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Stable water isotopes (δ18Ow and δDw) have been successfully implemented for the first time in a high-resolution model of the Mediterranean Sea (NEMO-MED12). In this numerical study, model results are compared with available in situ observations to evaluate the model performance of the present-day distribution of stable water isotopes and their relationship with salinity on a sub-basin scale. There is good agreement between the modelled and observed distributions of δ18Ow in the surface water. The model successfully simulates the observed east–west gradient of δ18Ow characterising surface, intermediate, and deep waters. The results also show good agreement between the simulated δDw and the in situ data. The δDw shows a strong linear relationship with δ18Ow (r2=0.98) and salinity (r2=0.94) for the whole Mediterranean Sea. Moreover, the modelled relationships between δ18Ow and salinity agree well with observations, with a weaker slope in the eastern basin than in the western basin. We investigate the relationship of the isotopic signature of the planktonic foraminifera shells (δ18Oc) with temperature and the influence of seasonality. Our results suggest a more quantitative use of δ18O records, combining reconstruction with modelling approaches.

The South Asian summer monsoon (SASM) significantly intensified during the Middle Miocene (17–12 Ma), but the driver of this change remains an open question. The uplift of the Himalaya (HM) and the Iranian Plateau (IP) and global CO2 variation are prominent factors among suggested drivers. Particularly, the impact of high CO2 levels on the Miocene SASM has been little studied, despite the wide range of reconstructed CO2 values around this period. Here we investigate their effects on the SASM using the fully coupled Ocean–Atmosphere Global Climate Model, CESM1.2, through a series of 12 sensitivity experiments. Our simulations show that the IP uplift plays a dominant role in the intensification of the SASM, mainly in the region around northwestern India. The effect of the HM uplift is confined to the range of the HM and its vicinity, producing orographic precipitation change. The topography forcing overall out-competes CO2 variation in driving the intensification of the SASM. In the case of extremely strong CO2 variation, the effects of these two factors are comparable in the core SASM region, while in the western region, the topographic forcing is still the dominant driver. We propose a thermodynamical process linking the uplift of the IP and the enhanced SASM through the release of latent heat. When compared with reconstructions, the simulated response of SASM to the IP uplift is in good agreement with observed precipitation and wind field, while the effects of the HM uplift and CO2 variation are inadequate to interpret the proxies.

The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period in which the atmospheric CO2 concentration was approximately equal to the concentration we measure today (ca. 400 ppm). Sea surface temperature (SST) proxies indicate above-average warming over the North Atlantic in the mid-Pliocene with respect to the pre-industrial period, which may be linked to an intensified Atlantic Meridional Overturning Circulation (AMOC). Earlier results from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2) show that the ensemble simulates a stronger AMOC in the mid-Pliocene than in the pre-industrial. However, no consistent relationship between the stronger mid-Pliocene AMOC and either the Atlantic northward ocean heat transport (OHT) or average North Atlantic SSTs has been found. In this study, we look further into the drivers and consequences of a stronger AMOC in mid-Pliocene compared to pre-industrial simulations in PlioMIP2. We find that all model simulations with a closed Bering Strait and Canadian Archipelago show reduced freshwater transport from the Arctic Ocean into the North Atlantic. This contributes to an increase in salinity in the subpolar North Atlantic and Labrador Sea that can be linked to the stronger AMOC in the mid-Pliocene. To investigate the dynamics behind the ensemble's variable response of the total Atlantic OHT to the stronger AMOC, we separate the Atlantic OHT into two components associated with either the overturning circulation or the wind-driven gyre circulation. While the ensemble mean of the overturning component is increased significantly in magnitude in the mid-Pliocene, it is partly compensated by a reduction in the gyre component in the northern subtropical gyre region. This indicates that the lack of relationship between the total OHT and AMOC is due to changes in OHT by the subtropical gyre. The overturning and gyre components should therefore be considered separately to gain a more complete understanding of the OHT response to a stronger mid-Pliocene AMOC. In addition, we show that the AMOC exerts a stronger influence on North Atlantic SSTs in the mid-Pliocene than in the pre-industrial, providing a possible explanation for the improved agreement of the PlioMIP2 ensemble mean SSTs with reconstructions in the North Atlantic.

The study of past climates has demonstrated the occurrence of Heinrich events during which major ice discharges occurred at the polar ice sheet, leading to significant additional sea level rise. Heinrich events strongly influenced the oceanic circulation and global climate. However, standard climate change scenarios (Representative Concentration Pathways or RCPs) do not consider such potential rapid ice sheet collapse; RCPs only consider the dynamic evolution of greenhouse gas emissions. We carried out water-hosing simulations using the Institute Pierre Simon Laplace global Climate Model (IPSL-CM5A) to simulate a rapid melting of the Greenland and Antarctic ice sheets, equivalent to +1 and +3 m additional sea level rise (SLR). Freshwater inputs were added to the standard RCP8.5 emission scenario over the 21st century. The contribution to the SLR from Greenland or from Antarctic ice sheets has differentiated impacts. The freshwater input in the Antarctic is diluted by the circumpolar current, and its global impact is moderate. Conversely, a rapid melting of the ice sheet in the North Atlantic slows down the Atlantic Meridional Overturning Circulation. This slowdown leads to changes in winds, inter-hemispheric temperature and pressure gradients, resulting in a southward shift of the tropical rain belt over the Atlantic and eastern Pacific region. The American and African monsoons are strongly affected and shift to the south. Changes in the North American monsoon occur later, while changes in the South American monsoon start earlier. The North African monsoon is drier during boreal summer, while the southern African monsoon intensifies during austral summer. Simulated changes were not significant for the Asian and Australian monsoons.

The mid-Pliocene warm period (3.264–3.025 Ma) is the most recent geological period during which atmospheric CO2 levels were similar to recent historical values (∼400 ppm). Several proxy reconstructions for the mid-Pliocene show highly reduced zonal sea surface temperature (SST) gradients in the tropical Pacific Ocean, indicating an El Niño-like mean state. However, past modelling studies do not show these highly reduced gradients. Efforts to understand mid-Pliocene climate dynamics have led to the Pliocene Model Intercomparison Project (PlioMIP). Results from the first phase (PlioMIP1) showed clear El Niño variability (albeit significantly reduced) and did not show the greatly reduced time-mean zonal SST gradient suggested by some of the proxies. In this work, we study El Niño–Southern Oscillation (ENSO) variability in the PlioMIP2 ensemble, which consists of additional global coupled climate models and updated boundary conditions compared to PlioMIP1. We quantify ENSO amplitude, period, spatial structure and “flavour”, as well as the tropical Pacific annual mean state in mid-Pliocene and pre-industrial simulations. Results show a reduced ENSO amplitude in the model-ensemble mean (−24 %) with respect to the pre-industrial, with 15 out of 17 individual models showing such a reduction. Furthermore, the spectral power of this variability considerably decreases in the 3–4-year band. The spatial structure of the dominant empirical orthogonal function shows no particular change in the patterns of tropical Pacific variability in the model-ensemble mean, compared to the pre-industrial. Although the time-mean zonal SST gradient in the equatorial Pacific decreases for 14 out of 17 models (0.2 ∘C reduction in the ensemble mean), there does not seem to be a correlation with the decrease in ENSO amplitude. The models showing the most “El Niño-like” mean state changes show a similar ENSO amplitude to that in the pre-industrial reference, while models showing more “La Niña-like” mean state changes generally show a large reduction in ENSO variability. The PlioMIP2 results show a reasonable agreement with both time-mean proxies indicating a reduced zonal SST gradient and reconstructions indicating a reduced, or similar, ENSO variability.

The mid-Pliocene (∼3 Ma) is one of the most recent warm periods with high CO2 concentrations in the atmosphere and resulting high temperatures, and it is often cited as an analog for near-term future climate change. Here, we apply a moisture budget analysis to investigate the response of the large-scale hydrological cycle at low latitudes within a 13-model ensemble from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The results show that increased atmospheric moisture content within the mid-Pliocene ensemble (due to the thermodynamic effect) results in wetter conditions over the deep tropics, i.e., the Pacific intertropical convergence zone (ITCZ) and the Maritime Continent, and drier conditions over the subtropics. Note that the dynamic effect plays a more important role than the thermodynamic effect in regional precipitation minus evaporation (PmE) changes (i.e., northward ITCZ shift and wetter northern Indian Ocean). The thermodynamic effect is offset to some extent by a dynamic effect involving a northward shift of the Hadley circulation that dries the deep tropics and moistens the subtropics in the Northern Hemisphere (i.e., the subtropical Pacific). From the perspective of Earth's energy budget, the enhanced southward cross-equatorial atmospheric transport (0.22 PW), induced by the hemispheric asymmetries of the atmospheric energy, favors an approximately 1∘ northward shift of the ITCZ. The shift of the ITCZ reorganizes atmospheric circulation, favoring a northward shift of the Hadley circulation. In addition, the Walker circulation consistently shifts westward within PlioMIP2 models, leading to wetter conditions over the northern Indian Ocean. The PlioMIP2 ensemble highlights that an imbalance of interhemispheric atmospheric energy during the mid-Pliocene could have led to changes in the dynamic effect, offsetting the thermodynamic effect and, hence, altering mid-Pliocene hydroclimate.

The mid-Pliocene warm period (mPWP; ∼3.2 million years ago) is seen as the most recent time period characterized by a warm climate state, with similar to modern geography and ∼400 ppmv atmospheric CO2 concentration, and is therefore often considered an interesting analogue for near-future climate projections. Paleoenvironmental reconstructions indicate higher surface temperatures, decreasing tropical deserts, and a more humid climate in West Africa characterized by a strengthened West African Monsoon (WAM). Using model results from the second phase of the Pliocene Modelling Intercomparison Project (PlioMIP2) ensemble, we analyse changes of the WAM rainfall during the mPWP by comparing them with the control simulations for the pre-industrial period. The ensemble shows a robust increase in the summer rainfall over West Africa and the Sahara region, with an average increase of 2.5 mm/d, contrasted by a rainfall decrease over the equatorial Atlantic. An anomalous warming of the Sahara and deepening of the Saharan Heat Low, seen in >90 % of the models, leads to a strengthening of the WAM and an increased monsoonal flow into the continent. A similar warming of the Sahara is seen in future projections using both phase 3 and 5 of the Coupled Model Intercomparison Project (CMIP3 and CMIP5). Though previous studies of future projections indicate a west–east drying–wetting contrast over the Sahel, PlioMIP2 simulations indicate a uniform rainfall increase in that region in warm climates characterized by increasing greenhouse gas forcing. We note that this effect will further depend on the long-term response of the vegetation to the CO2 forcing.

In the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2), coupled climate models have been used to simulate an interglacial climate during the mid-Piacenzian warm period (mPWP; 3.264 to 3.025 Ma). Here, we compare the Atlantic Meridional Overturning Circulation (AMOC), poleward ocean heat transport and sea surface warming in the Atlantic simulated with these models. In PlioMIP2, all models simulate an intensified mid-Pliocene AMOC. However, there is no consistent response in the simulated Atlantic ocean heat transport nor in the depth of the Atlantic overturning cell. The models show a large spread in the simulated AMOC maximum, the Atlantic ocean heat transport and the surface warming in the North Atlantic. Although a few models simulate a surface warming of ∼ 8–12 ∘C in the North Atlantic, similar to the reconstruction from Pliocene Research, Interpretation and Synoptic Mapping (PRISM) version 4, most models appear to underestimate this warming. The large model spread and model–data discrepancies in the PlioMIP2 ensemble do not support the hypothesis that an intensification of the AMOC, together with an increase in northward ocean heat transport, is the dominant mechanism for the mid-Pliocene warm climate over the North Atlantic.

Palaeoclimate simulations improve our understanding of the climate, inform us about the performance of climate models in a different climate scenario, and help to identify robust features of the climate system. Here, we analyse Arctic warming in an ensemble of 16 simulations of the mid-Pliocene Warm Period (mPWP), derived from the Pliocene Model Intercomparison Project Phase 2 (PlioMIP2). The PlioMIP2 ensemble simulates Arctic (60–90∘ N) annual mean surface air temperature (SAT) increases of 3.7 to 11.6 ∘C compared to the pre-industrial period, with a multi-model mean (MMM) increase of 7.2 ∘C. The Arctic warming amplification ratio relative to global SAT anomalies in the ensemble ranges from 1.8 to 3.1 (MMM is 2.3). Sea ice extent anomalies range from −3.0 to -10.4×106 km2, with a MMM anomaly of -5.6×106 km2, which constitutes a decrease of 53 % compared to the pre-industrial period. The majority (11 out of 16) of models simulate summer sea-ice-free conditions (≤1×106 km2) in their mPWP simulation. The ensemble tends to underestimate SAT in the Arctic when compared to available reconstructions, although the degree of underestimation varies strongly between the simulations. The simulations with the highest Arctic SAT anomalies tend to match the proxy dataset in its current form better. The ensemble shows some agreement with reconstructions of sea ice, particularly with regard to seasonal sea ice. Large uncertainties limit the confidence that can be placed in the findings and the compatibility of the different proxy datasets. We show that while reducing uncertainties in the reconstructions could decrease the SAT data–model discord substantially, further improvements are likely to be found in enhanced boundary conditions or model physics. Lastly, we compare the Arctic warming in the mPWP to projections of future Arctic warming and find that the PlioMIP2 ensemble simulates greater Arctic amplification than CMIP5 future climate simulations and an increase instead of a decrease in Atlantic Meridional Overturning Circulation (AMOC) strength compared to pre-industrial period. The results highlight the importance of slow feedbacks in equilibrium climate simulations, and that caution must be taken when using simulations of the mPWP as an analogue for future climate change.

The Pliocene epoch has great potential to improve our understanding of the long-term climatic and environmental consequences of an atmospheric CO2 concentration near ∼400 parts per million by volume. Here we present the large-scale features of Pliocene climate as simulated by a new ensemble of climate models of varying complexity and spatial resolution based on new reconstructions of boundary conditions (the Pliocene Model Intercomparison Project Phase 2; PlioMIP2). As a global annual average, modelled surface air temperatures increase by between 1.7 and 5.2 ∘C relative to the pre-industrial era with a multi-model mean value of 3.2 ∘C. Annual mean total precipitation rates increase by 7 % (range: 2 %–13 %). On average, surface air temperature (SAT) increases by 4.3 ∘C over land and 2.8 ∘C over the oceans. There is a clear pattern of polar amplification with warming polewards of 60∘ N and 60∘ S exceeding the global mean warming by a factor of 2.3. In the Atlantic and Pacific oceans, meridional temperature gradients are reduced, while tropical zonal gradients remain largely unchanged. There is a statistically significant relationship between a model's climate response associated with a doubling in CO2 (equilibrium climate sensitivity; ECS) and its simulated Pliocene surface temperature response. The mean ensemble Earth system response to a doubling of CO2 (including ice sheet feedbacks) is 67 % greater than ECS; this is larger than the increase of 47 % obtained from the PlioMIP1 ensemble. Proxy-derived estimates of Pliocene sea surface temperatures are used to assess model estimates of ECS and give an ECS range of 2.6–4.8 ∘C. This result is in general accord with the ECS range presented by previous Intergovernmental Panel on Climate Change (IPCC) Assessment Reports.

Recently, major progress has been made in the simulation of the ocean dynamics of the Mediterranean using atmospheric and oceanic models with high spatial resolution. High resolution is essential to accurately capture the synoptic variability required to initiate intermediate- and deep-water formation, the engine of the Mediterranean thermohaline circulation (MTC). In paleoclimate studies, one major problem with the simulation of regional climate changes is that boundary conditions are not available from observations or data reconstruction to drive high-resolution regional models. One consistent way to advance paleoclimate modelling is to use a comprehensive global-to-regional approach. However, this approach needs long-term integration to reach equilibrium (hundreds of years), implying enormous computational resources. To tackle this issue, a sequential architecture of a global–regional modelling platform has been developed for the first time and is described in detail in this paper. First of all, the platform is validated for the historical period. It is then used to investigate the climate and in particular, the oceanic circulation, during the Early Holocene. This period was characterised by a large reorganisation of the MTC that strongly affected oxygen supply to the intermediate and deep waters, which ultimately led to an anoxic crisis (called sapropel). Beyond the case study shown here, this platform may be applied to a large number of paleoclimate contexts from the Quaternary to the Pliocene, as long as regional tectonics remain mostly unchanged. For example, the climate responses of the Mediterranean basin during the last interglacial period (LIG), the Last Glacial Maximum (LGM) and the Late Pliocene all present interesting scientific challenges which may be addressed using this numerical platform.

The mid-Piacenzian warm period (3.264 to 3.025 Ma) is the most recent geological period with present-like atmospheric pCO2 and is thus expected to have exhibited a warm climate similar to or warmer than the present day. On the basis of understanding that has been gathered on the climate variability of this interval, a specific interglacial (Marine Isotope Stage KM5c, MIS KM5c; 3.205 Ma) has been selected for the Pliocene Model Intercomparison Project phase 2 (PlioMIP 2). We carried out a series of experiments according to the design of PlioMIP2 with two versions of the Institut Pierre Simon Laplace (IPSL) atmosphere–ocean coupled general circulation model (AOGCM): IPSL-CM5A and IPSL-CM5A2. Compared to the PlioMIP 1 experiment, run with IPSL-CM5A, our results show that the simulated MIS KM5c climate presents enhanced warming in mid- to high latitudes, especially over oceanic regions. This warming can be largely attributed to the enhanced Atlantic Meridional Overturning Circulation caused by the high-latitude seaway changes. The sensitivity experiments, conducted with IPSL-CM5A2, show that besides the increased pCO2, both modified orography and reduced ice sheets contribute substantially to mid- to high latitude warming in MIS KM5c. When considering the pCO2 uncertainties (+/-50 ppmv) during the Pliocene, the response of the modeled mean annual surface air temperature to changes to pCO2 (+/-50 ppmv) is not symmetric, which is likely due to the nonlinear response of the cryosphere (snow cover and sea ice extent). By analyzing the Greenland Ice Sheet surface mass balance, we also demonstrate its vulnerability under both MIS KM5c and modern warm climate.

The mid-Holocene period (MH) has long been an ideal target for the validation of general circulation model (GCM) results against reconstructions gathered in global datasets. These studies aim to test GCM sensitivity, mainly to seasonal changes induced by the orbital parameters (longitude of the perihelion). Despite widespread agreement between model results and data on the MH climate, some important differences still exist. There is no consensus on the continental size (the area of the temperature anomaly) of the MH thermal climate response, which makes regional quantitative reconstruction critical to obtain a comprehensive understanding of the MH climate patterns. Here, we compare the annual and seasonal outputs from the most recent Paleoclimate Modelling Intercomparison Project Phase 3 (PMIP3) models with an updated synthesis of climate reconstruction over China, including, for the first time, a seasonal cycle of temperature and precipitation. Our results indicate that the main discrepancies between model and data for the MH climate are the annual and winter mean temperature. A warmer-than-present climate condition is derived from pollen data for both annual mean temperature (∼0.7 K on average) and winter mean temperature (∼1 K on average), while most of the models provide both colder-than-present annual and winter mean temperature and a relatively warmer summer, showing a linear response driven by the seasonal forcing. By conducting simulations in BIOME4 and CESM, we show that surface processes are the key factors creating the uncertainties between models and data. These results pinpoint the crucial importance of including the non-linear responses of the surface water and energy balance to vegetation changes.

The extent to which climate conditions influenced the spatial distribution of hominin populations in the past is highly debated. General circulation models (GCMs) and archaeological data have been used to address this issue. Most GCMs are not currently capable of simulating past surface climate conditions with sufficiently detailed spatial resolution to distinguish areas of potential hominin habitat, however. In this paper, we propose a statistical downscaling method (SDM) for increasing the resolution of climate model outputs in a computationally efficient way. Our method uses a generalised additive model (GAM), calibrated over present-day climatology data, to statistically downscale temperature and precipitation time series from the outputs of a GCM simulating the climate of the Last Glacial Maximum (19 000–23 000 BP) over western Europe. Once the SDM is calibrated, we first interpolate the coarse-scale GCM outputs to the final resolution and then use the GAM to compute surface air temperature and precipitation levels using these interpolated GCM outputs and fine-resolution geographical variables such as topography and distance from an ocean. The GAM acts as a transfer function, capturing non-linear relationships between variables at different spatial scales and correcting for the GCM biases. We tested three different techniques for the first interpolation of GCM output: bilinear, bicubic and kriging. The resulting SDMs were evaluated by comparing downscaled temperature and precipitation at local sites with paleoclimate reconstructions based on paleoclimate archives (archaeozoological and palynological data) and the impact of the interpolation technique on patterns of variability was explored. The SDM based on kriging interpolation, providing the best accuracy, was then validated on present-day data outside of the calibration period. Our results show that the downscaled temperature and precipitation values are in good agreement with paleoclimate reconstructions at local sites, and that our method for producing fine-grained paleoclimate simulations is therefore suitable for conducting paleo-anthropological research. It is nonetheless important to calibrate the GAM on a range of data encompassing the data to be downscaled. Otherwise, the SDM is likely to overcorrect the coarse-grain data. In addition, the bilinear and bicubic interpolation techniques were shown to distort either the temporal variability or the values of the response variables, while the kriging method offered the best compromise. Since climate variability is an aspect of the environment to which human populations may have responded in the past, the choice of interpolation technique is therefore an important consideration.

The role of the Tibetan Plateau (TP) in maintaining the large-scale overturning circulation in the Atlantic and Pacific is investigated using a coupled atmosphere–ocean model. For the present day with a realistic topography, model simulation shows a strong Atlantic meridional overturning circulation (AMOC) but a near absence of the Pacific meridional overturning circulation (PMOC), which are in good agreement with the present observations. In contrast, the simulation without the TP depicts a collapsed AMOC and a strong PMOC that dominates deep-water formation. The switch in deep-water formation between the two basins results from changes in the large-scale atmospheric circulation and atmosphere–ocean feedback over the Atlantic and Pacific. The intensified westerly winds and increased freshwater flux over the North Atlantic cause an initial slowdown of the AMOC, while the weakened East Asian monsoon circulation and associated decreased freshwater flux over the North Pacific give rise to the initial intensification of the PMOC. The further decreased heat flux and the associated increase in sea-ice fraction promote the final AMOC collapse over the Atlantic, while the further increased heat flux leads to the final PMOC establishment over the Pacific. Although the simulations were performed in a cold world, it still importantly implicates that the uplift of the TP alone could have been a potential driver for the reorganization of PMOC–AMOC between the late Eocene and early Oligocene.

During an interval of the Late Pliocene, referred to here as the mid-Pliocene Warm Period (mPWP; 3.264 to 3.025 million years ago), global mean temperature was similar to that predicted for the end of this century, and atmospheric carbon dioxide concentrations were higher than pre-industrial levels. Sea level was also higher than today, implying a significant reduction in the extent of the ice sheets. Thus, the mPWP provides a natural laboratory in which to investigate the long-term response of the Earth's ice sheets and sea level in a warmer-than-present-day world. At present, our understanding of the Greenland ice sheet during the mPWP is generally based upon predictions using single climate and ice sheet models. Therefore, it is essential that the model dependency of these results is assessed. The Pliocene Model Intercomparison Project (PlioMIP) has brought together nine international modelling groups to simulate the warm climate of the Pliocene. Here we use the climatological fields derived from the results of the 15 PlioMIP climate models to force an offline ice sheet model. We show that mPWP ice sheet reconstructions are highly dependent upon the forcing climatology used, with Greenland reconstructions ranging from an ice-free state to a near-modern ice sheet. An analysis of the surface albedo variability between the climate models over Greenland offers insights into the drivers of inter-model differences. As we demonstrate that the climate model dependency of our results is high, we highlight the necessity of data-based constraints of ice extent in developing our understanding of the mPWP Greenland ice sheet.

The Pliocene Model Intercomparison Project (PlioMIP) is the first coordinated climate model comparison for a warmer palaeoclimate with atmospheric CO2 significantly higher than pre-industrial concentrations. The simulations of the mid-Pliocene warm period show global warming of between 1.8 and 3.6 °C above pre-industrial surface air temperatures, with significant polar amplification. Here we perform energy balance calculations on all eight of the coupled ocean–atmosphere simulations within PlioMIP Experiment 2 to evaluate the causes of the increased temperatures and differences between the models. In the tropics simulated warming is dominated by greenhouse gas increases, with the cloud component of planetary albedo enhancing the warming in most of the models, but by widely varying amounts. The responses to mid-Pliocene climate forcing in the Northern Hemisphere midlatitudes are substantially different between the climate models, with the only consistent response being a warming due to increased greenhouse gases. In the high latitudes all the energy balance components become important, but the dominant warming influence comes from the clear sky albedo, only partially offset by the increases in the cooling impact of cloud albedo. This demonstrates the importance of specified ice sheet and high latitude vegetation boundary conditions and simulated sea ice and snow albedo feedbacks. The largest components in the overall uncertainty are associated with clouds in the tropics and polar clear sky albedo, particularly in sea ice regions. These simulations show that albedo feedbacks, particularly those of sea ice and ice sheets, provide the most significant enhancements to high latitude warming in the Pliocene.

The Middle Miocene Climatic Transition (MMCT, approximately 14 Ma) is a key period in Cenozoic cooling and cryospheric expansion. Despite being well documented in isotopic record, the causes of the MMCT are still a matter of debate. Among various hypotheses, some authors suggested that it was due the final closure of the eastern Tethys seaway and subsequent oceanic circulation reorganisation. The aim of the present study is to quantify the impact of varying Tethys seaway depths on middle Miocene ocean and climate, in order to better understand its role in the MMCT. We present four sensitivity experiments with a fully coupled ocean-atmosphere general circulation model. Our results indicate the presence of a warm and salty water source in the northern Indian Ocean when the eastern Tethys is deep open (4000 or 1000 m), which corresponds to the Tethyan Indian Saline Water (TISW) described on the basis of isotopic studies. This water source is absent in the experiments with shallow (250 m) and closed Tethys seaway, inducing strong changes in the latitudinal density gradient and ultimately the reinforcement of the Antarctic Circumpolar Current (ACC). Moreover, when the Tethys seaway is shallow or closed, there is a westward water flow in the Gibraltar Strait that strengthens the Atlantic Meridional Overturning Circulation (AMOC) compared to the experiments with deep-open Tethys seaway. Our results therefore suggest that the shoaling and final closure of the eastern Tethys seaway played a major role in the oceanic circulation reorganisation during the middle Miocene. The results presented here provide new constraints on the timing of the Tethys seaway closure and particularly indicate that, prior to 14 Ma, a deep-open Tethys seaway should have allowed the formation of TISW. Moreover, whereas the final closure of this seaway likely played a major role in the reorganisation of oceanic circulation, we suggest that it was not the main driver of the global cooling and Antarctica ice-sheet expansion during the MMCT. Here we propose that the initiation of the MMCT was caused by an atmospheric pCO2 drawdown and that the oceanic changes due to the Tethys seaway closure amplified the response of global climate and East Antarctic Ice Sheet.

Based on simulations with 15 climate models in the Pliocene Model Intercomparison Project (PlioMIP), the regional climate of East Asia (focusing on China) during the mid-Pliocene is investigated in this study. Compared to the pre-industrial, the multi-model ensemble mean (MMM) of all models shows the East Asian summer winds (EASWs) largely strengthen in monsoon China, and the East Asian winter winds (EAWWs) strengthen in south monsoon China but slightly weaken in north monsoon China in the mid-Pliocene. The MMM of all models also illustrates a warmer and wetter mid-Pliocene climate in China. The simulated weakened mid-Pliocene EAWWs in north monsoon China and intensified EASWs in monsoon China agree well with geological reconstructions. However, there is a large model–model discrepancy in simulating mid-Pliocene EAWW, which should be further addressed in the future work of PlioMIP.

European loess sequences of the Marine Isotope Stage 3 (~60–25 kyr BP) show periods of strong dust accumulation alternating with episodes of reduced sedimentation, favoring soil development. In the western part of the loess belt centered around 50° N, these variations appear to have been related to the North Atlantic rapid climate changes: the Dansgaard–Oeschger (DO) and Heinrich (H) events. It has been recently suggested that the North Atlantic climate signal can be detected further east, in loess deposits from Stayky (50°05.65' N, 30°53.92' E), Ukraine. Here we use climate and dust emission modeling to investigate this data interpretation. We focus on the areas north and northeast of the Carpathians, where loess deposits can be found, and the corresponding main dust sources must have been located as well. The simulations were performed with the LMDZ atmospheric general circulation model and the ORCHIDEE land surface model. They represent a reference "Greenland stadial" state and two perturbations, seen as sensitivity tests with respect to changes in the North Atlantic surface conditions between 30° and 63° N: a "Greenland interstadial" and an "H event". The main source for the loess deposits in the studied area is identified as a dust deflation band, with two very active spots located west-northwest from our reference site. Emissions only occur between February and June. Differences from one deflation spot to another, and from one climate state to another, are explained by analyzing the relevant meteorological and surface variables. Over most of the source region, the annual emission fluxes in the "interstadial" experiment are 30 to 50% lower than the "stadial" values; they would only be about 20% lower if the inhibition of dust uplift by the vegetation were not taken into account. Assuming that lower emissions result in reduced dust deposition leads us to the conclusion that the loess–paleosol stratigraphic succession in the Stayky area reflects indeed North Atlantic millennial variations. In the main deflation areas of Western Europe, the vegetation effect alone determined most of the (~50% on average) stadial–interstadial flux differences. Even if its impact in Eastern Europe is less pronounced, this effect remains a key factor in modulating aeolian emissions at the millennial timescale. Conditions favorable to initiating particularly strong dust storms within a few hundred kilometers upwind from our reference site, simulated in the month of April of the H event experiment, support the correlation of H events with peaks in grain size index in some very detailed loess profiles, indicating increased coarse sedimentation.

Given the growing evidence for megalakes in the geological record, assessing their impact on climate and vegetation is important for the validation of palaeoclimate simulations and therefore the accuracy of model–data comparison in lacustrine environments. Megalake Chad (MLC) occurrences are documented not only for the mid-Holocene but also for the Mio-Pliocene (Schuster et al., 2009). At this time, the surface covered by water would have reached up to ~350 000 km2 (Ghienne et al., 2002; Schuster et al., 2005; Leblanc et al., 2006), making it an important evaporation source, possibly modifying climate and vegetation in the Chad Basin. We investigated the impact of such a giant continental water area in two different climatic backgrounds within the Paleoclimate Model Intercomparison Project phase 3 (PMIP3): the late Pliocene (3.3 to 3 Ma, i.e. the mid-Piacenzian warm period) and the mid-Holocene (6 kyr BP). In all simulations including MLC, precipitation is drastically reduced above the lake surface because deep convection is inhibited by overlying colder air. Meanwhile, convective activity is enhanced around MLC because of the wind increase generated by the flat surface of the megalake, transporting colder and moister air towards the eastern shore of the lake. The effect of MLC on precipitation and temperature is not sufficient to widely impact vegetation patterns. Nevertheless, tropical savanna is present in the Chad Basin in all climatic configurations, even without MLC presence, showing that the climate itself is the driver of favourable environments for sustainable hominid habitats.

In the Pliocene Model Intercomparison Project (PlioMIP), eight state-of-the-art coupled climate models have simulated the mid-Pliocene warm period (mPWP, 3.264 to 3.025 Ma). Here, we compare the Atlantic Meridional Overturning Circulation (AMOC), northward ocean heat transport and ocean stratification simulated with these models. None of the models participating in PlioMIP simulates a strong mid-Pliocene AMOC as suggested by earlier proxy studies. Rather, there is no consistent increase in AMOC maximum among the PlioMIP models. The only consistent change in AMOC is a shoaling of the overturning cell in the Atlantic, and a reduced influence of North Atlantic Deep Water (NADW) at depth in the basin. Furthermore, the simulated mid-Pliocene Atlantic northward heat transport is similar to the pre-industrial. These simulations demonstrate that the reconstructed high-latitude mid-Pliocene warming can not be explained as a direct response to an intensification of AMOC and concomitant increase in northward ocean heat transport by the Atlantic.

The mid-Pliocene warm period (~ 3.3–3.0 Ma) is often considered as the last sustained warm period with close enough geographic configurations compared to the present one associated with atmospheric CO2 concentration (405 ± 50 ppm) higher than the modern level. For this reason, this period is often considered as a potential analogue for the future climate warming, with the important advantage that for mid-Pliocene many marine and continental data are available. To investigate this issue, we selected the RCP4.5 scenario, one of the current available future projections, to compare the pattern of tropical atmospheric response with the past warm mid-Pliocene climate. We use three Atmosphere-Ocean General Circulation Model (AOGCM) simulations (RCP4.5 scenario, mid-Pliocene and present-day simulation) carried out with the IPSL-CM5A model and investigate atmospheric tropical dynamics through Hadley and Walker cell responses to warmer conditions, considering that the analysis can provide some assessment of how these circulations will change in the future. Our results show that there is a damping of the Hadley cell intensity in the northern tropics and an increase in both subtropics. Moreover, northern and southern Hadley cells expand poleward. The response of the Hadley cells is stronger for the RCP4.5 scenario than for the mid-Pliocene, but in very good agreement with the fact that the atmospheric CO2 concentration is higher in the future scenario than in the mid-Pliocene (543 versus 405 ppm). Concerning the response of the Walker cell, we show that despite very large similarities, there are also some differences. Common features to both scenarios are: weakening of the ascending branch, leading to a suppression of the precipitation over the western tropical Pacific. The response of the Walker cell is stronger in the RCP4.5 scenario than in the mid-Pliocene but also depicts some major differences, as an eastward shift of its rising branch in the future scenario compared to the mid-Pliocene. In this paper, we explain the dynamics of the Hadley and Walker cells, and show that despite a minor discrepancy, the mid-Pliocene is certainly an interesting analogue for future climate changes in tropical areas.

Climate and environments of the mid-Pliocene warm period (3.264 to 3.025 Ma) have been extensively studied. Whilst numerical models have shed light on the nature of climate at the time, uncertainties in their predictions have not been systematically examined. The Pliocene Model Intercomparison Project quantifies uncertainties in model outputs through a coordinated multi-model and multi-model/data intercomparison. Whilst commonalities in model outputs for the Pliocene are clearly evident, we show substantial variation in the sensitivity of models to the implementation of Pliocene boundary conditions. Models appear able to reproduce many regional changes in temperature reconstructed from geological proxies. However, data/model comparison highlights that models potentially underestimate polar amplification. To assert this conclusion with greater confidence, limitations in the time-averaged proxy data currently available must be addressed. Furthermore, sensitivity tests exploring the known unknowns in modelling Pliocene climate specifically relevant to the high latitudes are essential (e.g. palaeogeography, gateways, orbital forcing and trace gasses). Estimates of longer-term sensitivity to CO2 (also known as Earth System Sensitivity; ESS), support previous work suggesting that ESS is greater than Climate Sensitivity (CS), and suggest that the ratio of ESS to CS is between 1 and 2, with a "best" estimate of 1.5.

The role of different sources and sinks of CH4 in changes in atmospheric methane ([CH4]) concentration during the last 100 000 yr is still not fully understood. In particular, the magnitude of the change in wetland CH4 emissions at the Last Glacial Maximum (LGM) relative to the pre-industrial period (PI), as well as during abrupt climatic warming or Dansgaard–Oeschger (D–O) events of the last glacial period, is largely unconstrained. In the present study, we aim to understand the uncertainties related to the parameterization of the wetland CH4 emission models relevant to these time periods by using two wetland models of different complexity (SDGVM and ORCHIDEE). These models have been forced by identical climate fields from low-resolution coupled atmosphere–ocean general circulation model (FAMOUS) simulations of these time periods. Both emission models simulate a large decrease in emissions during LGM in comparison to PI consistent with ice core observations and previous modelling studies. The global reduction is much larger in ORCHIDEE than in SDGVM (respectively −67 and −46%), and whilst the differences can be partially explained by different model sensitivities to temperature, the major reason for spatial differences between the models is the inclusion of freezing of soil water in ORCHIDEE and the resultant impact on methanogenesis substrate availability in boreal regions. Besides, a sensitivity test performed with ORCHIDEE in which the methanogenesis substrate sensitivity to the precipitations is modified to be more realistic gives a LGM reduction of −36%. The range of the global LGM decrease is still prone to uncertainty, and here we underline its sensitivity to different process parameterizations. Over the course of an idealized D–O warming, the magnitude of the change in wetland CH4 emissions simulated by the two models at global scale is very similar at around 15 Tg yr−1, but this is only around 25% of the ice-core measured changes in [CH4]. The two models do show regional differences in emission sensitivity to climate with much larger magnitudes of northern and southern tropical anomalies in ORCHIDEE. However, the simulated northern and southern tropical anomalies partially compensate each other in both models limiting the net flux change. Future work may need to consider the inclusion of more detailed wetland processes (e.g. linked to permafrost or tropical floodplains), other non-wetland CH4 sources or different patterns of D–O climate change in order to be able to reconcile emission estimates with the ice-core data for rapid CH4 events.

This paper describes the experimental design and model results of the climate simulations of the mid-Pliocene Warm Period (mPWP, ca. 3.3–3 Ma) using the Institut Pierre Simon Laplace model (IPSLCM5A), in the framework of the Pliocene Model Intercomparison Project (PlioMIP). We use the IPSL atmosphere ocean general circulation model (AOGCM), and its atmospheric component alone (AGCM), to simulate the climate of the mPWP. Boundary conditions such as sea surface temperatures (SSTs), topography, ice-sheet extent and vegetation are derived from the ones imposed by the Pliocene Model Intercomparison Project (PlioMIP), described in Haywood et al. (2010, 2011). We first describe the IPSL model main features, and then give a full description of the boundary conditions used for atmospheric model and coupled model experiments. The climatic outputs of the mPWP simulations are detailed and compared to the corresponding control simulations. The simulated warming relative to the control simulation is 1.94 °C in the atmospheric and 2.07 °C in the coupled model experiments. In both experiments, warming is larger at high latitudes. Mechanisms governing the simulated precipitation patterns are different in the coupled model than in the atmospheric model alone, because of the reduced gradients in imposed SSTs, which impacts the Hadley and Walker circulations. In addition, a sensitivity test to the change of land-sea mask in the atmospheric model, representing a sea-level change from present-day to 25 m higher during the mid-Pliocene, is described. We find that surface temperature differences can be large (several degrees Celsius) but are restricted to the areas that were changed from ocean to land or vice versa. In terms of precipitation, impact on polar regions is minor although the change in land-sea mask is significant in these areas.

Heinrich events, identified as enhanced ice-rafted detritus (IRD) in North Atlantic deep sea sediments (Heinrich, 1988; Hemming, 2004) have classically been attributed to Laurentide ice-sheet (LIS) instabilities (MacAyeal, 1993; Calov et al., 2002; Hulbe et al., 2004) and assumed to lead to important disruptions of the Atlantic meridional overturning circulation (AMOC) and North Atlantic deep water (NADW) formation. However, recent paleoclimate data have revealed that most of these events probably occurred after the AMOC had already slowed down or/and NADW largely collapsed, within about a thousand years (Hall et al., 2006; Hemming, 2004; Jonkers et al., 2010; Roche et al., 2004), implying that the initial AMOC reduction could not have been caused by the Heinrich events themselves. Here we propose an alternative driving mechanism, specifically for Heinrich event 1 (H1; 18 to 15 ka BP), by which North Atlantic ocean circulation changes are found to have strong impacts on LIS dynamics. By combining simulations with a coupled climate model and a three-dimensional ice sheet model, our study illustrates how reduced NADW and AMOC weakening lead to a subsurface warming in the Nordic and Labrador Seas resulting in rapid melting of the Hudson Strait and Labrador ice shelves. Lack of buttressing by the ice shelves implies a substantial ice-stream acceleration, enhanced ice-discharge and sea level rise, with peak values 500–1500 yr after the initial AMOC reduction. Our scenario modifies the previous paradigm of H1 by solving the paradox of its occurrence during a cold surface period, and highlights the importance of taking into account the effects of oceanic circulation on ice-sheets dynamics in order to elucidate the triggering mechanism of Heinrich events.

Here we perform a detailed comparison between climate model results and climate reconstructions in western Europe and the Mediterranean area for the mid-Piacenzian warm interval (ca 3 Myr ago) of the Late Pliocene epoch. This region is particularly well suited for such a comparison as several quantitative climate estimates from local pollen records are available. They show evidence for temperatures significantly warmer than today over the whole area, mean annual precipitation higher in northwestern Europe and equivalent to modern values in its southwestern part. To improve our comparison, we have performed high resolution simulations of the mid-Piacenzian climate using the LMDz atmospheric general circulation model (AGCM) with a stretched grid which allows a finer resolution over Europe. In a first step, we applied the PRISM2 (Pliocene Research, Interpretation, and Synoptic Mapping) boundary conditions except that we used modern terrestrial vegetation. Second, we simulated the vegetation for this period by forcing the ORCHIDEE (Organizing Carbon and Hydrology in Dynamic Ecosystems) dynamic global vegetation model (DGVM) with the climatic outputs from the AGCM. We then supplied this simulated terrestrial vegetation cover as an additional boundary condition in a second AGCM run. This gives us the opportunity to investigate the model's sensitivity to the simulated vegetation changes in a global warming context. Model results and data show a great consistency for mean annual temperatures, indicating increases by up to 4°C in the study area, and some disparities, in particular in the northern Mediterranean sector, as regards winter and summer temperatures. Similar continental mean annual precipitation and moisture patterns are predicted by the model, which broadly underestimates the wetter conditions indicated by the data in northwestern Europe. The biogeophysical effects due to the changes in vegetation simulated by ORCHIDEE are weak, both in terms of the hydrological cycle and of the temperatures, at the regional scale of the European and Mediterranean mid-latitudes. In particular, they do not contribute to improve the model-data comparison. Their main influence concerns seasonal temperatures, with a decrease of the temperatures of the warmest month, and an overall reduction of the intensity of the continental hydrological cycle.

A 2.5-dimensional climate model of intermediate complexity, CLIMBER-2, fully coupled with the GREMLINS 3-D thermo-mechanical ice sheet model is used to simulate the evolution of major Northern Hemisphere ice sheets during the last glacial-interglacial cycle and to investigate the ice sheets responses to both insolation and atmospheric CO2 concentration. This model reproduces the main phases of advance and retreat of Northern Hemisphere ice sheets during the last glacial cycle, although the amplitude of these variations is less pronounced than those based on sea level reconstructions. At the last glacial maximum, the simulated ice volume is 52.5×1015 m3 and the spatial distribution of both the American and Eurasian ice complexes is in reasonable agreement with observations, with the exception of the marine parts of these former ice sheets. A set of sensitivity studies has also been performed to assess the sensitivity of the Northern Hemisphere ice sheets to both insolation and atmospheric CO2. Our results suggest that the decrease of summer insolation is the main factor responsible for the early build up of the North American ice sheet around 120 kyr BP, in agreement with benthic foraminifera δ18O signals. In contrast, low insolation and low atmospheric CO2 concentration are both necessary to trigger a long-lasting glaciation over Eurasia.

The Snowball Earth theory initially proposed by Kirschvink (1992) to explain the Neoproterozoic glacial episodes, suggested that the Earth was fully ice-covered at 720 Ma (Sturtian episode) and 640 Ma (Marinoan episode). This succession of extreme climatic crises induced environmental perturbations which are considered as a strong selective pressure on the evolution of life (Hoffman et al., 1998). Using a numerical model of carbon-alkalinity global cycles, we quantify environmental stresses caused by a global glaciation. According to our results, we suggest that during global glaciations, the ocean becomes acidic (pH~6), and undersaturated with respect to carbonate minerals. Moreover the quick transition from ice-house to greenhouse conditions implies an abrupt and large shift of the oceanic surface temperature which causes an extended hypoxia. The intense continental weathering, in the aftermath of the glaciation, deeply affects the seawater composition inducing rapid changes in terms of pH and alkalinity. We also propose a new timing for post glacial perturbations and for the cap carbonates deposition, ~2 Myr instead of 200 kyr as suggested in a previous modelling study. In terms of Precambrian life sustainability, seawater pH modifications appear drastic all along the glaciation, but we suggest that the buffering action of the oceanic crust dissolution avoids a total collapse of biological productivity. But short-lived and large post-glacial perturbations are more critical and may have played the role of an environmental filter proposed in the classic snowball Earth theory. Although the link between environmental changes and life sustainability cannot be modelled accurately, we suggest that only a permissive life (Knoll, 2003) may explain the relative continuity in microfossils diversity observed before, during and after Neoproterozoic glaciation events.

A set of coupled ocean-atmosphere simulations using state of the art climate models is now available for the Last Glacial Maximum and the Mid-Holocene through the second phase of the Paleoclimate Modeling Intercomparison Project (PMIP2). This study presents the large-scale features of the simulated climates and compares the new model results to those of the atmospheric models from the first phase of the PMIP, for which sea surface temperature was prescribed or computed using simple slab ocean formulations. We consider the large-scale features of the climate change, pointing out some of the major differences between the different sets of experiments. We show in particular that systematic differences between PMIP1 and PMIP2 simulations are due to the interactive ocean, such as the amplification of the African monsoon at the Mid-Holocene or the change in precipitation in mid-latitudes at the LGM. Also the PMIP2 simulations are in general in better agreement with data than PMIP1 simulations.

The Last Glacial Maximum has been one of the first foci of the Paleoclimate Modelling Intercomparison Project (PMIP). During its first phase, the results of 17 atmosphere general circulation models were compared to paleoclimate reconstructions. One of the largest discrepancies in the simulations was the systematic underestimation, by at least 10°C, of the winter cooling over Europe and the Mediterranean region observed in the pollen-based reconstructions. In this paper, we investigate the progress achieved to reduce this inconsistency through a large modelling effort and improved temperature reconstructions. We show that increased model spatial resolution does not significantly increase the simulated LGM winter cooling. Further, neither the inclusion of a vegetation cover compatible with the LGM climate, nor the interactions with the oceans simulated by the atmosphere-ocean general circulation models run in the second phase of PMIP result in a better agreement between models and data. Accounting for changes in interannual variability in the interpretation of the pollen data does not result in a reduction of the reconstructed cooling. The largest recent improvement in the model-data comparison has instead arisen from a new climate reconstruction based on inverse vegetation modelling, which explicitly accounts for the CO2 decrease at LGM and which substantially reduces the LGM winter cooling reconstructed from pollen assemblages. As a result, the simulated and observed LGM winter cooling over Western Europe and the Mediterranean area are now in much better agreement.

A set of coupled ocean-atmosphere(-vegetation) simulations using state of the art climate models is now available for the Last Glacial Maximum (LGM) and the Mid-Holocene (MH) through the second phase of the Paleoclimate Modeling Intercomparison Project (PMIP2). Here we quantify the latitudinal shift of the location of the Intertropical Convergence Zone (ITCZ) in the tropical regions during boreal summer and the change in precipitation in the northern part of the ITCZ. For both periods the shift is more pronounced over the continents and East Asia. The maritime continent is the region where the largest spread is found between models. We also clearly establish that the larger the increase in the meridional temperature gradient in the tropical Atlantic during summer at the MH, the larger the change in precipitation over West Africa. The vegetation feedback is however not as large as found in previous studies, probably due to model differences in the control simulation. Finally, we show that the feedback from snow and sea-ice at mid and high latitudes contributes for half of the cooling in the Northern Hemisphere for the LGM, with the remaining being achieved by the reduced CO2 and water vapour in the atmosphere. For the MH the snow and albedo feedbacks strengthen the spring cooling and enhance the boreal summer warming, whereas water vapour reinforces the late summer warming. These feedbacks are modest in the Southern Hemisphere. For the LGM most of the surface cooling is due to CO2 and water vapour.

Genome-wide association study (GWAS) is a powerful tool for identifying marker-trait associations that can accelerate breeding progress. Yet, its power is typically constrained in newly established breeding programs where large phenotypic and genotypic datasets have not yet accumulated. Expanding the dataset by inclusion of data from well-established breeding programs with many years of phenotyping and genotyping can potentially address this problem. In this study we performed single- and multi-population GWAS on heading date and lodging in four barley breeding populations with varying combinations of row-type and growth habit. Focusing on a recently established 6-rowed winter (6RW) barley population, single-population GWAS hardly resulted in any significant associations. Nevertheless, the combination of the 6RW target population with other populations in multi-population GWAS detected four and five robust candidate quantitative trait loci for heading date and lodging, respectively. Of these, three remained undetected when analysing the combined populations individually. Further, multi-population GWAS detected markers capturing a larger proportion of genetic variance in 6RW. For multi-population GWAS, we compared the findings of a univariate model (MP1) with a multivariate model (MP2). While both models surpassed single-population GWAS in power, MP2 offered a significant advantage by having more realistic assumptions while pointing towards robust marker-trait associations across populations. Additionally, comparisons of GWAS findings for MP2 and single-population GWAS allowed identification of population-specific loci. In conclusion, our study presents a promising approach to kick-start genomics-based breeding in newly established breeding populations., Competing Interests: Competing interests: Nordic Seed A/S own and market the studied barley breeding programs. Ethics approval: All data presented in this manuscript required no ethical approval., (© 2024. The Author(s).)

The weakening and poleward expansion of the Hadley circulation (HC) are considered robust responses of atmospheric meridional circulation to anthropogenic warming. Climate impacts arising from these changes enhance drought conditions and reduce food production in the affected regions. Therefore, understanding the mechanisms of HC changes is critical to anticipating the resultant climate risks. First, we demonstrate that robust future HC changes in boreal winter, and the uncertainty in their future projections, are both largely related to sea surface temperature (SST) warming. Next, we investigate the impact of anthropogenic regional ocean warming on the future HC. Accordingly, we conduct a large ensemble of individual ocean basin perturbation experiments at 1.5°C, 2°C, and 3°C warming thresholds (as in the Paris Agreement). These experiments highlight (i) the leading role of tropical Indian Ocean warming in HC changes and (ii) inter-model differences in tropical Pacific warming as a source of uncertainty in HC projections., (© The Author(s) 2024. Published by Oxford University Press on behalf of China Science Publishing & Media Ltd.)

Rift Valley Fever (RVF) is a zoonosis transmitted by Aedes and Culex mosquitoes, and is considered a priority pathogen by the WHO. RVF epidemics mostly occur in Africa and can decimate livestock herds, causing significant economic losses and posing health risks for humans. RVF transmission is associated with the occurrence of El Niño events that cause floods in eastern Africa and favour the emergence of mosquitoes in wetlands. Different risk models have been developed to forecast RVF transmission risk but very few studies have validated models at pan-African scale. This study aims to validate the skill of the Liverpool Rift Valley Fever model (LRVF) in reproducing RVF epidemics over Africa and to explore the relationship between simulated climatic suitability for RVF transmission and large-scale climate modes of variability such as the El Niño Southern Oscillation (ENSO) and the Dipole Mode Index (DMI). Our results show that the LRVF model correctly simulates RVF transmission hotspots and reproduces large epidemics that affected African countries. LRVF was able to correctly reproduce major RVF epidemics in Somalia, Kenya, Zambia and to a lesser extent for Mauritania and Senegal. The positive phases of ENSO and DMI are associated with an increased risk of RVF over the Horn of Africa, with important time lags. Following research activities should focus on the development of predictive modelling systems at different time scales., (© 2024. The Author(s).)

Pleiotropy-when a single gene controls two or more seemingly unrelated traits-has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56-32.3% of intervals show some degree of pleiotropy. We then assess the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide and large effect variants, leaving the prevalence of detectable pleiotropy relatively low., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

Introduction: Cassava (Manihot esculenta) is an annual root crop which provides the major source of calories for over half a billion people around the world. Since its domestication ~10,000 years ago, cassava has been largely clonally propagated through stem cuttings. Minimal sexual recombination has led to an accumulation of deleterious mutations made evident by heavy inbreeding depression., Methods: To locate and characterize these deleterious mutations, and to measure selection pressure across the cassava genome, we aligned 52 related Euphorbiaceae and other related species representing millions of years of evolution. With single base-pair resolution of genetic conservation, we used protein structure models, amino acid impact, and evolutionary conservation across the Euphorbiaceae to estimate evolutionary constraint. With known deleterious mutations, we aimed to improve genomic evaluations of plant performance through genomic prediction. We first tested this hypothesis through simulation utilizing multi-kernel GBLUP to predict simulated phenotypes across separate populations of cassava., Results: Simulations showed a sizable increase of prediction accuracy when incorporating functional variants in the model when the trait was determined by<100 quantitative trait loci (QTL). Utilizing deleterious mutations and functional weights informed through evolutionary conservation, we saw improvements in genomic prediction accuracy that were dependent on trait and prediction., Conclusion: We showed the potential for using evolutionary information to track functional variation across the genome, in order to improve whole genome trait prediction. We anticipate that continued work to improve genotype accuracy and deleterious mutation assessment will lead to improved genomic assessments of cassava clones., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Long, Romay, Ramstein, Buckler and Robbins.)

Between the Last Glacial Maximum and the mid-Holocene, the Mediterranean Sea experienced major hydrological changes. The deposition of the last sapropel, S1, during the Early Holocene is a consequence of these changes. In order to cause anoxia in the Eastern Mediterranean Sea (EMS) bottom water, a long preconditioning period of a few thousand years would need to occur throughout the deglaciation prior to S1. It is generally believed that this freshwater was of North Atlantic origin, later supplemented by the African Humid period (AHP). Here, we investigate another potentially important source of freshwater to the EMS: the Fennoscandian ice sheet (FIS) meltwater, running into the Caspian and Black Seas. A few scenarios of continental hydrologic perturbation have been developed to drive a high-resolution Mediterranean Sea general circulation model. We demonstrate that, during the last deglaciation, FIS meltwater flowing into the Black Sea reduced surface salinity and ventilation over the main convection areas in the EMS. By including continental hydrological changes, a more consistent framework is produced to characterize the hydrology of the Mediterranean Sea during the last deglaciation and the Early Holocene., (© 2022. The Author(s).)

Web-based data analysis and visualization tools are mostly designed for specific purposes, such as the analysis of data from whole transcriptome RNA sequencing or single-cell RNA sequencing. However, generic tools designed for the analysis of common laboratory data for noncomputational scientists are also needed. The importance of such web-based tools is emphasized by the continuing increases in the sample capacity of conventional laboratory tools such as quantitative PCR, flow cytometry or ELISA instruments. We present a web-based application FaDA, developed with the R Shiny package that provides users with the ability to perform statistical group comparisons, including parametric and nonparametric tests, with multiple testing corrections suitable for most standard wet-laboratory analyses. FaDA provides data visualizations such as heatmaps, principal component analysis (PCA) plots, correlograms and receiver operating curves (ROCs). Calculations are performed through the R language. The FaDA application provides a free and intuitive interface that allows biologists without bioinformatic skill to easily and quickly perform common laboratory data analyses. The application is freely accessible at https://shiny-bird.univ-nantes.fr/app/Fada., Competing Interests: The authors have declared that no competing interests exist.

Key Message: Convolutional Neural Networks (CNNs) can perform similarly or better than standard genomic prediction methods when sufficient genetic, environmental, and management data are provided. Predicting phenotypes from genetic (G), environmental (E), and management (M) conditions is a long-standing challenge with implications to agriculture, medicine, and conservation. Most methods reduce the factors in a dataset (feature engineering) in a subjective and potentially oversimplified manner. Deep neural networks such as Multilayer Perceptrons (MPL) and Convolutional Neural Networks (CNN) can overcome this by allowing the data itself to determine which factors are most important. CNN models were developed for predicting agronomic yield from a combination of replicated trials and historical yield survey data. The results were more accurate than standard methods when tested on held-out G, E, and M data (r = 0.50 vs. r = 0.43), and performed slightly worse than standard methods when only G was held out (r = 0.74 vs. r = 0.80). Pre-training on historical data increased accuracy compared to trial data alone. Saliency map analysis indicated the CNN has "learned" to prioritize many factors of known agricultural importance., (© 2021. This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply.)

Studies about the impact of future climate change on diseases have mostly focused on standard Representative Concentration Pathway climate change scenarios. These scenarios do not account for the non-linear dynamics of the climate system. A rapid ice-sheet melting could occur, impacting climate and consequently societies. Here, we investigate the additional impact of a rapid ice-sheet melting of Greenland on climate and malaria transmission in Africa using several malaria models driven by Institute Pierre Simon Laplace climate simulations. Results reveal that our melting scenario could moderate the simulated increase in malaria risk over East Africa, due to cooling and drying effects, cause a largest decrease in malaria transmission risk over West Africa and drive malaria emergence in southern Africa associated with a significant southward shift of the African rain-belt. We argue that the effect of such ice-sheet melting should be investigated further in future public health and agriculture climate change risk assessments.

Warm periods in Earth's history offer opportunities to understand the dynamics of the Earth system under conditions that are similar to those expected in the near future. The Middle Pliocene warm period (MPWP), from 3.3 to 3.0 My B.P, is the most recent time when atmospheric CO 2 levels were as high as today. However, climate model simulations of the Pliocene underestimate high-latitude warming that has been reconstructed from fossil pollen samples and other geological archives. One possible reason for this is that enhanced non-CO 2 trace gas radiative forcing during the Pliocene, including from methane (CH 4 ), has not been included in modeling. We use a suite of terrestrial biogeochemistry models forced with MPWP climate model simulations from four different climate models to produce a comprehensive reconstruction of the MPWP CH 4 cycle, including uncertainty. We simulate an atmospheric CH 4 mixing ratio of 1,000 to 1,200 ppbv, which in combination with estimates of radiative forcing from N 2 O and O 3 , contributes a non-CO 2 radiative forcing of 0.9 [Formula: see text] (range 0.6 to 1.1), which is 43% (range 36 to 56%) of the CO 2 radiative forcing used in MPWP climate simulations. This additional forcing would cause a global surface temperature increase of 0.6 to 1.0 °C, with amplified changes at high latitudes, improving agreement with geological evidence of Middle Pliocene climate. We conclude that natural trace gas feedbacks are critical for interpreting climate warmth during the Pliocene and potentially many other warm phases of the Cenezoic. These results also imply that using Pliocene CO 2 and temperature reconstructions alone may lead to overestimates of the fast or Charney climate sensitivity., Competing Interests: The authors declare no competing interest.

Deep learning methodologies have revolutionized prediction in many fields and show potential to do the same in molecular biology and genetics. However, applying these methods in their current forms ignores evolutionary dependencies within biological systems and can result in false positives and spurious conclusions. We developed two approaches that account for evolutionary relatedness in machine learning models: ( i ) gene-family-guided splitting and ( ii ) ortholog contrasts. The first approach accounts for evolution by constraining model training and testing sets to include different gene families. The second approach uses evolutionarily informed comparisons between orthologous genes to both control for and leverage evolutionary divergence during the training process. The two approaches were explored and validated within the context of mRNA expression level prediction and have the area under the ROC curve (auROC) values ranging from 0.75 to 0.94. Model weight inspections showed biologically interpretable patterns, resulting in the hypothesis that the 3' UTR is more important for fine-tuning mRNA abundance levels while the 5' UTR is more important for large-scale changes., Competing Interests: The authors declare no conflict of interest.

It is generally considered that the perennial glaciation of Greenland lasting several orbital cycles began around 2.7 Ma along with the intensification of Northern Hemisphere glaciation (NHG). Both data and model studies have demonstrated that a decline in atmospheric pCO 2 was instrumental in establishing a perennial Greenland ice sheet (GrIS), yet models have generally used simplistic pCO 2 constraints rather than data-inferred pCO 2 evolution. Here, using a method designed for the long-term coupling of climate and cryosphere models and pCO 2 scenarios from different studies, we highlight the pivotal role of pCO 2 on the GrIS expansion across the Plio-Pleistocene Transition (PPT, 3.0-2.5 Ma), in particular in the range between 280 and 320 ppm. Good qualitative agreement is obtained between various IRD reconstructions and some of the possible evolutions of the GrIS simulated by our model. Our results underline the dynamism of the GrIS waxing and waning under pCO 2 levels similar to or lower than today, which supports recent evidence of a dynamic GrIS during the Plio-Pleistocene.