Disentangling influences of climate variability and lake-system evolution on climate proxies derived from isoprenoid and branched GDGTs: the 250-kyr Lake Chala record

Baxter, Allix Jean; Peterse, Francien; Verschuren, Dirk; Maitituerdi, Aihemaiti; Waldmann, Nicolas; Sinninghe Damsté, Jaap S.

doi:https://doi.org/10.5194/egusphere-2023-2486

Preprints

https://doi.org/10.5194/egusphere-2023-2486

Preprints

27 Oct 2023

| 27 Oct 2023

Disentangling influences of climate variability and lake-system evolution on climate proxies derived from isoprenoid and branched GDGTs: the 250-kyr Lake Chala record

Allix Jean Baxter, Francien Peterse, Dirk Verschuren, Aihemaiti Maitituerdi, Nicolas Waldmann, and Jaap S. Sinninghe Damsté

Abstract. High-resolution paleoclimate records from tropical continental settings are greatly needed to advance understanding of global climate dynamics. The International Continental Scientific Drilling Program (ICDP) project DeepCHALLA recovered a 214.8-meter long sediment sequence from Lake Chala, a deep and permanently stratified (meromictic) crater lake in equatorial East Africa, covering the past c. 250,000 years (250 kyr) of continuous lacustrine deposition since the earliest phase of lake-basin development. Lipid biomarker analyses on the sediments of this long-lived lake can provide much-needed records of past climate variability from this currently poorly documented region. However, the degree to which climate proxies derived from aquatically produced biomarkers are affected by aspects of lake developmental history is rarely considered, even though it may critically influence their ability to consistently register a particular climate variable through time. Modern-system studies in Lake Chala revealed crucial information about the mechanisms underpinning relationships between proxies based on isoprenoid (iso-) and branched (br-) glycerol dialkyl glycerol tetraethers (GDGTs) and the targeted climate variables, but the persistence of these relationships in the past remains unclear. To assess the reliability of long-term climate signals registered in the sediments of Lake Chala, we compared downcore variations in GDGT distributions with major phases in lake-system evolution as indicated by independent proxies of lake depth, mixing regime and nutrient dynamics: seismic reflection data, lithology and fossil diatom assemblages. Together, these records suggest that during early lake history (before c. 180–200 ka) the distinct mixing-related depth zones with which specific GDGT producers are associated in the modern-day lake were not yet formed, likely due to more open lake hydrology and absence of chemical water-column stratification. Consequently during this early phase the absolute GDGT concentrations are relatively low, proxies sensitive to water-column stratification (e.g., BIT index) display highly irregular temporal variability, and correlations between proxies are dissimilar to expectations based on modern-system understanding. A sequence of lake-system changes between c. 180–200 ka and c. 80 ka first established and then strengthened the chemical density gradient, promoting meromictic conditions despite the overall decrease in lake depth due to sediment accumulation. From c. 180 ka onward some GDGTs and derived proxies (e.g., crenarchaeol concentration, BIT index and IR_6Medisplay strong ~23-kyr periodicity, likely reflecting the predominantly precession-driven insolation forcing of Quaternary climate variability in low-latitude regions. Our results suggest that GDGT-based temperature and moisture-balance proxies in Lake Chala sediments reflect the climate history of eastern equatorial Africa from at least c. 160 ka onwards, i.e., covering the complete last glacial-interglacial cycle and the penultimate glacial maximum. This work confirms the potential of lacustrine GDGTs for elucidating the climate history of tropical regions at Quaternary timescales, provided they are applied to suitably high-quality sediment archives. Additionally, their interpretation should incorporate a broader understanding of the extent to which lake-system evolution limits the extrapolation back in time of proxy-climate relationships established in the modern system.

Received: 26 Oct 2023 – Discussion started: 27 Oct 2023

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Journal article(s) based on this preprint

14 Jun 2024

Disentangling influences of climate variability and lake-system evolution on climate proxies derived from isoprenoid and branched glycerol dialkyl glycerol tetraethers (GDGTs): the 250 kyr Lake Chala record

Allix J. Baxter, Francien Peterse, Dirk Verschuren, Aihemaiti Maitituerdi, Nicolas Waldmann, and Jaap S. Sinninghe Damsté

Biogeosciences, 21, 2877–2908, https://doi.org/10.5194/bg-21-2877-2024,https://doi.org/10.5194/bg-21-2877-2024, 2024

Short summary

Allix Jean Baxter, Francien Peterse, Dirk Verschuren, Aihemaiti Maitituerdi, Nicolas Waldmann, and Jaap S. Sinninghe Damsté

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2023-2486', Anonymous Referee #1, 13 Dec 2023

This is a very well written paper that details the pros and cons of using GDGTs to reconstruct temperature in the paleorecord from Lake Chala. The study highlights the complexities of the modern lake environment, and how variations in the system through time make application of GDGTs to temperature reconstruction only appropriate in some intervals.

In general, I find the discussion very thorough, using other types of data to support their interpretations of GDGT data. The discussion of both isoprenoid and branched GDGTs is welcome.

I find a few places in the discussion where it seems that the authors are speculating. For example, is there other evidence for the development of the strong chemical gradient over time? This is certainly possible, but I didn’t see any solid evidence for that. I don’t think it is a problem to speculate in this type of paper, but they should be clear when they are doing so.

The authors used the Pearson 2011 calibration to estimate temperature from brGDGTs, ultimately concluding that this “MST” reconstruction that combines the 5 and 6 Me GDGTs appears to be more appropriate to use in Lake Chala than MBT’5ME. This is somewhat surprising as there is substantial evidence that separating the two groups improves temperature reconstruction, though the logic they use is clearly laid out. I am very curious to see if either the Zhao et al 2023 (QSR), O’Beirne et al 2023 (GCA), or Wang et al 2024 (EPSL) calibrations provide more reasonable results. I fully understand that these calibrations were not yet published when this work was being performed, but now that they are out there I wonder if they do a better job that the Pearson calibration, which has issues of its own that compromise its application.

A few minor typos:
            Line 164 needs closing parenthesis after johnson et al., 2016
            Line 351: change to “…Similar to brGDGTs, isoGDGT-0 is also produced”
            Lines 361 and 372: change to “Table 1”
            Line 461: Change to “…The degree of cyclisation (DC) of brGDGT was also calculated…”
            Line 497: change to “…within…”
            Lines 652-653: sentence is unclear, use of “respectively” twice in once sentence
            Line 676: change to “confirms”
            Line 722: change to “Stage”
            Line 796: change to “from”
            Line 886-887: used “inferred” twice
            Line 923: change to “insolation”
            Line 924: change to “from around”

You use both “GDGT” and “GDGTs” when referring to them as plural. Choose one and use it consistently

Citation: https://doi.org/10.5194/egusphere-2023-2486-RC1
- AC2: 'Reply on RC1', Allix Baxter, 19 Jan 2024
  
  Referee comments are in italics and our responses are in bold.
  This is a very well written paper that details the pros and cons of using GDGTs to reconstruct temperature in the paleorecord from Lake Chala. The study highlights the complexities of the modern lake environment, and how variations in the system through time make application of GDGTs to temperature reconstruction only appropriate in some intervals.
  
  In general, I find the discussion very thorough, using other types of data to support their interpretations of GDGT data. The discussion of both isoprenoid and branched GDGTs is welcome.
  
  We are very thankful to the referee for their positive assessment of our work.
  I find a few places in the discussion where it seems that the authors are speculating. For example, is there other evidence for the development of the strong chemical gradient over time? This is certainly possible, but I didn’t see any solid evidence for that. I don’t think it is a problem to speculate in this type of paper, but they should be clear when they are doing so.
  
  We see the point of the reviewer and plan to strengthen the arguments for the development of the chemical gradient, partly, by referring to data on fossil diatom assemblages (Tanttu, 2022) and partly by more explicit description of i) the evolution in lake hydrology over time due to gradual infilling of the crater basin with sediments, and ii) the expected effects of major lake-level changes on the water column’s dissolved-ion content.
  The authors used the Pearson 2011 calibration to estimate temperature from brGDGTs, ultimately concluding that this “MST” reconstruction that combines the 5 and 6 Me GDGTs appears to be more appropriate to use in Lake Chala than MBT’_5ME. This is somewhat surprising as there is substantial evidence that separating the two groups improves temperature reconstruction, though the logic they use is clearly laid out. I am very curious to see if either the Zhao et al 2023 (QSR), O’Beirne et al 2023 (GCA), or Wang et al 2024 (EPSL) calibrations provide more reasonable results. I fully understand that these calibrations were not yet published when this work was being performed, but now that they are out there I wonder if they do a better job that the Pearson calibration, which has issues of its own that compromise its application.
  
  It is true that separating the 5- and 6-me brGDGTs has improved the statistical relationship between brGDGT distribution and temperature in calibration data sets, i.e. brGDGT distribution in recently deposited sediments has become a better ‘predictor’ of temperature measured today at the sites included in those calibration data sets. However, there is no concrete evidence (for example, through comparison with time series of instrumental temperature data or with parallel reconstructions based on independent temperature proxies) that this improvement in modern-day calibration leads to more accurate reconstructions in down-core applications. Instead, as discussed in our paper, our results highlight that optimizing the calibration does not guarantee a credible long-term reconstruction. Further, considering the multitude of data presented in this paper, the already lengthy discussion (which we deem necessary to drive home the point made above), and the fact that the brGDGT palaeotemperature record is not the main topic of the current manuscript, we choose to not incorporate and discuss temperature reconstructions based on alternative calibrations into the present manuscript. Instead we refer to the detailed justification provided in Baxter et al. (2023, Nature) for our selection of the Pearson et al. (2011) calibration over other calibrations, including three that are based on MBT’_5Me(Russell et al., 2018; Martínez-Sosa et al., 2021; Raberg et al., 2021). We showed there that any calibration based on the ‘classically’ defined MBT’_5Me will result in reconstructed temperature records that are likely incorrect. As to the possible merit of the three newest calibrations cited by the referee, we plan to discuss potential application of these new calibrations in a forthcoming publication in preparation which focusses primarily on the Lake Chala temperature record and its climatic implications.
  A few minor typos:
  
  Line 164 needs closing parenthesis after johnson et al., 2016
  
  Line 351: change to “…Similar to brGDGTs, isoGDGT-0 is also produced”
  
  Lines 361 and 372: change to “Table 1”
  
  Line 461: Change to “…The degree of cyclisation (DC) of brGDGT was also calculated…”
  
  Line 497: change to “…within…”
  
  Lines 652-653: sentence is unclear, use of “respectively” twice in once sentence
  
  Line 676: change to “confirms”
  
  Line 722: change to “Stage”
  
  Line 796: change to “from”
  
  Line 886-887: used “inferred” twice
  
  Line 923: change to “insolation”
  
  Line 924: change to “from around”
  
  We will change all outlined minor corrections as suggested by the reviewer in the revised manuscript.
  You use both “GDGT” and “GDGTs” when referring to them as plural. Choose one and use it consistently
  
  We reviewed this inconsistency and will use “GDGTs” for the plural form in the revised manuscript.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2486-AC2
- AC3: 'Reply on RC1', Allix Baxter, 19 Jan 2024
  
  Referee comments are in italics and our responses are in bold.
  This is a very well written paper that details the pros and cons of using GDGTs to reconstruct temperature in the paleorecord from Lake Chala. The study highlights the complexities of the modern lake environment, and how variations in the system through time make application of GDGTs to temperature reconstruction only appropriate in some intervals.
  
  In general, I find the discussion very thorough, using other types of data to support their interpretations of GDGT data. The discussion of both isoprenoid and branched GDGTs is welcome.
  
  We are very thankful to the referee for their positive assessment of our work.
  I find a few places in the discussion where it seems that the authors are speculating. For example, is there other evidence for the development of the strong chemical gradient over time? This is certainly possible, but I didn’t see any solid evidence for that. I don’t think it is a problem to speculate in this type of paper, but they should be clear when they are doing so.
  
  We see the point of the reviewer and plan to strengthen the arguments for the development of the chemical gradient, partly, by referring to data on fossil diatom assemblages (Tanttu, 2022) and partly by more explicit description of i) the evolution in lake hydrology over time due to gradual infilling of the crater basin with sediments, and ii) the expected effects of major lake-level changes on the water column’s dissolved-ion content.
  The authors used the Pearson 2011 calibration to estimate temperature from brGDGTs, ultimately concluding that this “MST” reconstruction that combines the 5 and 6 Me GDGTs appears to be more appropriate to use in Lake Chala than MBT’_5ME. This is somewhat surprising as there is substantial evidence that separating the two groups improves temperature reconstruction, though the logic they use is clearly laid out. I am very curious to see if either the Zhao et al 2023 (QSR), O’Beirne et al 2023 (GCA), or Wang et al 2024 (EPSL) calibrations provide more reasonable results. I fully understand that these calibrations were not yet published when this work was being performed, but now that they are out there I wonder if they do a better job that the Pearson calibration, which has issues of its own that compromise its application.
  
  It is true that separating the 5- and 6-me brGDGTs has improved the statistical relationship between brGDGT distribution and temperature in calibration data sets, i.e. brGDGT distribution in recently deposited sediments has become a better ‘predictor’ of temperature measured today at the sites included in those calibration data sets. However, there is no concrete evidence (for example, through comparison with time series of instrumental temperature data or with parallel reconstructions based on independent temperature proxies) that this improvement in modern-day calibration leads to more accurate reconstructions in down-core applications. Instead, as discussed in our paper, our results highlight that optimizing the calibration does not guarantee a credible long-term reconstruction. Further, considering the multitude of data presented in this paper, the already lengthy discussion (which we deem necessary to drive home the point made above), and the fact that the brGDGT palaeotemperature record is not the main topic of the current manuscript, we choose to not incorporate and discuss temperature reconstructions based on alternative calibrations into the present manuscript. Instead we refer to the detailed justification provided in Baxter et al. (2023, Nature) for our selection of the Pearson et al. (2011) calibration over other calibrations, including three that are based on MBT’_5Me(Russell et al., 2018; Martínez-Sosa et al., 2021; Raberg et al., 2021). We showed there that any calibration based on the ‘classically’ defined MBT’_5Me will result in reconstructed temperature records that are likely incorrect. As to the possible merit of the three newest calibrations cited by the referee, we plan to discuss potential application of these new calibrations in a forthcoming publication in preparation which focusses primarily on the Lake Chala temperature record and its climatic implications.
  A few minor typos:
  
  Line 164 needs closing parenthesis after johnson et al., 2016
  
  Line 351: change to “…Similar to brGDGTs, isoGDGT-0 is also produced”
  
  Lines 361 and 372: change to “Table 1”
  
  Line 461: Change to “…The degree of cyclisation (DC) of brGDGT was also calculated…”
  
  Line 497: change to “…within…”
  
  Lines 652-653: sentence is unclear, use of “respectively” twice in once sentence
  
  Line 676: change to “confirms”
  
  Line 722: change to “Stage”
  
  Line 796: change to “from”
  
  Line 886-887: used “inferred” twice
  
  Line 923: change to “insolation”
  
  Line 924: change to “from around”
  
  We will change all outlined minor corrections as suggested by the reviewer in the revised manuscript.
  You use both “GDGT” and “GDGTs” when referring to them as plural. Choose one and use it consistently
  
  We reviewed this inconsistency and will use “GDGTs” for the plural form in the revised manuscript.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2486-AC3
RC2:
'Comment on egusphere-2023-2486', Anonymous Referee #2, 30 Dec 2023

This paper assessed the reliability of GDGT-based proxies for paleoenvironmental reconstruction in a long sediment core from Lake Chala, a deep meromictic lake in equatorial East Africa covering the past 250 kyr. The GDGT-based proxies, including BIT, IR_6ME, MBT’_5ME, and TEX₈₆ over the past 250 kyrs, were interpreted based on previous modern system studies and compared with the evolution of the lake basin. They found that paleoclimate and lake evolution exert joint effects on these GDGT-based proxies and thus the use of these proxies in this lake appears to be complicated. This paper incorporates a wealth of data and very detailed data interpretation. Finishing such a paper would be a tough task. The paper is generally well-written. However, reading a paper like this would be a challenge to a reader because it is too long and there is too much information that needs to be considered. I do not have comments on the scientific issues. Instead, I strongly suggest the authors remove some unnecessary parts of the paper (moved to the supplementary material) and make the paper succinct and easy to read. That would attract a much wider interest to read through the paper.

Table 1 ‘%GDGT-2’ A bracket is missing. Two ‘iso-GDGT-2’ were in the denominator.
L110 ‘only few’ is not accurate. There are many downcore applications of brGDGTs in lakes.
L175 I suggest that you delete the detailed descriptions of all previous results or make a summary of them. Such a detailed description of previous GDGT work in Lake Chala makes the part look like a review. The paper is too long, which eliminates the interest of careful reading. This detailed description can be moved to the supplementary files.
L260 delete ‘then’
L439 following the method of Hopmans et al.(2016)
L459 calculated according to De Jonge et al.(2015).
Figure 10 in e) Stage VI should be stage IV
L796 from
L924 from around
L932 where these lipids
L951 Data on this chapter? Which chapter?
L955 ‘review and edited the?’
L1033 Chen et al…. This is a preprint. The paper has been published in GCA.

Citation: https://doi.org/10.5194/egusphere-2023-2486-RC2
- AC1: 'Reply on RC2', Allix Baxter, 19 Jan 2024
  
  Referee comments are in italics and our response is in bold.
  This paper assessed the reliability of GDGT-based proxies for paleoenvironmental reconstruction in a long sediment core from Lake Chala, a deep meromictic lake in equatorial East Africa covering the past 250 kyr. The GDGT-based proxies, including BIT, IR6ME, MBT’5ME, and TEX86 over the past 250 kyrs, were interpreted based on previous modern system studies and compared with the evolution of the lake basin. They found that paleoclimate and lake evolution exert joint effects on these GDGT-based proxies and thus the use of these proxies in this lake appears to be complicated. This paper incorporates a wealth of data and very detailed data interpretation. Finishing such a paper would be a tough task. The paper is generally well-written. However, reading a paper like this would be a challenge to a reader because it is too long and there is too much information that needs to be considered. I do not have comments on the scientific issues. Instead, I strongly suggest the authors remove some unnecessary parts of the paper (moved to the supplementary material) and make the paper succinct and easy to read. That would attract a much wider interest to read through the paper.
  
  We appreciate the compliments made by the referee about the quality of our manuscript. We would like to stress that, although focused on Lake Chala, our demonstration that lake evolution influences GDGT-based records of climate proxies is likely widely applicable to other lake systems.
  
  Crucially, this demonstration required thorough analysis of multiple GDGT compounds and proxies in relation to multiple independent sources of information on lake-system variation through time. Although we acknowledge that this may have rendered the length of the paper challenging for some readers, we feel that most sections (in particular the discussion) would lose in clarity or persuasiveness if shortened considerably. See also our reply to referee #2 for question relating to L175 below.
  Table 1 ‘%GDGT-2’ A bracket is missing. Two ‘iso-GDGT-2’ were in the denominator.
  
  We will correct this.
  L110 ‘only few’ is not accurate. There are many downcore applications of brGDGTs in lakes.
  
  We will change this sentence as follows: “The strong correlation between MBT′ _5Mein lacustrine surface sediments and temperature (Russell et al., 2018; Martínez-Sosa et al., 2021; Raberg et al., 2021) has led to successful downcore applications of lake-based temperature calibrations since discovery of the 5-Me and 6-Me isomers (Feakins et al., 2019; Stockhecke et al., 2021; Zhao et al., 2021; Zhang et al., 2021; Garelick et al., 2021; Ramos-Roman et al., 2022; Parish et al., 2023), although uncertainties about the exact source(s) of brGDGTs in lakes still complicate interpretation of these records”.
  
  Although there may now be several applications of brGDGT temperature calibrations to lake sediments, we would like to again stress that often these studies do not settle on the classical MBT′_5Me model, but used modified calibrations they deem more suitable for their lake records (e.g., Ramos-Roman et al., 2022, Parish et al 2023, Bittner et al., 2022).
  L175 I suggest that you delete the detailed descriptions of all previous results or make a summary of them. Such a detailed description of previous GDGT work in Lake Chala makes the part look like a review. The paper is too long, which eliminates the interest of careful reading. This detailed description can be moved to the supplementary files
  
  We agree with the referee that the paper is long but it should be realized that this is the first GDGT lake record where so many sediment horizons have been analyzed, resulting in an unprecedented resolution. In addition, the present-day lake has been studied extensively in many aspects including extensive studies of GDGT production and settling over various time scales. Hence, it is likely fair to say that Lake Chala is the best studied lake in the world in this respect. The >15 years of work has resulted in an enormous amount of background information that actually allowed the detailed interpretation of the 250-kyr GDGT record. We feel that the reader of the paper will require a summarized form of this previous work to understand the interpretation of the record. Putting section 2 in a supplemental would make it much harder for the reader to follow the argumentation in the manuscript. Well-informed readers can simply pass over section 2, hence our choice to put this description in a separate section and not in the introduction.
  L260 delete ‘then’
  
  L439 following the method of Hopmans et al.(2016)
  
  L459 calculated according to De Jonge et al. (2015).
  
  Figure 10 in e) Stage VI should be stage IV
  
  L796 from
  
  L924 from around
  
  L932 where these lipids
  
  L951 Data on this chapter? Which chapter?
  
  L955 ‘review and edited the?’
  
  L1033 Chen et al…. This is a preprint. The paper has been published in GCA.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2486-RC2
  
  We will correct all these minor changes in the final submission.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2486-AC1

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2023-2486', Anonymous Referee #1, 13 Dec 2023

This is a very well written paper that details the pros and cons of using GDGTs to reconstruct temperature in the paleorecord from Lake Chala. The study highlights the complexities of the modern lake environment, and how variations in the system through time make application of GDGTs to temperature reconstruction only appropriate in some intervals.

In general, I find the discussion very thorough, using other types of data to support their interpretations of GDGT data. The discussion of both isoprenoid and branched GDGTs is welcome.

I find a few places in the discussion where it seems that the authors are speculating. For example, is there other evidence for the development of the strong chemical gradient over time? This is certainly possible, but I didn’t see any solid evidence for that. I don’t think it is a problem to speculate in this type of paper, but they should be clear when they are doing so.

The authors used the Pearson 2011 calibration to estimate temperature from brGDGTs, ultimately concluding that this “MST” reconstruction that combines the 5 and 6 Me GDGTs appears to be more appropriate to use in Lake Chala than MBT’5ME. This is somewhat surprising as there is substantial evidence that separating the two groups improves temperature reconstruction, though the logic they use is clearly laid out. I am very curious to see if either the Zhao et al 2023 (QSR), O’Beirne et al 2023 (GCA), or Wang et al 2024 (EPSL) calibrations provide more reasonable results. I fully understand that these calibrations were not yet published when this work was being performed, but now that they are out there I wonder if they do a better job that the Pearson calibration, which has issues of its own that compromise its application.

A few minor typos:
            Line 164 needs closing parenthesis after johnson et al., 2016
            Line 351: change to “…Similar to brGDGTs, isoGDGT-0 is also produced”
            Lines 361 and 372: change to “Table 1”
            Line 461: Change to “…The degree of cyclisation (DC) of brGDGT was also calculated…”
            Line 497: change to “…within…”
            Lines 652-653: sentence is unclear, use of “respectively” twice in once sentence
            Line 676: change to “confirms”
            Line 722: change to “Stage”
            Line 796: change to “from”
            Line 886-887: used “inferred” twice
            Line 923: change to “insolation”
            Line 924: change to “from around”

You use both “GDGT” and “GDGTs” when referring to them as plural. Choose one and use it consistently

Citation: https://doi.org/10.5194/egusphere-2023-2486-RC1
- AC2: 'Reply on RC1', Allix Baxter, 19 Jan 2024
  
  Referee comments are in italics and our responses are in bold.
  This is a very well written paper that details the pros and cons of using GDGTs to reconstruct temperature in the paleorecord from Lake Chala. The study highlights the complexities of the modern lake environment, and how variations in the system through time make application of GDGTs to temperature reconstruction only appropriate in some intervals.
  
  In general, I find the discussion very thorough, using other types of data to support their interpretations of GDGT data. The discussion of both isoprenoid and branched GDGTs is welcome.
  
  We are very thankful to the referee for their positive assessment of our work.
  I find a few places in the discussion where it seems that the authors are speculating. For example, is there other evidence for the development of the strong chemical gradient over time? This is certainly possible, but I didn’t see any solid evidence for that. I don’t think it is a problem to speculate in this type of paper, but they should be clear when they are doing so.
  
  We see the point of the reviewer and plan to strengthen the arguments for the development of the chemical gradient, partly, by referring to data on fossil diatom assemblages (Tanttu, 2022) and partly by more explicit description of i) the evolution in lake hydrology over time due to gradual infilling of the crater basin with sediments, and ii) the expected effects of major lake-level changes on the water column’s dissolved-ion content.
  The authors used the Pearson 2011 calibration to estimate temperature from brGDGTs, ultimately concluding that this “MST” reconstruction that combines the 5 and 6 Me GDGTs appears to be more appropriate to use in Lake Chala than MBT’_5ME. This is somewhat surprising as there is substantial evidence that separating the two groups improves temperature reconstruction, though the logic they use is clearly laid out. I am very curious to see if either the Zhao et al 2023 (QSR), O’Beirne et al 2023 (GCA), or Wang et al 2024 (EPSL) calibrations provide more reasonable results. I fully understand that these calibrations were not yet published when this work was being performed, but now that they are out there I wonder if they do a better job that the Pearson calibration, which has issues of its own that compromise its application.
  
  It is true that separating the 5- and 6-me brGDGTs has improved the statistical relationship between brGDGT distribution and temperature in calibration data sets, i.e. brGDGT distribution in recently deposited sediments has become a better ‘predictor’ of temperature measured today at the sites included in those calibration data sets. However, there is no concrete evidence (for example, through comparison with time series of instrumental temperature data or with parallel reconstructions based on independent temperature proxies) that this improvement in modern-day calibration leads to more accurate reconstructions in down-core applications. Instead, as discussed in our paper, our results highlight that optimizing the calibration does not guarantee a credible long-term reconstruction. Further, considering the multitude of data presented in this paper, the already lengthy discussion (which we deem necessary to drive home the point made above), and the fact that the brGDGT palaeotemperature record is not the main topic of the current manuscript, we choose to not incorporate and discuss temperature reconstructions based on alternative calibrations into the present manuscript. Instead we refer to the detailed justification provided in Baxter et al. (2023, Nature) for our selection of the Pearson et al. (2011) calibration over other calibrations, including three that are based on MBT’_5Me(Russell et al., 2018; Martínez-Sosa et al., 2021; Raberg et al., 2021). We showed there that any calibration based on the ‘classically’ defined MBT’_5Me will result in reconstructed temperature records that are likely incorrect. As to the possible merit of the three newest calibrations cited by the referee, we plan to discuss potential application of these new calibrations in a forthcoming publication in preparation which focusses primarily on the Lake Chala temperature record and its climatic implications.
  A few minor typos:
  
  Line 164 needs closing parenthesis after johnson et al., 2016
  
  Line 351: change to “…Similar to brGDGTs, isoGDGT-0 is also produced”
  
  Lines 361 and 372: change to “Table 1”
  
  Line 461: Change to “…The degree of cyclisation (DC) of brGDGT was also calculated…”
  
  Line 497: change to “…within…”
  
  Lines 652-653: sentence is unclear, use of “respectively” twice in once sentence
  
  Line 676: change to “confirms”
  
  Line 722: change to “Stage”
  
  Line 796: change to “from”
  
  Line 886-887: used “inferred” twice
  
  Line 923: change to “insolation”
  
  Line 924: change to “from around”
  
  We will change all outlined minor corrections as suggested by the reviewer in the revised manuscript.
  You use both “GDGT” and “GDGTs” when referring to them as plural. Choose one and use it consistently
  
  We reviewed this inconsistency and will use “GDGTs” for the plural form in the revised manuscript.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2486-AC2
- AC3: 'Reply on RC1', Allix Baxter, 19 Jan 2024
  
  Referee comments are in italics and our responses are in bold.
  This is a very well written paper that details the pros and cons of using GDGTs to reconstruct temperature in the paleorecord from Lake Chala. The study highlights the complexities of the modern lake environment, and how variations in the system through time make application of GDGTs to temperature reconstruction only appropriate in some intervals.
  
  In general, I find the discussion very thorough, using other types of data to support their interpretations of GDGT data. The discussion of both isoprenoid and branched GDGTs is welcome.
  
  We are very thankful to the referee for their positive assessment of our work.
  I find a few places in the discussion where it seems that the authors are speculating. For example, is there other evidence for the development of the strong chemical gradient over time? This is certainly possible, but I didn’t see any solid evidence for that. I don’t think it is a problem to speculate in this type of paper, but they should be clear when they are doing so.
  
  We see the point of the reviewer and plan to strengthen the arguments for the development of the chemical gradient, partly, by referring to data on fossil diatom assemblages (Tanttu, 2022) and partly by more explicit description of i) the evolution in lake hydrology over time due to gradual infilling of the crater basin with sediments, and ii) the expected effects of major lake-level changes on the water column’s dissolved-ion content.
  The authors used the Pearson 2011 calibration to estimate temperature from brGDGTs, ultimately concluding that this “MST” reconstruction that combines the 5 and 6 Me GDGTs appears to be more appropriate to use in Lake Chala than MBT’_5ME. This is somewhat surprising as there is substantial evidence that separating the two groups improves temperature reconstruction, though the logic they use is clearly laid out. I am very curious to see if either the Zhao et al 2023 (QSR), O’Beirne et al 2023 (GCA), or Wang et al 2024 (EPSL) calibrations provide more reasonable results. I fully understand that these calibrations were not yet published when this work was being performed, but now that they are out there I wonder if they do a better job that the Pearson calibration, which has issues of its own that compromise its application.
  
  It is true that separating the 5- and 6-me brGDGTs has improved the statistical relationship between brGDGT distribution and temperature in calibration data sets, i.e. brGDGT distribution in recently deposited sediments has become a better ‘predictor’ of temperature measured today at the sites included in those calibration data sets. However, there is no concrete evidence (for example, through comparison with time series of instrumental temperature data or with parallel reconstructions based on independent temperature proxies) that this improvement in modern-day calibration leads to more accurate reconstructions in down-core applications. Instead, as discussed in our paper, our results highlight that optimizing the calibration does not guarantee a credible long-term reconstruction. Further, considering the multitude of data presented in this paper, the already lengthy discussion (which we deem necessary to drive home the point made above), and the fact that the brGDGT palaeotemperature record is not the main topic of the current manuscript, we choose to not incorporate and discuss temperature reconstructions based on alternative calibrations into the present manuscript. Instead we refer to the detailed justification provided in Baxter et al. (2023, Nature) for our selection of the Pearson et al. (2011) calibration over other calibrations, including three that are based on MBT’_5Me(Russell et al., 2018; Martínez-Sosa et al., 2021; Raberg et al., 2021). We showed there that any calibration based on the ‘classically’ defined MBT’_5Me will result in reconstructed temperature records that are likely incorrect. As to the possible merit of the three newest calibrations cited by the referee, we plan to discuss potential application of these new calibrations in a forthcoming publication in preparation which focusses primarily on the Lake Chala temperature record and its climatic implications.
  A few minor typos:
  
  Line 164 needs closing parenthesis after johnson et al., 2016
  
  Line 351: change to “…Similar to brGDGTs, isoGDGT-0 is also produced”
  
  Lines 361 and 372: change to “Table 1”
  
  Line 461: Change to “…The degree of cyclisation (DC) of brGDGT was also calculated…”
  
  Line 497: change to “…within…”
  
  Lines 652-653: sentence is unclear, use of “respectively” twice in once sentence
  
  Line 676: change to “confirms”
  
  Line 722: change to “Stage”
  
  Line 796: change to “from”
  
  Line 886-887: used “inferred” twice
  
  Line 923: change to “insolation”
  
  Line 924: change to “from around”
  
  We will change all outlined minor corrections as suggested by the reviewer in the revised manuscript.
  You use both “GDGT” and “GDGTs” when referring to them as plural. Choose one and use it consistently
  
  We reviewed this inconsistency and will use “GDGTs” for the plural form in the revised manuscript.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2486-AC3
RC2:
'Comment on egusphere-2023-2486', Anonymous Referee #2, 30 Dec 2023

This paper assessed the reliability of GDGT-based proxies for paleoenvironmental reconstruction in a long sediment core from Lake Chala, a deep meromictic lake in equatorial East Africa covering the past 250 kyr. The GDGT-based proxies, including BIT, IR_6ME, MBT’_5ME, and TEX₈₆ over the past 250 kyrs, were interpreted based on previous modern system studies and compared with the evolution of the lake basin. They found that paleoclimate and lake evolution exert joint effects on these GDGT-based proxies and thus the use of these proxies in this lake appears to be complicated. This paper incorporates a wealth of data and very detailed data interpretation. Finishing such a paper would be a tough task. The paper is generally well-written. However, reading a paper like this would be a challenge to a reader because it is too long and there is too much information that needs to be considered. I do not have comments on the scientific issues. Instead, I strongly suggest the authors remove some unnecessary parts of the paper (moved to the supplementary material) and make the paper succinct and easy to read. That would attract a much wider interest to read through the paper.

Table 1 ‘%GDGT-2’ A bracket is missing. Two ‘iso-GDGT-2’ were in the denominator.
L110 ‘only few’ is not accurate. There are many downcore applications of brGDGTs in lakes.
L175 I suggest that you delete the detailed descriptions of all previous results or make a summary of them. Such a detailed description of previous GDGT work in Lake Chala makes the part look like a review. The paper is too long, which eliminates the interest of careful reading. This detailed description can be moved to the supplementary files.
L260 delete ‘then’
L439 following the method of Hopmans et al.(2016)
L459 calculated according to De Jonge et al.(2015).
Figure 10 in e) Stage VI should be stage IV
L796 from
L924 from around
L932 where these lipids
L951 Data on this chapter? Which chapter?
L955 ‘review and edited the?’
L1033 Chen et al…. This is a preprint. The paper has been published in GCA.

Citation: https://doi.org/10.5194/egusphere-2023-2486-RC2
- AC1: 'Reply on RC2', Allix Baxter, 19 Jan 2024
  
  Referee comments are in italics and our response is in bold.
  This paper assessed the reliability of GDGT-based proxies for paleoenvironmental reconstruction in a long sediment core from Lake Chala, a deep meromictic lake in equatorial East Africa covering the past 250 kyr. The GDGT-based proxies, including BIT, IR6ME, MBT’5ME, and TEX86 over the past 250 kyrs, were interpreted based on previous modern system studies and compared with the evolution of the lake basin. They found that paleoclimate and lake evolution exert joint effects on these GDGT-based proxies and thus the use of these proxies in this lake appears to be complicated. This paper incorporates a wealth of data and very detailed data interpretation. Finishing such a paper would be a tough task. The paper is generally well-written. However, reading a paper like this would be a challenge to a reader because it is too long and there is too much information that needs to be considered. I do not have comments on the scientific issues. Instead, I strongly suggest the authors remove some unnecessary parts of the paper (moved to the supplementary material) and make the paper succinct and easy to read. That would attract a much wider interest to read through the paper.
  
  We appreciate the compliments made by the referee about the quality of our manuscript. We would like to stress that, although focused on Lake Chala, our demonstration that lake evolution influences GDGT-based records of climate proxies is likely widely applicable to other lake systems.
  
  Crucially, this demonstration required thorough analysis of multiple GDGT compounds and proxies in relation to multiple independent sources of information on lake-system variation through time. Although we acknowledge that this may have rendered the length of the paper challenging for some readers, we feel that most sections (in particular the discussion) would lose in clarity or persuasiveness if shortened considerably. See also our reply to referee #2 for question relating to L175 below.
  Table 1 ‘%GDGT-2’ A bracket is missing. Two ‘iso-GDGT-2’ were in the denominator.
  
  We will correct this.
  L110 ‘only few’ is not accurate. There are many downcore applications of brGDGTs in lakes.
  
  We will change this sentence as follows: “The strong correlation between MBT′ _5Mein lacustrine surface sediments and temperature (Russell et al., 2018; Martínez-Sosa et al., 2021; Raberg et al., 2021) has led to successful downcore applications of lake-based temperature calibrations since discovery of the 5-Me and 6-Me isomers (Feakins et al., 2019; Stockhecke et al., 2021; Zhao et al., 2021; Zhang et al., 2021; Garelick et al., 2021; Ramos-Roman et al., 2022; Parish et al., 2023), although uncertainties about the exact source(s) of brGDGTs in lakes still complicate interpretation of these records”.
  
  Although there may now be several applications of brGDGT temperature calibrations to lake sediments, we would like to again stress that often these studies do not settle on the classical MBT′_5Me model, but used modified calibrations they deem more suitable for their lake records (e.g., Ramos-Roman et al., 2022, Parish et al 2023, Bittner et al., 2022).
  L175 I suggest that you delete the detailed descriptions of all previous results or make a summary of them. Such a detailed description of previous GDGT work in Lake Chala makes the part look like a review. The paper is too long, which eliminates the interest of careful reading. This detailed description can be moved to the supplementary files
  
  We agree with the referee that the paper is long but it should be realized that this is the first GDGT lake record where so many sediment horizons have been analyzed, resulting in an unprecedented resolution. In addition, the present-day lake has been studied extensively in many aspects including extensive studies of GDGT production and settling over various time scales. Hence, it is likely fair to say that Lake Chala is the best studied lake in the world in this respect. The >15 years of work has resulted in an enormous amount of background information that actually allowed the detailed interpretation of the 250-kyr GDGT record. We feel that the reader of the paper will require a summarized form of this previous work to understand the interpretation of the record. Putting section 2 in a supplemental would make it much harder for the reader to follow the argumentation in the manuscript. Well-informed readers can simply pass over section 2, hence our choice to put this description in a separate section and not in the introduction.
  L260 delete ‘then’
  
  L439 following the method of Hopmans et al.(2016)
  
  L459 calculated according to De Jonge et al. (2015).
  
  Figure 10 in e) Stage VI should be stage IV
  
  L796 from
  
  L924 from around
  
  L932 where these lipids
  
  L951 Data on this chapter? Which chapter?
  
  L955 ‘review and edited the?’
  
  L1033 Chen et al…. This is a preprint. The paper has been published in GCA.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2486-RC2
  
  We will correct all these minor changes in the final submission.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2486-AC1

Peer review completion

AR: Author's response | RR: Referee report | ED: Editor decision | EF: Editorial file upload

ED: Reconsider after major revisions (30 Jan 2024) by Cindy De Jonge

AR by Allix Baxter on behalf of the Authors (04 Mar 2024) Author's response Author's tracked changes Manuscript

ED: Publish subject to minor revisions (review by editor) (18 Mar 2024) by Cindy De Jonge

Dear Allix Baxter and co-authors, thank you for responding to the comments of the co-authors in a timely fashion, and for accepting the suggestion to shorten and streamline the manuscript. Following this major revision I have read through the resubmitted version, and only have a few small editorial comments, as well as a suggestion to make the relevance of this study for globally distributed lake systems even more clear. I invite the authors to correct these small typo's and address my suggestion below.

L 132: “subapine zone” seems to be a typo
L 144, check punctuation around the Sepulchre reference.
L 193, check punctuation around Moernaut reference.
L 479, Table number is missing
L 492: %isoGDGT2: the ecological relevance of this ratio is not introduced.
L 564: Rewrite as: ‘niches of GDGT producers’.
L 784: check punctuation around Baxter et al. reference.

Suggestion for making global relevance more clear:
Throughout the discussion there is not many comparisons made with other lakes. Is this because similar water column and/or sediment studies in the framework of the lake system evolution are uncommon? Or because Challa behaves differently than other lakes?
To address the ‘uniqueness’ of Lake Challa, could the authors include a statement in their conclusion whether the interpretations on GDGT niches and derived temperature ratios based on low latitude meromictic Lake Challa are fully/in part/not at all applicable to shallow (seasonally stratified or fully mixed) lakes or lakes at higher latitudes (seasonally variable temperature and a colder hypolimnion)? Would a shallow lake be comparable with a Lake Challa Zone 1-3 for instance?
Furthermore, the authors might want to ‘philosophize’ how we interpret the fact that the reconstructed sedimentary temperatures (based on brGDGTs) rely on the contribution of two different water layers and potentially different communities of producers (zone 3 vs zone 5 and 6)? How does this for instance relate back to the mechanism that a single brGDGT producer modulates the lipid composition of their membrane to regulate the membrane fluidity?

Hide

AR by Allix Baxter on behalf of the Authors (03 Apr 2024) Author's response Author's tracked changes Manuscript

ED: Publish as is (16 Apr 2024) by Cindy De Jonge

AR by Allix Baxter on behalf of the Authors (25 Apr 2024) Manuscript

Journal article(s) based on this preprint

14 Jun 2024

Allix J. Baxter, Francien Peterse, Dirk Verschuren, Aihemaiti Maitituerdi, Nicolas Waldmann, and Jaap S. Sinninghe Damsté

Biogeosciences, 21, 2877–2908, https://doi.org/10.5194/bg-21-2877-2024,https://doi.org/10.5194/bg-21-2877-2024, 2024

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Allix Jean Baxter, Francien Peterse, Dirk Verschuren, Aihemaiti Maitituerdi, Nicolas Waldmann, and Jaap S. Sinninghe Damsté

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https://doi.org/10.5194/egusphere-2023-2486-supplement

Allix Jean Baxter, Francien Peterse, Dirk Verschuren, Aihemaiti Maitituerdi, Nicolas Waldmann, and Jaap S. Sinninghe Damsté

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This study investigates the impact of long-term lake system evolution on the climate signal recorded by GDGTs, a popular biomarker in paleoclimate research. It compares downcore changes in GDGTs in the 250,000-year Lake Chala (Kenya/Tanzania) sediment sequence to independent data for lake mixing and water column chemistry. These factors critically influence the GDGT proxies during the earliest depositional phases (before ~180,000 ka), confounding the climate signal.


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