The Dungeness crab fishery is the most economically important on the West Coast; however, it has experienced dramatic fluctuations in annual catch. Previous research has shown the annual catch of megalopae is correlated with the commercial catch. The catch of megalopae is correlated with the phase of the Pacific Decadal Oscillation (PDO), the day of the year of the spring transition and the amount of upwelling following the spring transition. Further, the daily catch of megalopae is correlated with the internal tide. We developed individual based models of Dungeness crab dispersal, which we validated with results from a light trap. We demonstrated that the retention of larvae in the California Current is enhanced during negative phase PDOs. Further, we suggest that larvae migrate to or almost to the bottom each day. Specifically, megalopae exhibit a twilight vertical migration off of the continental shelf and remain in the neuston on the continental shelf. This concentrates megalopae at the continental shelf break. We also observed megalopae in situ and demonstrated that they swim in the neuston with the surface current at speeds of ~ 10 cm s-1. Using these results and data from a mooring, we demonstrated that this behavior would increase the distance internal waves would transport larvae. We analyzed mooring data and suggest that catch of megalopae is greater when the thermocline is deep and weak and there is less horizontal shear. We hypothesize this allows internal waves to remain coherent longer on the continental shelf. We show that the spring transition coincides with a shallowing of the thermocline, which would ultimately lead to the development of internal waves of depression rather than elevation. We hypothesize that the change in surface flow, based on whether the wave is one of elevation or depression, explains why most megalopae are caught following the spring transition. In general, these findings help us better understand the dispersal of Dungeness crabs. We suggest the dispersal patterns support Michael Sinclair’s member vagrant hypothesis. Further, we suggest these findings apply to many of the continental shelf species in the California Current. This dissertation includes both published and unpublished co-authored materials.

Marine protected areas (MPAs) have proliferated in the past decades to protect biodiversity and sustain fisheries. However, most of the MPA networks have been designed without taking into account a critical factor: the larval dispersal patterns of populations within and outside the reserves. The scale and predictability of larval dispersal, however, remain unknown due to the difficulty of measuring dispersal when larvae are minute (~ cm) compared to the potential scale of dispersal (~ km). Nevertheless, genetic approaches can now be used to make estimates of larval dispersal. The following thesis describes self-recruitment and connectivity patterns of a coral reef fish species (Centropyge bicolor) in Kimbe Bay, Papua New Guinea. To do this, microsatellite markers were developed to evaluate fine-scale genetics and recruit assignment via genetic parentage analysis. In this method, offspring are assigned to potential parents, so that larval dispersal distances can then be inferred for each individual larvae. From a total of 255 adults and 426 juveniles collected only 2 parentoffspring pairs were assigned, representing less than 1% self-recruitment. Previous data from the same study system showed that both Chaetodon vagagundus and Amphiprion percula have consistent high self-recuitment rates (~ 60%), despite having contrasting life history traits. Since C. bicolor and C. vagabundus have similar characteristics (e.g. reproductive mode, pelagic larval duration), comparable results were expected. On the contrary, the results of this study showed that dispersal patterns cannot be generalized across species. Hence the importance of studying different species and seascapes to better understand the patterns of larval dispersal. This, in turn, will be essential to improve the design and implementation of MPAs as conservation and management tools.

With a dramatic decrease of biodiversity as a result of the increase in exploitation of marine ecosystems, the establishment of marine protected areas (MPAs) serves as an important means of protecting those resources. Although there is support for the effectiveness of these MPAs and MPA networks, there is room for improvement in terms of MPA management and design. For example, a better understanding of the dispersal dynamics of targeted species across these MPAs will serve as a more accurate means of reserve as well as fisheries management. While there have been many methods used to determine the larval dispersal of a certain species, parentage analysis is becoming the most robust. In this thesis, I attempt to determine the patterns of self-recruitment and larval dispersal of the Longfin Grouper (Epinephelus quoyanus) in one focal marine reserve within the Great Keppel Island group through the method of parentage. For this, I developed 14 microsatellite markers and with those, genotyped 610 adults as well as 478 juveniles from the study site. These genotypes allowed me to assign offspring to their potential parents, which then allowed me to measure the self-recruitment, local retention as well as larval dispersal percentages of this species from and within the reserve. My results indicate that there is 32% local retention to the reserve while 68% of the assigned juveniles were dispersed to other areas (4% of which dispersed to another reserve). Previous studies conducted in the same area showed higher reserve self-recruitment rates for both Plectropomus maculatus (~30%) and Lutjanus carponotatus (64%) despite their similar life history traits. The results from this study add to the growing evidence that dispersal patterns cannot be generalized across marine systems or even between species within a single system.

The field of marine population connectivity is receiving growing attention from ecologists worldwide. The degree to which metapopulations are connected via larval dispersal has vital ramifications for demographic and evolutionary dynamics and largely determines the way we manage threatened coastal ecosystems. Here we addressed different questions relating to connectivity by integrating direct and indirect genetic approaches over different spatial and ecological scales in a coral reef fish in the Red Sea. We developed 35 novel microsatellite loci for our study organism the two-band anemonefish Amphiprion bicinctus (Rüppel 1830), which served as the basis of the following approaches. First, we collected nearly one thousand samples of A. bicinctus from 19 locations across 1500 km along the Saudi Arabian coast to infer population genetic structure. Genetic variability along the northern and central coast was weak, but showed a significant break at approximately 20°N. Implementing a model of isolation by environment with chlorophyll-a concentrations and geographic distance as predictors we were able to explain over 90% of the genetic variability in the data (R2 = 0.92). For the second approach we sampled 311 (c. 99%) putative parents and 172 juveniles at an isolated reef, Quita al Girsh (QG), to estimate self-recruitment using genetic parentage analysis. Additionally we collected 176 juveniles at surrounding locations to estimate larval dispersal from QG and ran a biophysical dispersal model of the system with real5 time climatological forcing. In concordance with model predictions, we found a complete lack (c. 0.5%) of self-recruitment over two sampling periods within our study system, thus presenting the first empirical evidence for a largely open reef fish population. Lastly, to conceptualize different hypotheses regarding the underlying processes and mechanisms of self-recruitment versus long-distance dispersal in marine organisms with pelagic larval stages, I introduce and discuss the concept of “origin effects”, providing the theoretical background to some of the questions that have arisen during this research. Overall, this thesis has generated significant new insights into the patterns of coral reef fish connectivity, specifically for the Red Sea, where such information has previously been scarce.

Connectivity is a major contributor to the overall dynamics of marine populations. However, it still remains challenging to describe connectivity on ecologically meaningful scales of time and space. This is a major impediment to evaluating the impacts of marine protected area with respect to fisheries management objectives. This dissertation brings together a wide array of spatial and connectivity information in the Gulf of Mexico (GOM) with the goal of 1) understanding the spatial distribution of fish populations and source-sink dynamics and 2) evaluating whether this information can be integrated, through a modeling framework, to identify closed areas that could be beneficial to fisheries management in the Gulf of Mexico. First, a generalized additive modelling (GAM) approach is used to describe the distribution of a large number of species groups (i.e. functional groups) across the Gulf of Mexico (GOM) using a large fisheries independent data set (SEAMAP) and climate scale (decades) oceanographic conditions. Next a numerical Lagrangian particle transport model was developed that incorporates two major connectivity processes; site specific larval production and oceanographic transport for an entire large marine ecosystem and over multiple years. The two components are then combined to develop larval dispersal patterns for the entire GOM and identify areas operating as larval sources and sinks. Last, this information is integrated into an end-to-end ecosystem model to evaluate effectiveness of closing source and sink areas for the management of reef fish fisheries. Closed area managemeny simlautions for reef fish indicated closing reef fish source areas, as opposed to sinks, in the GOM is most efficient method of increasing total biomass and yield. However, the impacts across individual functional groups were site specific. Ultimately, these simulations demonstrate the inclusion of connectivity information could improve fishery management objectives in an ecosystem context.

Nearshore populations have been depleted and some have not yet recovered. Therefore, theoretical studies focus on improving fisheries management and designing marine protected areas (MPAs). Depleted populations may be undergoing an Allee effect, i.e. a decrease in fitness at low densities. Here, I constructed a marine metapopulation model that included pre- and post-dispersal Allee effects using a network theory approach. Networks represent metapopulations as groups of nodes connected by dispersal paths. With this model I answered four questions: What is the role of Allee effects on habitat occupancy? Are MPAs effective in recovering exploited populations? What is the importance of larval dispersal patterns in preventing local extinctions due to exploitation and Allee effects? Can exploitation fragment nearshore metapopulations? When weak Allee effects are included, habitat occupancy drops as larval retention decreases because more larvae are lost to unsuitable habitat. With strong Allee effects habitat occupancy also drops at high larval retention because more larvae are needed to overcome the Allee effect. Post-dispersal Allee effects seem more detrimental for nearshore metapopulations. MPA effectiveness seems also lower in a post-dispersal Allee effect scenario. In overexploited systems, local populations that go extinct are also less likely to recover even after protecting the whole coastline. In exploited nearshore metapopulations with Allee effects, local occupancy or the recovery of local populations depends not only on larval inflow from neighbor populations, but also on larval inflow for these neighbors. Nearshore metapopulations with intense fishing mortality and Allee effects may also suffer a decrease in dispersal strength and fragmentation. Population fragmentation occurs when large populations are split into smaller groups. A tool for detecting partitioning in a network is modularity. The modularity analysis performed for red abalone in the Southern California Bight showed that exploitation increases partitioning through time before the entire metapopulation collapses. These findings call for research effort in estimating the strength of potential Allee effects to prevent stock collapse and assess MPA effectiveness, evaluating the predictability of local occupancy by centrality metrics to help identify important sites for conservation, and using modularity analysis to quantify the health of exploited metapopulations to prevent their collapse. / text

There is currently worldwide pressure to establish Marine Protected Area (MPA) networks which are self-sustaining and will persistently protect habitats and species. In order for MPA networks to be effective, the species targeted for conservation must be able to disperse between protected areas and maintain a gene-flow necessary for population sustainability and persistence. This warrants new research on how to quantify and map faunal dispersal to ensure that protection will be effective and sustainable. Population genetic methods have merit, with the ability to track parentage and gene flow between areas directly. However the costs, quantity of samples, and time required to genetically quantify dispersal for multiple species make these approaches prohibitive as the only method of assessment, especially in relatively inaccessible offshore waters. Dispersal modelling is now becoming more accessible and may fulfil immediate needs in this field (although ground truthing will be necessary in the future). There have been very few dispersal modelling studies focussed on deep sea or offshore areas, predominantly due to the lack of high resolution hydrodynamic models with sufficient geographic extent away from shore. Current conclusions have been drawn based on shallow water coastal studies, informing offshore MPA network size and spacing. However the differences between these two environments may mean that dispersal abilities are not comparable. Deep water receives less influence from wind and weather, and the scales are vastly different in terms of a) the depth ranges covered, b) the planktonic larval durations (PLDs) of animals, and c) the geographic areas concerned as a consequence. Global hydrodynamic models with reasonable resolution are now becoming more accessible. With the outputs from these models, and freely available particle simulators, it is becoming more practical to undertake offshore deep water dispersal studies. This thesis aims to undertake an analysis of these accessible modelling tools within a deep sea context. The guidelines which are currently available to dispersal modellers are yet to encompass the needs of deep water modellers which may require some additional considerations given the extended depth range covered and the different hydrodynamic drivers away from the air/sea interface. Chapter 1 reviews the larval dispersal process, the factors which may affect dispersal success, and those which should be incorporated into future predictions of dispersal. The current methods for assessing larval dispersal are explored covering genetics, elemental tagging and modelling approaches with an extended look at modelling considerations. Existing marine conservation policy is also touched on in the context of connectivity and larval dispersal. Chapter 2 is designed to inform future deep sea modellers on how to parameterise and understand a dispersal model. As models appear as a ‘black box’ to the majority of users, sensitivity tests can offer a way of scaling model inputs and tempering expectations from model outputs. A commonly used model pairing (the HYCOM hydrodynamic model and the Connectivity Modeling System) is assessed, using parameters which link to the temporal and spatial scales of mixing in the modelled system: timestep of particle tracer, horizontal and vertical positioning of release points, release frequency of larvae, and temporal range of simulation. All parameters were shown to have a decreased sensitivity with depth, with patterns reflecting local watermass structure. Future studies observing similar hydrodynamic conditions seeking to optimise their model set up would be advised to stratify their model release locations with depth. A means to incorporate all sensitivity test results into optimal input parameters for future studies is demonstrated. Chapter 3 investigates whether dispersal models provide any advantage over a “sphere of influence” estimate based on average current speeds and PLDs: there is no use pursuing dispersal modelling if the outputs are too erroneous to provide any advantage over a back-of-the-envelope calculation. This chapter examines the outputs of two dispersal models driven by two different hydrodynamic models in order to observe the variability in prediction between models. This model comparison revealed a greater disparity between hydrodynamic model predictions than has been previously understood by ecologists. The two models compared (POLCOMS and HYCOM) may equally be considered as suitable to promote realism in the study region, but slight differences in resolution and numerical error handling resulted in dispersal predictions from which opposing conclusions can be drawn. This chapter therefore emphasises the necessity for model ground truthing before predictions can be trusted. Chapter 4 assimilates the findings of the previous chapters and applies their advice to a study of MPA network dispersal connectivity. Using the hydrodynamic model which performed best in chapter 3 (HYCOM), a simulation was undertaken for cold water coral (Lophelia pertusa (Linnaeus 1758)) larval dispersal between already established MPAs in the NE Atlantic. As larval characters have only been observed ex situ, dispersal was simulated using two null models (passive and active vertical migration) and averaged to provide an intermediate prediction. A method for assessing dispersal within MPAs and MPA networks is offered based on the intermediate prediction, as well as a network wide assessment of the difference in dispersal patterns for passive and active larvae. It was found that the existing network performs well at supplying larvae to non-networked sites, but performs poorly at supplying other MPAs. The ‘best’ MPAs were central to the network and facilitated the traverse of regional gaps in suitable habitat. The ‘worst’ MPAs were peripheral to the network and small in size. Network-wide passive and active dispersal matrices had no significant difference between them. However site specific variability in the effect of vertical migration was detected subject to variability in local topographic barriers to dispersal, only some of which could be surmounted with vertical migration. All chapters aim to inform future deep sea dispersal modellers, and encourage exploration of this tool in other contexts, as well as marine conservation. The thesis cautions against the transplantation of shallow water assumptions to deep water environments, and advocates region specific studies and mandatory ground truthing of predictions. An upcoming study will ground truth the findings of this thesis with both genetic and oceanographic data, allowing the accuracy of study results to be quantified.

Comprendre la dynamique des populations marines est essentiel à une gestion efficaceet requiert des connaissances sur la dispersion et la connectivité entre populationsqui sont encore très lacunaires. Beaucoup d’organismes marins ont un cycle de viebipartite avec une phase larvaire pélagique qui représente souvent la seule possibilitéde dispersion. De nouvelles techniques de mesure de la dispersion larvaire, parmarquage ou modélisation, ont été développées durant ces quinze dernières années.Cependant, les résultats de ces deux types d’approches ont rarement été comparésau sein d’un même système marin, limitant l’utilisation des modèles de dispersiondans les modèles de métapopulation. Dans cette thèse, nous utilisons ces deux typesd’approches pour étudier la connectivité larvaire d’un poisson de récif corallien,Dascyllus aruanus, dans le lagon sud-ouest de Nouvelle-Calédonie. Notre modèle dedispersion montre que la rétention larvaire présente une variabilité temporelle élevéeà l’échelle lagonaire et à l’échelle d’un patch de récif, et atteint périodiquement desvaleurs élevées malgré des temps moyens de résidence courts. Le marquage artificieltransgénérationnel des otolithes montre des taux d’auto-recrutement relativementbas à l’échelle de la saison reproductive, suggérant une ouverture importante despopulations, et une variabilité temporelle considérable de l’auto-recrutement. Enfin,les grandes différences entre les résultats du modèle et ceux des marquages appuientle besoin de mieux comprendre les processus qui facilitent la rétention larvaire commeles comportements de homing et la circulation des courants à très petite échelle. / Understanding marine populations dynamics is critical to their effective management,and requires information on patterns of dispersal and connectivity that are still poorlyknown. Many marine organisms have a bipartite life history with a pelagic larvalstage that often represents the only opportunity for dispersal. In the last decade,new empirical and simulation approaches to measuring larval dispersal have beendeveloped, but results from these two different approaches have rarely been comparedin the context of a single marine system, impeding the use of larval dispersal modelsin metapopulation models supporting decision making. In this doctoral research, weused both approaches to investigate larval connectivity for a coral reef fish, Dascyllusaruanus, in the South-West Lagoon of New Caledonia. Our biophysical dispersalmodel shows that larval retention exhibits considerable temporal variability at bothlagoon and patch reef scales and periodically reaches large values despite low averagewater residence time. Artificial transgenerational marking of embryonic otoliths inthe wild also showed relatively low self-recruitment rates indicating high populationopenness at the reproductive season scale, with considerable monthly variability ofself-recruitment. Large quantitative discrepancies between simulations and empiricalresults emphasize the need to better understand processes that facilitate local retention,such as homing behavior and very small scale circulation patterns.

This thesis aims to increase our understanding of mechanisms that influence larval dispersal in marine benthic invertebrates, particularly in the absence of strong oceanographic features (e.g. estuarine plumes, upwelling events, or markedly different water masses). Laboratory experiments identified behavioural mechanisms that regulate the vertical distribution of larvae in response to thermal stratification, and field studies in St. George’s Bay, Nova Scotia (NS), Canada, examined the relationship between larval abundance and physical variables (temperature, salinity, fluorescence, etc) and identified mechanisms that regulate larval distributions in situ. In the laboratory, I demonstrated that thermal stratification affects the vertical distribution of larvae by acting as a barrier to migration, or through temperature-dependent vertical swimming velocities. I also developed a random walk based model which highlighted that the key to successfully simulating larval response to temperature was 1) determining the temperature-dependent distribution of vertical swimming velocities and 2) the temporal autocorrelation in these velocities. In the field, the most striking pattern was that the larval distributions for species with similar swimming abilities were significantly correlated to one another at all scales (0.5 to 40 km). This suggests a common mechanism, related to larval swimming ability, which greatly influences the horizontal larval distribution. I found that the spatial scale of variability in larval distributions (~ 3 km) matches that in both the environmental variables and of coherent structures in current velocities (i.e. the tidal excursion). Results from an aggregation-diffusion model suggest that horizontal larval swimming could not be responsible for the observed level of aggregation in the larval horizontal distributions. I suggest that these horizontal patterns are the result of 1) an aggregative process (i.e. larvae swimming against a vertical current and maintaining their vertical position) and 2) a diffusive process which scales the aggregations to the scale of the coherent structures in current velocity (i.e. tidal excursion). In conclusion, this thesis increases our understanding of larval behaviour and its effects on larval dispersal. The results will be particularly useful to those who are interested in mechanisms regulate population connectivity, particularly those using bio-physical models to model dispersal trajectories.

Orientador: Claudio José Von Zuben / Banca: Aricio Xavier Linhares / Banca: Wesley Augusto Conde Godoy / Resumo: A ordem Diptera desperta grande interesse nos estudos científicos devido à importância agrícola, sanitária, veterinária e forense, dependendo da espécie em estudo. A espécie Chrysomya megacephala (Fabricius) foi introduzida há cerca de 30 anos no Brasil e é de considerável importância médico-sanitária, além de poder ser utilizada em estudos forenses, na estimativa de intervalo pós-morte (IPM) em humanos. A espécie Musca domestica (Linnaeus) tem distribuição cosmopolita e é bastante comum no ambiente urbano e pode também transportar formas infectantes de muitas doenças. Nessas moscas, após o desenvolvimento dos imaturos em substratos discretos e efêmeros, as larvas abandonam o substrato alimentar em busca de um sítio para pupação, processo chamado de dispersão larval pós-alimentar. No entanto, em ambiente natural, tanto a fonte alimentar como o substrato de pupação podem estar contaminados com substâncias químicas, sendo que algumas destas podem ser de interesse forense ou ser aplicadas no controle de pragas. Assim, o principal objetivo do presente trabalho é procurar dar contribuição a um melhor conhecimento dos efeitos do ansiolítico Diazepam [Diazepam NQ® 10mg] sobre o desenvolvimento larval e comportamento de dispersão larval e do inseticida Fipronil [Regent 800 WG®] sobre a dispersão pós-alimentar das larvas de duas espécies de moscas (C. megacephala e M. domestica). Na análise do desenvolvimento larval, pôde-se observar que a presença de Diazepam no substrato alimentar aumenta o tempo de desenvolvimento larval, retardando o ganho de massa por tempo nas duas espécies estudadas, quando se compara ao grupo controle. Já o comportamento de dispersão larval foi alterado na presença de Fipronil ou de Diazepam, em relação ao controle, sendo que a profundidade de enterramento e a distância das pupas do centro de irradiação... (Resumo completo, clicar acesso eletrônico abaixo) / Abstract: Some species of Diptera have a great medical and veterinary importance, acting as vectors of many diseases, addiction of having a considerable agricultural, commercial and ecological importance and other ones having forensic importance. Flies utilize discrete and ephemeral breeding sites for larval nutrition. After the exhaustion of food, larvae begin dispersing in search of sites to pupate or to additional food sources, a process referred as post feeding larval dispersal. However, in natural environments these breeding or feeding sites can be contaminated with chemical substances. Some of these substances can be of forensic interest or be applied in pest control. In the present study, the main objective was to investigate the effect of Diazepam® [Diazepam NQ® 10mg] and Fipronil® [Regent 800 WG®] on immature stages of Chrysomya megacephala (Diptera: Calliphoridae) and Musca domestica (Diptera: Muscidae). The larvae were reared on artificial diet and rabbit liver on which different dosages of Diazepam were administrated in order to study the effects of this drug on the development and post feeding larval dispersal of the two species. Different dosages of the insecticide Fipronil were disposed in circular arena used as pupation substrate to investigate the effects on post feeding larval dispersal. The results showed that time required for larval development were significantly longer in colonies fed in contact with Diazepam than in the control ones, delaying the increase of mass per unit time in the two studied species. The larval dispersal behavior was modified in the presence of Fipronil and Diazepam, in comparison to arenas without the drugs. It was also observed that the burial depth and distance of the irradiation center were shorter than in the control groups for the two species... (Complete abstract click electronic address below) / Mestre