Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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The way forward : Can connectivity be useful to design better measuring and modelling schemes for water and sediment dynamics?
Keesstra, Saskia ; Nunes, Joao P. ; Saco, Patricia ; Parsons, Tony ; Poeppl, Ronald ; Masselink, Rens ; Cerdà, Artemi - \ 2018
Science of the Total Environment 644 (2018). - ISSN 0048-9697 - p. 1557 - 1572.
Agricultural impacts - Boundary conditions - Catchment systems - Co-evolution - Connectivity - Fire effects - Management - Measuring and modelling approaches - Pollutant transport

For many years, scientists have tried to understand, describe and quantify water and sediment fluxes, with associated substances like pollutants, at multiple scales. In the past two decades, a new concept called connectivity has been used by Earth Scientists as a means to describe and quantify the influences on the fluxes of water and sediment on different scales: aggregate, pedon, location on the slope, slope, watershed, and basin. A better understanding of connectivity can enhance our comprehension of landscape processes and provide a basis for the development of better measurement and modelling approaches, further leading to a better potential for implementing this concept as a management tool. This paper provides a short review of the State-of-the-Art of the connectivity concept, from which we conclude that scientists have been struggling to find a way to quantify connectivity so far. We adapt the knowledge of connectivity to better understand and quantify water and sediment transfers in catchment systems. First, we introduce a new approach to the concept of connectivity to study water and sediment transfers and the associated substances. In this approach water and sediment dynamics are divided in two parts: the system consists of phases and fluxes, each being separately measurable. This approach enables us to: i) better conceptualize our understanding of system dynamics at different timescales, including long timescales; ii) identify the main parameters driving system dynamics, and devise monitoring strategies which capture them; and, iii) build models with a holistic approach to simulate system dynamics without excessive complexity. Secondly, we discuss the role of system boundaries in designing measurement schemes and models. Natural systems have boundaries within which sediment connectivity varies between phases; in (semi-)arid regions these boundaries can be far apart in time due to extreme events. External disturbances (eg. climate change, changed land management) can change these boundaries. It is therefore important to consider the system state as a whole, including its boundaries and internal dynamics, when designing and implementing comprehensive monitoring and modelling approaches. Connectivity is a useful tool concept for scientists that must be expanded to stakeholder and policymakers.

Towards acoustic monitoring of a mixed demersal fishery based on commercial data: The case of the Northern Demersal Scalefish Fishery (Western Australia)
Gastauer, Sven ; Scoulding, Ben ; Parsons, Miles - \ 2017
Fisheries Research 195 (2017). - ISSN 0165-7836 - p. 91 - 104.
Ongoing monitoring of complex, mixed species environments is a challenging task. In this study, the potential of acoustic and catch data collected aboard a commercial fishing vessel, in combination with geostatistical variance estimates, are explored as a means to derive information on the distribution and abundance of key species groups within selected fishing regions. The FV Carolina M, a trap fishing vessel which operates in waters off Broome, Western Australia, in the Northern Demersal Scalefish Fishery, was equipped with Simrad ES70 echosounders, operated at 38 and 120 kHz. Optical recordings of catch were also obtained, in addition to the acoustic data, during routine fishing operations in 2014. Three regions, where both optical and acoustic datasets were available, were selected for analysis. Geostatistical conditional simulations were used to combine acoustic density information with species composition proportions and length distributions within the catch. For each of the input datasets 250 simulations were conducted, from which individual and combined sampling CVs were derived. Conversion of acoustic densities into abundance estimates was achieved through application of target strength to length relationships (TS-L). Where TS-L was unavailable in the literature for a particular species it was estimated through a Kirchhoff-ray mode model. TS-L equations were estimated for rankin cod (Epinephelus multinotatus)(TSRC = 20 log10(L) − 79.6), triggerfish (Balistidae) (TSTF = 20 log10(L) − 77.7) and spangled emperor (Lethrinus nebulosus) (TSSE = 20 log10(L) − 70.8) at 38 kHz. Sampling error was found to be generally low for catch proportions (<12%) and acoustic densities (<10%). Total sampling error CV for species group abundances within each of the three regions was 9%–38%, which is similar to typical estimates reported for acoustic surveys.
An Unsupervised Acoustic Description of Fish Schools and the Seabed in Three Fishing Regions Within the Northern Demersal Scalefish Fishery (NDSF, Western Australia)
Gastauer, Sven ; Scoulding, Ben ; Parsons, Miles - \ 2017
Acoustics Australia 45 (2017)2. - ISSN 0814-6039 - p. 363 - 380.
Fisheries acoustics is now a standard tool for monitoring marine organisms. Another use of active-acoustics techniques is the potential to qualitatively describe fish school and seafloor characteristics or the distribution of fish density hotspots. Here, we use a geostatistical approach to describe the distribution of acoustic density hotspots within three fishing regions of the Northern Demersal Scalefish Fishery in Western Australia. This revealed a patchy distribution of hotspots within the three regions, covering almost half of the total areas. Energetic, geometric and bathymetric descriptors of acoustically identified fish schools were clustered using robust sparse k-means clustering with a Clest algorithm to determine the ideal number of clusters. Identified clusters were mainly defined by the energetic component of the school. Seabed descriptors considered were depth, roughness, first bottom length, maximum Sv, kurtosis, skewness and bottom rise time. The ideal number of bottom clusters (maximisation rule with D-Index, Hubert Score and Weighted Sum of Squares), following the majority rule, was three. Cluster 1 (mainly driven by depth) was the sole type present in Region 1, Cluster 2 (mainly driven by roughness and maximum Sv) dominated Region 3, while Region 2 was split up almost equally between Cluster 2 and 3. Detection of indicator species for the three seabed clusters revealed that the selected clusters could be related to biological information. Goldband snapper and miscellaneous fish were indicators for Cluster 1; Cods, Lethrinids, Red Emperor and other Lutjanids were linked with Cluster 2, while Rankin Cod and Triggerfish were indicators for Cluster 3.
Estimates of variability of goldband snapper target strength and biomass in three fishing regions within the Northern Demersal Scalefish Fishery (Western Australia)
Gastauer, Sven ; Scoulding, Ben ; Parsons, Miles - \ 2017
Fisheries Research 193 (2017). - ISSN 0165-7836 - p. 250 - 262.
Error estimates - Fisheries acoustics - Fishing vessel - Geostatistics - Goldband snapper - NDSF - Target strength
Goldband snapper (Pristipomoides multidens) is an ecologically and economically important species in the Northern Demersal Scalefish Fishery (NDSF). The Carolina M, a trap fishing vessel operating in the NDSF, was equipped with Simrad ES70 echosounders, operated at 38 and 120 kHz. In 2014 acoustic data, in combination with optical recordings of the catch, were opportunistically collected during routine fishing operations. In December 2014 pure, low density goldband snapper schools were observed on the echograms. In situ target strength (TS) estimates were derived and linked to length distributions of catch information with the curve fitting method. Estimated TS-Length (L) at 38 kHz was 20.1 log10(L)-70.5 and 16.4 log10(L)-77 at 120 kHz. Three fishing grounds, where near simultaneously recorded acoustic and optical information was available were selected. Fish school densities observed within the 38 kHz acoustic data were disaggregated according to catch proportions using kriging. Goldband snapper density estimates ranged between 9518 individuals per nmi2 in the high-density fishing region and 2512 and 945 individuals per nmi2 in the two low density fishing regions. Sampling variance was estimated using geostatistics (coefficient of variance, CV = 10–20.9%). Other errors considered were signal-to-noise ratio (CV < 1%), variation in the acoustic signal due to fluctuations in temperature and salinity (CV = 0.5–1.15%), effects of diurnal vertical migration and variability of catch information (CV = 1.2–2%). A total CV of 28.2–50.6% was estimated for all considered sources, for the three fishing regions.
Scenarios in tropical forest degradation : Carbon stock trajectories for REDD+
Andrade, Rafael B. ; Balch, Jennifer K. ; Parsons, Amoreena L. ; Armenteras, Dolors ; Roman-Cuesta, Rosa Maria ; Bulkan, Janette - \ 2017
Carbon Balance and Management 12 (2017)1. - ISSN 1750-0680
Background: Human-caused disturbance to tropical rainforests-such as logging and fire-causes substantial losses of carbon stocks. This is a critical issue to be addressed in the context of policy discussions to implement REDD+. This work reviews current scientific knowledge about the temporal dynamics of degradation-induced carbon emissions to describe common patterns of emissions from logging and fire across tropical forest regions. Using best available information, we: (i) develop short-term emissions factors (per area) for logging and fire degradation scenarios in tropical forests; and (ii) describe the temporal pattern of degradation emissions and recovery trajectory post logging and fire disturbance. Results: Average emissions from aboveground biomass were 19.9 MgC/ha for logging and 46.0 MgC/ha for fire disturbance, with an average period of study of 3.22 and 2.15 years post-disturbance, respectively. Longer-term studies of post-logging forest recovery suggest that biomass accumulates to pre-disturbance levels within a few decades. Very few studies exist on longer-term (>10 years) effects of fire disturbance in tropical rainforests, and recovery patterns over time are unknown. Conclusions: This review will aid in understanding whether degradation emissions are a substantial component of country-level emissions portfolios, or whether these emissions would be offset by forest recovery and regeneration.
Linking Statistical and Ecological Theory : Hubbell's Unified Neutral Theory of Biodiversity as a Hierarchical Dirichlet Process: This paper addresses the issue of a species occupying a specific ecological niche by introducing a new algorithmic model that overcomes shortcomings of the traditional neutral models
Harris, Keith ; Parsons, Todd L. ; Ijaz, Umer Z. ; Lahti, Leo ; Holmes, Ian ; Quince, Christopher - \ 2017
Proceedings of the IEEE 105 (2017)3. - ISSN 0018-9219 - p. 516 - 529.
Diversity - ecological modelling - hierarchical Dirichlet process - Hubbell's unified neutral theory of biodiversity - microbial communities

Neutral models which assume ecological equivalence between species provide null models for community assembly. In Hubbell's unified neutral theory of biodiversity (UNTB), many local communities are connected to a single metacommunity through differing immigration rates. Our ability to fit the full multisite UNTB has hitherto been limited by the lack of a computationally tractable and accurate algorithm. We show that a large class of neutral models with this mainland-island structure but differing local community dynamics converge in the large population limit to the hierarchical Dirichlet process. Using this approximation we developed an efficient Bayesian fitting strategy for the multisite UNTB. We can also use this approach to distinguish between neutral local community assembly given a nonneutral metacommunity distribution and the full UNTB where the metacommunity too assembles neutrally. We applied this fitting strategy to both tropical trees and a data set comprising 570 851 sequences from 278 human gut microbiomes. The tropical tree data set was consistent with the UNTB but for the human gut neutrality was rejected at the whole community level. However, when we applied the algorithm to gut microbial species within the same taxon at different levels of taxonomic resolution, we found that species abundances within some genera were almost consistent with local community assembly. This was not true at higher taxonomic ranks. This suggests that the gut microbiota is more strongly niche constrained than macroscopic organisms, with different groups adopting different functional roles, but within those groups diversity may at least partially be maintained by neutrality. We also observed a negative correlation between body mass index and immigration rates within the family Ruminococcaceae. This provides a novel interpretation of the impact of obesity on the human microbiome as a relative increase in the importance of local growth versus external immigration within this key group of carbohydrate degrading organisms.

Urban bird conservation : presenting stakeholder-specific arguments for the development of bird-friendly cities
Snep, Robbert P.H. ; Kooijmans, Jip Louwe ; Kwak, Robert G.M. ; Foppen, Ruud P.B. ; Parsons, Holly ; Awasthy, Monica ; Sierdsema, Henk L.K. ; Marzluff, John M. ; Fernandez-Juricic, Esteban ; Laet, Jenny de - \ 2016
Urban Ecosystems 19 (2016)4. - ISSN 1083-8155 - p. 1535 - 1550.
Argument - Conservation strategy - Stakeholder - Urban biodiversity - Urban bird conservation - Urban green

Following the call from the United Nations Convention on Biological Diversity “Cities & Biodiversity Outlook” project to better preserve urban biodiversity, this paper presents stakeholder-specific statements for bird conservation in city environments. Based upon the current urban bird literature we focus upon habitat fragmentation, limited habitat availability, lack of the native vegetation and vegetation structure as the most important challenges facing bird conservation in cities. We follow with an overview of the stakeholders in cities, and identify six main groups having the greatest potential to improve bird survival in cities: i) urban planners, urban designers and (landscape) architects, ii) urban developers and engineers, iii) homeowners and tenants, iv) companies and industries, v) landscaping and gardening firms, vi) education professionals. Given that motivation to act positively for urban birds is linked to stakeholder-specific advice, we present ten statements for bird-friendly cities that are guided by an action perspective and argument for each stakeholder group. We conclude with a discussion on how the use of stakeholder-specific arguments can enhance and rapidly advance urban bird conservation action.

Target strength estimates of red emperor (Lutjanus sebae) with Bayesian parameter calibration
Gastauer, Sven ; Scoulding, Ben ; Fassler, Sascha ; Benden, Daniel P.L.D. ; Parsons, Miles - \ 2016
Aquatic Living Resources 29 (2016)3. - ISSN 0990-7440
Bayesian inference - Fisheries acoustics - KRM - Lutjanus sebae - Target Strength - Vessel of opportunity

Red emperor (Lutjanus sebae) is a long-lived tropical demersal snapper which is widely distributed in the Western Pacific and Indian Ocean. Despite the commercial and recreational importance of the species for the Northern Demersal Scalefish Fishery off the Northwest coast of Western Australia, we still lack a thorough understanding of its distribution and abundance in the area. To better understand the acoustic scattering properties of red emperor its acoustic backscattering characteristics were modelled based on swimbladder and body morphology, determined using computed tomography scans. A Kirchhoff-ray mode approximation was coupled with empirical (ex situ) measurements of target strength (TS) obtained from a 38 and 120 kHz split-beam echosounder on board a fishing vessel. Bayesian methods were used for model parameter calibration, which provided uncertainty estimates for some of the TS-model parameters. The derived TS-length relationships were 19.7log 10(L)-75.5 (C.I. 5.9 dB) at 120 kHz and 14.6 log10(L)-64.9 (C.I. 5.8 dB) at 38 kHz. The study demonstrated that small commercial fishing vessels can be used to conduct ex situ experiments and target strength modelling can be effectively based on computer tomography scans. This relatively low cost approach could be applied to other species.

Analysis of fullerenes in soils samples collected in The Netherlands
Carboni, Andrea ; Helmus, Rick ; Emke, Erik ; Brink, Nico van den; Parsons, John R. ; Kalbitz, Karsten ; Voogt, Pim de - \ 2016
Environmental Pollution 219 (2016). - ISSN 0269-7491 - p. 47 - 55.
Fullerenes - Monitoring - Soil - Terrestrial environment - Transformation products

Fullerenes are carbon based nanoparticles that may enter the environment as a consequence of both natural processes and human activities. Although little is known about the presence of these chemicals in the environment, recent studies suggested that soil may act as a sink. The aim of the present work was to investigate the presence of fullerenes in soils collected in The Netherlands. Samples (n = 91) were taken from 6 locations and analyzed using a new developed LC-QTOF-MS method. The locations included highly trafficked and industrialized as well as urban and natural areas. In general, C60 was the most abundant fullerene found in the environment, detected in almost a half of the samples and at concentrations in the range of ng/kg. Other fullerenes such as C70 and an unknown structure containing a C60 cage were detected to a lower extent. The highest concentrations were found in the proximity of combustion sites such as a coal power plant and an incinerator, suggesting that the nanoparticles were unintentionally produced during combustions processes and reached the soil through atmospheric deposition. Consistent with other recent studies, these results show that fullerenes are widely present in the environment and that the main route for their entrance may be due to human activities. These data will be helpful in the understanding of the distribution of fullerenes in the environment and for the study of their behavior and fate in soil.

Properties of a clay soil from 1.5 to 3.5 years after biochar application and the impact on rice yield
Carvalho, M.T.M. ; Madari, B.E. ; Bastiaans, L. ; Oort, P.A.J. van; Leal, W.G.O. ; Heinemann, A.B. ; Silva, M.A.S. da; Maia, A.H.N. ; Parsons, D. ; Meinke, H. - \ 2016
Geoderma 276 (2016). - ISSN 0016-7061 - p. 7 - 18.
Crop yield - Soil C - Soil water retention capacity - Wood biochar

We assessed the impact of a single application of wood biochar on soil chemical and physical properties and aerobic rice grain yield on an irrigated kaolinitic clay Ferralsol in a tropical Savannah. We used linear mixed models to analyse the response of soil and plant variables to application rates of biochar (0, 8, 16 and 32 t ha-1) and mineral N fertilization (0, 30, 60 and 90 kg N ha-1), and their interaction. The response was analysed within three aerobic rice-growing seasons (S), equivalent to 1.5, 2.5 and 3.5 years after biochar application (S1.5, S2.5 and S3.5). The fraction of oxidisable C in soil increased with biochar application rate, irrespective of N fertilization, at S2.5 and S3.5, whereas the rice stress-free available water (soil water retention between -6 and -100 kPa) decreased with biochar application rate at S1.5 and S2.5. Rice grain yield and yield components varied with the seasons according to the changes in soil properties and weather conditions. A single application rate up to 32 t ha-1 of the wood biochar type used in this study had no impact on aerobic rice yield increase on a kaolinitic clay Ferralsol under the climatic conditions of the Brazilian Savannah prone to dry spells. Most likely, the beneficial effects of wood biochar on soil chemical properties on rice production were offset by a decrease in soil water retention capacity and N uptake by the crop.

From bioavailability science to regulation of organic chemicals in Session Bioavailability
Harmsen, J. ; Ortega Calvo, J.J. ; Parsons, J.R. ; Semple, K.T. - \ 2015
Introduction to special issue on connectivity in water and sediment dynamics
Parsons, A.J. ; Bracken, L. ; Peopple, R. ; Wainwright, J. ; Keesstra, S.D. - \ 2015
Earth Surface Processes and Landforms 40 (2015)9. - ISSN 0197-9337 - p. 1275 - 1277.
Connectivity has emerged in recent years as a significant conceptual framework within which to address the spatial and temporal variability in runoff and sediment transport. This special issue draws together several of the papers that were presented in the session “Connectivity in water and sediment dynamics: how do we move forwards?” at the 2012 General Assembly of the European Geosciences Union in Vienna, Austria. The papers submitted for this special issue fall into three groups: empirical studies, modelling studies, and conceptual development. Although it may be evident that the concept of connectivity helps us to express the complexity (in terms of water and sediment yields) of landscape responses to rainfall inputs, does it improve our ability to understand or predict those responses? There would still seem to be some way to go in connectivity research before this nagging concern can be assuaged. That it can be will undoubtedly be an important task for a number of ongoing research initiatives.
From Bioavailability Science to Regulation of Organic Chemicals
Ortega-Calvo, J.J. ; Harmsen, J. ; Parsons, J.R. ; Semple, K.T. ; Aitken, M.D. ; Ajao, C. ; Eadsforth, C. ; Galay-Burgos, M. ; Naidu, R. ; Oliver, R. ; Peijnenburg, W.J.G.M. ; Römbke, J. ; Streck, G. ; Versonnen, B. - \ 2015
Environmental Science and Technology 49 (2015)17. - ISSN 0013-936X - p. 10255 - 10264.
The bioavailability of organic chemicals in soil and sediment is an important area of scientific investigation for environmental scientists, although this area of study remains only partially recognized by regulators and industries working in the environmental sector. Regulators have recently started to consider bioavailability within retrospective risk assessment frameworks for organic chemicals; by doing so, realistic decision-making with regard to polluted environments can be achieved, rather than relying on the traditional approach of using total-extractable concentrations. However, implementation remains difficult because scientific developments on bioavailability are not always translated into ready-to-use approaches for regulators. Similarly, bioavailability remains largely unexplored within prospective regulatory frameworks that address the approval and regulation of organic chemicals. This article discusses bioavailability concepts and methods, as well as possible pathways for the implementation of bioavailability into risk assessment and regulation; in addition, this article offers a simple, pragmatic and justifiable approach for use within retrospective and prospective risk assessment
Strategic double cropping on Vertisols: A viable rainfed cropping option in the Indian SAT to increase productivity and reduce risk
Nageswara Rao, V. ; Meinke, H.B. ; Craufurd, P.Q. ; Parsons, D. ; Kropff, M.J. ; Anten, N.P.R. ; Wani, S.P. ; Rego, T.J. - \ 2015
European Journal of Agronomy 62 (2015). - ISSN 1161-0301 - p. 26 - 37.
nitrogen - field - soil - management - tillage - residue - maize - wheat - yield - corn
Our study suggests the possibility for transformational change in the productivity and risk profile of someof India’s rainfed cropping systems. In the semi-arid regions of Southern India, farmers traditionally cropsorghum or chickpea on Vertisols during the post-rainy season, keeping the fields fallow during the rainyseason. This practice avoids land management problems, but limits the potential for crop intensifica-tion to increase systems productivity. A long-term (15 year) experiment at ICRISAT demonstrated thatcropping during the rainy season is technically feasible, and that grain productivity of double croppedsorghum + chickpea (SCP–SCP) and mung bean + sorghum (MS–MS) sequential systems were higher thantheir conventional counterparts with rainy season fallow, i.e. fallow + post-rainy sorghum (FS–FS) and fal-low + post-rainy chickpea (FS–FCP). Without N application, mean grain yield of post-rainy sorghum in theMS–MS system was significantly greater (2520 kg ha-1per two-year rotation) than in the FS–FS system(1940 kg ha-1per two-year rotation), with the added benefit of the mung bean grain yield (1000 kg ha-1per two-year rotation) from the MS–MS system. In the SCP–SCP system the additional grain yield ofrainy sorghum (3400 kg ha-1per two-year rotation) ensured that the total productivity of this systemwas greater than all other systems. Double cropping MS–MS and SCP–SCP sequential systems had sig-nificantly higher crop N uptake compared to traditional fallow systems at all rates of applied nitrogen(N).The intensified MS–MS and SCP–SCP sequential systems without any N fertilizer applied recorded amuch higher median gross profit of Rs. 20,600 (US $ 375) and Rs. 15,930 (US $ 290) ha-1yr-1, respectively,compared to Rs. 1560 (US $ 28) ha-1yr-1) with the FS–FS system. Applying 120 kg of N ha-1considerablyincreased the profitability of all systems, lifting median gross profits of the sorghum + chickpea systemover Rs. 60,000 (US $ 1091) ha-1yr-1and the conventional system to Rs. 20,570 (US $ 374) ha-1yr-1. Thegross profit margin analysis showed that nitrogen is a key input for improving productivity, particularlyfor the double cropping systems. However, traditional systems are unviable and risky without N appli-cation in the variable climates of the semi-arid tropics. Together, our results show that on Vertisols insemi-arid India, double cropping systems increase systems’ productivity, and are financially more pro-fitability and less risky than traditional fallow post-rainy systems while further benefits can be achievedthrough fertilizer application.
(Social) Norm Dynamics
Andrighetto, G. ; Castelfranchi, C. ; Mayor, E. ; McBreen, J. ; Lopez-Sanchez, M. ; Parsons, S. - \ 2013
In: Normative Multi-Agent systems / Adrighetto, G., Governatori, G., Noriega, P., van der Torre, L.W.N., Dagstuhl Publishing (Dagstuhl Follow-Ups 4) - ISBN 9783939897514 - p. 135 - 170.
Enhancing selective breeding for growth, slaughter traits and overall survival in rainbow trout (Oncorhynchus mykiss)
Sae-Lim, P. ; Komen, J. ; Kause, A. ; Martin, K.E. ; Crooijmans, R.P.M.A. ; Arendonk, J.A.M. van; Parsons, J.E. - \ 2013
Aquaculture 372-375 (2013). - ISSN 0044-8486 - p. 89 - 96.
polymorphic microsatellite markers - oreochromis-niloticus l. - cultured atlantic salmon - expressed sequence tags - carcass quality traits - genetic-parameters - body-weight - parental allocation - water temperature - 2-stage selection
Enhancing selection using two-stage selection is normally implemented by pre-selection for tagging weight (BWT) and by final selection for ungutted harvest weight (BWH) and thermal growth coefficient from tagging to harvest (TGCTH). However, selection on harvest traits, i.e., gutted weight (GBWH), visceral percentage (VISW%), condition factor (CFH), and overall survival (SURV), can be enhanced by exploiting correlated traits. It can be hypothesized that the efficiency of two-stage selection on genetic response in BWH and TGCTH is dependent on their genetic (rg) and phenotypic (rp) correlations with BWT and therefore dependent on the time point of pre-selection. The aims of this study were, first, to estimate genetic parameters (heritability: h2, rp, and rg) for BWT (7 months), BWS (weight at sorting, 9 months), BWH (14 months), TGCTH, GBWH, VISW%, CFH, and SURV. Second, these genetic parameters were used in two deterministic simulation studies; i) one- and two-stage selections to compare genetic responses in BWH and TGCTH, and ii) alternative selection indices using correlated traits to compare corresponding accuracy of selection (rIH) for slaughter traits, CFH, and SURV. Genetic parameters were estimated using an animal mixed model in ASReml on 2,041 fish records. The main results showed that, first, rg of BWT was 0.35 with BWH but - 0.25 with TGCTH, whereas the rg of BWS was 0.72 with BWH but 0.39 with TGCTH. Pre-selection for BWS led to genetic response of 54.15 g in BWH which was higher than the genetic response from pre-selection for BWT (51.90 g). Similarly, pre-selection on BWS enhanced correlated genetic response in TGCTH to 0.30 g(1/3)/°C*day. In contrast, pre-selection for BWT resulted in lower correlated genetic response in TGCTH of 0.20 g(1/3)/°C*day. It can be concluded that genetic improvement of BWH and TGCTH can be enhanced by postponing pre-selection to a later age. However, an optimal time point for tagging and pre-selection should be found to minimize common environmental effects and rearing costs during communal rearing of full-sibs. Second, including GBWH in a selection index can reduce unfavourable selection responses in VISW%. The GBWH is highly genetically correlated with BWH and can be easily indirectly selected. TGCTH is a good predictor for selection for lower VISW%, and higher SURV, but not for higher CFH. To control genetic changes in the condition factor, it should be included to the selection index.
Genotype-by-environment interaction for growth traits in rainbow trout: a continental scale study
Sae-Lim, P. ; Mulder, H.A. ; Komen, J. ; Kause, A. ; Arendonk, J.A.M. van; Martin, K.E. ; Parsons, J.E. - \ 2012
In: Book of Abstracts of the International symposium on genetics in aquaculture XI, 24-30 june 2012, Auburn University, Alabama, USA. - - p. 36 - 36.
Effect of high-sugar grasses on methane emissions simulated using a dynamic model
St-Pierre, J.L. ; Dijkstra, J. ; France, J. ; Parsons, A.J. ; Edwards, G.R. ; Rasmussen, S. ; Kebreab, E. ; Bannink, A. - \ 2012
Journal of Dairy Science 95 (2012)1. - ISSN 0022-0302 - p. 272 - 285.
perennial ryegrass cultivars - water-soluble carbohydrate - neutral detergent fiber - offered lolium-perenne - dairy-cows - milk-production - mechanistic model - lactating cow - in-vitro - nitrogen-utilization
High-sugar grass varieties have received considerable attention for their potential ability to decrease N excretion in cattle. However, feeding high-sugar grasses alters the pattern of rumen fermentation, and no in vivo studies to date have examined this strategy with respect to another environmental pollutant: methane (CH4). Modeling allows us to examine potential outcomes of feeding strategies under controlled conditions, and can provide a useful framework for the development of future experiments. The purpose of the present study was to use a modeling approach to evaluate the effect of high-sugar grasses on simulated CH4 emissions in dairy cattle. An extant dynamic, mechanistic model of enteric fermentation and intestinal digestion was used for this evaluation. A simulation database was constructed and analysis of model behavior was undertaken to simulate the effect of (1) level of water-soluble carbohydrate (WSC) increase in dietary dry matter, (2) change in crude protein (CP) and neutral detergent fiber (NDF) content of the plant with an increased WSC content, (3) level of N fertilization, and (4) presence or absence of grain feeding. Simulated CH4 emissions tended to increase with increased WSC content when CH4 was expressed as megajoules per day or percent of gross energy intake, but when CH4 was expressed in terms of grams per kilogram of milk, results were much more variable due to the potential increase in milk yield. As a result, under certain conditions, CH4 (g/kg of milk) decreased. The largest increases in CH4 emissions (MJ/d or % gross energy intake) were generally seen when WSC increased at the expense of CP in the diet and this can largely be explained by the representation in the model of the type of volatile fatty acid produced. Effects were lower when WSC increased at the expense of NDF, and intermediary when WSC increased at the expense of a mixture of CP and NDF. When WSC increased at the expense of NDF, simulated milk yield increased and, therefore, CH4 (g/kg of milk) tended to decrease. Diminished increases of CH4 (% gross energy intake or g/kg of milk) were simulated when DMI was increased with elevated WSC content. Simulation results suggest that high WSC grass, as a strategy to mitigate N emission, may increase CH4 emissions, but that results depend on the grass composition, DMI, and the units chosen to express CH4. Overall, this project demonstrates the usefulness of modeling for hypothesis testing in the absence of observed experimental results.
Defining desired genetic gains for rainbow trout breeding objective using analytic hierarchy process
Sae-Lim, P. ; Komen, J. ; Kause, A. ; Arendonk, J.A.M. van; Barfoot, A.J. ; Martin, K.E. ; Parsons, A.J. - \ 2012
Journal of Animal Science 90 (2012)6. - ISSN 0021-8812 - p. 1766 - 1776.
goal-programming approach - salmon salmo-salar - oncorhynchus-mykiss - atlantic salmon - environment interactions - sexual-maturity - body traits - fuzzy ahp - parameters - growth
Distributing animals from a single breeding program to a global market may not satisfy all producers, as they may differ in market objectives and farming environments. Analytic hierarchy process (AHP) is used to estimate preferences, which can be aggregated to consensus preference values using weighted goal programming (WGP). The aim of this study was to use an AHP-WGP based approach to derive desired genetic gains for rainbow trout breeding, and to study whether breeding trait preferences vary depending on commercial products and farming environments. Two questionnaires were sent out, Q-A and Q-B. Q-A was distributed to 178 farmers from 5 continents and used to collect information on commercial products and farming environments. In this questionnaire, farmers were asked to rank the 6 most important traits for genetic improvement from a list of 13 traits. Questionnaire B (Q-B) was sent to all farmers who responded to Q-A (53 in total). For Q-B, preferences of the 6 traits were obtained using pairwise comparison. Preference intensity was given in order to quantify (in % of a trait mean; G%) the degree to which one trait is preferred over the other. Individual preferences (Ind-P), social preferences (Soc-P), and consensus preferences (Con-P) were estimated using AHP and WGP. Desired gains were constructed by multiplying Con-P with G%. The analysis revealed that the 6 most important traits were thermal growth coefficient (TGC), survival (Surv), feed conversion ratio (FCR), condition factor (CF), fillet percentage (F%), and late maturation (LMat). Ranking of traits based on average Con-P values were Surv (0.271), FCR (0.246), TGC (0.246), LMat (0.090), F% (0.081), and CF (0.067). Corresponding desired genetic gains (in % of trait mean) were 1.63%, 1.87%, 1.67%, 1.29%, 0.06%, and 0.33%, respectively. The results from Con-P values show that trait preferences may vary for different types of commercial production or farming environments. This study demonstrated that combination of AHP and WGP can be used to derive desired gains for a breeding program, and to quantify differences due to variations market demand or production environment
Ecotoxicological assessment of grey water treatment systems with Daphnia magna and Chironomus riparius
Hernandez Leal, L. ; Soeter, A.M. ; Kools, S.A.E. ; Kraak, M.H.S. ; Parsons, J.R. ; Temmink, B.G. ; Zeeman, G. ; Buisman, C.J.N. - \ 2012
Water Research 46 (2012)4. - ISSN 0043-1354 - p. 1038 - 1044.
afvalwaterbehandeling - afvalwater - huishoudens - waterkwaliteit - bepaling - chironomus riparius - daphnia magna - ecotoxicologie - testen - biologische behandeling - fysisch-chemische behandeling - waste water treatment - waste water - households - water quality - determination - ecotoxicology - testing - biological treatment - physicochemical treatment - micropollutants - removal
In order to meet environmental quality criteria, grey water was treated in four different ways: 1) aerobic 2) anaerobic + aerobic 3) aerobic + activated carbon 4) aerobic + ozone. Since each treatment has its own specific advantages and disadvantages, the aim of this study was to compare the ecotoxicity of differently treated grey water using Chironomus riparius (96 h test) and Daphnia magna (48 h and 21d test) as test organisms. Grey water exhibited acute toxicity to both test organisms. The aerobic and combined anaerobic + aerobic treatment eliminated mortality in the acute tests, but growth of C. riparius was still affected by these two effluents. Post-treatment by ozone and activated carbon completely removed the acute toxicity from grey water. In the chronic toxicity test the combined anaerobic + aerobic treatment strongly affected D. magna population growth rate (47%), while the aerobic treatment had a small (9%) but significant effect. Hence, aerobic treatment is the best option for biological treatment of grey water, removing most of the toxic effects of grey water. If advanced treatment is required, the treatment with either ozone or GAC were shown to be very effective in complete removal of toxicity from grey water.
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