FBIP: Holothrix  herbarium specimen and DNA barcoding dataset

Benny Bytebier1, Mahlatse Kgatla2

1 University of KwaZulu-Natal Bews Herbarium, UKZN-School of Life Sciences, Pr. Bag X01, Scottsville, 3209, Pietermaritzburg, South Africa; 2 SANBI, 2 Cussonia Avenue, Brummeria, 0184, Pretoria, South Africa

Corresponding author(s): Benny Bytebier (bytebier@ukzn.ac.za)

Received {date}; Revised {date}; Accepted {date}; Published {date}

Citation: Combination of authors, year of data paper publication (in parentheses), Title, Journal Name, Volume, Issue number (in parentheses), and doi of the data paper.

Resource Citation

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

Abstract

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

Keywords: Orchidaceae, Specimen

Project details

Project title: Holothrix  herbarium specimen and DNA barcoding dataset
Personnel: Benny Bytebier
Funding: Funding from Foundational Biodiversity Information Programme (FBIP)
Study area descriptions/descriptor: South Africa (Eastern Cape, Western Cape, KwaZulu Natal, Gauteng, Mpumalanga, Northern Cape)

Data published through GBIF: http://ipt.sanbi.org.za/iptsanbi/resource?r=holothrix

Taxonomic coverage

General taxonomic coverage description: All specimen are identified to species level.
Taxonomic ranks
Family: Orchidaceae
Common names: Orchids

Spatial coverage

General spatial coverage: South Africa (Eastern Cape, Western Cape, KwaZulu Natal, Gauteng, Mpumalanga, Northern Cape)
Coordinates: 34°48'50.4''S and 21°56'34.8''S Latitude; 16°15'36''E and 32°46'58.8''E Longitude 

Temporal coverage: 1800 - 2016

Methods

Method step description: 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.
Study extent description: South Africa (Eastern Cape, Western Cape, KwaZulu Natal, Gauteng, Mpumalanga, Northern Cape)
Sampling description: 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.

Datasets

Dataset description
Object name: Darwin Core Archive FBIP: Holothrix  herbarium specimen and DNA barcoding dataset
Character encoding: UTF-8
Format name: Darwin Core Archive format
Format version: 1.0
Distribution: http://ipt.sanbi.org.za/iptsanbi/archive.do?r=holothrix
Publication date of data: 2019-09-30
Language: English
Licences of use: Creative Commons Attribution (CC-BY) 4.0 License

Metadata language: English
Date of metadata creation: 2019-06-21
Hierarchy level: Dataset