Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2009. / Includes bibliographical references. / Iron availability and primary productivity in the oceans are intricately linked through photosynthesis. At the global scale we understand how iron addition induces phytoplankton blooms through meso-scale iron-addition experiments. At the atomic scale, we can describe the length and type of bonds that connect iron atoms to components of photosystem I, the most efficient light-harvesting complex in nature. Yet, we know little of how iron influences microbial diversity and distribution in the open ocean. In this study, we assess the influence of iron on the ecology of the numerically abundant marine cyanobacterium, Prochlorococcus. With its minimal genome and ubiquity in the global ocean, Prochlorococcus represents a model system in which to study the dynamics of the link between iron and primary productivity. To this end, we tested the iron physiology of two closely-related Prochlorococcus ecotypes. MED4 is adapted to high-light environments while MIT9313 lives best in low-light conditions. We determined that MIT9313 is capable of surviving at low iron concentrations that completely inhibit MED4. Furthermore, concentrations of Fe' that inhibit growth in culture are sufficient to support Prochlorococcus growth in the field, which raises questions about the species of iron available to Prochlorococcus. We then examined the molecular basis for the ability of MIT9313 to grow at lower iron concentrations than MED4 by assessing whole-genome transcription in response to changes in iron availability in the two ecotypes. / Genes that were differentially expressed fell into two categories: those that are shared by all (Prochlorococcus core genome) and those that are not (non-core genome). Only three genes shared between MED4 and MIT9313 were iron-responsive in both strains. We then tested the iron physiology of picocyanobacteria in the field and found that Synechococcus is iron-stressed in samples where Prochlorococcus is not. Finally, we propose a method to measure how iron stress in Prochlorococcus changes over natural gradients of iron in the oligotrophic ocean by quantifying transcription of the iron-stress induced gene, isiB. Taken together, our studies demonstrate that iron metabolism influences the ecology of Prochlorococcus both by contributing to its diversity and distinguishing it from other marine cyanobacteria. / by Anne Williford Thompson. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 149-162). / Trichodesmium is a colonial, N2-fixing cyanobacterium found in tropical oceans. Species of Trichodesmium are genetically similar but several species exist together in the same waters. In order to coexist, Trichodesmium spp. may occupy different niche spaces through differential utilization of resources such as nutrients and light, and through responses to physical characteristics such as temperature and turbulence. To investigate niche differentiation in Trichodesmium, I characterized cultured strains of Trichodesmium, identified and enumerated Trichodesmium clades in the field, and investigated P stress and N2 fixation in field populations. Species of Trichodesmium grouped into two clades based on sequences from 16S rDNA, the internal transcribed spacer (ITS), and the heterocyst differentiation gene hetR. Clade I contained Trichodesmium erythraeum and Trichodesmium contortum, and clade II contained Trichodesmium thiebautii, Trichodesmium tenue, Trichodesmium hildebrandtii, and Trichodesmium pelagicum. Each clade was morphologically diverse, but species within each clade had similar pigmentation. I developed a quantitative polymerase chain reaction (qPCR) method to distinguish between these two clades. In field populations of the Atlantic and Pacific Oceans, the qPCR method revealed that clade II Trichodesmium spp. were more prominent than clade I in the open ocean. Concentrations of Trichodesmium did not correlate with nutrient concentrations, but clade I had wider temperature and depth distributions than clade II. / (cont.) Temperature and light are physical characteristics that may define niche spaces for species of Trichodesmium. Clade I and II concentrations correlated with each other in the Pacific but not in the Atlantic, indicating that the two clades were limited by the same factors in the Pacific while different factors were limiting the abundance of the two clades in the Atlantic. Trichodesmium populations in the North Atlantic were more P stressed and had higher N2 fixation rates than populations in the western Pacific. While nutrient concentrations didn't directly correlate with Trichodesmium concentrations, the contrasting nutrient regimes found in the Atlantic and Pacific Oceans might influence distributions of the two clades differently. Unraveling the differences among species of Trichodesmium begins to explain their coexistence and enables us to understand factors controlling global N2 fixation. / by Annette Michelle Hynes. / Ph.D.

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Viral predation on bacteria in the ocean liberates carbon from the particulate fraction, where it is accessible to higher trophic levels, and redirects it to the dissolved fraction, where it supports microbial growth. Although viruses are highly abundant in the ocean little is known about how their interactions with bacteria are structured. This challenge arises because the diversity of both bacteria and viruses is exceedingly high and interactions between them are mediated by specific molecular interactions. This thesis uses heterotrophic bacteria of the genus Vibrio as a model to quantify virus-host interactions in light of host population structure and ecology. The methods developed in this thesis include streamlining of standard bacteriophage protocols, such as the agar overlay, and facilitate higher throughput in the isolation and characterization of novel environmental virus-host systems. Here, >1300 newly isolated Vibrio are assayed for infection by viral predators and susceptibility is found to be common, though total concentrations of predators are highly skewed, with most present at low abundance. The largest phylogenetically-resolved host range cross test available to date is conducted, using 260 viruses and 277 bacterial strains, and highly-specific viruses are found to be prevalent, with nearly half infecting only a single host in the panel. Observations of blocks of multiple viruses with nearly identical infection profiles infecting sets of highly-similar hosts suggest that increases in abundance of particular lineages of bacteria may be important in supporting the replication of highly specific viruses. The identification of highly similar virus genomes deriving from different sampling time points also suggests that interactions for some groups of viruses and hosts may be stable and persisting. Genome sequencing reveals that members of the largest broad host-range viral group recovered in the collection have sequence homology to non-tailed viruses, which have been shown to be dominant in the surface oceans but are underrepresented in culture collections. By integrating host population structure with sequencing of over 250 viral genomes it is found that viral groups are genomically cohesive and that closely-related and co-occurring populations of bacteria are subject to distinct regimes of viral predation. / by Anne Kathryn Marie Kauffman. / Ph. D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Includes bibliographical references (p. 157-171). / Bacteriophage have been proposed to be the most abundant organisms on the planet, at an estimated 10³¹ particles globally (Hendrix et al., 1999). The majority of bacteriophage isolates (96%) are double-stranded DNA tailed phages (Caudovirales). These phages possess a distinctive icosehedral head, with a protein tail structure protruding from a single vertex. This organelle determines host specificity and provides the mechanism of passage of the phage genome into the host cell. Phages infecting differing microbial hosts may have access to a global pool of genes, albeit at different levels. Marine cyanobacteria of the genera Prochlorococcus and Synechococcus are numerically dominant photosynthetic cells in the large oligotrophic gyres of the open oceans, and contribute an estimated 30% to the oceanic photosynthetic budget. Cyanophages have been isolated which propagate on many strains of Synechococcus and Prochlorococcus. Cyanophages can effect community structure and succession through lytic infection of their hosts, and have implications in lateral gene transfer, mediated through lysogeny, mixed infections, pseudolysogeny, and transduction. / (cont.) The broad host ranges (between genera) observed in some phages indicates that lateral gene transfer is not confined to cells of the same strain. These phage/host interactions begin by host recognition by the tail of the infecting phage. Few studies have examined the structural proteins of cyanophage, partially due to the lack of a robust protocol for the growth and purification of phage particles. Cyanophage Syn5 is a short-tailed phage isolated from the Sargasso Sea by Waterbury and Valois (1993) which infects Synechococcus strain WH8109. Methods of growing the host cells and the phage, and concentrating the phage by PEG precipitation were developed. These methods led to highly concentrated purified phage stocks, to titers of 1012 particles/ml. Preliminary characterization of the growth of Syn5 gave a burst size of approximately 30 phage/cell and a lytic period of approximately 10 hours when inoculated into exponentially growing host cells acclimated to a temperature of 26⁰C and a light intensity of 50[mu]E m⁻² s⁻¹. Isolation of the phage nucleic acid yielded dsDNA molecules of approximately 40kb. The Syn5 particles were comprised of twelve structural proteins, as determined by SDS-PAGE. / (cont.) The most intense band on the gel was assigned to the capsid protein of Syn5 ([approx.] 35kDa). However, it was not possible to distinguish putative tail proteins via this method. Purified Syn5 particles were sent to the Pittsburgh Bacteriophage Institute for genome sequencing. The completed Syn5 genome was 46,214 bp long with a 237bp terminal repeat. Annotation of the completed Syn5 genome identified 61 putative ORFs, and revealed that Syn5 appeared closely related to the enteric phage T7 and cyanophages P-SSP7 and P60, as determined by gene similarity and synteny, although the genome was [approx.] 10kb longer than T7. Syn5 appeared to possess a more extensive DNA replisome that T7, containing copies of genes that encoded proteins of known T7 host co-factors, such as thioredoxin, utilized by the T7 DNAP. Several large ORFs were identified between the gene encoding the putative tail fiber and the gene encoding the putative terminase. These ORFs encoded proteins similar to some fibrous sequences within the NCBI non- redundant (nr) gene sequence database as of March, 2005; but had unknown functions within the phage. Unlike other recently sequenced cyanophages, SynS did not contain any photosynthetic genes. / (cont.) The structural proteins of SynS, as visualized by SDS-PAGE, were characterized by mass-spectroscopy and N-terminal sequencing. This allowed the assignment of sequences to putative ORFs within the Syn5 genome. The Syn5 particle was comprised of eleven discreet protein chains of molecular weight 152kDa, 139kDa, 99kDa, 90kDa, 66kDa, 60kDa, 47kDa, 35kDa, 22kDa, 21kDa, and 16kDa. The identified proteins included the portal, capsid, two tail tube proteins, and three internal virion proteins. Each of the genes encoding these proteins were found in the same gene order in the Syn5 genome as the corresponding genes were ordered in the T7 genome. There were three unidentifiable proteins within the particle (66kDa, 47kDa, and 16kDa). These mapped to the area of the SynS genome between the gene encoding the putative tail fiber and the gene encoding the putative terminase. No minor capsid or decorative capsid proteins were detected. The copy numbers of the corresponding protein chains were similar to those known for T7, with the exception of the tail fiber, which was present at a number of three chains per particle in comparison to T7's eighteen per particle. / (cont.) Polyclonal antibodies were raised against Syn5 particles. A Western blot with these antibodies showed that the tail fiber and the two unknown fibrous sequences were highly antigenic. This evidence implies that the unknown structures may act as host recognition proteins in addition to the tail fiber. Characterization of these novel proteins may provide insight to the host recognition abilities of cyanophages. An additional study was also carried out, investigating the high temperature limit of the growth of phage P22. The results revealed that the production of infectious particles was limited by the temperature sensitivity of the folding and assembly of the P22 tailspike protein. This work has been published and is included in the Appendix. / by Welkin Hazel Pope. / Ph.D.

<p>The timing of the spring phytoplankton bloom in the subpolar North Atlantic Ocean has important consequences for the marine carbon cycle and ecosystems. There are currently several proposed mechanisms to explain the timing of this bloom. The conventional theory holds that the bloom begins when the ocean warms and the seasonal mixed layer shoals in the spring, decreasing the depth to which phytoplankton are mixed and increasing the light available to the population. Recent work has attributed the beginning of the bloom to decreases in turbulence within the upper ocean, driven by the onset of positive heat fluxes or decreases in the strength of local winds. Other studies have focused on the increase in the seasonal mixed layer in the winter as a driver of changes in ecosystem interactions and a control on the spring bloom. Finally, submesoscale eddies, occurring as a result of lateral density gradients, have been proposed as a stratification mechanism that can create phytoplankton blooms prior to the onset of ocean surface warming.</p><p>This dissertation critically examines and compares the proposed theories for the initiation of the spring bloom and draws on these theories to propose a new framework: that blooms begin when the active mixing depth shoals, a process generally driven by a weakening of surface heat fluxes and consequent shift from convective mixing to wind-driven mixing. Using surface forcing data, we develop a parameterization for the active mixing depth from estimates of the largest energy-containing eddies in the upper ocean. </p><p>Using in situ records of turbulent mixing and biomass, we find that the spring phytoplankton bloom occurs after mixing shifts from being driven by convection to being driven by wind, and that biomass increases as the active mixing depth shoals. Using remote sensing data, we examine patterns of bloom initiation in the North Atlantic at the basin scale, compare current theories of bloom initiation, and find that the shoaling of the active mixing depth better predicts the onset of the bloom across the North Atlantic subpolar basin and over multiple years than do other current theories. Additionally, using a process study model, we evaluate the importance of submesoscale eddy-driven stratification as a control on the initiation of the spring bloom, determining that this mechanism has a relatively minor effect on alleviation of phytoplankton light limitation. Finally, we describe potential techniques and tools to examine whether interannual variability in the active mixing depth acts as a control on variability in the timing of the spring bloom.</p> / Dissertation

<p> There is a broad perception that many of the greatest knowledge gaps in marine conservation are in understanding and integrating human dimensions. Marine governance must go beyond the rhetoric that conservation will benefit from including human dimensions, and dig deeper into social science disciplines to find specific tools that may be useful. Bennett et al. (2017) advocate for &ldquo;fostering knowledge on the scope and contributions of the social sciences to conservation&rdquo; from the inception of conservation projects, during all stages of planning and implementation and at all scales, and encourage the mainstreaming of social science into conservation. However, the fractured nature of literature pointing to the importance of social science has left many unsure what is really important or what to do. This dissertation seeks to remedy this, first by mainstreaming how to strategically consider social equity, and second by learning from collective action studies. </p><p> Social equity is increasingly included in conservation mission statements &ndash; either because it is an intrinsic goal or because it is believed to have functional value to help reach other objectives. Until now, social equity has been vaguely defined, and therefore been difficult to include, monitor and evaluate in environmental governance. Chapter 1 presents a theoretical foundation for defining and distinguishing between different types of social equity and considering social equity&rsquo;s role in conservation outcomes. First, we introduce the <i>equity landscape</i> as a way to describe the distributions of resources and participation rights in a society supported by social norms in a given community. We use case studies to illustrate how environmental management can benefit from considering the equity landscape in both short- and long-term strategy. Through collaborative efforts, we also describe social equity to include several dimensions &ndash; including participation (or input to conservation interventions), and spatial, access, and financial outcomes of a conservation intervention (Klein et al. 2015). Chapter 1 motivates collecting empirical evidence of how different types of equity are experienced in a community and their influence on stakeholder behavior. </p><p> Therefore, in Chapter 2 we investigate how fishers perceive and experience these different dimensions of equity, and how different dimensions of equity influence fisher compliance with social norms and willingness to punish defectors. Our interdisciplinary approach combines a behavioral experiment and surveys, and informs important decisions on critical design elements, such as should the intervention focus on participation, or outcomes of the intervention, such as access or financial benefits? Should equity objectives be equal or fair? And, how should managers measure these objectives? This research provides important empirical insight on how equity and conservation outcomes are interlinked and how management actions may influence stakeholder cooperation, thus presenting a unique insight into equity that is applicable to a wide range of settings. </p><p> Second, this dissertation highlights the potential benefits of integrating collective action literature in fisheries management. Most problems in fisheries management are rooted in some sort of tragedy of the commons. Understanding the conditions under which cooperation can emerge and how to create policies around those conditions is extremely important for successful fisheries governance. The collective action literature contains a wealth of knowledge on how diverse types of societies can solve cooperation problems and real-world management questions. </p><p> Chapter 3 investigates two such applied questions: Do self-assembled or randomly assigned groups cooperate better? And, if there are costs to random assignment, what strategies might help offset some of these costs? We show that self-assembly and the ability to communicate face-to-face both increase compliance with rules and punishment of defectors, although self-assembly has a greater effect. </p><p> This work is specific to artisanal fishing communities in Ta&ntilde;on Strait, Philippines, but provides an approach to solving questions managers have to make on a range of key issues that likely have big consequences on conservation outcomes. By combining interdisciplinary theory and methods, my dissertation highlights how social science can both integrate into and aid conservation efforts.</p><p>

abstract: Sea ice algae dominated by diatoms inhabit the brine channels of the Arctic sea ice and serve as the base of the Arctic marine food web in the spring. I studied sea ice diatoms in the bottom 10 cm of first year land-fast sea ice off the coast of Barrow, AK, in spring of 2011, 2012, and 2013. I investigated the variability in the biomass and the community composition of these sea-ice diatoms between bloom phases, as a function of overlying snow depth and over time. The dominant genera were the pennate diatoms Nitzschia, Navicula, Thalassiothrix, and Fragilariopsis with only a minor contribution by centric diatoms. While diatom biomass as estimated by organic carbon changed significantly between early, peak, and declining bloom phases (average of 1.6 mg C L-1, 5.7 mg C L-1, and 1.0 mg C L-1, respectively), the relative ratio of the dominant diatom groups did not change. However, after export, when the diatoms melt out of the ice into the underlying water, diatom biomass dropped by ~73% and the diatom community shifted to one dominated by centric diatoms. I also found that diatom biomass was ~77% lower under high snow cover (>20 cm) compared to low snow cover (<8 cm); however, the ratio of the diatom categories relative to particulate organic carbon (POC) was again unchanged. The diatom biomass was significantly different between the three sampling years (average of 2.4 mg C L-1 in 2011, 1.1 mg C L-1 in 2012, and 5.4 mg C L-1 in 2013, respectively) as was the contribution of all of the dominant genera to POC. I hypothesize the latter to be due to differences in the history of ice sheet formation each year. The temporal variability of these algal communities will influence their availability for pelagic or benthic consumers. Furthermore, in an Arctic that is changing rapidly with earlier sea ice and snowmelt, this time series study will constitute an important baseline for further studies on how the changing Arctic influences the algal community immured in sea ice. / Dissertation/Thesis / Masters Thesis Biology 2014

abstract: This thesis research focuses on developing a single-cell gene expression analysis method for marine diatom Thalassiosira pseudonana and constructing a chip level tool to realize the single cell RT-qPCR analysis. This chip will serve as a conceptual foundation for future deployable ocean monitoring systems. T. pseudonana, which is a common surface water microorganism, was detected in the deep ocean as confirmed by phylogenetic and microbial community functional studies. Six-fold copy number differences between 23S rRNA and 23S rDNA were observed by RT-qPCR, demonstrating the moderate functional activity of detected photosynthetic microbes in the deep ocean including T. pseudonana. Because of the ubiquity of T. pseudonana, it is a good candidate for an early warning system for ocean environmental perturbation monitoring. This early warning system will depend on identifying outlier gene expression at the single-cell level. An early warning system based on single-cell analysis is expected to detect environmental perturbations earlier than population level analysis which can only be observed after a whole community has reacted. Preliminary work using tube-based, two-step RT-qPCR revealed for the first time, gene expression heterogeneity of T. pseudonana under different nutrient conditions. Heterogeneity was revealed by different gene expression activity for individual cells under the same conditions. This single cell analysis showed a skewed, lognormal distribution and helped to find outlier cells. The results indicate that the geometric average becomes more important and representative of the whole population than the arithmetic average. This is in contrast with population level analysis which is limited to arithmetic averages only and highlights the value of single cell analysis. In order to develop a deployable sensor in the ocean, a chip level device was constructed. The chip contains surface-adhering droplets, defined by hydrophilic patterning, that serve as real-time PCR reaction chambers when they are immersed in oil. The chip had demonstrated sensitivities at the single cell level for both DNA and RNA. The successful rate of these chip-based reactions was around 85%. The sensitivity of the chip was equivalent to published microfluidic devices with complicated designs and protocols, but the production process of the chip was simple and the materials were all easily accessible in conventional environmental and/or biology laboratories. On-chip tests provided heterogeneity information about the whole population and were validated by comparing with conventional tube based methods and by p-values analysis. The power of chip-based single-cell analyses were mainly between 65-90% which were acceptable and can be further increased by higher throughput devices. With this chip and single-cell analysis approaches, a new paradigm for robust early warning systems of ocean environmental perturbation is possible. / Dissertation/Thesis / Ph.D. Civil and Environmental Engineering 2013

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2005. / Page 296 blank. / Includes bibliographical references. / Marine thecate heterotrophic dinoflagellates likely play an important role in the consumption of primary productivity and in the trophic structure of the plankton, yet we know little about these species. This thesis expanded our understanding of the autecology and evolutionary history of the Protoperidinium and diplopsalids. The distributions of Protoperidinium species off the southwestern coast of Ireland were influenced by physical oceanographic conditions coupled with the availability of preferred prey. The distributions of individual Protoperidinium species varied widely from the distribution of total Protoperidinium, indicating differences in ecologies among species. Certain species of Protoperidinium co-occurred with known preferred phytoplankton prey species. Concentrations of other Protoperidinium species were not related to those of any particular phytoplankton species, indicating that these Protoperidinium may rely on phytoplankton or other food sources beyond those already known, may not be species specific selective feeders, or may have become uncoupled from their preferred prey. The description of the sexual and asexual life history of Protoperidinium steidingerae provided the first account of the life history of any Protoperidinium species. / (cont.) Asexual division occurred by eleutheroschisis within a temporary, immotile cyst, yielding two daughter cells. Daughter cells were initially round and half to two-thirds the size of parent cells, then rapidly increased in size, forming horns before separating. Sexual reproduction was constitutive in clonal cultures, indicating that the species may be homothallic. Fusing gametes were isogamous, and resulted in a planozygote with two longitudinal flagella. Hypnozygotes had a mandatory dormancy period of ca. 70 days. Germination resulted in planomeiocytes with two longitudinal flagella. Nuclear cyclosis may occur in the planomeiocyte stage. A high level of morphological diversity among life history stages of P. steidingerae has led to mis-classification and taxonomic inaccuracy of Protoperidinium species identified from field samples. The large subunit ribosomal DNA (LSU rDNA) molecular phylogeny of the heterotrophic dinoflagellates revealed that the genus Protoperidinium appeared to be recently diverged within the dinoflagellates. In maximum parsimony and neighbor joining analysis, Protoperidinium formed a monophyletic group, evolving from diplopsalid dinoflagellates. / (cont.) In maximum likelihood and Bayesian analyses, however, Protoperidinium was polyphyletic, as the lenticular, diplopsalid heterotroph, Diplopsalis lenticula Bergh, was inserted within the Protoperidinium clade basal to Protoperidinium excentricum (Paulsen) Balech, and Preperidinium meunieri (Pavillard) Elbrichter fell within a separate clade as a sister to the Oceanica section and Protoperidinium steidingerae Balech. In all analyses, the Protoperidinium were divided into two major clades, with members in the Oceanica group and subgenus Testeria in one clade, and the Excentrica, Conica, Pellucida, Pyriforme, and Divergens sections in another clade. The LSU rDNA molecular phylogeny supported the historical morphologically determined sections, but not a simple morphology-based model of evolution based on thecal plate shape. LSU rDNA gene sequences are frequently used to infer the phylogeny of organisms. The many copies of the LSU rDNA found in the genome are thought to be kept homogenous by concerted evolution. In Protoperidinium species, however, there was high intragenomic diversity in the D1-D6 region of the LSU rDNA. For each species, the clone library was usually comprised of one highly represented copy and many unique sequences. / (cont.) Sequence differences were primarily characterized by single base pair substitutions, single base pair insertion/deletions (indels), and/or large indels. Phylogenetic analysis of all clones gave strong support for monophyly of the polymorphic copies of each species, and recovered the same species tree as an analysis using just one sequence per species. Analysis of LSU rDNA gene expression in three species by RT-PCR indicated that copies with fewer substitutions and fewer and smaller indels are expressed, and that 50% or more of the copies are pseudogenes. High intraspecific and intraindividual LSU rDNA sequence variability could lead to inaccurate species phylogenies and over-estimation of species diversity in environmental sequencing studies. This thesis has explored the ecology, life history, molecular phylogeny, and intraspecific DNA sequence variability of marine thecate heterotrohic dinoflagellates using a wide range of methodologies, including field sampling, culturing, microscopy, morphological analyses, histological staining, and molecular biology. The work here has broadened our understanding of the Protoperidinium and diplopsalids, providing new insights into the ecological and evolutionary relationships of these heterotrophs with other plankton species. / by Kristin Elizabeth Gribble. / Ph.D.

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2008. / Includes bibliographical references. / In this dissertation, I explored metapopulation dynamics and population connectivity, with a focus on the softshell clam, Mya arenaria. I first worked towards developing a method for using elemental signatures retained in the larval shell as a tag of natal habitat. I designed and implemented an experiment to determine whether existing methods commonly used for fishes would be applicable to bivalves. I found that the instrumentation and setup I used were not able to isolate and measure the first larval shell of M. arenaria. In concert with developing this method for bivalves, I reared larval M. arenaria in the laboratory under controlled conditions to understand the environmental and biological factors that may influence elemental signatures in shell. My results show that growth rate and age have significant effects on juvenile shell composition, and that temperature and salinity affect larval and juvenile shell composition in variable ways depending on the element evaluated. I also examined the regional patterns of diversity over the current distribution of M. arenaria using the mitochondrial gene, cytochrome oxidase I (COI). I found minimal variability across all populations sampled, suggesting a recent population expansion in the Northwest Atlantic. Finally, I employed theoretical approaches to understand patch dynamics in a two-patch metapopulation when one patch is of high quality and the other low quality. I developed a matrix metapopulation model and compared growth rate elasticity to patch parameters under variable migration scenarios. I then expanded the model to include stochastic disturbance. I found that in many cases, the spatial distribution of individuals within the metapopulation affects whether growth rate is most elastic to parameters in the good or bad patch. / by Carly A. Strasser. / Ph.D.