Combining population genomics and biophysical modelling to assess connectivity patterns in an Antarctic fish

Connectivity is a fundamental process of population dynamics in marine ecosystems. In the last decade, with the emergence of new methods, combining different approaches to understand the patterns of connectivity among populations and their regulation has become increasingly feasible. The Western Antarctic Peninsula (WAP) is characterized by complex oceanographic dynamics, where local conditions could act as barriers to population connectivity. Here, the notothenioid fish Harpagifer antarcticus, a demersal species with a complex life cycle (adults with poor swim capabilities and pelagic larvae), was used to assess connectivity along the WAP by combining biophysical modelling and population genomics methods. Both approaches showed congruent patterns. Areas of larvae retention and low potential connectivity, observed in the biophysical model output, coincide with four genetic groups within the WAP: (1) South Shetland Islands, (2) Bransfield Strait, (3) the central and (4) the southern area of WAP (Marguerite Bay). These genetic groups exhibited limited gene flow between them, consistent with local oceanographic conditions, which would represent barriers to larval dispersal. The joint effect of geographic distance and larval dispersal by ocean currents had a greater influence on the observed population structure than each variable evaluated separately. The combined effect of geographic distance and a complex oceanographic dynamic would be generating limited levels of population connectivity in the fish H. antarcticus along the WAP. Based on this, population connectivity estimations and priority areas for conservation were discussed, considering the marine protected area proposed for this threatened region of the Southern Ocean.

Genomic assessment of larval odyssey: self-recruitment and biased settlement in the Hawaiian surgeonfish Acanthurus triostegus sandvicensis

The gap between spawning and settlement location of marine fishes, where the larvae occupy an oceanic phase, is a great mystery in both natural history and conservation. Recent genomic approaches provide some resolution, especially in linking parent to offspring with assays of nucleotide polymorphisms. Here, the authors applied this method to the endemic Hawaiian convict tang (Acanthurus triostegus sandvicensis), a surgeonfish with a long pelagic larval stage of c. 54-77 days. They collected 606 adults and 607 juveniles from 23 locations around the island of O'ahu, Hawai'i. Based on 399 single nucleotide polymorphisms, the authors assigned 68 of these juveniles back to a parent (11.2% assignment rate). Each side of the island showed significant population differentiation, with higher levels in the west and north. The west and north sides of the island also had little evidence of recruitment, which may be due to westerly currents in the region or an artefact of uneven sampling. In contrast, the majority of juveniles (94%) sampled along the eastern shore originated on that side of the island, primarily within semi-enclosed Kāne'ohe Bay. Nearly half of the juveniles assigned to parents were found in the southern part of Kāne'ohe Bay, with local settlement likely facilitated by extended water residence time. Several instances of self-recruitment, when juveniles return to their natal location, were observed along the eastern and southern shores. Cumulatively, these findings indicate that most dispersal is between adjacent regions on the eastern and southern shores. Regional management efforts for Acanthurus triostegus and possibly other reef fishes will be effective only with collaboration among adjacent coastal communities, consistent with the traditional moku system of native Hawaiian resource management.

Persistence of a reef fish metapopulation via network connectivity: theory and data

Determining metapopulation persistence requires understanding both demographic rates and patch connectivity. Persistence is well understood in theory but has proved challenging to test empirically for marine and other species with high connectivity that precludes classic colonisation-extinction dynamics. Here, we assessed persistence for a yellowtail anemonefish (Amphiprion clarkii) metapopulation using 7 years of annual sampling data along 30 km of coastline. We carefully accounted for uncertainty in demographic rates. Despite stable population abundances through time and sufficient production of surviving offspring for replacement, the pattern of connectivity made the metapopulation unlikely to persist in isolation and reliant on immigrants from outside habitat. To persist in isolation, the metapopulation would need higher fecundity or to retain essentially all recruits produced. This assessment of persistence in a marine metapopulation shows that stable abundance alone does not indicate persistence, emphasising the necessity of assessing both demographic and connectivity processes to understand metapopulation dynamics.

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.

Local adaptation of antipredator behaviors in populations of a temperate reef fish

The temperament of animals can vary among individuals and among populations, but it is often unclear whether spatial variation in temperament is the result of acclimation to local environmental conditions or genetic adaptation to spatial differences in natural selection. This study tested whether populations of a marine fish that experience different levels of mortality and fishing exhibited local adaptation in behaviors related to predator avoidance and evasion. First, we measured variation in reactivity to perceived risk in wild populations of black surfperch (Embiotoca jacksoni). We compared flight initiation distances (FID) between populations with significantly different mortality rates. After finding that FID values were substantially lower in the low-risk locations, we tested for local adaptation by rearing lab-born offspring from both high- and low-risk populations in a common environment before measuring their behavior. Lab-reared offspring from high- and low-risk populations exhibited significant differences in several behaviors related to reactivity. Between 23 and 43% of the total variation in behaviors we measured could be attributed to source population. These results thus suggest that a substantial amount of spatial variation in behaviors related to predator evasion may represent local adaptation. In addition, behaviors we measured had an average, broad-sense heritability of 0.24, suggesting that the behavioral tendencies of these populations have some capacity to evolve further in response to any changes in selection.

Combining agent-based, trait-based and demographic approaches to model coral-community dynamics

The complexity of coral-reef ecosystems makes it challenging to predict their dynamics and resilience under future disturbance regimes. Models for coral-reef dynamics do not adequately account for the high functional diversity exhibited by corals. Models that are ecologically and mechanistically detailed are therefore required to simulate the ecological processes driving coral reef dynamics. Here, we describe a novel model that includes processes at different spatial scales, and the contribution of species' functional diversity to benthic-community dynamics. We calibrated and validated the model to reproduce observed dynamics using empirical data from Caribbean reefs. The model exhibits realistic community dynamics, and individual population dynamics are ecologically plausible. A global sensitivity analysis revealed that the number of larvae produced locally, and interaction-induced reductions in growth rate are the parameters with the largest influence on community dynamics. The model provides a platform for virtual experiments to explore diversity-functioning relationships in coral reefs.

Disturbance size and frequency mediate the coexistence of benthic spatial competitors

Disturbance plays a key role in structuring community dynamics and is central to conservation and natural resource management. However, ecologists continue to debate the importance of disturbance for species coexistence and biodiversity. Such disagreements may arise in part because few studies have examined variation across multiple dimensions of disturbance (e.g., size, frequency) and how the effects of disturbance may depend on species attributes (e.g., competitiveness, dispersal ability). In light of this gap in understanding and accelerating changes to disturbance regimes worldwide, we used spatial population models to explore how disturbance size and frequency interact with species attributes to affect coexistence between seagrass (Zostera marina) and colonial burrowing shrimp (Neotrypaea californiensis) that compete for benthic space in estuaries throughout the west coast of North America. By simulating population dynamics under a range of ecologically relevant disturbance regimes, we discovered that intermediate disturbance (approximately 9-23% of landscape area per year) to short-dispersing, competitively dominant seagrass can foster long-term stable coexistence with broad-dispersing, competitively inferior burrowing shrimp via the spatial storage effect. When holding the total extent of disturbance constant, the individual size and annual frequency of disturbance altered landscape spatial patterns and mediated the dominance and evenness of competitors. Many small disturbances favored short-dispersing seagrass by hastening recolonization, whereas fewer large disturbances benefited rapidly colonizing burrowing shrimp by creating temporary refugia from competition. As a result, large, infrequent disturbances generally improved the strength and stability of coexistence relative to small, frequent disturbances. Regardless of disturbance size or frequency, the dispersal ability of the superior competitor (seagrass), the competitive ability of the inferior competitor (burrowing shrimp), and the reproduction and survival of both species strongly influenced population abundances and coexistence. Our results show that disturbance size and frequency can promote or constrain coexistence by altering the duration of time over which inferior competitors can escape competitive exclusion, particularly when colonization depends on the spatial pattern of disturbance due to dispersal traits. For coastal managers and conservation practitioners, our findings indicate that reducing particularly large disturbances may help conserve globally imperiled seagrass meadows and control burrowing shrimp colonies that can threaten the viability of oyster aquaculture.

Accounting for ocean connectivity and hydroclimate in fish recruitment fluctuations within transboundary metapopulations

Marine resources stewardships are progressively becoming more receptive to an effective incorporation of both ecosystem and environmental complexities into the analytical frameworks of fisheries assessment. Understanding and predicting marine fish production for spatially and demographically complex populations in changing environmental conditions is however still a difficult task. Indeed, fisheries assessment is mostly based on deterministic models that lack realistic parameterizations of the intricate biological and physical processes shaping recruitment, a cornerstone in population dynamics. We use here a large metapopulation of a harvested fish, the European hake (Merluccius merluccius), managed across transnational boundaries in the northwestern Mediterranean, to model fish recruitment dynamics in terms of physics-dependent drivers related to dispersal and survival. The connectivity among nearby subpopulations is evaluated by simulating multi-annual Lagrangian indices of larval retention, imports, and self-recruitment. Along with a proxy of the regional hydroclimate influencing early life stages survival, we then statistically determine the relative contribution of dispersal and hydroclimate for recruitment across contiguous management units. We show that inter-annual variability of recruitment is well reproduced by hydroclimatic influences and synthetic connectivity estimates. Self-recruitment (i.e., the ratio of retained locally produced larvae to the total number of incoming larvae) is the most powerful metric as it integrates the roles of retained local recruits and immigrants from surrounding subpopulations and is able to capture circulation patterns affecting recruitment at the scale of management units. We also reveal that the climatic impact on recruitment is spatially structured at regional scale due to contrasting biophysical processes not related to dispersal. Self-recruitment calculated for each management unit explains between 19% and 32.9% of the variance of recruitment variability, that is much larger than the one explained by spawning stock biomass alone, supporting an increase of consideration of connectivity processes into stocks assessment. By acknowledging the structural and ecological complexity of marine populations, this study provides the scientific basis to link spatial management and temporal assessment within large marine metapopulations. Our results suggest that fisheries management could be improved by combining information of physical oceanography (from observing systems and operational models), opening new opportunities such as the development of short-term projections and dynamic spatial management.

Modeled larval connectivity of a multi-species reef fish and invertebrate assemblage off the coast of Moloka'i, Hawai'i

We use a novel individual-based model (IBM) to simulate larval dispersal around the island of Moloka‘i in the Hawaiian Archipelago. Our model uses ocean current output from the Massachusetts Institute of Technology general circulation model (MITgcm) as well as biological data on four invertebrate and seven fish species of management relevance to produce connectivity maps among sites around the island of Moloka‘i. These 11 species span the range of life history characteristics of Hawaiian coral reef species and show different spatial and temporal patterns of connectivity as a result. As expected, the longer the pelagic larval duration (PLD), the greater the proportion of larvae that disperse longer distances, but regardless of PLD (3–270 d) most successful dispersal occurs either over short distances within an island (<30 km) or to adjacent islands (50–125 km). Again, regardless of PLD, around the island of Moloka‘i, connectivity tends to be greatest among sites along the same coastline and exchange between northward, southward, eastward and westward-facing shores is limited. Using a graph-theoretic approach to visualize the data, we highlight that the eastern side of the island tends to show the greatest out-degree and betweenness centrality, which indicate important larval sources and connectivity pathways for the rest of the island. The marine protected area surrounding Kalaupapa National Historical Park emerges as a potential source for between-island larval connections, and the west coast of the Park is one of the few regions on Moloka‘i that acts as a net larval source across all species. Using this IBM and visualization approach reveals patterns of exchange between habitat regions and highlights critical larval sources and multi-generational pathways to indicate priority areas for marine resource managers.