<p> Shallow subtidal epibenthic communities worldwide are under threat from exploitation, pollution, eutrophication, acidification, climate change, and invasive species, with implications for ecosystem diversity, productivity, function, and services. Subtidal ecosystems in the Gulf of Maine are particularly impacted, making it crucial to understand these habitats so that our impacts can be predicted and mitigated. I investigated the basic ecological forces that structure shallow subtidal epibenthic communities in this region, and how invasive species integrate themselves into these communities. I used community phylogenetic and functional trait analyses to investigate if invertebrate communities in the rocky subtidal are assembled via deterministic or random forces, experimental manipulations to quantify how macroalgae might influence sessile invertebrates on subtidal surfaces, and measurements of life history traits of <i>Botrylloides violaceus</i>, an invasive colonial ascidian, to estimate whether growth of this species differs among man-made versus natural habitats. Based on community phylogenetic analyses, rocky subtidal invertebrate communities appear to be structured by deterministic forces, with evidence for both competitive exclusion and environmental filtering operating at different spatial scales. These findings support existing studies that show that competition structures communities at local scales, and also expand our knowledge of the processes that act regionally, i.e. environmental filtering. On shallow sunlit experimental surfaces suspended from floating docks, macroalgae had little effect on invertebrate abundance or diversity, contrary to findings from experiments in the rocky subtidal. Macroalgae did influence composition as well as enhance invertebrate colonization in the early stages of community assembly. Different factors appear to influence the balance between heterotrophs and autotrophs in floating dock and rocky subtidal systems with implications for community structure, function and productivity. In different habitats, colonies of the invasive ascidian B. violaceus exhibited differences in life history traits. It grew faster and attained larger sizes in man-made floating dock versus natural rocky subtidal and eelgrass bed habitats. Again, differences among habitats appear to influence invasion success. In conclusion, competitive exclusion, facilitation, and environmental filtering play key roles in controlling the structure, composition, and function of shallow subtidal communities. Invasive species have the potential to disrupt these forces as they integrate themselves into man-made and subsequently natural habitats.</p>

<p>Most of the seafloor is soft sediment, so hard substrata are isolated and island-like. In this dissertation, I explore how species distribution patterns on isolated marine hard substrata resemble terrestrial island communities, drawing on classical island biogeography theory and assembly rules, and describe how benthic invertebrate communities assemble in these island-like habitats. Higher species richness occurred on larger substrata (dropstones and shipwrecks), paralleling terrestrial island communities. However, while larger islands have greater habitat diversity and primary productivity, marine hard substrata are simpler habitats. Greater elevation in the benthic boundary layer may expose fauna to faster current, higher food supply and larval flux. Substrata located closer together had more similar communities, another pattern that resembles terrestrial islands. Dropstone fauna had a clumped distribution, indicating that larvae may disperse among substrata located close together, resulting in similar communities. In Svalbard fjords, benthic megafaunal communities were significantly different between Arctic- and Atlantic-influenced fjords. Depth and temperature had the greatest influence, with the highest diversity occurring in cold Rijpfjorden and on the north Svalbard shelf. Recruitment in Svalbard fjords was spatially and temporally variable, with lower recruitment in Rijpfjorden than in Atlantic-influenced fjords and lower recruitment at greater depth. Most of the recruits in Svalbard fjords were fast-growing, poor-competitive opportunists. On shipwrecks, communities showed two mechanisms of colonization: mobile fauna with long-dispersing planktotrophic larvae, and encrusting fauna with lecithotrophic larvae. Encrusting species reproduce asexually to cover the wreck surface, and philopatry may build up dense populations, leading to uneven communities. On terrestrial islands, non-random co-occurrence is attributed to interspecific competition, but for marine substrata, there may not be a relationship. Fauna were distributed randomly on settlement plates in Svalbard fjords, even when interspecific competition was observed. On dropstones, some morphotypes co-occurred non-randomly in the absence of overgrowth competition. Non-random co-occurrence on isolated marine hard substrata may be a result of restricted larval dispersal (for pairs co-occurring less than by chance) or epibiontism (for pairs co-occurring more often than by chance). While species distribution patterns on island-like marine hard substrata resemble terrestrial islands, the mechanisms are not necessarily the same.

<p> Recruitment of marine fishes is largely determined by biological and oceanographic factors acting on early life stages. Coastal upwelling has long been recognized as a critical factor influencing the survival of larvae and recruitment to adult populations. Dynamics in regional upwelling influence the magnitude and timing of primary productivity, affecting the availability of critical food sources for larval fish. In addition, upwelling-relaxation cycles affect the dispersal of marine larvae and their onshore delivery prior to settlement. Challenges with tracking larvae, however, have limited our understanding of how oceanography influences the early life stages of fishes. The objective of this dissertation is to evaluate the biological and oceanographic drivers of larval growth, settlement, and recruitment, using rockfishes (<i> Sebastes</i> spp.) as model organisms. </p><p> Overlap of larval production and favorable feeding conditions may drive recruitment for many temperate marine fishes, as small changes in larval growth can result in order-of-magnitude differences in year-class-strength. In Chapter 1, I assess the influence of regional productivity, temperature, and larval condition in explaining growth in rockfishes. I employ a combination of otolith microstructure and satellite imagery to measure initial larval growth and estimate the productivity and temperature experienced by individuals to determine their relative importance in subsequent growth at metamorphosis. I compare model performance using indexed environmental conditions scaled over three different regions. In both years of study, net primary productivity explained the most variation in pre-metamorphic growth relative to temperature and initial growth. This relationship was consistent across spatial regions. Recent settlement, juvenile recruitment, and individual growth were significantly higher in a year when productivity bloomed earlier and individual larvae experienced higher levels of productivity. These results support the hypothesis that large-scale oceanographic processes that stimulate upwelling and secondary production are primary drivers of larval growth and subsequent year-class strength in rockfishes.</p><p> Characterizing the behavior of larvae prior to settlement is integral to understanding population dynamics because coastal oceanography may facilitate or limit settlement. Otolith microchemistry can be used to determine patterns of fish movement, although there is a limited understanding of how this tool can be applied in coastal marine systems. My goal in Chapter 2 is to evaluate the application of otolith microchemistry to characterize water mass associations of settlement-stage marine fish in a coastal upwelling region using a three-step approach. First, I characterize seawater chemistry of coastal water masses across multiple years, finding significant differences in the chemical signatures of strong upwelling, weak upwelling, and relaxation. Second, I experimentally determine the effect of temperature on the partitioning of trace elements in otoliths for two rockfishes to find that the effect of temperature on otolith partition coefficients was element- and species-specific. Finally, I compare the synchrony in seawater and otolith chemistry of settlement-stage rockfishes that were exposed to naturally variable conditions over an upwelling-relaxation cycle. I subsequently evaluate whether laser ablation inductively coupled plasma mass spectrometry effectively measures otolith chemistry over ecologically relevant time scales. I discovered that elemental concentrations in otoliths respond rapidly to changes in seawater chemistry and reflect equivalent proportional changes. This study provides evidence that elemental signatures are valuable tools for reconstructing larval histories of marine fish.</p><p> In Chapter 3, I use otolith chemistry to examine water mass associations of two juvenile rockfishes during onshore transport and settlement in an upwelling region. I develop a chemical proxy for upwelling and relaxation by characterizing Sr/Ca and Ba/Ca signatures of otoliths collected during these oceanographic conditions. Otolith chemistry differed between rockfishes collected during upwelling and relaxation, with signatures unique to each year. I subsequently compare otolith signatures of rockfishes collected during high and low settlement periods to determine whether specific water masses affect settlement. I provide evidence that copper rockfish associate with upwelling currents during periods of high settlement, suggesting that upwelling may facilitate settlement for these species. Conversely, I found evidence that the closely related gopher rockfish associate with relaxation events during peak settlement periods. This research takes an important first step at in evaluating the utility of trace element signatures to characterize larval fish movement during onshore delivery and settlement in marine systems. Together, these studies improve our understanding of how coastal upwelling impacts larval growth, settlement, and recruitment, which provides important information for understanding population dynamics in marine ecosystems.</p>