Agroecology offers a scientific and operational framework for redesigning animal production systems (APS) so that they better cope with the coming challenges. Grounded in the stimulation and valorization of natural processes to reduce inputs and pollutions in agroecosystems, it opens a challenging research agenda for the animal science community. In this paper, we identify key research issues that define this agenda. We first stress the need to assess animal robustness by measurable traits, to analyze trade-offs between production and adaptation traits at within-breed and between-breed level, and to better understand how group selection, epigenetics and animal learning shape performance. Second, we propose research on the nutritive value of alternative feed resources, including the environmental impacts of producing these resources and their associated non-provisioning services. Third, we look at how the design of APS based on agroecological principles valorizes interactions between system components and promotes biological diversity at multiple scales to increase system resilience. Addressing such challenges requires a collection of theories and models (concept-knowledge theory, viability theory, companion modeling, etc.). Acknowledging the ecology of contexts and analyzing the rationales behind traditional small-scale systems will increase our understanding of mechanisms contributing to the success or failure of agroecological practices and systems. Fourth, the large-scale development of agroecological products will require analysis of resistance to change among farmers and other actors in the food chain. Certifications and market-based incentives could be an important lever for the expansion of agroecological alternatives in APS. Finally, we question the suitability of current agriculture extension services and public funding mechanisms for scaling-up agroecological practices and systems.

There are numerous recent studies highlighting sustainability problems for the development of ruminant production systems (RPS) while facing increasing human food necessities and global climate change. Despite the complexity of the context, in our view the main objectives of the ruminants' physiologist should be convergent for both industrialized (IC) and developing countries (DC) in a common and global strategy of advancing knowledge. In DC, this means improving the efficiency of RPS, taking into account the unique possibility of using rangelands. For IC settings, RPS should be revisited in terms of autonomy and environment- friendly feeding and managing practices. Assuming that competition for feed/food use is still a crucial criterion, future ruminant feeding systems (FeSyst) should preferably focus on lignocellulosic sources. According to biome distributions, and the recent increases in volumes of crop residues and their by-products, the annually renewed volumes of these biomasses are considerable. Therefore, we need to redesign our strategies for their efficient utilization at the local level. For this purpose, digestion processes and rumen functioning need to be better understood. The renewed vision of ruminal digestion through the reduction of greenhouse gas emissions is also a key aspect as it is an environmental demand that cannot be ignored. With regard to other ruminants' physiological functions, accumulated knowledge could be mobilized into an integrative approach that puts forward the adaptive capacities of animals to face variability in quantity and quality of supplied feeds. Basically, the reduction of inputs that were traditionally used to ensure FeSyst will need more flexible animals. In that sense, the concepts of homeostasis and teleophorhesis need to be updated and adapted to domestic species and breeds that were until now largely excluded from the dominant productive systems. In conclusion, a more holistic approach of research targets is required in which physiological functions and farmers' practices must converge and respond to each particular situation in an integral, dynamic and flexible conceptual perspective. From a scientific point of view, both for ICs and DCs, a broader range of experimental scenarios should be explored in order to arrive at innovative practices and solutions that respect environmental, ethical and economical issues. The clear challenge is to in evaluate the sustainability of RPSs. This includes, in our opinion, a strong interaction with other disciplines (multi- and trans-disciplinary conception), thus structuring new relevant indicators for the evaluation sustainability.

Agroecology uses natural processes and local resources rather than chemical inputs to ensure production while limiting the environmental footprint of livestock and crop production systems. Selecting to achieve a maximization of target production criteria has long proved detrimental to fitness traits. However, since the 1990s, developments in animal breeding have also focussed on animal robustness by balancing production and functional traits within overall breeding goals. We discuss here how an agroecological perspective should further shift breeding goals towards functional traits rather than production traits. Breeding for robustness aims to promote individual adaptive capacities by considering diverse selection criteria which include reproduction, animal health and welfare, and adaptation to rough feed resources, a warm climate or fluctuating environmental conditions. It requires the consideration of genotype×environment interactions in the prediction of breeding values. Animal performance must be evaluated in low-input systems in order to select those animals that are adapted to limiting conditions, including feed and water availability, climate variations and diseases. Finally, we argue that there is no single agroecological animal type, but animals with a variety of profiles that can meet the expectations of agroecology. The standardization of both animals and breeding conditions indeed appears contradictory to the agroecological paradigm that calls for an adaptation of animals to local opportunities and constraints in weakly artificialized systems tied to their physical environment.

Characterizing and understanding the complexity of numerous interactions occurring in mixed farming systems is still a methodological challenge. We hypothesize that farm functioning features in terms of crop-livestock integration practices impact the agroecological performance of the system, which will be also affected by the farm context. In order to analyze crop-livestock integration in a holistic way, a set of seventeen mixed farming systems from three contrasting socioeconomic regions of the humid tropics (Guadeloupe, Brazilian Amazonia, and Cuba) was selected in order to cover a wide range of crop-livestock integration situations. The ecological network analysis was applied to each farm in order to study the nutrient flow networks, expressed in nitrogen. The activity and flow organization of crop-livestock integration practices were characterized and the agroecological performance has been evaluated in terms of efficiency, resilience, productivity, and dependency of N flow networks. Here, we show for the first time that the range of crop-livestock integration is well characterized by the activity and organization of flows. Gradients of crop-livestock integration were well detected and described. Some agroecological performances were related to a particular socioeconomic context. Resource endowment influenced efficiency, according to the intensification level. The crop-livestock integration however contributed partially to the productivity of the system, being especially effective in promoting resilience. This study applies a suitable framework to analyze complex farming systems while linking their functioning and performance in an agroecological approach. Thus, comparison of contrasting systems was feasible here with the support of numerical and tangible figures for interpreting complex indicators (e.g., resilience), representing a useful tool for monitoring sustainability of agricultural systems in a dynamic and holistic way.