the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Disentangling environmental drivers of Subarctic dinocyst assemblage compositional change during the Holocene
Abstract. Analysis of compositional changes in fossil organic-walled dinoflagellate cyst (dinocysts) assemblages is a widely used tool for the quantitative reconstruction of past environmental parameters. This approach assumes that the assemblage composition is significantly and independently related to the reconstructed environmental parameters. Theoretically, dinocyst assemblages can be used to reconstruct multiple environmental variables. However, there is evidence that primary and subordinate drivers for assemblage compositions differ regionally and it remains unclear whether a significant relationship to specific parameters in the present ocean always implies that this relationship is significant in fossil assemblages, questioning if past changes in these multiple parameters can be reconstructed simultaneously from fossil assemblages. Here, we analysed a local subset of the Northern Hemisphere dinocyst calibration dataset (n =1968), including samples from the Baffin Bay area (n = 421), and evaluated the benefits of a local versus a more regional or global calibration for the environmental reconstruction of Baffin Bay oceanography during the Holocene. We determined the dimensionality of the dinocyst ecological response and identified environmental drivers in the Baffin Bay area for the modern dataset. We analysed four existing Holocene records along a North-South transect in the area and evaluated the statistical significance of downcore reconstructions by applying the local and global datasets with different techniques: the modern analogue technique (MAT), the weighted average partial least square (WA-PLS), and maximum likelihood (ML). We evaluate reconstructions tested as significant in the light of the existing state of knowledge about West Greenland’s Holocene paleoceanography. Our analyses imply that present-day and Holocene dinocyst assemblages in the Baffin Bay area are primarily driven by salinity changes; other parameters were less important in driving assemblage compositions and their contribution differed among the studied records. We show that the objectively occurring and temporally coherent shifts in dinocyst assemblages in the Holocene of Baffin Bay can be interpreted robustly only by transfer functions that are calibrated locally. Transfer functions based on the broad North Hemisphere calibration yielded many insignificant environmental reconstructions. At the same time, we show that even in the local calibration, not all parameters that appear to significantly affect dinocyst assemblages in the calibration dataset can be meaningfully reconstructed in the fossil record. A thorough evaluation of the calibration dataset and the significance of downcore applications is necessary to reveal the region-specific information contained in dinocyst assemblage composition.
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RC1: 'Comment on egusphere-2023-561', Anonymous Referee #1, 15 Jun 2023
This paper aims to assess whether a local database would be more suitable to use for quantitatively reconstruct past environmental conditions based on organic-walled dinoflagellate cyst assemblages. The Holocene studied cores are located in Baffin Bay, along a north-south transect and the “modern” assemblages are situated in that region but also including some samples from the Arctic, Hudson Bay and NW Atlantic. The statistical methodology is quite rigorous and relatively well explained (see comments on the pdf) and does highlight some interesting considerations about the use of local versus global databases. A number of suggestions are made in the text, mostly the expression and some clarification. Overall, this is a solid paper, demonstrating the value of using a structured approach with ecological statistics to understand which driver(s) explain dinoflagellate cyst distribution and assemblage composition. This paper should be accepted after some minor editorial corrections.
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AC2: 'Reply on RC1', Sabrina Hohmann, 10 Aug 2023
This referee’s comments offer constructive suggestion for the improvement of the manuscript regarding clarifications of poorly expressed or not in enough detail explained descriptions. These comments and suggestions will help to improve the final version of the manuscript.
Responses to comments are made directly in the pdf version of the manuscript annotated by the reviewer.
We thank the referee for the comments and helpful propositions!
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AC2: 'Reply on RC1', Sabrina Hohmann, 10 Aug 2023
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RC2: 'Comment on egusphere-2023-561', Anonymous Referee #2, 19 Jun 2023
This preprint carefully examines the relationship between dinoflagellate cyst assemblages and environmental variables so that it can develop transfer functions to reconstruct palaeoceangraphic conditions in Baffin Bay.
One of the main findings is that a local calibration set gives more significant reconstructions that the northern hemisphere calibration set.Dinocysts have been used, perhaps more than other microfossil indicator groups, to reconstruct many environmental variables, often from the same core.
Whether these reconstructions were robust and independent of each other was doubtful.
This preprint moves dinocyst reconstructions onto a more realistic basis.One of the premises for the preprint is that there are "regionally different relationships between assemblages and environmental conditions." (line 78). My interpretation is subtlety different: that the relationship between assemblage and the environment is global, but regionally, different variables are important, because they have more variance (perhaps after an appropriate transformation) in that region. This interpretation changes little of the analysis, but does make the possibility of different environmental conditions having similar assemblages (the multiple analogues problem, line 94) less likely.
The preprint argues that areas with suspected advected dinocysts could be removed from local calibration sets. True, but they could also be removed from hemispheric calibration sets (and obviously dinocyst stratigraphies from cores in such regions needed to be treated with caution).
In general, I like the preprint.
My main concern is that it is rather too long.
The preprint can, and should, be shortened by not reporting numbers in both tables and the text, and removing some unnecessary methods.With regard to doubly reported numbers, the size of the calibration set is reported 10 times!
I know the authors want to distinguish which version of the calibration set is used, but still, I think it reasonable to assume that readers won't instantly forget, just be consistent with the naming.The data analysis starts with a multiple factor analysis, to find correlation structures without "reference to the directionality of possible causal relationships".
Since we do know the direction of causality, it is not clear that this analysis adds anything to the redundancy analysis.Fig. 1A is a bit busy; I didn't notice the core names initially.
Perhaps swap panels A and B, and show the site map without the bathymetry and increase the labels' contrast.Some methods use log-transformed permil data, others use Hellinger transformed data.
It is not clear what transformation is used for the transfer function (hopefully none for ML).
Would it not make sense to be, as far as possible, consistent?Line 368.
I'm unclear what is referred to as variance in this context.Fig 5.
I don't think you need to show axes 2 vs 3.
Removing this would make the species and sample plots comparable.The caption for figure S5 is insufficient.
Variogram of what?Table 5. four or five WAPLS components is excessive, probably driven by the autocorrelation. I'm particularly surprised about how many components appear to be useful with h-block cross-validation.
Line 440, fig 8 The preprint seems to use zero crossing of the PCA axes to delimit the core into zones.
I'm not convinced this is a good method - there is nothing particularly special about zero.
There are several ways to zone microfossil, for example CONISS which is implemented in the rioja R package.It is possible to run the reconstruction significance test with an autocorrelated null model (also the PCA). This is generally a little more conservative than running them against the default white noise null, but is more effort to set up. It is also possible to test if reconstructions are significant after partially another reconstruction out. This makes it possible to test if there is an independent signal in the second or third reconstruction.
Fig S7 is described as a "cross-correlation plot".
Cross-correlation is a method for describing the relationship between two time series at different lags, which does not describe S7.
A more fundamental issues with this plot is that as the reconstructions and ordination axes are not independent, the p-values are not correct.
They can be corrected by using simulations, but that would give a method that is analagous to, but less powerful, than the significance test for reconstructions shown in figure 7.
In short, the enormous and difficult to read fig.
S7 and related text can be deleted without loss.I don't fully understand the purpose and interpretation of the q-mode factor analysis (~ line 560).
In several places, the preprint states that the code and data will be available on publication.
The preprint is published.
So the data and code should also be published, at least with a private link for review.
The zenodo archive linked to has been removed as spam.Citation: https://doi.org/10.5194/egusphere-2023-561-RC2 -
AC1: 'Reply on RC2', Sabrina Hohmann, 10 Aug 2023
In general, this referee, like the first, also offers some comments with constructive suggestion for the improvement of the manuscript regarding clarifications of poorly expressed or not in enough detail explained/ illustrated descriptions.
The detailed comments, suggestions and concerns are answered below (comments in italic).
- “One of the premises for the preprint is that there are "regionally different relationships between assemblages and environmental conditions." (line 78). My interpretation is subtlety different: that the relationship between assemblage and the environment is global, but regionally, different variables are important, because they have more variance (perhaps after an appropriate transformation) in that region. This interpretation changes little of the analysis, but does make the possibility of different environmental conditions having similar assemblages (the multiple analogues problem, line 94) less likely.”
- I agree with the reviewer that the relationship between the assemblage and the environment is global, because a specific taxon does not respond differently to a given environmental parameter - meaning its behavior stays within its environmental gradient. But, as also mentioned by the reviewer, different environmental parameters are important in different regions because of a higher variance of some of these environmental variables. This causes the assemblage to “react” mostly to these variables. In other regions, other parameters may have larger gradients, causing the assemblage to “react” more to these variables. Theoretically, this may lead to situations where the assemblages are the same, although some parameters in the environment were different. This will result in a seemingly "regionally different relationship between the assemblages and the environmental conditions".
- In my opinion the reviewers and my interpretation are not really different, although this should be expressed more explicitly in the final version.
- “The preprint argues that areas with suspected advected dinocysts could be removed from local calibration sets. True, but they could also be removed from hemispheric calibration sets (and obviously dinocyst stratigraphies from cores in such regions needed to be treated with caution).”
- The reviewer is correct and I will add a couple of sentences about that into the final version. It would be interesting to test how the statistics turn out, when we remove areas with suspected advected assemblages from the hemispheric calibration dataset, but this will be done in another study.
- “The preprint can, and should, be shortened by not reporting numbers in both tables and the text, and removing some unnecessary methods.”
The reviewer mentions also other parts that should be shortened or changed to achieve a better understanding.
- After some reflection, I think that the referee is right. Although, all of the added analyses and data are informative, not all are necessary to illustrate the essential messages of the study.
- It is feasible to remove the multiple factor analysis (and the q-mode factor analysis) as suggested by the referee without losing any important information.
- We will also consider shortening of other parts.
- “Fig. 1A is a bit busy; I didn't notice the core names initially. Perhaps swap panels A and B, and show the site map without the bathymetry and increase the labels' contrast.”
- This will be changed in the final version
- ”Some methods use log-transformed per mil data, others use Hellinger transformed data. It is not clear what transformation is used for the transfer function (hopefully none for ML).”
- In general, we applied Hellinger transformation to quantify the relationship between species variances and forcing parameters because the species data do not indicate linear distribution although they are not clearly unimodal either. The Hellinger transformation preserves the Euclidean distance in the linear ordination in case the data “behaves” rather unimodal.
- We did not give the detailed information for the transfer functions as it is given in Hohmann et al. (2020). For WA-PLS and ML no transformation was applied. For MAT the estimates were determined using a log-transformed distance calculation for the analogue selection as we followed the method in de Vernal et al. (2005).
- In the final version, this will be presented more explicitly.
Hohmann, S., Kucera, M., de Vernal, A.: Identifying the signature of sea-surface properties in dinocyst assemblages: Implications for quantitative palaeoceanographical reconstructions by transfer functions and analogue techniques, Mar. Micropaleontol., 159, 101816, https://doi.org/https://doi.org/10.1016/j.marmicro.2019.101816, 2020.
de Vernal, A., Eynaud, F., Henry, M., Hillaire-Marcel, C., Londeix, L., Mangin, S., Matthiessen, J., Marret, F., Radi, T., Rochon, A., Solignac, S., Turon, J.L.: Reconstruction of sea-surface conditions at middle to high latitudes of the Northern Hemisphere during the Last Glacial Maximum (LGM) based on dinoflagellate cyst assemblages, Quat. Sci. Rev., 24, 897–924, https://doi.org/10.1016/j.quascirev.2004.06.014, 2005.
- ”Line 440, fig 8 The preprint seems to use zero crossing of the PCA axes to delimit the core into zones. I'm not convinced this is a good method - there is nothing particularly special about zero. There are several ways to zone microfossil, for example CONISS which is implemented in the rioja R package.”
- Thank you for mentioning this! As this is a common practice (e.g., Allan et al., 2018, 2021), we followed this procedure. For future studies, the suggestion to use CONISS is relevant, but for our study the “0-method” is still appropriate. All PC-axes of the four cores center around the zero crossing and a shift from one side to the other clearly depicts a change in the assemblage composition which is related to a change in the environment. Nevertheless, I understand the concearn about “zones” and it is probably better to keep the expression “assemblage shifts”.
Allan, E., Vernal, A. De, Knudsen, M.F., Hillaire-Marcel, C., 2018. Late Holocene sea-surface instabilities in the Disko Bugt area, west Greenland, in phase with d18O-oscillations at Camp Century. Paleogeography and Paleoclimatology 33, 227–243. https://doi.org/10.1002/2017PA003289
Allan, E., de Vernal, A., Seidenkrantz, M. ‐S., Briner, J.P., Hillaire‐Marcel, C., Pearce, C., Meire, L., Røy, H., Mathiasen, A.M., Nielsen, M.T., Plesner, J.L., Perner, K., 2021. Insolation vs . meltwater control of productivity and sea surface conditions off SW Greenland during the Holocene. Boreas. https://doi.org/10.1111/bor.12514
- “In several places, the preprint states that the code and data will be available on publication. The preprint is published. So the data and code should also be published, at least with a private link for review. The zenodo archive linked to has been removed as spam.”
- Thank you for bringing this to my attention. I have no idea why this happened. Apparently, my whole account has been removed. I contacted the support from zenodo. Now the link is active again and my accound has been restored. The code is available now. The data will be published in PANGAEA as soon as possible in September.
We thank the referee for the comments and helpful propositions!
Citation: https://doi.org/10.5194/egusphere-2023-561-AC1
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AC1: 'Reply on RC2', Sabrina Hohmann, 10 Aug 2023
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2023-561', Anonymous Referee #1, 15 Jun 2023
This paper aims to assess whether a local database would be more suitable to use for quantitatively reconstruct past environmental conditions based on organic-walled dinoflagellate cyst assemblages. The Holocene studied cores are located in Baffin Bay, along a north-south transect and the “modern” assemblages are situated in that region but also including some samples from the Arctic, Hudson Bay and NW Atlantic. The statistical methodology is quite rigorous and relatively well explained (see comments on the pdf) and does highlight some interesting considerations about the use of local versus global databases. A number of suggestions are made in the text, mostly the expression and some clarification. Overall, this is a solid paper, demonstrating the value of using a structured approach with ecological statistics to understand which driver(s) explain dinoflagellate cyst distribution and assemblage composition. This paper should be accepted after some minor editorial corrections.
-
AC2: 'Reply on RC1', Sabrina Hohmann, 10 Aug 2023
This referee’s comments offer constructive suggestion for the improvement of the manuscript regarding clarifications of poorly expressed or not in enough detail explained descriptions. These comments and suggestions will help to improve the final version of the manuscript.
Responses to comments are made directly in the pdf version of the manuscript annotated by the reviewer.
We thank the referee for the comments and helpful propositions!
-
AC2: 'Reply on RC1', Sabrina Hohmann, 10 Aug 2023
-
RC2: 'Comment on egusphere-2023-561', Anonymous Referee #2, 19 Jun 2023
This preprint carefully examines the relationship between dinoflagellate cyst assemblages and environmental variables so that it can develop transfer functions to reconstruct palaeoceangraphic conditions in Baffin Bay.
One of the main findings is that a local calibration set gives more significant reconstructions that the northern hemisphere calibration set.Dinocysts have been used, perhaps more than other microfossil indicator groups, to reconstruct many environmental variables, often from the same core.
Whether these reconstructions were robust and independent of each other was doubtful.
This preprint moves dinocyst reconstructions onto a more realistic basis.One of the premises for the preprint is that there are "regionally different relationships between assemblages and environmental conditions." (line 78). My interpretation is subtlety different: that the relationship between assemblage and the environment is global, but regionally, different variables are important, because they have more variance (perhaps after an appropriate transformation) in that region. This interpretation changes little of the analysis, but does make the possibility of different environmental conditions having similar assemblages (the multiple analogues problem, line 94) less likely.
The preprint argues that areas with suspected advected dinocysts could be removed from local calibration sets. True, but they could also be removed from hemispheric calibration sets (and obviously dinocyst stratigraphies from cores in such regions needed to be treated with caution).
In general, I like the preprint.
My main concern is that it is rather too long.
The preprint can, and should, be shortened by not reporting numbers in both tables and the text, and removing some unnecessary methods.With regard to doubly reported numbers, the size of the calibration set is reported 10 times!
I know the authors want to distinguish which version of the calibration set is used, but still, I think it reasonable to assume that readers won't instantly forget, just be consistent with the naming.The data analysis starts with a multiple factor analysis, to find correlation structures without "reference to the directionality of possible causal relationships".
Since we do know the direction of causality, it is not clear that this analysis adds anything to the redundancy analysis.Fig. 1A is a bit busy; I didn't notice the core names initially.
Perhaps swap panels A and B, and show the site map without the bathymetry and increase the labels' contrast.Some methods use log-transformed permil data, others use Hellinger transformed data.
It is not clear what transformation is used for the transfer function (hopefully none for ML).
Would it not make sense to be, as far as possible, consistent?Line 368.
I'm unclear what is referred to as variance in this context.Fig 5.
I don't think you need to show axes 2 vs 3.
Removing this would make the species and sample plots comparable.The caption for figure S5 is insufficient.
Variogram of what?Table 5. four or five WAPLS components is excessive, probably driven by the autocorrelation. I'm particularly surprised about how many components appear to be useful with h-block cross-validation.
Line 440, fig 8 The preprint seems to use zero crossing of the PCA axes to delimit the core into zones.
I'm not convinced this is a good method - there is nothing particularly special about zero.
There are several ways to zone microfossil, for example CONISS which is implemented in the rioja R package.It is possible to run the reconstruction significance test with an autocorrelated null model (also the PCA). This is generally a little more conservative than running them against the default white noise null, but is more effort to set up. It is also possible to test if reconstructions are significant after partially another reconstruction out. This makes it possible to test if there is an independent signal in the second or third reconstruction.
Fig S7 is described as a "cross-correlation plot".
Cross-correlation is a method for describing the relationship between two time series at different lags, which does not describe S7.
A more fundamental issues with this plot is that as the reconstructions and ordination axes are not independent, the p-values are not correct.
They can be corrected by using simulations, but that would give a method that is analagous to, but less powerful, than the significance test for reconstructions shown in figure 7.
In short, the enormous and difficult to read fig.
S7 and related text can be deleted without loss.I don't fully understand the purpose and interpretation of the q-mode factor analysis (~ line 560).
In several places, the preprint states that the code and data will be available on publication.
The preprint is published.
So the data and code should also be published, at least with a private link for review.
The zenodo archive linked to has been removed as spam.Citation: https://doi.org/10.5194/egusphere-2023-561-RC2 -
AC1: 'Reply on RC2', Sabrina Hohmann, 10 Aug 2023
In general, this referee, like the first, also offers some comments with constructive suggestion for the improvement of the manuscript regarding clarifications of poorly expressed or not in enough detail explained/ illustrated descriptions.
The detailed comments, suggestions and concerns are answered below (comments in italic).
- “One of the premises for the preprint is that there are "regionally different relationships between assemblages and environmental conditions." (line 78). My interpretation is subtlety different: that the relationship between assemblage and the environment is global, but regionally, different variables are important, because they have more variance (perhaps after an appropriate transformation) in that region. This interpretation changes little of the analysis, but does make the possibility of different environmental conditions having similar assemblages (the multiple analogues problem, line 94) less likely.”
- I agree with the reviewer that the relationship between the assemblage and the environment is global, because a specific taxon does not respond differently to a given environmental parameter - meaning its behavior stays within its environmental gradient. But, as also mentioned by the reviewer, different environmental parameters are important in different regions because of a higher variance of some of these environmental variables. This causes the assemblage to “react” mostly to these variables. In other regions, other parameters may have larger gradients, causing the assemblage to “react” more to these variables. Theoretically, this may lead to situations where the assemblages are the same, although some parameters in the environment were different. This will result in a seemingly "regionally different relationship between the assemblages and the environmental conditions".
- In my opinion the reviewers and my interpretation are not really different, although this should be expressed more explicitly in the final version.
- “The preprint argues that areas with suspected advected dinocysts could be removed from local calibration sets. True, but they could also be removed from hemispheric calibration sets (and obviously dinocyst stratigraphies from cores in such regions needed to be treated with caution).”
- The reviewer is correct and I will add a couple of sentences about that into the final version. It would be interesting to test how the statistics turn out, when we remove areas with suspected advected assemblages from the hemispheric calibration dataset, but this will be done in another study.
- “The preprint can, and should, be shortened by not reporting numbers in both tables and the text, and removing some unnecessary methods.”
The reviewer mentions also other parts that should be shortened or changed to achieve a better understanding.
- After some reflection, I think that the referee is right. Although, all of the added analyses and data are informative, not all are necessary to illustrate the essential messages of the study.
- It is feasible to remove the multiple factor analysis (and the q-mode factor analysis) as suggested by the referee without losing any important information.
- We will also consider shortening of other parts.
- “Fig. 1A is a bit busy; I didn't notice the core names initially. Perhaps swap panels A and B, and show the site map without the bathymetry and increase the labels' contrast.”
- This will be changed in the final version
- ”Some methods use log-transformed per mil data, others use Hellinger transformed data. It is not clear what transformation is used for the transfer function (hopefully none for ML).”
- In general, we applied Hellinger transformation to quantify the relationship between species variances and forcing parameters because the species data do not indicate linear distribution although they are not clearly unimodal either. The Hellinger transformation preserves the Euclidean distance in the linear ordination in case the data “behaves” rather unimodal.
- We did not give the detailed information for the transfer functions as it is given in Hohmann et al. (2020). For WA-PLS and ML no transformation was applied. For MAT the estimates were determined using a log-transformed distance calculation for the analogue selection as we followed the method in de Vernal et al. (2005).
- In the final version, this will be presented more explicitly.
Hohmann, S., Kucera, M., de Vernal, A.: Identifying the signature of sea-surface properties in dinocyst assemblages: Implications for quantitative palaeoceanographical reconstructions by transfer functions and analogue techniques, Mar. Micropaleontol., 159, 101816, https://doi.org/https://doi.org/10.1016/j.marmicro.2019.101816, 2020.
de Vernal, A., Eynaud, F., Henry, M., Hillaire-Marcel, C., Londeix, L., Mangin, S., Matthiessen, J., Marret, F., Radi, T., Rochon, A., Solignac, S., Turon, J.L.: Reconstruction of sea-surface conditions at middle to high latitudes of the Northern Hemisphere during the Last Glacial Maximum (LGM) based on dinoflagellate cyst assemblages, Quat. Sci. Rev., 24, 897–924, https://doi.org/10.1016/j.quascirev.2004.06.014, 2005.
- ”Line 440, fig 8 The preprint seems to use zero crossing of the PCA axes to delimit the core into zones. I'm not convinced this is a good method - there is nothing particularly special about zero. There are several ways to zone microfossil, for example CONISS which is implemented in the rioja R package.”
- Thank you for mentioning this! As this is a common practice (e.g., Allan et al., 2018, 2021), we followed this procedure. For future studies, the suggestion to use CONISS is relevant, but for our study the “0-method” is still appropriate. All PC-axes of the four cores center around the zero crossing and a shift from one side to the other clearly depicts a change in the assemblage composition which is related to a change in the environment. Nevertheless, I understand the concearn about “zones” and it is probably better to keep the expression “assemblage shifts”.
Allan, E., Vernal, A. De, Knudsen, M.F., Hillaire-Marcel, C., 2018. Late Holocene sea-surface instabilities in the Disko Bugt area, west Greenland, in phase with d18O-oscillations at Camp Century. Paleogeography and Paleoclimatology 33, 227–243. https://doi.org/10.1002/2017PA003289
Allan, E., de Vernal, A., Seidenkrantz, M. ‐S., Briner, J.P., Hillaire‐Marcel, C., Pearce, C., Meire, L., Røy, H., Mathiasen, A.M., Nielsen, M.T., Plesner, J.L., Perner, K., 2021. Insolation vs . meltwater control of productivity and sea surface conditions off SW Greenland during the Holocene. Boreas. https://doi.org/10.1111/bor.12514
- “In several places, the preprint states that the code and data will be available on publication. The preprint is published. So the data and code should also be published, at least with a private link for review. The zenodo archive linked to has been removed as spam.”
- Thank you for bringing this to my attention. I have no idea why this happened. Apparently, my whole account has been removed. I contacted the support from zenodo. Now the link is active again and my accound has been restored. The code is available now. The data will be published in PANGAEA as soon as possible in September.
We thank the referee for the comments and helpful propositions!
Citation: https://doi.org/10.5194/egusphere-2023-561-AC1
-
AC1: 'Reply on RC2', Sabrina Hohmann, 10 Aug 2023
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Cited
Michal Kucera
Anne de Vernal
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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Supplement
(1008 KB) - BibTeX
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- Final revised paper