Harnessing ecological theory to enhance ecosystem restoration.

Ecosystem restoration can increase the health and resilience of nature and humanity. As a result, the international community is championing habitat restoration as a primary solution to address the dual climate and biodiversity crises. Yet most ecosystem restoration efforts to date have underperformed, failed, or been burdened by high costs that prevent upscaling. To become a primary, scalable conservation strategy, restoration efficiency and success must increase dramatically. Here, we outline how integrating ten foundational ecological theories that have not previously received much attention - from hierarchical facilitation to macroecology - into ecosystem restoration planning and management can markedly enhance restoration success. We propose a simple, systematic approach to determining which theories best align with restoration goals and are most likely to bolster their success. Armed with a century of advances in ecological theory, restoration practitioners will be better positioned to more cost-efficiently and effectively rebuild the world's ecosystems and support the resilience of our natural resources.

Scale-dependent topographic complexity underpins abundance and spatial distribution of ecosystem engineers on natural and artificial structures.

In response to ongoing coastal urbanization, it is critical to develop effective methods to improve the biodiversity and ecological sustainability of artificial shorelines. Enhancing the topographic complexity of coastal infrastructure through the mimicry of natural substrata may facilitate the establishment of ecosystem engineering species and associated biogenic habitat formation. However, interactions between ecosystem engineers and their substratum are likely determined by organismal size and resource needs, thus making responses to topography highly scale-dependent. Here, we assessed the topographic properties (rugosity, surface area, micro-surface orientations) that underpin the abundance and distribution of two ecosystem engineers (fucoids, limpets) across six spatial scales (1-500 mm). Furthermore, we assessed the 'biogenic' rugosity created by barnacle matrices across fine scales (1-20 mm). Field surveys and 3D scanning, conducted across natural and artificial substrata, showed major effects of rugosity and associated topographic variables on ecosystem engineer assemblages and spatial occupancy, while additional abiotic environmental factors (compass direction, wave exposure) and biotic associations only had weak influences. Natural substrata exhibited ≤67 % higher rugosity than artificial ones. Fucoid-covered patches were predominantly associated with high-rugosity substrata and horizontal micro-surfaces, while homescars of limpets (≥15 mm shell length) predominated on smoother substratum patches. Barnacle-driven rugosity homogenized substrata at scales ≤10 mm. Our findings suggest that scale-dependent rugosity is a key driver of fucoid habitat formation and limpet habitat use, with wider eco-engineering applications for mimicking ecologically impactful topography on coastal infrastructure.

Topography-based modulation of environmental factors as a mechanism for intertidal microhabitat formation: A basis for marine ecological design.

Topographic complexity is often considered to be closely associated with habitat complexity and niche diversity; however, complex topography per se does not imply habitat suitability. Rather, ecologically suitable habitats may emerge if topographic features interact with environmental factors and thereby alter their surrounding microenvironment to the benefit of local organisms (e.g., resource provisioning, stress mitigation). Topography may thus act as a key modulator of abiotic stressors and biotic pressures, particularly in environmentally challenging intertidal systems. Here, we review how topography can alter microhabitat conditions with respect to four resources required by intertidal organisms: a source of energy (light, suspended food particles, prey, detritus), water (hydration, buffering of light, temperature and hydrodynamics), shelter (temperature, wave exposure, predation), and habitat space (substratum area, propagule settlement, movement). We synthesize mechanisms and quantitative findings of how environmental factors can be altered through topography and suggest an organism-centered 'form-follows-ecological-function' approach to designing multifunctional marine infrastructure.

Functional diversity of sharks and rays is highly vulnerable and supported by unique species and locations worldwide.

Elasmobranchs (sharks, rays and skates) are among the most threatened marine vertebrates, yet their global functional diversity remains largely unknown. Here, we use a trait dataset of >1000 species to assess elasmobranch functional diversity and compare it against other previously studied biodiversity facets (taxonomic and phylogenetic), to identify species- and spatial- conservation priorities. We show that threatened species encompass the full extent of functional space and disproportionately include functionally distinct species. Applying the conservation metric FUSE (Functionally Unique, Specialised, and Endangered) reveals that most top-ranking species differ from the top Evolutionarily Distinct and Globally Endangered (EDGE) list. Spatial analyses further show that elasmobranch functional richness is concentrated along continental shelves and around oceanic islands, with 18 distinguishable hotspots. These hotspots only marginally overlap with those of other biodiversity facets, reflecting a distinct spatial fingerprint of functional diversity. Elasmobranch biodiversity facets converge with fishing pressure along the coast of China, which emerges as a critical frontier in conservation. Meanwhile, several components of elasmobranch functional diversity fall in high seas and/or outside the global network of marine protected areas. Overall, our results highlight acute vulnerability of the world's elasmobranchs' functional diversity and reveal global priorities for elasmobranch functional biodiversity previously overlooked.

Top ten priorities for global saltmarsh restoration, conservation and ecosystem service research.

Coastal saltmarshes provide globally important ecosystem services including 'blue carbon' sequestration, flood protection, pollutant remediation, habitat provision and cultural value. Large portions of marshes have been lost or fragmented as a result of land reclamation, embankment construction, and pollution. Sea level rise threatens marsh survival by blocking landward migration where coastlines have been developed. Research-informed saltmarsh conservation and restoration efforts are helping to prevent further loss, yet significant knowledge gaps remain. Using a mixed methods approach, this paper identifies ten research priorities through an online questionnaire and a residential workshop attended by an international, multi-disciplinary network of 35 saltmarsh experts spanning natural, physical and social sciences across research, policy, and practitioner sectors. Priorities have been grouped under four thematic areas of research: Saltmarsh Area Extent, Change and Restoration Potential (including past, present, global variation), Spatio-social contexts of Ecosystem Service delivery (e.g. influences of environmental context, climate change, and stakeholder groups on service provisioning), Patterns and Processes in saltmarsh functioning (global drivers of saltmarsh ecosystem structure/function) and Management and Policy Needs (how management varies contextually; challenges/opportunities for management). Although not intended to be exhaustive, the challenges, opportunities, and strategies for addressing each research priority examined here, providing a blueprint of the work that needs to be done to protect saltmarshes for future generations.

Abrogation of MAP4K4 protein function causes congenital anomalies in humans and zebrafish.

We report 21 families displaying neurodevelopmental differences and multiple congenital anomalies while bearing a series of rare variants in mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4). MAP4K4 has been implicated in many signaling pathways including c-Jun N-terminal and RAS kinases and is currently under investigation as a druggable target for multiple disorders. Using several zebrafish models, we demonstrate that these human variants are either loss-of-function or dominant-negative alleles and show that decreasing Map4k4 activity causes developmental defects. Furthermore, MAP4K4 can restrain hyperactive RAS signaling in early embryonic stages. Together, our data demonstrate that MAP4K4 negatively regulates RAS signaling in the early embryo and that variants identified in affected humans abrogate its function, establishing MAP4K4 as a causal locus for individuals with syndromic neurodevelopmental differences.

Are shark teeth proxies for functional traits? A framework to infer ecology from the fossil record.

Modern sharks have an evolutionary history of at least 250 million years and are known to play key roles in marine systems, from controlling prey populations to connecting habitats across oceans. These ecological roles can be quantified based on their functional traits, which are typically morphological (e.g., body size) or behavioural (e.g., feeding and diet). Nonetheless, the understanding of such roles of extinct sharks is limited due to the inherent incompleteness of their fossil record, which consists mainly of isolated teeth. As such, establishing links between tooth morphology and ecological traits in living sharks could provide a useful framework to infer sharks' ecology from the fossil record. Here, based on extant sharks from which morphological and behavioural characteristics are known, the authors assess the extent to which isolated teeth can serve as proxies for functional traits. To do so, they first review the scientific literature on extant species to evaluate the use of shark dental characters as proxies for ecology to then perform validation analyses based on an independent data set collected from museum collections. Their results reveal that 12 dental characters have been used in shark literature as proxies for three functional traits: body size, prey preference and feeding mechanism. From all dental characters identified, tooth size and cutting edge are the most widely used. Validation analyses suggest that seven dental characters - crown height, crown width, cutting edge, lateral cusplets, curvature, longitudinal outline and cross-section outline - are the best proxies for the three functional traits. In particular, tooth size (crown height and width) was found to be a reliable proxy of all three traits; the presence of serrations on the cutting edge was one of the best proxies for prey preference; and tooth shape (longitudinal outline) and the presence of lateral cusplets were among the best indicators of feeding mechanism. Overall, the authors' results suggest that in the absence of directly measurable traits in the fossil record, these seven dental characters (and different combinations of them) can be used to quantify the ecological roles of extinct sharks. This information has the potential to provide key insights into how shark functional diversity has changed through time, including their ecological responses to extinction events.

Wrack enhancement of post-hurricane vegetation and geomorphological recovery in a coastal dune.

Coastal ecosystems such as sand dunes, mangrove forests, and salt marshes provide natural storm protection for vulnerable shorelines. At the same time, storms erode and redistribute biological materials among coastal systems via wrack. Yet how such cross-ecosystem subsidies affect post-storm recovery is not well understood. Here, we report an experimental investigation into the effect of storm wrack on eco-geomorphological recovery of a coastal embryo dune in north-eastern Florida, USA, following hurricane Irma. We contrasted replicated 100-m2 wrack-removal and unmanipulated (control) plots, measuring vegetation and geomorphological responses over 21 months. Relative to controls, grass cover was reduced 4-fold where diverse storm wrack, including seagrass rhizomes, seaweed, and wood, was removed. Wrack removal was also associated with a reduction in mean elevation, which persisted until the end of the experiment when removal plots had a 14% lower mean elevation than control plots. These results suggest that subsides of wrack re-distributed from other ecosystem types (e.g. seagrasses, macroalgae, uplands): i) enhances the growth of certain dune-building grasses; and ii) boosts the geomorphological recovery of coastal dunes. Our study also indicates that the practice of post-storm beach cleaning to remove wrack-a practice widespread outside of protected areas-may undermine the resilience of coastal dunes and their services.

A Pleistocene legacy structures variation in modern seagrass ecosystems.

Distribution of Earth's biomes is structured by the match between climate and plant traits, which in turn shape associated communities and ecosystem processes and services. However, that climate-trait match can be disrupted by historical events, with lasting ecosystem impacts. As Earth's environment changes faster than at any time in human history, critical questions are whether and how organismal traits and ecosystems can adjust to altered conditions. We quantified the relative importance of current environmental forcing versus evolutionary history in shaping the growth form (stature and biomass) and associated community of eelgrass (Zostera marina), a widespread foundation plant of marine ecosystems along Northern Hemisphere coastlines, which experienced major shifts in distribution and genetic composition during the Pleistocene. We found that eelgrass stature and biomass retain a legacy of the Pleistocene colonization of the Atlantic from the ancestral Pacific range and of more recent within-basin bottlenecks and genetic differentiation. This evolutionary legacy in turn influences the biomass of associated algae and invertebrates that fuel coastal food webs, with effects comparable to or stronger than effects of current environmental forcing. Such historical lags in phenotypic acclimatization may constrain ecosystem adjustments to rapid anthropogenic climate change, thus altering predictions about the future functioning of ecosystems.

The biogeography of community assembly: latitude and predation drive variation in community trait distribution in a guild of epifaunal crustaceans.

While considerable evidence exists of biogeographic patterns in the intensity of species interactions, the influence of these patterns on variation in community structure is less clear. Studying how the distributions of traits in communities vary along global gradients can inform how variation in interactions and other factors contribute to the process of community assembly. Using a model selection approach on measures of trait dispersion in crustaceans associated with eelgrass (Zostera marina) spanning 30° of latitude in two oceans, we found that dispersion strongly increased with increasing predation and decreasing latitude. Ocean and epiphyte load appeared as secondary predictors; Pacific communities were more overdispersed while Atlantic communities were more clustered, and increasing epiphytes were associated with increased clustering. By examining how species interactions and environmental filters influence community structure across biogeographic regions, we demonstrate how both latitudinal variation in species interactions and historical contingency shape these responses. Community trait distributions have implications for ecosystem stability and functioning, and integrating large-scale observations of environmental filters, species interactions and traits can help us predict how communities may respond to environmental change.

Functional diversity of habitat formers declines scale-dependently across an environmental stress gradient.

Marine habitat formers such as seaweeds and corals are lynchpins of coastal ecosystems, but their functional diversity and how it varies with scale and context remains poorly studied. Here, we investigate the functional diversity of seaweed assemblages across the rocky intertidal stress gradient at large (zones) and small (quadrat) scales. We quantified complementary metrics of emergent group richness, functional richness (functional space occupied) and functional dispersion (trait complementarity of dominant species). With increasing shore height, under species loss and turnover, responses of functional diversity were scale- and metric-dependent. At the large scale, functional richness contracted while-notwithstanding a decline in redundancy-emergent group richness and functional dispersion were both invariant. At the small scale, all measures declined, with the strongest responses evident for functional and emergent group richness. Comparisons of observed versus expected values based on null models revealed that functional richness and dispersion were greater than expected in the low shore but converged with expected values higher on the shore. These results show that functional diversity of assemblages of marine habitat formers can be especially responsive to environmental stress gradients at small scales and for richness measures. Furthermore, niche-based processes at the small-neighbourhood-scale can favour co-occurrence of functionally distinctive species under low, but not high, stress, magnifying differences in functional diversity across environmental gradients. As assemblages of marine habitat formers face accelerating environmental change, further studies examining multiple aspects of functional diversity are needed to elucidate patterns, processes, and ecosystem consequences of community (dis-)assembly across diverse groups.

Loss of function mutations in CCDC32 cause a congenital syndrome characterized by craniofacial, cardiac and neurodevelopmental anomalies.

Despite the wide use of genomics to investigate the molecular basis of rare congenital malformations, a significant fraction of patients remains bereft of diagnosis. As part of our continuous effort to recruit and perform genomic and functional studies on such cohorts, we investigated the genetic and mechanistic cause of disease in two independent consanguineous families affected by overlapping craniofacial, cardiac, laterality and neurodevelopmental anomalies. Using whole exome sequencing, we identified homozygous frameshift CCDC32 variants in three affected individuals. Functional analysis in a zebrafish model revealed that ccdc32 depletion recapitulates the human phenotypes. Because some of the patient phenotypes overlap defects common to ciliopathies, we asked if loss of CCDC32 might contribute to the dysfunction of this organelle. Consistent with this hypothesis, we show that ccdc32 is required for normal cilia formation in zebrafish embryos and mammalian cell culture, arguing that ciliary defects are at least partially involved in the pathomechanism of this disorder.

Novel truncating mutations in CTNND1 cause a dominant craniofacial and cardiac syndrome.

CTNND1 encodes the p120-catenin (p120) protein, which has a wide range of functions, including the maintenance of cell-cell junctions, regulation of the epithelial-mesenchymal transition and transcriptional signalling. Due to advances in next-generation sequencing, CTNND1 has been implicated in human diseases including cleft palate and blepharocheilodontic (BCD) syndrome albeit only recently. In this study, we identify eight novel protein-truncating variants, six de novo, in 13 participants from nine families presenting with craniofacial dysmorphisms including cleft palate and hypodontia, as well as congenital cardiac anomalies, limb dysmorphologies and neurodevelopmental disorders. Using conditional deletions in mice as well as CRISPR/Cas9 approaches to target CTNND1 in Xenopus, we identified a subset of phenotypes that can be linked to p120-catenin in epithelial integrity and turnover, and additional phenotypes that suggest mesenchymal roles of CTNND1. We propose that CTNND1 variants have a wider developmental role than previously described and that variations in this gene underlie not only cleft palate and BCD but may be expanded to a broader velocardiofacial-like syndrome.

Below-ground biomass of plants, with a key contribution of buried shoots, increases foredune resistance to wave swash.

BACKGROUND AND AIMS: Sand dunes reduce the impact of storms on shorelines and human infrastructure. The ability of these ecosystems to provide sustained coastal protection under persistent wave attack depends on their resistance to erosion. Although flume experiments show that roots of perennial plants contribute to foredune stabilization, the role of other plant organs, and of annual species, remains poorly studied. Furthermore, it remains unknown if restored foredunes provide the same level of erosion resistance as natural foredunes. We investigated the capacity of three widespread pioneer foredune species (the perennial Ammophila arenaria and the annuals Cakile maritima and Salsola kali) to resist dune erosion, and compared the erosion resistance of Ammophila at natural and restored sites. METHODS: Cores collected in the field were tested in a flume that simulated a wave swash. A multi-model inference approach was used to disentangle the contributions of different below-ground compartments (i.e. roots, rhizomes, buried shoots) to erosion resistance. KEY RESULTS: All three species reduced erosion, with Ammophila having the strongest effect (36 % erosion reduction versus unvegetated cores). Total below-ground biomass (roots, rhizomes and shoots), rather than any single compartment, most parsimoniously explained erosion resistance. Further analysis revealed that buried shoots had the clearest individual contribution. Despite similar levels of total below-ground biomass, coarser sediment reduced erosion resistance of Ammophila cores from the restored site relative to the natural site. CONCLUSIONS: The total below-ground biomass of both annual and perennial plants, including roots, rhizomes and buried shoots, reduced dune erosion under a swash regime. Notably, we show that (1) annual pioneer species offer erosion protection, (2) buried shoots are an important plant component in driving sediment stabilization, and (3) management must consider both biological (plants and their traits) and physical (grain size) factors when integrating dunes into schemes for coastal protection.

Alkylglycerol monooxygenase, a heterotaxy candidate gene, regulates left-right patterning via Wnt signaling.

Congenital heart disease (CHD) is a major cause of morbidity in the pediatric population yet its genetic and molecular causes remain poorly defined. Previously, we identified AGMO as a candidate heterotaxy disease gene, a disorder of left-right (LR) patterning that can have a profound effect on cardiac function. AGMO is the only known alkylglycerol monooxygenase, an orphan tetrahydrobiopterin dependent enzyme that cleaves the ether linkage in alkylglycerols. However, whether AGMO plays a role in LR patterning was unexplored. Here we reveal that Agmo is required for correct development of the embryonic LR axis in Xenopus embryos recapitulating the patient's heterotaxy phenotype. Mechanistically, we demonstrate that Agmo is a regulator of canonical Wnt signaling, required during gastrulation for normal formation of the left - right organizer. Mutational analysis demonstrates that this function is dependent on Agmo's alkylglycerol monooxygenase activity. Together, our findings identify Agmo as a regulator of canonical Wnt signaling, demonstrate a role for Agmo in embryonic axis formation, and provide insight into the poorly understood developmental requirements for ether lipid cleavage.

Induction of Neural Crest Stem Cells From Bardet-Biedl Syndrome Patient Derived hiPSCs.

Neural crest cells arise in the embryo from the neural plate border and migrate throughout the body, giving rise to many different tissue types such as bones and cartilage of the face, smooth muscles, neurons, and melanocytes. While studied extensively in animal models, neural crest development and disease have been poorly described in humans due to the challenges in accessing embryonic tissues. In recent years, patient-derived human induced pluripotent stem cells (hiPSCs) have become easier to generate, and several streamlined protocols have enabled robust differentiation of hiPSCs to the neural crest lineage. Thus, a unique opportunity is offered for modeling neurocristopathies using patient specific stem cell lines. In this work, we make use of hiPSCs derived from patients affected by the Bardet-Biedl Syndrome (BBS) ciliopathy. BBS patients often exhibit subclinical craniofacial dysmorphisms that are likely to be associated with the neural crest-derived facial skeleton. We focus on hiPSCs carrying variants in the BBS10 gene, which encodes a protein forming part of a chaperonin-like complex associated with the cilium. Here, we establish a pipeline for profiling hiPSCs during differentiation toward the neural crest stem cell fate. This can be used to characterize the differentiation properties of the neural crest-like cells. Two different BBS10 mutant lines showed a reduction in expression of the characteristic neural crest gene expression profile. Further analysis of both BBS10 mutant lines highlighted the inability of these mutant lines to differentiate toward a neural crest fate, which was also characterized by a decreased WNT and BMP response. Altogether, our study suggests a requirement for wild-type BBS10 in human neural crest development. In the long term, approaches such as the one we describe will allow direct comparison of disease-specific cell lines. This will provide valuable insights into the relationships between genetic background and heterogeneity in cellular models. The possibility of integrating laboratory data with clinical phenotypes will move us toward precision medicine approaches.

Expression of the guanine nucleotide exchange factor, RAPGEF5, during mouse and human embryogenesis.

Rap GTPases mediate fundamental cellular processes, including cell adhesion, migration and intracellular signal transduction. The subcellular activity of these GTPases is regulated by dedicated activators (guanine nucleotide exchange factors, GEFs) and deactivators (GTPase-activating proteins, GAPs). RAPGEF5 is a potent activator of Rap proteins and mutations in RAPGEF5 have been linked to both neurological disorders and congenital heart disease. In the frog model, Xenopus tropicalis, Rapgef5 is a critical regulator of the canonical Wnt signalling pathway and is required for normal gastrulation and correct establishment of the left-right body axis. However, requirements for RAPGEF5 in other developmental contexts, and in mammalian embryogenesis in particular, remain undefined. Here, we describe RAPGEF5 mRNA expression patterns during mouse (E9.5 - E16.5) and human (Carnegie stage 21) development, as an initial step towards better understanding its developmental functions.

RPSA, a candidate gene for isolated congenital asplenia, is required for pre-rRNA processing and spleen formation in Xenopus.

A growing number of tissue-specific inherited disorders are associated with impaired ribosome production, despite the universal requirement for ribosome function. Recently, mutations in RPSA, a protein component of the small ribosomal subunit, were discovered to underlie approximately half of all isolated congenital asplenia cases. However, the mechanisms by which mutations in this ribosome biogenesis factor lead specifically to spleen agenesis remain unknown, in part due to the lack of a suitable animal model for study. Here we reveal that RPSA is required for normal spleen development in the frog, Xenopus tropicalis Depletion of Rpsa in early embryonic development disrupts pre-rRNA processing and ribosome biogenesis, and impairs expression of the key spleen patterning genes nkx2-5, bapx1 and pod1 in the spleen anlage. Importantly, we also show that whereas injection of human RPSA mRNA can rescue both pre-rRNA processing and spleen patterning, injection of human mRNA bearing a common disease-associated mutation cannot. Together, we present the first animal model of RPSA-mediated asplenia and reveal a crucial requirement for RPSA in pre-rRNA processing and molecular patterning during early Xenopus development.

Multiple dimensions of biodiversity drive human interest in tide pool communities.

Activities involving observation of wild organisms (e.g. wildlife watching, tidepooling) can provide recreational and learning opportunities, with biologically diverse animal assemblages expected to be more stimulating to humans. In turn, more diverse communities may enhance human interest and facilitate provisioning of cultural services. However, no experimental tests of this biodiversity-interest hypothesis exist to date. We therefore investigated the effects of different dimensions of animal biodiversity (species richness, phyletic richness and functional diversity) on self-reported interest using tide pools as a model system. We performed two experiments by manipulating: (1) the richness of lower (species) and higher taxonomic levels (phyla) in an image based, online survey, and (2) the richness of the higher taxonomic level (phyla) in live public exhibits. In both experiments, we further quantified functional diversity, which varied freely, and within the online experiment we also included the hue diversity and colourfulness arising from the combination of organisms and the background scenes. Interest was increased by phyletic richness (both studies), animal species richness (online study) and functional diversity (online study). A structural equation model revealed that functional diversity and colourfulness (of the whole scene) also partially mediated the effects of phyletic richness on interest in the online study. In both studies, the presence of three of four phyla additively increased interest, supporting the importance of multiple, diverse phyla rather than a single particularly interesting phylum. These results provide novel experimental evidence that multiple dimensions of biodiversity enhance human interest and suggest that conservation initiatives that maintain or restore biodiversity will help stimulate interest in ecosystems, facilitating educational and recreational benefits.