This paper by David De Vleeschouwer et al. presents new stable oxygen isotope data and clumped isotope data generated on mixed-layer dwelling foraminifera, and discusses the Pliocene to early Pleistocene evolution of the Leeuwin Current offshore northwestern Australia. This period is an important one in terms of northern hemisphere glacial intensification and the evolution of Indonesian Throughflow, and the study site is well placed to track potential changes in the latter (related to sea level and tectonics). The paper is well written and contains interesting, high-quality new data. New foraminiferal clumped isotope data will certainly contribute to the growing body of data that will allow us to better constrain absolute ocean temperatures in the pre-Pleistocene, and also provide important information on depth habitats of particular species. I find it interesting that there is no clear unidirectional trend in isotopic gradient over the intensification of northern hemisphere glaciation interval, and LC current intensity on secular timescales thus seems to be almost independent of this (although LC intensity is apparently strongly linked to sea level changes at the G-IG scale) – this aspect is not discussed much. I think the paper is suitable for consideration in Climate of the Past after minor revisions, see comments below.

Comments on temperature reconstructions

Figure 4a: perhaps add modern SST and T at proposed calcification depth of T. sacculifer (base of mixed layer) onto the Figure for comparison.

Fig. 5: Calcification temperature reconstruction based on d18Oplanktic and Rohling Sea Level curve: I had a hard time assessing the robustness of this. Is the calculation of T in this way therefore based on the assumption that local d18Osw (i.e. the part of d18Osw related to local hydrological cycle effects and not global sea level) was constant? Is this assumption reasonable both on the long-term and on G-IG timescales (in the context of salinity/water mass changes associated with L current and upwelling changes in your study area) at your site? I think some discussion of expected local d18Osw changes on G-IG timescales, and how this would impact the temperature reconstruction, would be nice.

In Figures 5 and 6, different sea-level reconstructions appear to be shown or used in calculations – Rohling 2014 in Fig. 5 and Rohling 2021 in Fig. 6. Is the more up-to-date sea-level record not also suitable for calculating the glacial contribution to d18Osw in Fig. 5?



It would be interesting to consider the G-IG amplitude of the G. sacculifer d18O signal in the context of contemporaneous and/or regional records from surface-dwelling species such as G. ruber, to see if this can give you any support for the proposed deep mixed layer depth habitat or relatively constant d18Osw conditions. Also, in the methods, it is not mentioned whether individuals with gametogenic calcite final chambers were avoided or included during picking.



It may also be relevant to consider and compare the new paper by Meinicke et al. (2021, already cited) that also contains D47 measurements on Trilobatus trilobus and a deeper-dwelling species for the Plio-Pleistocene from the Western Pacific Warm Pool - I think their interpretations re: depth habitat for T. trilobus are not the same as in this paper, are the two interpretations compatible?

Line 349: This is interesting, I wonder is there any evidence in support of the hypothesis that Thaumarchaeota thrive/are more successful when phytoplankton biomass is low under oligotrophic conditions?

Line 361: Perhaps add that diagenesis (seafloor recrystallisation?) of foraminifera would specifically lead to a cool bias on D47 temperatures.



Line 362: please briefly define “isotopic scrambling” for non-clumped specialists



Line 498: Not clear how exactly low-resolution clumped isotope and TEX86 temperatures “demonstrate that the LC continued to operate […]” – do you deduce this from absolute temperatures? Or latitudinal gradients?

Minor comments

The last sentence of the abstract is not clear to me. “The common ITF forcing explains the observed coherence of Southern Hemisphere ocean and climate records.” – do you mean ocean vs atmospheric records in the Southern Ocean? or ITF/low-latitude vs higher southern latitude records?

 line 65 – north

line 67 – do you mean between Indo-Pacific paleoceanography and paleogeographic/gateway changes?

line 76 – “Pliocene aridity is punctuated” sounds strange to me. Do you mean that aridity is intensified/magnified during glacials?

line 85 – might be useful to add Site U1461 to the map? Also names mentioned in the text such as Carnarvon/Perth Basins

Figure 1 caption: (a) and (b) January vs June don’t seem to match up with the text in the figure panels.

Fig. 1c: the depth/time plot y-axis extends to >500m water depth, yet the site U1459 is according to the methods at 192m water depth. Is the profile from further offshore? Is this because of the paleodepth? Maybe add details to the caption.

line 195 – misplaced comma?

“Composite forcing” record: did you assume equal weighting of the two forcings? (maybe I missed this)

Regional increases in PP – how can we tell if they are Leeuwin Current eddy-mixing driven, or “weak Leeuwin Current” SAMW upwelling driven?

The focus of the manuscript “Plio-Pleistocene Perth Basin water temperatures and Leeuwin Current dynamics (Indian Ocean) derived from oxygen and clumped isotope paleothermometry” by De Vleeschouwer et al. is the calculation of planktonic foraminiferal d¹⁸O gradients between IODP Site 1459 located off the western coast of Australia and previously published records from more northern located sites. These gradients are intended to provide new insights into temporal changes in the Leeuwin Current strength during the time-period 4- 2 Ma. The authors present a new planktonic foraminiferal d¹⁸O record from IODP Site 1459 in orbital resolution that extends a previously published record from the same Site. Also, eight clumped isotope SST reconstructions are presented and compared to previously published TEX 86 SST reconstructions from the same Site.

While the data presented here are from an interesting location and time period the used methods, and interpretations are very uncertain, and claims are not well supported by the data. The manuscript is generally written well. Major comments:

• A planktonic d¹⁸O record is presented from core depths (55-105 mcd) where partly severe dolomitization was reported previously (Proceedings of the International Ocean Discovery Program, vol. 356). Further, all samples are from a shallow carbonate rich ocean region close to coral reefs where carbonate diagenesis is very common. It is well known that diagenesis and recrystallisation at sea bottom alter foraminiferal d¹⁸O towards heavier values (e.g., Edgar et al., 2015, Geochimica et Cosmochimica Acta). It is also clear that these alterations (solution, recrystallisation) are not always visible in the crystal structure of the foraminifers (Kozdon et al., 2011, and refs. therein, Paleoceanography). The comparison to clumped isotope temperatures is not convincing to rule out diagenesis as there are only eight data points shown and it has been shown that clumped isotope temperatures from planktonic foraminifers are also biased towards colder temperatures by diagenesis (Leutert et al., 2019, Geochimica et Cosmochimica Acta). Hence, at least parts of the paleoclimatic interpretations with relatively high d¹⁸O during the warm Pliocene might be probably related to diagenesis.

• I see the method of calculating planktonic foraminiferal gradients to reconstruct changes in the paleo-Leeuwin Current (warmer-colder) very problematic. It is known that the d¹⁸O of planktonic foraminifers are dependent on local temperature changes, local salinity changes and the global ice volume. Even if the global ice volume is known from the past there are still two variables which are unknown for each site location (local temperature and local salinity). Also, the clumped isotope temperatures do not really support the presented d¹⁸O record from Site 1459 as a temperature signal. This is due to the very few (eight) data points over the whole time period studied, that makes it impossible to compare long-term trends in temperature.  Additionally, these data points show a huge error bar of up to 10°C.  

• It was not clear to me why the d¹⁸O gradient between sites at 29° S and 19 ° S reflect the evolution of the Leeuwin Current better than the difference between sites located northwards (sites 1463 and 763). Presented model simulations (Fig. 2b) show miniscule temperature changes at about 29° S at Site 1459 between cold and warm stages but the gradients presented by the authors are mostly driven by huge changes in the planktonic foraminiferal d¹⁸O of Site 1459.  

• A recent study by He et al., (2021, EPSL, mentioned by the authors) presented alkenone derived SST gradients from regions close to what the authors used to reconstruct their planktonic foraminiferal d¹⁸O gradients. However, the temporal development of these alkenone SST gradients is different from what the authors show from their d¹⁸O gradients.

 Some more detailed comments:

Line 21: Here the authors should make clear that clumped isotopes are not in an orbital resolution. The reader might be confused.

Line 39: Clearly, the boundary currents facilitated the conditions for humans in Australia but that it is only habitable because of these is exaggerated.

Lines 81-86: The authors discuss here a point of the study of He et al., (2021) which focuses on a time period that is not covered by their data so it’s not really relevant.

Lines 245- 255: This might be more suitable for the methods section

First paragraph of Chapter 3.2: Parts can be moved into the methods section

Lines 280-288: Unclear and confusing, please describe more clear

Lines 297-301: Not clear to me how the authors calculated d¹⁸O_sw

Line 334: Indicate how much is “slightly warmer”

Lines 361-367: See mayor comments

Lines 372-388: Confusing paragraph about the habitat depth of sacculifer. The authors already mention that it is not a close surface dweller as G. ruber, but there is poor evidence of making it a subsurface water species.

Lines 460-461: Not very convincing for me.

Lines 464-471: I would like to see these comparisons in a figure. Which age models are used for these reconstructions?

Lines 472-473: This correlation is not really convincing for me.

Figure 1C:

The authors should clarify why the depth scale is from 100 to more than 500 m water depths if the present water depth of Site 1459 is only about 192 m.

Figure 3C:

It is not clear which data is new and which has been already published. I recommend indicating this with different colors.

Figure 4B:

I can’t see a good “coherence” of the two records. Yes, the lowest clumped isotope temperature data point is at the same time when d¹⁸O values appear low. However, other data points don’t really match, for instance the data point at 2.25 Ma. Also, the marks of the clumped isotope temperatures are too thick to really can correlate them to the d¹⁸O record.

Figure 7A:

Especially the long-term trends do not show a good correlation.

Figure 8B-D:

Colors of the records are difficult to distinguish. Scales are all different. Records do not show a good correlation.

Dear Erin McClymont, dear authors,

Over the past week, I have read the manuscript by De Vleeschouwer et al., submitted for review to Climate of the Past, with interest. In their manuscript, the authors present new stable oxygen isotope and clumped isotope data from Pliocene to Pleistocene planktic foraminifera microfossils from the IODP core drilled at Site U1459 off the western coast of Australia. This site is interesting, because it is placed within a framework of other IODP records in the region and by comparison potentially allows the strength of the Leeuwin current to be constrained over this important time period, which covers the transition from the comparatively warm Pliocene to the Pleistocene icehouse climate.

The addition of clumped isotope analyses to the (partly previously established) stable oxygen isotope records is useful as it potentially allows the effects of temperature and seawater isotopic composition on the stable oxygen isotope records to be disentangled. This is especially important in this setting, since one of the main aims the authors put forward is to reconstruct the isotopic gradient along the Australian western margin as a proxy for the strength of the Leeuwin current.

Overall, I think the authors present a valuable dataset embedded in the context of ongoing research in this area. The subject of the study definitely fits within the scope of Climate of the Past. However, I do think that some revisions are required to the manuscript before it can be accepted for publication, as I believe some of the conclusions the authors put forward are not (yet) fully supported by the data as it now stands. Below, I highlight some major concerns I have with the discussion of the data, followed by some more minor line-by-line changes I suggest the authors implement to improve the readability of their text.

Major comments

TEX₈₆ vs. clumped temperatures

Firstly, I have some concerns about the authors’ conclusions that TEX₈₆ likely reflects sea surface temperatures while the clumped isotope analyses are indicative of the temperatures in the lower mixed layer, as put forward in the abstract (lines 24-26). In their discussion about the discrepancy between TEX₈₆ and clumped temperatures, the authors put forward the hypothesis that TEX₈₆ may be seasonally biased (lines 343-350). In fact, previous studies have suggested that a summer bias on TEX₈₆ is likely and explains the consistent difference between TEX₈₆ and stable isotope paleotemperature estimates found in other studies (Jia et al., 2017; O’Brien et al., 2017). While they disregard their other working hypothesis about the southward displacement of sinking particles, it seems that the authors cannot exclude the possibility of seasonal bias in their TEX₈₆ data (see line 387), which could easily explain the ~5°C difference between TEX₈₆ and clumped results (line 283) if TEX₈₆ represents summer SST and clumped records MAT (see Fig. 1). In absence of clear evidence about the living habitat of T. sacculifer (lines 371-385), and with the only other line of evidence being that the TEX₈₆ temperatures “seem reasonable compared to the present-day mean annual temperatures” (lines 341-342), I think the conclusion that clumped isotope temperatures represent the lower mixed layer and TEX₈₆ represents the mean annual SST is not sufficiently supported.

Isotopic gradients

While I understand that the authors only measured clumped isotope temperatures in one site, it is a shame that their discussion of the isotopic gradient along the Leeuwin Current does not benefit from the addition of clumped isotope analyses. My very first question on reading this discussion after the discussion on the clumped isotope results is how much of this isotopic gradient reflects temperature gradient and how much reflects the difference in seawater isotopic composition. Would a strengthening or weakening of the Leeuwin Current affect both these variables similarly? Would it somehow be possible to infer from the changes in temperature and seawater oxygen isotope composition over time, which the authors can infer from their clumped isotope record, whether the changes observed in δ¹⁸O over time are mostly driven by temperature or water composition? And by extension, could this evidence be used to say something about which factor predominantly forced the changes in isotopic gradient? Finally, if the author’s hypothesis that the foraminifera calcify in the lower mixed layer is correct (see previous comment), how does this impact the discussion of isotopic gradient? Can the authors somehow exclude that changes in the calcification depth or the depth of the mixed layer between the two sites which are compared affect the difference in δ¹⁸O without the need for a change in the strength of the Leeuwin Current? I feel that there is some untapped opportunity for discussion on this topic which would integrate the clumped isotope analyses more firmly into the main discussion of the manuscript.

Clumped isotope statistics

I had some concerns about the way the statistics and uncertainty of the clumped isotope analyses were presented in the manuscript:

First of all, the caption of Table 2 (line 309) and the methods description (line 277) list different reproducibility errors for the clumped isotope measurements. I assume that the standard deviations cited in line 277 are one order of magnitude too high (e.g. 0.0314‰ instead of 0.314‰, as in line 309).

Secondly, I noticed that the authors used the reproducibility of their standards for calculating the standard errors in Table 2 (see lines 307-309) instead of the within-sample reproducibility. This method is likely to underestimate the uncertainty on the ∆₄₇ values in the samples, as the homogenized ETH-4 standard on which the standard deviation is based will likely reproduce better than the samples consisting of foraminifera pooled from up to four adjacent samples (line 189; up to 60 cm core depth when using the median sampling resolution from line 177). The authors should at least report the reproducibility of clumped isotope analyses within their samples.

Thirdly, in the clumped community it is common practice to report uncertainties at the 95% confidence level (e.g. Fernandez et al., 2017). Instead, the authors report uncertainties at ±1 standard error in Tables 2 and 3. The captions of Figures 4 and 5 do not show what the error bars on the clumped datapoints represent, but from comparison with the tables I infer that these are also 1 SE. This reporting makes the uncertainty look smaller than in other studies using 95% confidence level and in my opinion the reporting of ±1 SE (“68% CL”) is less intuitive. I realize that calculating 95% CL, or even the within-sample standard deviation, of samples with 2 or 3 replicates (PB03, PB05, PB06 and PB08) is challenging due to the lack of statistics. This problem illustrates the risk of analyzing small numbers of replicates of samples and will make it challenging to assess the confidence on these clumped isotope datapoints, or to compare the results amongst themselves (e.g. via a Student’s T-test) or with other data. I do not know how this issue can be resolved without adding additional replicates, and I do sympathize with the authors given how much work it is to gather enough foraminifera for these measurements. At the very least, I would therefore urge the authors to add information about their within-sample reproducibility (standard deviations) for all samples and calculate 95% confidence levels for those samples for which this is feasible (sample size > 3), in addition to making the clumped isotope results available in an open-access repository (now, only regular stable isotope data is archived).

Finally, while not (yet) a standard in the clumped isotope community, it would be good practice if the uncertainty on the clumped isotope calibration(s) used in the study were to be propagated on the clumped isotope result. This uncertainty is not contained within the measurement uncertainty and is usually relatively small (<5 ppm). However, given the differences between the sample sizes and temperature ranges between the calibrations cited in Table 3, the differences in uncertainties of these calibrations could be discussed.

Recalculated clumped isotope calibration

It is a really nice addition that the authors compare the results of applying difference clumped isotope calibrations on their data (Table 3). This gives the reader a good intuition of the difference using different calibration makes in the study. Unfortunately, the I-CDES-scale updated calibration of Peral et al. (2018) is not provided in the paper. This makes it impossible to verify the temperature results of this calibration. For the sake of open science, I urge the authors to make the I-CDES-scale referenced calibration dataset on which the updated Peral et al. (2018) calibration is based available in an open repository (e.g. Pangaea or EarthChem database) and to cite the new calibration formula with uncertainties on slopes and intercepts (sensu Equation 1) in the manuscript text or in Table 1 (as in Meinicke et al., 2021). Providing the calibration dataset is especially important as the uncertainties on the calibration (see previous comment) cannot be propagated from the errors on the slopes and intercepts of the calibration formula alone, as information about the covariation of slope and intercept are missing from this information.

Minor comments

Line 24-26: I am not sure this conclusion about the explanation of the difference between TEX₈₆ and clumped results is currently supported by the data

Line 39: “habitable” seems a bit overstated. Would the continent be wholly unhabitable without the boundary currents?

Line 136-137: Please refer to the repository where the re-calculated calibration dataset of Peral et al. 2018 can be accessed.

Line 195: Rephrase “carbonate, power reacts” to “carbonate powder reacts”

Line 215-216: Why was an acid fractionation factor used? The new values of the ETH standards in Bernasconi et al. (2021) should not require the use of a factor if the reaction of the carbonate took place at 70°C. Please double-check if the acid fractionation factor is not wrongly applied as this would offset the temperature reconstructions which can have big implications for the discussion in the manuscript!

Line 250-251: I agree that this method of tuning the record runs the risk of circular reasoning, but I think the fact that the authors limit their tuning to only 2 astronomical tie points renders this risk fairly limited.

Line 275-279: “The reported uncertainties scale to the number of repeated measurements” I think this statement is redundant given the fact that the SE are calculated from the reproducibility of the standards, which is the same for all samples except PB03, hence yielding lower SE for samples with higher N. What would be more interesting here is to report the reproducibility of the replicates within the samples (see major comment).

Line 292: I find it confusing that the clumped isotope data are presented with a ±1 SE error while for TEX₈₆ the full 95% confidence level is reported. This makes comparison between the proxies difficult (see major comment).

Line 300-301: The fact that the δ¹⁸O-based reconstructions are more similar to clumped than to TEX₈₆ is not really surprising, since these isotope proxies are measured on the same material (foraminifer carbonate).

Table 2: I suggest the authors also provide their uncertainties (1 standard deviation) on the three ETH standards used in the ETF-calibration of the clumped result to give the reader an idea of the reproducibility of the clumped isotope measurements on different standards.

Line 356-359: I agree that the TEX₈₆ data looks to be of high quality and likely reflects SST. However, I think the authors did not sufficiently disprove the hypothesis that the TEX₈₆ temperatures may be seasonally baised (see major comment). A seasonal bias in SST can be substantial and I would not label such a potential bias as a “minor warm-bias” (line 357).

Line 451: “This interpretation is endorsed by…” I would rephrase this. A causal relationship between two parameters (as stated in the previous sentence) cannot be (dis)proven by the similarity of the powerspectra of these parameters. Spectral analysis is a powerful and useful statistical tool, but it cannot be used to infer causal relationships.

Line 457: “remarkable co-variation between…” A statement like this should be backed up with statistical proof of this co-variation. For example by an R² and p-value and/or by means of cross-spectral analysis.

Figure 7: The vertical axes of these plots require units. I assume the isotopic gradient is in ‰ and the composite is unitless (-).

Lines 524-525: Please include the potential for seasonal bias in the TEX₈₆ reconstructions more prominently here in the conclusion (see major comment). Perhaps the authors could estimate the size of the warm bias if the TEX₈₆ would record summer temperatures and compare that with the difference between the proxies to show whether or not this bias is small enough to be neglected.

Line 535: “Current” rephrase to “Currently”

Figure C1: From the caption it is not clear if these pictures are from Gallagher et al. or from this study. Please clarify.

References

Fernandez, A., Müller, I. A., Rodríguez-Sanz, L., van Dijk, J., Looser, N., and Bernasconi, S. M.: A reassessment of the precision of carbonate clumped isotope measurements: implications for calibrations and paleoclimate reconstructions, 18, 4375–4386, 2017.

Jia, G., Wang, X., Guo, W., and Dong, L.: Seasonal distribution of archaeal lipids in surface water and its constraint on their sources and the TEX86 temperature proxy in sediments of the South China Sea, 122, 592–606, https://doi.org/10.1002/2016JG003732, 2017.

Meinicke, N., Reimi, M. A., Ravelo, A. C., and Meckler, A. N.: Coupled Mg/Ca and Clumped Isotope Measurements Indicate Lack of Substantial Mixed Layer Cooling in the Western Pacific Warm Pool During the Last ∼5 Million Years, 36, e2020PA004115, https://doi.org/10.1029/2020PA004115, 2021.

O’Brien, C. L., Robinson, S. A., Pancost, R. D., Sinninghe Damsté, J. S., Schouten, S., Lunt, D. J., Alsenz, H., Bornemann, A., Bottini, C., Brassell, S. C., Farnsworth, A., Forster, A., Huber, B. T., Inglis, G. N., Jenkyns, H. C., Linnert, C., Littler, K., Markwick, P., McAnena, A., Mutterlose, J., Naafs, B. D. A., Püttmann, W., Sluijs, A., van Helmond, N. A. G. M., Vellekoop, J., Wagner, T., and Wrobel, N. E.: Cretaceous sea-surface temperature evolution: Constraints from TEX 86 and planktonic foraminiferal oxygen isotopes, 172, 224–247, https://doi.org/10.1016/j.earscirev.2017.07.012, 2017.