the karoo biogaps project making big strides for the...
TRANSCRIPT
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