Predicting ecological responses in a changing ocean: the effects of future climate uncertainty

Climate change drives fish communities: Changing multiple facets of fish biodiversity in the Northwest Pacific Ocean

Global marine biodiversity is experiencing significant alterations due to climate change. Incorporating phylogenetic and functional diversity may provide novel insights into these impacts. This study used an ensemble model approach (random forest and boosted regression tree), to predict the habitat distribution of 47 fish species in the Northwestern Pacific under contemporary (2000-2014) and future scenarios (2040-2050, 2090-2100). We first examined the relationship between eleven functional traits and habitat changes, predicting the spatial distribution of functional traits within fish communities. A significant correlation was observed between temperature preference and habitat changes, highlighting the vulnerability of cold-water species and potential advantages for warm-water species in the future. Moreover, fish communities exhibited a spatial gradient distribution with southern regions characterized by shorter-lived and earlier maturity, contrasting with longer-lived and later maturity species in the north. Secondly, to assess the impact of climate change on marine biodiversity, we explored the taxonomic, phylogenetic, and functional diversity under contemporary and future scenarios, revealing higher indices in the East China Sea (ECS) and the coastal sea of Japan, with the Taiwan Strait emerging as a contemporary biodiversity hotspot. In future scenarios, the three biodiversity indices would decline in the Yellow Sea and ECS, but increase in the sea beyond the continental shelf, coastal sea of Hokkaido, and Sea of Okhotsk. Lastly, we explored processes and mechanisms in the change of community composition. By quantifying β-diversity, we identified species loss (nestedness) as the primary driver of fish community change by 2040-2050, with species replacement (turnover) predicted to become dominant in the far future. Our results explore the potential changes in multiple facets of fish biodiversity, providing crucial insights for policymakers aiming to protect fish resources and biodiversity.

Incorporating mesopelagic fish into the evaluation of conservation areas for marine living resources under climate change scenarios

Mesopelagic fish (meso-fish) are central species within the Southern Ocean (SO). However, their ecosystem role and adaptive capacity to climate change are rarely integrated into protected areas assessments. This is a pity given their importance as crucial prey and predators in food webs, coupled with the impacts of climate change. Here, we estimate the habitat distribution of nine meso-fish using an ensemble model approach (MAXENT, random forest, and boosted regression tree). Four climate model simulations were used to project their distribution under two representative concentration pathways (RCP4.5 and RCP8.5) for short-term (2006-2055) and long-term (2050-2099) periods. In addition, we assess the ecological representativeness of protected areas under climate change scenarios using meso-fish as indicator species. Our models show that all species shift poleward in the future. Lanternfishes (family Myctophidae) are predicted to migrate poleward more than other families (Paralepididae, Nototheniidae, Bathylagidae, and Gonostomatidae). In comparison, lanternfishes were projected to increase habitat area in the eastern SO but lose area in the western SO; the opposite was projected for species in other families. Important areas (IAs) of meso-fish are mainly distributed near the Antarctic Peninsula and East Antarctica. Negotiated protected area cover 23% of IAs at present and 38% of IAs in the future (RCP8.5, long-term future). Many IAs of meso-fish still need to be included in protected areas, such as the Prydz Bay and the seas around the Antarctic Peninsula. Our results provide a framework for evaluating protected areas incorporating climate change adaptation strategies for protected areas management.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00188-9.

Modeling present and future distribution of plankton populations in a coastal upwelling zone: the copepod Calanus chilensis as a study case

Predicting species distribution in the ocean has become a crucial task to assess marine ecosystem responses to ongoing climate change. In the Humboldt Current System (HCS), the endemic copepod Calanus chilensis is one of the key species bioindicator of productivity and water masses. Here we modeled the geographic distribution of Calanus chilensis for two bathymetric ranges, 0-200 and 200-400 m. For the 0-200 m layer, we used the Bayesian Additive Regression Trees (BART) method, whereas, for the 200-400 m layer, we used the Ensembles of Small Models (ESMs) method and then projected the models into two future scenarios to assess changes in geographic distribution patterns. The models were evaluated using the multi-metric approach. We identified that chlorophyll-a (0.34), Mixed Layer Depth (0.302) and salinity (0.36) explained the distribution of C. chilensis. The geographic prediction of the BART model revealed a continuous distribution from Ecuador to the southernmost area of South America for the 0-200 m depth range, whereas the ESM model indicated a discontinuous distribution with greater suitability for the coast of Chile for the 200-400 m depth range. A reduction of the distribution range of C. chilensis is projected in the future. Our study suggests that the distribution of C. chilensis is conditioned by productivity and mesoscale processes, with both processes closely related to upwelling intensity. These models serve as a tool for proposing indicators of changes in the ocean. We further propose that the species C. chilensis is a high productivity and low salinity indicator at the HCS. We recommend further examining multiple spatial and temporal scales for stronger inference.

Mapping and assessment of future changes in the coastal and marine ecosystem services supply in Lithuania

Assessing and mapping ecosystem services (ES) became an integral part of coastal and marine management practices. Hence, quantitative and validated approaches are lacking, especially to address future conditions. The objective of this study is to apply further existing and develop new methodological frameworks to quantitatively assess and map the current and future supply of 3 ES in the coastal zone of Lithuania: coastal flood protection, nutrient regulation, and maintenance of nursery conditions. For coastal flood ES modelling, 2 time periods (1990 and 2018) and 4 scenarios (A0, A1 A2, A3 - based on future socio-economic changes in Lithuania) were analysed. The coastal flood protection ES model was validated (r² = 0.30) using tree cover density. The results showed spatial differences among the analysed periods but no statistical differences. High supply areas are located in the southern coastal area, while the central part displays a low supply. For nutrient regulation and maintenance of nursery conditions, 7 time periods were analysed: a historical period and 6 scenarios based on Representative Concentration Pathway 4.5 and 8.5 and 3 Shared Socioeconomic Pathways. The nutrient regulation ES model was validated (r² = 0.85) using in situ nutrient. Statistical differences were observed for this ES, but a similar spatial distribution of high and low supply areas. A decrease in the supply was observed comparing the historical period and future scenarios. Maintenance of nursery conditions was validated (r² = 0.72) based on the protection status of the coastal zone. Results show no statistical differences and similar spatial patterns among the periods. Rocky and sandbank areas show a high supply for this ES. Limitations of our work are mainly related to the resolution of the utilised indicators. Nevertheless, the information obtained from our models can support spatial planning and decision-making processes.

Seeing the forest for the trees: Assessing genetic offset predictions from gradient forest

Gradient Forest (GF) is a machine learning algorithm designed to analyze spatial patterns of biodiversity as a function of environmental gradients. An offset measure between the GF-predicted environmental association of adapted alleles and a new environment (GF Offset) is increasingly being used to predict the loss of environmentally adapted alleles under rapid environmental change, but remains mostly untested for this purpose. Here, we explore the robustness of GF Offset to assumption violations, and its relationship to measures of fitness, using SLiM simulations with explicit genome architecture and a spatial metapopulation. We evaluate measures of GF Offset in: (1) a neutral model with no environmental adaptation; (2) a monogenic "population genetic" model with a single environmentally adapted locus; and (3) a polygenic "quantitative genetic" model with two adaptive traits, each adapting to a different environment. We found GF Offset to be broadly correlated with fitness offsets under both single locus and polygenic architectures. However, neutral demography, genomic architecture, and the nature of the adaptive environment can all confound relationships between GF Offset and fitness. GF Offset is a promising tool, but it is important to understand its limitations and underlying assumptions, especially when used in the context of predicting maladaptation.

Modeling the impact of climate change on mussel aquaculture in a coastal upwelling system: A critical assessment

Forecasting of climate change impacts on marine aquaculture production has become a major research task, which requires taking into account the biases and uncertainties arising from ocean climate models in coastal areas, as well as considering culture management strategies. Focusing on the suspended mussel culture in the NW Iberian coastal upwelling system, we simulated current and future mussel growth by means of a multistructural net production Dynamic Energy Budget (DEB) model. We considered two scenarios and three ocean climate models to account for climate uncertainty, and applied a bias correction to the climate models in coastal areas. Our results show that the predicted impact of climate change on mussel growth is low compared with the role of the seeding time. However, the response of mussels varied across climate models, ranging from a minor growth decline to a moderate growth increase. Therefore, this work confirms that an accurate forecasting of climate change impacts on shellfish aquaculture should take into account the variability linked to both management strategies and climate uncertainty.

Potential changes in the connectivity of marine protected areas driven by extreme ocean warming

Projected future climate scenarios anticipate a warmer tropical ocean and changes in surface currents that will likely influence the survival of marine organisms and the connectivity of marine protected areas (MPAs) networks. We simulated the regional effects of climate change on the demographic connectivity of parrotfishes in nine MPAs in the South Atlantic through downscaling of the HadGEM2-ES Earth System Model running the RCP 8.5 greenhouse gas trajectory. Results indicate a tropicalization scenario over the tropical southwest Atlantic following an increase of sea surface temperature (SST) between 1.8 and 4.5 °C and changes in mean surface currents between - 0.6 to 0.5 m s^-1 relative to present conditions. High mortality rates will reduce demographic connectivity and increase the isolation of oceanic islands. The simulation of organismal response to ocean warming shows that acclimation can significantly improve (p < 0.001) particle survival, promoting connectivity and tropicalization of MPAs, with potential impacts on their functional integrity and long-term resilience.

Multiple facets of marine biodiversity in the Pacific Arctic under future climate

Climate change is triggering a global reorganization of marine life. Biogeographical transition zones, diversity-rich regions straddling biogeographical units where many species live at, or close to, their physiological tolerance limits (i.e., range distribution edges), are redistribution hotspots that offer a unique opportunity to understand the mechanisms and consequences of climate-driven thermophilization processes in natural communities. In this context, we examined the impacts of climate change projections in the 21st century (2026-2100) on marine biodiversity in the Eastern Bering and Chukchi seas within the Pacific Arctic, a climatically exposed and sensitive boreal-to-Arctic transition zone. Overall, projected changes in species distributions, modeled using species distribution models, resulted in poleward increases in species richness and functional redundancy, along with pronounced reductions in phylogenetic distances by century's end (2076-2100). Future poleward shifts of boreal species in response to warming and sea ice changes are projected to alter the taxonomic and functional biogeography of contemporary Arctic communities as larger, longer-lived and more predatory taxa expand their leading distributional margins. Drawing from the existing evidence from other Arctic regions, these changes are anticipated to increase the susceptibility and vulnerability of the Arctic ecosystems, as trophic connectance between biological components increases, thus decreasing the modularity of Arctic food webs. Our results demonstrate how integrating multiple diversity facets can provide key insights into the relationships between climate change, species composition and ecosystem functioning across marine biogeographic regions.

Projecting global mariculture diversity under climate change

Previous studies have focused on changes in the geographical distribution of terrestrial biomes and species targeted by marine capture fisheries due to climate change impacts. Given mariculture's substantial contribution to global seafood production and its growing significance in recent decades, it is essential to evaluate the effects of climate change on mariculture and their socio-economic consequences. Here, we projected climate change impacts on the marine aquaculture diversity for 85 of the currently most commonly farmed fish and invertebrate species in the world's coastal and/or open ocean areas. Results of ensemble projections from three Earth system models and three species distribution models show that climate change may lead to a substantial redistribution of mariculture species richness potential, with an average of 10%-40% decline in the number of species being potentially suitable to be farmed in tropical to subtropical regions. In contrast, mariculture species richness potential is projected to increase by about 40% at higher latitudes under the 'no mitigation policy' scenario (RCP 8.5) by the mid-21st century. In Exclusive Economic Zones where mariculture is currently undertaken, we projected an average future decline of 1.3% and 5% in mariculture species richness potential under RCP 2.6 ('strong mitigation') and RCP 8.5 scenarios, respectively, by the 2050s relative to the 2000s. Our findings highlight the opportunities and challenges for climate adaptation in the mariculture sector through the redistribution of farmed species and expansion of mariculture locations. Our results can help inform adaptation planning and governance mechanisms to minimize local environmental impacts and potential conflicts with other marine and coastal sectors in the future.

Harmful algae at the complex nexus of eutrophication and climate change

Climate projections suggest-with substantial certainty-that global warming >1.5 °C will occur by mid-century (2050). Population is also projected to increase, amplifying the demands for food, fuel, water and sanitation, which, in turn, escalate nutrient pollution. Global projections of nutrient pollution, however, are less certain than those of climate as there are regionally decreasing trends projected in Europe, and stabilization of nutrient use in North America and Australia. In this review of the effects of eutrophication and climate on harmful algae, some of the complex, subtle, and non-intuitive effects and interactions on the physiology of both harmful and non-harmful taxa are emphasized. In a future ocean, non-harmful diatoms may be disproportionately stressed and mixotrophs advantaged due to changing nutrient stoichiometry and forms of nutrients, temperature, stratification and oceanic pH. Modeling is advancing, but there is much yet to be understood, in terms of physiology, biogeochemistry and trophodynamics and how both harmful and nonharmful taxa may change in an uncertain future driven by anthropogenic activities.

Discovering millions of plankton genomic markers from the Atlantic Ocean and the Mediterranean Sea

Comparison of the molecular diversity in all plankton populations present in geographically distant water columns may allow for a holistic view of the connectivity, isolation and adaptation of organisms in the marine environment. In this context, a large-scale detection and analysis of genomic variants directly in metagenomic data appeared as a powerful strategy for the identification of genetic structures and genes under natural selection in plankton. Here, we used discosnp++, a reference-free variant caller, to produce genetic variants from large-scale metagenomic data and assessed its accuracy on the copepod Oithona nana in terms of variant calling, allele frequency estimation and population genomic statistics by comparing it to the state-of-the-art method. discosnp ++ produces variants leading to similar conclusions regarding the genetic structure and identification of loci under natural selection. discosnp++ was then applied to 120 metagenomic samples from four size fractions, including prokaryotes, protists and zooplankton sampled from 39 tara Oceans sampling stations located in the Atlantic Ocean and the Mediterranean Sea to produce a new set of marine genomic markers containing more than 19 million of variants. This new genomic resource can be used by the community to relocate these markers on their plankton genomes or transcriptomes of interest. This resource will be updated with new marine expeditions and the increase of metagenomic data (availability: http://bioinformatique.rennes.inria.fr/taravariants/).