Claire B. Paris

Bio: Claire B. Paris is an academic researcher from University of Miami. The author has contributed to research in topics: Population & Biological dispersal. The author has an hindex of 48, co-authored 143 publications receiving 9492 citations. Previous affiliations of Claire B. Paris include State University of New York System & Florida International University.

Scaling of Connectivity in Marine Populations

Abstract: Defining the scale of connectivity, or exchange, among marine populations and determining the factors driving this exchange are pivotal to our understanding of the population dynamics, genetic structure, and biogeography of many coastal species. Using a high-resolution biophysical model for the Caribbean region, we report that typical larval dispersal distances of ecologically relevant magnitudes are on the scale of only 10 to 100 kilometers for a variety of reef fish species. We also show the importance of the early onset of active larval movement mediating the dispersal potential. In addition to self-recruitment, larval import from outside the local area is required to sustain most populations, although these population subsidies are very limited in particular systems. The results reveal distinct regions of population isolation based on larval dispersal that also correspond to genetic and morphological clines observed across a range of marine organisms.

Connectivity of marine populations: open or closed?

Abstract: Most marine populations are thought to be well connected via long-distance dispersal of larval stages. Eulerian and Lagrangian flow models, coupled with linear mortality estimates, were used to examine this assumption. The findings show that when simple advection models are used, larval exchange rates may be overestimated; such simplistic models fail to account for a decrease of up to nine orders of magnitude in larval concentrations resulting from diffusion and mortality. The alternative process of larval retention near local populations is shown to exist and may be of great importance in the maintenance of marine population structure and management of coastal marine resources.

Trophic cascade facilitates coral recruitment in a marine reserve

Abstract: Reduced fishing pressure and weak predator–prey interactions within marine reserves can create trophic cascades that increase the number of grazing fishes and reduce the coverage of macroalgae on coral reefs. Here, we show that the impacts of reserves extend beyond trophic cascades and enhance the process of coral recruitment. Increased fish grazing, primarily driven by reduced fishing, was strongly negatively correlated with macroalgal cover and resulted in a 2-fold increase in the density of coral recruits within a Bahamian reef system. Our conclusions are robust because four alternative hypotheses that may generate a spurious correlation between grazing and coral recruitment were tested and rejected. Grazing appears to influence the density and community structure of coral recruits, but no detectable influence was found on the overall size-frequency distribution, community structure, or cover of corals. We interpret this absence of pattern in the adult coral community as symptomatic of the impact of a recent disturbance event that masks the recovery trajectories of individual reefs. Marine reserves are not a panacea for conservation but can facilitate the recovery of corals from disturbance and may help sustain the biodiversity of organisms that depend on a complex three-dimensional coral habitat.

Direct evidence of a biophysical retention mechanism for coral reef fish larvae

Abstract: We examine the hypothesis that reef fish larvae have some direct influence on their own dispersal and ability to recruit to their natal reef by tracking cohorts of bicolor damselfish (Stegastes partitus) from hatching to settlement onto the reef, about 30 d later. We conducted high-resolution sampling during two consecutive years in a small area (15 km 3 20 km) off the west coast of Barbados, extending from depths of 0 to 100 m. Observations of discrete stage-specific larval patches of mean size of 29.4 and 13.2 km 2 for preflexion (1‐5-d old) and flexion/postflexion (.5-d old) stages extending ca. 30 m in the vertical indicated that larvae initially dispersing as patches tend to stay in coherent patches throughout their pelagic duration. Highest concentrations of preflexion larvae within a patch were in the upper 20 m, while those of older larvae were always deeper. Downward migration of about 60 m throughout ontogeny within stratified currents represented a retention mechanism for locally spawned larvae. Most of the variability in estimated retention rates between daily cohorts occurred during the earliest stages as a result of the dynamic nature of surface currents experienced by larvae prior to the onset of vertical migration. Differences in residence time between experiments were consistent with observed intermonthly variability in recruitment strength, implying that pelagic processes can explain recruitment rates. These results provide empirical evidence for larval retention of coral reef fishes and stress the role of active behavior in larval transport.

Connectivity and resilience of coral reef metapopulations in marine protected areas: matching empirical efforts to predictive needs.

Abstract: Design and decision-making for marine protected areas (MPAs) on coral reefs require prediction of MPA effects with population models. Modeling of MPAs has shown how the persistence of metapopulations in systems of MPAs depends on the size and spacing of MPAs, and levels of fishing outside the MPAs. However, the pattern of demographic connectivity produced by larval dispersal is a key uncertainty in those modeling studies. The information required to assess population persistence is a dispersal matrix containing the fraction of larvae traveling to each location from each location, not just the current number of larvae exchanged among locations. Recent metapopulation modeling research with hypothetical dispersal matrices has shown how the spatial scale of dispersal, degree of advection versus diffusion, total larval output, and temporal and spatial variability in dispersal influence population persistence. Recent empirical studies using population genetics, parentage analysis, and geochemical and artificial marks in calcified structures have improved the understanding of dispersal. However, many such studies report current self-recruitment (locally produced settlement/settlement from elsewhere), which is not as directly useful as local retention (locally produced settlement/total locally released), which is a component of the dispersal matrix. Modeling of biophysical circulation with larval particle tracking can provide the required elements of dispersal matrices and assess their sensitivity to flows and larval behavior, but it requires more assumptions than direct empirical methods. To make rapid progress in understanding the scales and patterns of connectivity, greater communication between empiricists and population modelers will be needed. Empiricists need to focus more on identifying the characteristics of the dispersal matrix, while population modelers need to track and assimilate evolving empirical results.

Coral Reefs Under Rapid Climate Change and Ocean Acidification

Abstract: Atmospheric carbon dioxide concentration is expected to exceed 500 parts per million and global temperatures to rise by at least 2 degrees C by 2050 to 2100, values that significantly exceed those of at least the past 420,000 years during which most extant marine organisms evolved. Under conditions expected in the 21st century, global warming and ocean acidification will compromise carbonate accretion, with corals becoming increasingly rare on reef systems. The result will be less diverse reef communities and carbonate reef structures that fail to be maintained. Climate change also exacerbates local stresses from declining water quality and overexploitation of key species, driving reefs increasingly toward the tipping point for functional collapse. This review presents future scenarios for coral reefs that predict increasingly serious consequences for reef-associated fisheries, tourism, coastal protection, and people. As the International Year of the Reef 2008 begins, scaled-up management intervention and decisive action on global emissions are required if the loss of coral-dominated ecosystems is to be avoided.

The value of estuarine and coastal ecosystem services

Abstract: The global decline in estuarine and coastal ecosystems (ECEs) is affecting a number of critical benefits, or ecosystem services. We review the main ecological services across a variety of ECEs, including marshes, mangroves, nearshore coral reefs, seagrass beds, and sand beaches and dunes. Where possible, we indicate estimates of the key economic values arising from these services, and discuss how the natural variability of ECEs impacts their benefits, the synergistic relationships of ECEs across seascapes, and management implications. Although reliable valuation estimates are beginning to emerge for the key services of some ECEs, such as coral reefs, salt marshes, and mangroves, many of the important benefits of seagrass beds and sand dunes and beaches have not been assessed properly. Even for coral reefs, marshes, and mangroves, important ecological services have yet to be valued reliably, such as cross-ecosystem nutrient transfer (coral reefs), erosion control (marshes), and pollution control (mangroves). An important issue for valuing certain ECE services, such as coastal protection and habitat-fishery linkages, is that the ecological functions underlying these services vary spatially and temporally. Allowing for the connectivity between ECE habitats also may have important implications for assessing the ecological functions underlying key ecosystems services, such coastal protection, control of erosion, and habitat-fishery linkages. Finally, we conclude by suggesting an action plan for protecting and/or enhancing the immediate and longer-term values of ECE services. Because the connectivity of ECEs across land-sea gradients also influences the provision of certain ecosystem services, management of the entire seascape will be necessary to preserve such synergistic effects. Other key elements of an action plan include further ecological and economic collaborative research on valuing ECE services, improving institutional and legal frameworks for management, controlling and regulating destructive economic activities, and developing ecological restoration options.

Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Abstract: Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

Larval Dispersal and Marine Population Connectivity

Abstract: Connectivity, or the exchange of individuals among marine populations, is a central topic in marine ecology. For most benthic marine species with complex life cycles, this exchange occurs primarily during the pelagic larval stage. The small size of larvae coupled with the vast and complex fluid environment they occupy hamper our ability to quantify dispersal and connectivity. Evidence from direct and indirect approaches using geochemical and genetic techniques suggests that populations range from fully open to fully closed. Understanding the biophysical processes that contribute to observed dispersal patterns requires integrated interdisciplinary approaches that incorporate high-resolution biophysical modeling and empirical data. Further, differential postsettlement survival of larvae may add complexity to measurements of connectivity. The degree to which populations self recruit or receive subsidy from other populations has consequences for a number of fundamental ecological processes that affect population regulation and persistence. Finally, a full understanding of population connectivity has important applications for management and conservation.

Geophysical fluid dynamics.

Abstract: The potential for sea ice-albedo feedback to give rise to nonlinear climate change in the Arctic Ocean – defined as a nonlinear relationship between polar and global temperature change or, equivalently, a time-varying polar amplification – is explored in IPCC AR4 climate models. Five models supplying SRES A1B ensembles for the 21 st century are examined and very linear relationships are found between polar and global temperatures (indicating linear Arctic Ocean climate change), and between polar temperature and albedo (the potential source of nonlinearity). Two of the climate models have Arctic Ocean simulations that become annually sea ice-free under the stronger CO 2 increase to quadrupling forcing. Both of these runs show increases in polar amplification at polar temperatures above-5 o C and one exhibits heat budget changes that are consistent with the small ice cap instability of simple energy balance models. Both models show linear warming up to a polar temperature of-5 o C, well above the disappearance of their September ice covers at about-9 o C. Below-5 o C, surface albedo decreases smoothly as reductions move, progressively, to earlier parts of the sunlit period. Atmospheric heat transport exerts a strong cooling effect during the transition to annually ice-free conditions. Specialized experiments with atmosphere and coupled models show that the main damping mechanism for sea ice region surface temperature is reduced upward heat flux through the adjacent ice-free oceans resulting in reduced atmospheric heat transport into the region.