Linking habitat mosaics and connectivity in a coral reef seascape

Author Posting. © The Author(s), 2012. This is the author's version of the work. It is posted here by permission of National Academy of Sciences for personal use, not for redistribution. The definitive version was published in Proceedings of the National Academy of Sciences of the United States of America 109 (2012): 15372-15376, doi:10.1073/pnas.1206378109.Tropical marine ecosystems are under mounting anthropogenic pressure from overfishing and habitat destruction, leading to declines in their structure and function on a global scale. While maintaining connectivity among habitats within a seascape is necessary for preserving population resistance and resilience, quantifying movements of individuals within seascapes remains challenging. Traditional methods of identifying and valuing potential coral reef fish nursery habitats are indirect, often relying on visual surveys of abundance and correlations of size and biomass among habitats. We used compound-specific stable isotope analyses to determine movement patterns of commercially important fish populations within a coral reef seascape. This approach allowed us to quantify the relative contributions of individuals from inshore nurseries to reef populations and identify migration corridors among important habitats. Our results provided direct measurements of remarkable migrations by juvenile snapper of over 30 km between nurseries and reefs. We also found significant plasticity in juvenile nursery residency. While a majority of individuals on coastal reefs had used seagrass nurseries as juveniles, many adults on oceanic reefs had settled directly into reef habitats. Moreover, seascape configuration played a critical but heretofore unrecognized role in determining connectivity among habitats. Finally, our approach provides key quantitative data necessary to estimate the value of distinctive habitats to ecosystem services provided by seascapes.This research was based on work supported by Award Nos. USA 00002 and KSA 00011 made by King Abdullah University of Science and Technology (KAUST). Additional funding was provided by Woods Hole Oceanographic Institution and an International Society for Reef Studies-Ocean Conservancy Coral Reef Fellowship. K. McMahon received support from the National Science Foundation Graduate Research Fellowship Program

HMMoce : an R package for improved geolocation of archival-tagged fishes using a hidden Markov method

Author Posting. © The Author(s), 2017. This is the author's version of the work. It is posted here under a nonexclusive, irrevocable, paid-up, worldwide license granted to WHOI. It is made available for personal use, not for redistribution. The definitive version was published in Methods in Ecology and Evolution 9 (2018): 1212-1220, doi:10.1111/2041-210X.12959.Electronic tagging of marine fishes is commonly achieved with archival tags that rely on light levels and sea surface temperatures to retrospectively estimate movements. However, methodological issues associated with light-level geolocation have constrained meaningful inference to species where it is possible to accurately estimate time of sunrise and sunset. Most studies have largely ignored the oceanographic profiles collected by the tag as a potential way to refine light-level geolocation estimates. Open-source oceanographic measurements and outputs from high-resolution models are increasingly available and accessible. Temperature and depth profiles recorded by electronic tags can be integrated with these empirical data and model outputs to construct likelihoods and improve geolocation estimates. The R package HMMoce leverages available tag and oceanographic data to improve position estimates derived from electronic tags using a hidden Markov approach. We illustrate the use of the model and test its performance using example blue and mako shark archival tag data. Model results were validated using independent, known tracks and compared to results from other geolocation approaches. HMMoce exhibited as much as 6-fold improvement in pointwise error as compared to traditional light-level geolocation approaches. The results demonstrated the general applicability of HMMoce to marine animals, particularly those that do not frequent surface waters during crepuscular periods.This work was funded by awards to C. Braun from the Martin Family Society of Fellows for Sustainability Fellowship at the Massachusetts Institute of Technology, the Grassle Fellowship and Ocean Venture Fund at the Woods Hole Oceanographic Institution, and the NASA Earth and Space Science Fellowship

Response of Otolith Microchemistry to Environmental Variations Experienced by Larval and Juvenile Atlantic Croaker (Micropogonias Undulatus)

Minor and trace elements incorporated into otoliths during growth may permanently record environmental conditions experienced by fishes. To determine the validity of this approach, we used laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) to assay sectioned otoliths from juvenile Atlantic croaker (Micropogonias undulatus) collected from each of three sites in the Neuse River, North Carolina, and the Elizabeth River, Virginia. Elemental concentrations at the center of the otoliths did not differ between locations, although both Mg : Ca and Ba : Ca were significantly higher at the edge of otoliths from the Neuse River than from the Elizabeth River. Three of the elements (Mg : Ca, Sr : Ca, and Ba : Ca) showed significant variation across otoliths. Sr : Ca, and to a lesser extent Mg : Ca, showed progressive decreases as the fish moved from offshore spawning sites to estuarine nursery areas. The opposite pattern was shown by Ba : Ca. We hypothesize that these patterns were related to the elemental concentrations within oceanic and estuarine water masses. Although both Sr : Ca and Ba : Ca seem to be useful tracers of offshore-inshore migration of estuarine-dependent species, the sensitivity of the technique to more subtle changes in water chemistry remains to be determined

Geochemical signatures in otoliths record natal origins of American shad

Author Posting. © American Fisheries Society, 2008. This article is posted here by permission of American Fisheries Society for personal use, not for redistribution. The definitive version was published in Transactions of the American Fisheries Society 137 (2008): 57–69, doi:10.1577/T07-029.1.Population connectivity is a critical component in the life history dynamics of anadromous fishes and in the persistence of local populations. We used geochemical signatures in the otoliths of American shad Alosa sapidissima to determine natal origins and estimate rates of straying among river-specific populations along the U.S. Atlantic coast. Stable isotope (δ13C, δ18O and 87Sr:86Sr) and elemental (Mg:Ca, Mn:Ca, Sr:Ca and Ba:Ca) signatures in otoliths of juvenile American shad from rivers from Georgia to New Hampshire varied significantly, allowing for an average of 91% cross-validated accuracy when classifying individual fish to their natal rivers. We also found significant interannual variability in the geochemical signatures from several rivers, due largely to differences in δ18O values among years. We then used the ground-truthed geochemical signatures in the otoliths of juvenile American shad to identify the natal origins of spawning adults in the York River system in Virginia. Approximately 6% of the spawning adults collected in the York River were strays from other rivers. Of the remaining fish, 79% were spawned in the Mattaponi River and 21% in the Pamunkey River. The combined results of this and other recent studies suggest that although most American shad spawning in the York River were homing to their natal river, there was much less fidelity to individual tributaries. Small-scale straying could allow fish spawned in the Mattaponi River to subsidize spawning in the Pamunkey River, which has experienced persistent recruitment failureThis work was funded by National Science Foundation grants OCE-0215905 and OCE-0134998 to SRT and by the Wallop–Breaux Program of the U.S. Fish and Wildlife Service through the Virginia Marine Resources Commission to J.E.O

Accelerator mass spectrometry 14C determination in CO2 produced from laser decomposition of aragonite

Author Posting. © John Wiley & Sons, 2008. This is the author's version of the work. It is posted here by permission of John Wiley & Sons for personal use, not for redistribution. The definitive version was published in Rapid Communications in Mass Spectrometry 22 (2008): 3443-3449, doi:10.1002/rcm.3745.Determination of 14C in aragonite (CaCO3) decomposed thermally to CO2 using an yttrium‐aluminum‐garnet doped neodymium laser is reported. Laser decomposition accelerator mass spectrometer (LD‐AMS) measurements reproduce AMS determinations of 14C from conventional reaction of aragonite with concentrated phosphoric acid. The lack of significant differences between these sets of measurements indicate that LD‐AMS radiocarbon dating can overcome the significant fractionation that has been observed during stable isotope (C and O) laser decomposition analysis of different carbonate minerals. The laser regularly converted nearly 30% of material removed to CO2 despite being optimized for ablation, where laser energy breaks material apart rather than chemically altering it. These results illustrate promise for using laser decomposition on the front‐end of AMS systems that directly measure CO2 gas. The feasibility of such measurements depends on 1. the improvement of material removal and/or CO2 generation efficiency of the laser decomposition system and 2. the ionization efficiency of AMS systems measuring continuously flowing CO2.This work was funded on a competitive basis by the Cecil H. and Ida M. Green Technology Innovation Award of Woods Hole Oceanographic Institution

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.)

Markov Chain Monte Carlo methods for assigning larvae to natal sites using natural geochemical tags

Author Posting. © Ecological Society of America, 2008. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecological Applications 18 (2008): 1901–1913, doi:10.1890/07-1792.1.Geochemical signatures deposited in otoliths are a potentially powerful means of identifying the origin and dispersal history of fish. However, current analytical methods for assigning natal origins of fish in mixed-stock analyses require knowledge of the number of potential sources and their characteristic geochemical signatures. Such baseline data are difficult or impossible to obtain for many species. A new approach to this problem can be found in iterative Markov Chain Monte Carlo (MCMC) algorithms that simultaneously estimate population parameters and assign individuals to groups. MCMC procedures only require an estimate of the number of source populations, and post hoc model selection based on the deviance information criterion can be used to infer the correct number of chemically distinct sources. We describe the basics of the MCMC approach and outline the specific decisions required when implementing the technique with otolith geochemical data. We also illustrate the use of the MCMC approach on simulated data and empirical geochemical signatures in otoliths from young-of-the-year and adult weakfish, Cynoscion regalis, from the U.S. Atlantic coast. While we describe how investigators can use MCMC to complement existing analytical tools for use with otolith geochemical data, the MCMC approach is suitable for any mixed-stock problem with a continuous, multivariate data.J. W. White was supported by NSF Predoctoral, UC Regents, and UCSB Affiliates fellowships

Effect of ocean acidification on otolith development in larvae of a tropical marine fish

© The Author(s), 2011. This article is distributed under the terms of the Creative Commons Attribution 3.0 License. The definitive version was published in Biogeosciences 8 (2011): 1631-1641, doi:10.5194/bg-8-1631-2011.Calcification in many invertebrate species is predicted to decline due to ocean acidification. The potential effects of elevated CO2 and reduced carbonate saturation state on other species, such as fish, are less well understood. Fish otoliths (earbones) are composed of aragonite, and thus, might be susceptible to either the reduced availability of carbonate ions in seawater at low pH, or to changes in extracellular concentrations of bicarbonate and carbonate ions caused by acid-base regulation in fish exposed to high pCO2. We reared larvae of the clownfish Amphiprion percula from hatching to settlement at three pHNBS and pCO2 levels (control: ~pH 8.15 and 404 μatm CO2; intermediate: pH 7.8 and 1050 μatm CO2; extreme: pH 7.6 and 1721 μatm CO2) to test the possible effects of ocean acidification on otolith development. There was no effect of the intermediate treatment (pH 7.8 and 1050 μatm CO2) on otolith size, shape, symmetry between left and right otoliths, or otolith elemental chemistry, compared with controls. However, in the more extreme treatment (pH 7.6 and 1721 μatm CO2) otolith area and maximum length were larger than controls, although no other traits were significantly affected. Our results support the hypothesis that pH regulation in the otolith endolymph can lead to increased precipitation of CaCO3 in otoliths of larval fish exposed to elevated CO2, as proposed by an earlier study, however, our results also show that sensitivity varies considerably among species. Importantly, our results suggest that otolith development in clownfishes is robust to even the more pessimistic changes in ocean chemistry predicted to occur by 2100

Accurate Classification of Juvenile Weakfish Cynoscion regalis to Estuarine Nursery Areas Based on Chemical Signatures in Otoliths

We investigated the ability of trace element and isotopic signatures in otoliths to record the nursery areas of juvenile (young-of-the-year) weakfish Cynoscion regalis from the east coast of the USA. Juvenile C. regalis were captured with otter trawls at multiple sites in Doboy Sound (Georgia), Pamlico Sound (North Carolina), Chesapeake Bay (Virginia), Delaware Bay (Delaware) and Peconic Bay (New York), from July to September 1996. One sagittal otolith from each specimen was assayed for Mg/Ca, Mn/Ca, Sr/Ca and Ba/Ca ratios using inductively coupled plasma mass spectrometry (ICP-MS), while delta 13 C and delta 18 O values from the other sagittal otolith in the pair were determined using isotope ratio mass spectrometry (IR-MS). A multivariate analysis of variance determined that there were significant differences in trace element signatures among locations. Bootstrapped 95% confidence ellipses on canonical variates indicated that all 5 locations were significantly isolated in discriminant space. On the basis of these differences, linear discriminant function analysis (LDFA) and artificial neural network (ANN) models were used to classify individual fish to their natal estuary with an overall error rate of 37% for LDFA and 29.6% for ANN. Addition of delta 13C and delta 18O values to the LDFA and ANN models derived from the trace element data resulted in overall error around 10%. We will, therefore, be able to use chemical signatures from the juvenile portion of adult C. regalis otoliths to accurately classify these fish to their natal estuary

Estimating westslope cutthroat trout (Oncorhynchus clarkii lewisi) movements in a river network using strontium isoscapes

This paper is not subject to U.S. copyright. The definitive version was published in Canadian Journal of Fisheries and Aquatic Sciences 69 (2012): 906-915, doi:10.1139/f2012-033.We used natural variation in the strontium concentration (Sr:Ca) and isotope composition (87Sr:86Sr) of stream waters and corresponding values recorded in otoliths of westslope cutthroat trout (Oncorhynchus clarkii lewisi) to examine movements during their life history in a large river network. We found significant spatial differences in Sr:Ca and 87Sr:86Sr values (strontium isoscapes) within and among numerous spawning and rearing streams that remained relatively constant seasonally. Both Sr:Ca and 87Sr:86Sr values in the otoliths of juveniles collected from nine natal streams were highly correlated with those values in the ambient water. Strontium isoscapes measured along the axis of otolith growth revealed that almost half of the juveniles had moved at least some distance from their natal streams. Finally, otolith Sr profiles from three spawning adults confirmed homing to natal streams and use of nonoverlapping habitats over their migratory lifetimes. Our study demonstrates that otolith geochemistry records movements of cutthroat trout through Sr isoscapes and therefore provides a method that complements and extends the utility of conventional tagging techniques in understanding life history strategies and conservation needs of freshwater fishes in river networks.Bonneville Power Administration, Montana Fish, Wildlife & Parks, and the US Geological Survey funded this work. Partial support was provided by NSF grants OCE-0134998 and OCE-0215905 to SRT