Peer review of: The coincidence of ecological opportunity with hybridization explains rapid adaptive (2019)

Reviewers' Comments:  
 
Reviewer #1:  
Remarks to the Author:  
This is a very nice and important piece of work documenting the role of hybridization in cichlid fish 
radiations. The authors sought to tease apart the question of whether adaptive radiation is limited by 
ecological (niche preemption, competition) constraints or alternatively by genetic constraints (limited 
genetic variation). They examine this by comparing two lakes, Lake Mweru and Lake Bangweulu, 
which are geographically close and climatically similar. The primary difference is that Lake Mweru was 
colonized by from multiple sources, while Lake Bangweulu was colonized by a single source. The 
particular significance is that the authors are able to tease apart the precise history of hybridization in 
Lake Mweru, and hence its role in feeding the genetic diversity in a given lake, while also comparing 
this to a lake system within which hybridization has not occurred.  
 
The authors do a great job of detailing the hybridization events in Lake Mweru. Somewhat less 
convincing was the comparison with Lake Bangweulu in the context of ecological opportunity. 
Ecological opportunity refers to the resources that can be exploited as a result of a combination of 
isolation (reduces the number of competitors/ predators, etc) and resources available. The opportunity 
for adaptive radiation appears to require both these factors; thus, in terrestrial landscapes, adaptive 
radiation has not been documented on the most isolated atolls, presumably due to the limited area 
and resource availability. For the current study, the comparison is between Lake Bangweulu and Lake 
Mweru, with the idea that Lake Bangweulu should provide greater opportunity because it is more 
isolated than Lake Mweru. The problem here is twofold: (1) the authors do not talk about what factors 
were used to define “isolation”, and hence how Bangweulu is considered to be more isolated than 
Mweru. Moreover, (2) there is no information provided on the relative volumes of these lakes, which 
seems to be critical to the manuscript given the test of the role of ecological opportunity. In the 
supplemental material the authors say that Lake Bangweulu has an area of 3,000 km2 surface 
(expanding in the wet season), max depth 10 m; Lake Mweru has an area of 4,400 km2 surface, max 
depth 27 m. I could not find references to these values given in the text. However, in checking 
Shiklomanov and Rodda (2004), these authors give Bangweulu as having an area of 4920 km2 surface 
area, depth 5 m and volume 5 km3; Lake Mweru having an area of 5,100 km2 surface, depth 15 m, 
and volume 32 km3. If this is correct, then - although the areas are roughly comparable - the huge 
differences in volumes would mean that Lake Mweru would likely provide much more opportunity 
compared to Lake Bangweulu. Therefore, could not the finding that diversity is much higher in Lake 
Mweru be explained simply by the much greater lake size (volume)?  
 
The real strength of the paper is the novelty of the adaptive radiation in Lake Mweru and the history of 
hybridization that has fed into this lake. I think that the paper would be a significant contribution if the 
authors focused on this element. Yes, it would be great to tease apart the effects of ecological and 
genetic opportunity, but I’m not convinced that this system is the best for doing that.  
 
Specific points:  
 
Line 80: To what does “They” refer?  
“ … provide ecological opportunities such as opportunities ..” Reword  
Line 82 “Here, we test if co-occurrence of multiple lineages facilitated or impeded ..” Not clear from 
this as to the goal. If we’re thinking 2-3 lineages, the answer would be very different if we’re thinking 
500k – 10,000k ..  
Line 84 Why cichlids?  
Line 99 “despite the presence”  
Line 100 “favorable conditions for radiation (e.g. lake size, latitude, ..” Clarify. What about lake size, 

latitude, etc, makes it favorable (presumably not small size and high latitude)  
 
Line 114. I am not sure that the large differences in lake volume (and presumed associated ecological 
opportunity) allow you to separate out this particular effect. As mentioned above, there is no definition 
of isolation, so it is difficult to see how this differs between the lakes. Moreover, the volume of Lake 
Mweru seems to be much larger than Bangweulu, so the prediction based on this alone would be that 
the Mweru would have a much greater diversity of species (as reported).  
Line 136 Not clear as to the significance of the point that, while > 600 individuals were caught, only 
400 were collected; likewise > 1200 compared to 1066  
Line 192. Not clear what is complemnatry to what.  
Line 199 (& 255). What are “Aufwuchs”  
Line 241: Overlap in species?  
 
Lines 251-269 - Patterns of diversity in Orthochromis and Pseudocrenilabrus are suggestive of 
evolutionary effects of competition in sympatry because in sympatry the two lineages do not overlap 
in morphospace, but the “Orthochromis” in allopatry overlaps in morphospace tremendously with 
Pseudocrenilabrus. That’s fine. Certainly consistent with competition, but there is no actual evidence 
of competition. So the statement that competition among lineages appears to have constrained the 
adaptive radiations in Lake Mweru seems highly speculative. Likewise that interactions among the 
most distantly related lineages may have facilitated radiation.  
 
Line 310 serranochromines  
 
Line 411: occurred  
 
Line 413: Keep in mind the work on many plant radiations that indicate both early and ongoing 
hybridization in adaptive radiation.  
 
Line 441. “despite ecological opportunity” – Looks like there would be a lot less ecological opportunity 
in Bangweulu given the much smaller volume?  
 
Line 456 Say what is complementary to what.  
 
Line 482. The evidence is really not sufficient to say that the opportunity for hybridization is more 
important than ecological opportunity.  
 
 
 
Reviewer #2:  
Remarks to the Author:  
In this interesting paper, Joana Meier and co-workers provide an in-depth examination of the cichlid 
fish faunas of two so far underexplored African Lakes, Lake Mweru and Lake Bangweulu, which are 
situated at a biogeographically interesting region between the Congo and the Zambezi drainage 
systems. Based on an impressive sample size, the authors report a major difference between these 
two lakes with respect to cichlid adaptive radiation: While there are only few and usually non-endemic 
cichlid species in Bangweulu, Lake Mweru is home to a large species assemblage mainly derived from 
intralacustrine radiation events. The authors relate this pattern to the much higher potential for 
(historical) gene flow between species in Lake Mweru. This observation is not particularly novel, given 
that the same authors have previously shown that hybridization can fuel adaptive radiation. What is 
new in this study is the suggestion that the co-existence of several closely related lineages in the 
same water body is conducive for radiation (because of the possibility to exchange genes) rather than 

preventing it (as would be expected from ecological theory).  
 
Overall, I find this integrative study very well conducted, the methods are sound, and the results are 
of broad interest. I do have a few points, though, which would need further clarifications or which the 
authors should consider to incorporate in a revised version of their work:  
 
(1) I do think that the authors should not dismiss the differences between the two lakes in their 
consideration of whether or not an adaptive radiation takes place (that is, the abiotic factors). Lake 
Mweru is certainly larger, probably more stable over geological times, it is deeper (so there is real 
deep-water/open water niche), and it is situated at a lower altitude (these are all factors that 
contribute to adaptive radiation according to previous work by the same group; see Wagner et al.). 
Bangweulu, on the other hand, is a swamp after all. While I don't think that these abiotic factors are 
crucial for the story, these should be discussed in more detail.  
 
(2) Although not particularly important for the general interpretation of the results, I did not get the 
point why exactly the four age calibrations presented in Table S1 were chosen, as these do not include 
the minimum possible, nor the most up-to-date or the ones based on the largest data-sets. I would 
suggest to have a look at Michael Matschiner's review on that matter (Hydrobiologia cichlid special 
issue). Wouldn't it be possible to also try a demographic estimate of diversification times?  
 
(3) As mentioned above, I am generally quite happy with the methods. Nevertheless, I thought that 
the data-set at hand would ideally be run through Milan Malinsky et al.'s fineRADstructure software, 
which is specifically tailored for the RAD data such as the ones presented in this study. Such an 
analysis would allow for a detailed view on the co-ancestry of the taxa.  
 
(4) I feel that the authors should go over the taxonomy once more and provide updates, where 
necessary. For example, I believe that the taxon labelled as "New Lufubu" is in fact O. indermauri 
(Schedel et al. 2018); and perhaps some other taxa have been described (I might be wrong, though, 
but was not able to trace this back further).  
 
In addition, I have some rather minor comments/suggestions:  
 
- 95: I don't want to advertise work on which I am co-author, but I think that Britta Meyer's PhD work 
(the Systematic Biology paper) is relevant here.  
- 108/109: Out of interest: How do we know that Tylochromis is a strong swimmer compared to other 
cichlids? Is there a reference for this statement?  
- 239: there's a double space before "paleolake"  
- 279: To be fair, I think you should cite the original papers from where this number comes from, the 
Nagel paper (200k) and the Verheyen paper, which first reported this exact number (again, I am a co-
author on the latter)  
- 310: Chilwa or Chila? I think this makes a big difference (see also our latest work on sex 
chromosome evolution in P. philander...)  
- 476, etc.: very good point.  
- 646: AFLP's: I see the point that you don't have the extracts anymore, but is it really necessary to 
report these outdated results and methods?  
- It would be great if you could improve a bit the .pdf of the detailed nuclear versus mitochondrial 
tree. Node labels, symbols and especially the branch support values are really difficult to read.  
 
I very much hope that my comments are useful.  
With best wishes,  
Walter  

 
 
 
Reviewer #3:  
Remarks to the Author:  
I read carefully the manuscript entitled "The coincidence of ecological opportunity with hybridization 
explains the prevalence of rapid adaptive radiation". This study showed that adaptive radiations of 
four haplochromine lineages from Lake Mweru experienced hybridization in ancestral species with 
other cichlid lineages, but non-radiated haplochromine lineages from Lake Bangweulu haven't 
experienced hybridization. Ecological opportunity for adaptive radiation may not be different so much 
between the lakes; therefore, not only ecological opportunity but also hybridization is likely to be a 
key factor facilitating adaptive radiation. I didn't find problems in analyses and conclusion but very 
minor points regarding explanation.  
 
Line 151-154: This study called Pseudocrenilabrus radiation, Sargochromis radiation, large-tooth 
serranochromines, and small-tooth serranochromines "lacustrine radiations" of Lake Mweru. This 
information is very important in this study, but I didn't understand which are lacustrine radiations 
when I read the text first. Showing these radiations in this sentence, or marking these radiations with 
"L" or some character in Figure 1b will be helpful for readers.  
 
Line 192: It is difficult to follow this section. For example, I confused "Orthochromis species (line 
198)" with orthochromines species at first. In the previous section, eight radiations were defined. In 
this section, explanation for each radiation may be easier to understand.