity Council (Research licence JKM/MBS.1000 2/2 (34))
• Sabah Biodiversity Council (Research licence JKM/MBS.1000 2/3 JLD.2 (107))
• Sabah Biodiversity Council (Export licence JKM/MBS.1000 2/3 JLD.3 (44))
• Danum Valley Conservation Area (Research licence YS/DVMC/2016/253)

XML metadata: GEMINI compliant metadata for this dataset is available here

Files: This consists of 1 file: Drinkwater2020-iDNA_diversity3.xlsx

Drinkwater2020-iDNA_diversity3.xlsx

This file contains dataset metadata and 3 data tables:

1. UNFILTERED Taxonomic assignment of iDNA sequences (described in worksheet ecoTAG_output_raw)

   Description: UNFILTERED This dataset is the raw output of the in silico PCR using the programs ecoPCR and the OBITOOLS package. The exact primers are matched against all mammal sequences in GenBank (NCBI) using a minimum of three mismatches between primer and query sequence and a quality filter of a minimum identity of 0.95. This dataset was subsequently filtered for contaminant, geographically implausible mammals and collapsed by haplotype per pool

   Number of fields: 15

   Number of data rows: 3454

   Fields:

   • id: Unique sequence ID within leech pool (Field type: id)
   • site: The site at the SAFE project from which the pool of leeches was collected (Field type: id)
   • hab: The habitat type of the site at the SAFE project from which the pool of leeches was collected (Field type: id)
   • count: Count of the times this sequence was found - UNFILTERED (Field type: numeric)
   • best_identity: Percent identity match between query and database sequence - UNFILTERED (Field type: numeric)
   • family: Family taxid - following GenBank (Field type: id)
   • family_name: Family name (Field type: id)
   • genus: Genus taxid - following GenBank (Field type: id)
   • genus_name: Genus name (Field type: id)
   • order: Order taxid - following GenBank (Field type: id)
   • order_name: Order name (Field type: id)
   • species: Species taxid - following GenBank (Field type: id)
   • species_name: Species name (Field type: id)
   • Assigned_name: Assigned taxonomic name (Field type: id)
   • sequence: Query sequence (Field type: id)

2. Mammal detections recorded in each pool (described in worksheet detections)

   Description: From the taxonomic assignment list, the unique sequences identfied in each pool are are recorded as detections. The value is a count of the numebr of time the unique sequence for that taxon was recorded in the pool. Geographically implausible mammals have been removed and taxa which agree per site have been collapsed. This give a detections by pool matrix. For analyses these counts were converted into presence/absence data.

   Number of fields: 19

   Number of data rows: 57

   Fields:

   • pool: This is the pool name given to the leech pool for sequencing (Field type: id)
   • site: The site at the SAFE project from which the pool of leeches was collected (Field type: id)
   • leeches: This is the number of individual leeches which make up the pool (Field type: numeric)
   • habitat: Habitat type - classification used in the paper to describe the quality of forest in the sites where the leeches were collected (Field type: id)
   • Arctogalidia: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Elephas: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Felidae: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Helarctos: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Hemigalus: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Hystrix: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Macaca: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Manis: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Muntiacus: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Rusa: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Sus: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Paguma: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Tragulus: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Trichys: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)
   • Viverra: Occurrence of detections of this taxon in a leech pool, as determined from leech-based iDNA (Field type: abundance)

3. Microclimate variables (described in worksheet microclimate)

   Description: Mean and maximum temperature and mean and maximum VPD extracted at each of the second order points used in the study. These values were extracted from microclimate surfaces generated in Jucker et al., (2018), using the coordinates from the centre of each of the 25m2 plots. For the values in Danum Valley Conservation Area (DVCA), these were extracted from the nearest river point (coordinates given).

   Number of fields: 6

   Number of data rows: 92

   Fields:

   • Code: SAFE second order points including LOMBOK points at RLFE and three river sites at DVCA (Field type: location)
   • site: The site at the SAFE project from which the pool of leeches was collected (Field type: id)
   • T_max_raster: The maximum daily temperature at each second order point (Field type: numeric)
   • T_mean_raster: The mean daily temperature at each second order point (Field type: numeric)
   • VPD_max_raster: The maximum daily vapour pressure deficit (VPD) at each second order point (Field type: numeric)
   • VPD_mean_raster: The mean daily vapour pressure deficit (VPD) at each second order point (Field type: numeric)

Date range: 2016-01-01 to 2016-12-31

Latitudinal extent: 4.5000 to 5.0700

Longitudinal extent: 116.7500 to 117.8200

Taxonomic coverage:
All taxon names are validated against the GBIF backbone taxonomy. If a dataset uses a synonym, the accepted usage is shown followed by the dataset usage in brackets. Taxa that cannot be validated, including new species and other unknown taxa, morphospecies, functional groups and taxonomic levels not used in the GBIF backbone are shown in square brackets.