Diversity and Big Tree Patterns in the Brazilian Amazon
, Eric Bastos Görgens 2, Anderson Pedro Bernardina Batista 3, Diego Armando Silva da Silva 3, Cinthia Pereira de Oliveira 1 and Carla Samara Campelo de Sousa 3
Round 1
Reviewer 1 Report
General comments
The manuscript presents an analysis of the relation between the occurrence of big trees (with DBH> 70cm with wood density, tree density and species diversity in several plots of the Amazonian forest. The main conclusions were that there was a negative correlation between DBH and species diversity and that big trees represent a large proportion of the biomass (75%), even if they represent less than 10% of the species. The data is interesting, but I think the authors can improve the manuscript with a better exploitation of the results and discussion. Some parts of the data analysis need to be better explained.
Specific comments
The abstract does not highlight the main conclusions of the analysis.
Line 21: If you want to include the concept of regions of Morrone in the abstract, you need to briefly explain that this is a biogeographical classification of the author Morrone. Those that are not so familiar with tropical regions do not understand what you mean by “regions of Morrone”. Additionally, in the end you could not find a simple relation between the attributes you have measured (diameter, wood density and diversity) and the regions of Morrone (line 221), if I understood well.
Line 35: You say that “Big trees help the kickstart of the succession by improving microclimate and soil conditions, attracting frugivorous seed dispersers, and favoring regeneration of old-growth species.” You use the reference of Poorter et al. (2021). This manuscript is about tropical forest recovery after agricultural abandonment. Those authors use several indicators to evaluate the recovery of a tropical forest and they say that “Dmax (maximum tree size) and SH (structural heterogeneity) are robust indicators of structural recovery” but “Dmax is weakly linked to recovery of biodiversity attributes.” But they also say that “Aboveground attributes such as structure and diversity had low starting values because of the nearly complete removal of woody vegetation for agricultural use, whereas soil attributes had high starting values because of belowground legacies.” So how can big trees “help the kickstart of the succession”? Can you explain better?
Line 67: You have used data from the plots of the project forestplots.net. Can you briefly characterize the plots in terms of management? Were they similar in terms of anthropogenic use (agriculture, wood extraction – in this sense big trees are important targets).
Line 95-96: When you refer density, you refer wood density?
Line 96-97: Please explain better what variables were computed. 100 variables of species density? What was the difference of the 100 variables of species density? 6 variables of diversity? What variables? And 10 variables of structure? DBH and what else?
Line 103: The attributes of structure were d – what is d? – and wood density – I count two variables, diameter and wood density (not 10 variables as previously mentioned); and the relative density of top 50 species for all trees. When you say “relative density” you refer to the wood density? Please explain better.
Figure 1: Can you distinguish better the symbols of the different biogeographic regions? In legend of the map you highlight altitude but in the analysis of the results you do not relate the occurrence of a higher percentage of big trees with altitude (or any other abiotic parameter). Is it really important to have the altitude in the map?
Figure 3D: How did you calculate the tree biomass?
Figure 4: If you did a K-mean cluster analysis, can you show the clusters? Figure 4 is just a way to determine the best k-number, that is, how many groups are clustered. But can you show which clusters did you obtained? Explain better the results of this analysis.
Line 182-183: What about anthropogenic impact?
Line 199: In what way big trees are important to the biogeochemical cycle? Can you detail?
Line 201-202: You saw a positive relation between big tree species diversity and aboveground total biomass. If you have more species of big trees, you increase the probability of having a higher number of big trees, thus an increase in total aboveground biomass. Please explain better why this result is interesting.
Line 204: Where can I see this result, that the 4 groups did not match the biogeographical regions?
Line 210-211: You say that “The northeastern Amazon site exhibit patterns of diversity and structure that are more evident than in other regions.” What do you mean by “more evident”?
Line 222: What are these regions, Madeira, Pará, etc. Are regions of plots? Why do you highlight these particular plots (or regions)? Where are these regions located in Figure 1?
Line 241-242: The authors say that “Big trees are long-term survivors, suggesting that they may be more adapted to local factors”. An interesting question is why there are big trees? A simple answer is that they are strong competitors for light. But how did they become so big? Is it because they have higher growth rates and/or because they are older? Size and age in trees do not have a direct correlation. Size is strongly modulated by environmental conditions that is why you can have a large and a smaller tree diameter and the smaller one can be older. Another interesting question, concerning big trees in tropical forests is why they are associated with certain species, that is, the presence of big trees is not randomly associated with the identity of the species. Why some species are more associated with big trees? What are their characteristics?
Author Response
Big trees patterns in the Brazilian Amazon
Lima et al. 2022
Author's Reply to the Review Report (Reviewer 1)
Line 21: If you want to include the concept of regions of Morrone in the abstract, you need to briefly explain that this is a biogeographical classification of the author Morrone. Those that are not so familiar with tropical regions do not understand what you mean by “regions of Morrone”. Additionally, in the end you could not find a simple relation between the attributes you have measured (diameter, wood density and diversity) and the regions of Morrone (line 221), if I understood well.
Reply: In summary, we corrected the Morrone regions by adding the term biogeographical. Due to the word limit in the abstract, we could not describe a specific concept, limiting ourselves to implying that Morrone's biogeographic regions are domains or ecological zones of taxa of terrestrial plants and animals that divide the Brazilian Amazon. Regarding the relationship between structure and diversity attributes, we found that some dominant large species occur more frequently in these biogeographic regions. The structure attributes are a complement to respond to these formations through the groups generated by k-means. For example, the Guiana shield region comprises the largest trees and the most significant species richness. At the same time, the central Amazon province is less rich, probably due to the devastating action of anthropic activities.
Line 35: You say that “Big trees help the kickstart of the succession by improving microclimate and soil conditions, attracting frugivorous seed dispersers, and favoring regeneration of old-growth species.” You use the reference of Poorter et al. (2021). This manuscript is about tropical forest recovery after agricultural abandonment. Those authors use several indicators to evaluate the recovery of a tropical forest and they say that “Dmax (maximum tree size) and SH (structural heterogeneity) are robust indicators of structural recovery” but “Dmax is weakly linked to recovery of biodiversity attributes.” But they also say that “Aboveground attributes such as structure and diversity had low starting values because of the nearly complete removal of woody vegetation for agricultural use, whereas soil attributes had high starting values because of belowground legacies.” So how can big trees “help the kickstart of the succession”? Can you explain better?
Reply: Large trees are the final stage of ecological succession when they reach maximum heights (climax). The microclimatic conditions provided by the size of the crown and trunk are great drivers of smaller species of the understory that are of secondary succession (early and late) and need shade for their initial development. These species classified as secondary succession make up the vegetation canopy in tropical primary forests.
Line 67: You have used data from the plots of the project forestplots.net. Can you briefly characterize the plots in terms of management? Were they similar in terms of anthropogenic use (agriculture, wood extraction – in this sense big trees are important targets).
Reply: The field inventory data obtained by the ForesPlots platform's plot network originated with different research objectives. In some cases, the data are from permanent plots monitored annually by principal researchers funded by long-term ecological projects. In these projects, some topics are addressed, such as the effect of anthropic activities (burning, logging) on vegetation dynamics. Other projects mainly address the structure and diversity of primary and secondary forests. The sampling or inventoried plots are usually at least 1 hectare of forest sampled for the different locations and analyses. As our work is to compare the structures and diversities of these communities, we do not work with secondary data on the effect of anthropic activities in each area, even though large trees are routinely affected by these activities, especially those of commercial value.
Line 95-96: When you refer density, you refer wood density?
Reply: In this case, we refer to the relative density of species (Number of individuals of the species/total number of species). The basic density of wood is characterized as an attribute of structure (wood density).
Line 96-97: Please explain better what variables were computed. 100 variables of species.
Reply: Our analysis comprises splitting the complete database into two subsets. One dataset with all trees with DBH > 10 cm and a second dataset with DBH > 70 cm (big trees). In each data set, we analyzed the 50 main dominant species (totaling 100) and the attributes of diameter (mean, maximum and standard deviation) structure and wood density.
Line 103: The attributes of structure were d – what is d? – and wood density – I count two variables, diameter and wood density (not 10 variables as previously mentioned); and the relative density of top 50 species for all trees. When you say “relative density” you refer to the wood density? Please explain better.
Reply: Similar to the answer to the previous question. The d is the diameter (dbh). This information has already been corrected in the main text where: dmean, dmax, and dsd are respectively the mean, maximum, and standard deviation of the diameters.
Figure 1: Can you distinguish better the symbols of the different biogeographic regions? In legend of the map you highlight altitude but in the analysis of the results you do not relate the occurrence of a higher percentage of big trees with altitude (or any other abiotic parameter). Is it really important to have the altitude in the map?
Reply: We have not looked directly at the effect of altitude on the structure and diversity components because this approach is being implemented in another paper investigating the effect of environmental factors on the large tree community in Amazonia. Therefore figure 1 has been modified.
Figure 3D: How did you calculate the tree biomass?
Reply: The individual tree-level biomass for each plot was obtained using the pan-tropical allometric model developed by Chave et al.(2014):
where D is in cm, H is in m and ρ is the basic density of wood and is in g cm3. This model performed well in all forest types and bioclimatic conditions (Chave et al. 2014). This information was added in the paper.
Figure 4: If you did a K-mean cluster analysis, can you show the clusters? Figure 4 is just a way to determine the best k-number, that is, how many groups are clustered. But can you show which clusters did you obtained? Explain better the results of this analysis.
Reply: The figure of the formed groups is shown as supplementary information. We corrected and added this figure to the main manuscript.
Line 182-183: What about anthropogenic impact?
Reply: We did not directly assess the effect of anthropic activities as an input variable for K-means
Line 199: In what way big trees are important to the biogeochemical cycle? Can you detail?
Reply: Plant growth dynamics generally drive the biogeochemical cycle in forest ecosystems. Large trees make up the forest canopy and absorb more sunlight, favoring their three-dimensional growth. The fallen leaves from the canopy of these trees are the primary source of nutrients for many microorganisms and plants of different sizes and contribute to the soil's respiration and the accumulation of nutrients and organic carbon. The cycling and distribution of nutrients promoted by the roots of these trees can condition the growth of other plants. The percentage of soil water uptake by its large roots contributes to its biomass productivity and the water cycle on continental scales. This and other information shows the importance of large trees in biogeochemical cycles.
Line 201-202: You saw a positive relation between big tree species diversity and aboveground total biomass. If you have more species of big trees, you increase the probability of having a higher number of big trees, thus an increase in total aboveground biomass. Please explain better why this result is interesting.
Reply: The relationship between species richness and the proportion of biomass of the largest trees is significantly driven by the data on the low occurrence of large trees in the largest DBH classes (Fig. 2c,d). Over 75% of the biomass is concentrated in less than 10% of large species. Therefore, our results suggest that the variation in the richness of large species between size classes and locations may reflect the biomass of the largest trees. An increase in the occurrence of large species in the largest classes can result in a significant increase in total biomass and, consequently, can decrease species diversity over time (Fig. 2b).
Line 204: Where can I see this result, that the 4 groups did not match the biogeographical regions?
Reply: Further details on the biogeographic groups and regions can be found in the supplementary information (xlsx).
Line 210-211: You say that “The northeastern Amazon site exhibit patterns of diversity and structure that are more evident than in other regions.” What do you mean by “more evident”?
Reply: This region is known for its high biodiversity conservation status. This area generally presents richness, diversity, and forest biomass values more evident than in other places in the region.
Line 222: What are these regions, Madeira, Pará, etc. Are regions of plots? Why do you highlight these particular plots (or regions)? Where are these regions located in Figure 1?
Reply: We have made the changes in Figure 1 and have already provided information about these biogeographic regions.
Line 241-242: The authors say that “Big trees are long-term survivors, suggesting that they may be more adapted to local factors”. An interesting question is why there are big trees? A simple answer is that they are strong competitors for light. But how did they become so big? Is it because they have higher growth rates and/or because they are older? Size and age in trees do not have a direct correlation. Size is strongly modulated by environmental conditions that is why you can have a large and a smaller tree diameter and the smaller one can be older. Another interesting question, concerning big trees in tropical forests is why they are associated with certain species, that is, the presence of big trees is not randomly associated with the identity of the species. Why some species are more associated with big trees? What are their characteristics?
Reply: These questions are fascinating and sharpen our curiosity about the big trees. As mentioned, the size of these giant trees is often driven by environmental factors, which are being investigated in another paper. However, knowing why large tree species are restricted to a individuals low number are gaps that are still difficult to fill and need more data for a more robust analysis. Both competitive superiority and widespread cultivation before 1492 by humans are compelling hypotheses worth testing.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
Comments for author File: Comments.pdf
Author Response
Big trees patterns in the Brazilian Amazon
Lima et al. 2022
Author's Reply to the Review Report (Reviewer 2)
L32: “Big trees is”: suggested to change the subject verb agreement.
Reply: Fixed in main text
L32: “since it provide”: suggested to change the subject verb agreement.
Reply: Fixed in main text
L33: “store”: suggested to change the subject verb agreement.
Reply: Fixed in main text
L33 to L34: “The presence of big trees also influence”: suggested to change the subject verbagreement.
Reply: Fixed in main text
L35: “Bit trees”: suggested to correct the spelling.
Reply: Fixed in main text
L64: “70 cm in diameter”: specify where this diameter was measured.
Reply: Fixed in main text
L67: “ForestPlots plot”: should be written as “ForestPlots” only.
Reply: Fixed in main text
L68: “Brazilian Amazon (https://www.forestplots.net/).” Provide the reference not the website.
Reply: Fixed in main text
L70: “diameter (d) recorded”. Need to specify the height at which the diameter was measured.
Reply: Fixed in main text
L72: “Resolution Service (https://tnrs.iplantcollaborative.org)”: Provide the reference not the website.
Reply: Fixed in main text
L73: Missouri Botanical Garden (https://www.missouribotanicalgarden.org/): Provide the
reference not the website.
Reply: Fixed in main text
L126: “(DBH ≥ 70 cm)”: the fullform of dbh is not defined. I hope it is diameter at breast height. But it should be defined when used for the first time. In some of the previous lines, authors have written as diameter or only “d”. The diameter is not consistently written, but it should be.
Reply: is the diameter measured at the level of 1.3 m above ground level, or at breast height. Fixed in main text
L131-L137: Present these types of information either in table or in figure.
Reply: These results are presented in supplementary figures and tables. We did not put it in the manuscript's main text because the tables are too big.
L174: “figure s2”. You presented figure S2 before figure S1. If I am not wrong, you should present figure S1 first and then figure S2, S3 …….
Reply: Fixed in main text
L180: Same issues (L174) here also.
Reply: Fixed in main text
L189: I don’t think your proportion was superior. It is just greater than those reported by Harris et al. (2021).
Reply: Fixed in main text
L193: “(d ≥ 80 cm)”. Its very confusing. Sometimes you stated DBH and only d. Most probably both are DBH but you should write consistently the same abbreviations.
Reply: All are dbh and have been fixed in the main text
Author Response File: 
Author Response.docx
Reviewer 3 Report
Rewrite the abstract and use some of the results obtained in the abstract. The information in this article will advance the field.Author Response
All changes and recommendations have been made to the main text
Reviewer 4 Report
The title is too general, and the targeted research content should be refined.
There have been many researches on big trees, but the highlight of this paper is not very prominent.
The presentation and interpretation of the research results need to be further improved.
I prefer to have an independent conclusion part, although I don't know whether it is caused by the requirements of the journal.
Author Response
Big trees patterns in the Brazilian Amazon
Lima et al. 2022
Author's Reply to the Review Report (Reviewer 4)
The title is too general, and the targeted research content should be refined.
Reply: Although the title is presented in a more general way, we seek to reformulate and synthesize the main information presented in the manuscript, making the main content addressed about the large trees in the Amazon clear. Therefore, the final title of the manuscript can be described as follows:
Diversity and big trees patterns in the Brazilian Amazon.
This change was made in the main document
There have been many researches on big trees, but the highlight of this paper is not very prominent.
Reply: We believe that the information presented in this manuscript is necessary for the Amazon to understand the pattern and diversity of large trees, especially at regional scales of the ecosystem.
The presentation and interpretation of the research results need to be further improved.
Reply: We made some changes to the main document to improve the discussion of the results
I prefer to have an independent conclusion part, although I don't know whether it is caused by the requirements of the journal.
Reply: The conclusion is presented at the end of the discussion.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Can be accepted after minor corrections for spelling and grammars.
