Peer review of: An excess of niche differences maximizes ecosystem functioning (2020)

Peer Review File - Reviewers' comments first round 
 
 
Reviewer #1 (Remarks to the Author): 
 
The authors present an empirical comparison of two areas of modern community ecology: 
coexistence theory (e.g. Chesson 2000) and BEF theory (e.g. Loreau & Hector 2001). 
Unfortunately, the authors seem focused on testing how these two theories compare to one 
another for their own sake, not because the comparison reflects an interesting mechanistic 
question. While unifying community ecology is important, doing it phenomenologically (instead of 
mechanistically) will lead us down a path of wasted time and money. I would recommend that the 
authors dig deeper into the mechanisms underlying both Chesson’s stabilizing vs. equalizing 
framework and Loreau & Hector’s complementarity vs. selection framework. For example, 
facilitation can be a stabilizing mechanism, but only when interspecific facilitation is greater than 
intraspecific facilitation. In either case, the alpha terms must be less than 0, but this is 
systematically prohibited in the coding of their model. The authors are familiar with the 
applications of these theories, but I would also recommend they consult with a mathematical 
ecologist to further understand the implications of the assumptions they are embedding in their 
models. Beyond this, a single year of data is insufficient to test the proposed theories. 
 
Major errors/issues: 
 
1. Introduction and framework: Complementarity effects as calculated by Loreau & Hector are not 
mechanistic. At least three classes of mechanisms fall under this umbrella: resource partitioning, 
abiotic facilitation, and pathogen pressures. Importantly, recent work has shown that resource 
partitioning is likely not the most important of these mechanisms (e.g. Barry et al. 2019). 
Furthermore, both Chesson’s stabilizing mechanisms and equalizing mechanisms could include 
abiotic facilitation: if interspecific facilitation is greater than intraspecific facilitation, this would be 
stabilizing, but if microclimate amelioration homogenizes a plot and makes demographic rates 
more similar to each other, this would be an equalizing mechanism. The authors need to take a 
surgical approach to this problem in order to not further muddy an already muddy subject. 
 
Some examples: Lines 59-61: Complementarity effects (as calculated by Loreau & Hector) are not 
mechanistic. Lines 66-67: Because complementarity effects are not mechanistic, this doesn’t seem 
like the right place to start. Lines 68-73: this is all assuming that the most important mechanisms 
are driven by competition…but this is likely not the case. Lines 74-76: Linking these two theories 
to one another is not interesting a priori… 
 
2. Methods: Overall the biggest methodological issue is that the experiment only ran for one year. 
Even in an annual plant community, there is no reasonable way to parameterize a model about 
stability in a one-year-old community. An ecological community results from more than just a 
single life cycle of plants (e.g. leaf litter accumulation, pathogens, soil community, etc). Plenty of 
work in the BEF literature demonstrated that BEF effects don’t stabilize for at least several years 
(probably closer to 10 years). 
 
Beyond this, the modelling approach had some issues and needed clarification in some areas. 
 
Line 314: shared mutualisms would not result in niche differences, please clarify 
Line 318: Be clear in your discussion of competitive dominance (relative values for alpha) vs. 
higher fitness values. You use them interchangeably in the text and this has serious implications 
for interpretation of the model 
Lines 324-327: when there is perfect niche difference (species only compete with conspecifics, the 
competitive response ratio goes towards infinity, how is this handled? 
Lines 360-361: you cannot restrict alpha values to be greater than 0 and compare this with 
complementarity effects. Complementarity effects are likely strongly driven by facilitation and 
facilitation in this framework is represented by negative alpha values. 
 
3. Results: the lack of clear mechanistic justification for these comparisons becomes very clear in 
your results. Also, you overstate the results repeatedly, which makes the reader less confident in 

the work in general. For example, in Figure 2, complementarity effects are ONLY clearly linked to 
niche differences for biomass production. For both litter decomposition and soil nitrogen, selection 
effects are much more clearly correlated with niche differences (while in a negative direction the 
correlation is still clear). This means that you have more support for a link between selection 
effects and niche differences. There is no mechanistic reason why that would happen and also no 
theoretical underpinning for why that would happen. Again, this makes the lack of theoretical 
underpinning for the whole paper particularly clear. Similar issues are repeated throughout Figure 
2. 
 
In Figure 3, it does look like there is an interesting pattern in control climate conditions in terms of 
biomass production, but then the rest of the figures make it seem like this could just as easily 
have been a spurious correlation. None of the rest of the relationships support the proposed 
hypothesis at all. 
 
 
 
 
Reviewer #2 (Remarks to the Author): 
 
 
The manuscript by Godoy and colleagues is a novel attempt to combine predictions and insights 
from coexistence theory to understand complementarity and selection effects for biodiversity-
ecosystem function studies. This work uses an elegant experiment to parameterize two sets of 
models and shows how complementarity/selection are related to niche and fitness differences. This 
is a much-needed experiment and an extremely valuable contribution to the literature. I really like 
this study, though I do have some suggestions for improvement. 
 
The environmental treatment seemed to come out of nowhere in the introduction but is actually a 
cool feature of the experiment. That you can create different scenarios of niche and fitness 
differences with the same species is a powerful way to test some of the central questions. The 
importance of environmental differences for influencing both sets of mechanisms (niche and fitness 
differences and complementarity/select) should be introduced earlier. 
 
The final analyses looking at competitive networks and equilibrium coexistence, to me, seem 
underdeveloped and the main finding, that the full community will not coexist and thus diversity 
and function are transient, do not come across as robust. My general concern about niche/fitness 
difference experiments is that they are temporally and spatially limited and that parameter 
estimates are biassed by local conditions without accounting for coexistence mechanisms 
influenced by spatial or temporal niche differences. None of these types of experiments has been 
able to fully account for full community coexistence, and I believe that the methodology is too 
limited. Thus, I recommend removing this test (lines 150-156, 221-229), as, to me, it doesn’t 
really test the main hypothesis anyway. 
 
In general, I found that the discussion lacked biology, as opposed to ecological theory. I think it 
would be helpful to bring the results back to the system and species manipulated and to put the 
mechanisms into terms that are germane about this system. A little more about species and those 
contributing to selection effects and the different ecosystem functions for example. In another 
example, the section on the environmental variability again lacks biology from the species, which 
least sensitive and how did they contribute to selection effects and functioning. And again, like the 
introduction, the environment treatments seems disconnected from the other results, rather than 
being a way to strengthen the findings. 
 
 
Abstract -second sentence seems too obtuse. Please be more precise about mechanisms/classes. 
And the third sentence - what the prediction refers to is not clear. 
Line 67-68: not clear what ‘its effects’ is referring to exactly. 
Line 72: ‘may’ to ‘might’ 
Line 73: maybe give a mechanistic explanation or example of how this could happen. 
Lines 77-89: great paragraph explaining your questions and motivation. 

Lines 95-96: Seems a little obtuse, please be more precise on how Environmental variation 
influences the link between diversity and productivity. 
Lines 127-130: Even though described in methods, I think a little more description of what was 
meant by demographic and competitive response ratios and how these were quantified. 
Lines 142-145: you state twice ‘species pairs predicted to stably coexist’, which is a mouthful. Why 
stably, is it necessary, just ‘predicted to coexist’ should be sufficient. 
Line 161: “Both fields’ -I know what you mean, but you haven’t really said what these are in the 
previous sentence. 
Lines 207-219: I’m sure you can say a little more about the likely mechanisms. Which species 
maximized these and what is known about them? 
 
 
 
 
 
 
 
Reviewer #3 (Remarks to the Author): 
 
I have read “A mechanistic path to maximize biomass production while maintaining species 
diversity” by Godoy et al. In this contribution, the authors put to the test a number of ideas that 
have received recent theoretical attention on the relationship between coexistence mechanisms 
and diversity effects of ecosystem functioning. In this sense, the contribution is timely and 
important. The experiment is well designed, and the methods seem correct (although there is a 
critical issue that is not clearly explained, making it impossible to provide a complete assessment 
in this regard), and the statistical methods are correct given the data. I have some doubts on the 
hypothesis that ecosystem functioning increases when niche differences overcome fitness 
differences, allowing for stable coexistence, rather than increasing as a result of adding the effects 
of niche and fitness differences considered separately. There is no clear reasoning behind this idea, 
previous theoretical work does not support it (and rather contradicts it), and the results do not 
support it clearly. However, this is not a critical issue, and it does not reduce the merit of the 
contribution. There is also an issue on a possible extrapolation that could cast doubts on one 
important result. Below I list my comments as issues appear in the manuscript. The ones with an 
asterisk are the ones that I believe are most important. 
 
1. Title: when I first read the title I thought that a path was being proposed to explain some kind 
of paradox precluding coexistence in productive systems. I would prefer something in the lines of 
“Coexistence stabilization has a positive effect on ecosystem functioning in diverse annual-plant 
communities”. 
2. Abstract: The problem is posed as “it is important to know how these two things relate to each 
other”. I would prefer to see an argument for why they should relate at all (especially if we are 
told in the abstract that theory states that they do not “map to each other”). Fitness differences 
(sensu Chesson), complementarity and selection (sensu diversity-functioning theory) are not 
widely used terms that may require a definition in the abstract. I can see that this is a challenge 
given 150 words. Please conduct some copyediting for grammar. 
3. L31: Plants or plant species? 
4. L63: Isn’t it the other way around? Niche differences strengthen stabilization. 
5. L82: large niche differences promote evenness. Yes, in relative terms when compared to a very 
specific community (one with less differentiation, ceteris paribus; see Turnbull et al 2013). In 
general, there is no reason to expect evenness in absolute terms if niches are different. Population 
sizes would depend on the availability of the resources used by the different species, which is an 
environmental factor independent of niche differentiation. The authors have tried to be very 
concise in the presentation of their hypotheses and predictions, but I feel that more space is 
needed to explain them clearly. Please see comments 6 and 7. 
6. L82: You have not argued for evenness before as a factor that increases functioning. The 
function-evenness relationship needs to be clearly stated before (Turnbull et al 2013, Connolly et 
al 2013 may be cited). 
7. *General hypothesis: Perhaps I am not getting something right, but I am not convinced about 
the way the argument presented. In L82-84, niche and fitness differentiation are discussed as 

having somehow independent effects on functioning: function increases with niche differences 
(ND) and decreases with fitness differences (FD.) The expected pattern (greater function as ND 
increases relative FD) would be expected if the “independent” effects of ND and FD are simply 
added, but also if it is the difference ND-FD that matters. However, you favor the latter 
alternative. Please state more clearly the biology behind this argument. 
8. *L84: (In line with previous comment) “sufficient niche differentiation to offset fitness 
differences”. This is a binary variable (sufficient vs insufficient), while I believe that, from the 
argumentation in L 82-84, it follows that a greater difference between niche differences (ND) and 
fitness differences (FD) should result in a greater functioning: no digital divide expected, gradual 
change instead. Se also Turnbull et al. 2013. They show that overyielding is related to ND, 
regardless of whether ND is sufficient to grant stable coexistence (i.e., no need for ND>FD). In 
fact, overyielding does not provide evidence on stable coexistence at all. 
9. L123: The way this is written suggests that p value should be used as effect size. In any case, p 
values are not as important as effect sizes in this context. Please rewrite. 
10. *L141-148, Fig. 3A-B. You would expect to see more biomass towards the bottom-right corner 
of the graphs if the effects of ND and FD just add up or if yield only increases when there 
“sufficient niche differentiation to offset fitness differences” (L84). Therefore, I do not see any 
reason to conclude in favor of the second alternative. A more sophisticated analysis would be 
required to tell between both hypotheses because their predictions are so similar (gradual increase 
towards the coexistence region of the graphs vs. a sharp increase at the divide between 
coexistence and exclusion). The pattern seems quite noisy to provide a clear cut between both 
patterns. 
11. L359: (20)? 
12. Equation after L359 (and elsewhere): When the experiment was set up, seeds of the focal and 
interactin species were added in different amounts measured as mass of seeds (2-16 g m-2), but 
the fitted model requires numbers (not mass) of individuals. Did you count the number of 
interacting individuals that got established in each plot, and used that number to fit your models? 
Please explain. 
13. L360-61. I guess that the parentheses should close after “greater or equal to zero” rather than 
after “BFGS-B”). 
14. L363: gi was calculated as the fraction of seeds that germinated out of the five that were sown 
in each plot, from the number of seeds added when setting the density treatment (those added as 
grams per m), or both? 
15. L389 and ss: I did not follow clearly how was litter manipulated and decomposition measured. 
16. *L416 and ss: I like the idea of resorting to a procedure such as that proposed by Connolly et 
al. 2013 to solve the problem, and the fact that the procedure proposed here correlates with the 
“canonic” procedure of Loreau and Hector (although sometimes the correlation is quite weak, 
something that merits some comment from the authors) suggests that the Godoy et al.’s method 
used is appropriate. However, much more detail is required here. Connolly et al.’s procedure needs 
to be explained for the reader, and, very importantly, the way in which it was adapted/interpreted 
in terms of complementarity and selection needs to be thoroughly explained. In eq. 1 in Connolly’s 
paper, the model for no diversity effects is explained. I can but guess that the model used by 
Godoy et al is eq. 2b from Connolly, which is the same as eq 1 with only one more term 
comprising diversity effects (delta*Pi*Pj to the power theta). If I get it right, positive deltas result 
in overyielding and thus indicate complementarity, and theta is a shape parameter. I can’t see 
where the measurements of selection come from (unless theta can be interpreted in this way, but 
it is not obvious why). These things need to be explained, especially because Connolly et al. do not 
propose any interpretation of their model as a partition of diversity effects into complementarity 
and selection effects and thus Godoy et al.’s proposal seems to be entirely novel. 
17. L421: “because it possesses” 
18. L428: Please provide a short explanation of what Loreau and Hector do, and why the results of 
your procedure needs to be compared with those derived from their method. 
19. L447: delete “this means that a” 
20. L451: This is probably a personal bias, but I find the term “network analysis” a bit misleading 
here. What you are using here has long been known simply as stability analysis. Network analysis 
suggests to me the study of the structure of the matrix such as compartmentalization, 
connectivity, nestedness, small-word structure etc. 
21. Fig 1“Non-linear instead regressions fitted the data better” remove “instead” and: better than 
what? 

22. *Fig 3: If there are no species pairs in the coexistence region under drought conditions (Figure 
S3), the complementarity effect observed in the coexistence region in panel B may be a strong 
extrapolation and thus may not be trusted. This would cast doubts on some important conclusions 
of the manuscript. Am I missing something? 
23. Fig S1: I am a bit surprised by the fact that the relationships between diversity and functioning 
are straight lines. Connolly et al model corresponds to a not linear relationship. What model are 
you using here? 
24. The caption of figure S5 states “see Figure S5”, which is odd. Is this an error and you want the 
reader to see some other figure instead? Besides, I find the figure unclear.