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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.

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].

Archer, SK, Allgeier JE, Semmens BX, Heppell SA, Pattengill-Semmens CV, Rosemond AD, Bush PG, McCoy CM, Johnson BC, Layman CA.  2015.  Hot moments in spawning aggregations: implications for ecosystem-scale nutrient cycling. Coral Reefs. 34:19-23.   10.1007/s00338-014-1208-4   AbstractWebsite

Biogeochemical hot moments occur when a temporary increase in availability of one or more limiting reactants results in elevated rates of biogeochemical reactions. Many marine fish form transient spawning aggregations, temporarily increasing their local abundance and thus nutrients supplied via excretion at the aggregation site. In this way, nutrients released by aggregating fish could create a biogeochemical hot moment. Using a combination of empirical and modeling approaches, we estimate nitrogen and phosphorus supplied by aggregating Nassau grouper (Epinephelus striatus). Data suggest aggregating grouper supply up to an order-of-magnitude more nitrogen and phosphorus than daily consumer-derived nutrient supply on coral reefs without aggregating fish. Comparing current and historic aggregation-level excretion estimates shows that overfishing reduced nutrients supplied by aggregating fish by up to 87 %. Our study illustrates a previously unrecognized ecosystem viewpoint regarding fish spawning aggregations and provides an additional perspective on the repercussions of their overexploitation.

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.

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Bellquist, L, Semmens B, Stohs S, Siddall A.  2017.  Impacts of recently implemented recreational fisheries regulations on the Commercial Passenger Fishing Vessel fishery for Paralabrax sp. in California. Marine Policy. 86:134-143.   10.1016/j.marpol.2017.09.017   AbstractWebsite

The California Commercial Passenger Fishing Vessel (CPFV) fleet is unique in scale of operation, extensive fishing history, and economic impacts. The basses (Paralabrax sp.), which represent a principal target for the CPFV fleet, recently gained more stringent size limits and bag limits. The goal of this study was to conduct a survey of CPFV captains to assess perceptions regarding the status of two Paralabrax species, as well as the impacts of the new regulations. Catch and effort estimates were also obtained using CPFV logbook data to compare captains' perceptions with actual changes in the fishery. The captains agreed that both species are vital to recreational fishing, and that the Barred Sand Bass stock is less healthy than Kelp Bass. Catch and effort analyses were consistent with this perception, with more dramatic declines in CPUE exhibited by Barred Sand Bass. The most experienced captains perceived the status of each species to be in a less healthy state than the less experienced captains, suggesting that shifting baselines are occurring. Most of the captains thought the increased minimum size limits had the greatest short-term impact on the fishing experience. The CPFV logbook data summaries support this assertion, but Kelp Bass CPUE showed a trend reversal. In contrast, Barred Sand Bass CPUE has precipitously declined, and spawning aggregations have been absent since 2013. The agreement between captains' perceptions and logbook analyses strengthens the overall findings, and suggests captains are a valuable resource for informing fisheries management, especially in future studies with data-limited stocks.

Bellquist, LF, Graham JB, Barker A, Ho J, Semmens BX.  2016.  Long-term dynamics in "trophy" sizes of pelagic and coastal pelagic fishes among California recreational fisheries (1966-2013). Transactions of the American Fisheries Society. 145:977-989.   10.1080/00028487.2016.1185035   AbstractWebsite

In California, recreational fisheries contribute a significant amount to coastal economies, with pelagic and coastal pelagic species constituting a principal set of target species during summer and fall. Although traditional catch frequency (landings) data sets exist for these species, size-specific information is limited, especially for the largest size-classes. We digitized weekly records of trophy catch reported in the "Whoppers of the Week" section of the Western Outdoor News, a California fishing and hunting newspaper published since 1953. The resulting database contained catch records that described the largest fish caught at each sportfishing landing site along the California coast during 1966-2013. We then assessed the temporal dynamics in trophy size of the top-15 pelagic and coastal pelagic species, with a combined total of 21,440 individual catch records. Among the 15 pelagic and coastal pelagic species examined, the Yellowfin Tuna Thunnus albacares and Striped Bass Morone saxatilis were the only species that showed clear long-term declines in trophy size over the study period, whereas the Pacific Bluefin Tuna Thunnus orientalis, White Seabass Atractoscion nobilis, and Yellowtail Jack Seriola lalandi exhibited long-term increases in size. In general, the trophy sizes of pelagic species were more variable than those of coastal pelagic species and were not as consistently correlated with oceanographic conditions; both findings likely reflect the fact that oceanography drives the availability but not necessarily the size of pelagic species catch. In contrast, coastal pelagic species demonstrated trends in trophy sizes that were more consistently responsive to both oceanography and fisheries management. Our results suggest that oceanographic processes, natural history characteristics, fishing, and fisheries regulations each play a role in trophy size dynamics, but their relative influences vary among species.

Blake, WH, Boeckx P, Stock BC, Smith HG, Bode S, Upadhayay HR, Gaspar L, Goddard R, Lennard AT, Lizaga I, Lobb DA, Owens PN, Petticrew EL, Kuzyk ZZA, Gari BD, Munishi L, Mtei K, Nebiyu A, Mabit L, Navas A, Semmens BX.  2018.  A deconvolutional Bayesian mixing model approach for river basin sediment source apportionment. Scientific Reports. 8   10.1038/s41598-018-30905-9   AbstractWebsite

Increasing complexity in human-environment interactions at multiple watershed scales presents major challenges to sediment source apportionment data acquisition and analysis. Herein, we present a step-change in the application of Bayesian mixing models: Deconvolutional-MixSIAR (D-MIXSIAR) to underpin sustainable management of soil and sediment. This new mixing model approach allows users to directly account for the 'structural hierarchy' of a river basin in terms of sub-watershed distribution. It works by deconvoluting apportionment data derived for multiple nodes along the stream-river network where sources are stratified by sub-watershed. Source and mixture samples were collected from two watersheds that represented (i) a longitudinal mixed agricultural watershed in the south west of England which had a distinct upper and lower zone related to topography and (ii) a distributed mixed agricultural and forested watershed in the mid-hills of Nepal with two distinct sub-watersheds. In the former, geochemical fingerprints were based upon weathering profiles and anthropogenic soil amendments. In the latter compound-specific stable isotope markers based on soil vegetation cover were applied. Mixing model posterior distributions of proportional sediment source contributions differed when sources were pooled across the watersheds (pooled-MixSIAR) compared to those where source terms were stratified by sub-watershed and the outputs deconvoluted (D-MixSIAR). In the first example, the stratified source data and the deconvolutional approach provided greater distinction between pasture and cultivated topsoil source signatures resulting in a different posterior distribution to non-deconvolutional model (conventional approaches over-estimated the contribution of cultivated land to downstream sediment by 2 to 5 times). In the second example, the deconvolutional model elucidated a large input of sediment delivered from a small tributary resulting in differences in the reported contribution of a discrete mixed forest source. Overall D-MixSIAR model posterior distributions had lower (by ca 25-50%) uncertainty and quicker model run times. In both cases, the structured, deconvoluted output cohered more closely with field observations and local knowledge underpinning the need for closer attention to hierarchy in source and mixture terms in river basin source apportionment. Soil erosion and siltation challenge the energy-food-water-environment nexus. This new tool for source apportionment offers wider application across complex environmental systems affected by natural and human-induced change and the lessons learned are relevant to source apportionment applications in other disciplines.

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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.

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Diffendorfer, JE, Loomis JB, Ries L, Oberhauser K, Lopez-Hoffman L, Semmens D, Semmens B, Butterfield B, Bagstad K, Goldstein J, Wiederholt R, Mattsson B, Thogmartin WE.  2014.  National valuation of Monarch butterflies indicates an untapped potential for incentive-based conservation. Conservation Letters. 7:253-262.   10.1111/conl.12065   AbstractWebsite

The annual migration of monarch butterflies (Danaus plexippus) has high cultural value and recent surveys indicate monarch populations are declining. Protecting migratory species is complex because they cross international borders and depend on multiple regions. Understanding how much, and where, humans place value on migratory species can facilitate market-based conservation approaches. We performed a contingent valuation study of monarchs to understand the potential for such approaches to fund monarch conservation. The survey asked U.S. respondents about the money they would spend, or have spent, growing monarch-friendly plants, and the amount they would donate to monarch conservation organizations. Combining planting payments and donations, the survey indicated U.S. households valued monarchs as a total one-time payment of $4.78-$6.64 billion, levels similar to many endangered vertebrate species. The financial contribution of even a small percentage of households through purchases or donations could generate new funding for monarch conservation through market-based approaches.

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Egerton, JP, Johnson AF, Le Vay L, McCoy CM, Semmens BX, Heppell SA, Turner JR.  2017.  Hydroacoustics for the discovery and quantification of Nassau grouper (Epinephelus striatus) spawning aggregations. Coral Reefs. :1-12.   10.1007/s00338-017-1542-4   Abstract

Fish spawning aggregations (FSAs) are vital life-history events that need to be monitored to determine the health of aggregating populations; this is especially true of the endangered Nassau grouper (Epinephelus striatus). Hydroacoustics were used to locate Nassau grouper FSAs at sites on the west end of Little Cayman (LCW), and east ends of Grand Cayman (GCE) and Cayman Brac (CBE). Fish abundance and biomass at each FSA were estimated via echo integration and FSA extent. Acoustic mean fish abundance estimates (±SE) on the FSA at LCW (893 ± 459) did not differ significantly from concurrent SCUBA estimates (1150 ± 75). Mean fish densities (number 1000 m−3) were significantly higher at LCW (33.13 ± 5.62) than at the other sites (GCE: 7.01 ± 2.1, CBE: 4.61 ± 1.16). We investigate different acoustic post-processing options to obtain target strength (TS), and we examine the different TS to total length (TL) formulas available. The SCUBA surveys also provided measures of TL through the use of laser callipers allowing development of an in situ TS to TL formula for Nassau grouper at the LCW FSA. Application of this formula revealed mean fish TL was significantly higher at LCW (65.4 ± 0.7 cm) than GCE (60.7 ± 0.4 cm), but not CBE (61.1 ± 2.5 cm). Use of the empirical TS to TL formula resulted in underestimation of fish length in comparison with diver measurements, highlighting the benefits of secondary length data and deriving specific TS to TL formulas for each population. FSA location examined with reference to seasonal marine protected areas (Designated Grouper Spawning Areas) showed FSAs were partially outside these areas at GCE and very close to the boundary at CBE. As FSAs often occur at the limits of safe diving operations, hydroacoustic technology provides an alternative method to monitor and inform future management of aggregating fish species.

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Fontes, J, Semmens B, Caselle JE, Santos RS, Prakya R.  2016.  Ocean productivity may predict recruitment of the rainbow wrasse (coris julis). Plos One. 11   10.1371/journal.pone.0165648   AbstractWebsite

Predicting recruitment fluctuations of fish populations remains the Holy Grail of fisheries science. While previous work has linked recruitment of reef fish to environmental variables including temperature, the demonstration of a robust relationship with productivity remains elusive. Despite decades of research, empirical evidence to support this critical link remains limited. Here we identify a consistent and strong relationship between recruitment of a temperate wrasse Coris julis, from temperate reefs in the mid-Atlantic region, with Chlorophyll, over contrasting scales, across multiple years. Additionally, we find that the correlation between Chlorophyll and recruitment is not simply masking a temperature-recruitment relationship. Understanding the potential mechanisms underlying recruitment variability, particularly as it relates to changing climate and ocean regimes, is a critical first step towards characterizing species' vulnerability to mismatches between pulsed planktonic production and early pelagic life stages.

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.

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Gruss, A, Robinson J, Heppell SS, Heppell SA, Semmens BX.  2014.  Conservation and fisheries effects of spawning aggregation marine protected areas: What we know, where we should go, and what we need to get there. Ices Journal of Marine Science. 71:1515-1534.   10.1093/icesjms/fsu038   AbstractWebsite

There is a global trend in the depletion of transient reef fish spawning aggregations ("FSAs"), making them a primary target for management with marine protected areas (MPAs). Here, we review the observed and likely effectiveness of FSA MPAs, discuss how future studies could fill knowledge gaps, and provide recommendations for MPA design based on species' life history and behaviour, enforcement potential, and management goals. Modelling studies indicate that FSA MPAs can increase spawning-stock biomass and normalize sex ratio in protogynous fish populations, unless fishing mortality remains high outside protected FSA sites and spawning times. In the field, observations of no change or continued decline in spawning biomass are more common than population recovery. When empirical studies suggest that FSA MPAs may not benefit fish productivity or recovery, extenuating factors such as insufficient time since MPA creation, poor or lack of enforcement, inadequate design, and poorly defined management objectives are generally blamed rather than failure of the MPA concept. Results from both the empirical and modelling literature indicate that FSA MPAs may not improve exploitable biomass and fisheries yields; however, investigations are currently too limited to draw conclusions on this point. To implement effective FSA MPAs, additional modelling work, long-term monitoring programmes at FSA sites, and collections of fisheries-dependent data are required, with greater attention paid to the design and enforcement of area closures. We recommend a harmonized, adaptive approach that combines FSA MPA design with additional management measures to achieve explicitly stated objectives. Conservation objectives and, therefore, an overall reduction in mortality rates should be targeted first. Fisheries objectives build on conservation objectives, in that they require an overall reduction in mortality rates while maintaining sufficient access to exploitable biomass. Communication among researchers, regulatory agencies, park authorities, and fishers will be paramount for effective action, along with significant funds for implementation and enforcement.

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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.

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.

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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Jackson, AM, Semmens BX, de Mitcheson YS, Nemeth RS, Heppell SA, Bush PG, Aguilar-Perera A, Claydon JAB, Calosso MC, Sealey KS, Scharer MT, Bernardi G.  2014.  Population structure and phylogeography in Nassau grouper (Epinephelus striatus), a mass-aggregating marine fish. Plos One. 9   10.1371/journal.pone.0097508   AbstractWebsite

To address patterns of genetic connectivity in a mass-aggregating marine fish, we analyzed genetic variation in mitochondrial DNA (mtDNA), microsatellites, and single nucleotide polymorphisms (SNPs) for Nassau grouper (Epinephelus striatus). We expected Nassau grouper to exhibit genetic differentiation among its subpopulations due to its reproductive behavior and retentive oceanographic conditions experienced across the Caribbean basin. All samples were genotyped for two mitochondrial markers and 9 microsatellite loci, and a subset of samples were genotyped for 4,234 SNPs. We found evidence of genetic differentiation in a Caribbean-wide study of this mass-aggregating marine fish using mtDNA (F-ST = 0.206, p<0.001), microsatellites (F-ST = 0.002, p = 0.004) and SNPs (F-ST = 0.002, p = 0.014), and identified three potential barriers to larval dispersal. Genetically isolated regions identified in our work mirror those seen for other invertebrate and fish species in the Caribbean basin. Oceanographic regimes in the Caribbean may largely explain patterns of genetic differentiation among Nassau grouper subpopulations. Regional patterns observed warrant standardization of fisheries management and conservation initiatives among countries within genetically isolated regions.

Johnson, DW, Grorud-Colvert K, Sponaugle S, Semmens BX.  2014.  Phenotypic variation and selective mortality as major drivers of recruitment variability in fishes. Ecology Letters. 17:743-755.   10.1111/ele.12273   AbstractWebsite

An individual's phenotype will usually influence its probability of survival. However, when evaluating the dynamics of populations, the role of selective mortality is not always clear. Not all mortality is selective, patterns of selective mortality may vary, and it is often unknown how selective mortality compares or interacts with other sources of mortality. As a result, there is seldom a clear expectation for how changes in the phenotypic composition of populations will translate into differences in average survival. We address these issues by evaluating how selective mortality affects recruitment of fish populations. First, we provide a quantitative review of selective mortality. Our results show that most of the mortality during early life is selective, and that variation in phenotypes can have large effects on survival. Next, we describe an analytical framework that accounts for variation in selection, while also describing the amount of selective mortality experienced by different cohorts recruiting to a single population. This framework is based on reconstructing fitness surfaces from phenotypic selection measurements, and can be employed for either single or multiple traits. Finally, we show how this framework can be integrated with models of density-dependent survival to improve our understanding of recruitment variability and population dynamics.

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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.

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.

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Nosrati, K, Govers G, Semmens BX, Ward EJ.  2014.  A mixing model to incorporate uncertainty in sediment fingerprinting. Geoderma. 217:173-180.   10.1016/j.geoderma.2013.12.002   AbstractWebsite

Information on sediment sources is required for effective sediment control strategies, to understand nutrient and pollutant transport, and for developing soil erosion models. Uncertainty associated with sediment fingerprinting mixing models is often substantial, but this uncertainty has not yet been fully incorporated in these models. The main objectives of this study are to apply geochemical fingerprints to determine relative contributions of sediment sources and to develop a Bayesian-mixing model that estimates probability distributions of source contributions to a mixture associated with multiple sources for assessing the uncertainty estimation in sediment fingerprinting in the Hiv catchment, Iran. In this analysis, 28 tracers were measured in 42 different sampling sites from three sediment sources (rangeland, orchard and stream bank) and 12 sediment samples from reservoir check dams. Discriminant analysis provided an important data reduction as it identified four tracers, i.e. B, C, Sr and Tl, that afforded more than 97% correct assignations in discriminating between the sediment sources in the study area. Using a stable isotope mixing model, the median contribution from rangeland, orchard and stream bank sources was 20.8%, 11.2% and 68%, respectively. Sediment source fingerprinting was used to explore the uncertainty in the contributions of sediment from the three sources. Uncertainty is considerable, as the range of probable values was wide: 2-24% for rangeland, 1-26% for orchards and 66-83% for stream banks respectively. While these results can be useful as a scientific basis of sediment management and selecting the soil erosion control methods for decision makers of natural resources they also show that it may not always be possible to identify sediment sources with great precision. Consequently, uncertainty needs to be accounted for when evaluating different management options. (C) 2013 Elsevier B.V. All rights reserved.

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Oberhauser, K, Wiederholt R, Diffendorfer JE, Semmens D, Ries L, Thogmartin WE, Lopez-Hoffman L, Semmens B.  2017.  A trans-national monarch butterfly population model and implications for regional conservation priorities. Ecological Entomology. 42:51-60.   10.1111/een.12351   AbstractWebsite

1. The monarch has undergone considerable population declines over the past decade, and the governments of Mexico, Canada, and the United States have agreed to work together to conserve the species. 2. Given limited resources, understanding where to focus conservation action is key for widespread species like monarchs. To support planning for continental-scale monarch habitat restoration, we address the question of where restoration efforts are likely to have the largest impacts on monarch butterfly (Danaus plexippusLinn.) population growth rates. 3. We present a spatially explicit demographic model simulating the multi-generational annual cycle of the eastern monarch population, and use the model to examine management scenarios, some of which focus on particular regions of North America. 4. Improving the monarch habitat in the north central or southern parts of the monarch range yields a slightly greater increase in the population growth rate than restoration in other regions. However, combining restoration efforts across multiple regions yields population growth rates above 1 with smaller simulated improvements in habitat per region than single-region strategies. 5. Synthesis and applications:These findings suggest that conservation investment in projects across the full monarch range will be more effective than focusing on one or a few regions, and will require international cooperation across many land use categories.

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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.

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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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.