FBIP: Holothrix herbarium specimen and DNA barcoding dataset

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 43 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.

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:

Bytebier B (2019): FBIP: Holothrix herbarium specimen and DNA barcoding dataset. v1.1. South African National Biodiversity Institute. Dataset/Occurrence. http://ipt.sanbi.org.za/iptsanbi/resource?r=holothrix&v=1.1

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: a71aeb4a-46bc-43b0-b752-c6f5e0d6561c.  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

Orchidaceae; Specimen

Contacts

Geographic Coverage

South Africa (Eastern Cape, Western Cape, KwaZulu Natal, Gauteng, Mpumalanga, Northern Cape)

Taxonomic Coverage

All specimen are identified to species level.

Temporal Coverage

Project Data

A compilation of herbarium specimen records of the orchid genus Holothrix from different herbaria

The personnel involved in the project:

Sampling Methods

We propose a holistic approach to revising Holothrix and Bartholina by combining field work with the study and digitization of herbarium specimens, and with modern tools such as DNA barcoding and computer-aided identification keys. Specifically, this project aims at: (i) Digitising herbarium specimens to synthetize all available knowledge about distribution, morphology and ecology of Holothrix and Bartholina; (ii) Undertaking field work to study the ecology and collect plant material for analysis (iii) Generating a large molecular dataset to test and enable barcode identification; (iv) Constructing a computerized knowledge base, using freely available software, to store, edit, analyse and distribute descriptive data on-line; (v) Proposing a comprehensive taxonomic revision on the basis of morphological and molecular analyses; (vi) Constructing a freely accessible, electronic, multi access identification key for South African Holothrix and Bartholina species ; (vii) Compiling species pages for all South African taxa for publication in the e-Flora of South Africa and/or Encyclopedia of Life; (viii) Making all these results freely accessible on-line.

Method step description:

1. Digitisation and morphological analysis of herbarium specimens: Herbarium specimens will be requested on loan from various local and international herbaria (BM, BOL, EA, GRA, K, NBG, NH, P, PRE and SAM). They will be used to evaluate (i) taxon boundaries and the morphological diversity of the different taxonomic entities, (ii) the ecological characteristics, and (iii) the distribution. All specimen information including images of the specimens, will be captured in the BRAHMS (Botanical Research and Herbarium Management System) database of the Bews Herbarium (http://herbaria.plants.ox.ac.uk/bol/brahms/) and will be made available on-line pending approval of various herbaria. Specimen data in Brahms can be easily exported in a variety of formats including Darwin Core for uploading to the SANBI’s national specimen database, GBIF and other biodiversity data aggregators. Field work and collection of plant material: On the basis of distribution information from the literature, herbarium specimen and through collaboration with citizen scientists such as the CREW teams, new and existing populations of the various Holothrix species will be identified and visited during four field sessions (two in the Cape Floristic Region and two along the Drakensberg escarpment). In order to evaluate morphological and genetic variation, several populations will be visited per species whenever possible. Plant material (herbarium vouchers, spirit material, tissue samples and photographs) will be collected from the field and deposited at the Bews Herbarium (NU) of the University of KwaZulu-Natal. Duplicates will be distributed to other relevant SA herbaria. Tissue will be dried using silicagel and stored at -20°C. Particular attention will be paid to rare species for which only one reference specimen will be collected. Timeline: during the flowering season i.e. January and March-April 2016 along the Drakensberg Escarpment; September-October in the GCFR. DNA sequence data for phylogenetic analysis and the Barcode of Life project DNA will be extracted from tissue preserved in silicagel using the Qiagen DNeasy plant mini kit following the manufacturer’s protocol. Three gene regions will be amplified by standard PCR techniques and will be sequenced at the Central Analytical Facility of Stellenbosch University. Two plastid regions (matK and trnL-F) and one nuclear marker (ITS) have been selected for their discriminative power, based on the recommendations of the Consortium for the Barcode of Life and our own experience for African Orchidaceae. Revising the taxonomy and compilation of computerized knowledge database: Morphological descriptions of the various taxa will be compiled using the free software package Xper2 (http://infosyslab.fr/lis/?q=en/resources/software/xper2). Xper2 is a taxonomic software platform that enables the compilation of standardized species descriptions from specimen measurements. It can also generate interactive dichotomous or multi-access keys that allow for computer-aided-identification. The knowledge database and interactive keys will be made freely accessible online. Species pages and distribution maps: Species pages, images and distribution maps will be compiled in BRAHMS and initially made available through BRAHMS online (BOL). BOL is used to publish BRAHMS databases online and the Bews Herbarium has its own server to do so. BOL websites can be richly developed with text, images, hyperlinks, tables, file downloads and indeed any standard website feature. Websites can be linked to one or more BRAHMS databases and the online data query tools search these data and present the results in flexible text pages and data grids. Since the e-Flora of South Africa project also uses BRAHMS, species pages can be easily be transferred and integrated into the e-Flora project and, later on, into the World Online Flora as well. Furthermore, generating files from BRAHMS for uploading in other biodiversity data management systems (e.g. Scratchpads) is pre-programmed in BRAHMS and thus straightforward.

Additional Metadata