BDATA

BIODIVERSITY DATA

FBIP: DNA barcode reference library for plants from Addo Elephant National Park for herbivore diet studies

Latest version published by South African National Biodiversity Institute on Jun 28, 2019 South African National Biodiversity Institute

Identifying their diet resources is key to understanding how a high diversity of herbivore species can co-exist without competition, as well as in terms of predicting their impacts on plant species and communities. To date describing the diets of herbivores has been slow, cumbersome and probably biased. The use of DNA metabarcoding of diet samples however overcomes these limits, but is dependent on the availability of a comprehensive reference collection of DNA sequenced material for the potentially consumed plant species. To date no such reference collection exists for Subtropical Thicket in the Eastern Cape. This project therefore aimed to establish such a reference collection, for the plant community in the Addo Elephant National Park (AENP). The data set represents the plant voucher specimens collected from two localities, their identities, and DNA sequences. The voucher specimens have been deposited in the Ria Olivier Herbarium at NMMU.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 357 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 357 records in English (24 KB) - Update frequency: unknown
Metadata as an EML file download in English (12 KB)
Metadata as an RTF file download in English (10 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Kerley G (2019): FBIP: DNA barcode reference library for plants from Addo Elephant National Park for herbivore diet studies. v1.0. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=dna_barcoding&v=1.0

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is South African National Biodiversity Institute. This work is licensed under a Creative Commons Attribution (CC-BY) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 2dd5d605-ce02-4496-bbba-b4723a3709c0.  South African National Biodiversity Institute publishes this resource, and is itself registered in GBIF as a data publisher endorsed by South African Biodiversity Information Facility.

Keywords

Addo Elephant National Park; herbivore diet reference collection for DNA barcoding; Specimen

Contacts

Who created the resource:

Graham Kerley
Professor and Director of Centre for African Conservation Ecology
Nelson Mandela Metropolitan University Summerstrand Campus (South), Department of Zoology, Room 12-114c Port Elizabeth Eastern Cape ZA +27 41 504 2308
http://ace.mandela.ac.za/

Who can answer questions about the resource:

Graham Kerley
Professor and Director of Centre for African Conservation Ecology
Nelson Mandela Metropolitan University Summerstrand Campus (South), Department of Zoology, Room 12-114c Port Elizabeth Eastern Cape ZA +27 41 504 2308
http://ace.mandela.ac.za/

Who filled in the metadata:

Graham Kerley
Professor and Director of Centre for African Conservation Ecology
Nelson Mandela Metropolitan University Summerstrand Campus (South), Department of Zoology, Room 12-114c Port Elizabeth Eastern Cape ZA +27 41 504 2308
http://ace.mandela.ac.za/

Who else was associated with the resource:

Content Provider
Mahlatse Kgatla
FBIP Data Specialist
SANBI 2 Cussonia Avenue, Brummeria 0184 Pretoria Gauteng ZA 0128435196
http://fbip.co.za/contact/

Geographic Coverage

Addo Elephant National Park, two localities: Main Camp and Colchester

Bounding Coordinates South West [-33.631, 25.703], North East [-33.442, 25.917]

Taxonomic Coverage

Most specimen have been identified to Genus level while others to Species and Subspecies level.

Kingdom  Plantae

Temporal Coverage

Start Date 2014-01-01

Project Data

Identifying their diet resources is key to understanding how a high diversity of herbivore species can co-exist without competition, as well as in terms of predicting their impacts on plant species and communities. To date describing the diets of herbivores has been slow, cumbersome and probably biased. The use of DNA metabarcoding of diet samples however overcomes these limits, but is dependent on the availability of a comprehensive reference collection of DNA sequenced material for the potentially consumed plant species. To date no such reference collection exists for Subtropical Thicket in the Eastern Cape. This project therefore aimed to establish such a reference collection, for the plant community in the Addo Elephant National Park (AENP). The data set represents the plant voucher specimens collected from two localities, their identities, and DNA sequences. The voucher specimens have been deposited in the Ria Olivier Herbarium at NMMU.

Title DNA barcode reference library for plants from Addo Elephant National Park for herbivore diet studies
Identifier IBIP-BS13100452303
Funding Foundational Biodiversity Information Programme
Study Area Description Addo Elephant National Park, two localities: Main Camp and Colchester

The personnel involved in the project:

Principal Investigator
Graham Kerley

Sampling Methods

Data from specimen labels / datasheets. DNA barcoding done by Prof P Taberlet of Centre National de la Recherche Scientifique, France. Specimens vouchered in Ria Olivier Herbarium, identified by PhD student (C. Weatherall-Thomas), Prof E. Campbell. Specimens that could not be identified based on morphology were barcoded and barcodes used to obtain identifications

Study Extent Addo Elephant National Park, two localities: Main Camp and Colchester

Method step description:

  1. This survey will be undertaken throughout the Addo Main Camp and Colchester Sections of the Addo Elephant National Park, this to cover 8 vegetation types that occur here. An initial literature and expert-based survey indicates that approximately 500 plant species should be sampled, these reflecting both dominant plant species, plant species of conservation significance and plants that are potentially consumed by the herbivores (the latter comprising 13 species) Sampling will comprise the collection of tissue and herbarium samples. Samples will be located in the field by local experts, tissues samples stored in labelled, silica-dried tubes and matched plant species will be prepared for herbarium curation in the Ria Olivier Herbarium at the Nelson Mandela Metropolitan University. This phase (plant collection, identification and curation) will be undertaken by a team of botanists and ecologists, including Profs Campbell and Kerley, Dr Landman together with postgraduate and undergraduate students. SANParks Regional Ecologist A Gaylard will also assist with this phase, together with SANParks Field Rangers (for protection of researchers). The field work will be initiated in January 2014 (or as soon as funds are released) and will run for 12 months. In this period there will be at least three major sampling trips to cover the phenological patterns of the plant communities. The tissue samples will then be sent to France, under a BABS permit, for analysis. The DNA barcoding itself will be supported by a separate project and will be undertaken in collaboration with Dr Pierre Taberlet of the Joseph Fourier University, France. The DNA analysis will be divided into three sub-tasks: (i) DNA extraction, (ii) DNA amplification, and (iii) DNA sequencing. Sequence reads will be analysed using tools specifically designed for such analyses, including http://www.grenoble.prabi.fr/trac/OBITools. It is anticipated that these DNA analyses will require an additional 6 months.

Additional Metadata

Alternative Identifiers http://ipt.sanbi.org.za/iptsanbi/resource?r=dna_barcoding