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Supplementary Fig. 2. An alternative biostratigraphic age model for the NKK-1 borehole (age model 'Option-1'). Age-depth tie points are plotted as event mid-points (see Table 3) with associated depth error ranges shown. T = top, B = base. Planktonic foraminifera biozones are shown against the age scale. See Fig. 6 for nannofossil zone distribution. Grey circles identify the calibrated datum events used to constrain the numerical age model. Other planktonic foraminiferal events used in to construct the biozonation are also named. Dashed biozone separators indicate low certainty bioevent positions in the core. HCO = highest common occurrence, and is an alternative interpretation of the Psuedohastigerina naguewichiensis range data, using the HCO of this species as the calibrated age-depth tie-point rather than the last rare occurrence above the sandstone/basalt (Option - 2).

Supplementary Fig. 3. Foraminifera stable isotopes across the NKK-1 borehole EOT succession on the depth scale. The zone of faded isotopic data points highlights where extensive infilling with sparry calcite is associated with isotopically depleted ε18O and ε13C values even in separated test fragments (c. 53–47 mbs), masking the primary foraminiferal/ocean signal. The dashed vertical pale blue and pale grey lines (planktonic and benthic respectively) represent late Eocene ‘base-line’ ‘unaltered values’ used as a threshold for determining which data points contain significant diagenetic calcite bias and, thus, should be excluded from our interpretation (see Supplementary Fig. 3).

Supplementary Fig 1. A selection of middle Eocene to lower Oligocene light microscope images of some biostratigraphically useful calcareous nannofossils (and others) from the NKK-1 borehole, central Java. Figs. 1 & 2. Reticulofenestra reticulata (Fig. 1, reproduced from *, Pl. 1, fig. 38; and **, Pl. 1, fig. 1). Fig. 2 reproduced from *, Pl. 1, fig. 44 and **, Pl. 1, fig. 8), Figs. 3 & 4. R. nanggulanensis (reproduced from Jones & Dunkley Jones (2020) Pl. 1, fig 40-41), Fig. 5. R. bisecta (reproduced from **, Pl. 1 fig. 32), Fig. 6. R. umbilicus (reproduced from **, Pl. 1, fig. 35), Fig. 7. Coccolithus pelagicus (reproduced from *, Pl. 1, fig. 12; and **, Pl. 2, fig. 3), Fig. 8. C. formosus (reproduced from *, Pl. 1, fig. 16; and **, Pl. 2, fig. 23), Figs. 9, 27 & 28. Reticulofenestra isabellae, (Fig. 9, reproduced from *, Pl. 1, fig. 9; and of **, Pl. 1, fig. 45; Fig 27 reproduced from *, Pl. 1, fig. 10; and of **, Pl. 1, fig. 46; Fig 28 reproduced from *, Pl. 1, fig. 11; and **, Pl. 1, fig. 47). Fig. 10. Calcidiscus bicircus (reproduced from **, Pl. 3, fig. 12) Fig. 11. Umbilicosphaera bramletti, Fig. 12. U. detecta, (reproduced from **, Pl. 3, fig. 19) Figs. 13 & 14. Discoaster saipanensis, Figs. 15 & 16. D. barbadiensis, (Fig. 15, reproduced from **, Pl. 6, fig. 3; Fig. 16, reproduced from **, Pl. 6, fig.6), Figs. 17 & 18. Clausicoccus subdistichus, (Fig. 17, reproduced from **, Pl. 3, fig. 1; Fig. 18 reproduced from **, Pl. 3, fig. 4), Figs. 19 & 20 Sphenolithus obtusus, (Fig. 19, reproduced from *, Pl. 1 fig. 31; and **, Pl. 6, fig. 29; Fig. 20, reproduced from *, Pl. 1 fig. 32; and **, Pl. 6, fig. 30), Figs. 21 & 22. S. akropodus, (Fig. 21, reproduced from *, Pl. 1 fig. 33; and **; Pl. 6, fig. 41; Fig. 22, reproduced *, Pl. 1 fig. 34; and **, Pl. 6, fig. 42), Figs. 23 & 24. S. tribulosus, (Fig. 23, reproduced from *, Pl. 1 fig. 35; and ** Pl. 6, fig. 35; Fig. 24, reproduced from *, Pl. 1 fig. 36; and ** Pl. 6, fig. 36), Figs. 25 & 26. Chiasmolithus grandis, (Fig. 25, reproduced ** Pl. 2, fig. 45; Fig. 26, reproduced ** Pl. 2, fig. 44). Sample information recorded under each image pertaining to each species. Where an image is a rotation of the same specimen as the preceding image, the sample information is not replicated. The same applies to different specimens that are the same species. * Jones et al., (2019); ** Jones & Dunkley Jones (2020).

Supplementary Fig. 4. Foraminifera carbon and oxygen stable isotope cross plot identifying possible diagenetic calcite influence in the basal Oligocene of the NKK-1 borehole. Planktonic foraminifera δ18O values (T. ampliapertura, ‘whole-sparr fill’, ‘empty’ and ‘fragments’) with δ18O > 1 ‰ that is negatively offset from the late Eocene ‘base-line’ 1 (i.e. left of the dashed blue vertical line, as defined in Supplementary Fig. 2), and/or having paired sparite infill samples with δ18O that is > 1 ‰ negatively offset from the foraminifera values, are suspected to include a significant diagenetic calcite component. These are excluded from our downhole EOT isotope stratigraphy interpretation. The matching δ13C for these samples is also excluded. Benthic foraminifera δ18O from this ‘alteration interval’ should likely also be treated with caution, although the more enclosed tests with smaller internal spaces for diagenetic calcite to form, appear to result in a smaller diagenetic deviations.

Appendix 1: NKK-1 lithological log sheets, Cores 1-21.

Appendix 3: NKK-1 core photos, Cores 11-21.