TITLE: Initial PhD ideas
DATE: 2017-09-25
AUTHOR: John L. Godlee
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I'm now just over 1 month into my 48 month PhD program. I've spent 
a lot of time reading and trying to wrap my head around my project. 
Now I feel like I'm ready to at least have a stab at saying what my 
PhD is going to be about. Though this all might change again over 
the next few months as I start to write my PhD plan and 
confirmation report.

The original title of the PhD I applied for was "Biodiversity – 
Ecosystem Function Relationships in Southern African Woodlands". 
The basic idea that has been reported by lots of independent 
studies is that as biodiversity increases, so do the levels of 
various ecosystem functions. Biodiversity is most commonly measured 
as species richness (i.e. the number of species in a given area). 
Ecosystem functions are just any rate process that the ecosystem 
performs, one of the most commonly used is the rate at which CO2 is 
fixed into biomass via photosynthesis, taking into account respired 
CO2. This idea has been used a lot to justify biodiversity 
conservation work, under the assumption that if biodiversity 
declines, ecosystem functions and their associated benefits to 
humankind will also decline.

There is however, still lots of controversy about how strong the 
effects of the BEFR are in natural systems and what the drivers of 
the BEFR are. A lot of studies of the BEFR have been in mesocosms, 
or small grassland patches. These studies are often criticised for 
not mirroring natural systems enough to be used to inform policy. 
Often they study one ecosystem function within a limited timeframe 
and with a small species richness. Often species addition/removal 
is random, which doesn't mirror what happens in natural systems 
under stress.

In the past, studies have identified the following as potential 
drivers of the BEFR:

-   Niche complementarity - As more species are added, they 
necessarily differ in the niche space they occupy so they can fill 
more of the total niche space and optimise resource usage.
-   Selection effects - As more species are added, there is a 
higher probability that one of those species will maximise 
productivity. e.g. Grimes 1998

The above potential drivers of the BEFR differ in their reasoning. 
Niche complementarity doesn't take into account community 
composition, while Selection effects realy on community 
composition. Of course, it's likely that in a natural system it's 
probably a combination of the two.

Of course there are other reasons why ecosystem functioning, e.g. 
productivity might vary over space:

-   Resource availability - As resource availability increases, 
productivity responds to that by increasing productivity
-   Environmental stress - An increase in environmental stress such 
as fire intensity might lead to an increase or a decrease in 
productivity, the exact mechanisms behind this are complex.

Southern African Woodlands are understudied and unique

The "Southern African Woodlands" bit is part of why this project is 
interesting. The map below from (Clarke et al. 2017) shows that 
African study sites (and the tropics in general) are severely under 
represented in the Biodiversity - Ecosystem Function (BEFR) 
literature.

  ![World map of studies of the 
BEFR](https://johngodlee.xyz/img_full/phd_ideas/clarke_studyloc.png)

Also, a lot of these theories about the BEFR were drawn from 
studies in temperate environments, so it's not a given that the 
same processes will occur in the dry tropics. Indeed, in the wet 
tropics, there isn't such a strong BEFR, and there are various 
reasons for that. One of the trains of thought that is getting a 
lot of attention at the moment is the role of the environment in 
mediating the strength (i.e. the steepness of the slope), of the 
BEFR. In the temperate studies, it's often found that as you 
decrease resource availability, facilitation effects become 
stronger than competition effects, so that if you add another 
species to the ecosystem, the ecosystem functioning is likely to go 
up more than if the community was under no stress and species were 
competing more. I'm not sure I agree with that idea, surely in a 
woodland, even if there is drought stress, the trees are still 
going to compete for that little water availability because they 
are close together. The competition effect might even increase.

There isn't much data on the traits of different species in African 
woodlands, but it makes sense that species with different traits 
would react differently to environmental change, so the structure 
of the woodland is going to change as different populations change 
in abundance depending on their response to environmental change. 
It also makes sense that as the relative abundance of each species 
changes under environmental change, the level of various ecosystem 
functions will also change at the plot level, because different 
species provide different ecosystem functions. These two sources of 
variation between woodlands muddy the waters in the search for a 
general BEFR, but possibly if you can control for those sources of 
variation, or at least account for them properly in statistical 
analysis you could go some way to teasing out a relationship.

Possible studies

Obviously one of the main jobs of this PhD is to use data from many 
woodland plots across Southern Africa to try to quantify the BEFR, 
and figure out what the drivers of the BEFR are. For example, does 
the shape of the BEFR vary across space according to water 
availability. How does it vary according to woodland type.

I'd like to do a study that looks at how different woodland types 
and their species composition (i.e. their biodiversity) affect how 
they will respond to increasing atmospheric CO2 concentrations. For 
example, some woodlands might be made up predominantly by a single 
species that is very fast growing and can take advantage of the 
extra CO2, while others might not. I suppose leaf traits would also 
have a lot ot do with this. I've heard of a general distinction 
between species that invest in woody growth, and those that invest 
in leafy growth, maybe that has something to do with it.

I think that the understorey of savanna-woodland mosaics is 
understudied. You might expect that the structural aspects and 
diversity of a woodland canopy might affect the diversity and 
composition of the understorey. Understorey species might affect 
the provision of rare ecosystem services and functions, they will 
also have a big role in the spread of fire through those 
understories.

Lastly, it looks like I might be going to Angola for 2 weeks in 
January, to get involved in overseeing the collection of some data 
that will get put into the SEOSAW database. The trip should be a 
good chance for me to get some more fieldwork experience (go to a 
cool place) and make some connections with the people who are 
collecting the data. Making these measurements will be one of the 
first cataloging efforts in the woodlands in this part of the 
African continent and could be a neat paper in itself if I can make 
some connection between the initial biomass and its partitioning 
amongst species of different traits. That study would also be a 
nice way to kick off a second PhD chapter on the role of community 
composition on the BEFR. Then I'd have a chapter on the role of 
environmental variation on the BEFR.

The lack of a BEFR in the wet tropics, possibly worldwide

In the wet tropics, species richness is very high to begin with. 
Many studies of the BEFR in experimental landscapes have shown that 
the BEFR saturates at high biodiversity, so maybe if you take away 
a species it won't actually make any difference. This equates to 
there being high functional redundancy in the wet tropics. The most 
plausible theory in my mind as to why this is the case is that 
because environmental conditions are quite amenable, it is likely 
that competition interactions are powerful enough that species 
co-exist, even within the same niche space, at least at the plot 
scale and higher, this leads to a lot of functional redundancy. If 
you remove a species from the niche space, a suitably similar 
species will have the ability to fill that niche space quickly, so 
there is no loss of function.

In dry ecosystems however, there aren't that many tree species to 
begin with, so you would expect there to be a big effect on 
productivity if you removed a species, as a big area of niche space 
has been removed. However, this line of reasoning relies on the 
assumption that the tree species occupy different niches, while 
occupying adjacent space, but adult trees in savannahs might not 
compete with each other due to them being so spaced apart. So, 
instead of there being a species richness - function relationship, 
maybe there is a composition - function relationship, and the 
function merely relies on the presence of certain species over 
others.

Early predictions

y thoughts at the moment are that because African woodlands are 
quite species poor to begin with, the addition of a tree species 
could greatly increase the productivity of the woodland. But I also 
expect that this effect will depend on a minimum threshold of tree 
density to begin with. At really low tree densities the effect of 
adding a species would depend more on the productivity of that 
species, because the niche space isn't filled enough to promote 
niche partitioning.