Publications

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1998
Pattengill-Semmens, CV, Semmens BX.  1998.  An Analysis of Fish Survey Data Generated by Nonexpert Volunteers in the Flower Garden Banks National Marine Sanctuary. Gulf of Mexico Science. 16:196-207. Abstract
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2001
Salomon, AK, Ruesink JL, Semmens BX, Paine RT.  2001.  Incorporating human and ecological communities in marine conservation: An alternative to Zacharias and Roff. Conservation Biology. 15:1452-1455.   10.1111/j.1523-1739.2001.00555.x   AbstractWebsite
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2003
Pattengill-Semmens, CV, Semmens BX.  2003.  Conservation and management applications of the reef volunteer fish monitoring program. Environmental Monitoring and Assessment. 81:43-50.   10.1023/a:1021300302208   AbstractWebsite

The REEF Fish Survey Project is a volunteer fish monitoring program developed by the Reef Environmental Education Foundation ( REEF). REEF volunteers collect fish distribution and abundance data using a standardized visual method during regular diving and snorkeling activities. Survey data are recorded on preprinted data sheets that are returned to REEF and optically digitized. Data are housed in a publicly accessible database on REEF's Web site (http:// www. reef. org). Since the project's inception in 1993, over 40,000 surveys have been conducted in the coastal waters of North America, tropical western Atlantic, Gulf of California and Hawaii. The Fish Survey Project has been incorporated into existing monitoring programs through partnerships with government agencies, scientists, conservation organizations, and private institutions. REEF's partners benefit from the educational value and increased stewardship resulting from volunteer data collection. Applications of the data include an evaluation of fish/habitat interactions in the Florida Keys National Marine Sanctuary, the development of a multi-species trend analysis method to identify sites of management concern, assessment of the current distribution of species, status reports on fish assemblages of marine parks, and the evaluation of no-take zones in the Florida Keys. REEF's collaboration with a variety of partners, combined with the Fish Survey Project's standardized census method and database management system, has resulted in a successful citizen science monitoring program.

2004
Semmens, BX, Buhle ER, Salomon AK, Pattengill-Semmens CV.  2004.  A hotspot of non-native marine fishes: evidence for the aquarium trade as an invasion pathway. Marine Ecology-Progress Series. 266:239-244.   10.3354/meps266239   AbstractWebsite

Invasions of non-native species in marine ecosystems can be ecologically damaging and economically costly. Identifying 'hot-spots' of non-native species and their sources of introduction is necessary to maximize the effectiveness of invasion quarantine programs. We use a large spatially explicit marine fish database to show that there are a surprising number of non-native fishes on the reefs of southeast Florida, USA. Two likely sources explain the occurrence of non-native marine fishes in this region: introductions through ballast-water exchange, and introductions from aquaria. Data on international shipping patterns and marine fish imports were used to evaluate the culpability of these 2 vectors. Our results suggest that the introductions are the result of aquarium releases. Prevention of further releases and invasions will require education, outreach, and enforcement efforts directed at marine aquarists and the aquarium industry.

Holmes, E, Semmens BX.  2004.  Viability analysis for endangered metapopulations: a diffusion approximation approach. Ecology, genetics, and evolution of metapopulations. ( Hanski I, Gaggiotti OE, Eds.)., Burlington, MA: Elsevier Abstract
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Whaylen, L, Pattengill-Semmens CV, Semmens BX, Bush PG, Boardman MR.  2004.  Observations of a Nassau grouper, Epinephelus striatus, spawning aggregation site in Little Cayman, Cayman Islands, including multi-species spawning information. Environmental Biology of Fishes. 70:305-313.   10.1023/B:EBFI.0000033341.57920.a8   AbstractWebsite

Mass spawning aggregations of Caribbean grouper species are a conservation priority because of declines due to over-fishing. Previous studies have documented five historical aggregation sites in the Cayman Islands. Today, three of these sites are inactive or commercially extinct. In January 2002, the Reef Environmental Education Foundation led an expedition to Little Cayman Island to document a recently re-discovered spawning aggregation of Nassau grouper, Epinephelus striatus. A team of divers estimated the abundance, color phase composition, and courtship and spawning behavior of the aggregating grouper. The color phase composition of the aggregation shifted both during the course of each evening and throughout the 10-day project. Divers documented atypical coloration and courtship behavior in 10 additional fish species, of which five were seen spawning. Artisanal fishing occurred daily on the aggregation. The Cayman Islands Department of the Environment collected landings data and sampled catches to obtain length and sex ratios. The Cayman fishing fleet, while small, had a significant impact on the aggregation with a harvest of almost 2 000 Nassau grouper during the 10-day project. The study site supports the largest known Nassau grouper aggregation in the Cayman Islands. The relatively large size of fish and the high proportion of males indicate that this site supports a relatively healthy aggregation compared to other Nassau grouper aggregation sites throughout the Caribbean.

2005
Auster, PJ, Semmens BX, Barber K.  2005.  Pattern in the co-occurrence of fishes inhabiting the coral reefs of Bonaire, Netherlands Antilles. Environmental Biology of Fishes. 74:187-194.   10.1007/s10641-005-8078-0   AbstractWebsite

We conducted an analysis of species associations using fish diversity and abundance surveys conducted in Bonaire Marine Park by recreational divers. We used data from the REEF (Reef Environmental Education Foundation) Fish Survey Project to compute Bray-Curtis similarity coefficients for all species pairs for the 100 most abundant species. We quantified relationships between species using hierarchical agglomerative clustering and non-metric multidimensional scaling (MDS) of the matrix of Bray-Curtis similarity coefficients. We identified three clusters of species from the analysis. MDS results showed species clusters occupied distinct regions across a continuous gradient of species in two-dimensional space, rather than form distinct clusters. While differences in habitat requirements can explain some of the pattern in pairwise species interactions, these results suggest that there are significant direct and indirect behavioral interactions mediating the distribution and abundance of species. Studies conducted to elucidate patterns of species-habitat relationships have been central to conservation planning for marine protected areas (MPAs). However, the role of behavioral interactions between species driving the dynamics of species composition within MPA networks, designed for representation of biological diversity, should be considered when selecting sites in order to be effective.

Semmens, BX, Brumbaugh DR, Drew JA.  2005.  Interpreting space use and behavior of blue tang, Acanthurus coeruleus, in the context of habitat, density, and intra-specific interactions. Environmental Biology of Fishes. 74:99-107.   10.1007/s10641-005-6467-z   AbstractWebsite

We hypothesized that blue tang, Acanthurus coeruleus, territories on sites with low biogenic structure would be larger than territories on sites with relatively high biogenic structure due to differences in the amount and distribution of resources. We tested this hypothesis by tracking blue tang over uncolonized pavement and reef crest, two habitat types at opposite ends of the habitat structure spectrum. We recorded density, feeding rates and aggression events in order to evaluate our findings in the context of a territory model and the ideal free distribution model. Territories of A. coeruleus averaged nearly four times larger on pavement sites than on reef crest sites. Conversely, densities of A. coeruleus were significantly lower on pavement sites. While there was no significant difference in the average rates of movement between habitats, average turning angles were significantly higher on reef crest. There were no significant differences in feeding rates between habitats, suggesting that higher territory sizes and lower densities may allow fish on uncolonized pavement to match resource acquisition of fish on reef crest. The insignificant difference of aggression encounters between habitats suggests that movement and density differences among habitats are not solely legacies of differential settlement.

2006
Semmens, BX, Luke KE, Bush PG, McCoy CMR, Johnson BC.  2006.  Isopod infestation of postspawning Nassau grouper around little Cayman Island. Journal of Fish Biology. 69:933-937.   10.1111/j.1095-8649.2006.01129.x   AbstractWebsite

Attacks by the isopod Excorallana tricornis tricornis on Nassau grouper Epinephelus striatus caught in Antillean fish traps around Little Cayman Island, Cayman Islands, are recorded. Divers reported heavily parasitized fish during the study period, suggesting that trapping did not exclusively precipitate parasitism. Parasitic infestations were reported to be common in Nassau grouper immediately following their spawning season in mid-winter. (c) 2006 The Authors Journal compilation (c) 2006 The Fisheries Society of the British Isles.

2008
Moore, JW, Semmens BX.  2008.  Incorporating uncertainty and prior information into stable isotope mixing models. Ecology Letters. 11:470-480.   10.1111/j.1461-0248.2008.01163.x   AbstractWebsite

Stable isotopes are a powerful tool for ecologists, often used to assess contributions of different sources to a mixture (e.g. prey to a consumer). Mixing models use stable isotope data to estimate the contribution of sources to a mixture. Uncertainty associated with mixing models is often substantial, but has not yet been fully incorporated in models. We developed a Bayesian-mixing model that estimates probability distributions of source contributions to a mixture while explicitly accounting for uncertainty associated with multiple sources, fractionation and isotope signatures. This model also allows for optional incorporation of informative prior information in analyses. We demonstrate our model using a predator-prey case study. Accounting for uncertainty in mixing model inputs can change the variability, magnitude and rank order of estimates of prey (source) contributions to the predator (mixture). Isotope mixing models need to fully account for uncertainty in order to accurately estimate source contributions.

Semmens, BX.  2008.  Acoustically derived fine-scale behaviors of juvenile Chinook salmon (Oncorhynchus tshawytscha) associated with intertidal benthic habitats in an estuary. Canadian Journal of Fisheries and Aquatic Sciences. 65:2053-2062.   10.1139/f08-107   AbstractWebsite

Given the presumed importance of benthic and epibenthic estuarine habitats in Chinook salmon (Oncorhynchus tshawytscha) smolt growth and survival, resource managers would be well served by an improved understanding of how smolts use such habitats. A cabled acoustic positioning system was used to precisely track (<1 m resolution) the movement of seventeen 0-aged hatchery-reared fall Chinook smolts in a large (similar to 400 m(2)) enclosure over a period of 10 days in Willapa Bay, Washington, USA. A hierarchical Bayesian state-space model of movement was subsequently developed to associate the behaviors of tagged salmon with characteristics of benthic habitat in the enclosure. Model results indicated that smolts had a strong preference for remaining in native eelgrass (Zostera marina). Conversely, no such preference existed for other structured benthic habitats such as oyster (Crassostrea gigas) beds, non-native eelgrass (Zostera japonica), and non-native smooth crodgrass (Spartina alterniflora). There was a positive relationships between individual survivorship in the enclosure and the strength of behavioral preference for native eelgrass, suggesting that predator avoidance may be the evolutionary mechanism driving behavioral responses of smolts to benthic habitats.

2009
Semmens, BX, Ward EJ, Moore JW, Darimont CT.  2009.  Quantifying Inter- and Intra-Population Niche Variability Using Hierarchical Bayesian Stable Isotope Mixing Models. Plos One. 4   10.1371/journal.pone.0006187   AbstractWebsite

Variability in resource use defines the width of a trophic niche occupied by a population. Intra-population variability in resource use may occur across hierarchical levels of population structure from individuals to subpopulations. Understanding how levels of population organization contribute to population niche width is critical to ecology and evolution. Here we describe a hierarchical stable isotope mixing model that can simultaneously estimate both the prey composition of a consumer diet and the diet variability among individuals and across levels of population organization. By explicitly estimating variance components for multiple scales, the model can deconstruct the niche width of a consumer population into relevant levels of population structure. We apply this new approach to stable isotope data from a population of gray wolves from coastal British Columbia, and show support for extensive intra-population niche variability among individuals, social groups, and geographically isolated subpopulations. The analytic method we describe improves mixing models by accounting for diet variability, and improves isotope niche width analysis by quantitatively assessing the contribution of levels of organization to the niche width of a population.

Semmens, BX, Moore JW, Ward EJ.  2009.  Improving Bayesian isotope mixing models: a response to Jackson et al. (2009). Ecology Letters. 12:E6-E8.   10.1111/j.1461-0248.2009.01283.x   AbstractWebsite

We recently described a Bayesian framework for stable isotope mixing models and provided a software tool, MixSIR, for conducting such analyses (Ecol. Lett., 2008; 11:470). Jackson et al. (Ecol. Lett., 2009; 12:E1) criticized the performance of our software based on tests using simulated data. However, their simulation data were flawed, rendering claims of erroneous behaviour inaccurate. A re-evaluation of the MixSIR source code did, however, uncover two minor coding errors, which we have fixed. When data are correctly simulated according to eqns (1)-(4) in Jackson et al. (2009), MixSIR consistently and accurately estimated the proportional contribution of prey to a predator diet, and was surprisingly robust to additional unquantified error. Jackson et al. (2009) also suggested we use a Dirichlet prior on the source proportion parameters, which we agree with. Finally, Jackson et al. (2009) propose adding additional error parameters to our mixing model framework. We caution that such increases in model complexity should be evaluated based on data support.

2010
Semmens, BX, Auster PJ, Paddack MJ.  2010.  Using Ecological Null Models to Assess the Potential for Marine Protected Area Networks to Protect Biodiversity. Plos One. 5   10.1371/journal.pone.0008895   AbstractWebsite

Marine protected area (MPA) networks have been proposed as a principal method for conserving biological diversity, yet patterns of diversity may ultimately complicate or compromise the development of such networks. We show how a series of ecological null models can be applied to assemblage data across sites in order to identify non-random biological patterns likely to influence the effectiveness of MPA network design. We use fish census data from Caribbean fore-reefs as a test system and demonstrate that: 1) site assemblages were nested, such that species found on sites with relatively few species were subsets of those found on sites with relatively many species, 2) species co-occurred across sites more than expected by chance once species-habitat associations were accounted for, and 3) guilds were most evenly represented at the richest sites and richness among all guilds was correlated (i.e., species and trophic diversity were closely linked). These results suggest that the emerging Caribbean marine protected area network will likely be successful at protecting regional diversity even if planning is largely constrained by insular, inventory-based design efforts. By recasting ecological null models as tests of assemblage patterns likely to influence management action, we demonstrate how these classic tools of ecological theory can be brought to bear in applied conservation problems.

Ward, EJ, Semmens BX, Schindler DE.  2010.  Including Source Uncertainty and Prior Information in the Analysis of Stable Isotope Mixing Models. Environmental Science & Technology. 44:4645-4650.   10.1021/es100053v   AbstractWebsite

Stable isotope mixing models offer a statistical framework for estimating the contribution of multiple sources (such as prey) to a mixture distribution. Recent advances in these models have estimated the source proportions using Bayesian methods, but have not explicitly accounted for uncertainty in the mean and variance of sources. We demonstrate that treating these quantities as unknown parameters can reduce bias in the estimated source contributions, although model complexity is increased (thereby increasing the variance of estimates). The advantages of this fully Bayesian approach are particularly apparent when the source geometry is poor or sample sizes are small. A second benefit to treating source quantities as parameters is that prior source information can be included. We present findings from 9 lake food-webs, where the consumer of interest (fish) has a diet composed of 5 sources: aquatic insects, snails, zooplankton, amphipods, and terrestrial insects. We compared the traditional Bayesian stable isotope mixing model with fixed source parameters to our fully Bayesian model with and without an informative prior. The informative prior has much less impact than the choice of model the traditional mixing model with fixed source parameters estimates the diet to be dominated by aquatic insects, while the fully Bayesian model estimates the diet to be more balanced but with greater importance of zooplankton. The findings from this example demonstrate that there can be stark differences in inference between the two model approaches, particularly when the source geometry of the mixing model is poor. These analyses also emphasize the importance of investing substantial effort toward characterizing the variation in the isotopic characteristics of source pools to appropriately quantify uncertainties in their contributions to consumers in food webs.

2011
Ward, EJ, Semmens BX, Holmes EE, Balcomb KC.  2011.  Effects of Multiple Levels of Social Organization on Survival and Abundance. Conservation Biology. 25:350-355.   10.1111/j.1523-1739.2010.01600.x   AbstractWebsite

Identifying how social organization shapes individual behavior, survival, and fecundity of animals that live in groups can inform conservation efforts and improve forecasts of population abundance, even when the mechanism responsible for group-level differences is unknown. We constructed a hierarchical Bayesian model to quantify the relative variability in survival rates among different levels of social organization (matrilines and pods) of an endangered population of killer whales (Orcinus orca). Individual killer whales often participate in group activities such as prey sharing and cooperative hunting. The estimated age-specific survival probabilities and survivorship curves differed considerably among pods and to a lesser extent among matrilines (within pods). Across all pods, males had lower life expectancy than females. Differences in survival between pods may be caused by a combination of factors that vary across the population's range, including reduced prey availability, contaminants in prey, and human activity. Our modeling approach could be applied to demographic rates for other species and for parameters other than survival, including reproduction, prey selection, movement, and detection probabilities.

Francis, TB, Schindler DE, Holtgrieve GW, Larson ER, Scheuerell MD, Semmens BX, Ward EJ.  2011.  Habitat structure determines resource use by zooplankton in temperate lakes. Ecology Letters. 14:364-372.   10.1111/j.1461-0248.2011.01597.x   AbstractWebsite

P>While the importance of terrestrial linkages to aquatic ecosystems is well appreciated, the degree of terrestrial support of aquatic consumers remains debated. Estimates of terrestrial contributions to lake zooplankton have omitted a key food source, phytoplankton produced below the mixed layer. We used carbon and nitrogen stable isotope data from 25 Pacific Northwest lakes to assess the relative importance of particulate organic matter (POM) from the mixed layer, below the mixed layer and terrestrial detritus to zooplankton. Zooplankton and deep POM were depleted in 13C relative to mixed layer POM in lakes that can support deep primary production. A Bayesian stable isotope mixing model estimated that terrestrial detritus contributed < 5% to zooplankton production, and confirms the role of lake optical and thermal properties; deep POM accounted for up to 80% of zooplankton production in the clearest lakes. These results suggest terrestrial support of lake zooplankton production is trivial.

Yeakel, JD, Novak M, Guimaraes PR, Dominy NJ, Koch PL, Ward EJ, Moore JW, Semmens BX.  2011.  Merging Resource Availability with Isotope Mixing Models: The Role of Neutral Interaction Assumptions. Plos One. 6   10.1371/journal.pone.0022015   AbstractWebsite

Background: Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predator's diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values. Methodology: We develop a procedure to incorporate prey availability data into Bayesian mixing models conditional on the similarity of isotope values between two prey. If a pair of prey have similar isotope values (resulting in highly uncertain mixing model results), our model increases the weight of availability data in estimating the contribution of prey to a predator's diet. We test the utility of this method in an intertidal community against independently measured feeding rates. Conclusions: Our results indicate that our weighting procedure increases the accuracy by which consumer diets can be inferred in situations where multiple prey have similar isotope values. This suggests that the exchange of formalism for predictive power is merited, particularly when the relationship between prey availability and a predator's diet cannot be assumed for all species in a system.

2012
Hass, T, Hyman J, Semmens BX.  2012.  Climate change, heightened hurricane activity, and extinction risk for an endangered tropical seabird, the black-capped petrel Pterodroma hasitata. Marine Ecology-Progress Series. 454:251-261.   10.3354/meps09723   AbstractWebsite

The destructiveness of major (Category 3 to 5) hurricanes along the United States Atlantic Ocean seaboard has been recognized for centuries. While the effects of hurricanes on coastal ecosystems are well known, the influence of hurricanes on pelagic seabirds is difficult to assess. During the annual Atlantic hurricane season (similar to 1 June to 30 November), the endangered black-capped petrel Pterodroma hasitata aggregates in Gulf Stream habitats from Florida to North Carolina. On at least 8 occasions over the past century, hurricanes have driven petrels far inland (sometimes as far as the Great Lakes), suggesting the demise of 10s to 100s of individuals. This paper models >100 yr of data to characterize and compare key aspects of hurricanes that did and did not drive petrels inland. Our model suggests that the predicted increase in the frequency of Category 3 to 5 hurricanes in the region due to climate change could nearly double the expected number of wrecked petrels over the next century and place an endangered species at greater risk of extinction.

Archer, SK, Heppell SA, Semmens BX, Pattengill-Semmens CV, Bush PG, McCoy CM, Johnson BC.  2012.  Patterns of color phase indicate spawn timing at a Nassau grouper Epinephelus striatus spawning aggregation. Current Zoology. 58:73-83. AbstractWebsite

Nassau grouper Epinephelus striatus are a large bodied, top level predator that is ecologically important throughout the Caribbean. Although typically solitary, Nassau grouper form large annual spawning aggregations at predictable times in specific locations. In 2003, The Cayman Islands Marine Conservation Board established protection for a newly rediscovered Nassau grouper spawning aggregation on Little Cayman, British West Indies. The large size of this aggregation provides a unique opportunity to study the behavior of Nassau grouper on a relatively intact spawning aggregation. During non-spawning periods Nassau grouper display a reddish-brown-and-white barred coloration. However, while aggregating they exhibit three additional color phases: "bicolor", "dark", and "white belly". We video sampled the population on multiple days leading up to spawning across five spawning years. Divers focused a laser caliper equipped video camera on individual fish at the aggregation. We later analyzed the video to determine the length of the fish and record the color phase. Our observations show that the relative proportion of fish in the bicolor color phase increases significantly on the day leading up to the primary night of spawning. The increase in the proportion of the bicolor color phase from 0.05 early in the aggregation to 0.40 on the day of spawning suggests that this color phase conveys that a fish is behaviorally and physiologically prepared to spawn. Additionally, 82.7% of fish exhibiting dark or white belly coloration early in the aggregation period suggests that these color phases are not only shown by female fish as was previously posited [Current Zoology 58 (1): 73-83, 2012].

Carlisle, AB, Kim SL, Semmens BX, Madigan DJ, Jorgensen SJ, Perle CR, Anderson SD, Chapple TK, Kanive PE, Block BA.  2012.  Using Stable Isotope Analysis to Understand the Migration and Trophic Ecology of Northeastern Pacific White Sharks (Carcharodon carcharias). Plos One. 7   10.1371/journal.pone.0030492   AbstractWebsite

The white shark (Carcharodon carcharias) is a wide-ranging apex predator in the northeastern Pacific (NEP). Electronic tagging has demonstrated that white sharks exhibit a regular migratory pattern, occurring at coastal sites during the late summer, autumn and early winter and moving offshore to oceanic habitats during the remainder of the year, although the purpose of these migrations remains unclear. The purpose of this study was to use stable isotope analysis (SIA) to provide insight into the trophic ecology and migratory behaviors of white sharks in the NEP. Between 2006 and 2009, 53 white sharks were biopsied in central California to obtain dermal and muscle tissues, which were analyzed for stable isotope values of carbon (delta C-13) and nitrogen (delta N-15). We developed a mixing model that directly incorporates movement data and tissue incorporation (turnover) rates to better estimate the relative importance of different focal areas to white shark diet and elucidate their migratory behavior. Mixing model results for muscle showed a relatively equal dietary contribution from coastal and offshore regions, indicating that white sharks forage in both areas. However, model results indicated that sharks foraged at a higher relative rate in coastal habitats. There was a negative relationship between shark length and muscle delta C-13 and delta N-15 values, which may indicate ontogenetic changes in habitat use related to onset of maturity. The isotopic composition of dermal tissue was consistent with a more rapid incorporation rate than muscle and may represent more recent foraging. Low offshore consumption rates suggest that it is unlikely that foraging is the primary purpose of the offshore migrations. These results demonstrate how SIA can provide insight into the trophic ecology and migratory behavior of marine predators, especially when coupled with electronic tagging data.

Heppell, SA, Semmens BX, Archer SK, Pattengill-Semmens CV, Bush PG, McCoy CM, Heppell SS, Johnson BC.  2012.  Documenting recovery of a spawning aggregation through size frequency analysis from underwater laser calipers measurements. Biological Conservation. 155:119-127. Abstract

Many spawning aggregations of marine fishes have been fished beyond the point of sustainability, leading to increased calls for protection through seasonal and/or site-specific fishery closures. Once a closure has been put in place, monitoring the aggregation is imperative in order to learn whether protection leads to the recovery of the population. Current methods for monitoring the status of spawning aggregations rely largely on counts, either subsample or census, usually combined with capturing a subset of the fish to assess individual traits such as length and weight. Handling fish during the spawning aggregation can be stressful for the fish, and can ultimately lead to decreased spawning success, increased susceptibility to predators, or increased mortality through capture trauma or infection. Here we present a novel analysis for monitoring fish on a spawning aggregation that does not require the capture and handling of fish. Following a recovering aggregation of Nassau grouper (Epinephelus striatus) over seven spawning seasons, we show that length-distribution data can be collected by divers using a video-based system with parallel lasers calibrated to a specific distance apart, and subsequently use those data to monitor changes in the size distribution over time. We detected recruitment of new fish to the grouper spawning aggregation in the fourth year of monitoring. In addition to tracking size distribution trends over time, the length distribution information could be combined with an established length-weight regression and an estimate of total abundance to estimate spawning stock biomass. We qualitatively cross-validate this method with census data to evaluate its effectiveness in monitoring the recovery or decline of aggregating species that can be visually observed. (C) 2012 Elsevier Ltd. All rights reserved.

McCauley, DJ, Young HS, Dunbar RB, Estes JA, Semmens BX, Michel F.  2012.  Assessing the effects of large mobile predators on ecosystem connectivity. Ecological Applications. 22:1711-1717. AbstractWebsite

Large predators are often highly mobile and can traverse and use multiple habitats. We know surprisingly little about how predator mobility determines important processes of ecosystem connectivity. Here we used a variety of data sources drawn from Palmyra Atoll, a remote tropical marine ecosystem where large predators remain in high abundance, to investigate how these animals foster connectivity. Our results indicate that three of Palmyra's most abundant large predators (e.g., two reef sharks and one snapper) use resources from different habitats creating important linkages across ecosystems. Observations of cross-system foraging such as this have important implications for the understanding of ecosystem functioning, the management of large-predator populations, and the design of conservation measures intended to protect whole ecosystems. In the face of widespread declines of large, mobile predators, it is important that resource managers, policy makers, and ecologists work to understand how these predators create connectivity and to determine the impact that their depletions may be having on the integrity of these linkages.

Abello, P, Ai WM, Altmann C, Bernardi G, Bonato O, Burchhardt KM, Chen X, Chen ZJ, Cizkova D, Clouet C, Cubeta MA, Garcia-Merchan V, Gauthier N, Gibson S, Halacka K, Hamdi F, Hankeln T, Hochkirch A, Hrbek T, Jackson AM, Lin CW, Lin SM, Macpherson E, Macrander J, Maresova E, Mendel J, Nowak M, Orti G, Palero F, Papousek I, Pascual M, Schmitt T, Semmens BX, Streito JC, Tian EW, Tseng SP, Veith M, Vetesnik L, Wang HY, Weyer J, Willis S, Yu H, Zhou ZM, Mol Ecology Resources Primer Dev C.  2012.  Permanent Genetic Resources added to Molecular Ecology Resources Database 1 April 2012-31 May 2012. Molecular Ecology Resources. 12:972-974.   10.1111/j.1755-0998.2012.03173.x   AbstractWebsite

This article documents the addition of 123 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Brenthis ino, Cichla orinocensis, Cichla temensis, Epinephelus striatus, Gobio gobio, Liocarcinus depurator, Macrolophus pygmaeus, Monilinia vaccinii-corymbosi, Pelochelys cantorii, Philotrypesis josephi, Romanogobio vladykovi, Takydromus luyeanus and Takydromus viridipunctatus. These loci were cross-tested on the following species: Cichla intermedia, Cichla ocellaris, Cichla pinima, Epinephelus acanthistius, Gobio carpathicus, Gobio obtusirostris, Gobio sp. 1, Gobio volgensis, Macrolophus costalis, Macrolophus melanotoma, Macrolophus pygmaeus, Romanogobio albipinnatus, Romanogobio banaticus, Romanogobio belingi, Romanogobio kesslerii, Romanogobio parvus, Romanogobio pentatrichus, Romanogobio uranoscopus, Takydromus formosanus, Takydromus hsuehshanesis and Takydromus stejnegeri.

2013
Parnell, AC, Phillips DL, Bearhop S, Semmens BX, Ward EJ, Moore JW, Jackson AL, Grey J, Kelly DJ, Inger R.  2013.  Bayesian stable isotope mixing models. Environmetrics. 24:387-399. AbstractWebsite

In this paper, we review recent advances in stable isotope mixing models (SIMMs) and place them into an overarching Bayesian statistical framework, which allows for several useful extensions. SIMMs are used to quantify the proportional contributions of various sources to a mixture. The most widely used application is quantifying the diet of organisms based on the food sources they have been observed to consume. At the centre of the multivariate statistical model we propose is a compositional mixture of the food sources corrected for various metabolic factors. The compositional component of our model is based on the isometric log-ratio transform. Through this transform, we can apply a range of time series and non-parametric smoothing relationships. We illustrate our models with three case studies based on real animal dietary behaviour. Copyright (c) 2013 John Wiley & Sons, Ltd.