Variation in behaviour and growth of common sole : genetic and environmental influences

Common sole (Solea solea) has a high potential for commercial aquaculture because of its consumer popularity and high market values in Europe. However, a major economic constraint for the culture of sole is its slow and variable growth. The aim of this thesis was to investigate: 1) the importance of (non-) feeding behaviour of sole in relation to variation in growth; 2) the effect of (social and physical) environmental factors on behaviour, growth and the relation between them; 3) the existence of GE interaction regarding growth. Feeding consistency, swimming activity in the tank, and boldness during (novel environment and light avoidance) behavioural tests explained variation in feed intake and thereby growth of individually housed sole. For communally housed sole, behavioural factors derived from individual behavioural tests and sex also explained variation in growth. The motivation to bury was negatively related to growth, whereas the motivation to explore a novel environment was positively related. Social interactions, both in quality (i.e., size hierarchies) and in quantity (i.e.,stocking density), influenced (non-) feeding behaviour and growth of sole. High stocking density in sole reared without substrate results in more fish-fish interactions, which increases swimming activity, FCR and variation in growth. These conditions seem to induce social stress in sole, which is alleviated when sand is provided. Environmental factors which differ between nature and farming conditions, such as food type, sand and variability of environmental conditions, influenced individual behavioural responses of sole to a novel environment test but did not induce variation in growth. Results suggest that consistent relationships between behaviour and growth develop when fish are reared in stable barren environments but not when fish experience more variable, enriched/natural environments. The role of environmental factors in the relationship between (non)-feeding behaviour and growth was supported by strong genotype by environment interaction for growth of sole reared in a semi-natural or an intensive aquaculture environment. In conclusion, the effect of (non-) feeding behaviour on growth should be taken into account to foster progress in the farming of sole. Environmental factors (i.e., substrate, stocking density) that influence behaviour and growth should be used to optimize culture systems. Future genetic selection strategies should focus more on behavioural characteristics to select sole which will be able to cope and grow best in the different rearing conditions present in commercial aquaculture. </p

Tree-based ensembles unveil the microhabitat suitability for the invasive bleak (Alburnus alburnus L.) and pumpkinseed (Lepomis gibbosus L.): Introducing XGBoost to eco-informatics

[EN] Random Forests (RFs) and Gradient Boosting Machines (GBMs) are popular approaches for habitat suitability modelling in environmental flow assessment. However, both present some limitations theoretically solved by alternative tree-based ensemble techniques (e.g. conditional RFs or oblique RFs). Among them, eXtreme Gradient Boosting machines (XGBoost) has proven to be another promising technique that mixes subroutines developed for RFs and GBMs. To inspect the capabilities of these alternative techniques, RFs and GBMs were compared with: conditional RFs, oblique RFs and XGBoost by modelling, at the micro-scale, the habitat suitability for the invasive bleak (Alburnus alburnus L.) and pumpkinseed (Lepomis gibbosus L). XGBoost outperformed the other approaches, particularly conditional and oblique RFs, although there were no statistical differences with standard RFs and GBMs. The partial dependence plots highlighted the lacustrine origins of pumpkinseed and the preference for lentic habitats of bleak. However, the latter depicted a larger tolerance for rapid microhabitats found in run-type river segments, which is likely to hinder the management of flow regimes to control its invasion. The difference in the computational burden and, especially, the characteristics of datasets on microhabitat use (low data prevalence and high overlapping between categories) led us to conclude that, in the short term, XGBoost is not destined to replace properly optimised RFs and GBMs in the process of habitat suitability modelling at the micro-scale.This project had the support of Fundacion Biodiversidad, of Spanish Ministry for Ecological Transition. We want to thank the volunteering students of the Universitat Politecnica de Valencia, Marina de Miguel, Carlos A. Puig-Mengual, Cristina Barea, Rares Hugianu, and Pau Rodriguez. R. Munoz-Mas benefitted from a postdoctoral Juan de la Cierva fellowship from the Spanish Ministry of Science, Innovation and Universities (ref. FJCI-2016-30829). This research was supported by the Government of Catalonia (ref. 2017 SGR 548).Muñoz-Mas, R.; Gil-Martínez, E.; Oliva-Paterna, FJ.; Belda, E.; Martinez-Capel, F. (2019). Tree-based ensembles unveil the microhabitat suitability for the invasive bleak (Alburnus alburnus L.) and pumpkinseed (Lepomis gibbosus L.): Introducing XGBoost to eco-informatics. Ecological Informatics. 53:1-12. https://doi.org/10.1016/j.ecoinf.2019.100974S1125

Search for Blue Compact Dwarf Galaxies During Quiescence

Blue Compact Dwarf (BCD) galaxies are metal poor systems going through a major starburst that cannot last for long. We have identified galaxies which may be BCDs during quiescence (QBCD), i.e., before the characteristic starburst sets in or when it has faded away. These QBCD galaxies are assumed to be like the BCD host galaxies. The SDSS/DR6 database provides ~21500 QBCD candidates. We also select from SDSS/DR6 a complete sample of BCD galaxies to serve as reference. The properties of these two galaxy sets have been computed and compared. The QBCD candidates are thirty times more abundant than the BCDs, with their luminosity functions being very similar except for the scaling factor, and the expected luminosity dimming associated with the end of the starburst. QBCDs are redder than BCDs, and they have larger HII region based oxygen abundance. QBCDs also have lower surface brightness. The BCD candidates turn out to be the QBCD candidates with the largest specific star formation rate (actually, with the largest H_alpha equivalent width). One out of each three dwarf galaxies in the local universe may be a QBCD. The properties of the selected BCDs and QBCDs are consistent with a single sequence in galactic evolution, with the quiescent phase lasting thirty times longer than the starburst phase. The resulting time-averaged star formation rate is low enough to allow this cadence of BCD -- QBCD phases during the Hubble time.Comment: Accepted for publication in ApJ. 17 pages. 13 Fig

Combining literature-based and data-driven fuzzy models to predict brown trout (salmo trutta l.) spawning habitat degradation induced by climate change

[EN] A fuzzy rule-based system combining empirical data on hydraulic preferences and literature information on temperature requirements was used to foresee the brown trout (Salmo trutta L.) spawning habitat degradation induced by climate change. The climatic scenarios for the Cabriel River (Eastern Iberian Peninsula) corresponded to two Representative Concentration Pathways (4.5 and 8.5) for the short (2011¿2040) and mid (2041¿2070) term horizons. The hydraulic and hydrologic modelling were undertaken with process-based numerical models (i.e., River2D© and HBV-light) while the water temperature was modelled by assembling the predictions of three machine learning techniques (M5, Multi-Adaptive Regression Splines and Support Vector Regression). The predicted rise in the water temperature will not be compensated by the more benign lower flows. Consequently, the suitable spawning habitat will be reduced between 15.4¿48.7%. The entire population shall suffer the effects of climate change and will probably be extirpated from the downstream segments of the river.The study has been partially funded by the IMPADAPT project (CGL2013-48424-C2-1-R) with Spanish MINECO (Ministerio de Economía y Competitividad) and FEDER funds and by the Confederación Hidrográfica del Júcar (Spanish Ministry of Agriculture, Food and Environment). The authors thank AEMET and UC for the data provided for this work (dataset Spain02). Finally, we are grateful to the colleagues who worked in the field and in preliminary data analyses; especially Marcello Minervini (funded by the EU programme of Erasmus Traineeships, at the Dept. of Hydraulic Engineering and Environment, Universitat Politècnica de València).Muñoz Mas, R.; Marcos-García, P.; Lopez-Nicolas, A.; Martínez-García, F.; Pulido-Velazquez, M.; Martinez-Capel, F. (2018). Combining literature-based and data-driven fuzzy models to predict brown trout (salmo trutta l.) spawning habitat degradation induced by climate change. Ecological Modelling. 386:98-114. https://doi.org/10.1016/j.ecolmodel.2018.08.012S9811438

Search for blue compact dwarf galaxies during quiescence II: metallicities of gas and stars, ages, and star-formation rates

We examine the metallicity and age of a large set of SDSS/DR6 galaxies that may be Blue Compact Dwarf (BCD) galaxies during quiescence (QBCDs).The individual spectra are first classified and then averaged to reduce noise. The metallicity inferred from emission lines (tracing ionized gas) exceeds by ~0.35 dex the metallicity inferred from absorption lines (tracing stars). Such a small difference is significant according to our error budget estimate. The same procedure was applied to a reference sample of BCDs, and in this case the two metallicities agree, being also consistent with the stellar metallicity in QBCDs. Chemical evolution models indicate that the gas metallicity of QBCDs is too high to be representative of the galaxy as a whole, but it can represent a small fraction of the galactic gas, self enriched by previous starbursts. The luminosity weighted stellar age of QBCDs spans the whole range between 1 and 10 Gyr, whereas it is always smaller than 1 Gyr for BCDs. Our stellar ages and metallicities rely on a single stellar population spectrum fitting procedure, which we have specifically developed for this work using the stellar library MILES.Comment: Accepted for publication in ApJ. 20 pages. 16 figures (corrected typos

Exploring the key drivers of riparian woodland successional pathways across three European river reaches

"This is the peer reviewed version of the following article: Muñoz-Mas, R., V. Garófano-Gómez, I. Andrés-Doménech, D. Corenblit, G. Egger, F. Francés, M.T. Ferreira, et al. 2017. ¿Exploring the Key Drivers of Riparian Woodland Successional Pathways across Three European River Reaches.¿ Ecohydrology 10 (8). Wiley: e1888. doi:10.1002/eco.1888, which has been published in final form at https://doi.org/10.1002/eco.1888. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving."[EN] Climate change and river regulation are negatively impacting riparian vegetation. To evaluate these impacts, process-based models are preferred over data-driven approaches. However, they require extensive knowledge about ecohydrological processes. To facilitate the implementation of such process-based models, the key drivers of riparian woodland successional pathways across three river reaches, in Austria, Portugal, and Spain, were explored, employing two complementary approaches. The principal component analyses highlighted the importance of the physical gradients determining the placement of the succession phases within the riparian and floodplain zones. The generalized additive models revealed that the initial and pioneer succession phases, characteristic of the colonization stage, appeared in areas highly morphodynamic, close in height and distance to the water table, and with coarse substrate, whereas elder phases within the transitional and mature stages showed incremental differences, occupying less dynamic areas with finer substrate. The Austrian site fitted well the current successional theory (elder phases appearing sequentially further up and distant), but at the Portuguese site, the tolerance of the riparian species to drought and flash flood events governed their placement. Finally, at the Spanish site, the patchy distribution of the elder phases was the remnants of formative events that reshaped the river channel. These results highlight the complex relationships between flow regime, channel morphology, and riparian vegetation. The use of succession phases, which rely on the sequential evolution of riparian vegetation as a response to different drivers, may be potentially better reproducible, within numerical process-based models, and transferable to other geographical regions.This work was supported by the IWRM Era-NET Funding Initiative through the RIPFLOW project (references ERACCT-2005-026025, ERA-IWRM/0001/2008, CGL2008-03076-E/BTE), http://www.old.iwrm-net.eu/spip.php, by the Spanish Ministry of Economy and Competitiveness through the project SCARCE (Consolider¿Ingenio 2010 CSD2009-00065), and by the project ¿Natural and anthropogenic changes in Mediterranean river drainage basins: historical impacts on rivers morphology, sedimentary flows and vegetation¿ of the Spanish MINECO (CGL2013-44917-R). Virginia Garófano-Gómez received a postdoctoral grant from the Université Blaise Pascal (now: Université Clermont Auvergne). Rui Rivaes benefited from a PhD grant (SFRH/BD/52515/2014) sponsored by Fundação para a Ciência e Tecnologia (FCT) under the FCT PhD programme FLUVIO¿River Restoration and Management. Patricia María Rodríguez González was funded by FCT through an SFRH/BPD/47140/2008 postdoctoral fellowship and through an FCT Investigator Programme grant (IF/00059/2015). The authors also thank all the colleagues and master students who contributed enthusiastically to the field campaigns of this study.Muñoz Mas, R.; Garófano-Gómez, V.; Andrés Doménech, I.; Corenblit, D.; Egger, G.; Francés, F.; Ferreira, M.... (2017). Exploring the key drivers of riparian woodland successional pathways across three European river reaches. Ecohydrology. 10(8):1-19. https://doi.org/10.1002/eco.1888S11910

Evolution of innovation policy in Emilia-Romagna and Valencia: Similar reality, similar results?

This is an author's accepted manuscript of an article published in: “European Planning Studies"; Volume 22, Issue 11, 2014; copyright Taylor & Francis; available online at: http://dx.doi.org/10.1080/09654313.2013.831398[EN] This paper examines the evolution of regional innovation policy in Emilia-Romagna and Valencia, two regions with similar economic features that implemented close innovation policies in the 1970s and 1980s. We investigate whether their similarities have led to parallel targets, policy tools and governance developments. We show that innovation policy in both regions suffered from the effects of privatization, budget constraints and changes to manufacturing during the 1990s and we highlight the consequences. Although Emilia-Romagna experienced deeper changes to its innovation policy, privatizations and/or the replacement of public funds promoted commercial approaches and induced market failures in both regions. The worst effects of these policies were the implementation of less-risky innovation projects, the shift towards extraregional projects and markets, and the favouring of large firms.López Estornell, M.; Barberá Tomás, JD.; Garcia Reche, A.; Mas Verdú, F. (2013). Evolution of innovation policy in Emilia-Romagna and Valencia: Similar reality, similar results?. European Planning Studies. 22(11):2287-2304. doi:10.1080/09654313.2013.831398S22872304221

Use or abuse of bioinformatic tools: A response to Samach

In a recent paper, we described for the first time the effects of fruit on the expression of putative homologues of genes involved in flowering pathways. It was our aim to provide insight into the molecular mechanisms underlying alternate bearing in citrus. However, a bioinformatics-based critique of our and other related papers has been given by Samach in the preceding Viewpoint article in this issue of Annals of Botany. The use of certain bioinformatic tools in a context of structural rather than functional genomics can cast doubts about the veracity of a large amount of data published in recent years. In this response, the contentions raised by Samach are analysed, and rebuttals of his criticisms are presented.Muñoz Fambuena, N.; Mesejo Conejos, C.; Gonzalez Más, MC.; Primo-Millo, E.; Agustí Fonfría, M.; Iglesias, DJ. (2013). Use or abuse of bioinformatic tools: A response to Samach. Annals of Botany. 111(3):335-336. doi:10.1093/aob/mct020S3353361113Aleza, P., Juárez, J., Hernández, M., Pina, J. A., Ollitrault, P., & Navarro, L. (2009). Recovery and characterization of a Citrus clementina Hort. ex Tan. «Clemenules» haploid plant selected to establish the reference whole Citrus genome sequence. BMC Plant Biology, 9(1), 110. doi:10.1186/1471-2229-9-110Huang, X. (1999). CAP3: A DNA Sequence Assembly Program. Genome Research, 9(9), 868-877. doi:10.1101/gr.9.9.868Muñoz-Fambuena, N., Mesejo, C., Carmen González-Mas, M., Primo-Millo, E., Agustí, M., & Iglesias, D. J. (2011). Fruit regulates seasonal expression of flowering genes in alternate-bearing ‘Moncada’ mandarin. Annals of Botany, 108(3), 511-519. doi:10.1093/aob/mcr164Rafalski, J. A. (2002). Plant genomics: Present state and a perspective on future developments. Briefings in Functional Genomics and Proteomics, 1(1), 80-94. doi:10.1093/bfgp/1.1.80Rhee, S. Y. (2005). Bioinformatics. Current Limitations and Insights for the Future: Figure 1. Plant Physiology, 138(2), 569-570. doi:10.1104/pp.104.900153Samach, A. (2012). Congratulations, you have been carefully chosen to represent an important developmental regulator! Annals of Botany, 111(3), 329-333. doi:10.1093/aob/mcs161Vassilev, D., Leunissen, J., Atanassov, A., Nenov, A., & Dimov, G. (2005). Application of Bioinformatics in Plant Breeding. Biotechnology & Biotechnological Equipment, 19(sup3), 139-152. doi:10.1080/13102818.2005.1081729

On the equivalence between Implicit Regularization and Constrained Differential Renormalization

Constrained Differential Renormalization (CDR) and the constrained version of Implicit Regularization (IR) are two regularization independent techniques that do not rely on dimensional continuation of the space-time. These two methods which have rather distinct basis have been successfully applied to several calculations which show that they can be trusted as practical, symmetry invariant frameworks (gauge and supersymmetry included) in perturbative computations even beyond one-loop order. In this paper, we show the equivalence between these two methods at one-loop order. We show that the configuration space rules of CDR can be mapped into the momentum space procedures of Implicit Regularization, the major principle behind this equivalence being the extension of the properties of regular distributions to the regularized ones.Comment: 16 page

Behavioural syndrome in a solitary predator is independent of body size and growth rate.

Models explaining behavioural syndromes often focus on state-dependency, linking behavioural variation to individual differences in other phenotypic features. Empirical studies are, however, rare. Here, we tested for a size and growth-dependent stable behavioural syndrome in the juvenile-stages of a solitary apex predator (pike, Esox lucius), shown as repeatable foraging behaviour across risk. Pike swimming activity, latency to prey attack, number of successful and unsuccessful prey attacks was measured during the presence/absence of visual contact with a competitor or predator. Foraging behaviour across risks was considered an appropriate indicator of boldness in this solitary predator where a trade-off between foraging behaviour and threat avoidance has been reported. Support was found for a behavioural syndrome, where the rank order differences in the foraging behaviour between individuals were maintained across time and risk situation. However, individual behaviour was independent of body size and growth in conditions of high food availability, showing no evidence to support the state-dependent personality hypothesis. The importance of a combination of spatial and temporal environmental variation for generating growth differences is highlighted