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.

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

BioGaps: Filling biodiversity information

gaps to support development decision

making in the Karoo FBIP Integrated Team Projects grant 2016-2018

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 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

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.

• Records for rare taxa

• Range extensions:

Several reptile, scorpion, spider, butterfly and nematode species.

• Taxonomic updates: 2 lizards, several snakes, some agile

grasshoppers, 2 stream fish.

(Photo: Ismail Ebrahim)

Stasimopus species.

(Photo: Ian Engelbrecht)

Redfin Minnows

(Photo: Dr Martin Jordaan)

Pseudocordylus microlepidotus namaquensis

(Photo: Nicolas Telford)

Digitising

Someleze – Schonland Tebogo – Ditsong Refiloe - Bolus

And several research assistants

at Bews Herbarium

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

Inverts labels imaged/databased = ~15 000

Plant labels imaged/databased = ~97 000

TOTAL imaged/databased = 112 000

Electronic image of the specimen/label

in the collection

1) Imaging

http://transcribe.sanbi.org

Register and start transcribing

Take a trip into

history: see

photos of old

specimens!

2) Transcribing

~ 46 000 uploaded

~21 000 transcribed (45%)

Geo-referencing

Average rate ~150/day – varies.

Inverts + frogs = 38 000

Plants = 77 000

TOTAL georeferenced = 115 000

Nkhume Given Sphelele

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