Paleoclimatic Reconstruction Based on the Late Pleistocene San Josecito Cave Stratum 720 Fauna Using Fossil Mammals, Reptiles, and Birds

Round 1

Reviewer 1 Report

see comments in the word file

Comments for author File: Comments.pdf

Author Response

Responses for Reviewer #1:

Comment 1. This must be rewritten; First, I do not agree that paleontology is considered a descriptive science until recently, more than a century ago it is at the core of evolutionary discussion. In some other instances, the journal Paleobiology has more than 50 years. Paleontology has played a significant role in the field of evolutionary biology for many years. While it is true that paleontology involves the description and analysis of fossil remains, it is much more than just a descriptive science. Paleontologists use their findings to reconstruct past environments, study evolutionary processes, and contribute to our understanding of the history of life on Earth. Paleontology provides critical evidence for the theory of evolution by documenting the existence of extinct species and transitional forms. Fossils help us trace the evolution of various organisms and understand how they adapted and diversified over time. This information has been instrumental in shaping our understanding of evolutionary processes and the interconnectedness of life on our planet. Moreover, paleontology often involves interdisciplinary research, combining techniques from geology, biology, chemistry, biomechanics, thus physics and engineering, and other fields. Palaeontologists may use methods such as radiometric dating, stable isotope analysis, and genetic studies to gain insights into the biology and ecology of extinct organisms. Publications like the journal Paleobiology, with its long history, demonstrate the continuous advancements in paleontological research. These publications showcase the diverse research conducted in thetifield, including studies on macroevolutionary patterns, paleoecology, functional morphology, and phylogenetics. Such research is not limited to descriptive work but involves hypothesis testing, statistical analyses, and theoretical modeling. Overall, while paleontology does involve describing and documenting fossil remains, it is far from being merely descriptive. It is a dynamic scientific discipline that contributes significantly to our understanding of evolution, past ecosystems, and the history of life on Earth. Second, I do not know what the authors mean by “housed within geological sciences rather than biological sciences”. In my opinion, of course, paleontology is at the core of geology: biostratigraphy, climate reconstruction, correlation, relative age, and evolution…. Having in mind it was the core of geology and the main argument for the old age of the Earth. Paleontology was the core of the Principles of Geology of Lyell, etc. It is true that in the Quaternary, most fossil genera and species have extant relatives. It is the reason for the paleontology of the Quaternary in the Frontier of Geology and Biology.

R= We rewritten the sentence about paleontology such as a descriptive topic avoids any such reaction in readers as well as misinterpretation. We are completely agreeing with the Reviewer about the evolution of paleontology and the importance in the evolutionary theory and its inclusion in current biology, as in the case of conservation paleobiology, where geological and paleontological data are necessary to know the response of biodiversity to recent climate change. It´s very interesting that in Europe (Iberian Peninsula for example) the development of paleoenvironmental, paleoclimatic, and paleobiogeographical studies with small vertebrates has been impressive; if we compare the studies about the paleoclimatic reconstructions with vertebrates in Europe with America, in North America the studies are scarcer and in Latin America the studies are almost nil. Therefore, if the Reviewer wanted to do a paleoecological comparation at the subcontinental level, we would be willing to collaborate.

Comment 2. To answer these questions, microvertebrates are worthy proxies to reconstruct past environments [10](Blain et al. 2018), and caves are an excellent place for their preservation. In the Quaternary of Europe, there is much more literature dealing with proxies to reconstruct past environments using small vertebrates, some examples:

Baca, Mateusz; Popovic, Danijela; Lemanik, Anna; et al; Nadachowski, Adam. 2023. Ancient DNA reveals interstadials as a driver of common vole population dynamics during the last glacial period. JOURNAL OF BIOGEOGRAPHY. 50-1, pp.183-196. https://doi.org/10.1111/jbi.14521

Cuenca-Bescós G; Lawrence G; Straus González Morales MR; García Pimienta JC. 2009. The

reconstruction of past environments through small mammals: from the Mousterian to the

Bronze Age in El Mirón Cave (Cantabria Spain). Journal of Archaeological Science 36 947-955.

https://doi.org/10.1016/j.jas.2008.09.025

R = We add the literature suggested by Reviewer because are a good example about other paleoenvironmental reconstructions with biogeographical, ecological, and paleogenomic information. We used to Blain et al. (2018) because is a good revision about the paleoenvironmental reconstruction with vertebrates in the world but in this paper the articles mentioned by the Reviewer are not included.

Comment 3. Material Information is used about the fossil small mammals, reptiles, and birds from stratum 720 (Table 1; [20](Arroyo-Cabrales et al. 2021). Who and how identified the fossil remains?

R = The fossil material used in this manuscript is the recompilation of species of different articles that are summarized in Arroyo-Cabrales et al. (2021) and defined to stratum 720. We add this information in the main text.

Comment 4. Fossil presence data were not used because the recent ecological information of a species was needed to project that species into the past. Understanding the meaning of the pronouncement here is difficult. Fossil presence not used? why? What then is the fauna of San Josecito cave?

R = We remove this sentence because as de reviewer mentions it causes confusion.

Comment 5. Table 1. This is a table. Tables should be placed in the main text near to the first time they are cited. It must be table 2?

R = We corrected the observation of Reviewer and changed Table 1 by Table 2. In addition, we add the captions in the tables.

Comment 6. In Figure 2 the authors should add SJC, stratum 720 assemblage community. The Paleoclimatic reconstruction from San Josecito Cave (SJC) with the different groups of vertebrates (A) including the Mean Annual Temperature (MAT, red squares) and Annual Precipitation (AP, blue circles) compared with the current climate at the fossil locality. The paleoclimatic values inferred with the all-vertebrate community were used to reconstruct the paleotemperature and precipitation of the Late Pleistocene from San Josecito Cave.

R = We did the changes suggested by the Reviewer.

Author Response File: Author Response.pdf

Reviewer 2 Report

This manuscript describes a novel palaeoenvironmental approach to a well-known site of the Mexican Late Pleistocene. The use of MER and ENM applied to all the groups provides a good general picture about the past environment and the work includes an interesting comparison between the results obtained with each group.

The work is original and very interesting, the text is well written and well structured, and it should be accepted for publication after some really minor changes.

Lines 6 to 15: the numbers of the affiliation do not coincide with the ones in the author´s names.

Abstract:

The first sentence of the abstract is too general, and it does not provide relevant information about the paper. Also, is almost the same one than the first sentence of the introduction.

Depending on the geographic area and the temporal context birds are not the second-best group studied. In fact, within my personal experience, they are more often ignored than the reptiles. I would rephrase the sentence to say that they are also a well-studied, although I leave that to the authors decision.

It would be interesting to add some highlights about the main differences found between the three studied groups in the abstract, as it is a central part of the work.

Introduction:

Line 57: Although it is true that birds are considered a poor proxy, here are many works which use the analysis of birds to reconstruct past environment. I list you here some recent examples that maybe can be useful for the discussion.

Carrera, L., Scarponi, D., Martini, F., Sarti, L., Pavia, M. 2021. Mid-Late Pleistocene Neanderthal landscapes in southern Italy: Palaeocological contributions of the avian assemblage from Grotta del Cavallo, Apulia, Southern Italy. Palaeogeography, Palaeoclimatology, Palaeoecology 567, 110256

Núñez-Lahuerta, C., Galán, J., Cuenca-Bescós, G., García-Medrano, P., Cáceres, I. 2022, A bird asseblage across the MIS9/8 boundary: The Middle Pleistocene of Galería (Atapuerca). Quaternary Science Reviews 293, 107708

Pavia, M., Val, A., Carrera, L., Steininger, C.M. 2022. Fossil birds from Cooper´s D aid in reconstructing the Early Pleistocene palaeoenvironment in the Cradle of Humankind (Gauteng, South Africa). Journal of Human Evolution 167, 103185

Tomek, T., Bochenski, Z.M., Socha, P., Stefaniak, K. 2012. Continous 300.000-year fossil record changes in the ornithofauna of Bisnik Cave, Poland. Palaeontologia Electronica 15(1), 2A, 20p.

Study Area: A picture of the entrance and a planimetry of the cave would be very useful for this part of the manuscript.

Material: Desmodus does not appear listed in the Table 1, an example which appear in the analysis would be more representative for this part.

The table 1 caption is missing (same case in line 173, with table 2)

I think that adding the number of identified specimens to the table 1 would provide useful information about the level 720 assemblage, although I am aware that this information is included in the work of Arroyo-Cabrales et al. 2021.

I am not an expert on MER or the use of R packages, I think that the methodology used is well explained. But I think that the used data-base should be available as supplementary information, for the reproducibility of the analysis.

Line 203: the name of the figure should be figure 4.

Line 221: “Birds and mammals individually have similar precipitation values (AP=664.2 mm and 617.7 mm respectively)”. I think the sentence is more understandable in this form.

Lines 229 to 232: this set of bibliographical references belongs to the discussion.

Discussion:

The taphonomic origin of the remains and its possible bias to the results should be discussed in the work.

Line 246: I think the sentence should be rephrased to: “San Josecito Cave is one of the best-studied Late Pleistocene localities in Mexico, with six new fossil species, eight extinct birds and 19 extinct mammals”.

Paleoclimatic inferences between vertebrate groups:

Line 292: the authors provide a list of works concerning palaeoenvironmental reconstruction based on bird fossil remains from north America, but the data are not discussed. There is a huge contrast with the start of the next paragraph in which a long list of mammal-based palaeoenvironmental reconstruction works from the Iberian Peninsula are listed and discussed.  I do not understand why this difference when discussing the obtained results, the same geographical extension should be used for both groups.

 Also, I don´t think that there is need to cite so many mammal-based works, but this is up to the authors.

Please note that I did not check that all the references are correct and cited within the text, this is up to the editors.

Author Response

Responses for Reviewer #2:

Comment 1. Lines 6 to 15: the numbers of the affiliation do not coincide with the ones in the author´s names.

R = We add the changes suggested by the Reviewer.

Comment 2. Abstract: The first sentence of the abstract is too general, and it does not provide relevant information about the paper. Also, is almost the same one than the first sentence of the introduction.

R = We rewritten the sentence about paleontology such as a descriptive topic. For us is very important mention the lack of paleoecological studies with vertebrates because we have the Latin American point of view. It´s very interesting that in Europe (Iberian Peninsula for example) the development of paleoenvironmental, paleoclimatic, and paleobiogeographical studies with small vertebrates has been impressive; if we compare the studies about the paleoclimatic reconstructions with vertebrates in Europe with America, in North America the studies are scarcer and in Latin America the studies are almost nil.

Comment 3. Depending on the geographic area and the temporal context birds are not the second-best group studied. In fact, within my personal experience, they are more often ignored than the reptiles. I would rephrase the sentence to say that they are also a well-studied, although I leave that to the authors decision.

R = We add the American continent in the phrase because in this continent the birds are the second-best group studied after mammals. However, it is very interesting that the study of different groups depending on the geographic study area.

Comment 4. It would be interesting to add some highlights about the main differences found between the three studied groups in the abstract, as it is a central part of the work.

R = We add the highlights about the main differences between different groups of vertebrates in the abstract.

Comment 5. Introduction: Line 57: Although it is true that birds are considered a poor proxy, here are many works which use the analysis of birds to reconstruct past environment. I list you here some recent examples that maybe can be useful for the discussion.

Carrera, L., Scarponi, D., Martini, F., Sarti, L., Pavia, M. 2021. Mid-Late Pleistocene Neanderthal landscapes in southern Italy: Palaeocological contributions of the avian assemblage from Grotta del Cavallo, Apulia, Southern Italy. Palaeogeography, Palaeoclimatology, Palaeoecology 567, 110256

Núñez-Lahuerta, C., Galán, J., Cuenca-Bescós, G., García-Medrano, P., Cáceres, I. 2022, A bird asseblage across the MIS9/8 boundary: The Middle Pleistocene of Galería (Atapuerca). Quaternary Science Reviews 293, 107708

Pavia, M., Val, A., Carrera, L., Steininger, C.M. 2022. Fossil birds from Cooper´s D aid in reconstructing the Early Pleistocene palaeoenvironment in the Cradle of Humankind (Gauteng, South Africa). Journal of Human Evolution 167, 103185

Tomek, T., Bochenski, Z.M., Socha, P., Stefaniak, K. 2012. Continous 300.000-year fossil record changes in the ornithofauna of Bisnik Cave, Poland. Palaeontologia Electronica 15(1), 2A, 20p.

R = We add the literature suggested in the discussion section.

Comment 6. Study Area: A picture of the entrance and a planimetry of the cave would be very useful for this part of the manuscript.

R = This information is extensively documented in Arroyo-Cabrales et al. (2021) and it is not the main goal of this manuscript to show the geology of the study area.

Comment 7. Material: Desmodus does not appear listed in the Table 1, an example which appear in the analysis would be more representative for this part.

R = Thank you so much for the observation, this was my mistake. I add Desmodus stocki in the Table 1.

Comment 8. The table 1 caption is missing (same case in line 173, with table 2).

R = We add the table caption.

Comment 9. I think that adding the number of identified specimens to the table 1 would provide useful information about the level 720 assemblage, although I am aware that this information is included in the work of Arroyo-Cabrales et al. 2021.

R = Yes, this information is included in Arroyo-Cabrales et al. (2021) and in this manuscript we only use species presence data.

Comment 10. I am not an expert on MER or the use of R packages, I think that the methodology used is well explained. But I think that the used data-base should be available as supplementary information, for the reproducibility of the analysis.

R = We add the link to access for all information about the taxa used, R script, rasters, shapes, and all documents necessary for the reproducibility in data availability statement. https://drive.google.com/drive/folders/17-YhZoEaLd-KVtxNcJfBZPqmE9Aqkkga?usp=sharing

Comment 11. Line 203: the name of the figure should be figure 4.

R = Thank you for the observation. We corrected the number of figure.

Comment 12. Line 221: “Birds and mammals individually have similar precipitation values (AP=664.2 mm and 617.7 mm respectively)”. I think the sentence is more understandable in this form.

R = We are agreeing with the review and change the sentence.

Comment 13. Lines 229 to 232: this set of bibliographical references belongs to the discussion.

R = We have these bibliographical references in the discussion too. We think that these references are appropriate in this section to justify the combination of mammals and reptiles in the analysis.

Comment 14. Line 246: I think the sentence should be rephrased to: “San Josecito Cave is one of the best-studied Late Pleistocene localities in Mexico, with six new fossil species, eight extinct birds and 19 extinct mammals”.

R = We change the sentence as suggested by the reviewer

Comment 15. Paleoclimatic inferences between vertebrate groups: Line 292: the authors provide a list of works concerning palaeoenvironmental reconstruction based on bird fossil remains from north America, but the data are not discussed. There is a huge contrast with the start of the next paragraph in which a long list of mammal-based palaeoenvironmental reconstruction works from the Iberian Peninsula are listed and discussed.  I do not understand why this difference when discussing the obtained results, the same geographical extension should be used for both groups.

R = The reviewer is absolutely right and with the reference add in the comment 5 we include studies in the Europe and South Africa. Is very interesting that exist a strong research group in Iberian Peninsula that study the paleoenvironmental evolution of Europe using different vertebrates’ groups, which is needed in other parts of the world.

Comment 16. Also, I don´t think that there is need to cite so many mammal-based works, but this is up to the authors.

R = We think that the difference between works of different groups reflects which are the most studied and which are not, as the Reviewer showed us in comment 5 where the studies with birds in quantitative paleoenvironmental reconstructions are very recent.

Author Response File: Author Response.pdf

Reviewer 3 Report

Alberto Cruz and colleagues provide an interesting multiproxy paleoclimatic reconstruction of one layer of the Late Pleistocene San Josecito Cave (Mexico), where the multiple proxies are different vertebrate groups, namely small mammals, birds, and reptiles.

This paleoecological study is a worth addiction for San Josecito, which will be relevant for future considerations on the Late Pleistocene of the region, while the use of different vertebrate groups is not often attempted and could thus be generalized and quoted in other case studies.

The main problem I notice is in the interpretations provided in the results, especially section 3.2, and more precisely from Line 208 onwards, when the authors compare the results from the different groups and respect to all groups together.

The problem is that we do not know the real environmental conditions of the past, so whether they were closer to the average estimates provided by all groups or to those inferred from a single group cannot be stated a priori.

For instance, the authors commented that reptiles-based predictions of annual-precipitation are higher than other groups and hence they are overestimation, but this is not conceptually correct. Perhaps reptiles provide the closest value to the real past conditions, while other groups underestimate it. This cannot be inferred with the approach chosen. To test it, the authors should have compared their results to another proxy independent from their models.

This does not undermine the value of the work, but the authors should rephrase all relevant passages to express a proxy-to-proxy comparison, rather than a proxy-to-climate.

The interpretations on what group (or if all groups together) provide the best estimates, with justification, should be placed in the discussion.

Save for this point, I do not have great concerns, I listed below some further things:

In the abstract:

I do not get why the authors write specifically about birds and then argue that "to probe that view" (what? that birds are worser than mammals as paleoenvironmental proxy?) different groups are considered. I would rephrase the abstract stating that investigating multiple groups is important but not often attempted.

Line 32: 

Ecological niche modelling (rather than models)

Line 44:

remove methods (proxy is just fine)

Line 48:

different scales, otherwise means nothing

Line 50:

remove "the use of"

Line 52:

remove "in the past" 

Lines 103-104:

The caption is missing

Lines 173-174:

The caption is missing

minor editing needed

Author Response

Responses for Reviewer #3:

Comment 1. The main problem I notice is in the interpretations provided in the results, especially section 3.2, and more precisely from Line 208 onwards, when the authors compare the results from the different groups and respect to all groups together. The problem is that we do not know the real environmental conditions of the past, so whether they were closer to the average estimates provided by all groups or to those inferred from a single group cannot be stated a priori. For instance, the authors commented that reptiles-based predictions of annual-precipitation are higher than other groups and hence they are overestimation, but this is not conceptually correct. Perhaps reptiles provide the closest value to the real past conditions, while other groups underestimate it. This cannot be inferred with the approach chosen. To test it, the authors should have compared their results to another proxy independent from their models. This does not undermine the value of the work, but the authors should rephrase all relevant passages to express a proxy-to-proxy comparison, rather than a proxy-to-climate.

The interpretations on what group (or if all groups together) provide the best estimates, with justification, should be placed in the discussion.

R = In the second paragraph of 4.1. Paleoclimatic inferences between vertebrate groups section, we discuss that the paleoclimatic inference with all groups is the correct because the values that we obtained are very similar with other quantitative inferences obtained using diatoms and speleothems in sites relatively close to San Josecito Cave. Also, add the sentence “The concordance of the paleoclimatic inference in this study with other proxies reflects that the presence of several taxa in the same site contain the information of all environmental filters that species has had to pass to be present in a determinate time and geographical space” that indicates the importance of using as many taxa as possible to infer the paleoclimate of a fossil site.

Comment 2. In the abstract: I do not get why the authors write specifically about birds and then argue that "to probe that view" (what? that birds are worser than mammals as paleoenvironmental proxy?) different groups are considered. I would rephrase the abstract stating that investigating multiple groups is important but not often attempted.

R = We add the sentence “Investigating multiple groups is important but not often attempted, hence” as suggested by the Reviewer and better reflects the study that we presented.

Comment 3. Line 32: Ecological niche modelling (rather than models)

R = We make the change the reviewer suggests.

Comment 4. Line 44: remove methods (proxy is just fine)

R = We make the change the reviewer suggests.

Comment 5. Line 48: different scales, otherwise means nothing

R = We make the change the reviewer suggests.

Comment 6. Line 50: remove "the use of"

R = We remove the sentence as the reviewer suggests.

Comment 7. Line 52: remove "in the past"

R = We remove the sentence as the reviewer suggests.

Comment 8. Lines 103-104: The caption is missing

R = We add the caption in the table 1

Comment 9. Lines 173-174: The caption is missing

R = We add the caption in the table 2