François Chevenet
email: francois.chevenet@ird.fr

Jean-Philippe Doyon

Celine Scornavacca

Edwin Jacox

Emma- Nuelle Jousselin

Vincent Berry

Prof Valencia Alfonso

SylvX: a viewer for phylogenetic tree reconciliations

Motivation:

Reconciliation methods aim at recovering the evolutionary processes that shaped the history of a given gene family including events such as duplications, transfers and losses by comparing the discrepancies between the topologies of the associated gene and species trees. These methods are also used in the framework of host/parasite studies to recover co-diversification scenarios including co-speciation events, host-switches and extinctions. These evolutionary processes can be graphically represented as nested trees. These interconnected graphs can be visually messy and hard to interpret, and despite the fact that reconciliations are increasingly used, there is a shortage of tools dedicated to their graphical management. Here we present SylvX, a reconciliation viewer which implements classical phylogenetic graphic operators (swapping, highlighting, etc.) and new methods to ease interpretation and comparison of reconciliations (multiple maps, moving, shrinking subreconciliations). SylvX is an open source, cross-platform, standalone editor available for Windows and Unix-like systems including OSX.

INTRODUCTION

Reconciliation methods compare gene trees and species trees to recover the history of gene families. Such a history is composed of speciation events, duplications, losses, transfers and other evolutionary events affecting particular genes at specific times in evolution [START_REF] Page | Trees within trees: phylogeny and historical associations[END_REF]. Reconciliation methods are also used in co-diversification studies where the phylogeny of parasite species is compared to that of host species infected by these parasites. Here a different set of evolutionary events is considered including cospeciation events, duplications, extinctions and host switches. Few tools are currently available to visualize reconciliations: Tarzan/CoRe-PA [START_REF] Merkle | Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information[END_REF], Jane [START_REF] Conow | Jane: a new tool for the cophylogeny reconstruction problem[END_REF] and PrIMETV (Sennblad et al., 2007) packages use a two dimensional Euclidean slanted layout for the representation of reconciliations; the 3DPE editor [START_REF] Kim | Three-Dimensional Phylogeny Explorer: Distinguishing paralogs, lateral transfer, and violation of "molecular clock" assumption with 3D visualization[END_REF] uses a 2.5D representation of a slanted layout, crossing species (X) vs. evolutionary distance (Y) vs. paralogs (Z). In spite of these powerful tools for illustrating how a "guest" tree (e.g. a gene history) evolves inside a host tree (e.g. a species tree), these interconnected graphs can be visually hard to interpret when the number of evolutionary events depicted is high. Another issue is that the available viewers lack the ability to compare reconciliations obtained under different settings (e.g. different event costs) or to compare reconciliations for different genes families (or parasite taxa) on the same species tree. The goal of SylvX is the graphical management of such drawings and the generation of publication-ready illustrations.

METHODS

SylvX is written in Tcl/Tk. The required input is a species tree (Newick format) and one or several reconciliations in the format outputted by Mowgli [START_REF] Doyon | An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers[END_REF]. Mowgli is included and dynamically linked to SylvX. TERA [START_REF] Scornavacca | Joint amalgamation of most parsimonious reconciled gene trees[END_REF] and NOTUNG [START_REF] Vernot | Reconciliation with Non-Binary Species Trees[END_REF] output can be imported. SylvX output format is PostScript or SVG (easily editable with many drawing package and keeping a high quality graphics). The reconciliation graphs are based on a species tree (host) using a rectangular layout with a variable thickness line, and a gene history (parasite tree), embedded in the species tree, which is composed of horizontal segments linked by vertical versatile connectors. The algorithm displaying reconciliations is based on vertical translation of segments following evolutionary events. For instance, both segments of a duplication are shifted, one upwards and the other downwards. This offset is then inherited by all the subsequent nodes and is cumulative with posterior events.

RESULTS

SylvX's consists of three toolboxes (Fig. 1). The first one is related to maps. A map is a resizable and scrollable display space showing a species tree with one superimposed gene reconciliation. The user can add/remove maps and choose which reconciliation to display on a given map from the reconciliation toolbox (see below). Both the species tree and its gene reconciliation are updated by applying a tool (e.g. zoom) from this map toolbox. The second toolbox is specific to reconciliations. In order to display a reconciliation, first, the user needs to target one or several map(s) from the map toolbox, and secondly, select a reconciliation from the list of available ones. The reconciliation toolbox offers graphical operators such as highlighting (line thickness, dash line, foreground color), shrinking, translation or annotation that can be applied to internal nodes of a reconciliation. These operations take into account evolutionary events, including horizontal transfers. For instance, setting a new color to an internal node of a reconciliation also updates the color of all the subsequent horizontal transfers and their descendants. Reconciliations can be synchronized, meaning that a graphical modification on a reconciliation from a given map can be automatically conducted on a selection of maps displaying the same reconciliation. The third toolbox is dedicated to the species tree. A species subtree can be swapped, hidden, highlighted, colored and annotated. Like reconciliations, species trees from several maps can be synchronized.

DISCUSSION

The main feature of SylvX is the ability to manage multiple interactive maps of reconciliations. Synchronous highlighting operations between juxtaposed maps ease their comparison. Zooming, annotating (color, text), shrinking sub-parts of the trees help in the interpretation of chains of events. The SylvX method for displaying reconciliations is based on upward and downward translations of segments linked by versatile connectors. Displaying reconciliations having a high number of evolutive events, such as a set of successive duplications, within one (short) species tree segment is still a challenge (superimpositions of a high number of graphical items in a small drawing area). More elaborated methods available in the field of information visualization will be useful, such as the production of symbolic views (e.g. replacing a set of duplications by one « hot spot » in the tree) or tree navigation tools based on Focus+Context distortion such as the accordion zoom (Munzer et al., 2003). Another challenge is a global view of multiple genes histories on a single map/species tree. In this context, flattening or smoothing reconciliation graphs and its evolutionary events will be required to avoid messy visualizations and graphical operators acting locally, manually or automatically must be developed. In the short term, one priority is the ability to import reconciliations from other packages such as PrIMETV (Sennblad et al., 2007).

Figure 1 .

 1 Figure 1. Screenshot of a SylvX session. The left side of the interface gathers the Map toolbox, the Reconciliation(s) toolbox and the Species tree toolbox. The right side stacks maps. Duplications are represented by blue squares, losses by red crosses and transfers by arrows (variable colors). The "host-parasite" dataset used in the figure consists of the Ficus/fig wasp dataset by Cruaud et al. (2012). Two maps are in use: the one on the left displays a species tree with a superimposed reconciliation having a color coding based on transfers. The second map displays a reconciliation for the same gene but with a different costs for evolutionary events. at INRA Institut National de la Recherche Agronomique on November 4, 2015 http://bioinformatics.oxfordjournals.org/ Downloaded from

at INRA Institut National de la Recherche Agronomique on November 4, 2015 http://bioinformatics.oxfordjournals.org/ Downloaded from

ACKNOWLEDGEMENTS

We thank Astrid Cruaud & coll. for sharing the fig/fig-wasp dataset. Funding: ANR Phylospace.


domain: sdv shs

text:
Rosalia Filippini
email: rosalia.filippini@gmail.com

Elisa Marraccini

Sylvie Lardon

Elisa Bonari

Enrico Bonari

Is the choice of a farm's commercial market an indicator of agricultural intensity? Conventional and short food supply chains in periurban farming systems

Keywords: Periurban agriculture, food supply chains, farm management, Tuscany

Short food supply chains (SFSCs) have been identified as an economic opportunity for agriculture under urban pressure, as well as drivers for more sustainable farming systems. However, few studies have focused on the intensity of periurban farms that participate in such SFSCs, compared with the performance of the other farms. In this paper, we examined the relationship between agricultural intensity and the market orientation in a representative sample of farms in the urban area of Pisa (Italy). We define agricultural intensity as the intensity of land use and its main drivers (e.g., farm management or the individual characteristics of farmers), and market orientation as the ratio of farm produce within conventional, short or mixed foodsupply chains. The results suggest that the market orientation of periurban farming systems is more correlated to the indicators of farm management and land use intensity than to the individual farmer's characteristics. This result provides the first evidence that market orientation is a driver of intensity, and that individual farmer's characteristics are not significantly different in the three groups of market orientation. These findings could be generalised to other urban areas and correlated with the main orientation of farming systems in order to support both the assessment of farming systems and the implementation of innovative urban food policies.

Introduction

The European Environmental Agency (EEA, 2010) has highlighted that periurban agricultural areas are affected by urbanisation in terms farmland loss and fragmentation. These dynamics are particularly pronounced in Mediterranean countries [START_REF] Marraccini | Common features and different trajectories of land cover changes in six Western Mediterranean urban regions[END_REF]. Urbanisation affects not only ecosystem services [START_REF] Foley | Global consequences of land use[END_REF][START_REF] Zasada | Peri-urbanisation and multifunctional adaptation of agriculture around Copenhagen[END_REF], but also the potential productivity of agricultural areas by impacting on farmers' choices and environmental resources [START_REF] Agrawal | Effect of air pollution on peri-urban agriculture: a case study[END_REF]Akimowitz, 2012). These dynamics of urban growth are thus threatening agriculture in periurban areas. However, several studies have also pointed out how urbanisation has redesigned the economic relationships in these areas, offering new opportunities for agriculture [START_REF] Soulard | Quelle utilisation de l'espace en zones rurales et péri-urbaines?[END_REF].

More recently the function of periurban agriculture in terms of food production has been studied, linked to the opportunities offered by short food supply chains (SFSCs) [START_REF] Paül | Peri-urban farmland conservation and development of alternative food networks: Insights from a casestudy area in metropolitan Barcelona (Catalonia, Spain)[END_REF]. SFSCs are defined as innovative food chains characterised by a restored and more direct connection between producers and consumers [START_REF] Renting | Understanding alternative food networks: exploring the role of short food supply chains in rural development[END_REF]. Especially in periurban areas, the adoption of SFSCs has been seen as an indicator of the farmer's adaptation to being in proximity to an urban area [START_REF] Lamine | Les AMAP: un nouveau pacte entre producteurs et consommateurs? Available from[END_REF]. It is generally stated within the literature on SFSCs that these farming systems are beneficial for the environment [START_REF] Renting | Understanding alternative food networks: exploring the role of short food supply chains in rural development[END_REF][START_REF] Cleveland | Operationalizing local food: goals, actions, and indicators for alternative food systems[END_REF] and they are generally associated with more sustainable rural development [START_REF] Sundkvist | On the importance of tightening feedback loops for sustainable development of food systems[END_REF][START_REF] Maréchal | Les circuits courts favorisent-ils l'adoption de pratiques agricoles plus respectueuses de l'environnement?[END_REF]Forrssel and Lankoski, 2014). Although SFSCs could represent a real market opportunity for periurban farmers, and thus they could prevent agricultural abandonment in urban areas, periurban farming systems oriented to SFSCs have been often neglected by mainstream agronomic literature. Indeed, traditional approaches on SFSCs are more focused on how the relationships are established, and their social and economical benefits. A more in-depth study on the farming systems is thus necessary in order to properly assess their sustainability [START_REF] Goodman | Rural Europe redux? Reflections on alternative agrofood networks and paradigm change[END_REF][START_REF] Simoncini | Introducing territorial and historical contexts and critical thresholds in the analysis of conservation of agro-biodiversity by Alternative Food Networks, in Tuscany, Italy[END_REF].

The aim of this study is to carry out a preliminary study on the relationship between the market's orientation and the agricultural intensity of periurban farming systems. We define the agricultural intensity of farming systems as both the intensity of land use and its drivers, i.e., the farm structure, farm management, and the individual farmer's characteristics. We define market orientation according to [START_REF] Renting | Understanding alternative food networks: exploring the role of short food supply chains in rural development[END_REF], i.e., as the conscious market destination either locally in SFSCs or in conventional food supply chains where the producer relies on traders, or producer's cooperatives. The paper is organised as follows. In Materials and methods section we describe the methodology developed in terms of indicators, case study and statistical analysis. In Results section we discuss the main results obtained in the case study of the urban area of Pisa. Finally, we discuss our method and main results and draw conclusions on the agricultural intensity of periurban farming systems.

Materials and methods

The urban area of Pisa (Italy): a representative area of Mediterranean urbanised coastal plains

The case study is the urban area of Pisa, a medium-sized city in Tuscany (Italy). As already described by [START_REF] Filippini | Assessing food production capacity of farms in periurban areas[END_REF], this region has a surface of 500 km 2 and consists of six municipalities located in the coastal plain of the Arno river and on the hilly area known as the Monte Pisano (917 m a.s.l). The area has a population density of almost 400 inhabitants per km 2 and follows the European urban demographic trend for the last decade: a decrease in the city-centre inhabitants (-4% in the last decade) and a significant increase in the periur-ban areas (+8% in the last decade). Local farming systems are typically Mediterranean and oriented to cereal production, livestock, industrial crops or specialised crops such as horticultural or olive groves [START_REF] Marraccini | Durabilité de l'agriculture dans les territoires périurbains méditerranéens: enjeux et projets agriurbains dans la région de Pise (Toscane, Italie)[END_REF]. The case study is representative of the transition of the main farming systems: a decrease in hectares of usable agricultural area (UAA) (-16%) and above all in the number of farms particularly in more intensive productions such as horticultural and fruit groves (-94%), while cereal and industrial crops farms has decreased less (-50%).

The case study is also relevant considering the interest of local institutions in developing a food plan of the area, which included the contribution of local food supply to feed the inhabitants of the area (Di [START_REF] Iacovo | Le strategie urbane: il piano del cibo[END_REF].

Data collection

The analysis was based on 31 variables measured through 55 semistructured farm interviews. The interviews were carried out in 2013 and represented almost 10% of the total number of farms in the area according to the last agricultural census. We sampled the surveyed farms not for their market orientation but rather considering their dominant land use (e.g., industrial crops, cereals, fodder, olive groves and horticultural crops), the size of the farm according to the UAA and the distance of the farmstead from the main city centre. These three

Short Communication

Table 1. List of the selected indicators used in the analysis. The questionnaire was based on the main characteristics of the farm, the crop management, the marketing of the products, the farmer projects and the main advantages and disadvantages of being near an urban centre. For more details, see [START_REF] Filippini | Assessing food production capacity of farms in periurban areas[END_REF].

Type of indicator

The sampled farms were thus classified in three groups, considering the marketing of the farm products declared by the farmers: conventional (CFC), if the farm produce is allotted totally to conventional food supply chains; short (SFC) it is devolved totally to short food supply chains, mixed (MFC) if it is devolved to both conventional and short food supply chains.

Analysis of the relationships between agricultural intensity and the market orientation of farms

The agricultural intensity was assessed with four groups of indicators without combining them with an overall score of intensity. A total of 31 indicators were calculated for each farm, referring to four items: the farm structure (e.g., farm size, land use); the farm management (e.g., crop management, livestock management, multifunctionality); the land use intensity (e.g., livestock density, irrigation) and the individual farmer characteristics (e.g., age, agricultural background). Indicators were identified by literature [START_REF] Dumanski | Land quality indicators: research plan[END_REF][START_REF] Herzog | Assessing the intensity of temperate European agriculture at the landscape scale[END_REF]; thus they have been selected considering their capacity in discriminate between farms using analysis of the variation coefficient (cv) and excluding those indicators with a cv lower than 0.30 (little diversity).

Table 1 provides a list of the indicators used in the analysis, and the motivation for their adoption.

A descriptive analysis has been performed (data not shown) in order to characterise our farm sample. Afterwards, the relation between each indicator of agricultural intensity and the three market orientations identified was assessed using a Kruskal-Wallis test, since the indicators generally had a non-normal distribution [START_REF] Kruskal | Use of ranks in one-criterion variance analysis[END_REF].

Results

Characteristics of farms and localisation for the three market orientations

Considerable differentiation was found in the number of farms belonging to each group: only 10% of the farms sell the total production in SFCs, versus 47% of farms that sell exclusively in CFCs. An interesting result was the huge percentage of farmers (43%) that mix short and conventional food supply chains. We also found a difference in the type of farms belonging to each group. In fact, farmers that are exclusively in CFCs generally grow cereals and industrial crops (respectively 26% and 34%). On the other hand, horticulture seems to be more rep- resented by farmers selling in SFCs and MFCs, although in both these groups this represents only about 20%. Both groups have a greater percentage of producers of fodder -livestock orientation and olive groves: 29% in MFCs and 40% in SFCs. The only difference between the two groups is that in the MFC group, there are producers of industrial and cereal crops (16%), while no cereal or industrial crop farms participate exclusively in SFCs.

The distance from the urban area does not seem to affect the three groups and producing close to the urban city does not affect the market orientation of farms.

Land use intensity and farm management provide statistically significant differences in the market orientation of farms

Figure 1 shows the main results of the statistical analysis. It is possible to observe two main results. The first result concerns the group of indicators with significant differences depending on the market orientation. We found that land use intensity (4 significant indicators out of 6) and farm management (6 indicators out of 10) were the agricultural intensity groups most related to market orientation. However, farm structure and individual farmers' characteristics were less related to market orientation (respectively 3 out of 10, and 1 out of 6). This result is important because it is the first evidence that market orientation could be a driver of agricultural intensity. Farms exclusively in CFCs generally have higher values of intensity, but this is not the case for all the indicator values. Livestock density and tree density for olive groves have higher values for farms exclusively in alternative food chains, thus suggesting that even farms in SFCs can have an intensive farming practice or land use. However, since an overall score was not calculated, we were not able to predict which market orientation was more or less intensive. This opens up a new research area for the assessment of the agricultural intensity of periurban farming systems.

Moreover we demonstrated that in this case study, the farm structure or the individual farmer's characteristics are not significantly different in the three groups of market orientation, which in fact is more related to the type of farming system.

The second result concerns the differences in the indicator values within each market orientation group. We found very different dynamics unrelated to the indicator group. In fact, in some cases, there is a regular gradient between the indicator values within each group (e.g., the ratio of cereal surface within the UAA, which decreases from the CSC farms to the SFCs), or a similar value in two out of the three groups (e.g., the average number of multifunctional activities, which has almost the same value in MFCs and SFCs whereas it decreases for CFCs). Our interpretation is that this result may depend on the nature of the MFC, which was not completely defined in this work. In fact, MFC may be related to a different food chain for different farm product (e.g., cereals and milk or meat for livestock farms) or for a market diversification strategy for each kind of products (e.g., a market orientation in SFCs and CFCs for vegetables in horticultural farms). An in-depth analysis of MFCs is needed in order to understand their type and frequency within each farming system.

Conclusions

In this preliminary study, we have demonstrated that there is a relationship between market orientation and the agricultural intensity of periurban farming systems. Moreover we have shown that this relationship is more complex than what several scholars have claimed, promoting SFCs as tool for a less intensive farming in periurban areas: considering our results there is no evidence that a farming system in CFC is more intense than another oriented to SFC. This contribution leaves for further analysis to investigate the nature of this link. We suggest two possible ways to deep the analysis: firstly, to assess a single agricultural intensity index and secondly, to extend the statistical analysis using a multivariate model in order to consider other environmental and agricultural variables. We finally suggest that further agronomical research on periurban agriculture should be more focused on periurban farming systems, in order to assess their intensity, the services they provide, and their real contribution to local food policies.

  land use Usable agricultural area UAA On farm surface used for arable and permanent crops ha Share of the UAA owned SUAAp Percentage of the UAA owned by the farms % Number of landowners Np Number of different landowners on the farmland Value Share of UAA in winter cereals SUAAwc Percentage of winter cereals in UAA % Share of UAA in horticultural crops SUAAho Percentage of horticultural crops in UAA % Share of UAA in olive groves SUAAog Percentage of olive groves in UAA % Share of UAA in fodder SUAAf Percentage of fodder in UAA % Number of farm blocks Nblocks Number of adjacent groups of fields belonging Value to the same farmer and managed in the same way Distance between blocks Dblocks Maximum distance of blocks between different on-farm blocks km Distance from the city Durb Distance of the farmstead from the main city centre km Farm management Livestock unit UGBT Number of livestock units on the farm Value Type of machinery Equip Main types of machinery available on the farm Value Share of full-time workers Nftw Share of full time workers out of the total workers of the farm % Number of seasonal workers Nsw Number of seasonal workers per farm Value Number of food chains Nfc Number of different food chains of the farm Value (on-farm direct selling, shops, cooperatives, etc.) Number of cultivated products Nsp Number of different crops cultivated on the farm Value Number of labels Nlabel Number of different labels on one or several farm produce Value Number of other activities Nact Number of different on-farm activities Value Innovation dynamics DynInn Dynamics of innovation on the farm (0=decreasingapplications Nphyto Number of pesticide applications on the more intensive crops Value Individual farmer's characteristics Number of years Nyears On-farm work experience Value Type of education Tedu Type of educational background (0=no; 1=basic no agri; 0 to 4 2=advanced no agri; 3=agri; 4=advanced agri) Age Age Age of the farmer or the main farmer manager (0=<40; 1=40-65; 2=>65) 0/1/2 Number of networks Nnet Number of networks the farmer belongs to Value Agricultural background Agri Agricultural background of family (0=no, 1=yes) 0/1 Type of enterprise Tjury Type of farm (0=family; 1=cooperative; 2=enterprise; Value 3=technical agricultural; 4=other) to select those farms more illustrative of the local farming systems and at the same time differently constrained by the proximity to the city.

  Figure 1. Main results of the statistical analysis (for each indicators' code see Table1).

the authors acknowledge ANR funding via the DAUME project n° ANR-2010-STRA-007-01 and the Scuola Superiore Sant'Anna for RF PhD grant.


Editorial: Agroecology for producing goods and services in sustainable animal farming systems Agroecology was initially defined as a scientific discipline that applies ecological theory to the design and management of agroecosystems in order to enhance their sustainability [START_REF] Altieri | Agroecology: the scientific basis of alternative agriculture[END_REF]. It then gradually emerged both as a movement and as a set of practices, and moved beyond the agroecosystem scale toward a wider focus on the whole food system, encompassing food production, distribution and consumption [START_REF] Wezel | Agroecology as a science, a movement and a practice. A review[END_REF]. The recent surge in academic literature on agroecology has ignored animal production systems despite their direct or indirect dependency on natural processes. Animal production systems have indisputable negative impacts on the environment, but as underlined by [START_REF] Gliessman | Animals in agroecosystems[END_REF] the problem lies not so much with the animals themselves or their use as food, but with the ways animals are incorporated in agroecosystems and food systems. Animal agriculture needs to be reconfigured to minimize its negative impacts, produce food and other ecosystem services and increase their adaptive capacity to face an increasingly uncertain future (markets, climate change, demands for food security, shifts in dietary preferences in the developing world). The integration of animals in an agroecosystem can often make the difference in realizing long-term ecological sustainability and socio-economic viability goals. To extend ecological thinking into animal production systems, [START_REF] Dumont | Prospects from agroecology and industrial ecology for animal production in the 21 st century[END_REF] recently proposed five principles based on the identification of key ecological processes that need to be optimized: (i) adopt management practices aiming to improve animal health, (ii) decrease the inputs needed for production, (iii) decrease pollution by optimizing the metabolic functioning of farming systems, (iv) enhance diversity within animal production systems to strengthen their resilience and (v) preserve biological diversity in agroecosystems by adapting management practices. In this special issue, 19 papers investigate how the issues above can contribute to the design of innovative, adaptive and resilient farming systems in ruminants, pigs, horses and aquaculture across temperate, Mediterranean and tropical areas.

Integration of cropping and livestock farming systems allows better regulation of biochemical cycles and environmental fluxes to the atmosphere and hydrosphere through interactions among farm units, and mobilizes biodiversity to supply ecosystem services. To reach these objectives, [START_REF] Moraine | Farming system design for innovative crop-livestock integration in Europe[END_REF] propose a participatory design method that was implemented across a diversity of European case studies in which diversity of crops and grasslands interacting with animals appeared central. Cooperation and collective structuration between farmers and with other actors of territories reveal opportunities for smart social innovation. [START_REF] Veysset | Mixed crop-livestock farming systems: a sustainable way to produce beef? Commercial farm results, questions and perspectives[END_REF] and [START_REF] Ripoll-Bosch | Role of self-sufficiency, productivity and diversification on the economic sustainability of farming systems with autochthonous sheep breeds in less favoured areas in Southern Europe[END_REF] analyze the economic performance of mixed crop-livestock farming systems in temperate and Mediterranean areas. Both studies find that the economic profitability of mixed crop-livestock farms is not related to the diversity of production or to animal productivity, the main driver of farm sustainability rather being the low dependency on off-farm inputs (feed self-sufficiency). However, the diversity of production enhances farm flexibility, with organic farms being the ones that exploit the diversity of herd feed resources (grasslands, cereals, legume crops) more efficiently. Oosting et al. (2014) aim to analyze the constraints to production increases from the farm and the farmers' perspective in smallholder mixed crop-livestock systems in the tropics. They show that maximum herd output is not achieved at the highest production per individual animal. They also present a framework linking farming systems to value chains. The 'system jump' from subsistence to commercial livestock production would lead to lower prices, more competition and higher demands for product quality requiring investments that not all farmers can afford. Changing a system also requires a deeper understanding of the attitudes of farmers. For instance, [START_REF] Gizaw | Efficiency of selection for body weight in a cooperative village breeding program of Menz sheep under smallholder farming system[END_REF] show that collective breeding programs in Ethiopia lead to genetic improvement that cannot be achieved through individual efforts of smallholder farmers, and that the integration of farmers' own criteria (pelvic width, body length, color, horn) to select rams does not affect the program efficiency but makes it socially acceptable. Latawiec et al. (2014) review the main constraints for sustainable intensification of cattle grazing in Brazil in terms of productivity, pasture management, socio-economic impacts and climate change mitigation. Adopting practices like rotational grazing, incorporation of legumes and integrated crop-livestock-forestry systems can enable higher yields and higher economic outcomes to be obtained while reversing degradation and protecting the environment. Technical assistance is however essential, particularly for small-and medium-scale farmers. An example also in Brazil is presented by [START_REF] Paciullo | Sward characteristics and performance of dairy cows in organic grass-legume pastures shaded by tropical trees[END_REF], who illustrate how organic dairy production that incorporates several herbaceous (legumes and grasses) and tree species in a silvopastoral system can improve animal nutrition, helping to reconcile animal production and environmental conservation. Accatino et al. (2014) present a dynamic model of rangelands to which they apply the mathematical framework of viability theory to quantify the management adaptability of the system. They conclude that cattle grazing is viable only for high-rainfall regimes, and that the use of mixed herds composed of cattle and goats increases the adaptability of management. In tropical grasslands, combining goats and heifers offers a promising alternative for increased production of goats and overall animal production, and also represents an option for the lower use of chemical anthelmintics (d'Alexis et al., 2014). In temperate conditions, [START_REF] Collas | How does the suppression of energy supplementation affect herbage intake, performance and parasitism in lactating saddle mares?[END_REF] analyze the consequences of suppressing energy complementation at pasture on the performance of saddle mares. Under high herbage allowance, the mare's adaptive capacities allow requirements to be met and produce foals with satisfying growth and conformation while relying on grass only. Supplementation should thus not be systematic, which appears an efficient way to increase farmers' incomes and decrease the environmental footprint of horse farming systems.

The use of forage plants as an alternative to concentrate feeds constitutes a relevant strategy to decrease the inputs needed for feeding pigs in tropical areas. [START_REF] Kambashi | Forage plants as an alternative feed resource for sustainable pig production in the tropics: a review[END_REF] review a number of issues related to the high fibre and low-energy contents of tropical forages and to the presence of plant secondary metabolites. They conclude on the need for a proper assessment at the farm level of the social, economic and environmental consequences of such nutritional changes. [START_REF] Agostini | Management factors affecting mortality, feed intake and feed conversion ratio of grow-finishing pigs[END_REF] illustrate how grow-finishing pig farms can increase their technical and economic performance by improving farm facilities and modifying batch management practices. [START_REF] Gilles | An integrated closed system for fish-plankton aquaculture in Amazonian fresh water[END_REF] discuss how an integrated, self-contained, fish-plankton system can provide technical, environmental and economic advantages for fish aquaculture in Amazonia compared with the traditional outdoor production.

Innovative farming systems need to be evaluated for both their economic performance and their environmental footprint. [START_REF] Henriksson | Carbon footprint and land requirement for dairy herd rations: impacts of feed production practices and regional climate variations[END_REF] and [START_REF] Sasu-Boakye | Localising livestock protein feed production and the impact on land use and greenhouse gas emissions[END_REF] use Life Cycle Assessment (LCA) to quantify the impacts of various feed rations for dairy cows and pigs in Sweden. The carbon footprint varies according to cultivation practices and climate conditions. Authors stress that land use change must be considered in carbon footprinting as goal conflicts often arise. For instance, localising protein feed production reduces greenhouse gas emissions and improves some ecological processes (e.g. nutrient recycling), but at a cost of increasing land occupation for local feed production. Beyond the use of LCA, the five principles mentioned above can be used to setup multi-criteria evaluation methods. [START_REF] Botreau | Towards an agroecological assessment of dairy systems: proposal for a set of criteria suited to mountain farming[END_REF] identify a number of criteria and organize them to form the architecture of an evaluation framework for dairy systems in mountain environments, which measures the level of system compliance with agroecological principles.

Agroecology considers pasture-based livestock systems as multifunctional, delivering not only food and fiber but also a wide range of public goods. [START_REF] Rodríguez-Ortega | Applying of the ecosystem services framework to pasturebased livestock farming systems in Europe[END_REF] review the Ecosystem Service framework for integrating market and non-market functions, which allows the multiple trade-offs and synergies that can exist to be considered. They point at the multidimensionality of livestock production and present different methodologies to value ecosystem services from the biophysical, socio-cultural and economic perspectives. An example of economic valuation of public goods associated to livestock production is the study by [START_REF] Martin-Collado | Determination of non-market values to inform conservation strategies for the threatened Alistana-Sanabresa cattle breed[END_REF] that calculate the Total Economic Value of an endangered breed, and propose considering the existence and cultural values associated to local breeds to inform conservation strategies.

We conclude this special issue by identifying key research areas on the technical and organizational innovations that are needed to scale-up the use of agroecology principles in livestock farming systems [START_REF] Dumont | Forty research issues for the redesign of animal production systems in the 21 st century[END_REF]. Designing robust and resilient animal production systems able to face increasing uncertainty and handle various types of disturbances will demand a paradigm shift in many scientific disciplines. We should quickly progress toward holistic and interdisciplinary research methods, involving animal scientists, ecologists, economists and sociologists. The authors also call for a new approach for the whole researchdevelopment-innovation chain to bridge the gap between science and practice.

  Herbivores, Theix, 63122 Saint-Genès-Champanelle, France; 2 Department of Animal and Aquacultural Sciences, Norwegian University of Life Science (NMBU), 1432 Ås, Norway