Monday, 8 May 2017

Karoo Biogaps experience

By Thaakira Samodien

Our first pentad was Rietfontein farm, South of Colesberg. The weather was extremely humid and the sun was at its peak while we were out in the field. The first plant species that stood out for me as we drove to our site was the Brunsvigia radulosa. Its shape, size and beautiful colour caught my eye immediately and I was in utter awe that such beauty exists in the Karoo. As we got to the site, we got all our equipment ready and started our day. I was amazed at how many different species there were that were flowering. Aspalathus, Selago, Hermannia, Jamesbrittenia, Gnidia, and lots of different grasses were some of the species that we collected on the first day. In total we found about over 130 species on the first day. 

The second day was the best Karoo experience I had. This site was on Doornberg farm in Nieu Bethesda. It was a beautiful hot day and we found lots of special flowers. Although it was hot, it rained while we were in the field which made the day even more special. The site was a beautiful site; flat dry land with hill tops filled with lots of grasses. We reached a river area as well where we found different types of Cyperus and dragonflies. My favourite flower that we found on that site was a tiny little Hermannia species. We called it Hermannia candy-like, because its colour was a combination of white, yellow and a reddish-pink.

The next few days it rained quite a bit which made some of the sites very difficult to gain access to, but we still managed to collect some species on the wetter sites. 

We found some succulents and more grasses. We saw lots of different Aloes; Aloe ferox, Aloe broomii and Aloe striata. The flora field trip experience overall was amazing and fulfilling. Being a part of the BioGaps project has taught me a lot and it gives me motivation to do more to protect the flora of Southern Africa. 

Thursday, 4 May 2017

Behind the scene supporters of Team Spider-by Robin Lyle

Fieldwork is the fun, hard and dirty part of an arachnologist’s job. However, have you ever wondered what happens to the spiders once they are collected? As part of the Karoo BioGap project, all spiders collected are deposited into the National Collection of Arachnida (NCA) that is housed in the Biosystematics building at the Agricultural Research Council.
Background of the collection
The National Collection of Arachnida (non-Acari) was established in 1976, the under Plant Protection Research Institute, which later became the Agricultural Research Council. It was established by Dr Ansie Dippenaar-Schoeman and is a comprehensive and fast growing collection in South Africa. It contains 70,200 accessions represented by approximately 210,600 alcohol-preserved specimens. Sampling of spiders has focused mainly on South Africa.
The NCA is one of South Africa’s Agricultural National Public Assets and it is maintained on behalf of the Department of Agriculture, Forestry and Fisheries (DAFF) and the Department of Science and Technology (DST). The collection contains a wealth of information, ranging from taxonomic names, biological and biogeographical information.

Process of accessioning a specimen
A specimen collected in the field follows a set procedure before it is included in the NCA. These steps are as follows:
1.       Specimens are sorted and placed into a glass container suitable for the collection.
2.       Specimen is identified to include order, family, genus and species name, where possible.
3.       Specimen information is written into a catalogue and given a unique accession number.
4.       Correct locality and identification labels, including accession number, are generated.
5.       Specimen and all associated data is captured into the NCA database.
6.       Specimen is stored in the collection.

The people behind the scene at NCA

The growth and upkeep of the collection is always ongoing. The National Collection of Arachnida is lucky to have a small team that helps in this task.

 Ezekia Sgudhla (left), Joel Mooka (middle) and Sma Chiloane (right) help with different aspects of accessioning a specimen. Responsibilities include basic sorting, label generation and identification to family level. 

Petro Marais (left), the collection manager of the National Collection of Arachnida, and Maggie Menyatso (right) who is responsible for databasing accessioned specimens. 

Small impoundments: a necessary evil for fish conservation in a global biodiversity hotspot

Small impoundments represent one of the most widespread anthropogenic changes to the riverscapes in the Cape Fold Ecoregion (CFE) at the southern tip of Africa - a region which originally lacked natural standing water bodies. These impoundments were primarily built for agricultural and livestock farming and have proliferated with increasing demand for water. Consequently, there are few free-flowing streams in the CFE. Construction of small impoundments has been widely documented to have serious ecological and biodiversity impacts, including changes in hydrologic regimes and fragmentation of historically connected populations of stream-inhabiting fishes, with adverse effects on their genetic characteristics. Small impoundments have also created favourable habitats that have facilitated the proliferation and spread of non-native species. 

While these negative impacts cannot be denied, observations and preliminary results from a recent comprehensive survey of the Great Fish River system by researchers and students from the South African Institute for Aquatic Biodiversity and Rhodes University are showing that small impoundments can also benefit biodiversity. This survey was conducted in January 2017 as part of Delsy Sifundza’s MSc research (funded by the NRF-FBIP Karoo BioGaps Project) to map the distribution and determine the status of remnant populations of the Eastern Cape Rocky, Sandelia bainsii (Figure 1). The Eastern Cape Rocky is a highly threatened endemic stream fish which has been listed by the IUCN as Endangered since 1987 due to rapid decline in population sizes and severe decline in its historical distribution range.

A picture of the Eastern Cape Rocky, Sandelia bainsii, showing the species’ live colour pattern.

Our survey indicated that the Kat River is the remaining stronghold of the Eastern Cape Rocky in the Great Fish River system. The survival of this species in the upper section of the Kat River has been facilitated by the presence of several impoundments of various sizes (Figure 2) which have prevented the spread of non-native fishes, such as the sharptooth catfish, small-mouth yellowfish and banded tilapia which are now dominant in the mainstem Great Fish River. Sandelia bainsii was abundant at sites above the weirs that formed the upper limit of non-native fishes in the Kat River. In these river sections, S. bainsii occurred with three other native fishes of the Great Fish River system: Labeo umbratus (moggel), Enteromius anoplus (chubby head barb) and Glossogobius callidus (river goby). Some of these impoundments are therefore likely to have formed effective barriers that could have protected the genetic integrity of the original L. umbratus genetic lineage in the Great Fish River which is threatened by potential hybridisation with a genetically distinct lineage of this species that was introduced into the Great Fish through the Orange-Fish tunnel Inter-Basin Transfer. The Kat River therefore represents an important sanctuary of highly threatened endemic fishes of the eastern CFE and should be prioritised for protection. There is critical need for building awareness among the communities to prevent the spread non-native fishes in the Kat River catchment. There is also need for establishing collaboration between researchers, conservation authorities and the local farming communities and land owners to identify the weirs that are preventing the upstream migration of non-native fishes to ensure that they are effectively secured and protected from potential breach or flood damage.

 A. A major weir in the lower Kat River close to the confluence with the Great Fish River is an impassable barrier for fishes from the mainstem Great Fish; B. a moderately sized weir in the Upper Kat where the lower distribution limit of Sandelia bainsii was recorded during the survey in January 2017.  

Research Team
Miss Delsy Sifundza (MSc candidate, Department of Ichthyology and Fisheries Science, Rhodes University)
Mr Tadiwa Mutizwa (MSc candidate, Department of Ichthyology and Fisheries Science, Rhodes University)
Dr Albert Chakona (South African Institute for Aquatic Biodiversity)
Dr Wilbert Kadye (Department of Ichthyology and Fisheries Science, Rhodes University)

Tuesday, 25 April 2017

Team Mammal's surveys for BioGaps-Zoe Woodgate and Nadine Hassan

It constantly amazes me how time flies. Indeed, our months spent trapesing across the Karoo feel like a lifetime ago- and yet we’ve only been back home for three weeks.

Since October last year, Nadine Hassan and myself have been surveying the Karoo for mammal species as part of SANBIs Karoo BioGaps project. In total we’ve been on five fieldtrips, with each one taking a few weeks due to the great distances we needed to transverse each day. To help us in this end the EWT Drylands programme kindly lent us their vehicle for the duration of the fieldwork. The Mazda (affectionately known as ‘Karoo Bean’) has been both gutsy and reliable.

The two main tools of our trade, so to speak, are camera traps and Sherman small mammal traps. Camera traps stand on an allocated site for a minimum of 30 days, dutifully taking photographs of all that moves past. Interestingly, whilst many photographs were of the usual suspects (steenbok, kudu, black-backed Jackal, scrub hare and the like), there were the occasional novelties. In particular rock monitor lizard, secretary bird and bush pig made cameo appearances. As expected, the sheer amount of data collected has been immense. Approximately 400 gigabytes of photographs lie in wait on my hard-drive. As one can imagine, going through them all is proving to be quite the challenge.

Nadine’s Sherman traps have produced equally important data. At each site she patiently baited and left 120 traps overnight, scattered amongst the various micro-habitats available. Pre-dawn every morning we checked each one, carefully processing and releasing any live captures. What a pleasure to be up close and personal with these fluffy creatures, whom are so often over-looked in mammal surveys. Despite the drought Nadine captured at least 10 micromammal species. The most cosmopolitan species for the drylands, the Namaqua rock mouse (Micaelamys namaquensis) was found around the various rock formations that characterise much of the Karoo landscape.

As winter approaches it becomes too cold to sample for the small mammals. Thus for now we must take a step away from the Karoo and turn our attention back towards our laptops. Fieldwork was only half the story- now begins a rigorous session of data cataloguing and analysis. Nonetheless we are both excited to see the result of our hard work, and eagerly await our next fieldtrip come spring.

Wednesday, 19 April 2017

Karoo BioGaps - Press Release -How you can help

How you can help:

We are calling on the public to be part of the Karoo BioGaps Project and help us undertake fieldwork in the Karoo and/or help us integrate existing data from museums and herbaria. We will study 12 different taxonomic groups: plants, mammals, amphibians, reptiles, freshwater fish, birds, bees, spiders, dragonflies, scorpions, grasshoppers and butterflies. By the end of the project, approximately 200,000 new records will inform species occupancy and habitat richness models.  These, along with approximately 300 Red List assessments of species of conservation concern, will be given to decision makers. The project also provides research opportunities for postgraduate students, building critical capacity for converting foundational biodiversity science into policy advice.

1.     You can photograph Karoo species and post your observations on
Why would posting observations on iSpot help? Any record of any species in the Karoo is useful to us, particularly those in the 12 taxonomic groups. By posting your picture of a species with its location information onto iSpot, you will be adding to the knowledge about the distribution range of that species.  Species experts will have access to your image on the website, and will identify it for you. You might spot something really unique!

2.     You can help transcribe data from museum and herbaria collections using the online platform
Why do we need help transcribing? There are thousands of historical museum and herbaria specimens collected before the time of computers! The information in these specimen records is critical to understand previous distribution patterns of species, but the information is inaccessible if it remains in hard copy only.  We need to digitise all museum and herbaria records so that scientists can analyse the data. Photographs of the specimen have been uploaded onto this website, but we need your help to type the data from the specimen label into the database. By doing this transcribing, you are helping to make species information as old as 1830 available to scientists and the general public!

Prizes are available for the most iSpot uploads and the most records transcribed!

The Karoo BioGaps Project led by the South African National Biodiversity Institute (SANBI) in partnership with a consortium of research institutions, and is funded by the Foundational Biodiversity Information Programme (FBIP), a joint initiative of the Department of Science of Technology (DST), the National Research Foundation (NRF) and SANBI.

Tuesday, 4 April 2017

The Bee Team

Bees tend to have a high species diversity in arid areas, particularly those with a mediterranean climate. South Africa, being a largely arid country, has its fair share of bee species, but when there are no rains and consequently no flowers, they cannot be found. As with most insects, solitary bees breed through the summer and their progeny emerge during the following summer to reproduce. Therefore, productive bee collecting has much to do with the previous summer’s weather.
During 21 November to 1 December 2016 the bee team began fieldwork. The team consisted of Elisabeth Khumo Mwase and Connal Eardley, who spent a day collecting at each site. One day is adequate to sample a square kilometre for bees.

The trip focussed on the East Karoo BioGaps sites. The area was dry, with some sites being very dry, except for the Black Hill farm that had received rain. Surprisingly, bee collecting was not much better on Black Hill than on the other farms, but the results were different because we collected many more small carpenter bees than elsewhere. With one or two exceptions, bee collecting was average. A few sites were very dry and bee collecting was poor.

The second BioGaps bee trip took place in the Central Karoo during 30 January to 4 February 2017. The team consisted of Reinette Swanepoel and Connal Eardley. . Although flowers were plentiful near Victoria West, bees were scarce in that area. We had sampled bees there during the previous summer and had found the area very dry with few flowers; hence the knock-on effect described above. The other sites, near Beaufort West, Fraserburg and Loxton were devastatingly dry and bees were non-existent (because we could not find any bees we sampled more than one site per day). This was disappointing as we now have no bee records from those areas. It will be interesting to see how long it takes after good rains have fallen for the bee populations to recover. Let’s hope that the rains come soon and that long-term sampling can be undertaken.

Near the BioGaps site on Chris Hayward’s farm

Wednesday, 22 March 2017

Historical data add value to BioGaps

The BioGaps project not only has teams of experts going out into the field in the Karoo to collect new data. It also has a team working hard on mobilizing historical data in herbaria, museums and other research institutions.

There are many specimens of plants and invertebrates, relevant to BioGaps, which are not yet databased and thus not usable. In order to be able to use these data for BioGaps, four digitisers started on the project around September last year to either capture label information onto computer, or else take images of labels for transcribing later on.

Three digitisers have been focusing on herbarium specimens only. They are Someleze Mgcuwa stationed at Selmar Shonland Herbarium at Rhodes University in Grahamstown, Sifiso Mnxati stationed at Bews Herbarium at the University of KwaZulu-Natal in Pietermartizburg, and Mpumelele Gumede stationed at Compton Herbarium at SANBI Kirstenbosch in Cape Town. The Cape Town digitiser will also be working on specimens at the Bolus Herbarium at the University of Cape Town.


They recently attended a training course at SANBI Kirstenbosch to be shown how to use the new imaging equipment that has arrived. This equipment will speed up the pace for photographing plant specimen labels.

Plant digitisers being trained on how to use the imaging equipment

The fourth digitizer is Tebogo Ledwaba who is stationed at the Ditsong Natural History Museum in Pretoria, and she is focusing purely on bee and grasshopper specimens from the museum and from the Agricultural Research Institute. She has completed imaging all the relevant specimen labels and will now image representative specimens per species. She is also lucky enough to jet off to New York in a few months time where she will image scorpion specimens at the American Natural History Museum.


All images of specimen labels will be made available via SANBI’s new online transcribing platform called Transcribe. Transcribe will allow citizen scientists to assist with capturing label information into useable digital fields.

Once specimen labels are digitized they are ready to have latitude and longitude coordinates assigned to them. For this, BioGaps has employed two geo-referencers, Nkhume Ramavhunga and Given Leballo who are both based at SANBI in Pretoria, and SANBI intern Portia Mailula has also been assisting.


Given hard at work


They have been working tirelessly since last year July in adding coordinates to each data record. They started with datasets that were already digitized and soon will move over to the specimen data made available via Transcribe.

The geo-referencing lab

MSc student Precious Tshililo, from the Univeristy of Stellenbosch, has also help geo-reference grasshopper specimens for her research.


Recently volunteer Jill Earle also joined the team, as well as Lesiba Papo, and with their help we’ll get closer to our data targets for BioGaps.

Overall, there are about 100 000 plants specimens that require imaging of their labels and then geo-referncing, and a further 100 000 already-digitised plants that require geo-referencing. And for the invertebrates there are about 20 000 which require imaging of labels and a further 40 000 that requiregeo-referencing.

The task is large, but with our great team of digitisers and geo-referencers we are sure to make good progress.