Functional connectivity of coral reef fishes in a tropical seascape assessed by compound-specific stable isotope analyses

Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution February 2011The ecological integrity of tropical habitats, including mangroves, seagrass beds and coral reefs, is coming under increasing pressure from human activities. Many coral reef fish species are thought to use mangroves and seagrass beds as juvenile nurseries before migrating to coral reefs as adults. Identifying essential habitats and preserving functional linkages among these habitats is likely necessary to promote ecosystem health and sustainable fisheries on coral reefs. This necessitates quantitative assessment of functional connectivity among essential habitats at the seascape level. This thesis presents the development and first application of a method for tracking fish migration using amino acid (AA) δ13C analysis in otoliths. In a controlled feeding experiment with fish reared on isotopically distinct diets, we showed that essential AAs exhibited minimal trophic fractionation between consumer and diet, providing a δ13C record of the baseline isoscape. We explored the potential for geochemical signatures in otoliths of snapper to act as natural tags of residency in seagrass beds, mangroves and coral reefs in the Red Sea, Caribbean Sea and Eastern Pacific Ocean. The δ13C values of otolith essential AAs varied as a function of habitat type and provided a better tracer of residence in juvenile nursery habitats than conventional bulk stable isotope analyses (SIA). Using our otolith AA SIA approach, we quantified the relative contribution of coastal wetlands and reef habitats to Lutjanus ehrenbergii populations on coastal, shelf and oceanic coral reefs in the Red Sea. L. ehrenbergii made significant ontogenetic migrations, traveling more than 30 km from juvenile nurseries to coral reefs and across deep open water. Coastal wetlands were important nurseries for L. ehrenbergii; however, there was significant plasticity in L. ehrenbergii juvenile habitat requirements. Seascape configuration played an important role in determining the functional connectivity of L. ehrenbergii populations in the Red Sea. The compound-specific SIA approach presented in this thesis will be particularly valuable for tracking the movement of species and life-stages not amenable to conventional tagging techniques. This thesis provides quantitative scientific support for establishing realistic population connectivity models that can be used to design effective marine reserve networks.I have been supported by an Ocean Life Institute Fellowship, a National Science Foundation Graduate Research Fellowship, and the WHOI Academic Programs Office. The research presented in this thesis was supported by an Ocean Life Institute student research grant to K. McMahon, an International Society for Reef Studies-Ocean Conservancy Coral Reef Research Fellowship to K. McMahon, and King Abdullah University of Science and Technology (KAUST) Award Nos. USA 00002 and KSA 00011 to S. Thorrold. Additional support came from the Woods Hole Oceanographic Institution, the Large Pelagics Research Center at the University of New Hampshire, the Carnegie Institution of Washington and the W.M. Keck Foundation

Scaling properties of critical bubble of homogeneous nucleation in stretched fluid of square-gradient density-functional model with triple-parabolic free energy

The square-gradient density-functional model with triple-parabolic free energy is used to study homogeneous bubble nucleation in a stretched liquid to check the scaling rule for the work of formation of the critical bubble as a function of scaled undersaturation $\Delta\mu/\Delta\mu_{\rm spin}$, the difference in chemical potential $\Delta\mu$ between the bulk undersaturated and saturated liquid divided by $\Delta\mu_{\rm spin}$ between the liquid spinodal and saturated liquid. In contrast to our study, a similar density-functional study for a Lennard-Jones liquid by Shen and Debenedetti [J. Chem. Phys. {\bf 114}, 4149 (2001)] found that not only the work of formation but other various quantities related to the critical bubble show the scaling rule, however, we found virtually no scaling relationships in our model near the coexistence. Although some quantities show almost perfect scaling relations near the spinodal, the work of formation divided by the value deduced from the classical nucleation theory shows no scaling in this model even though it correctly vanishes at the spinodal. Furthermore, the critical bubble does not show any anomaly near the spinodal as predicted many years ago. In particular, our model does not show diverging interfacial width at the spinodal, which is due to the fact that compressibility remains finite until the spinodal is reached in our parabolic models.Comment: 10 pages, 10 figures, Journal of Chemical Physics accepted for publicatio

Direct numerical simulation of homogeneous nucleation and growth in a phase-field model using cell dynamics method

Homogeneous nucleation and growth in a simplest two-dimensional phase field model is numerically studied using the cell dynamics method. Whole process from nucleation to growth is simulated and is shown to follow closely the Kolmogorov-Johnson-Mehl-Avrami (KJMA) scenario of phase transformation. Specifically the time evolution of the volume fraction of new stable phase is found to follow closely the KJMA formula. By fitting the KJMA formula directly to the simulation data, not only the Avrami exponent but the magnitude of nucleation rate and, in particular, of incubation time are quantitatively studied. The modified Avrami plot is also used to verify the derived KJMA parameters. It is found that the Avrami exponent is close to the ideal theoretical value m=3. The temperature dependence of nucleation rate follows the activation-type behavior expected from the classical nucleation theory. On the other hand, the temperature dependence of incubation time does not follow the exponential activation-type behavior. Rather the incubation time is inversely proportional to the temperature predicted from the theory of Shneidman and Weinberg [J. Non-Cryst. Solids {\bf 160}, 89 (1993)]. A need to restrict thermal noise in simulation to deduce correct Avrami exponent is also discussed.Comment: 9 pages, 8 figures, Journal of Chemical Physics to be publishe

Steady-state nucleation rate and flux of composite nucleus at saddle point

The steady-state nucleation rate and flux of composite nucleus at the saddle point is studied by extending the theory of binary nucleation. The Fokker-Planck equation that describes the nucleation flux is derived using the Master equation for the growth of the composite nucleus, which consists of the core of the final stable phase surrounded by a wetting layer of the intermediate metastable phase nucleated from a metastable parent phase recently evaluated by the author [J. Chem. Phys. {\bf 134}, 164508 (2011)]. The Fokker-Planck equation is similar to that used in the theory of binary nucleation, but the non-diagonal elements exist in the reaction rate matrix. First, the general solution for the steady-state nucleation rate and the direction of nucleation flux is derived. Next, this information is then used to study the nucleation of composite nucleus at the saddle point. The dependence of steady-state nucleation rate as well as the direction of nucleation flux on the reaction rate in addition to the free-energy surface is studied using a model free-energy surface. The direction of nucleation current deviates from the steepest-descent direction of the free-energy surface. The results show the importance of two reaction rate constants: one from the metastable environment to the intermediate metastable phase and the other from the metastable intermediate phase to the stable new phase. On the other hand, the gradient of the potential $\Phi$ or the Kramers crossover function (the commitment or splitting probability) is relatively insensitive to reaction rates or free-energy surface.Comment: 12 pages, 6 figures, to be published in Journal of Chemical Physic

A review of ecogeochemistry approaches to estimating movements of marine animals

Author Posting. © Association for the Sciences of Limnology and Oceanography, 2013. This article is posted here by permission of Association for the Sciences of Limnology and Oceanography for personal use, not for redistribution. The definitive version was published in Limnology and Oceanography 58 (2013): 697-714, doi:10.4319/lo.2013.58.2.0697.Ecogeochemistry—the application of geochemical techniques to fundamental questions in population and community ecology—has been used in animal migration studies in terrestrial environments for several decades; however, the approach has received far less attention in marine systems. This review includes comprehensive meta-analyses of organic zooplankton δ13C and δ15N values at the base of the food web, dissolved inorganic carbon δ13C values, and seawater δ18O values to create, for the first time, robust isoscapes for the Atlantic Ocean. These isoscapes present far greater geographic variability in multiple geochemical tracers than was previously thought, thus forming the foundation for reconstructions of habitat use and migration patterns of marine organisms. We review several additional tracers, including trace-element-to-calcium ratios and heavy element stable isotopes, to examine anadromous migrations. We highlight the value of the ecogeochemistry approach by examining case studies on three components of connectivity: dispersal and natal homing, functional connectivity, and migratory connectivity. We also discuss recent advances in compound-specific stable carbon and nitrogen isotope analyses for tracking animal movement. A better understanding of isotopic routing and fractionation factors, particularly of individual compound classes, is necessary to realize the full potential of ecogeochemistry.We were supported by funding from the National Science Foundation (Division of Ocean Sciences–0825148 to S.R.T.), Award USA 00002 and KSA 00011 from the King Abdullah University of Science and Technology (to S.R.T.), and a National Science Foundation Graduate Research Fellowship (to L.H.)

Tracing carbon flow through coral reef food webs using a compound-specific stable isotope approach

Author Posting. © The Author(s), 2015. This is the author's version of the work. It is posted here by permission of Springer for personal use, not for redistribution. The definitive version was published in Oecologia 180 (2016): 809-821, doi:10.1007/s00442-015-3475-3.Coral reefs support spectacularly productive and diverse communities in tropical and sub26 tropical waters throughout the world’s oceans. Debate continues, however, on the degree to which reef biomass is supported by new water column production, benthic primary production, and recycled detrital carbon. We coupled compound-specific δ13C analyses with Bayesian mixing models to quantify carbon flow from primary producers to coral reef fishes across multiple feeding guilds and trophic positions in the Red Sea. Analyses of reef fishes with putative diets composed primarily of zooplankton (Amblyglyphidodon indicus), benthic macroalgae (Stegastes nigricans), reef-associated detritus (Ctenochaetus striatus), and coral tissue (Chaetodon trifascialis) confirmed that δ13C values of essential amino acids from all baseline carbon sources were both isotopically diagnostic and accurately recorded in consumer tissues. While all four source end-members contributed to the production of coral reef fishes in our study, a single source end-member often dominated dietary carbon assimilation of a given species, even for highly mobile, generalist top predators. Microbially-reworked detritus was an important secondary carbon source for most species. Seascape configuration played an important role in structuring resource utilization patterns. For instance, L. ehrenbergii, showed a significant shift from a benthic macroalgal food web on shelf reefs (71 ± 13% of dietary carbon) to a phytoplankton-based food web (72 ± 11%) on oceanic reefs. Our work provides insights into the roles that diverse carbon sources play in the structure and function of coral reef ecosystems and illustrates a powerful fingerprinting method to develop and test nutritional frameworks for understanding resource utilization.This research was based on work supported by Awards USA 00002 and KSA 00011 from King Abdullah University of Science and Technology (KAUST); additional funding was provided by the Woods Hole Oceanographic Institution (WHOI), a KAUST-WHOI award (SPCF-7000000104), and KAUST baseline research funds.2016-11-2

Crystallization Mechanism of Hard Sphere Glasses

In supercooled liquids, vitrification generally suppresses crystallization. Yet some glasses can still crystallize despite the arrest of diffusive motion. This ill-understood process may limit the stability of glasses, but its microscopic mechanism is not yet known. Here we present extensive computer simulations addressing the crystallization of monodisperse hard-sphere glasses at constant volume (as in a colloid experiment). Multiple crystalline patches appear without particles having to diffuse more than one diameter. As these patches grow, the mobility in neighbouring areas is enhanced, creating dynamic heterogeneity with positive feedback. The future crystallization pattern cannot be predicted from the coordinates alone: crystallization proceeds by a sequence of stochastic micro-nucleation events, correlated in space by emergent dynamic heterogeneity.Comment: 4 pages 4 figures Accepted for publication in Phys. Rev. Lett., April 201

Major shifts in nutrient and phytoplankton dynamics in the North Pacific Subtropical Gyre over the last 5000 years revealed by high-resolution proteinaceous deep-sea coral δ\u3csup\u3e15\u3c/sup\u3eN and δ\u3csup\u3e13\u3c/sup\u3eC records

The North Pacific Subtropical Gyre (NPSG) is the largest continuous ecosystem on Earth and is a critical component of global oceanic biogeochemical cycling and carbon sequestration. We report here multi-millennial-scale, sub-decadal-resolution records of bulk stable nitrogen (δ15N) and carbon (δ13C) isotope records from proteinaceous deep-sea corals. Data from three Kulamanamana haumeaae specimens from the main Hawaiian Islands extend the coral-based time-series back ∼5000 yrs for the NPSG and bypass constraints of low resolution sediment cores in this oligotrophic ocean region. We interpret these records in terms of shifting biogeochemical cycles and plankton community structure, with a main goal of placing the extraordinarily rapid ecosystem biogeochemical changes documented by recent coral records during the Anthropocene in a context of broader Late-Holocene variability. During intervals where new data overlaps with previous records, there is strong correspondence in isotope values, indicating that this older data represents a direct extension of Anthropocene records. These results reveal multiple large isotopic shifts in both δ15N and δ13C values similar to or larger in magnitude to those reported in the last 150 yrs. This shows that large fluctuations in the isotopic composition of export production in this region are not unique to the recent past, but have occurred multiple times through the Mid- to Late-Holocene. However, these earlier isotopic shifts occurred over much longer time intervals (∼millennial vs. decadal timescales). Further, the δ15N data confirm that the extremely low present day δ15N values recorded by deep sea corals (∼8‰) are unprecedented for the NPSG, at least within the past five millennia. Together these records reveal centennial to millennial-scale oscillations in NPSG biogeochemical cycles. Further, these data also suggest a number of independent biogeochemical regimes during which δ15N and δ13C trends were synchronous (similar to recent coral records) or distinctly decoupled. We propose that phytoplankton species composition and nutrient source changes are the dominant mechanisms controlling the coupling and de-coupling of δ15N and δ13C values, likely primarily influenced by changing oceanographic conditions (e.g., stratification vs. entrainment). The decoupling observed in the past further suggests that oceanographic forcing and ecosystem responses controlling δ15N and δ13C values of export production have been substantially different earlier in the Holocene compared to mechanisms controlling the present day system

Why simheuristics? : Benefits, limitations, and best practices when combining metaheuristics with simulation

Many decision-making processes in our society involve NP-hard optimization problems. The largescale, dynamism, and uncertainty of these problems constrain the potential use of stand-alone optimization methods. The same applies for isolated simulation models, which do not have the potential to find optimal solutions in a combinatorial environment. This paper discusses the utilization of modelling and solving approaches based on the integration of simulation with metaheuristics. These 'simheuristic' algorithms, which constitute a natural extension of both metaheuristics and simulation techniques, should be used as a 'first-resort' method when addressing large-scale and NP-hard optimization problems under uncertainty -which is a frequent case in real-life applications. We outline the benefits and limitations of simheuristic algorithms, provide numerical experiments that validate our arguments, review some recent publications, and outline the best practices to consider during their design and implementation stages

Carbon and nitrogen isotope fractionation of amino acids in an avian marine predator, the gentoo penguin (Pygoscelis papua)

© The Author(s), 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ecology and Evolution 5 (2015): 1278–1290, doi:10.1002/ece3.1437.Compound-specific stable isotope analysis (CSIA) of amino acids (AA) has rapidly become a powerful tool in studies of food web architecture, resource use, and biogeochemical cycling. However, applications to avian ecology have been limited because no controlled studies have examined the patterns in AA isotope fractionation in birds. We conducted a controlled CSIA feeding experiment on an avian species, the gentoo penguin (Pygoscelis papua), to examine patterns in individual AA carbon and nitrogen stable isotope fractionation between diet (D) and consumer (C) (Δ13CC-D and Δ15NC-D, respectively). We found that essential AA δ13C values and source AA δ15N values in feathers showed minimal trophic fractionation between diet and consumer, providing independent but complimentary archival proxies for primary producers and nitrogen sources respectively, at the base of food webs supporting penguins. Variations in nonessential AA Δ13CC-D values reflected differences in macromolecule sources used for biosynthesis (e.g., protein vs. lipids) and provided a metric to assess resource utilization. The avian-specific nitrogen trophic discrimination factor (TDFGlu-Phe = 3.5 ± 0.4‰) that we calculated from the difference in trophic fractionation (Δ15NC-D) of glutamic acid and phenylalanine was significantly lower than the conventional literature value of 7.6‰. Trophic positions of five species of wild penguins calculated using a multi-TDFGlu-Phe equation with the avian-specific TDFGlu-Phe value from our experiment provided estimates that were more ecologically realistic than estimates using a single TDFGlu-Phe of 7.6‰ from the previous literature. Our results provide a quantitative, mechanistic framework for the use of CSIA in nonlethal, archival feathers to study the movement and foraging ecology of avian consumers.This research was funded by National Science Foundation Office of Polar Programs [grants ANT-0125098, ANT-0739575] and the 2013 Antarctic Science Bursaries