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Environmental variability controls recruitment but with different drivers among spawning components in Gulf of St. Lawrence herring stocks

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FISHERIES OCEANOGRAPHY 2019年第1期28卷 1-17页

作者： Brosset, Pablo Doniol-Valcroze, Thomas Swain, Douglas P. Lehoux, Caroline Van Beveren, Elisabeth Mbaye, Baye C. Emond, Kim Plourde, Stephane Fisheries & Oceans Canada Maurice Lamontagne Inst Mont Joli PQ Canada Fisheries & Oceans Canada Gulf Fisheries Ctr Moncton NB Canada Fisheries & Oceans Canada Pacific Biol Stn Nanaimo BC Canada

The factors affecting herring recruitment are still poorly understood, complicating the prediction of stock dynamics and the choice of operational management strategies. We investigated effects of intrinsic (SSB) and extrinsic factors (physical and biological environments, including competition and predation) on recruitment of the spring and fall spawning components of each of the two herring stocks occurring in the Gulf of the St. Lawrence between 1971 and 2014. Effects of potential explanatory factors on recruit (age 2) abundance were tested using generalized additive models. Model fit was significantly improved by incorporating both physical and biological environmental variability, but effects of herring SSB and predation were not significant. Indices of zooplankton abundance and phenology explained more variance in recruitment than physical indices. Our results emphasize the dominance of bottom-up processes over SSB in the regulation of herring recruitment. Environmental variability did not seem to act uniformly on the recruitment of either stock or their respective spawning components. A long-term trend of decreasing recruitment in spring spawners was associated with a long-term decline in abundance of cold water copepods. In fall spawners, optimal recruitment was dependent on warmer environmental conditions combined with an adequate supply (species composition and phenology) of zooplankton. These results provide the first empirical evidence that spring and fall spawning herring are adapted to contrasting environmental conditions and shed light on the potential mechanisms linking herring recruitment to key zooplankton community characteristics and phenology. Management strategies can be improved by incorporating this new knowledge on environmental drivers of herring recruitment.

关键词： environment-recruitment models generalized additive models NW Atlantic pelagic fish population dynamics reproductive strategies zooplankton

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Benthic habitat modelling and mapping as a conservation tool for marine protected areas: A seamount in the western Mediterranean

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AQUATIC CONSERVATION-MARINE AND FRESHWATER ECOSYSTEMS 2019年第5期29卷 732-750页

作者： de la Torriente, Ana Manuel Gonzalez-Irusta, Jose Aguilar, Ricardo Miguel Fernandez-Salas, Luis Punzon, Antonio Serrano, Alberto Ctr Oceanog Santander Inst Espanol Oceanog Santander Spain Univ Cadiz Puerto Real Spain OCEANA Madrid Spain Ctr Oceanog Cadiz Inst Espanol Oceanog Cadiz Spain

An ecologically representative, well-connected, and effectively managed system of marine protected areas (MPAs) has positive ecological and environmental effects as well as social and economic benefits. Although progress in expanding the coverage of MPAs has been made, the application of management tools has not yet been implemented in most of these areas. In this work, distribution models were applied to nine benthic habitats on a Mediterranean seamount within an MPA for conservation purposes. Benthic habitat occurrences were identified from 55 remotely operated vehicle (ROV) transects, at depths from 76 to 700 m, and data derived from multibeam bathymetry. generalized additive models (GAMs) were applied to link the presence of each benthic habitat to local environmental proxies (depth, slope, backscatter, aspect, and bathymetric position index, BPI). The main environmental drivers of habitat distribution were depth, slope, and BPI. Based on this result, five different geomorphological areas were distinguished. A full coverage map indicating the potential benthic habitat distribution on the seamount was obtained to inform spatial management. The distribution of those habitats identified as vulnerable marine ecosystems (VMEs) was used to make recommendations on zonation for developing the management plan of the MPA. This process reveals itself as an appropriate methodological approach that can be developed in other areas of the Natura 2000 marine network.

关键词： benthic habitat generalized additive models mapping marine protected area seamount spatial management

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Semiparametric Regression Using Variational Approximations

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JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION 2019年第528期114卷 1765-1777页

作者： Hui, Francis K. C. You, C. Shang, H. L. Mueller, Samuel Australian Natl Univ Math Sci Inst Canberra ACT 2601 Australia Univ Nottingham Sch Math Sci Ningbo Zhejiang Peoples R China Australian Natl Univ Res Sch Finance Actuarial Studies & Stat Canberra ACT Australia Univ Sydney Sch Math & Stat Sydney NSW Australia

Semiparametric regression offers a flexible framework for modeling nonlinear relationships between a response and covariates. A prime example are generalized additive models (GAMs) where splines (say) are used to approximate nonlinear functional components in conjunction with a quadratic penalty to control for overfitting. Estimation and inference are then generally performed based on the penalized likelihood, or under a mixed model framework. The penalized likelihood framework is fast but potentially unstable, and choosing the smoothing parameters needs to be done externally using cross-validation, for instance. The mixed model framework tends to be more stable and offers a natural way for choosing the smoothing parameters, but for nonnormal responses involves an intractable integral. In this article, we introduce a new framework for semiparametric regression based on variational approximations (VA). The approach possesses the stability and natural inference tools of the mixed model framework, while achieving computation times comparable to using penalized likelihood. Focusing on GAMs, we derive fully tractable variational likelihoods for some common response types. We present several features of the VA framework for inference, including a variational information matrix for inference on parametric components, and a closed-form update for estimating the smoothing parameter. We demonstrate the consistency of the VA estimates, and an asymptotic normality result for the parametric component of the model. Simulation studies show the VA framework performs similarly to and sometimes better than currently available software for fitting GAMs. for this article are available online.

关键词： generalized additive models Mixed models Penalized splines Smoothing parameter

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Premium small scale: the trap fishery for Plesionika narval (Decapoda, Pandalidae) in the eastern Mediterranean Sea

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HYDROBIOLOGIA 2019年第1期826卷 279-290页

作者： Vasilakopoulos, Paraskevas Maravelias, Christos D. Anastasopoulou, Aikaterini Kapiris, Konstantinos Smith, Christopher J. Kalogirou, Stefanos Hellen Ctr Marine Res Inst Marine Biol Resources & Inland Waters 46-7 Km Athens Sounio Ave Anavyssos 19013 Greece European Commiss Joint Res Ctr Directorate Sustainable Resources D Unit Water & Marine Resources D 02 Via Enrico Fermi 2749 I-21027 Ispra VA Italy Hellen Ctr Marine Res Inst Marine Biol Resources & Inland Waters POB 2214 Iraklion 71003 Crete Greece Hellen Ctr Marine Res Inst Marine Biol Resources & Inland Waters Hydrobiol Stn Rhodes Rhodes Greece

Small-scale fisheries (SSFs) constitute a substantial component of European fisheries and have a high socioeconomic importance, especially for remote insular areas. Traps produce catches of high quality and value, associated with limited bycatch and low habitat impact. Long-standing trap SSFs in both the Mediterranean and the Atlantic showcase the potential of such SSFs to support remote fishing communities;however, trap SSFs remain relatively understudied. Here, we investigate the spatial and temporal dynamics of a Greek trap SSF targeting Plesionika narval (Fabricius, 1787) in the eastern Mediterranean, by means of generalized additive models fitted on fishers' logbook data from 2005 to 2014. The dynamics of both catch per unit effort (CPUE) and profits suggest a pronounced seasonality for this fishery, while there are also signs of local overexploitation in the traditional fishing grounds. Additionally, small vessels (< 12 m) report higher CPUEs than larger vessels. Our results point to management measures that could improve the sustainability of this valuable SSF, such as changes in the spatial and temporal allocation of fishing effort, and in fleet composition. The insights gained from this study are relevant to other localized trap SSFs and illustrate the socioeconomic potential of such fisheries for remote fishing communities.

关键词： Dodecanese generalized additive models Logbook data Narwal shrimp Small-scale fisheries

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Response of Scotian Shelf silver hake (Merluccius bilinearis) to environmental variability

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FISHERIES OCEANOGRAPHY 2019年第3期28卷 256-272页

作者： Reed, Daniel Plourde, Stephane Cook, Adam Pepin, Pierre Casault, Benoit Lehoux, Caroline Johnson, Catherine Fisheries & Oceans Canada Bedford Inst Oceanog 1 Challenger DrPOB 1006 Dartmouth NS B2Y 4A2 Canada Fisheries & Oceans Canada Inst Maurice Lamontagne Mont Joli PQ Canada Fisheries & Oceans Canada Northwest Atlantic Fisheries Ctr St John NF Canada

Commercially-exploited fish populations are not only shaped by fishing pressure, but also by the dynamics of their environment. By quantifying the influence of environmental variability, fisheries management advice can be improved and uncertainties reduced. To this end, we developed statistical models of the response of Scotian Shelf silver hake stock metrics to variability in zooplankton community composition and phenology over the past 18 years and in the physical environment since 1985. Dominant modes of variability in these pelagic habitat indicators were characterized using principal component analysis, and the relationships of silver hake condition, abundance, and recruitment to pelagic habitat variability were assessed using generalized additive models. Condition was largely modulated by the onset and duration of the spring bloom, which controls food availability. In contrast, adult abundance was governed by composition of the zooplankton community and bottom-water temperature, which dictates the distribution of silver hake. Finally, recruitment was affected by both thermal conditions and food availability. Our results presented here form the basis for qualitative assessment of ecosystem attributes and the influence on silver hake stock productivity.

关键词： adult abundance condition environmental variability generalized additive models recruitment Scotian Shelf silver hake

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Maintaining production while reducing local and global environmental emissions in dairy farming

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JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020年 272卷 111054页

作者： Soteriades, Andreas D. Foskolos, Andreas Styles, David Gibbons, James M. Bangor Univ Sch Nat Sci Deiniol Rd Bangor LL57 2UW Gwynedd Wales Bangor Univ Sir William Roberts Ctr Sustainable Land Use Deiniol Rd Bangor LL57 2DG Gwynedd Wales Univ Thessaly Dept Anim Sci Campus Gaiopolis Larisa 41110 Greece Aberystwyth Univ IBERS Aberystwyth SY23 3EB Dyfed Wales Univ Limerick Sch Engn Limerick V94 T9PX Ireland

While milk is a major agricultural commodity, dairy farming also supports a large share of global beef production. In Life Cycle Assessment (LCA) studies of dairy farming systems, dairy-beef production is often ignored or 'allocated off, which may give a distorted view of production efficiencies. This study combines LCA with Data Envelopment Analysis (DEA) to develop an indicator of eco-efficiency for each of 738 UK dairy farms (3624 data points in 15 years) that aggregates multiple burdens and expresses them per unit of milk and dairy-beef produced. Within the DEA framework, the importance (weight) of dairy-beef relative to milk is iteratively increased to quantify the environmental losses from heavily focussing on milk-production, via e.g. higher yields per cow, with consequent lower burdens per unit of milk, yet with lower dairy-beef production levels, where burdens for beef production are externalized. Then, the relationship between DEA eco-efficiency and a series of indicators of dairy farming intensity at animal- and farm-levels was studied with generalized additive models (GAM). For all sets of DEA weights (proportion of deviance explained ranged between 68% and 82%) indicate that milk yield per cow and forage area, and larger dairy herds all have a positive effect on eco-efficiency, while concentrate fed per unit of milk and the forage area both have a negative effect (p < 0.05 for all modelled relationships). These findings suggest that more intensive and consolidated dairy farms can positively impact on eco-efficiency. However, as the DEA weight for dairy-beef relative to milk increases, the relationship between environmental efficiency and farming specialization (expressed as L milk per kg dairy-beef produced) reverses from positive to negative. In conclusion, dairy-beef production is pivotal in determining the wider environmental efficiency of dairy (and ruminant food) systems, and its under-representation in efficiency studies has generated a misleading

关键词： Life Cycle Assessment Dairy-beef production Production intensity Commercial farm panel data Data Envelopment Analysis generalized additive models

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Variational Message Passing for Elaborate Response Regression models

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BAYESIAN ANALYSIS 2019年第2期14卷 371-398页

作者： McLean, M. W. Wand, M. P. Univ Technol Sydney Sch Math & Phys Sci POB 123 Broadway 2007 Australia

We build on recent work concerning message passing approaches to approximate fitting and inference for arbitrarily large regression models. The focus is on regression models where the response variable is modeled to have an elaborate distribution, which is loosely defined to mean a distribution that is more complicated than common distributions such as those in the Bernoulli, Poisson and Normal families. Examples of elaborate response families considered here are the Negative Binomial and t families. Variational message passing is more challenging due to some of the conjugate exponential families being non-standard and numerical integration being needed. Nevertheless, a factor graph fragment approach means the requisite calculations only need to be done once for a particular elaborate response distribution family. Computer code can be compartmentalized, including that involving numerical integration. A major finding of this work is that the modularity of variational message passing extends to elaborate response regression models.

关键词： Bayesian computing factor graph generalized additive models generalized linear mixed models mean field variational Bayes support vector machine classification

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Spatial segregation of striped marlin (Kajikia audax) by size in the eastern Pacific Ocean

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FISHERIES OCEANOGRAPHY 2019年第2期28卷 203-211页

作者： Acosta-Pachon, Tatiana A. Muzquiz-Villalobos, Mariana L. Ortega-Garcia, Sofia Martinez-Rincon, Raul O. Ctr Invest Biol Noroeste CIBNOR La Paz Mexico Inst Politecn Nacl CICIMAR Dept Pesquerias & Biol Marina La Paz Mexico CONACYT Ctr Invest Biol Noroeste CIBNOR La Paz Mexico

Striped marlin (Kajikia audax) is an epipelagic fish distributed in oceanic and coastal waters of the Pacific Ocean. This species is usually found in warm and coastal waters with high primary productivity. The main goal of this study was to describe the spatial segregation of striped marlin by average Eye-Fork length (EFL) in the eastern Pacific Ocean (EPO) and its relationship with environmental variables using EFL data obtained from tuna purse-seining and generalized additive models (GAMs). The model suggested that larger individuals of striped marlin were more likely to be found in waters with high Chlorophyll-a concentration (>2 mg/m(3)) and with temperatures lower than 25 degrees C, within a region known as the "cold tongue" and the Humboldt current system, while smaller individuals were more likely to be found in warmer and low productive areas within a region known as the "warm pool of the EPO." We observed that set type caused a large variation on average EFL of striped marlin;larger fish were captured in sets associated with floating objects (natural and manmade), while smaller fish were captured in sets associated with dolphins. Despite this, our findings suggest that striped marlin has a latitudinal gradient in average EFL;larger individuals occurred predominantly south of 10 degrees N, while smaller ones occurred predominantly in coastal waters between 10 degrees N and 20 degrees N, thus demonstrating a spatial segregation of the species affected by its maturity stage.

关键词： generalized additive models satellite imagery tuna purse-seine fishery

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Spatiotemporal patterns and environmental drivers of total and active bacterial abundances in Lake Taihu, China

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ECOLOGICAL INDICATORS 2020年 114卷

作者： Xie, Guijuan Tang, Xiangming Shao, Keqiang Hu, Yang Liu, Hao Martin, Robbie M. Gao, Guang Chinese Acad Sci Nanjing Inst Geog & Limnol State Key Lab Lake Sci & Environm Taihu Lab Lake Ecosyst Res Nanjing 210008 Peoples R China Univ Chinese Acad Sci Beijing 100049 Peoples R China Univ Tennessee Dept Microbiol Knoxville TN 37996 USA

Bacteria are a key component in lake ecosystems, playing a crucial role in driving biogeochemical and energy fluxes. In lake biomonitoring, false alarms have often been triggered due to the presence of abundant dead or dormant bacterial cells. Thus, quantification of the metabolically active and dormant cells is required for effective biomonitoring. In this study, 120 sites were seasonally sampled in a large, shallow, eutrophic lake (Taihu, China) to quantify the total bacterial (TB) and active bacterial (AB) abundances and explore their spatiotemporal distribution. generalized additive models (GAMS) were used to identify the major environmental drivers of TB and AB dynamics. TB ranged from 7.57 x 10(4) to 1.84 x 10(8) cells mL(-1), while AB ranged from 4.42 x 10(3) to 5.56 x 10(6) cells mL(-1). The proportion of AB was significantly higher in May (mean: 18.7%;cyanobacterial bloom thriving season) than in January or September (6.8% and 4.7%, respectively). GAMS indicated that dissolved oxygen, total dissolved nitrogen (TDN), total dissolved phosphorus and turbidity explained 47.8% of the TB variation, while TDN, dissolved organic carbon, water temperature and total phosphorus explained 72.7% of the AB variation. Our study showed that nutrients and physical factors are the major drivers of the TB and AB abundance variations in Lake Taihu. Bacterial responses to environmental variation were mostly nonlinear. The high proportion of AB variation (72.7%) explained by environmental parameters indicates that active bacteria are more sensitive to environmental changes and could be more effective bioindicators for long-term monitoring in shallow eutrophic lakes.

关键词： Total bacteria Active bacteria generalized additive models CTC Lake Taihu Eutrophic

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Time scales of external loading and spatial heterogeneity in nutrients-chlorophyll a response: Implication on eutrophication control in a large shallow lake

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ECOLOGICAL ENGINEERING 2020年 142卷

作者： Xu, Tao Yang, Tao Xiong, Manling Hohai Univ Ctr Global Change & Water Cycle State Key Lab Hydrol Water Resources & Hydraul En Nanjing 210098 Jiangsu Peoples R China

Nutrient over-enrichment of phosphorus (P) and nitrogen (N) makes phytoplankton proliferate, and is closely linked to algal blooms. Identifying effects of nutrients on algal biomass is necessary for eutrophication control. Long term (1994-2018) monitoring data of chlorophyll a (Chl-a), in-lake nutrient concentrations, and external phosphorus loading were leveraged in four ecological zones of Lake Okeechobee. generalized additive models (GAMs) were developed to detect the response of Chl-a to nutrients. Term of cumulative loading with different time scales was added for the first time into GAMs to study the legacy effect of P accumulation. We find that the added term of cumulative total phosphorus (TP) loading integrated over four years to one decade produced the GAM model with the best explanatory power. This result suggests that the long-term TP loading, rather than short-term external loading, has a more significant role on algal biomass in Lake Okeechobee. Our study also demonstrated the inhibition effect of ambient TP concentration and cumulative TP loading on Chl-a at their high values, while a positive impact of total nitrogen concentration in most circumstances. In addition, a threshold value of nitrate and nitrite in the response curve indicated the nitrogen fixing ability of some algae species. These findings imply that the delayed effects of restoration strategies can be up to one or two decades after external phosphorus loading reduction, and that inhibition phenomenon during high TP concentrations and cumulative loadings should be paid attention to when dealing with eutrophication problems in large and shallow lakes.

关键词： Algal biomass Cumulative external loading generalized additive models Timescale Nonlinear response

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