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 http://www.ispotnature.org/projects/karoo-biogap
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 http://transcribe.sanbi.org/
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.

Monday, 13 March 2017

Fynbos Endemic Birds Survey

Team spider

Team Spider on the move
Team Spider kicked off their fieldwork in early September for the Karoo BioGap project. The main area of focus was the eastern site because this part of the Karoo had received rain during summer. With rain in mind, the very first sampling day was a wet one. The rain, along with the fact that this was the first of the sites that were sampled, presented a few challenges that were however easily overcome.

Rain moving in towards the sampling site on the first day in the field for Team Spider

Tyrone Le Roux catches his first baboon spider ever!

During the second trip, two spider teams headed out and completed a site together as a training exercise and a bit of team building. The sampling protocol was carried out by each team. Methods such as pitfall trapping, sweeping, beating and active searching proved to be easy with so many helping hands. After completing the first site, the teams went their separate ways to cover more ground. In this way, ten sites were completed and more sites will be done later this summer.
One thing was clear from all the sites visited- the Karoo was very dry and the current drought is extremely serious. Many farmers cannot remember conditions ever being as bad.  The extent of the drought is not fully felt by those of us living in the city. 

Team members learning how to dig up a mygalomorph spider

Both teams hard at work digging in pitfall traps

Team members learning to looking through plant material for spiders collected by beating a tree and a bush

 Robin Lyle and Tyrone Le Roux, one of the teams, out in the middle of the Karoo

team spider