Ishii and co-authors have compiled isoGDGT data for the Southern Ocean to evaluate their relationship with temperature and water masses. The Southern Ocean is region sensitive to climate change, but reliable temperature reconstructions from this area are scares due to poor preservation of carbonates and deviating temperature sensitivity of lipid biomarker proxies compared to global trends.

They authors find that isoGDGTs in surficial sediments are different in sediments north and south of the Polar Front, and also have a different relationship with temperature. They subsequently propose an index that can be used to reconstruct the position of the Polar Front, and possibly reconstruct paleotemperatures.

The development of proxies to reliably reconstruct past temperatures in the Southern Ocean is very important. For that reason, I would say that this manuscript is worth publishing in Climate of the Past. However, the current version lacks crucial background information and context at several instances. Also, GDGTs are often written in singular form -also when the are referred to as plural-, which creates unnecessary confusion and ambiguity in the text. Finally, the text contains ‘the’ at places where it is not necessary, and misses this word at places where it is necessary. Please carefully reread the text before resubmission. Besides from these textual comments, my main points are:

• I am missing a mechanism supporting the definition for the proposed AIZ index. From the very *last* section of the discussion, it finally appears that GDGT-0 is a crucial compound in driving this index, but this is far too late in the manuscript. Please (at least try to) explain why GDGT-0 occurs more/less in certain water masses and state its relationship with temperature earlier on. This should also be mentioned in the abstract. Important here is to mention that GDGT-0 is deliberately not included in the TEX86 because it is produced by such a wide range of archaea (Schouten et al., 2002 EPSL, Schouten et al., 2013 Org Geochem). We as community should move on from merely reporting statistical relationships to truly understanding the mechanisms that drive TEX86 and GDGT distributions in the environment (and cultures) in general. 
• The AIZ index is used both to recognise water masses and to reconstruct temperature. However, there is no discussion on how these two different aspects can be disentangled. What is the primary control on the AIZ? And how does temperature (and all other environmental parameters mentioned in the text) vary between water masses? In short, the characteristics of the different water masses need to be better described. In the introduction and the Oceanographic setting, and should be used as context for the interpretation of surficial sediment data and downcore proxy results.
• The introduction is a bit sloppy and misses some crucial information and details on the development and use of the TEX86 as proxy for SST.
  
  L36: there are many more than 6 different isoGDGTs (isoGDGTs exist with up to 8 cyclisations, with additional branches, with hydroxy groups, with a c-c bond, etc etc). Please be correct in your statements.
  
  L37: cren only has 1 cyclohexane moiety.
  
  L38: cren’ is a stereoisomer, not a regioisomer (see Liu et al 2018 Org Geochem and Sinninghe Damsté et al 2018 Org. Geochem).
  
  L38: specify that it is the number of cyclisations that is related to temperature, not the isoGDGT distribution in general.
  
  L40: explain why there was a need for studies to further improve the proxy. What were the problems?
  
  L46: TEX86L is not generally used by the community and it is not recommended for use. The Southern Ocean seems to be an exception as unique region where some OK results have been obtained. Given the prominent role of TEX86L in this manuscript, some background information is warranted. See community discussion (section 7.2) in Bijl et al., in press, Biogeosciences (https://doi.org/10.5194/egusphere-2025-1467).
  
  L50 states that polar-specific factors should be taken into account, but it is not explained what their influence on TEX86 is.
  
  L53 mentions hydroxy GDGTs as promising addition to the TEX86 in polar regions, but leaves it at that. Explain the OH-TEX86 (Varma et al., 2024 GCA) and how it extends the linear response of GDGTs to temperatures <15C. This is one of the major advancements of the field of the past years and warrants more discussion and attention. I would even recommend including OH-GDGTs in the analyses here.
  
  L62: the Polar Front appears out of nowhere here. The different water masses and their characteristics need to be explained earlier on, possibly in relation with the deviating temperature-relationship of isoGDGTs compared to that in global oceans.
• I refered to the community-led paper sharing the best practices on the analysis and interpretation of isoGDGTs in marine sediments (Bijl et al., in press, see link above). It would make sense to follow those best practices here, too. For example in assessing outliers or for selecting the most appropriate calibration.
• Section 4.2 mentions export depth, but does not explain the principle, or what determines/influences export depth. Please add more context and explanation here, and make clear how export depth relates to the depth of maximum isoGDGT production, as well as whether these depths are expected to vary between water masses (and if so, how, and why).
• L239: the discussion suddenly shifts to differences in isoGDGTs north and south of the polar front, whereas these relations have not been shown or discussed yet. This only happens much later in the manuscript. Critically check the story line and adjust the order.
• AIZ index: it is not clear to me how one can distinguish a water mass signal vs a temperature signal from this index. Please elaborate. This is important given your finding that the AIZ index relates to temperature south of the PF. When applying this index downcore, it has to be clear how this record needs to be interpreted. Are we reconstructing the position of the PF? Or temperature? And can the temperature relationship be extrapolated (as suggested in L329), or is it only valid <4C/in sediments below water masses south of the PF? What does the record mean in terms of temperature when the AIZ index exceeds the PF threshold value over time?
• In section 4.6.2 should be made more clear that the temperature discussion is onnly valid for locations south of the PF. Also for the comparison with OPTIMAL: the record from north of the PF does not show clear G-IG cycles as suggested in the text. Please adjust.
• There are a lot of supplementary figures. Are they all necessary?