FBIP: Holothrix herbarium specimen and DNA barcoding dataset

出現紀錄
最新版本 published by South African National Biodiversity Institute on 九月 30, 2019 South African National Biodiversity Institute
發布日期:
2019年9月30日
授權條款:
CC-BY 4.0

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說明

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

資料紀錄

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版本

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如何引用

研究者應依照以下指示引用此資源。:

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

權利

研究者應尊重以下權利聲明。:

此資料的發布者及權利單位為 South African National Biodiversity Institute。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

此資源已向GBIF註冊,並指定以下之GBIF UUID: a71aeb4a-46bc-43b0-b752-c6f5e0d6561c。  South African National Biodiversity Institute 發佈此資源,並經由South African Biodiversity Information Facility同意向GBIF註冊成為資料發佈者。

關鍵字

Orchidaceae; Specimen

聯絡資訊

Benny Bytebier
  • 元數據提供者
  • 出處
  • 連絡人
Curator
University of KwaZulu-Natal Bews Herbarium
UKZN-School of Life Sciences, Pr. Bag X01, Scottsville
3209 Pietermaritzburg
KwaZulu-Natal
ZA
+27332605145
Mahlatse Kgatla
  • 內容提供者
FBIP Data Specialist
SANBI
2 Cussonia Avenue, Brummeria
0184 Pretoria
Gauteng
ZA
0128435196

地理涵蓋範圍

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

界定座標範圍 緯度南界 經度西界 [-34.814, 16.26], 緯度北界 經度東界 [-21.943, 32.783]

分類群涵蓋範圍

All specimen are identified to species level.

Family Orchidaceae (Orchids)

時間涵蓋範圍

起始日期 / 結束日期 1800-01-01 / 2016-01-01

計畫資料

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

計畫名稱 Holothrix herbarium specimen and DNA barcoding dataset
辨識碼 FBIS150618119652
經費來源 Funding from Foundational Biodiversity Information Programme (FBIP)
研究區域描述 South Africa (Eastern Cape, Western Cape, KwaZulu Natal, Gauteng, Mpumalanga, Northern Cape)

參與計畫的人員:

Benny Bytebier
  • 研究主持人

取樣方法

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.

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

方法步驟描述:

  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.

額外的詮釋資料