Incorporating seascape connectivity in conservation prioritisation

Linking tidal wetland vegetation mosaics to micro-topography and hydroperiod in a tropical estuary

Although saltmarshes are critical coastal ecosystems they are threatened by human activities and sea-level rise (SLR). Long-term restoration and management strategies are often hampered by an insufficient understanding of the past, present, and future processes that influence tidal wetland functionality and change. As understanding vegetation distribution in relation to elevation and tidal hydroperiod is often the basis of restoration and management decisions, this study investigated the relationships between micro-topography, tidal hydroperiod, and the distribution of saltmarshes, mangroves, and unvegetated flats in a tropical estuary situated within a Great Barrier Reef Catchment in North Queensland, Australia. A combination of high-resolution unattended-aerial-vehicle (UAV)-derived digital elevation model (DEMs) and land cover coupled with 2D hydrodynamic modelling was used to investigate these aspects. Zonation was more complex than generally recognised in restoration and legislation, with overlapping distribution across elevation. Additionally, although each type of tidal wetland cover had distinct mean hydroperiods, and elevation and hydroperiods were strongly correlated, elevation explained only 15% of the variability in tidal wetland cover distribution. This suggests that other factors (e.g., groundwater dynamics) likely contribute to tidal wetland cover zonation patterns. These findings underline that simplistic rules in the causality of tidal wetlands need to be applied with caution. Their applicability in management and restoration are likely to vary depending on contexts, as observed in our study site, with varying environmental and biological factors playing important roles in the distribution patterns of tidal wetland components. We also identified strong monthly variability in tidal hydroperiods and connectivity experienced by each tidal wetland cover (e.g., 10.26% of succulent saltmarshes were inundated during lower-than-average tides compared to 66% in higher than-average tides), highlighting the importance of integrating temporal dynamics in tidal wetland research and management. Additionally, we explored the potential effects of sea-level rise (SLR) on the tidal hydroperiods and connectivity of our study site. The results show that the inundation experienced by each tidal wetland cover may increase importantly if vegetation does not keep up with SLR (e.g., under a 0.8 m sea level scenarios, mean maximum depth of succulent saltmarsh in higher-than-average tides is 184.1 mm higher than the current mean-maximum inundation depth of mangroves). This underlines the importance of acquiring detailed spatio-temporally resolved data to enable the development of robust long-term and adaptive saltmarsh management strategies. Our results are discussed from a management and restoration perspective. We highlight the uncertainties and complexities in understanding the processes influencing tidal wetland functionality, and hence, their management and restoration prospects.

Aquatic connectivity: challenges and solutions in a changing climate

The challenge of managing aquatic connectivity in a changing climate is exacerbated in the presence of additional anthropogenic stressors, social factors, and economic drivers. Here we discuss these issues in the context of structural and functional connectivity for aquatic biodiversity, specifically fish, in both the freshwater and marine realms. We posit that adaptive management strategies that consider shifting baselines and the socio-ecological implications of climate change will be required to achieve management objectives. The role of renewable energy expansion, particularly hydropower, is critically examined for its impact on connectivity. We advocate for strategic spatial planning that incorporates nature-positive solutions, ensuring climate mitigation efforts are harmonized with biodiversity conservation. We underscore the urgency of integrating robust scientific modelling with stakeholder values to define clear, adaptive management objectives. Finally, we call for innovative monitoring and predictive decision-making tools to navigate the uncertainties inherent in a changing climate, with the goal of ensuring the resilience and sustainability of aquatic ecosystems.

Comparing spatial conservation prioritization methods with site- versus spatial dependency-based connectivity

Larval dispersal is an important component of marine reserve networks. Two conceptually different approaches to incorporate dispersal connectivity into spatial planning of these networks exist, and it is an open question as to when either is most appropriate. Candidate reserve sites can be selected individually based on local properties of connectivity or on a spatial dependency-based approach of selecting clusters of strongly connected habitat patches. The first acts on individual sites, whereas the second acts on linked pairs of sites. We used a combination of larval dispersal simulations representing different seascapes and case studies of biophysical larval dispersal models in the Coral Triangle region and the province of Southeast Sulawesi, Indonesia, to compare the performance of these 2 methods in the spatial planning software Marxan. We explored the reserve design performance implications of different dispersal distances and patterns based on the equilibrium settlement of larvae in protected and unprotected areas. We further assessed different assumptions about metapopulation contributions from unprotected areas, including the case of 100% depletion and more moderate scenarios. The spatial dependency method was suitable when dispersal was limited, a high proportion of the area of interest was substantially degraded, or the target amount of habitat protected was low. Conversely, when subpopulations were well connected, the 100% depletion was relaxed, or more habitat was protected, protecting individual sites with high scores in metrics of connectivity was a better strategy. Spatial dependency methods generally produced more spatially clustered solutions with more benefits inside than outside reserves compared with site-based methods. Therefore, spatial dependency methods potentially provide better results for ecological persistence objectives over enhancing fisheries objectives, and vice versa. Different spatial prioritization methods of using connectivity are appropriate for different contexts, depending on dispersal characteristics, unprotected area contributions, habitat protection targets, and specific management objectives. Comparación entre los métodos de priorización de la conservación espacial con sitio y la conectividad espacial basada en la dependencia.

Genomic assessment reveals signal of adaptive selection in populations of the Spotted rose snapper Lutjanus guttatus from the Tropical Eastern Pacific

Background

The lack of barriers in the marine environment has promoted the idea of panmixia in marine organisms. However, oceanographic conditions and habitat characteristics have recently been linked to genetic structure in marine species. The Tropical Eastern Pacific (TEP) is characterized by dynamic current systems and heterogeneous oceanographic conditions. The Gulf of Panama (part of the equatorial segment for the TEP) is influenced by a complex current system and heterogeneous environment, which has been shown to limit the gene flow for shoreline species. Next Generation Sequencing (NGS) has contributed to detect genetic differences in previously reported panmictic species by the assessment of loci associated with selection and to understand how selection acts affects marine populations. Lutjanus guttatus is a species distributed in the TEP for which previous studies using mitochondrial data recovered a panmictic pattern along its distributional range. In this study, we used SNP data of L. guttatus individuals sampled along its range to evaluate population genetic structure and investigate whether oceanographic factors influence the species’ genetic architecture. Finally, we assessed the role of adaptive selection by evaluating the contribution of outlier and neutral loci to genetic divergence.

Methods

The RADcap method was used to obtain 24 million paired reads for 123 individuals of L. guttatus covering nearly all its distributional area. Genetic variation was assessed using both spatial and non-spatial methods by comparing three different data sets: (i) a Combined Loci (CL dataset = 2003 SNPs); a search for putative loci under selection allowed the evaluation of (ii) Neutral Loci (NL dataset = 1858 SNPs) and (iii) Outlier Loci (OL dataset = 145 SNPs). We used the estimating effective migration surface (EEMS) approach to detect possible barriers to gene flow.

Results

Genetic differences were found in the OL dataset, showing two clusters (Northern and Southern), whereas NL showed no differences. This result may be related to the Selection-Migration balance model. The limit between the Northern and Southern groups was in the Gulf of Panama, which has been previously identified as a barrier to gene flow for other species, mainly due to its heterogeneous oceanographic conditions. The results suggest that selection plays an important role in generating genetic differences in Lutjanus guttatus. A migration corridor was detected that coincides with the Costa Rica Coastal Current that flows from Central America to the Gulf of California, allowing the homogenization of the northern population. In the Southern cluster, a migration corridor was observed with the OL from Panama to Colombia, which could be associated with the currents found in the Gulf of Panama. Genetic variation found in the OL of Lutjanus guttatus highlights the usefulness of NGS data in evaluating the role of selection in population differentiation.

Co-designing an Indicator of Habitat Connectivity for England

Landscapes have been drastically transformed by human activities, generally resulting in the loss of semi-natural habitat. In the United Kingdom, wildlife habitat mainly consists of small patches of semi-natural habitat that are poorly connected to each other. In May 2019 the United Kingdom Government published an outcome indicator framework for measuring progress against the goals and outcomes of the 25 Year Environment Plan (YEP) for England. The indicator of the Quantity, Quality and Connectivity of Habitats (D1) is one of seven indicators within the Wildlife theme and it follows the principle of making areas of semi-natural habitat “more, bigger, better and joined up.” In this study, we describe the process of co-designing the connectivity metric for indicator D1. In consultation with experts and stakeholders we selected three candidate landscape connectivity metrics to produce the indicator. The first metric comes from a suite of rules of thumb for practitioners and it is the proportion of habitat patches in the landscape that have a nearest neighbor ≤ 1 km away. The second metric is a habitat fragmentation index from the Natural England National Biodiversity Climate Change Vulnerability Assessment Tool (NBCCVAT). The third and final metric is from the software Condatis and it represents the ability of a species to move through a landscape. We tested each metric on a set of simulated landscapes representing different levels of habitat addition strategies and different spatial configurations. We asked if the metrics are able to detect changes in the connectivity of each of these landscapes after habitat addition. Two of the three metrics (NBCCVAT and Condatis) performed well and were sensitive to change. They both increased as the total extent of habitat increased and each showed particular sensitivity to one spatial arrangement over the other. Given these results, one or both of these metrics could be used to produce the indicator. We discuss the implications of using one or both of the metrics and highlight the fundamental choices that need to be made to produce the indicator.

Ecological connectivity of the marine protected area network in the Baltic Sea, Kattegat and Skagerrak: Current knowledge and management needs

Marine protected areas (MPAs) have become a key component of conservation and fisheries management to alleviate anthropogenic pressures. For MPA networks to efficiently promote persistence and recovery of populations, ecological connectivity, i.e. dispersal and movement of organisms and material across ecosystems, needs to be taken into account. To improve the ecological coherence of MPA networks, there is hence a need to evaluate the connectivity of species spreading through active migration and passive dispersal. We reviewed knowledge on ecological connectivity in the Baltic Sea, Kattegat and Skagerrak in the northeast Atlantic and present available information on species-specific dispersal and migration distances. Studies on genetic connectivity are summarised and discussed in relation to dispersal-based analyses. Threats to ecological connectivity, limiting dispersal of populations and lowering the resilience to environmental change, were examined. Additionally, a review of studies evaluating the ecological coherence of MPA networks in the Baltic Sea, Kattegat and Skagerrak was performed, and suggestions for future evaluations to meet management needs are presented.

Evolving spatial conservation prioritization with intraspecific genetic data

Spatial conservation prioritization (SCP) is a planning framework used to identify new conservation areas on the basis of the spatial distribution of species, ecosystems, and their services to human societies. The ongoing accumulation of intraspecific genetic data on a variety of species offers a way to gain knowledge of intraspecific genetic diversity and to estimate several population characteristics useful in conservation, such as dispersal and population size. Here, we review how intraspecific genetic data have been integrated into SCP and highlight their potential for identifying conservation area networks that represent intraspecific genetic diversity comprehensively and that ensure the long-term persistence of biodiversity in the face of global change.

Habitat Suitability Modeling to Inform Seascape Connectivity Conservation and Management

Coastal habitats have experienced significant degradation and fragmentation in recent decades under the strain of interacting ecosystem stressors. To maintain biodiversity and ecosystem functioning, coastal managers and restoration practitioners face the urgent tasks of identifying priority areas for protection and developing innovative, scalable approaches to habitat restoration. Facilitating these efforts are models of seascape connectivity, which represent ecological linkages across heterogeneous marine environments by predicting species-specific dispersal between suitable habitat patches. However, defining the suitable habitat patches and migratory pathways required to construct ecologically realistic connectivity models remains challenging. Focusing on two reef-associated fish species of the Florida Keys, United States of America (USA), we compared two methods for constructing species- and life stage-specific spatial models of habitat suitability—penalized logistic regression and maximum entropy (MaxEnt). The goal of the model comparison was to identify the modeling algorithm that produced the most realistic and detailed products for use in subsequent connectivity assessments. Regardless of species, MaxEnt’s ability to distinguish between suitable and unsuitable locations exceeded that of the penalized regressions. Furthermore, MaxEnt’s habitat suitability predictions more closely aligned with the known ecology of the study species, revealing the environmental conditions and spatial patterns that best support each species across the seascape, with implications for predicting connectivity pathways and the distribution of key ecological processes. Our research demonstrates MaxEnt’s promise as a scalable, species-specific, and spatially explicit tool for informing models of seascape connectivity and guiding coastal conservation efforts.

Drivers for genetic structure at different geographic scales for Pacific red snapper (Lutjanus peru) and yellow snapper (Lutjanus argentiventris) in the tropical eastern Pacific

The tropical eastern Pacific (TEP) is a highly dynamic region and a model system to study how habitat discontinuities affect the distribution of shorefishes, particularly for species that display ontogenetic habitat shifts, including snappers (Lutjanidae). To evaluate the genetic structure of the Pacific red snapper (Lutjanus peru) and the yellow snapper (Lutjanus argentiventris) throughout their distribution range along the TEP, 13 and 11 microsatellite loci were analysed, respectively. The genetic diversity of L. peru (N = 446) and L. argentiventris (N = 170) was evaluated in 10 and 5 localities, respectively, showing slightly higher but non-significant values in the Gulf of California for both species. The genetic structure analysis identified the presence of significant genetic structure in both species, but the locations of the identified barriers for the gene flow differed between species. The principal driver for the genetic structure at large scales >2500 km was isolation by distance. At smaller scales (<250 km), the habitat discontinuity for juveniles and adults and the environmental differences throughout the distribution range represented potential barriers to gene flow between populations for both species.

An appraisal of systematic conservation planning for Pacific Ocean Tropical Islands coastal environments

Systematic Conservation Planning (SCP) offers concepts and toolboxes to make spatial decisions on where to focus conservation actions while minimizing a variety of costs to stakeholders. Thirty-four studies of Pacific Ocean Tropical Islands were scrutinized to categorize past and current types of applications. It appeared that scenarios were often built on a biodiversity representation objective, opportunity costs for fishers was the most frequent cost factor, and an evolution from simple to sophisticated scenarios followed the need to maximize resilience and connectivity while mitigating climate change impacts. However, proxies and models were often not validated, pointing to data quality issues. Customary management by local communities motivated applications specific to the Pacific region, but several island features remained ignored, including invertebrate fishing, ciguatera poisoning and mariculture. Fourteen recommendations are provided to enhance scenarios' robustness, island specificities integration, complex modelling accuracy, and better use of SCP for island management.

Comparing abundance distributions and range maps in spatial conservation planning for migratory species

Most spatial conservation planning for wide-ranging or migratory species is constrained by poor knowledge of species' spatiotemporal dynamics and is only based on static species' ranges. However, species have substantial variation in abundance across their range and migratory species have important spatiotemporal population dynamics. With growing ecological data and advancing analytics, both of these can be estimated and incorporated into spatial conservation planning. However, there is limited information on the degree to which including this information affects conservation planning. We compared the performance of systematic conservation prioritizations for different scenarios based on varying the input species' distributions by ecological metric (abundance distributions versus range maps) and temporal sampling resolution (weekly, monthly, or quarterly). We used the example of a community of 41 species of migratory shorebirds that breed in North America, and we used eBird data to produce weekly estimates of species' abundances and ranges. Abundance distributions at a monthly or weekly resolution led to prioritizations that most efficiently protected species throughout the full annual cycle. Conversely, spatial prioritizations based on species' ranges required more sites and left most species insufficiently protected for at least part of their annual cycle. Prioritizations with only quarterly species ranges were very inefficient as they needed to target 40% of species' ranges to include 10% of populations. We highlight the high value of abundance information for spatial conservation planning, which leads to more efficient and effective spatial prioritization for conservation. Overall, we provide evidence that spatial conservation planning for wide-ranging migratory species is most robust and efficient when informed by species' abundance information from the full annual cycle.

Larval connectivity patterns of the North Indo-West Pacific coral reefs

Coral reefs of the North Indo-West Pacific provide important ecosystem services to the region but are subjected to multiple local and global threats. Strengthening management measures necessitate understanding the variability of larval connectivity and bridging global connectivity models to local scales. An individual-based Lagrangian biophysical model was used to simulate connectivity between coral reefs for three organisms with different early life history characteristics: a coral (Acropora millepora), a sea urchin (Tripneustes gratilla), and a reef fish (Epinephelus sp). Connectivity metrics and reef clusters were computed from the settlement probability matrices. Fitted power law functions derived from the dispersal kernels provided relative probabilities of connection given only the distance between reefs, and demonstrated that 95% of the larvae across organisms settled within a third of their maximum settlement distances. The magnitude of the connectivity metric values of reef cells were sensitive to differences both in the type of organism and temporal variability. Seasonal variability of connections was more dominant than interannual variability. However, despite these differences, the moderate to high correlation of metrics between organisms and seasonal matrices suggest that the spatial patterns are relatively similar between reefs. A cluster analysis based on the Bray-Curtis Dissimilarity of sink and source connections synthesized the inherent variability of these multiple large connectivity matrices. Through this, similarities in regional connectivity patterns were determined at various cluster sizes depending on the scale of interest. The validity of the model is supported by 1) the simulated dispersal kernels being within the range of reported parentage analysis estimates; and, 2) the clusters that emerged reflect the dispersal barriers implied by previously published population genetics studies. The tools presented here (dispersal kernels, temporal variability maps and reef clustering) can be used to include regional patterns of connectivity into the spatial management of coral reefs.

An approach to incorporating inferred connectivity of adult movement into marine protected area design with limited data

Marine protected areas (MPAs) are important conservation tools that can support the resilience of marine ecosystems. Many countries, including Canada, have committed to protecting at least 10% of their marine areas under the Convention on Biological Diversity's Aichi Target 11, which includes connectivity as a key aspect. Connectivity, the movement of individuals among habitats, can enhance population stability and resilience within and among MPAs. However, little is known about regional spatial patterns of marine ecological connectivity, particularly adult movement. We developed a method to assess and design MPA networks that maximize inferred connectivity within habitat types for adult movement when ecological data are limited. We used the Northern Shelf Bioregion in British Columbia, Canada, to explore two different approaches: (1) evaluating sites important for inferred regional connectivity (termed hotspots) and (2) assessing MPA network configurations based on their overlap with connectivity hotspots and interconnectedness between MPAs. To assess inferred connectivity via adult movement, we used two different threshold distances (15 and 50 km) to capture moderate home ranges, which are most appropriate to consider in MPA design. We applied graph theory to assess inferred connectivity within 16 habitat and depth categories (proxies for distinct ecological communities), and used novel multiplex network methodologies to perform an aggregated assessment of inferred connectivity. We evaluated inferred regional connectivity hotspots based on betweenness and eigenvector centrality metrics, finding that the existing MPA network overlapped a moderate proportion of these regional hotspots and identified key areas to be considered as candidate MPAs. Network density among existing MPAs was low within the individual habitat networks, as well as the multiplex. This work informs an ongoing MPA planning process, and approaches for incorporating connectivity into MPA design when data are limited, with lessons for other contexts.

Cross-shelf habitat shifts by red snapper (Lutjanus campechanus) in the Gulf of Mexico

Habitat shifts that occur during the life cycles of marine fishes influence population connectivity and structure. A generalized additive modeling approach was used to characterize relationships between environmental variables and the relative abundance of red snapper Lutjanus campechanus over unconsolidated substrate on the continental shelf (<150 m) of the U.S. Gulf of Mexico (GoM) at three different life stages: juvenile (age-0, <125 mm FL), sub-adult (age-1-2, 125-300 mm FL), and adult (age-2+, >300 mm FL). Fisheries independent data (2008-2014) were used to develop separate models for both the eastern and western GoM, and final models were used to predict the relative availability of suitable habitat for each life stage across the two regions. Predictor variables included in final models varied by age class and region, with depth, dissolved oxygen, longitude, and distance to artificial structure common to most models. Depth was among the most influential variables in all models, and preferred depth increased with increasing size/age. Regional differences in fish-habitat relationships were also observed, as relative abundance of larger red snapper over unconsolidated substrates was more closely linked to artificial structure in the eastern GoM. The location of predicted high quality habitat for juvenile red snapper was greatest on the inner Texas shelf and a smaller area east of the Mississippi River Delta, suggesting these two areas may represent important nursery grounds for the respective regions. Clear ontogenetic shifts in the spatial distribution of predicted high quality habitat were evident in both the eastern (expansion from west to east with age) and western (shift from inshore to offshore) GoM. Given the unique population dynamics between the eastern and western GoM, improving our understanding of spatial and temporal variability in habitat quality may be important to maintaining connectivity between juvenile and adult habitats, and may enhance recovery and management of red snapper stocks in the GoM.