Representing bird atlas data (SABAP2) on a map

In a previous post, I plotted maps of my sampling sites for fynbos-endemic birds on a map, overlaying a polygon representing the fynbos to get an idea of how well I was covering the range of these birds. Unfortunately, the polygon (downloaded from SANBI) delineates the fynbos “biome” rather than fynbos as a vegetation type, so it includes areas of lowland renosterveld and strandveld vegetation which are not utilised by fynbos endemic birds.

How then should I go about representing the ranges of these birds on my maps? The shapefiles I was using could delineate vegetation at a finer scale, so I could have plotted only those fynbos vegetation types suitable for my species (Cape sugarbird and orange-breasted sunbird). I struggled to get the subsetting to work for this though. I’m sure it could be done, but I  thought of a better resource that would show ranges based on actual obervations: atlas data. Continue reading


Southern Africa (South Africa, Lesotho, Swaziland, Namibia, Botswana, Zimbabwe and Mozambique south of the Zambezi) has a pretty rich diversity of birds. My third edition “Sasol Birds of Southern Africa” reports 951 species occurring in the region, 144 of which are endemics or breeding endemics. To put things into perspective, that’s more birds than there are in Canada and the USA combined! Given this plethora of birds, there have been surprisingly few phylogeographic studies conducted on them¹, especially considering the long history of avian research in the region.

Perhaps even more surprising is that among the small collection of phylogeographic work on our birds, not a single study has focussed on species occurring largely or only within the Cape Floristic Region (CFR), a global biodiversity hotspot2,3. The Percy FitzPatrick Institute of African Ornithology (PFIAO or Fitztitute) has been around for more than 50 years and, situated as it is at the University of Cape Town in the “heart” of the CFR, it really is a wonder that nobody has yet explored the phylogeography of any CFR-endemic birds. I’m not complaining though, since exploring the phylogeography of a fynbos endemic bird/s is exactly what I’ll be doing for my M.Sc.. It would be a lot less exciting, I think, if somebody had done it all before. Continue reading

My first field trip!

I’ve just started an M.Sc. project looking at genetic connectivity in fynbos endemic birds (starting with Cape sugarbird, Promerops cafer, and orange-breasted sunbird, Anthobaphes violacea). To do this, I will of course need DNA, for which I’ll need blood samples. This means I’ll have to go out and catch birds. Birds are normally caught using mist nets, usually by ringers (a bunch of people that fit numbered rings to birds and take all sorts of biometric measurements, building up a goldmine of useful information, especially through recaptures [check out SAFRING]).

Despite having attended as many ringing outings as possible over the past months, my ringing skills aren’t really on par yet, particularly not if I want to be able to catch birds in the field on my own (which was sort of the idea initially, though it’s looking less likely now). The biggest struggle for me is extracting birds from the tiny mesh of the mistnets, especially tiny birds like Cape white-eye (Zosterops capensis). Enter Alan Lee, a post-doc at the Fitz whose current research focusses on conservation of fynbos endemic birds, particularly in relation to climate change (click here and here). Alan played a major role in conceiving “my” project, and the bulk of the available blood samples were collected by him. He and his family live at Blue Hill Nature Reserve, a Cape Nature stewardship reserve bordering the renowned Baviaanskloof Nature Reserve. Alan kindly agreed to have me at Blue Hill to hone my bird ringing/handling skills and also organised a whole ringing road trip to collect samples from a variety of locations. Continue reading