Integrated Population Genomic Analysis and Numerical Simulation to Estimate Larval Dispersal of Acanthaster cf. solaris Between Ogasawara and Other Japanese Regions

The estimation of larval dispersal on an ecological timescale is significant for conservation of marine species. In 2018, a semi-population outbreak of crown-of-thorns sea star, Acanthaster cf. solaris, was observed on a relatively isolated oceanic island, Ogasawara. The aim of this study was to assess whether this population outbreak was caused by large-scale larval recruitment (termed secondary outbreak) from the Kuroshio region. We estimated larval dispersal of the coral predator A. cf. solaris between the Kuroshio and Ogasawara regions using both population genomic analysis and simulation of oceanographic dispersal. Population genomic analysis revealed overall genetically homogenized patterns among Ogasawara and other Japanese populations, suggesting that the origin of the populations in the two regions is the same. In contrast, a simulation of 26-year oceanographic dispersal indicated that larvae are mostly self-seeded in Ogasawara populations and have difficulty reaching Ogasawara from the Kuroshio region within one generation. However, a connectivity matrix produced by the larval dispersal simulation assuming a Markov chain indicated gradual larval dispersal migration from the Kuroshio region to Ogasawara in a stepping-stone manner over multiple years. These results suggest that the 2018 outbreak was likely the result of self-seeding, including possible inbreeding (as evidenced by clonemate analysis), as large-scale larval dispersal from the Kurishio population to the Ogasawara population within one generation is unlikely. Instead, the population in Ogasawara is basically sustained by self-seedings, and the outbreak in 2018 was also most likely caused by successful self-seedings including possible inbreeding, as evidenced by clonemate analysis. This study also highlighted the importance of using both genomic and oceanographic methods to estimate larval dispersal, which provides significant insight into larval dispersal that occurs on ecological and evolutionary timescales.

Testing the Influence of Seascape Connectivity on Marine-Based Species Distribution Models

Species distribution models (SDMs) are commonly used in ecology to predict species occurrence probability and how species are geographically distributed. Here, we propose innovative predictive factors to efficiently integrate information on connectivity into SDMs, a key element of population dynamics strongly influencing how species are distributed across seascapes. We also quantify the influence of species-specific connectivity estimates (i.e., larval dispersal vs. adult movement) on the marine-based SDMs outcomes. For illustration, seascape connectivity was modeled for two common, yet contrasting, marine species occurring in southeast Australian waters, the purple sea urchin, Heliocidaris erythrogramma, and the Australasian snapper, Chrysophrys auratus. Our models illustrate how different species-specific larval dispersal and adult movement can be efficiently accommodated. We used network-based centrality metrics to compute patch-level importance values and include these metrics in the group of predictors of correlative SDMs. We employed boosted regression trees (BRT) to fit our models, calculating the predictive performance, comparing spatial predictions and evaluating the relative influence of connectivity-based metrics among other predictors. Network-based metrics provide a flexible tool to quantify seascape connectivity that can be efficiently incorporated into SDMs. Connectivity across larval and adult stages was found to contribute to SDMs predictions and model performance was not negatively influenced from including these connectivity measures. Degree centrality, quantifying incoming and outgoing connections with habitat patches, was the most influential centrality metric. Pairwise interactions between predictors revealed that the species were predominantly found around hubs of connectivity and in warm, high-oxygenated, shallow waters. Additional research is needed to quantify the complex role that habitat network structure and temporal dynamics may have on SDM spatial predictions and explanatory power.

Kilometer-Scale Larval Dispersal Processes Predict Metapopulation Connectivity Pathways for Paramuricea biscaya in the Northern Gulf of Mexico

Fine-scale larval dispersal and connectivity processes are key to species survival, growth, recovery and adaptation under rapidly changing disturbances. Quantifying both are required to develop any effective management strategy. In the present work, we examine the dispersal pattern and potential connectivity of a common deep-water coral, Paramuricea biscaya, found in the northern Gulf of Mexico by evaluating predictions of physical models with estimates of genetic connectivity. While genetic approaches provide estimates of realized connectivity, they do not provide information on the dispersal process. Physical circulation models can now achieve kilometer-scale resolution sufficient to provide detailed insight into the pathways and scales of larval dispersal. A high-resolution regional ocean circulation model is integrated for 2015 and its advective pathways are compared with the outcome of the genetic connectivity estimates of corals collected at six locations over the continental slope at depths comprised between 1,000 and 3,000 m. Furthermore, the likely interannual variability is extrapolated using ocean hindcasts available for this basin. The general connectivity pattern exhibits a dispersal trend from east to west following 1,000 to 2,000-m isobaths, corresponding to the overall westward near-bottom circulation. The connectivity networks predicted by our model were mostly congruent with the estimated genetic connectivity patterns. Our results show that although dispersal distances of 100 km or less are common, depth differences between tens to a few hundred meters can effectively limit larval dispersal. A probabilistic graphic model suggests that stepping-stone dispersal mediated by intermediate sites provides a likely mechanism for long-distance connectivity between the populations separated by distances of 300 km or greater, such as those found in the DeSoto and Keathley canyons.

Seascape Genomics Reveals Metapopulation Connectivity Network of Paramuricea biscaya in the Northern Gulf of Mexico

The degree of connectivity among populations influences their ability to respond to natural and anthropogenic stressors. In marine systems, determining the scale, rate, and directionality of larval dispersal is therefore, central to understanding how coral metapopulations are interconnected and the degree of resiliency in the event of a localized disturbance. Understanding these source-sink dynamics is essential to guide restoration efforts and for the study of ecology and evolution in the ocean. The patterns and mechanisms of connectivity in the deep-sea (>200 m deep) are largely understudied. In this study, we investigated the spatial diversity patterns and metapopulation connectivity of the octocoral Paramuricea biscaya throughout the northern Gulf of Mexico (GoM). Paramuricea biscaya is one of the most abundant corals on the lower continental slope (between 1,200 and 2,500 m) in the GoM. The 2010 Deepwater Horizon oil spill (DWH) directly impacted populations of this species and thus are considered primary targets for restoration. We used a combination of seascape genomic analyses, high-resolution ocean circulation modeling, and larval dispersal simulations to quantify the degree of population structuring and connectivity among P. biscaya populations. Evidence supports the hypotheses that the genetic diversity of P. biscaya is structured by depth, and that larval dispersal among connected populations is asymmetric due to dominant ocean circulation patterns. Our results suggest that there are intermediate unsampled populations in the central GoM that serve as stepping stones for dispersal. The data suggest that the DeSoto Canyon area, and possibly the West Florida Escarpment, critically act as sources of larvae for areas impacted by the DWH oil spill in the Mississippi Canyon. This work illustrates that the management of deep-sea marine protected areas should incorporate knowledge of connectivity networks and depth-dependent processes throughout the water column.

Insights Into the Environmental Impact on Genetic Structure and Larval Dispersal of Crown-of-Thorns Starfish in the South China Sea

The coral-eating crown-of-thorns starfish (COTS; Acanthaster spp.) play a major role in coral reef degradation in the Indo-Pacific region. However, the impacts of environmental factors on the phylogenetic and genetic characteristics of COTS in the northern Indo-Pacific convergence region remains unclear. We used mitochondrial DNA (mtDNA) and microsatellite markers to analyze the phylogenetic relationship, demographic history, genetic diversity and genetic structure of COTS in the South China Sea (SCS) and explored the impact of environmental factors on historical population expansion, genetic differentiation and larval dispersal. There was a clear signature of a population expansion in the SCS using the mtDNA marker. According to microsatellite loci analysis, COTS have high genetic diversity in the SCS. STRUCTURE analysis indicated that COTS in the Pacific Ocean can be divided into four subgroups: the SCS, Western Pacific, Pacific equatorial current affected zone, and Pacific insular atolls populations in the Pacific Ocean. Fst-statistical analysis revealed positive correlations between the Fst values and geographic isolation for all sampling sites. Additionally, there were no clear associations between the Fst values and chlorophyll a concentrations among coral reefs in the SCS; however, there were significant positive associations between the Fst values and particulate organic carbon (POC) concentrations within small geographic distances. These results suggest that COTS underwent historical population expansion after the Last Glacial Maximum, possibly followed by coral population expansion. The genetic structure of COTS populations may have been shaped by distinct nutrient concentrations, particularly those of POC, over small geographic distances. Moreover, ocean currents provide a potential dispersal mechanism for COTS larvae in the SCS. This study demonstrates that environmental and oceanographic factors play important roles in shaping the genetic characteristics and larval dispersal of COTS populations in the northern Indo-Pacific convergence region.

An MPA Design Approach to Benefit Fisheries: Maximising Larval Export and Minimising Redundancy

In the design of marine protected areas (MPAs), tailoring reserve placement to facilitate larval export beyond reserve boundaries may support fished populations and fisheries through recruitment subsidies. Intuitively, capturing such connectivity could be purely based on optimising larval dispersal metrics such as export strength. However, this can lead to inefficient or redundant larval connectivity, as the subset of sites with the best connectivity metrics might share many of the same connections, making them, collectively, poor MPA candidates to provide recruitment subsidies to unprotected sites. We propose a simple, dynamic algorithm for reserve placement optimisation designed to select MPAs sequentially, maximising larval export to the overall network, whilst accounting for redundancy in supply from multiple sources. When applied to four regions in the Caribbean, the algorithm consistently outperformed approaches that did not consider supply redundancy, leading to, on average, 20% greater fished biomass in a simulated model. Improvements were most apparent in dense, strongly connected systems such as the Bahamas. Here, MPA placement without redundancy considerations produced fishery benefits worse than random MPA design. Our findings highlight the importance of considering redundancy in MPA design, and offer a novel, simple approach to improving MPA design for achieving fishery objectives.

The relationship between Oceanographic Parameters and Fish Larvae Dispersal in the Fisheries Management Area of the Republic Indonesia (FMA) 717

Cendrawasih Bay and the Pacific Ocean are known as potential fishing areas and as fish spawning locations in Fisheries Management Area 717. Larval dispersal in the waters is strongly influenced by oceanographic parameters. This study was conducted to examine the relationship between oceanographic parameters and fish larval dispersal in FMA 717. This research was conducted using KR Bawal Putih III in November 2019. A number of 42 stations were determined for observation. Environmental parameters included temperature, salinity, dissolved oxygen, chlorophyll-a, turbidity, and photosynthetic active radiation (PAR), were measured using SBE 19 plus V2 CTD while pelagic fish larvae were collected using a bonggo net. Analysis of the correlation of oceanographic parameters with pelagic fish larvae abundance and spatial distribution was calculated using PCA (Principal Component Analysis) statistical analysis. The results showed that the pelagic fish larvae was influenced by temperature, salinity, PAR, chlorophyll-a, turbidity, and DO. Temperature and salinity have a direct interaction to the abundance of pelagic fish larvae.

Strong horizontal and vertical connectivity in the coral Pocillopora verrucosa from Ludao, Taiwan, a small oceanic island

Mesophotic habitats could be sheltered from natural and anthropogenic disturbances and act as reproductive refuges, providing propagules to replenish shallower populations. Molecular markers can be used as proxies evaluating the connectivity and inferring population structure and larval dispersal. This study characterizes population structure as well as horizontal and vertical genetic connectivity of the broadcasting coral Pocillopora verrucosa from Ludao, a small oceanic island off the eastern coast of Taiwan. We genotyped 75 P. verrucosa specimens from three sites (Gongguan, Dabaisha, and Guiwan) at three depth ranges (Shallow: 7–15 m, Mid-depth: 23–30 m, and Deep: 38–45 m), spanning shallow to upper mesophotic coral reefs, with eight microsatellite markers. F-statistics showed a moderate differentiation (FST = 0.106, p<0.05) between two adjacent locations (Dabaisha 23–30 and Dabaisha 38–45 m), but no differentiation elsewhere, suggesting high levels of connectivity among sites and depths. STRUCTURE analysis showed no genetic clustering among sites or depths, indicating that all Pocillopora individuals could be drawn from a single panmictic population. Simulations of recent migration assigned 30 individuals (40%) to a different location from where they were collected. Among them, 1/3 were assigned to deeper locations, 1/3 to shallower populations and 1/3 were assigned to the right depth but a different site. These results suggest high levels of vertical and horizontal connectivity, which could enhance the recovery of P. verrucosa following disturbances around Ludao, a feature that agrees with demographic studies portraying this species as an opportunistic scleractinian.

Kilometer-scale larval dispersal processes predict metapopulation connectivity pathways for Paramuricea biscaya in the northern Gulf of Mexico

Fine-scale larval dispersal and connectivity processes are key to species survival, growth, recovery and adaptation under rapidly changing disturbances. Quantifying both are required to develop any effective management strategy. In the present work, we examine the dispersal pattern and potential connectivity of a common deep-water coral, Paramuricea biscaya, found in the northern Gulf of Mexico by evaluating predictions of physical models with estimates of genetic connectivity. While genetic approaches provide estimates of realized connectivity, they do not provide information on the dispersal process. Physical circulation models can now achieve kilometer-scale resolution sufficient to provide detailed insight into the pathways and scales of larval dispersal. A high-resolution regional ocean circulation model is integrated for 2015 and its advective pathways are compared with the outcome of the genetic connectivity estimates of corals collected at six locations over the continental slope at depths comprised between 1000 and 3000 meters. Furthermore, the likely interannual variability is extrapolated using ocean hindcasts available for this basin. The general connectivity pattern exhibits a dispersal trend from east to west following 1000 to 2000-meter isobaths, corresponding to the overall westward near-bottom circulation. The connectivity networks predicted by our model were mostly congruent with the estimated genetic connectivity patterns. Our results show that although dispersal distances of 100 km or less are common, depth differences between tens to a few hundred meters can effectively limit larval dispersal. A probabilistic graphic model suggests that stepping-stone dispersal mediated by intermediate sites provides a likely mechanism for long-distance connectivity between the populations separated by distances of 300 km or greater, such as those found in the DeSoto and Keathley canyons.

Seascape genomics reveals metapopulation connectivity network of Paramuricea biscaya in the northern Gulf of Mexico

The degree of connectivity among populations influences their ability to respond to natural and anthropogenic stressors. In marine systems, determining the scale, rate, and directionality of larval dispersal is therefore central to understanding how coral metapopulations are interconnected and the degree of resiliency in the event of a localized disturbance. Understanding these source-sink dynamics is essential to guide restoration efforts and for the study of ecology and evolution in the ocean. The patterns and mechanisms of connectivity in the deep-sea (> 200 meters deep) are largely understudied. In this study, we investigated the spatial diversity patterns and metapopulation connectivity of the octocoral Paramuricea biscaya throughout the northern Gulf of Mexico (GoM). Paramuricea biscaya is one of the most abundant corals on the lower continental slope (between 1200 and 2500 m) in the GoM. The 2010 Deepwater Horizon oil spill (DWH) directly impacted populations of this species and thus are considered primary targets for restoration. We used a combination of seascape genomic analyses, high-resolution ocean circulation modeling, and larval dispersal simulations to quantify the degree of population structuring and connectivity among P. biscaya populations. Evidence supports the hypotheses that the genetic diversity of P. biscaya is predominantly structured by depth, and that larval dispersal among connected populations is asymmetric due to dominant ocean circulation patterns. Our results suggest that there are intermediate unsampled populations in the central GoM that serve as stepping stones for dispersal. The data suggest that the DeSoto Canyon area, and possibly the West Florida Escarpment, critically act as sources of larvae for areas impacted by the DWH oil spill in the Mississippi Canyon. This work illustrates that the management of deep-sea marine protected areas should incorporate knowledge of connectivity networks and depth-dependent processes throughout the water column.