G. Allison, The Influence of Species Diversity and Stress Intensity on Community Resistance and Resilience, Ecological Monographs, vol.74, pp.117-134, 2004.

. Anses, , 2017.

M. H. Assouma, D. Serça, F. Guérin, V. Blanfort, P. Lecomte et al., Livestock induces strong spatial heterogeneity of soil CO2, N2O and CH4 emissions within a semi-arid sylvo-pastoral landscape in West Africa, Journal of Arid Land, vol.9, issue.2, pp.210-221, 2017.

A. O. Awiti, Biological Diversity and Resilience: Lessons from the Recovery of Cichlid Species in Lake Victoria, Ecology and Society, vol.16, p.9, 2011.

L. Bach and I. Dahllöf, Local contamination in relation to population genetic diversity and resilience of an arctic marine amphipod, Aquatic Toxicology, vol.114, pp.58-66, 2012.

C. Baggini, Y. Issaris, M. Salomidi, and J. Hall-spencer, Herbivore diversity improves benthic community resilience to ocean acidification, Journal of Experimental Marine Biology and Ecology, vol.469, pp.98-104, 2015.

C. Bellard, P. Cassey, and T. M. Blackburn, Alien species as a driver of recent extinctions, Biology Letters, vol.12, 2016.

D. R. Bellwood, A. S. Hoey, and J. H. Choat, Limited functional redundancy in high diversity systems: resilience and ecosystem function on coral reefs, Ecology Letters, vol.6, pp.281-285, 2003.

M. G. Betts, C. Wolf, W. J. Ripple, B. Phalan, K. A. Millers et al., Global forest loss disproportionately erodes biodiversity in intact landscapes, Nature, vol.547, pp.441-444, 2017.

J. Boissier, S. Grech-angelini, B. L. Webster, J. F. Allienne, T. Huyse et al., Outbreak of urogenital schistosomiasis in Corsica (France): an epidemiological case study, Lancet Infect Dis, vol.16, issue.8, pp.971-980, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01364002

M. R. Borchers, Y. M. Chang, I. C. Tsai, B. A. Wadsworth, and J. M. Bewley, A validation of technologies monitoring dairy cow feeding, ruminating, and lying behaviors, Journal of Dairy Science, vol.99, pp.7458-7466, 2016.

T. P. Bregman, A. C. Lees, H. E. Macgregor, B. Darski, N. G. De-moura et al., Using avian functional traits to assess the impact of land-cover change on ecosystem processes linked to resilience in tropical forests, Proceedings of the Royal Society -B, vol.283, 2017.

L. Carlisle, Diversity, flexibility, and the resilience effect: lessons from a social ecological case study of diversified farming in the northern Great Plains, USA. Ecology and Society, vol.19, p.45, 2014.

L. M. Chevin and A. P. Beckerman, From adaptation to molecular evolution, Heredity, vol.108, pp.457-459, 2011.

C. Chomba and V. Nyirenda, Game Ranching: A Sustainable Land Use Option and Economic Incentive for Biodiversity Conservation in Zambia, Open Journal of Ecology, vol.4, issue.9, pp.571-581, 2014.

C. Danchin-burge, G. Leroy, M. Brochard, S. Moureaux, and E. Verrier, Evolution of the genetic variability of eight French dairy cattle breeds assessed by pedigree analysis, J. Anim. Breed. Genet, vol.129, pp.206-217, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00999874

C. Darwin, On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, 1859.

P. C. De-faccio-carvalho, I. Anghinoni, A. De-moraes, D. Souza, E. D. Sulc et al., Managing grazing animals to achieve nutrient cycling and soil improvement in no-till integrated systems, Nutrient Cycling in Agroecosystems, vol.88, issue.2, pp.259-273, 2010.

S. De-juan, S. F. Thrush, and J. E. Hewitt, Counting on ?-diversity to safeguard the resilience of estuaries, PLoS ONE, vol.8, p.65575, 2013.

D. Destoumieux-garzón, P. Mavingui, G. Boetsch, J. Boissier, F. Darriet et al., The One Health concept: 10 years old and a long road ahead, Frontiers in Veterinary Science, vol.5, p.14, 2018.

B. Dumont, L. Fortun-lamothe, M. Jouven, M. Thomas, and M. Tichit, Prospects from agroecology and industrial ecology for animal production in the 21 st century, Animal, vol.7, pp.1028-1043, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01000394

. Fao, Second state of the world's animal genetic resources for food and agriculture, 2015.

I. Rome and F. ,

J. Fischer, D. B. Lindenmayer, and A. D. Manning, Biodiversity, ecosystem function, and resilience: ten guiding principles for commodity production landscapes, Frontiers in Ecology and the Environment, vol.4, pp.80-86, 2006.

P. G. Frost and I. Bond, The CAMPFIRE programme in Zimbabwe: Payments for wildlife services, Ecological Economics, vol.65, issue.4, pp.776-787, 2008.

V. Gagic, I. Bartomeus, T. Jonsson, A. Taylor, C. Winqvist et al., Functional identity and diversity of animals predict ecosystem functioning better than species-based indices, Proceedings of the Royal Society B: Biological Sciences, vol.282, 1801.

S. Génermont and P. Cellier, A mechanistic model for estimating ammonia volatilization from slurry applied to bare soil, Agricultural and Forest Meteorology, vol.88, issue.1, pp.145-167, 1997.

P. J. Gerber, H. Steinfeld, B. Henderson, A. Mottet, C. Opio et al., Tackling climate change through livestock -A global assessment of emissions and mitigation opportunities, 2013.

A. C. Gleiss, R. P. Wilson, and E. L. Shepard, Making overall dynamic body acceleration work: on the theory of acceleration as a proxy for energy expenditure, Methods in Ecology and Evolution, vol.2, issue.1, pp.23-33, 2011.

S. J. Gould and E. A. Lloyd, Individuality and adaptation across levels of selection: how shall we name and generalize the unit of Darwinism, Proceedings of the National Academy of Sciences, vol.96, pp.11904-11909, 1999.

P. R. Grant, B. R. Grant, R. B. Huey, M. T. Johnson, A. H. Knoll et al., , 2017.

, Evolution caused by extreme events, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.372, 20160146.

B. L. Greenfield, C. Kraan, C. A. Pilditch, and S. F. Thrush, Mapping functional groups can provide insight into ecosystem functioning and potential resilience of intertidal sandflats, Marine Ecology Progress Series, vol.548, pp.1-10, 2016.

D. Headon, Systems biology and lifestock production, Animal, vol.7, pp.1959-1963, 2013.

T. Heams, Variation, Les Mondes darwiniens, Editions Syllepse, pp.17-30, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01587879

S. Højsgaard and N. C. Friggens, Quantifying degree of mastitis from common trends in a panel of indicators for mastitis in dairy cows, Journal of Dairy Science, vol.93, pp.582-592, 2010.

C. S. Holling, Engineering resilience versus ecological resilience, Engineering within ecological constraints, pp.31-44, 1996.

S. Jenouvrier, C. Péron, and H. Weimerskirch, Extreme climate events and individual heterogeneity shape life-history traits and population dynamics, Ecological Monographs, vol.85, pp.605-624, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01326119

B. T. Jones, R. W. Diggle, and C. Thouless, From Exploitation to Ownership: WildlifeBased Tourism and Communal Area Conservancies in Namibia, In: Institutional Arrangements for Conservation, Development and Tourism in Eastern and Southern Africa, pp.17-37, 2015.

E. Kaarlejärvi, K. S. Hoset, and J. Olofsson, Mammalian herbivores confer resilience of Arctic shrub-dominated ecosystems to changing climate, Global Change Biology, vol.21, pp.3379-3388, 2015.

C. N. Kaiser-bunbury, J. Mougal, A. E. Whittington, T. Valentin, R. Gabriel et al., Ecosystem restoration strengthens pollination network resilience and function, Nature, vol.542, pp.223-229, 2017.

T. Kammili, B. Hubert, and J. F. Tourrand, A paradigm shift in livestock management: from resource sufficiency to functional integrity, pp.28-29, 2008.

B. S. Kaplan, M. K. Torchetti, K. M. Lager, R. J. Webby, and A. L. Vincent, Absence of clinical disease and contact transmission of North American clade H5NX HPAI in experimentally infected pigs. Influenza Other Respir Viruses, 2017.

B. A. Keating, P. S. Carberry, P. S. Bindraban, S. Asseng, H. Meinke et al., Ecoefficient agriculture: concepts, challenges, and opportunities, Crop Science, pp.50-109, 2010.

F. Keesing, L. K. Belden, P. Daszak, A. Dobson, C. D. Harvell et al., Impacts of biodiversity on the emergence and transmission of infectious diseases, Nature, vol.468, issue.7324, pp.647-652, 2010.

S. Kühsel and N. Blüthgen, High diversity stabilizes the thermal resilience of pollinator communities in intensively managed grasslands, Nature Communications, vol.6, p.7989, 2015.

F. Lamprianidou, T. Telfer, and L. G. Ross, A model for optimization of the productivity and bioremediation efficiency of marine integrated multitrophic aquaculture, Estuarine, Coastal and Shelf Science, vol.164, issue.C, pp.253-264, 2015.

R. Lande and S. J. Arnold, The measurement of selection on correlated characters, Evolution, vol.37, pp.1210-1226, 1983.

M. Lindegren, D. M. Checkley, . Jr, M. D. Ohman, J. A. Koslow et al., Resilience and stability of a pelagic marine ecosystem, Proceedings of the Royal Society -B, vol.283, 2016.

D. R. López, M. A. Brizuela, P. Willems, M. R. Aguiar, G. Siffredi et al., Linking ecosystem resistance, resilience, and stability in steppes of North Patagonia, Ecological Indicators, vol.24, pp.1-11, 2013.

S. J. Lycett, R. Bodewes, A. Pohlmann, J. Banks, C. Bányai et al., Role for migratory wild birds in the global spread of avian influenza H5N8. The Global Consortium for H5N8 and Related Influenza Viruses, Science, vol.354, p.6309, 2016.

J. S. Mackenzie and M. Jeggo, Reservoirs and vectors of emerging viruses, Curr Opin Virol, vol.3, issue.2, pp.170-179, 2013.

J. Martinez, P. Dabert, S. Barrington, and C. Burton, Livestock waste treatment systems for environmental quality, food safety, and sustainability, Bioresource technology, vol.100, issue.22, pp.5527-5536, 2009.

S. L. Maxwell, R. A. Fuller, T. M. Brooks, and J. E. Watson, The ravages of guns, nets and bulldozers, Nature, vol.536, pp.143-145, 2016.

A. E. Mckechnie and B. O. Wolf, Climate change increases the likelihood of catastrophic avian mortality events during extreme heat waves, Biology Letters, vol.6, pp.253-259, 2010.

D. Mijatovi?, F. Van-oudenhoven, P. Eyzaguirre, and T. Hodgkin, The role of agricultural biodiversity in strengthening resilience to climate change: towards an analytical framework, International Journal of Agricultural Sustainability, vol.11, pp.95-107, 2013.

H. Milhazes-cunha and A. Otero, Valorisation of aquaculture effluents with microalgae: The Integrated Multi-Trophic Aquaculture concept, Algal Research, vol.24, pp.416-424, 2017.

C. Mora, D. P. Tittensor, S. Adl, A. G. Simpson, and B. Worm, How many species are there on earth and in the ocean?, PLoS Biology, vol.9, issue.8, pp.1-8, 2011.

S. Morand, K. M. Mcintyre, and M. Baylis, Domesticated animals and human infectious diseases of zoonotic origins: Domestication time matters, Infection, Genetics and Evolution, vol.24, pp.76-81, 2014.

M. Moretti, P. Duelli, and M. K. Obrist, Biodiversity and resilience of arthropod communities after fire disturbance in temperate forests, Oecologia, vol.149, pp.312-327, 2006.

A. S. Mori, T. Furukawa, and T. Sasaki, Response diversity determines the resilience of ecosystems to environmental change, Biological Reviews, vol.88, pp.349-364, 2013.

M. B. Morrissey, L. E. Kruuk, and . A. Wilson, The danger of applying the breeder's equation in observational studies of natural populations, Journal of Evolutionary Biology, vol.23, pp.2277-2288, 2010.

L. Mouysset, L. Doyen, and F. Jiguet, From Population Viability Analysis to Coviability, Conservation Biology, vol.28, pp.187-201, 2013.
URL : https://hal.archives-ouvertes.fr/hal-01198099

. Oie, , 2016.

T. H. Oliver, M. S. Heard, N. J. Isaac, D. B. Roy, D. Procter et al., Biodiversity and resilience of ecosystem functions, Trends in Ecology & Evolution, vol.30, pp.673-684, 2015.

T. H. Oliver, M. S. Heard, N. J. Isaac, D. B. Roy, D. Procter et al., A synthesis is emerging between biodiversity-ecosystem function and ecological resilience research: Reply to Mori, Trends in Ecology & Evolution, vol.31, pp.89-92, 2016.

T. H. Oliver, N. J. Isaac, T. A. August, B. A. Woodcock, D. B. Roy et al., Declining resilience of ecosystem functions under biodiversity loss, Nature Communications, vol.6, p.10122, 2015.

P. A. Oltenacu and . Broom, The impact of genetic selection for increased milk yield on the welfare of dairy cows, Animal Welfare, vol.19, pp.39-49, 2010.

E. Ostrom, A General Framework for Analyzing Sustainability of Social-Ecological Systems, Science, vol.325, p.24, 2009.

D. R. Paini, A. W. Sheppard, D. C. Cook, P. J. De-barro, S. P. Worner et al., , 2016.

, Global threat to agriculture from invasive species, Proceedings of the National Academy of Sciences of the United States of America, vol.113, pp.7575-7579

S. R. Palumbi, Humans as the World's Greatest Evolutionary Force, Science, vol.293, pp.1786-1790, 2001.

D. Pauly, V. Christensen, S. Guenette, T. J. Pitcher, U. R. Sumaila et al., Towards sustainability in world fisheries, Nature, vol.418, pp.689-695, 2002.

J. M. Pearce-duvet, The origin of human pathogens: evaluating the role of agriculture and domestic animals in the evolution of human disease, Biol Rev Camb Philos Soc, vol.81, issue.3, pp.369-82, 2006.

O. L. Petchey and K. J. Gaston, Functional diversity: back to basics and looking forward, Ecology Letters, vol.9, pp.741-758, 2006.

P. Prunet, O. Overli, J. Douxfils, G. Bernardini, P. Kestemont et al., Fish welfare and genomics, Fish Physiology and Biochemistry, vol.38, issue.1, pp.43-60, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01205030

L. Puillet, D. Réale, and N. C. Friggens, Disentangling the relative roles of resource acquisition and allocation on animal feed efficiency: Insights from a dairy cow model, Genetics Selection Evolution, vol.48, pp.1-16, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01413578

B. Raymond, M. A. Lea, T. Patterson, V. Andrews-goff, R. Sharples et al., Important marine habitat off east Antarctica revealed by two decades of multi-species predator tracking, Ecography, vol.38, pp.121-129, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01076443

O. Rey, E. Danchin, M. Mirouze, C. Loot, and S. Blanchet, Adaptation to Global Change: A Transposable Element-Epigenetics Perspective, Trends in Ecology & Evolution, vol.31, pp.514-526, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02099870

G. Rezza, L. Nicoletti, R. Angelini, R. Romi, A. C. Finarelli et al., Infection with chikungunya virus in Italy: an outbreak in a temperate region, The Lancet, vol.370, issue.9602, pp.1840-1846, 2007.

S. Ripperger, D. Josic, M. Hierold, A. Koelpin, R. Weigel et al., , 2016.

, Automated proximity sensing in small vertebrates: design of miniaturized sensor nodes and first field tests in bats, Ecol Evol, vol.6, issue.7, pp.2179-89

R. Sabatier, L. Doyen, and M. Tichit, Heterogeneity and the trade-off between ecological and productive functions of agro-landscapes: A model of cattle-bird interactions in a grassland agroecosystem, Agric Systems, vol.126, pp.38-49, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01198013

B. Sadoul, P. Evouna-mengues, N. C. Friggens, P. Prunet, and V. Colson, A new method for measuring group behaviours of fish shoals from recorded videos taken in near aquaculture conditions, Aquaculture, vol.430, pp.179-187, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01173631

T. Sasaki, T. Furukawa, Y. Iwasaki, M. Seto, and A. S. Mori, Perspectives for ecosystem management based on ecosystem resilience and ecological thresholds against multiple and stochastic disturbances, Ecological Indicators, vol.57, pp.395-408, 2015.

P. Schippers, C. M. Van-der-heide, H. P. Koelewijn, M. A. Schouten, R. M. Smulders et al., Landscape diversity enhances the resilience of populations, ecosystems and local economy in rural areas, Landscape Ecology, vol.30, pp.193-202, 2015.

M. A. Schlaepfer, M. C. Runge, and P. W. Sherman, Ecological and evolutionary traps, Trends in Ecology & Evolution, vol.17, pp.474-480, 2002.

B. Sherf, World watch list for domestic animal diversity, 2000.

A. M. Siepielski, K. M. Gotanda, M. B. Morrissey, S. E. Diamond, J. D. Dibattista et al., The spatial patterns of directional phenotypic selection, Ecology Letters, vol.16, pp.1382-1392, 2013.

A. M. Siepielski, M. B. Morrissey, M. Buoro, S. M. Carlson, C. M. Caruso et al., Precipitation drives global variation in natural selection, Science, vol.355, pp.959-962, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01605014

A. D. Soteriades, A. W. Stott, S. Moreau, T. Charroin, M. Blanchard et al., The relationship of dairy farm eco-efficiency with intensification and selfsufficiency. Evidence from the French dairy sector using life cycle analysis, data envelopment analysis and partial least squares structural equation modelling, PLoS ONE, vol.11, p.166445, 2016.

C. Stahl, S. Fontaine, K. Klumpp, C. Picon-cochard, M. M. Grise et al., Continuous soil carbon storage of old permanent pastures in Amazonia, Global Change Biology, vol.23, issue.8, pp.3382-3392, 2017.

S. C. Stearns, The evolution of life history traits: A Critique of the Theory and a Review of the Data, Evolution, and Systematics, vol.8, pp.145-171, 1977.

E. Tabacchi, J. Steiger, D. Corenblit, M. T. Monaghan, and A. Planty-tabacchi, Implications of biological and physical diversity for resilience and resistance patterns within highly dynamic river systems, Aquatic Sciences, vol.71, pp.279-289, 2009.
URL : https://hal.archives-ouvertes.fr/hal-01514101

C. T. Thien-thu, P. H. Cuong, L. T. Hang, N. V. Chao, L. X. Anh et al., Manure management practices on biogas and non-biogas pig farms in developing countries -using livestock farms in Vietnam as an example, Journal of cleaner production, vol.27, issue.C, pp.64-71, 2012.

M. Troell, C. Halling, A. Neori, T. Chopin, A. H. Buschmann et al., Integrated mariculture: asking the right questions, Aquaculture, vol.226, issue.1, pp.69-90, 2003.

C. C. Ummenhofer and G. A. Meehl, Extreme weather and climate events with ecological relevance: a review, Phil. Trans. R. Soc. B, vol.372, p.20160135, 2017.

C. M. Valcu and B. Kempenaers, Proteomics in behavioral ecology, Behavioral Ecology, vol.26, pp.1-15, 2014.

J. A. Van-gils, S. Lisovski, T. Lok, W. Meissner, A. Ozarowska et al., Body shrinkage due to Arctic warming reduces red knot fitness in tropical wintering range, Science, vol.352, pp.819-821, 2016.

J. Vayssières, F. Guerrin, J. Paillat, and P. Lecomte, GAMEDE: A global activity model for evaluating the sustainability of dairy enterprises. Part I -Whole-farm dynamic model, Agricultural Systems, vol.101, pp.128-138, 2009.

C. Villars, A. Bergouignan, J. Dugas, E. Antoun, D. A. Schoeller et al.,

C. Simon, Validity of combining heart rate and uniaxial acceleration to measure free-living physical activity energy expenditure in young men, Journal of applied physiology, vol.113, issue.11, pp.1763-1771, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00751256

M. E. Visser, A. J. Noordwijk, J. M. Tinbergen, and C. M. Lessells, Warmer springs lead to mistimed reproduction in great tits (Parus major), Proceedings of the Royal Society B: Biological Sciences, vol.265, pp.1867-1870, 1998.

C. M. Wathes, H. H. Kristensen, J. M. Aerts, and D. Berckmans, Is precision livestock farming an engineer's daydream or nightmare, an animal's friend or foe, and a farmer's panacea or pitfall?, Computers and Electronics in Agriculture, vol.64, pp.2-10, 2008.

M. E. Woolhouse, D. T. Haydon, and R. Antia, Emerging pathogens: the epidemiology and evolution of species jumps, Trends in Ecol. Evol, vol.20, pp.238-244, 2005.