The El Niño-Southern Oscillation (ENSO) describes variation in tropical Pacific Ocean temperatures and the resulting changes in atmospheric pressure gradients. The atmospheric changes widely propagate the effects of ENSO variability, making ENSO a major component of regional climate across much of the world1. The impacts of changes in regional temperature and precipitation patterns associated with El Niño and La Niña phases of ENSO have wide-ranging environmental, societal and economic consequences. The El Niño phase manifests as a warming of central and/or eastern Pacific sea surface temperature (SST) with resulting increased precipitation in northern South America and western North America (Fig. 1). Conversely, the associated cooling in the western Pacific during El Niño events is associated with drought, forest fires and reduced agricultural yield in the western tropical Pacific, including the eastern half of Australia2. The opposing La Niña phase is equally important as a driver of drought in the eastern Pacific and positive precipitation anomalies in the west Pacific2. This was most recently evident during the 2010/11 La Niña, when the volume of precipitation over land was sufficient to reduce global sea levels by 5 mm, with much of this falling on Australia3. This resulted in catastrophic flooding in the sub-tropics and massive carbon uptake via greening of the vast arid and semi-arid regions of the continent4,5.

Figure 1 ENSO influence on surface precipitation. Spatial correlation between mean precipitation (Nov–Oct: the local hydrological year17) across the greater ENSO region and mean sea surface temperature for the Nino3.4 region (box) for the period 1980–2016 CE. Location of the study site and other locations mentioned in the text are illustrated. Full size image

Given these wide-ranging effects, it is essential to understand how both phases of ENSO will respond to future climate change. Reducing predictive model uncertainties requires proxy data of ENSO behaviour under different background states, as well as in response to local and extra-regional influences from all ENSO-sensitive areas6,7. The Holocene provides fruitful opportunities for this, with millennial-scale changes in orbital radiation forcing and centennial-scale global temperature changes, such as the Little Ice Age (~1450–1850)8. However, the evolution of ENSO through the Holocene remains unclear, with discrepancies between central Pacific SST proxies9 and eastern Pacific proxies of both precipitation10 and SST11, particularly during the mid-Holocene. Additionally, there are very few proxy ENSO records that can resolve centennial-scale trends in changing ENSO mean state. This is important as changes in the dominant phase of ENSO have been linked to solar irradiance12, orbital forcing13, average global temperatures14 and fresh water fluxes in the North Atlantic7.

We present a new ~7700-year quantitative precipitation record from subtropical eastern Australia, where La Niña and El Niño conditions are associated with positive and negative rainfall anomalies, respectively2 (Fig. 1). The precipitation reconstruction is derived from the carbon isotope ratio (δ13C) of leaves from the evergreen tree Melaleuca quinquenervia ((Cav.) S.T. Blake) preserved in the Holocene sediments of Swallow Lagoon on Minjerribah (North Stradbroke Island), the world’s second largest sand island. Swallow Lagoon (27°29′55″S: 153°27′17″E) is a small (0.27 ha), perched, freshwater lake that is isolated from the regional water table15. With no inflow or outflow streams, the balance of precipitation over evaporation determines lake level (Fig. S1) and moisture availability for the isolated stand of M. quinquenervia that fringes the lake (Supplementary Information). Sediments from a 370 cm core were sieved at contiguous one-centimetre resolution for M. quinquenervia leaf fragments, yielding 284 samples. Each datum represents the δ13C of all leaf fragments at that depth and is an average for the period encapsulated by that centimetre of sediment, which ranges from two to 77 years (avg. 24.4 yrs; s.d. 15.6 yrs). As such, these data do not represent El Niño or La Niña events, but represent mean conditions of individual time-slices. Age control is provided by 18 accelerator mass spectrometry 14C dates on short-lived terrestrial macrofossils, including M. quinquenervia leaves (Table S1).

Our new rainfall reconstruction builds on a well-established relationship between carbon isotope fractionation in C 3 plant leaves and moisture availability (e.g., ref.16). In a novel approach, we utilise a relationship established specifically for M. quinquenervia using a 12-year collection of monthly litterfall samples from a nearby south-east Queensland wetland, which demonstrated a linear relationship (r2 = 0.67, p = 0.002) between the carbon isotope discrimination of M. quinquenervia leaves, relative to atmosphere, and mean annual rainfall17. We apply this calibration to sub-fossil M. quinquenervia leaf fragments from Swallow Lagoon to derive a quantitative estimate of mean annual rainfall. The linear nature of the model may skew precipitation estimates to the lower end and affect apparent variability; however, our calibration has advantages over other potential datasets as it uses location-specific climate data and is species-specific, as opposed to using modelled rainfall estimates16 or averaged data from all C 3 plants at a location18. Comparing our results against various reconstructions from global datasets demonstrate that they consistently reconstruct higher precipitation estimates, however the patterns of change and variance, although accentuated, do not differ and our findings based on the species-specific calibration remain robust (Fig. S4).

The inferred rainfall record from Swallow Lagoon covers the last 7700 years (Fig. 2) and displays a transition from predominantly high precipitation with low frequency variability during the mid-Holocene, to a drier climate with enhanced centennial-scale variability after ca. 3200 cal yr before present (3.2 cal kyr BP, where ‘present’ is 1950 CE). However, both non-constant sampling through time and varying numbers of years per sample could affect the variability in our record. To assess the fidelity of this shift in variability, we use a generalized additive location scale model (GAM-LS) to simultaneously estimate trends in both the mean (μ) and the standard deviation (σ) of the rainfall record. We find a statistically significant trend in σ. To test if this trend was influenced by sampling resolution, the estimated model was tested against a null model using 1000 simulated time series that follow the nonlinear trend estimated by our GAM-LS model but importantly with constant variance. This process demonstrates the range of trends in σ we might expect if there were no systematic change in variance. Simulation results demonstrate the estimated trend in σ is not an artefact arising from varying sampling resolution in time (Fig. S5). The combination of the fidelity of the variability in the record, the similarities between this and the general pattern of Holocene ENSO variability seen in other proxy records11,19,20,21, and the ENSO-sensitive location of the study region, provide confidence that rainfall variability in the record reflects ENSO variability through the Holocene. We therefore interpret the record in terms of mean ENSO conditions of individual time slices, as discussed above. Alternative explanations involving changes in ENSO ‘flavour’22 or shifting teleconnection patterns23,24 are not as firmly grounded in the palaeoclimate literature, although we cannot rule these out.

Figure 2 The Swallow Lagoon precipitation record. (a) The number of individual samples per non-overlapping century. (b) The Swallow Lagoon rainfall reconstruction with standard error (±88 mm; grey shading) and generalised additive location-scale model (GAM-LS: orange line with 95% confidence level shaded) illustrating significant trends in the data. Horizontal black dashed lines indicate ±2σ of the record, dotted line is the mean (1742 mm). (c) Standard deviation (σ) in mean annual rainfall with 95% confidence level shaded (see methods). Full size image

The nature of Holocene ENSO variance remains a subject of debate; central Pacific coral records suggesting no change in variance9 contrast with eastern Pacific ENSO proxies indicating enhanced variance in the late Holocene11,19,25. A recent analysis of coral and mollusc δ18O records from across the Pacific concluded marked changes in variance are in fact evident between the middle and late Holocene, and that tropical Pacific climate was susceptible to millennial-scale quiescent periods unrelated to orbital forcing20. In contrast, model simulations suggest the discrepancies between variability in eastern and central Pacific palaeoclimate data may be due to a differential response to insolation changes driven by orbital forcing22. Our record provides a new perspective from the southwestern Pacific and clearly demonstrate marked changes in rainfall variability over the last ~7700 years (Fig. 2). Prior to 5 cal kyr BP, variability is low, before a gradual increase ~5–2.5 cal kyr BP, and a further increase from ~1.2 cal kyr BP to present. The similarities between the timing of onset and trends in the variance between the eastern and western Pacific SSTs and teleconnected precipitation (Fig. 3) imply a common forcing mechanism.

Figure 3 (a) Swallow Lagoon precipitation record (as per Fig. 2); (b) West Pacific warm pool SST32; (c) lake sediment sand content from El Junco Lake, Galápagos Islands19, and (d) sediment deposition at Laguna Pallcacocha, Ecuador25, as proxies for El Niño event frequency; (e) simulated amplitude of ENSO variability as reflected by Nino3.4 SST variability with 95% confidence interval shaded and, (f) simulated strength of the Pacific Walker circulation in the Nino4 region with 95% confidence interval shaded, according to the CSIRO Mk3L climate system model (see methods); (g) Standard deviation in mean annual rainfall record from Swallow Lagoon (as per Fig. 2c); eastern tropical Pacific measures of ENSO variability derived from (h) variance of individual foraminifera11 (grey bars; original sample at 7 cal kyr BP not shown as it is considered spurious by the authors), (i) bivalves63 (blue boxes), and (j) Laguna Pallcacocha variance, in 100-year non-overlapping windows, derived from normal-transformed data64 (black solid line). Inverted triangles represent the location of radiocarbon ages in the Swallow Lagoon record. LIA: Little Ice Age. Full size image

Model simulations at 6 kyr and 0 kyr identify a strengthened Pacific Walker Circulation (PWC), driven by high boreal summer insolation and a stronger monsoon system, as the primary driver of reduced ENSO variability evident in proxy records during the mid-Holocene7,26,27. In this setting, strengthened trade winds foster more La Niña-like conditions and restrict the formation of El Niño events. To investigate the evolution of this scenario over time, we expand on these simulations using nine equilibrium climate model simulations spanning 8 kyr to 0 kyr, and derive metrics for the amplitude of ENSO variability and strength of the PWC (methods). Each simulation consists of a 1200-year model simulation (with the last 1000 years being used for analysis) and differs only via changes in the Earth’s orbital parameters. The model reproduces the long-term trends in ENSO variability over the last 8000 years seen in proxy records, with lower variability during the mid-Holocene (8–5 kyr) and gradually increasing late Holocene variability (Fig. 3). Modelled PWC strength suggests it reached a peak at 5 kyr, before decreasing towards 0 kyr. However, there is little difference between simulations either side of this peak, with the largest changes evident after 3 kyr, mirroring the pattern of rainfall variability at Swallow Lagoon (Fig. 3). Though it is likely that other factors beyond orbital forcing also influence ENSO, and the PWC, during the Holocene28, the simulations provide a mechanistic explanation for the coeval changes noted in proxy-ENSO records and rainfall in the Australian subtropics.

As our record tracks both wet and dry anomalies, we can characterise the shift at 3.2 cal kyr BP in terms of changes in the distribution as well as the amplitude of extremes. Prior to 3.2 cal kyr BP, no events exceeded ±2σ of the record mean; after 3.2 cal kyr BP, there are 12 dry excursions greater than 2σ, but only one wet excursion of this magnitude. While an increase in resolution towards the top of the record will naturally lead to the preservation of more short-lived events, we note that dry anomalies dominate and the transition towards an overall drier mean state, as illustrated by the GAM-LS (Fig. 2b), remains evident when the data are interpolated to a common centennial scale (Fig. S6). This trend suggests that the enhanced amplitude of late Holocene variability evident at Swallow Lagoon, and in other equatorial Pacific palaeoclimate records19,20,21,25, is driven by increasing strength of the El Niño phase alone, rather than simply a more variable system. While this has previously been implied from a marked shift in vegetation across eastern Australia towards more drought tolerant species around 3 cal kyr BP29, the Swallow Lagoon record confirms the one-sided nature of late-Holocene ENSO intensification.

The mid-Holocene (~7.7–3.5 cal kyr BP) at Swallow Lagoon is dominated by precipitation estimates above the mean (analogous to La Niña conditions in the instrumental record) though some dry periods are evident. The most extensive of these are apparent around 6.9, 6.8 and 5.8 cal kyr BP, suggesting El Niño was still active at this time. During the period 5.5–3.5 cal kyr BP, rainfall at Swallow Lagoon was generally stable, around a wet La Niña-like mean state. This period closely corresponds with a time of low variance in eastern Pacific SSTs11 from ~6–4 cal kyr and when Galápagos lake sediments suggest both phases of ENSO were less frequent21. Though some temporal smoothing is expected in the Galápagos record, as well as at Swallow Lagoon, the timing is also in general agreement with a “quiescent period” evident in high-resolution carbonate δ18O records from discrete periods between 5–3 cal kyr BP20. The GAM-LS model illustrates a period of very high rainfall at Swallow Lagoon around 3.5–3.0 cal kyr BP, which corresponds with a marked cool and dry period reflected in Galápagos lake sediments, also at 3.5–3.0 cal kyr BP21. Taken together, these findings suggest a centennial-scale period of enhanced zonal SST gradient, a persistently strong PWC and a more La Niña-like mean state.

The shift towards drier climates at Swallow Lagoon aligns with increasing SST variability in the eastern equatorial Pacific11 and the onset of more frequent El Niño events evident in sediment records from the Galápagos19 and Ecuador25 (Fig. 3; although we note the veracity of the Ecuadorean record in documenting El Niño events has recently been challenged30). Enhanced El Niño conditions in the west Pacific warm pool are evident in discreet coral records from Papua New Guinea around this time31, with notable prolonged and extreme events at ~2.5 and 2.04 ka corresponding with dry periods that exceed 2σ of the Swallow Lagoon record around 2.47 and 2.04 cal kyr BP. These events at Swallow Lagoon occur in a cluster of dry events during the ~2.6–2.0 cal kyr BP period, suggesting prolonged or extreme El Niño events, such as those evident in the coral records, may have occurred more regularly during this time. An absence of long coral records from the west Pacific precludes precise correlation with subsequent late-Holocene dry extremes in the Swallow Lagoon record, though a general agreement between rainfall trends (as illustrated by the GAM-LS) and west Pacific warm pool SSTs32 is evident through this period (Fig. 3).

A notable exception to the drier and more variable climate in the late Holocene at Swallow Lagoon is the stable high rainfall phase during the Little Ice Age (LIA: ~1450–1850)8, a period of globally cool temperatures14,33. ENSO variability during the LIA has been debated in recent research8,14,34,35,36. Problems in interpretation arise because of the heterogeneous relationship among terrestrial hydroclimate proxies, oceanic SST proxies and theoretical and physical models of predicted responses to globally cool periods36,37,38. A strengthened zonal gradient is indicated by hydrological records of a generally dry eastern Pacific19,21,25 contrasting with a wet western Pacific34,36, whereas a weakened zonal gradient is indicated by proxy records of relatively cool eastern and western Pacific SSTs8,39. The Swallow Lagoon record indicates persistently high rainfall during the LIA (Fig. 3). This is consistent with lake40 and tree-ring41 records from southern Australia that also find wet and low-variability LIA climate, which is inconsistent with El Niño-like conditions14. However, dry climate in northern Australia during the LIA37 is inconsistent with La Niña-like conditions. Thompson et al. (ref.21) suggest the pattern of reduced SST gradient described above is reminiscent of El Niño Modoki conditions; these can drive large-scale decreases in precipitation over northern Australia42, although they are unable to explain a wet southeastern40 or subtropical Australia (Swallow Lagoon). Given the critical impacts ENSO has on water resources in teleconnected regions, understanding this apparent disparity between SST and hydroclimate proxies highlights the need for further research into the response of ENSO to changes in global climate.