Cenozoic history of the tropical marine biodiversity hotspot.

The region with the highest marine biodiversity on our planet is known as the Coral Triangle or Indo-Australian Archipelago (IAA)1,2. Its enormous biodiversity has long attracted the interest of biologists; however, the detailed evolutionary history of the IAA biodiversity hotspot remains poorly understood3. Here we present a high-resolution reconstruction of the Cenozoic diversity history of the IAA by inferring speciation-extinction dynamics using a comprehensive fossil dataset. We found that the IAA has exhibited a unidirectional diversification trend since about 25 million years ago, following a roughly logistic increase until a diversity plateau beginning about 2.6 million years ago. The growth of diversity was primarily controlled by diversity dependency and habitat size, and also facilitated by the alleviation of thermal stress after 13.9 million years ago. Distinct net diversification peaks were recorded at about 25, 20, 16, 12 and 5 million years ago, which were probably related to major tectonic events in addition to climate transitions. Key biogeographic processes had far-reaching effects on the IAA diversity as shown by the long-term waning of the Tethyan descendants versus the waxing of cosmopolitan and IAA taxa. Finally, it seems that the absence of major extinctions and the Cenozoic cooling have been essential in making the IAA the richest marine biodiversity hotspot on Earth.

Highest ocean heat in four centuries places Great Barrier Reef in danger.

Mass coral bleaching on the Great Barrier Reef (GBR) in Australia between 2016 and 2024 was driven by high sea surface temperatures (SST)1. The likelihood of temperature-induced bleaching is a key determinant for the future threat status of the GBR2, but the long-term context of recent temperatures in the region is unclear. Here we show that the January-March Coral Sea heat extremes in 2024, 2017 and 2020 (in order of descending mean SST anomalies) were the warmest in 400 years, exceeding the 95th-percentile uncertainty limit of our reconstructed pre-1900 maximum. The 2016, 2004 and 2022 events were the next warmest, exceeding the 90th-percentile limit. Climate model analysis confirms that human influence on the climate system is responsible for the rapid warming in recent decades. This attribution, together with the recent ocean temperature extremes, post-1900 warming trend and observed mass coral bleaching, shows that the existential threat to the GBR ecosystem from anthropogenic climate change is now realized. Without urgent intervention, the iconic GBR is at risk of experiencing temperatures conducive to near-annual coral bleaching3, with negative consequences for biodiversity and ecosystems services. A continuation on the current trajectory would further threaten the ecological function4 and outstanding universal value5 of one of Earth's greatest natural wonders.

Continental-scale nutrient and contaminant delivery by Pacific salmon.

The movement of large amounts of nutrients by migrating animals has ecological benefits for recipient food webs1,2 that may be offset by co-transported contaminants3,4. Salmon spawning migrations are archetypal of this process, carrying marine-derived materials to inland ecosystems where they stimulate local productivity but also enhance contaminant exposure5-7. Pacific salmon abundance and biomass are higher now than in the last century, reflecting substantial shifts in community structure8 that probably altered nutrient versus contaminant delivery. Here we combined nutrient and contaminant concentrations with 40 years of annual Pacific salmon returns to quantify how changes in community structure influenced marine to freshwater inputs to western North America. Salmon transported tonnes of nutrients and kilograms of contaminants to freshwaters annually. Higher salmon returns (1976-2015) increased salmon-derived nutrient and contaminant inputs by 30% and 20%, respectively. These increases were dominated by pink salmon, which are short-lived, feed lower in marine food webs than other salmon species, and had the highest nutrient-to-contaminant ratios. As a result, the delivery of nutrients increased at a greater rate than the delivery of contaminants, and salmon inputs became more ecologically beneficial over time. Even still, contaminant loadings may represent exposure concerns for some salmon predators. The Pacific salmon example demonstrates how long-term environmental changes interact with nutrient and contaminant movement across large spatial scales and provides a model for exploring similar patterns with other migratory species9.

Microbial iron limitation in the ocean's twilight zone.

Primary production in the sunlit surface ocean is regulated by the supply of key nutrients, primarily nitrate, phosphate and iron (Fe), required by phytoplankton to fix carbon dioxide into biomass1-3. Below the surface ocean, remineralization of sinking organic matter rapidly regenerates nutrients, and microbial metabolism in the upper mesopelagic 'twilight zone' (200-500 m) is thought to be limited by the delivery of labile organic carbon4,5. However, few studies have examined the role of nutrients in shaping microbial production in the mesopelagic6-8. Here we report the distribution and uptake of siderophores, biomarkers for microbial Fe deficiency9 across a meridional section of the eastern Pacific Ocean. Siderophore concentrations are high not only in chronically Fe-limited surface waters but also in the twilight zone underlying the North and South Pacific subtropical gyres, two key ecosystems for the marine carbon cycle. Our findings suggest that bacterial Fe deficiency owing to low Fe availability is probably characteristic of the twilight zone in several large ocean basins, greatly expanding the region of the marine water column in which nutrients limit microbial metabolism, with potential implications for ocean carbon storage.

Future increase in extreme El Niño supported by past glacial changes.

El Niño events, the warm phase of the El Niño-Southern Oscillation (ENSO) phenomenon, amplify climate variability throughout the world1. Uncertain climate model predictions limit our ability to assess whether these climatic events could become more extreme under anthropogenic greenhouse warming2. Palaeoclimate records provide estimates of past changes, but it is unclear if they can constrain mechanisms underlying future predictions3-5. Here we uncover a mechanism using numerical simulations that drives consistent changes in response to past and future forcings, allowing model validation against palaeoclimate data. The simulated mechanism is consistent with the dynamics of observed extreme El Niño events, which develop when western Pacific warm pool waters expand rapidly eastwards because of strongly coupled ocean currents and winds6,7. These coupled interactions weaken under glacial conditions because of a deeper mixed layer driven by a stronger Walker circulation. The resulting decrease in ENSO variability and extreme El Niño occurrence is supported by a series of tropical Pacific palaeoceanographic records showing reduced glacial temperature variability within key ENSO-sensitive oceanic regions, including new data from the central equatorial Pacific. The model-data agreement on past variability, together with the consistent mechanism across climatic states, supports the prediction of a shallower mixed layer and weaker Walker circulation driving more frequent extreme El Niño genesis under greenhouse warming.

Plastic pollution on the world's coral reefs.

Coral reefs are losing the capacity to sustain their biological functions1. In addition to other well-known stressors, such as climatic change and overfishing1, plastic pollution is an emerging threat to coral reefs, spreading throughout reef food webs2, and increasing disease transmission and structural damage to reef organisms3. Although recognized as a global concern4, the distribution and quantity of plastics trapped in the world's coral reefs remains uncertain3. Here we survey 84 shallow and deep coral ecosystems at 25 locations across the Pacific, Atlantic and Indian ocean basins for anthropogenic macrodebris (pollution by human-generated objects larger than 5 centimetres, including plastics), performing 1,231 transects. Our results show anthropogenic debris in 77 out of the 84 reefs surveyed, including in some of Earth's most remote and near-pristine reefs, such as in uninhabited central Pacific atolls. Macroplastics represent 88% of the anthropogenic debris, and, like other debris types, peak in deeper reefs (mesophotic zones at 30-150 metres depth), with fishing activities as the main source of plastics in most areas. These findings contrast with the global pattern observed in other nearshore marine ecosystems, where macroplastic densities decrease with depth and are dominated by consumer items5. As the world moves towards a global treaty to tackle plastic pollution6, understanding its distribution and drivers provides key information to help to design the strategies needed to address this ubiquitous threat.

Anthropogenic fingerprints in daily precipitation revealed by deep learning.

According to twenty-first century climate-model projections, greenhouse warming will intensify rainfall variability and extremes across the globe1-4. However, verifying this prediction using observations has remained a substantial challenge owing to large natural rainfall fluctuations at regional scales3,4. Here we show that deep learning successfully detects the emerging climate-change signals in daily precipitation fields during the observed record. We trained a convolutional neural network (CNN)5 with daily precipitation fields and annual global mean surface air temperature data obtained from an ensemble of present-day and future climate-model simulations6. After applying the algorithm to the observational record, we found that the daily precipitation data represented an excellent predictor for the observed planetary warming, as they showed a clear deviation from natural variability since the mid-2010s. Furthermore, we analysed the deep-learning model with an explainable framework and observed that the precipitation variability of the weather timescale (period less than 10 days) over the tropical eastern Pacific and mid-latitude storm-track regions was most sensitive to anthropogenic warming. Our results highlight that, although the long-term shifts in annual mean precipitation remain indiscernible from the natural background variability, the impact of global warming on daily hydrological fluctuations has already emerged.

Increased occurrences of consecutive La Niña events under global warming.

Most El Niño events occur sporadically and peak in a single winter1-3, whereas La Niña tends to develop after an El Niño and last for two years or longer4-7. Relative to single-year La Niña, consecutive La Niña features meridionally broader easterly winds and hence a slower heat recharge of the equatorial Pacific6,7, enabling the cold anomalies to persist, exerting prolonged impacts on global climate, ecosystems and agriculture8-13. Future changes to multi-year-long La Niña events remain unknown. Here, using climate models under future greenhouse-gas forcings14, we find an increased frequency of consecutive La Niña ranging from 19 ± 11% in a low-emission scenario to 33 ± 13% in a high-emission scenario, supported by an inter-model consensus stronger in higher-emission scenarios. Under greenhouse warming, a mean-state warming maximum in the subtropical northeastern Pacific enhances the regional thermodynamic response to perturbations, generating anomalous easterlies that are further northward than in the twentieth century in response to El Niño warm anomalies. The sensitivity of the northward-broadened anomaly pattern is further increased by a warming maximum in the equatorial eastern Pacific. The slower heat recharge associated with the northward-broadened easterly anomalies facilitates the cold anomalies of the first-year La Niña to persist into a second-year La Niña. Thus, climate extremes as seen during historical consecutive La Niña episodes probably occur more frequently in the twenty-first century.

Precipitation regime changes in High Mountain Asia driven by cleaner air.

High Mountain Asia (HMA) has experienced a spatial imbalance in water resources in recent decades, partly because of a dipolar pattern of precipitation changes known as South Drying-North Wetting1. These changes can be influenced by both human activities and internal climate variability2,3. Although climate projections indicate a future widespread wetting trend over HMA1,4, the timing and mechanism of the transition from a dipolar to a monopolar pattern remain unknown. Here we demonstrate that the observed dipolar precipitation change in HMA during summer is primarily driven by westerly- and monsoon-associated precipitation patterns. The weakening of the Asian westerly jet, caused by the uneven emission of anthropogenic aerosols, favoured a dipolar precipitation trend from 1951 to 2020. Moreover, the phase transition of the Interdecadal Pacific Oscillation induces an out-of-phase precipitation change between the core region of the South Asian monsoon and southeastern HMA. Under medium- or high-emission scenarios, corresponding to a global warming of 0.6-1.1 °C compared with the present, the dipolar pattern is projected to shift to a monopolar wetting trend in the 2040s. This shift in precipitation patterns is mainly attributed to the intensified jet stream resulting from reduced emissions of anthropogenic aerosols. These findings underscore the importance of considering the impact of aerosol emission reduction in future social planning by policymakers.

Forced changes in the Pacific Walker circulation over the past millennium.

The Pacific Walker circulation (PWC) has an outsized influence on weather and climate worldwide. Yet the PWC response to external forcings is unclear1,2, with empirical data and model simulations often disagreeing on the magnitude and sign of these responses3. Most climate models predict that the PWC will ultimately weaken in response to global warming4. However, the PWC strengthened from 1992 to 2011, suggesting a significant role for anthropogenic and/or volcanic aerosol forcing5, or internal variability. Here we use a new annually resolved, multi-method, palaeoproxy-derived PWC reconstruction ensemble (1200-2000) to show that the 1992-2011 PWC strengthening is anomalous but not unprecedented in the context of the past 800 years. The 1992-2011 PWC strengthening was unlikely to have been a consequence of volcanic forcing and may therefore have resulted from anthropogenic aerosol forcing or natural variability. We find no significant industrial-era (1850-2000) PWC trend, contrasting the PWC weakening simulated by most climate models3. However, an industrial-era shift to lower-frequency variability suggests a subtle anthropogenic influence. The reconstruction also suggests that volcanic eruptions trigger El Niño-like PWC weakening, similar to the response simulated by climate models.

A well-oxygenated eastern tropical Pacific during the warm Miocene.

The oxygen content of the oceans is susceptible to climate change and has declined in recent decades1, with the largest effect in oxygen-deficient zones (ODZs)2, that is, mid-depth ocean regions with oxygen concentrations <5 µmol kg-1 (ref. 3). Earth-system-model simulations of climate warming predict that ODZs will expand until at least 2100. The response on timescales of hundreds to thousands of years, however, remains uncertain3-5. Here we investigate changes in the response of ocean oxygenation during the warmer-than-present Miocene Climatic Optimum (MCO; 17.0-14.8 million years ago (Ma)). Our planktic foraminifera I/Ca and δ15N data, palaeoceanographic proxies sensitive to ODZ extent and intensity, indicate that dissolved-oxygen concentrations in the eastern tropical Pacific (ETP) exceeded 100 µmol kg-1 during the MCO. Paired Mg/Ca-derived temperature data suggest that an ODZ developed in response to an increased west-to-east temperature gradient and shoaling of the ETP thermocline. Our records align with model simulations of data from recent decades to centuries6,7, suggesting that weaker equatorial Pacific trade winds during warm periods may lead to decreased upwelling in the ETP, causing equatorial productivity and subsurface oxygen demand to be less concentrated in the east. These findings shed light on how warm-climate states such as during the MCO may affect ocean oxygenation. If the MCO is considered as a possible analogue for future warming, our findings seem to support models suggesting that the recent deoxygenation trend and expansion of the ETP ODZ may eventually reverse3,4.

Persistent equatorial Pacific iron limitation under ENSO forcing.

Projected responses of ocean net primary productivity to climate change are highly uncertain1. Models suggest that the climate sensitivity of phytoplankton nutrient limitation in the low-latitude Pacific Ocean plays a crucial role1-3, but this is poorly constrained by observations4. Here we show that changes in physical forcing drove coherent fluctuations in the strength of equatorial Pacific iron limitation through multiple El Niño/Southern Oscillation (ENSO) cycles, but that this was overestimated twofold by a state-of-the-art climate model. Our assessment was enabled by first using a combination of field nutrient-addition experiments, proteomics and above-water hyperspectral radiometry to show that phytoplankton physiological responses to iron limitation led to approximately threefold changes in chlorophyll-normalized phytoplankton fluorescence. We then exploited the >18-year satellite fluorescence record to quantify climate-induced nutrient limitation variability. Such synoptic constraints provide a powerful approach for benchmarking the realism of model projections of net primary productivity to climate changes.

Diagnosing destabilization risk in global land carbon sinks.

Global net land carbon uptake or net biome production (NBP) has increased during recent decades1. Whether its temporal variability and autocorrelation have changed during this period, however, remains elusive, even though an increase in both could indicate an increased potential for a destabilized carbon sink2,3. Here, we investigate the trends and controls of net terrestrial carbon uptake and its temporal variability and autocorrelation from 1981 to 2018 using two atmospheric-inversion models, the amplitude of the seasonal cycle of atmospheric CO2 concentration derived from nine monitoring stations distributed across the Pacific Ocean and dynamic global vegetation models. We find that annual NBP and its interdecadal variability increased globally whereas temporal autocorrelation decreased. We observe a separation of regions characterized by increasingly variable NBP, associated with warm regions and increasingly variable temperatures, lower and weaker positive trends in NBP and regions where NBP became stronger and less variable. Plant species richness presented a concave-down parabolic spatial relationship with NBP and its variability at the global scale whereas nitrogen deposition generally increased NBP. Increasing temperature and its increasing variability appear as the most important drivers of declining and increasingly variable NBP. Our results show increasing variability of NBP regionally that can be mostly attributed to climate change and that may point to destabilization of the coupled carbon-climate system.

Anticyclonic eddies aggregate pelagic predators in a subtropical gyre.

Ocean eddies are coherent, rotating features that can modulate pelagic ecosystems across many trophic levels. These mesoscale features, which are ubiquitous at mid-latitudes1, may increase productivity of nutrient-poor regions2,3, accumulate prey4 and modulate habitat conditions in the water column5. However, in nutrient-poor subtropical gyres-the largest marine biome-the role of eddies in modulating behaviour throughout the pelagic predator community remains unknown despite predictions for these gyres to expand6 and pelagic predators to become increasingly important for food security7. Using a large-scale fishery dataset in the North Pacific Subtropical Gyre, we show a pervasive pattern of increased pelagic predator catch inside anticyclonic eddies relative to cyclones and non-eddy areas. Our results indicate that increased mesopelagic prey abundance in anticyclone cores4,8 may be attracting diverse predators, forming ecological hotspots where these predators aggregate and exhibit increased abundance. In this energetically quiescent gyre, we expect that isolated mesoscale features (and the habitat conditions in them) exhibit primacy over peripheral submesoscale dynamics in structuring the foraging opportunities of pelagic predators. Our finding that eddies influence coupling of epi- to mesopelagic communities corroborates the growing evidence that deep scattering layer organisms are vital prey for a suite of commercially important predator species9 and, thus, provide valuable ecosystem services.

Cyclic evolution of phytoplankton forced by changes in tropical seasonality.

Although the role of Earth's orbital variations in driving global climate cycles has long been recognized, their effect on evolution is hitherto unknown. The fossil remains of coccolithophores, a key calcifying phytoplankton group, enable a detailed assessment of the effect of cyclic orbital-scale climate changes on evolution because of their abundance in marine sediments and the preservation of their morphological adaptation to the changing environment1,2. Evolutionary genetic analyses have linked broad changes in Pleistocene fossil coccolith morphology to species radiation events3. Here, using high-resolution coccolith data, we show that during the last 2.8 million years the morphological evolution of coccolithophores was forced by Earth's orbital eccentricity with rhythms of around 100,000 years and 405,000 years-a distinct spectral signature to that of coeval global climate cycles4. Simulations with an Earth System Model5 coupled with an ocean biogeochemical model6 show a strong eccentricity modulation of the seasonal cycle, which we suggest directly affects the diversity of ecological niches that occur over the annual cycle in the tropical ocean. Reduced seasonality in surface ocean conditions favours species with mid-size coccoliths, increasing coccolith carbonate export and burial; whereas enhanced seasonality favours a larger range of coccolith sizes and reduced carbonate export. We posit that eccentricity pacing of phytoplankton evolution contributed to the strong 405,000-year cyclicity that is seen in global carbon cycle records.

Enhanced ocean oxygenation during Cenozoic warm periods.

Dissolved oxygen (O2) is essential for most ocean ecosystems, fuelling organisms' respiration and facilitating the cycling of carbon and nutrients. Oxygen measurements have been interpreted to indicate that the ocean's oxygen-deficient zones (ODZs) are expanding under global warming1,2. However, models provide an unclear picture of future ODZ change in both the near term and the long term3-6. The paleoclimate record can help explore the possible range of ODZ changes in warmer-than-modern periods. Here we use foraminifera-bound nitrogen (N) isotopes to show that water-column denitrification in the eastern tropical North Pacific was greatly reduced during the Middle Miocene Climatic Optimum (MMCO) and the Early Eocene Climatic Optimum (EECO). Because denitrification is restricted to oxygen-poor waters, our results indicate that, in these two Cenozoic periods of sustained warmth, ODZs were contracted, not expanded. ODZ contraction may have arisen from a decrease in upwelling-fuelled biological productivity in the tropical Pacific, which would have reduced oxygen demand in the subsurface. Alternatively, invigoration of deep-water ventilation by the Southern Ocean may have weakened the ocean's 'biological carbon pump', which would have increased deep-ocean oxygen. The mechanism at play would have determined whether the ODZ contractions occurred in step with the warming or took centuries or millennia to develop. Thus, although our results from the Cenozoic do not necessarily apply to the near-term future, they might imply that global warming may eventually cause ODZ contraction.

Volcanic trigger of ocean deoxygenation during Cordilleran ice sheet retreat.

North Pacific deoxygenation events during the last deglaciation were sustained over millennia by high export productivity, but the triggering mechanisms and their links to deglacial warming remain uncertain1-3. Here we find that initial deoxygenation in the North Pacific immediately after the Cordilleran ice sheet (CIS) retreat4 was associated with increased volcanic ash in seafloor sediments. Timing of volcanic inputs relative to CIS retreat suggests that regional explosive volcanism was initiated by ice unloading5,6. We posit that iron fertilization by volcanic ash7-9 during CIS retreat fuelled ocean productivity in this otherwise iron-limited region, and tipped the marine system towards sustained deoxygenation. We also identify older deoxygenation events linked to CIS retreat over the past approximately 50,000 years (ref. 4). Our findings suggest that the apparent coupling between the atmosphere, ocean, cryosphere and solid-Earth systems occurs on relatively short timescales and can act as an important driver for ocean biogeochemical change.

Pliocene decoupling of equatorial Pacific temperature and pH gradients.

Ocean dynamics in the equatorial Pacific drive tropical climate patterns that affect marine and terrestrial ecosystems worldwide. How this region will respond to global warming has profound implications for global climate, economic stability and ecosystem health. As a result, numerous studies have investigated equatorial Pacific dynamics during the Pliocene (5.3-2.6 million years ago) and late Miocene (around 6 million years ago) as an analogue for the future behaviour of the region under global warming1-12. Palaeoceanographic records from this time present an apparent paradox with proxy evidence of a reduced east-west sea surface temperature gradient along the equatorial Pacific1,3,7,8-indicative of reduced wind-driven upwelling-conflicting with evidence of enhanced biological productivity in the east Pacific13-15 that typically results from stronger upwelling. Here we reconcile these observations by providing new evidence for a radically different-from-modern circulation regime in the early Pliocene/late Miocene16 that results in older, more acidic and more nutrient-rich water reaching the equatorial Pacific. These results provide a mechanism for enhanced productivity in the early Pliocene/late Miocene east Pacific even in the presence of weaker wind-driven upwelling. Our findings shed new light on equatorial Pacific dynamics and help to constrain the potential changes they will undergo in the near future, given that the Earth is expected to reach Pliocene-like levels of warming in the next century.

Genomic insights into population history and biological adaptation in Oceania.

The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes1. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago2-4. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.

Baleen whale prey consumption based on high-resolution foraging measurements.

Baleen whales influence their ecosystems through immense prey consumption and nutrient recycling1-3. It is difficult to accurately gauge the magnitude of their current or historic ecosystem role without measuring feeding rates and prey consumed. To date, prey consumption of the largest species has been estimated using metabolic models3-9 based on extrapolations that lack empirical validation. Here, we used tags deployed on seven baleen whale (Mysticeti) species (n = 321 tag deployments) in conjunction with acoustic measurements of prey density to calculate prey consumption at daily to annual scales from the Atlantic, Pacific, and Southern Oceans. Our results suggest that previous studies3-9 have underestimated baleen whale prey consumption by threefold or more in some ecosystems. In the Southern Ocean alone, we calculate that pre-whaling populations of mysticetes annually consumed 430 million tonnes of Antarctic krill (Euphausia superba), twice the current estimated total biomass of E. superba10, and more than twice the global catch of marine fisheries today11. Larger whale populations may have supported higher productivity in large marine regions through enhanced nutrient recycling: our findings suggest mysticetes recycled 1.2 × 104 tonnes iron yr-1 in the Southern Ocean before whaling compared to 1.2 × 103 tonnes iron yr-1 recycled by whales today. The recovery of baleen whales and their nutrient recycling services2,3,7 could augment productivity and restore ecosystem function lost during 20th century whaling12,13.