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2018
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.

Stock, BC, Jackson AL, Ward EJ, Parnell AC, Phillips DL, Semmens BX.  2018.  Analyzing mixing systems using a new generation of Bayesian tracer mixing models. Peerj. 6   10.7717/peerj.5096   AbstractWebsite

The ongoing evolution of tracer mixing models has resulted in a confusing array of software tools that differ in terms of data inputs, model assumptions, and associated analytic products. Here we introduce MixSIAR, an inclusive, rich, and flexible Bayesian tracer (e.g., stable isotope) mixing model framework implemented as an open-source R package. Using MixSIAR as a foundation, we provide guidance for the implementation of mixing model analyses. We begin by outlining the practical differences between mixture data error structure formulations and relate these error structures to common mixing model study designs in ecology. Because Bayesian mixing models afford the option to specify informative priors on source proportion contributions, we outline methods for establishing prior distributions and discuss the influence of prior specification on model outputs. We also discuss the options available for source data inputs (raw data versus summary statistics) and provide guidance for combining sources. We then describe a key advantage of MixSIAR over previous mixing model software-the ability to include fixed and random effects as covariates explaining variability in mixture proportions and calculate relative support for multiple models via information criteria. We present a case study of Alligator mississippiensis diet partitioning to demonstrate the power of this approach. Finally, we conclude with a discussion of limitations to mixing model applications. Through MixSIAR, we have consolidated the disparate array of mixing model tools into a single platform, diversified the set of available parameterizations, and provided developers a platform upon which to continue improving mixing model analyses in the future.

Semmens, DJ, Diffendorfer JE, Bagstad KJ, Wiederholt R, Oberhauser K, Ries L, Semmens BX, Goldstein J, Loomis J, Thogmartin WE, Mattsson BJ, Lopez-Hoffman L.  2018.  Quantifying ecosystem service flows at multiple scales across the range of a long-distance migratory species. Ecosystem Services. 31:255-264.   10.1016/j.ecoser.2017.12.002   AbstractWebsite

Migratory species provide ecosystem goods and services throughout their annual cycles, often over long distances. Designing effective conservation solutions for migratory species requires knowledge of both species ecology and the socioeconomic context of their migrations. We present a framework built around the concept that migratory species act as carriers, delivering benefit flows to people throughout their annual cycle that are supported by the network of ecosystems upon which the species depend. We apply this framework to the monarch butterfly (Danaus plexippus) migration of eastern North America by calculating their spatial subsidies. Spatial subsidies are the net ecosystem service flows throughout a species' range and a quantitative measure of the spatial mismatch between the locations where people receive most benefits and the locations of habitats that most support the species. Results indicate cultural benefits provided by monarchs in the U.S. and Canada are subsidized by migration and overwintering habitat in Mexico. At a finer scale, throughout the monarch range, habitat in rural landscapes subsidizes urban residents. Understanding the spatial distribution of benefits derived from and ecological support provided to monarchs and other migratory species offers a promising means of understanding the costs and benefits associated with conservation across jurisdictional borders. Published by Elsevier B.V.

2017
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.

Thogmartin, WE, Wiederholt R, Oberhauser K, Drum RG, Diffendorfer JE, Altizer S, Taylor OR, Pleasants J, Semmens D, Semmens B, Erickson R, Libby K, Lopez-Hoffman L.  2017.  Monarch butterfly population decline in North America: identifying the threatening processes. Royal Society Open Science. 4   10.1098/rsos.170760   AbstractWebsite

The monarch butterfly (Danaus plexippus) population in North America has sharply declined over the last two decades. Despite rising concern over the monarch butterfly's status, no comprehensive study of the factors driving this decline has been conducted. Using partial least-squares regressions and time-series analysis, we investigated climatic and habitat-related factors influencing monarch population size from 1993 to 2014. Potential threats included climatic factors, habitat loss (milkweed and overwinter forest), disease and agricultural insecticide use (neonicotinoids). While climatic factors, principally breeding season temperature, were important determinants of annual variation in abundance, our results

Stewart, JD, Rohner CA, Araujo G, Avila J, Fernando D, Forsberg K, Ponzo A, Rambahiniarison JM, Kurle CM, Semmens BX.  2017.  Trophic overlap in mobulid rays: insights from stable isotope analysis. Marine Ecology Progress Series. 580:131-151.   10.3354/meps12304   AbstractWebsite

Mobulid rays, a group of closely related filter-feeders, are threatened globally by bycatch and targeted fisheries. Their habitat use and feeding ecology are not well studied, and most efforts have focused on temporally limited stomach content analysis or inferences from tagging data. Previous studies demonstrate a variety of different diving behaviors across species, which researchers have interpreted as evidence of disparate foraging strategies. However, few studies have examined feeding habitats and diets of multiple mobulid species from a single location, and it is unclear if the proposed differences in diving and inferred foraging behavior are examples of variability between species or regional adaptations to food availability. Here, we use stable isotope data from mobulids landed in fisheries to examine the feeding ecology of 5 species at 3 sites in the Indo-Pacific. We use Bayesian mixing models and analyses of isotopic niche areas to demonstrate dietary overlap between sympatric mobulid species at all of our study sites. We show the degree of overlap may be inversely related to productivity, which is contrary to prevailing theories of niche overlap. We use isotope data from 2 tissues to examine diet stability of Manta birostris and Mobula tarapacana in the Philippines. Finally, we observe a significant but weak relationship between body size and isotope values across species. Our findings highlight challenges to bycatch mitigation measures for mobulid species and may explain the multi-species mobulid bycatch that occurs in a variety of fisheries around the world.

Thogmartin, WE, Lopez-Hoffman L, Rohweder J, Diffendorfer J, Drum R, Semmens D, Black S, Caldwell I, Cotter D, Drobney P, Jackson LL, Gale M, Helmers D, Hilburger S, Howard E, Oberhauser K, Pleasants J, Semmens B, Taylor O, Ward P, Weltzin JF, Wiederholt R.  2017.  Restoring monarch butterfly habitat in the Midwestern US: 'all hands on deck'. Environmental Research Letters. 12   10.1088/1748-9326/aa7637   AbstractWebsite

The eastern migratory population of monarch butterflies (Danaus plexippus plexippus) has declined by >80% within the last two decades. One possible cause of this decline is the loss of >= 1.3 billion stems of milkweed (Asclepias spp.), which monarchs require for reproduction. In an effort to restore monarchs to a population goal established by the US Fish and Wildlife Service and adopted by Mexico, Canada, and the US, we developed scenarios for amending the Midwestern US landscape with milkweed. Scenarios for milkweed restoration were developed for protected area grasslands, Conservation Reserve Program land, powerline, rail and roadside rights of way, urban/suburban lands, and land in agricultural production. Agricultural land was further divided into productive and marginal cropland. We elicited expert opinion as to the biological potential (in stems per acre) for lands in these individual sectors to support milkweed restoration and the likely adoption (probability) of management practices necessary for affecting restoration. Sixteen of 218 scenarios we developed for restoring milkweed to the Midwestern US were at levels (>1.3 billion new stems) necessary to reach the monarch population goal. One of these scenarios would convert all marginal agriculture to conserved status. The other 15 scenarios converted half of marginal agriculture (730 million stems), with remaining stems contributed by other societal sectors. Scenarios without substantive agricultural participation were insufficient for attaining the population goal. Agricultural lands are essential to reaching restoration targets because they occupy 77% of all potential monarch habitat. Barring fundamental changes to policy, innovative application of economic tools such as habitat exchanges may provide sufficient resources to tip the balance of the agro-ecological landscape toward a setting conducive to both robust agricultural production and reduced imperilment of the migratory monarch butterfly.

Upadhayay, HR, Bode S, Griepentrog M, Huygens D, Bajracharya RM, Blake WH, Dercon G, Mabit L, Gibbs M, Semmens BX, Stock BC, Cornelis W, Boeckx P.  2017.  Methodological perspectives on the application of compound-specific stable isotope fingerprinting for sediment source apportionment. Journal of Soils and Sediments. 17:1537-1553.   10.1007/s11368-017-1706-4   AbstractWebsite

Compound-specific stable isotope (CSSI) fingerprinting of sediment sources is a recently introduced tool to overcome some limitations of conventional approaches for sediment source apportionment. The technique uses the C-13 CSSI signature of plant-derived fatty acids (delta C-13-fatty acids) associated with soil minerals as a tracer. This paper provides methodological perspectives to advance the use of CSSI fingerprinting in combination with stable isotope mixing models (SIMMs) to apportion the relative contributions of different sediment sources (i.e. land uses) to sediments. CSSI fingerprinting allows quantitative estimation of the relative contribution of sediment sources within a catchment at a spatio-temporal resolution, taking into account the following approaches. First, application of CSSI fingerprinting techniques to complex catchments presents particular challenges and calls for well-designed sampling strategies and data handling. Hereby, it is essential to balance the effort required for representative sample collection and analyses against the need to accurately quantify the variability within the system. Second, robustness of the CSSI approach depends on the specificity and conservativeness of the delta C-13-FA fingerprint. Therefore, saturated long-chain (> 20 carbon atoms) FAs, which are biosynthesised exclusively by higher plants and are more stable than the more commonly used short-chain FAs, should be used. Third, given that FA concentrations can vary largely between sources, concentration-dependent SIMMs that are also able to incorporate delta C-13-FA variability should be standard operation procedures to correctly assess the contribution of sediment sources via SIMMs. This paper reflects on the use of delta C-13-FAs in erosion studies and provides recommendations for its application. We strongly advise the use of saturated long-chain (> 20 carbon atoms) FAs as tracers and concentration-dependent Bayesian SIMMs. We anticipate progress in CSSI sediment fingerprinting from two current developments: (i) development of hierarchical Bayesian SIMMs to better address catchment complexity and (ii) incorporation of dual isotope approaches (delta C-13- and delta H-2-FA) to improve estimates of sediment sources.

Thogmartin, WE, Diffendorfer JE, Lopez-Hoffman L, Oberhauser K, Pleasants J, Semmens BX, Semmens D, Taylor OR, Wiederholt R.  2017.  Density estimates of monarch butterflies overwintering in central Mexico. Peerj. 5   10.7717/peerj.3221   AbstractWebsite

Given the rapid population decline and recent petition for listing of the monarch butterfly (Danaus plexippus L.) under the Endangered Species Act, an accurate estimate of the Eastern, migratory population size is needed. Because of difficulty in counting individual monarchs, the number of hectares occupied by monarchs in the overwintering area is commonly used as a proxy for population size, which is then multiplied by the density of individuals per hectare to estimate population size. There is, however, considerable variation in published estimates of overwintering density, ranging from 6.9-60.9 million ha(-1). We develop a probability distribution for overwinter density of monarch butterflies from six published density estimates. The mean density among the mixture of the six published estimates was similar to 27.9 million butterflies ha(-1) (95% CI [2.4-80.7] million ha(-1)); the mixture distribution is approximately log-normal, and as such is better represented by the median (21.1 million butterflies ha(-1)). Based upon assumptions regarding the number of milkweed needed to support monarchs, the amount of milkweed (Asciepias spp.) lost (0.86 billion stems) in the northern US plus the amount of milkweed remaining (1.34 billion stems), we estimate >1.8 billion stems is needed to return monarchs to an average population size of 6 ha. Considerable uncertainty exists in this required amount of milkweed because of the considerable uncertainty occurring in overwinter density estimates. Nevertheless, the estimate is on the same order as other published estimates, The studies included in our synthesis differ substantially by year, location, method, and measures of precision. A better understanding of the factors influencing overwintering density across space and time would be valuable for increasing the precision of conservation recommendations.

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.

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.

2016
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.

Stock, BC, Semmens BX.  2016.  Unifying error structures in commonly used biotracer mixing models. Ecology. 97:2562-2569.   10.1002/ecy.1517   AbstractWebsite

Mixing models are statistical tools that use biotracers to probabilistically estimate the contribution of multiple sources to a mixture. These biotracers may include contaminants, fatty acids, or stable isotopes, the latter of which are widely used in trophic ecology to estimate the mixed diet of consumers. Bayesian implementations of mixing models using stable isotopes (e.g., MixSIR, SIAR) are regularly used by ecologists for this purpose, but basic questions remain about when each is most appropriate. In this study, we describe the structural differences between common mixing model error formulations in terms of their assumptions about the predation process. We then introduce a new parameterization that unifies these mixing model error structures, as well as implicitly estimates the rate at which consumers sample from source populations (i.e., consumption rate). Using simulations and previously published mixing modeldatasets, we demonstrate that the new error parameterization outperforms existing models and provides an estimate of consumption. Our results suggest that the error structure introduced here will improve future mixing model estimates of animal diet.

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.

Stewart, JD, Beale CS, Fernando D, Sianipar AB, Burton RS, Semmens BX, Aburto-Oropeza O.  2016.  Spatial ecology and conservation of Manta birostris in the Indo-Pacific. Biological Conservation. 200:178-183.   10.1016/j.biocon.2016.05.016   AbstractWebsite

Information on the movements and population connectivity of the oceanic manta ray (Manta birostris) is scarce. The species has been anecdotally classified as a highly migratory species based on the pelagic habitats it often occupies, and migratory behavior exhibited by similar species. As a result, in the absence of ecological data, population declines in oceanic manta have been addressed primarily with international-scale management and conservation efforts. Using a combination of satellite telemetry, stable isotope and genetic analyses we demonstrate that, contrary to previous assumptions, the species appears to exhibit restricted movements and fine scale population structure. M. birostris tagged at four sites in the Indo-Pacific exhibited no long-range migratory movements and had non-overlapping geographic ranges. Using genetic and isotopic analysis, we demonstrate that the observed movements and population structure persist on multi-year and generational time scales. These data provide the first insights into the long-term movements and population structure of oceanic manta rays, and suggest that bottom-up, local or regional approaches to managing oceanic mantas could prove more effective than existing, international-scale management strategies. This case study highlights the importance of matching the scales at which management and relevant ecological processes occur to facilitate the effective conservation of threatened species. (C) 2016 Elsevier Ltd. All rights reserved.

Semmens, BX, Semmens DJ, Thogmartin WE, Wiederholt R, López-Hoffman L, Diffendorfer JE, Pleasants JM, Oberhauser KS, Taylor OR.  2016.  Quasi-extinction risk and population targets for the Eastern, migratory population of monarch butterflies (Danaus plexippus). Scientific Reports. 6:23265.: The Author(s)   10.1038/srep23265   Abstract

The Eastern, migratory population of monarch butterflies (Danaus plexippus), an iconic North American insect, has declined by ~80% over the last decade. The monarch’s multi-generational migration between overwintering grounds in central Mexico and the summer breeding grounds in the northern U.S. and southern Canada is celebrated in all three countries and creates shared management responsibilities across North America. Here we present a novel Bayesian multivariate auto-regressive state-space model to assess quasi-extinction risk and aid in the establishment of a target population size for monarch conservation planning. We find that, given a range of plausible quasi-extinction thresholds, the population has a substantial probability of quasi-extinction, from 11–57% over 20 years, although uncertainty in these estimates is large. Exceptionally high population stochasticity, declining numbers, and a small current population size act in concert to drive this risk. An approximately 5-fold increase of the monarch population size (relative to the winter of 2014–15) is necessary to halve the current risk of quasi-extinction across all thresholds considered. Conserving the monarch migration thus requires active management to reverse population declines, and the establishment of an ambitious target population size goal to buffer against future environmentally driven variability.

Stanton, JC, Semmens BX, McKann PC, Will T, Thogmartin WE.  2016.  Flexible risk metrics for identifying and monitoring conservation-priority species. Ecological Indicators. 61:683-692.   10.1016/j.ecolind.2015.10.020   AbstractWebsite

Region-specific conservation programs should have objective, reliable metrics for species prioritization and progress evaluation that are customizable to the goals of a program, easy to comprehend and communicate, and standardized across time. Regional programs may have vastly different goals, spatial coverage, or management agendas, and one-size-fits-all schemes may not always be the best approach. We propose a quantitative and objective framework for generating metrics for prioritizing species that is straightforward to implement and update, customizable to different spatial resolutions, and based on readily available time-series data. This framework is also well-suited to handling missing-data and observer error. We demonstrate this approach using North American Breeding Bird Survey (NABBS) data to identify conservation priority species from a list of over 300 landbirds across 33 bird conservation regions (BCRs). To highlight the flexibility of the framework for different management goals and timeframes we calculate two different metrics. The first identifies species that may be inadequately monitored by NABBS protocols in the near future (TMT, time to monitoring threshold), and the other identifies species likely to decline significantly in the near future based on recent trends (TPD, time to percent decline). Within the individual BCRs we found up to 45% (mean 28%) of the species analyzed had overall declining population trajectories, which could result in up to 37 species declining below a minimum NABBS monitoring threshold in at least one currently occupied BCR within the next 50 years. Additionally, up to 26% (mean 8%) of the species analyzed within the individual BCRs may decline by 30% within the next decade. Conservation workers interested in conserving avian diversity and abundance within these BCRs can use these metrics to plan alternative monitoring schemes or highlight the urgency of those populations experiencing the fastest declines. However, this framework is adaptable to many taxa besides birds where abundance time-series data are available. Published by Elsevier Ltd.

2015
Scheuerell, MD, Buhle ER, Semmens BX, Ford MJ, Cooney T, Carmichael RW.  2015.  Analyzing large-scale conservation interventions with Bayesian hierarchical models: a case study of supplementing threatened Pacific salmon. Ecology and Evolution. 5:2115-2125.   10.1002/ece3.1509   AbstractWebsite

Myriad human activities increasingly threaten the existence of many species. A variety of conservation interventions such as habitat restoration, protected areas, and captive breeding have been used to prevent extinctions. Evaluating the effectiveness of these interventions requires appropriate statistical methods, given the quantity and quality of available data. Historically, analysis of variance has been used with some form of predetermined before-after control-impact design to estimate the effects of large-scale experiments or conservation interventions. However, ad hoc retrospective study designs or the presence of random effects at multiple scales may preclude the use of these tools. We evaluated the effects of a large-scale supplementation program on the density of adult Chinook salmon Oncorhynchus tshawytscha from the Snake River basin in the northwestern United States currently listed under the U.S. Endangered Species Act. We analyzed 43years of data from 22 populations, accounting for random effects across time and space using a form of Bayesian hierarchical time-series model common in analyses of financial markets. We found that varying degrees of supplementation over a period of 25years increased the density of natural-origin adults, on average, by 0-8% relative to nonsupplementation years. Thirty-nine of the 43year effects were at least two times larger in magnitude than the mean supplementation effect, suggesting common environmental variables play a more important role in driving interannual variability in adult density. Additional residual variation in density varied considerably across the region, but there was no systematic difference between supplemented and reference populations. Our results demonstrate the power of hierarchical Bayesian models to detect the diffuse effects of management interventions and to quantitatively describe the variability of intervention success. Nevertheless, our study could not address whether ecological factors (e.g., competition) were more important than genetic considerations (e.g., inbreeding depression) in determining the response to supplementation.

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.

2014
Thorson, JT, Scheuerell MD, Semmens BX, Pattengill-Semmens CV.  2014.  Demographic modeling of citizen science data informs habitat preferences and population dynamics of recovering fishes. Ecology. 95:3251-3258. AbstractWebsite

Managing natural populations and communities requires detailed information regarding demographic processes at large spatial and temporal scales. This combination is challenging for both traditional scientific surveys, which often operate at localized scales, and recent citizen science designs, which often provide data with few auxiliary information (i.e., no information about individual age or condition). We therefore combine citizen science data at large scales with the demographic resolution afforded by recently developed, site-structured demographic models. We apply this approach to categorical data generated from citizen science representing species density of two managed reef fishes in the Gulf of Mexico, and use a modified Dail-Madsen model to estimate demographic trends, habitat associations, and interannual variability in recruitment. This approach identifies strong preferences for artificial structure for the recovering Goliath grouper, while revealing little evidence of either habitat associations or trends in abundance for mutton snapper. Results are also contrasted with a typical generalized linear mixed-model (GLMM) approach, using real-world and simulated data, to demonstrate the importance of accounting for the statistical complexities implied by spatially structured citizen science data. We conclude by discussing the increasing potential for synthesizing demographic models and citizen science data, and the management benefits that can be accrued.

Phillips, DL, Inger R, Bearhop S, Jackson AL, Moore JW, Parnell AC, Semmens BX, Ward EJ.  2014.  Best practices for use of stable isotope mixing models in food-web studies. Canadian Journal of Zoology. 92:823-835.   10.1139/cjz-2014-0127   AbstractWebsite

Stable isotope mixing models are increasingly used to quantify consumer diets, but may be misused and misinterpreted. We address major challenges to their effective application. Mixing models have increased rapidly in sophistication. Current models estimate probability distributions of source contributions, have user-friendly interfaces, and incorporate complexities such as variability in isotope signatures, discrimination factors, hierarchical variance structure, covariates, and concentration dependence. For proper implementation of mixing models, we offer the following suggestions. First, mixing models can only be as good as the study and data. Studies should have clear questions, be informed by knowledge of the system, and have strong sampling designs to effectively characterize isotope variability of consumers and resources on proper spatio-temporal scales. Second, studies should use models appropriate for the question and recognize their assumptions and limitations. Decisions about source grouping or incorporation of concentration dependence can influence results. Third, studies should be careful about interpretation of model outputs. Mixing models generally estimate proportions of assimilated resources with substantial uncertainty distributions. Last, common sense, such as graphing data before analyzing, is essential to maximize usefulness of these tools. We hope these suggestions for effective implementation of stable isotope mixing models will aid continued development and application of this field.

Waterhouse, L, Sampson DB, Maunder M, Semmens BX.  2014.  Using areas-as-fleets selectivity to model spatial fishing: Asymptotic curves are unlikely under equilibrium conditions. Fisheries Research. 158:15-25.   10.1016/j.fishres.2014.01.009   AbstractWebsite

Most population models and stock assessment approaches assume that fish and fishing are spatially uniform. Here, we examine the effects of spatial structure on fishery selection (selectivity). Selectivity refers to the fact that age- or size-classes of fish are not equally vulnerable to fishing; such differences in class-specific vulnerabilities will influence the age-structure of a fish stock, which in turn will determine the stock's productivity and ability to sustain harvest. The selectivity of the gear produces a characteristic selection curve that is generally assumed to be asymptotic. However, population-level selection curves can deviate considerably from an asymptotic shape given spatial structure in the population. For example, given time-invariant recruitment and time-invariant age-specific survival, the shape of the selection curve at the level of the population will be dome-shaped under a wide range of conditions, even though the gear-selection curves operating in common in all areas within the population are asymptotic. This paper explores the factors, under equilibrium conditions, influencing the areas-as-fleets selection curves that result from using selectivity coefficients to represent spatial catch-at-age in a non-spatial population dynamics model. We use a simplified set of survival equations from Sampson and Scott (Can. J. Fish. Aquat. Sci. 68 (2011) 1077-1086), in which there are three distinct spatial regions with the same asymptotic selection curve operating in each region, and show that while the overall population-selectivity is typically dome shaped, the corresponding areas-as-fleets selection curve shapes differ from each other and from the population-selection and gear-selection curves. Factors that influence how much the selectivity curves differ from each other include the magnitude of the differences in the regional fishing mortality rates, the rates of fish movement and whether the movements are diffusive or directional, and the regional distribution of the recruits. If fish movement rates are relatively slow (say, less than 20% per time-step), then in nearly all cases areas-as-fleets selectivity will differ from the underlying gear-selectivity, except under the extraordinary conditions of equal recruitment and equal fishing mortality across all spatial regions. (C) 2014 Elsevier B.V. All rights reserved.

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.

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.

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.