Global marine protected areas do not secure the evolutionary history of tropical corals and fishes

Capturing diversity: Split systems and circular approximations for conservation

We investigated the implications of employing a circular approximation of split systems in the calculation of maximum diversity subsets of a set of taxa in a conservation biology context where diversity is measured using Split System Diversity (SSD). We conducted a comparative analysis between the maximum SSD score and the maximum SSD set(s) of size k, efficiently determined using a circular approximation, and the true results obtained through brute-force search based on the original data. Through experimentation on simulated datasets and SNP data across 50 Atlantic Salmon populations, our findings demonstrate that employing a circular approximation can lead to the generation of an incorrect max-SSD set(s). We built a graph-based split system whose circular approximation led to a max-SSD set of size k=4 that was less than the true max-SSD set by 17.6%. This discrepancy increased to 25% for k=11 when we used a hypergraph-based split system. The same comparison on the Atlantic salmon dataset revealed a mere 1% difference. However, noteworthy disparities emerged in the population composition between the two sets. These findings underscore the importance of assessing the suitability of circular approximations in conservation biology systems. Caution is advised when relying solely on circular approximations to determine sets of maximum diversity, and careful consideration of the data characteristics is crucial for accurate results in conservation biology applications.

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.

Shifting reef restoration focus from coral survivorship to biodiversity using Reef Carpets

To enhance the practice of farmed-coral transplantation, we conducted a trial of an approach called "Reef Carpets" (RC), which draws inspiration from the commercial turf-grass sod in land-based lawn gardening. Three 8.4m2 RCs were established on a sandy seabed, containing preselected combinations of branching corals (Acropora cf. variabilis, Pocillopora damicornis, Stylophora pistillata) with nursery recruited dwellers, and were monitored for 17-months. Corals within RCs grew, supported coral recruitment and offered ecological habitats for coral-associated organisms. While the unstable sediment underneath the RCs increased corals' partial mortalities, corals managed to grow and propagate. The extent of fish and gastropods corallivory varied among the coral species and planulation of Stylophora transplants was significantly higher than same-size natal-colonies. The RCs provided conducive environments for fish/invertebrate communities (183 taxa), and each coral species influenced specifically species-diversity and reef-associated communities. Even dead corals played crucial roles as habitats for reef biota, sustaining >80% of the RCs diversity; hence, they should not be considered automatically as indicators of failure. RCs scaled-up reef restoration and generated, in short periods, new reefs in denuded zones with enhanced biodiversity. Yet, RCs employment on soft-beds could be improved by using more structured artificial frameworks, requiring further research efforts.

Fish community structure and dynamics are insufficient to mediate coral resilience

Coral reefs are being impacted by myriad stressors leading to drastic changes to their structure and function. Fishes play essential roles in driving ecosystem processes on coral reefs but the extent to which these processes are emergent at temporal or ecosystem scales or otherwise masked by other drivers (for example, climatic events and crown-of-thorns starfish outbreaks) is poorly understood. Using time series data on fish community composition and coral and macroalgae percentage cover between 2006 and 2017 from 57 sites around Mo'orea, Polynesia, we found that fish community diversity predicts temporal stability in fish biomass but did not translate to temporal stability of coral cover. Furthermore, we found limited evidence of directional influence of fish on coral dynamics at temporal and ecosystem scales and no evidence that fish mediate coral recovery rate from disturbance. Our findings suggest that coral reef fisheries management will benefit from maintaining fish diversity but that this level of management is unlikely to strongly mediate coral loss or recovery over time.

How protected are marine protected areas: A case study of tributyltin in Latin America

Protected areas (PAs) are dedicated and managed to achieve long-term conservation of nature with associated ecosystem services and cultural values. However, few studies have assessed contamination/pollution, one of the top five biodiversity threats, within these areas. In fact, more than 100,000 molecules used in consumer goods are potentially affecting over 250,000 protected areas distributed worldwide. As a result, chemical appraisal within PAs require specific approaches to be feasible. Herein, an approach for assessment of contamination in marine protected areas (MPAs) spread over large continental and/or global areas was proposed and tested using, as a case study, the impact of tributyltin (TBT) within Latin America. This approach included area delimitation, bibliographic survey, construction of attribute tables, data insertion in a Geographic Information System, overlapping with worldwide shapefiles of PAs, identification of affected PAs and evaluation of impacts using the outcomes against specific environmental quality guidelines/directives. A total of 259 records of TBT occurrence and/or its biological effect within 53 marine protected areas (including biosphere reserves, Ramsar sites and National parks) were gathered. Among affected species, were recorded 18 gastropods exhibiting imposex. In addition, 6 bivalves, 1 crustacean, and 3 fish species presenting TBT residues in tissues were seen in MPAs from Brazil, Argentina, Ecuador, Peru, Chile and Venezuela. Since levels of TBT recorded in several studied MPAs were enough do induce deleterious biological responses over marine biota, it was clear that conservancy goals of some "protected" areas are under threat. Considering that only TBT exposure was appraised, and these areas are likely to be concomitantly exposed to other classes of contaminants, the actual scenario can be even more frightening. Although initially applied as a TBT case study, the present approach enables an overview for other chemicals within protected areas worldwide.

Area-based conservation in the twenty-first century

Humanity will soon define a new era for nature-one that seeks to transform decades of underwhelming responses to the global biodiversity crisis. Area-based conservation efforts, which include both protected areas and other effective area-based conservation measures, are likely to extend and diversify. However, persistent shortfalls in ecological representation and management effectiveness diminish the potential role of area-based conservation in stemming biodiversity loss. Here we show how the expansion of protected areas by national governments since 2010 has had limited success in increasing the coverage across different elements of biodiversity (ecoregions, 12,056 threatened species, 'Key Biodiversity Areas' and wilderness areas) and ecosystem services (productive fisheries, and carbon services on land and sea). To be more successful after 2020, area-based conservation must contribute more effectively to meeting global biodiversity goals-ranging from preventing extinctions to retaining the most-intact ecosystems-and must better collaborate with the many Indigenous peoples, community groups and private initiatives that are central to the successful conservation of biodiversity. The long-term success of area-based conservation requires parties to the Convention on Biological Diversity to secure adequate financing, plan for climate change and make biodiversity conservation a far stronger part of land, water and sea management policies.

The World Coral Conservatory (WCC): A Noah's ark for corals to support survival of reef ecosystems

Global change causes widespread decline of coral reefs. In order to counter the anticipated disappearance of coral reefs by the end of this century, many initiatives are emerging, including creation of marine protected areas (MPAs), reef restoration projects, and assisted evolution initiatives. Such efforts, although critically important, are locally constrained. We propose to build a “Noah's Ark” biological repository for corals that taps into the network of the world’s public aquaria and coral reef scientists. Public aquaria will serve not only as a reservoir for the purpose of conservation, restoration, and research of reef-building corals but also as a laboratory for the implementation of operations for the selection of stress-resilient and resistant genotypes. The proposed project will provide a global dimension to coral reef education and protection as a result of the involvement of a network of public and private aquaria.

Global change is causing a widespread decline in coral reefs. This Community Page article proposes to build the World Coral Conservatory, a “Noah's Ark” biological repository that taps into the network of the world’s public aquaria and coral reef scientists, in order to preserve the fast-disappearing biodiversity of coral reefs.

A thirteen-million-year divergence between two lineages of Indonesian coelacanths

Coelacanth fishes of the genus Latimeria are the only surviving representatives of a basal lineage of vertebrates that originated more than 400 million years ago. Yet, much remains to be unveiled about the diversity and evolutionary history of these ‘living fossils’ using new molecular data, including the possibility of ‘cryptic’ species or unknown lineages. Here, we report the discovery of a new specimen in eastern Indonesia allegedly belonging to the species L. menadoensis. Although this specimen was found about 750 km from the known geographical distribution of the species, we found that the molecular divergence between this specimen and others of L. menadoensis was great: 1.8% compared to 0.04% among individuals of L. chalumnae, the other living species of coelacanth. Molecular dating analyses suggested a divergence date of ca. 13 million years ago between the two populations of Indonesian coelacanths. We elaborate a biogeographical scenario to explain the observed genetic divergence of Indonesian coelacanth populations based on oceanic currents and the tectonic history of the region over Miocene to recent. We hypothesize that several populations of coelacanths are likely to live further east of the present capture location, with potentially a new species that remains to be described. Based on this, we call for an international effort to take appropriate measures to protect these fascinating but vulnerable vertebrates which represent among the longest branches on the Tree of Life.

Species diversity as a surrogate for conservation of phylogenetic and functional diversity in terrestrial vertebrates across the Americas

Preserving the evolutionary history and ecological functions that different species embody, in addition to species themselves, is a growing concern for conservation. Recent studies warn that conservation priority regions identified using species diversity differ from those based on phylogenetic or functional diversity. However, spatial mismatches in conservation priority regions need not indicate low surrogacy among these dimensions in conservation planning. Here, we use data for 10,213 terrestrial vertebrate species across the Americas to evaluate surrogacy; that is, the proportion of phylogenetic or functional diversity represented in conservation plans targeting species. We find that most conservation plans targeting species diversity also represent phylogenetic and functional diversity well, despite spatial mismatches in the priority regions identified by each plan. However, not all phylogenetic and functional diversity is represented within species-based plans, with the highest-surrogacy conservation strategy depending on the proportion of land area included in plans. Our results indicate that targeting species diversity could be sufficient to preserve much of the phylogenetic and functional dimensions of biodiversity in terrestrial vertebrates of the Americas. Incorporating phylogenetic and functional data in broad-scale conservation planning may not always be necessary, especially when the cost of doing so is high.

Tetrapods on the EDGE: Overcoming data limitations to identify phylogenetic conservation priorities

The scale of the ongoing biodiversity crisis requires both effective conservation prioritisation and urgent action. As extinction is non-random across the tree of life, it is important to prioritise threatened species which represent large amounts of evolutionary history. The EDGE metric prioritises species based on their Evolutionary Distinctiveness (ED), which measures the relative contribution of a species to the total evolutionary history of their taxonomic group, and Global Endangerment (GE), or extinction risk. EDGE prioritisations rely on adequate phylogenetic and extinction risk data to generate meaningful priorities for conservation. However, comprehensive phylogenetic trees of large taxonomic groups are extremely rare and, even when available, become quickly out-of-date due to the rapid rate of species descriptions and taxonomic revisions. Thus, it is important that conservationists can use the available data to incorporate evolutionary history into conservation prioritisation. We compared published and new methods to estimate missing ED scores for species absent from a phylogenetic tree whilst simultaneously correcting the ED scores of their close taxonomic relatives. We found that following artificial removal of species from a phylogenetic tree, the new method provided the closest estimates of their “true” ED score, differing from the true ED score by an average of less than 1%, compared to the 31% and 38% difference of the previous methods. The previous methods also substantially under- and over-estimated scores as more species were artificially removed from a phylogenetic tree. We therefore used the new method to estimate ED scores for all tetrapods. From these scores we updated EDGE prioritisation rankings for all tetrapod species with IUCN Red List assessments, including the first EDGE prioritisation for reptiles. Further, we identified criteria to identify robust priority species in an effort to further inform conservation action whilst limiting uncertainty and anticipating future phylogenetic advances.

A Global Synthesis Reveals Gaps in Coastal Habitat Restoration Research

Coastal ecosystems have drastically declined in coverage and condition across the globe. To combat these losses, marine conservation has recently employed habitat restoration as a strategy to enhance depleted coastal ecosystems. For restoration to be a successful enterprise, however, it is necessary to identify and address potential knowledge gaps and review whether the field has tracked scientific advances regarding best practices. This enables managers, researchers, and practitioners alike to more readily establish restoration priorities and goals. We synthesized the peer-reviewed, published literature on habitat restoration research in salt marshes, oyster reefs, and seagrasses to address three questions related to restoration efforts: (i) How frequent is cross-sector authorship in coastal restoration research? (ii) What is the geographic distribution of coastal restoration research? and (iii) Are abiotic and biotic factors equally emphasized in the literature, and how does this vary with time? Our vote-count survey indicated that one-third of the journal-published studies listed authors from at least two sectors, and 6% listed authors from all three sectors. Across all habitat types, there was a dearth of studies from Africa, Asia, and South America. Finally, despite many experimental studies demonstrating that species interactions can greatly affect the recovery and persistence of coastal foundation species, only one-fourth of the studies we examined discussed their effects on restoration. Combined, our results reveal gaps and discrepancies in restoration research that should be addressed in order to further propel coastal restoration science.

Acoustic telemetry and network analysis reveal the space use of multiple reef predators and enhance marine protected area design

Marine protected areas (MPAs) are commonly employed to protect ecosystems from threats like overfishing. Ideally, MPA design should incorporate movement data from multiple target species to ensure sufficient habitat is protected. We used long-term acoustic telemetry and network analysis to determine the fine-scale space use of five shark and one turtle species at a remote atoll in the Seychelles, Indian Ocean, and evaluate the efficacy of a proposed MPA. Results revealed strong, species-specific habitat use in both sharks and turtles, with corresponding variation in MPA use. Defining the MPA's boundary from the edge of the reef flat at low tide instead of the beach at high tide (the current best in Seychelles) significantly increased the MPA's coverage of predator movements by an average of 34%. Informed by these results, the larger MPA was adopted by the Seychelles government, demonstrating how telemetry data can improve shark spatial conservation by affecting policy directly.

Current limitations of global conservation to protect higher vulnerability and lower resilience fish species

Estuaries are threatened by intense and continuously increasing human activities. Here we estimated the sensitivity of fish assemblages in a set of estuaries distributed worldwide (based on species vulnerability and resilience), and the exposure to cumulative stressors and coverage by protected areas in and around those estuaries (from marine, estuarine and freshwater ecosystems, due to their connectivity). Vulnerability and resilience of estuarine fish assemblages were not evenly distributed globally and were driven by environmental features. Exposure to pressures and extent of protection were also not evenly distributed worldwide. Assemblages with more vulnerable and less resilient species were associated with estuaries in higher latitudes (in particular Europe), and with higher connectivity with the marine ecosystem, moreover such estuaries were generally under high intensity of pressures but with no concomitant increase in protection. Current conservation schemes pay little attention to species traits, despite their role in maintaining ecosystem functioning and stability. Results emphasize that conservation is weakly related with the global distribution of sensitive fish species in sampled estuaries, and this shortcoming is aggravated by their association with highly pressured locations, which appeals for changes in the global conservation strategy (namely towards estuaries in temperate regions and highly connected with marine ecosystems).

Multispecies genetic objectives in spatial conservation planning

Growing threats to biodiversity and global alteration of habitats and species distributions make it increasingly necessary to consider evolutionary patterns in conservation decision making. Yet, there is no clear-cut guidance on how genetic features can be incorporated into conservation-planning processes, despite multiple molecular markers and several genetic metrics for each marker type to choose from. Genetic patterns differ between species, but the potential tradeoffs among genetic objectives for multiple species in conservation planning are currently understudied. We compared spatial conservation prioritizations derived from 2 metrics of genetic diversity (nucleotide and haplotype diversity) and 2 metrics of genetic isolation (private haplotypes and local genetic differentiation) in mitochondrial DNA of 5 marine species. We compared outcomes of conservation plans based only on habitat representation with plans based on genetic data and habitat representation. Fewer priority areas were selected for conservation plans based solely on habitat representation than on plans that included habitat and genetic data. All 4 genetic metrics selected approximately similar conservation-priority areas, which is likely a result of prioritizing genetic patterns across a genetically diverse array of species. Largely, our results suggest that multispecies genetic conservation objectives are vital to creating protected-area networks that appropriately preserve community-level evolutionary patterns.

Integrating biogeography, threat and evolutionary data to explore extinction crisis in the taxonomic group of cycads

Will the ongoing extinction crisis cause a severe loss of evolutionary information accumulated over millions of years on the tree of life? This question has been largely explored, particularly for vertebrates and angiosperms. However, no equivalent effort has been devoted to gymnosperms. Here, we address this question focusing on cycads, the gymnosperm group exhibiting the highest proportion of threatened species in the plant kingdom. We assembled the first complete phylogeny of cycads and assessed how species loss under three scenarios would impact the cycad tree of life. These scenarios are as follows: (1) All top 50% of evolutionarily distinct (ED) species are lost; (2) all threatened species are lost; and (3) only all threatened species in each IUCN category are lost. Finally, we analyzed the biogeographical pattern of cycad diversity hotspots and tested for gaps in the current global conservation network. First, we showed that threatened species are not significantly clustered on the cycad tree of life. Second, we showed that the loss of all vulnerable or endangered species does not depart significantly from random loss. In contrast, the loss of all top 50% ED, all threatened or all critically endangered species, would result in a greater loss of PD (Phylogenetic Diversity) than expected. To inform conservation decisions, we defined five hotpots of diversity, and depending on the diversity metric used, these hotspots are located in Southern Africa, Australia, Indo‐Pacific, and Mexico and all are found within protected areas. We conclude that the phylogenetic diversity accumulated over millions of years in the cycad tree of life would not survive the current extinction crisis. As such, prioritizing efforts based on ED and concentrating efforts on critically endangered species particularly in southern Africa, Australia, Indo‐Pacific, and Mexico are required to safeguarding the evolutionary diversity in the cycad tree of life.