The Karoo Biogaps Project Making Big Strides for the Karoo

The Karoo BioGaps Project making big strides for the Karoo

Silvia Kirkman & Theresa Sethusa Motivation for project

Shale Gas Development Strategic Environment Assessment (SGD SEA) commissioned by Department of Environmental Affairs. SANBI worked with CSIR for biodiversity component during May 2015-January 2016. http://seasgd.csir.co.za/

Early on in the process it became apparent that the Karoo has a major data gap.

Only 3% of South Africa’s plant specimen records come from the Karoo even though this area covers 30% of the country.

BioGaps: Filling biodiversity information gaps to support development decision making in the Karoo FBIP Integrated Team Projects grant 2016-2018

Project aims: To mobilise foundational biodiversity data to support the SEAs for Shale Gas Development (SGD) and other infrastructure development projects in the Karoo basin.

The lack of biodiversity data for the Karoo region will be addressed through: 1) integrating and upgrading existing data located in museums and herbaria 2) conducting detailed surveys for 11 (now 14) representative taxonomic groups in areas targeted for shale gas exploration Karoo BioGaps Project Objectives 1. Establish a coordinated network of institutions to deliver foundational biodiversity information to decision makers (21 institutions). 2. Produce comprehensive high quality occurrence data for target taxa through national level specimen digitisation, geo-referencing and field sampling (200 000 records). 3. Enable species identification through DNA barcoding and develop a barcode library (barcodes added to BOLD). 4. Assess the threat status of species to identify those of conservation concern (RL and species pages for Species of Conservation Concern). 5. To identify core areas and habitats for species of conservation concern occurring within the Karoo, and assess functional diversity to be used as a baseline for monitoring ecosystem services and function (spp richness, functional diversity, critical habitats, species research). 6. Compile and serve species data and associated landuse guidelines to decision makers at the international, national, provincial and local levels. 7. Upskill young scientists in terms of data collection, field surveys, data management, analyses, and threat assessments through practical work and post-graduate studies (1 Postdoc, 2 PhD, 4 MSc, 1 Honours). Karoo BioGaps Project collaborative multi-institutional network • SANBI and the Botanical Society of South Africa – plants • SANBI, Port Elizabeth Museum at Bayworld, Stellenbosch University – amphibians and reptiles • University of Cape Town – mammals and species distribution modelling • The South African Institute for Aquatic Biodiversity (SAIAB) – freshwater fish • The Agricultural Research Council (ARC) – bees, spiders, fungi, nematodes • BirdLife South Africa – birds • The American Museum of Natural History – scorpions • Stellenbosch University – grasshoppers and dragonflies • Lepidopterists' Society of Africa / Brenton Blue Trust – butterflies • SAEON – fieldwork and monitoring of permanent long-term sites. Karoo BioGaps Project collaborative multi-institutional network Collections institutions involved in digitisation and specimen curation: • Selmar Schonland Herbarium (Rhodes University) • Bews Herbarium (University of KwaZulu-Natal) • Bolus Herbarium (University of Cape Town) • Compton Herbarium (SANBI) • Port Elizabeth Museum at Bayworld • Ditsong Museum • Iziko Museum • National Museum • Albany Museum • Agricultural Research Council

DNA barcoding: SANBI, National Zoological Gardens and University of Johannesburg. Occurrence records

• Field work: 2016, 2017, 2018

• Digitisation and georeferencing existing specimens: museums and herbaria

• Citizen scientists: iNat, ADU Field sampling 60 pentads (8 x 8 km) across the area zoned for potential shale gas exploration have been statistically selected to represent all different environments in the Karoo.

1x1 km sites within these pentads that must be visited by terrestrial taxonomic groups Field sampling Field sampling standardised (the same no matter who is in the field, repeatable), collector effort is quantified (i.e. time to detection), and additional covariates are recorded (e.g. weather on the day).

Field sampling is revealing • New species: 1 plant, 2 scorpions, 1 reptile, 2 freshwater fish, numerous trapdoor spiders and 2 ground wandering spiders, several grasshoppers, 3 nematodes, 1 fungus. Redfin Minnows Stasimopus species. (Photo: Dr Martin Jordaan) (Photo: Ian Engelbrecht)

• Records for rare taxa (Photo: Ismail Ebrahim) • Range extensions: Several reptile, scorpion, spider, butterfly and nematode species. Pseudocordylus microlepidotus namaquensis • Taxonomic updates: (Photo: Nicolas Telford) 2 lizards, several snakes, some agile grasshoppers, 2 stream fish.

Digitising

Someleze – Schonland Tebogo – Ditsong Refiloe - Bolus And several research assistants at Bews Herbarium Inverts labels imaged/databased = ~15 000 Plant labels imaged/databased = ~97 000 TOTAL imaged/databased = 112 000 Digitising consists of: 1. Imaging or photographing the specimen – so there is a digital version and anyone around the world can see the specimen 2. Transcribing or capturing the data from the specimen label into databases so that the information is accessible 1) Imaging

Electronic image of the specimen/label in the collection 2) Transcribing http://transcribe.sanbi.org

Take a trip into history: see photos of old specimens!

~ 46 000 uploaded ~21 000 transcribed (45%) Geo-referencing

Nkhume Given Sphelele

Average rate ~150/day – varies.

Inverts + frogs = 38 000 Plants = 77 000 TOTAL georeferenced = 115 000

iNaturalist / ADU virtual museums https://www.inaturalist.org/projects/biogaps-s-afr

http://vmus.adu.org.za/ Geospatial modelling

Detection probability (with variables that may affect detection of a taxon, e.g. length of transect, time, observer, temperature, etc.)

Occupancy probability (with covariates, e.g. rainfall, elevation, to determine what areas it may occupy) Geospatial modelling

Detection probability and Occupancy probability used to determine species richness and species occurrence Geospatial modelling At the end of the project

• Characterise & map critical habitat within the Karoo; functional diversity. • Species distribution database. • Landuse guidelines for decision makers. • Updated DNA barcodes (1 340 animal & 300 plant barcodes). • Updated species threat status (300 Red Lists). • Species pages (1 000 species pages; http://species.sanbi.org.za). • Publications (15 peer-reviewed scientific publications).

Thank you