Protecting connectivity promotes successful biodiversity and fisheries conservation

Marine megavertebrate migrations connect the global ocean

Animal migrations are extensive, ubiquitous, and in decline. To effectively protect migratory species, it is often crucial to identify the interconnected sets of sites they rely upon. Gaps between primary ecological research and synthesised information that is useful to policymakers has limited effective conservation of long-distance migrants, particularly in the marine realm. By synthesising 1304 references to identify 1787 sites and develop model migratory networks for 109 species, we show the minimum extent of marine megafauna connectivity across the global oceans. Our analyses underscore the importance of transboundary cooperation for migratory species conservation at scales larger than current regional structures afford and provide a free online system that will enable policymakers to efficiently summarise how marine migrants use and connect their jurisdictions.

Environmental DNA Epigenetics Accurately Predicts the Age of Cultured Fish Larvae

While acquiring age information is crucial for efficient stock management and biodiversity conservation, traditional aging methods fail to offer a universal, non-invasive, and precise way of estimating a wild animal's age. DNA methylation from tissue DNA (tDNA) was recently proposed as a method to overcome these issues and showed more accurate results than telomere-length-based age assessments. Here, we used environmental DNA (eDNA) for the first time as a template for age estimation, focusing on the larval phase (10-24 days post-hatch) of cultured Dicentrarchus labrax (seabass), a species of major economic and conservation interest. Using third-generation sequencing, we were able to directly detect various modification types (e.g., cytosine and adenosine methylation in all contexts) across the whole genome using amplification-free nanopore sequencing. However, aging sites were only present in the mitogenome, which could be a specific feature of eDNA methylation or the consequence of better DNA protection within mitochondria. By considering qualitative and quantitative information about aging sites according to an objective model selection framework, our epigenetic clock reached a cross-validated accuracy of 2.6 days (Median Absolute Error). Such performances are higher than those of previous clocks, notably for adult seabass even when scaling MAE to the age range, which could be linked to a more dynamic epigenome during early life stages. Overall, our pilot study proposes new methods to determine the potential of eDNA for simultaneous age and biodiversity assessments, although robust validation of our preliminary results along with methodological developments are needed before field applications can be envisaged.

The role of mesoscale-driven connectivity patterns in coral recovery around Moorea and Tahiti, French Polynesia

Coral reefs are declining due to anthropogenic warming. Nonetheless, some have recovered quickly from repeated bleaching events. Coral recovery depends on adaptation capabilities, fishing pressure, overall number of stressors, reef conditions before the event, and degree of connectivity. Coral reefs that are connected to many others can receive viable larvae and regain coverage faster. Around Moorea and Tahiti, within the Society Islands of French Polynesia, coral cover has regained its previous levels rapidly, despite several mass bleaching events over the past three decades. Here it is explored whether the connectivity with distant reefs may support such recovery by modeling the transport of coral larvae around the islands over 28 years. Ocean currents enable connectivity with the Tuamotu Islands, ~ 250 km to the northeast, that act as sources to Moorea and Tahiti for pelagic larval durations of three weeks or longer. The circulation around Moorea and Tahiti is very dynamic; mesoscale eddies can also halt the connectivity with the Tuamotu Islands and sporadically transport larvae from reefs to the west and southeast instead. With many undisturbed coral reefs within a 300 km radius and strong mesoscale variability, a dynamic, long-range connectivity may explain the recovery of reefs around Moorea and Tahiti.

Constructing wetland ecological corridor system based on hydrological connectivity with the goal of improving regional biodiversity

Hydrological connectivity is crucial for the healthy operation of wetland ecosystems. However, the current design of ecological corridors in wetland biodiversity networks is mostly based on species migration resistance, neglecting the important role of hydrological connectivity. How to incorporate hydrological connectivity into the wetland ecological corridor system (ECS) is still unclear. To answer the question, we proposed a framework for constructing a wetland ECS with the goal of improving conservation value of previously identified wetland biodiversity hotspots based on hydrological connectivity. In the proposed framework, we clarified the function-level-dimension of each corridor based on the dynamics of conservation value of biodiversity hotspots, the hierarchical classification of rivers and the dimension of hydrological connectivity. Then we determined the spatial distribution and functional zoning of the corridors by least cost model (LCM) using indicators that reflect wetland hydrological connectivity resistance, including water coverage, water use efficiency of vegetation, and land use suitability. The results are as follows: (1) to improve the overall hydrological connectivity and conservation value of biodiversity hotspots, 25 corridors should be constructed for vertical hydrological connectivity (with 3 for maintaining the status quo, 6 for improving and 16 for restoring connectivity) and 3 corridors should be constructed for lateral hydrological connectivity; (2) total area of all corridors are 11 km2, accounting for 6.79% of the study area (2.47% of core zone and 4.32% of buffer zone); (3) low suitability areas of hydrological vegetation gradient (HVG) are the most extensive, followed by low suitability areas of land use/cover change (LUCC) and the average fraction coverage of water surface (AFCW), accounting for 65.08%, 47.87% and 6.76% of the corridor coverage, respectively. The proposed framework of constructing wetland ECS in this study has the potential to provide the post-2020 global biodiversity framework and sustainable development goals with specific technical support and more targeted-control strategies for building a hydrological connected wetland biodiversity network.

Testing for concordance between predicted species richness, past prioritization, and marine protected area designations in the western Indian Ocean

Scientific advances in environmental data coverage and machine learning algorithms have improved the ability to make large-scale predictions where data are missing. These advances allowed us to develop a spatially resolved proxy for predicting numbers of tropical nearshore marine taxa. A diverse marine environmental spatial database was used to model numbers of taxa from ∼1000 field sites, and the predictions were applied to all 7039 6.25-km2 reef cells in 9 ecoregions and 11 nations of the western Indian Ocean. Our proxy for total numbers of taxa was based on the positive correlation (r2 = 0.24) of numbers of taxa of hard corals and 5 highly diverse reef fish families. Environmental relationships indicated that the number of fish species was largely influenced by biomass, nearness to people, governance, connectivity, and productivity and that coral taxa were influenced mostly by physicochemical environmental variability. At spatial delineations of province, ecoregion, nation, and strength of spatial clustering, we compared areas of conservation priority based on our total species proxy with those identified in 3 previous priority-setting reports and with the protected area database. Our method identified 119 locations that fit 3 numbers of taxa (hard coral, fish, and their combination) and 4 spatial delineations (nation, ecoregion, province, and reef clustering) criteria. Previous publications on priority setting identified 91 priority locations of which 6 were identified by all reports. We identified 12 locations that fit our 12 criteria and corresponded with 3 previously identified locations, 65 that aligned with at least 1 past report, and 28 that were new locations. Only 34% of the 208 marine protected areas in this province overlapped with identified locations with high numbers of predicted taxa. Differences occurred because past priorities were frequently based on unquantified perceptions of remoteness and preselected priority taxa. Our environment-species proxy and modeling approach can be considered among other important criteria for making conservation decisions.

Invasive species drive cross-ecosystem effects worldwide

Invasive species are pervasive around the world and have profound impacts on the ecosystem they invade. Invasive species, however, can also have impacts beyond the ecosystem they invade by altering the flow of non-living materials (for example, nutrients or chemicals) or movement of organisms across the boundaries of the invaded ecosystem. Cross-ecosystem interactions via spatial flows are ubiquitous in nature, for example, connecting forests and lakes, grasslands and rivers, and coral reefs and the deep ocean. Yet, we have a limited understanding of the cross-ecosystem impacts invasive species have relative to their local effects. By synthesizing emerging evidence, here we demonstrate the cross-ecosystem impacts of invasive species as a ubiquitous phenomenon that influences biodiversity and ecosystem functioning around the world. We identify three primary ways by which invasive species have cross-ecosystem effects: first, by altering the magnitude of spatial flows across ecosystem boundaries; second, by altering the quality of spatial flows; and third, by introducing novel spatial flows. Ultimately, the strong impacts invasive species can drive across ecosystem boundaries suggests the need for a paradigm shift in how we study and manage invasive species around the world, expanding from a local to a cross-ecosystem perspective.

Directed conservation of the world's reef sharks and rays

Many shark populations are in decline around the world, with severe ecological and economic consequences. Fisheries management and marine protected areas (MPAs) have both been heralded as solutions. However, the effectiveness of MPAs alone is questionable, particularly for globally threatened sharks and rays ('elasmobranchs'), with little known about how fisheries management and MPAs interact to conserve these species. Here we use a dedicated global survey of coral reef elasmobranchs to assess 66 fully protected areas embedded within a range of fisheries management regimes across 36 countries. We show that conservation benefits were primarily for reef-associated sharks, which were twice as abundant in fully protected areas compared with areas open to fishing. Conservation benefits were greatest in large protected areas that incorporate distinct reefs. However, the same benefits were not evident for rays or wide-ranging sharks that are both economically and ecologically important while also threatened with extinction. We show that conservation benefits from fully protected areas are close to doubled when embedded within areas of effective fisheries management, highlighting the importance of a mixed management approach of both effective fisheries management and well-designed fully protected areas to conserve tropical elasmobranch assemblages globally.

Life goes on: Spatial heterogeneity promotes biodiversity in an urbanized coastal marine ecosystem

Both human populations and marine biodiversity are concentrated along coastlines, with growing conservation interest in how these ecosystems can survive intense anthropogenic impacts. Tropical urban centres provide valuable research opportunities because these megacities are often adjacent to mega-diverse coral reef systems. The Pearl River Delta is a prime exemplar, as it encompasses one of the most densely populated and impacted regions in the world and is located just northwest of the Coral Triangle. However, the spatial and taxonomic complexity of this biodiversity, most of which is small, cryptic in habitat and poorly known, make comparative analyses challenging. We deployed standardized settlement structures at seven sites differing in the intensity of human impacts and used COI metabarcoding to characterize benthic biodiversity, with a focus on metazoans. We found a total of 7184 OTUs, with an average of 665 OTUs per sampling unit; these numbers exceed those observed in many previous studies using comparable methods, despite the location of our study in an urbanized environment. Beta diversity was also high, with 52% of the OTUs found at just one site. As expected, we found that the sites close to point sources of pollution had substantially lower diversity (44% less) relative to sites bathed in less polluted oceanic waters. However, the polluted sites contributed substantially to the total animal diversity of the region, with 25% of all OTUs occurring only within polluted sites. Further analysis of Arthropoda, Annelida and Mollusca showed that phylogenetic clustering within a site was common, suggesting that environmental filtering reduced biodiversity to a subset of lineages present within the region, a pattern that was most pronounced in polluted sites and for the Arthropoda. The water quality gradients surrounding the PRD highlight the unique role of in situ studies for understanding the impacts of complex urbanization pressures on biodiversity.

Quantifying larval dispersal portfolio in seabass nurseries using otolith chemical signatures

The temporal asynchronies in larvae production from different spawning areas are fundamental components for ensuring stability and resilience of marine metapopulations. Such a concept, named portfolio effect, supposes that diversifying larval dispersal histories should minimize the risk of recruitment failure by increasing the probability that at least some larvae successfully settle in nursery. Here, we used a reconstructive approach based on otolith chemistry to quantify the larval dispersal portfolio of the European seabass, Dicentrarchus labrax, across six estuarine nursery areas of the northeast Atlantic Ocean. The analysis of natal and trajectory signatures indicated that larvae hatch in distinct environments and then dispersed in water masses featured by contrasting chemical signatures. While some trace elements appeared affected by temporal changes (Mn and Sr), others varied spatially during the larval stage but remained poorly affected by temporal fluctuation and fish physiology (Ba, Cu, Rb and Zn). We then proposed two diversity metrics based on richness and variations of chemical signatures among populations to reflect spatio-temporal diversity in natal origins and larval trajectories (i.e., estimates of dispersal portfolio). Along the French coast, the diversity estimates were maximum in nurseries located at proximity of offshore spawning sites and featured by complex offshore hydrodynamic contexts, such as the Mont St-Michel bay. Finally, our findings indicate that the dispersal portfolio was positively related with the local abundance of seabass juveniles, supporting the assumption that heterogeneity in dispersal history contributes to promote recruitment success in nurseries.

Predation and spatial connectivity interact to shape ecosystem resilience to an ongoing regime shift

Ecosystem regime shifts can have severe ecological and economic consequences, making it a top priority to understand how to make systems more resilient. Theory predicts that spatial connectivity and the local environment interact to shape resilience, but empirical studies are scarce. Here, we use >7000 fish samplings from the Baltic Sea coast to test this prediction in an ongoing, spatially propagating shift in dominance from predatory fish to an opportunistic mesopredator, with cascading effects throughout the food web. After controlling for the influence of other drivers (including increasing mesopredator densities), we find that predatory fish habitat connectivity increases resilience to the shift, but only when densities of fish-eating top predators (seals, cormorants) are low. Resilience also increases with temperature, likely through boosted predatory fish growth and recruitment. These findings confirm theoretical predictions that spatial connectivity and the local environment can together shape resilience to regime shifts.

Marine protected areas are a useful tool to protect coral reef fishes but not representative to conserve their functional role

Anthropogenic actions have direct and indirect impacts on natural systems, leading to significant alterations in marine ecosystems worldwide. One of the most notable problems is species loss, as the disappearance of species from an area can compromise ecological functions. This is at the core of a severe biodiversity crisis. To address and reverse these processes, marine protected areas (MPAs) have been utilized as a crucial tool to mitigate species loss, increase biomass, and serve as a fisheries management tool. However, there is a lack of information assessing MPAs from the perspective of their contribution to maintaining ecological functions. In recent decades, functional diversity (FD) indices have been widely used to assess ecosystem functioning. In this paper, we conducted an assessment using a global database of reef fish abundance to analyze the effect of No-Take Zones (NTZ) on the FD and "true" diversity (TD) indices of tropical reef fish assemblages in seven tropical biogeographic regions. We found a significant protective effect for some indices, although these responses were dependent on the bioregion. At the bioregional level, NTZs included lower numbers of species and functional entities than open access areas. Consequently, the functional richness protected within these zones partially represented the functional diversity in each biogeographic province. However, smaller-scale functional diversity indices responded to NTZ protection depending on the bioregion. Therefore, these results reinforce that the assessed NTZs are responsive to the protection of functional diversity, although they are not sufficient for safeguarding ecosystem functions in tropical reefs. This highlights the importance of expanding the number of protection entities worldwide with management strategies focused on coral reef fish functionality, as well as effective local/regional assessments. Thus, a new paradigm is necessary in the planning and creation of MPAs to safeguard ecosystem functions, with a priority given to the protection of ecosystem functions and habitats.

Effects of Madagascar marine reserves on juvenile and adult coral abundance, and the implication for population regulation

Recruitment is a critical component in the dynamics of coral assemblages, and a key question is to determine the degree to which spatial heterogeneity of adults is influenced by pre-vs. post-settlement processes. We analyzed the density of juvenile and adult corals among 18 stations located at three regions around Madagascar, and examined the effects of Marine Protected Areas (MPAs). Our survey did not detect a positive effect of MPAs on juveniles, except for Porites at the study scale. The MPA effect was more pronounced for adults, notably for Acropora, Montipora, Seriatopora, and Porites at the regional scale. For most dominant genera, densities of juveniles and adults were positively correlated at the study scale, and at least at one of the three regions. These outcomes suggest recruitment-limitation relationships for several coral taxa, although differences in post-settlement events may be sufficiently strong to distort the pattern established at settlement for other populations. The modest benefits of MPAs on the density of juvenile corals demonstrated here argue in favor of strengthening conservation measures more specifically focused to protect recruitment processes.

Disparate genetic divergence patterns in three corals across a pan-Pacific environmental gradient highlight species-specific adaptation

Tropical coral reefs are among the most affected ecosystems by climate change and face increasing loss in the coming decades. Effective conservation strategies that maximize ecosystem resilience must be informed by the accurate characterization of extant genetic diversity and population structure together with an understanding of the adaptive potential of keystone species. Here we analyzed samples from the Tara Pacific Expedition (2016-2018) that completed an 18,000 km longitudinal transect of the Pacific Ocean sampling three widespread corals-Pocillopora meandrina, Porites lobata, and Millepora cf. platyphylla-across 33 sites from 11 islands. Using deep metagenomic sequencing of 269 colonies in conjunction with morphological analyses and climate variability data, we can show that despite a targeted sampling the transect encompasses multiple cryptic species. These species exhibit disparate biogeographic patterns and, most importantly, distinct evolutionary patterns in identical environmental regimes. Our findings demonstrate on a basin scale that evolutionary trajectories are species-specific and can only in part be predicted from the environment. This highlights that conservation strategies must integrate multi-species investigations to discern the distinct genomic footprints shaped by selection as well as the genetic potential for adaptive change.

Integrating larval connectivity into the marine conservation decision-making process across spatial scales

Larval dispersal connectivity is typically integrated into spatial conservation decisions at regional or national scales, but implementing agencies struggle with translating these methods to local scales. We used larval dispersal connectivity at regional (hundreds of kilometers) and local (tens of kilometers) scales to aid in design of networks of no-take reserves in Southeast Sulawesi, Indonesia. We used Marxan with Connectivity informed by biophysical larval dispersal models and remotely sensed coral reef habitat data to design marine reserve networks for 4 commercially important reef species across the region. We complemented regional spatial prioritization with decision trees that combined network-based connectivity metrics and habitat quality to design reserve boundaries locally. Decision trees were used in consensus-based workshops with stakeholders to qualitatively assess site desirability, and Marxan was used to identify areas for subsequent network expansion. Priority areas for protection and expected benefits differed among species, with little overlap in reserve network solutions. Because reef quality varied considerably across reefs, we suggest reef degradation must inform the interpretation of larval dispersal patterns and the conservation benefits achievable from protecting reefs. Our methods can be readily applied by conservation practitioners, in this region and elsewhere, to integrate connectivity data across multiple spatial scales.

Machine learning prediction of connectivity, biodiversity and resilience in the Coral Triangle

Even optimistic climate scenarios predict catastrophic consequences for coral reef ecosystems by 2100. Understanding how reef connectivity, biodiversity and resilience are shaped by climate variability would improve chances to establish sustainable management practices. In this regard, ecoregionalization and connectivity are pivotal to designating effective marine protected areas. Here, machine learning algorithms and physical intuition are applied to sea surface temperature anomaly data over a twenty-four-year period to extract ecoregions and assess connectivity and bleaching recovery potential in the Coral Triangle and surrounding oceans. Furthermore, the impacts of the El Niño Southern Oscillation (ENSO) on biodiversity and resilience are quantified. We find that resilience is higher for reefs north of the Equator and that the extraordinary biodiversity of the Coral Triangle is dynamic in time and space, and benefits from ENSO. The large-scale exchange of genetic material is enhanced between the Indian Ocean and the Coral Triangle during La Niña years, and between the Coral Triangle and the central Pacific in neutral conditions. Through machine learning the outstanding biodiversity of the Coral Triangle, its evolution and the increase of species richness are contextualized through geological times, while offering new hope for monitoring its future.

A contemporary baseline of Madagascar's coral assemblages: Reefs with high coral diversity, abundance, and function associated with marine protected areas

Madagascar is a major hotspot of biodiversity in the Western Indian Ocean, but, as in many other regions, coral reefs surrounding the island confront large-scale disturbances and human-induced local stressors. Conservation actions have been implemented with encouraging results for fisheries, though their benefit on coral assemblages has never been rigorously addressed. In this context, we analyzed the multiscale spatial variation of the composition, generic richness, abundance, life history strategies, and cover of coral assemblages among 18 stations placed at three regions around the island. The potential influences of marine protected areas (MPAs), algal cover, substrate rugosity, herbivorous fish biomass, and geographic location were also analyzed. Our results highlight the marked spatial variability, with variation at either or both regional and local scales for all coral descriptors. The northeast coastal region of Masoala was characterized by the high abundance of coral colonies, most notably of the competitive Acropora and Pocillopora genera and stress-tolerant taxa at several stations. The southwest station of Salary Nord was distinguished by lower abundances, with depauperate populations of competitive taxa. On the northwest coast, Nosy-Be was characterized by higher diversity and abundance as well as by high coral cover (~42-70%) recorded at unfished stations. Results clearly underline the positive effects of MPAs on all but one of the coral descriptors, particularly at Nosy-Be where the highest contrast between fished and unfished stations was observed. Biomass of herbivorous fishes, crustose coralline algae cover, and substrate rugosity were also positively related to several coral descriptors. The occurrence of reefs with high diversity, abundance, and cover of corals, including the competitive Acropora, is a major finding of this study. Our results strongly support the implementation of locally managed marine areas with strong involvement by primary users, particularly to assist in management in countries with reduced logistic and human resources such as Madagascar.