Thursday, 9 August 2018

The Fynbos Forum Turns 40 — But the Conservation Fight is Far From Over

By Alastair Potts

I've attended many of the Fynbos Forums over the years. It's a fantastic place where scientists, managers, government officials, and NGOs get to meet and share ideas about the Cape Floristic Region. Overseas researchers, e.g. from the US or Europe, are blown away by this conference concept. The Forum can be seen as a think-tank for research and conservation. Many ideas generated at the Forum have gone on to grow into major globally recognised initiatives (e.g. the Working for Water program).  These successes have been documented by Caroline Gelderblom & Julia Wood in their recent book "The Fynbos Forum: Its Impacts and History" (Available for free download in coming months).

The Forum has always had an upbeat vibe as it is where all those at the frontline of the conservation battle get to meet, share war stories, the successes, the losses, and all the interesting facts that we continue to learn about nature. 

This year felt different. Very different. In reviewing the amazing work of dealing with alien invasive plant species (the biggest threat to Fynbos!), the continued glaring omission of pine trees in the biocontrol list is devastating. Pine trees have escaped plantations, gone feral in the Fynbos, and are marching on unabated. (The reason for this is the plantation industry's fears around biocontrol affecting their plantations).

But these policy-level problems have been around for a long time. But this year, the problems were more personal, more devastating to the psyche. Those at the conservation frontline are hurting. There were many stories, and I list a few below for a feeling of them...

  • A site monitored by the CREW due to its rare plants was bulldozed by order of a local council in the Western Cape to make a parking lot for a water collection point. The bulldozers worked carefully around the large information signs explaining the unique heritage of the site. When confronted, the council apologised, and is "restoring" the veld, but the damage is irreversibly done. It is likely that these plant populations have been lost for good.
  • The City of Cape Town's biodiversity management department has put in years of effort and energy to conserve important open spaces in the City. The City of Cape Town is largely built on lowland Sand Fynbos, and this vegetation type is nearly extinct within the City's footprint — this is an incredibly rich vegetation with many endemics (most of which are now extinct). The biodiversity management department would always have an uphill battle against the needs of a growing city compared with the generally globally unique situation of incredibly high levels of biodiversity that is also spatially restricted. But the water crisis has brought on a mass flouting of environmental regulations and resulted in the ruining of many sites and threatening of plant species. But more worrying is the growing land appropriation question. There are land grabs in the city, and these naturally focus on the open undeveloped areas — but these are the exact same pieces of land that the biodiversity team have spent years in obtaining and managing for conservation. With single swoops, these areas are invaded and shacks are built on them. Evictions are nearly impossible as this is politically-sensitive topic, and what politician is going to stick his or her neck out to evict illegal land grabbers "for a few plants". The twin onslaughts are juggernauts that are impossible to stop. So while the City deals with the water crisis, and our Nation deals with the land crisis, we're losing our natural heritage.
  • There are also development plans for Kenilworth racecourse which is driven by the government, despite the obvious and documented conservation of the racecourse.  
  • Phosphate mining has reached the border of the West Coast National Park, and there are moves afoot to de-proclaim sections of the Park to allow the miners in...
  • The scuttlebutt is the Dr Guy Preston (Deputy Director General in the DEA) is being sued in his personal capacity by trout enthusiasts for his work on trying to get trout out of South African rivers where they are causing harm. Trout, an alien and invasive fish species, has caused huge amounts of biodiversity harm to the unique fauna of Cape rivers and there is a strong environmental case for their removal. But to attack conservationists in their personal capacity sets a worrying precedent for those who are willing to stand up against the "mighty" (the trout associations are backed by big money as is the case for most of those involved in major despoiling the environment!).
With all of these frontline stories shared at the Forum, it was apt that the concept of "ecological grief" has just been defined and Rupert Koopman shared this at the Forum. As Neville Ellis and Ashlee Cunsolo write..
"Research shows that people increasingly feel the effects of these planetary changes and associated ecological losses in their daily lives, and that these changes present significant direct and indirect threats to mental health and well-being. Climate change, and the associated impacts to land and environment, for example, have recently been linked to a range of negative mental health impacts, including depression, suicidal ideation, post-traumatic stress, as well as feelings of anger, hopelessness, distress, and despair."
Those in the conservation sector aren't in it for the money. The aren't in it for the fame. They're there because they can see the tidal wave of destruction that humans are unleashing and they know what it means. They are not "doing it" for us, but for future generations who are going to look back in despair at what our century destroyed. They can see the long view, the big picture, which gets lost in the day to day need to "make" money, whatever the cost.

Our environment needs help, but our conservationists also need help. This is not a war they can win on their own. And it is a war that is going on in your back yard, no matter where you live.

Glenn Moncrieff shared the following quote during his keynote address by Gus Speth (a leading US environmentalist):
I used to think that top environmental problems were biodiversity loss, ecosystem collapse and climate change. I thought that thirty years of good science could address these problems. I was wrong. The top environmental problems are selfishness, greed and apathy, and to deal with these we need a cultural and spiritual transformation. And we scientists don’t know how to do that.” - Gus Speth
Although the Fynbos Forum has been an amazingly successful think-tank for scientific and conservation issues, as well as making substantial progress highlighting the value of biodiversity to politicians and the public, there are still missing elements. The psychologists, the advertisers, the graphic designers, the famous, and the trend setters need to become part of the Forum's fellowship. It is no longer about what we know, but rather how we can capture minds across all walks of life. A difficult task given the pressing issues facing the world (the gross inequality in South Africa being especially prominent), and it is a task that both scientists and conservation managers are poorly equipped to do. We need to re-think who can really have the biggest impact on conserving biodiversity.

Imagine if Schalk Burger were to adopt a plant species and he took part in surveying it each year... :)

Thursday, 2 August 2018

The origins of flammable vegetation

by Alastair Potts

Examples of plant communities that require fire for sustained existence are found around the world. In South Africa, both fynbos and savanna ecosystems need fire at some point for their component species to either complete their life history cycle or reduce competition with other plants. Thus, some vegetation types have  traits that make them more flammable than others (think of fynbos [e.g. small leaves = "fine" fuel] versus forest [e.g. large leaves = "coarse" fuel]).

However, the evolution of these flammable traits at a community level is an evolutionary conundrum. In a seminal paper published in 1970, Robbert Mutch from the U.S. Department of Agriculture (Forest Service), proposed that...
"Fire-dependent plant communities burn more readily than non-fire-dependent communities because natural selection has favoured the development of characteristics that make them more flammable."
 A straightforward argument on the surface. But as dip a bit deeper into this idea, problems arise. This has primarily to do with what is the biological unit that is being selected?

Mutch opens his paper with the following bold proposition...

"If species have developed reproductive mechanisms (underground rhizomes, root sprouting, serotinous cones) and anatomical mechanisms (thick bark, epicormic sprouting) to survive periodic fires, then fire-dependant plants might also possess characteristics obtained through natural selection that actually enhance the flammability of these communities." [emphasis added]
Thus,  he suggests in a vague way that plant communities, and not species, are the units under selection. This type of argument is known as "group selection"; this type of selection has experienced extreme criticism in the literature, as altruistic behaviour where, in its extreme form, an individual sacrifices itself "for the good of the species" does not make evolutionary sense: if any individuals evolve that do not behave altruistically, then they will have a higher likelihood of passing on their genes in a population of altruistic kamikazis — and thereby such defectors will, over generations, come to dominate the population.

What is additionally interesting is that group selection usually applied to a group within the same species. However, almost all flammable vegetation types are comprise a highly diverse suite of species which have flammable traits. So even arguments of "kin selection" (i.e. sacrificing individuals do pass on their gene via relatives who survive), which is another angle of group selection, still fail to explain such behaviour.

Enter the "kill-thy-neighbour" hypothesis proposed by Bond and Midgley in 1995. This hypothesis that
"...flammability may enhance inclusive fitness if the resulting fires kill neighbouring less flammable individuals and also open up recruitment possibilities".
They also state that
"Alteration of the fire regime through the evolution of flammability, even in a single species contributing heavily to fuel loads,would result in the selective exclusion or admission of other species to an ecosystem depending on the compatibility of their pre-existing traits with fire."
Yet how does this hypothesis apply within a flammable fire-driven community? [Note: flammability and fire-surviving traits need to be considered separately]. If flammable traits are costly to maintain (e.g. dead branch retention), then defectors (in this case, species with low flammability but fire-surviving traits [either of the current individual or of seeds]) should come to dominate the community and thereby decrease its overall flammability. This would allow the invasion of other species that were previously excluded by fire; for example, remove fire from fynbos vegetation and forest species invade and ultimately transform the vegetation into a forest community.  Thus, flammable species need to remain dominant components of the community, and non-flammable defectors a minority component. Thus, from the Bond and Midgley model, we can predict that there should be a combination of flammable and non-flammable fire-adapted (or pre-existing fire survival traits) species.

But this is where the "kill-thy-neighbour" model ends. It still does not adequately explain how flammability and the necessary post-fire seedling advantage could co-evolve. This is where I think there is a geological explanation for the origin of flammable vegetation with fire-adapted traits, but that is a blog for another day...


Sunday, 4 February 2018

(oranges versus thicket) OR (oranges and thicket)?

by Alastair Potts

Much pristine thicket vegetation has been cleared for agriculture. This includes for the cultivation of oranges — which is major land-use option in the Sundays and Gamtoos drainage basins due to the availability of irrigated water. (There are other land uses, including melons, but that is a blog for another day).

The standard approach for obtaining land for orange farming in the Eastern Cape has been to clear large tracts of thicket.

However, would there be any benefit to farmers to maintain tracts of thicket — for example, in linear strips of 10-20 m in width? Would these strips have any conservation value? 

A provide a list of points below of possible benefits that thicket vegetation may have for orange groves if these occur side-by-side (the configuration still needs some thought, but there are lots of options).
  • Wind damage. Citrus trees and oranges can sustain significant damaged from high winds. Thicket vegetation is a dense matrix that grows between 2 - 3 m in height. It is an excellent wind buffer — anyone who experienced the thicket matrix on a windy day can attest to this. The ratio of thicket to grove size and the shape of groves could be used to drastically reduce the wind speeds in the grove.
  • Pest protection. Globally, citrus is either directly threatened by a range of insects or other invertebrates, or the bacteria they carry. For example, the invasion of the exotic Asian citrus psyllid (an insect) has led to the spread of  bacteria responsible for "Citrus greening". Such invasions can occur in systems do not have a functioning food-chain. By maintaining thicket vegetation, one maintains a food-web plus the predators that may feed on citrus pests. By keeping thicket vegetation, farmers may be able to reduce the susceptibility to such threats. This is the basis for concepts such as organic farming. (Note that there may be local potential pests in the thicket vegetation — but it would need to be investigated whether these represent a major threat to citrus; this probably involves asking the citrus growers)
  • Improved water availability. Intact thicket plays an important role in absorption and slow release of water, especially in the more arid forms of thicket (e.g. van Luijk et al. 2013). This may provide orange groves with more water. Alternatively, the evapotranspiration from thicket may lead to localised cooling thus ameliorating high temperatures.  
  • Improved pollination (?). The level of self-pollination appears to vary across different cultivars of citrus (e.g. this report). Where cross-pollination (pollination needs to travel from on plant to another) may increase yields, then maintaining thicket vegetation and all the associated pollinators could very well increase the pollination rate. 
There may be other points to consider on the citrus side of the equation (please share these!), but what about on the value of retaining tracts of thicket for conservation? 
  • Biodiversity. Thicket vegetation occurs as a solid type and in a mosaic with other vegetation types (e.g. grassland, fynbos, Nama-karoo). In the mosaic form, distinct thicket clumps are nested within a matrix of another vegetation type. What is crucial to understand is that these thicket clumps can maintain their biodiversity without any management — in contrast, fynbos or grassland patches need fire (a management headache!) to maintain their species. The patch size to maintain species is surprising small. In his PhD on bontveld (a vegetation type with thicket clumps in the mosaic), Justin Watson demonstrated that a surprisingly small area is required to maintain a high species diversity: 10 ✕ 10 m (with over 200 sqm consistently having high diversity; 2002, pg 129).  
  • Ecological functioning. Thicket operates as isolated patches in many landscapes (the "mosaics" mentioned above). Thus, irrespective of the system, thicket should be able to maintain its ecological functioning — this may also include when thicket grows in a mosaic with orange groves. (Although some thought of the role of pesticides may play needs to be considered).
Thus, there may be a a rare economic and conservation opportunity here where conservation goals with economic growth are achieved by maintaining thicket in a landscape with cultivation. To achieve this, we need to investigate the the size, shape, and co-benefits for both conservation and agriculture.

 If I may end with an example of economic utilisation and biodiversity conservation that coexist in harmony. In a Costa Rican National Park, containing some of highest biodiversity estimates on the planet, sits a power station. Dan Janzen, one of the world's leading scientists, has demonstrated that —with the right mitigation measures in place — there has been no loss in biodiversity or ecosystem functioning. Forests and thicket operate on similar principles: maybe one day say the same about thicket and oranges...

Thursday, 21 September 2017

Spekboom rooting — testing the stem-damage hypothesis.

In a previous post (To the root of the problem...), I highlighted that the roots of planted truncheons invariably only grow from the very base of the stem — thus, rooting takes place 15-20 cm below the soil surface where the stem has been cut. This was based on a few field observations that have been bolstered by digging up many more plants (must be over 50 by now, all in very different environments). In that same post, I suggested that damage to the stem was required for roots to develop. Together with Nicholas Galuszynski, we had an Honours student conduct a series of treatments to determine if this stem-damage for rooting was correct. Unfortunately, the Honours student left with all the data (another lesson on data management for me), so I'm left with a few photos — but the results are, nonetheless, quite clear.

We had five treatments:

  1. Control, where the truncheon was cut and planted with no addition damaging.
  2. Vertical slits, where two shallow vertical slits were cut (quite shallow: <0.5 cm) for ~10 cm length-ways along the stem ending at the base where using the sharp blade of a pair of secateurs.
  3. Horizontal slits, where a number of horizontal slits were cut (also shallow) cross-ways across the stem. 
  4. Peeling, where the sharp secateur-blade was used to shallowly peel (or skin) the outer bark, and,  
  5. Deep gouging, where deep cuts were gouged into the stem.

And the overall results are summarised below with photos of single replicates.
1. Control: no roots along the stem

2. Vertical (or longitudinal cuts): no roots along the stem
However, there was some swelling at the base with more (visually assessed) root biomass.

3. Horizontal (or perpendicular cuts): no roots along the stem

4. Scraping: no roots along the stem

5. Vertical (or longitudinal cuts): hooray! roots along the stem
Rooting was consistent across stems with gouges, but not every gouge developed roots. Nonetheless, those that did not develop roots still healed over.

So, the deep gouging makes a substantial contribution to stimulating rooting. The great thing about these results is that they've been replicate by an independent experiment!

Thankfully, Yondela Norman — an Honours student at Rhodes University — conducted a completely independent and different experiment on rooting (at the same time as we were!) and also found that the deep gouges substantially promoted root growth. So, my predictions in this earlier blog were correct. It's great when the data actually supports a hypothesis.  

Wednesday, 20 September 2017

Thicket Restoration: Is Spekboom the only answer?

Restoring thicket has largely focused on using Portulacaria afra (spekboom), and to a much lesser extent on "late-successional" tree species, as the agents for returning ecosystem functioning. I write "late-successional" because we are a far way off from understanding the successional patterns in thicket; nonetheless, the case is quite well established that, in arid thicket, the presence of many tree species — such as Pappea capensis — is due to the presence of spekboom (e.g. van der Vyver et al., 2013). This is largely due to the increase in available soil moisture that is a by-product of a spekboom dominant layer (van Luijk et al., 2013; Wilman et al., 2014).

However, does this necessarily mean that spekboom is the best pioneer species to re-introduce or bolster into degraded lands? Recent field observations lead me to think that we might have overlooked an pioneer candidate: Crassula tetragona.

While looking investigating a donga (a dry gulley formed by erosion) in Addo that was surrounded by dense intact thicket, it struck me that although there were plenty of spekboom plants in the vicinity (e.g. the orange arrow in the picture below), I could only find one small individual in the donga — although, I argue elsewhere (The number one invasive species in arid lands globally: Spekboom?) that this is due to a lack of an adequate dispersal agent. What had colonised this inhospitable environment was Crassula tetragona (blue arrow in the picture below). Also, where it had colonised, colonies of clonelets were forming wherever leaf-clusters had broken off the parent plant. This clump is acting as a silt and litter trap, with the soil already at least 5 cm above the surrounding soil. This is an example of spontaneous rehabilitation and C. tetragona is changing the microclimate of this eroded donga testing.

However, this is in a herbivore-exclusion area and along a drainage line where there will be some moisture and soil (the donga had not hit bed rock yet). How will this species fair in a harsher environment?

Well, the images below were taken from Kaboega Private Game Reserve on a heavily eroded north-facing (and so hot!) slope. There is no topsoil - it is right down to the eroding shale bedrock.  The light green plants in the image below are C. tetragona. These plants are filling up the small rills on a slope where all the topsoil has been stripped off  — and they are doing it via vegetation growth: a crown piece gets knocked off (falls off?), and this readily takes root. This is an environment where a range of herbivores are present, including kudu and impala. Why is it not being eaten? This species is likely to be unpalatable (however, Curtis & Perrin, 1979, do list it as a preferred species for rodents).

In discussing this as an option with Jan Vlok, he highlighted that this is a species that does not do well in areas with high herbivore activity due to trampling. So some activity is okay, but not too much.

Given that this is a species that has is readily self-propagating across a range of arid and hot environments, it should certainly be considered as part of the rehabilitation suite. Coupling this with erosion control measures, such as mini-ponds, could provide the boost to create vegetated hotspots. 

  • Curtis BA & Perrin MR (1979) Food preferences of the vlei rat (Otomys Irroratus) and the four-striped mouse (Rhabdomys pumilio). South African Journal of Zoology, 14:224-229. DOI: 10.1080/02541858.1979.11447675
  • van der Vyver ML, Cowling RM, Mills AJ, Difford M (2013) Spontaneous return of biodiversity in restored subtropical thicket: Portulacaria afra as an ecosystem engineer. Restoration Ecology 21:736-744.
  • van Luijk G, Cowling RM, Riksen MJPM & Glenday J (2013) Hydrological implications of desertification: Degradation of South African semi-arid subtropical thicket. Journal of Arid Environments 91:14-21.
  • Wilman, V, Campbell EE, Potts AJ & Cowling, RM (2014) A mismatch between germination requirements and environmental conditions: Niche conservatism in xeric subtropical thicket canopy species? South African Journal of Botany 92: 1-6.

Dr John Kani: why science and universities have failed South Africa

by Alastair Potts

I had the unusual pleasure of attending an awards ceremony for researchers and lecturers where the guest speaker, Dr John Kani, berated us in an unstinting barrage of uncomfortable truth. His voice, as unique as that of Morgan Freeman, captivated us as he poured his scorn and derision upon the state of the country  and how the universities are, in part, to blame. An interesting choice of topic to an event aimed at celebrating research, teaching and engagement  but an entirely necessary call to arms.

So what did John Kani say? It was a wide ranging talk, but below are two of the highlights that stuck with me (Crucial note: I was not prepared for note taking  it was an awards event after all  and although I've remembered these points, they are [largely] in my own words):

  • Scientists — what is it that you actually do? Dr Kani highlighted that scientists get so wrapped up in their private worlds [and usually only hang out with other scientists] that they forget to explain what it is they do and why it is important. But worse, we don't give much thought on how to make our research accessible to the lay person, or school children. We publish in rarefied journals that the even the most ardent of non-scientist science enthusiasts will a. battle to understand, and (even worse) b. won't have access to [locked behind publisher paywalls]. He shares the story of the selection committee for the prestigious Order of Mapungubwe battling to understand what it is that any given scientist has done that may warrant the bestowing of such an award. If we cannot (do not?) share our research findings with the public at large, then what is the point of science? I feel that this point is spot on: we cannot expect non-specialists to rise to the level of specialists (who have spent years learning the theory and jargon). It is the specialists who need to rise to the level of simplicity [Einstein had much to say about simplicity!].   

  • Universities — why are you so quiet? Another point that that he raised was that Universities have, in his view, shied away from politics and advising government. He makes a good point: where are the qualification specially designed for councillors and others in public service? Surely it is the universities who have the responsibility to create the diploma and degree benchmarks to ensure that those in public service are qualified to serve the public. Dr Kani relates the historical narrative of the NATS gaining power, based on a large part to the argument of the Afrikaans culture being under threat of erosion or extinction  and within a few years (six?) it was possible to study from pre-primary all the way through to University in Afrikaans. The NATS did this by pouring money into this agenda — i.e. into Universities, the Arts etc. Dr Kani believes that no such effort, nor commitment, has been made by the current government, and that universities have accepted this. Universities have not made a strong enough call to demand to be the agents of change for the country. [Rather, the funding for universities has declined without much active outcry which led to the burden being passed onto students]. 

Dr Kani left us with a challenge: be the driving agents of change in South Africa. We have the most powerful tool available  education. Given the new name of Nelson Mandela University and the university's slogan, "Change the World", this message could not have come at a more appropriate  time.

It is time to to turn the ivory towers into the pillars that support a better nation.  

Wednesday, 7 June 2017

The joys of recieving DNA sequences.

by Nicholas Galuszynski

The struggle is real! Image courtesy Sketching Science.
So you've done it!
After hours (that felt like years) battling with DNA extraction methods and PCR protocols you have finally received the sacred e-mail, "please see attached sequences..." and it all starts seeming worthwhile, maybe.
But now what, you've done the lab work but what are you supposed to do with these .ab1 files? What are .ab1 files any way? I WANT MY SEQUENCES!!!

So firstly, .ab1 files are are the output format for raw DNA data produced by Applied Biosystems' Sequencing Analysis Software. These files contain an electropherogram as well as the DNA base sequence, which can be viewed using a DNA viewer program. Secondly, there are many ways of opening these files, however, freely available software options for handling your .ab1 files, normally have limited capabilities compared to their expensive counterparts such as CodonCode Aligner

So I've recently been using the trial version of Codon to check out some Cyclopia sequences, and damn this program is easy to use once you know where and what the different functions do. After checking out a few tutorial video on YouTube, I was able to do the basics such as import my sequences, create contigs based on names and visually inspect and correct these contigs. If you are starting out with Codon, watch those videos! From that base you can start trouble shooting and finding your own ways to do things, which is made much easier with the wide range to tutorials available from the manufacturers.

Oddly enough, one of the most useful features of the software, comparing all the contigs you've assembled, needs to be added to the toolbar. But this is easily explained by CodonCode. Before you get too into creating contigs and aligning them all to each other, it is often really useful to run a base call on your freshly relieved sequences. This can improve the quality of your sequence, resulting in better alignment of the forward and reverse sequence. I tended to have a lot of strange indels pop up in the sequences for a cDNA region, possible due to sequencing errors in highly repetitive A and T rich sections. These made contig comparisons difficult and I ended up selecting the best quality sequence as a reference sequence (make a reference seq by selecting the sample and pressing ctrl+alt+m), I then selected the Clustal-Omega method of aligning the contigs as apparently this option handles these gaps a bit better than Muscle that tends to delete them. But maybe deleting them isn't the worst option if all you're interested in is detecting SNPs and if that is your desire, you can then use Codon to find primer sites around those SNPs without even having to open another program. That is however, until the end of the 30 day trial after which you'll have to buy a licence or like reinstall windows or something.

So CodonCode is a pretty useful tool for the molecular biologist, offering a lot of functionality in one neat package. This however, comes at a price so make the best use of your trial and check out the helpful link's in this post before you activate your copy.