R. K. Suarez and C. D. Moyes, Metabolism in the age of "omes, J Exp Biol, vol.215, pp.2351-2357, 2012.

A. Sboner, X. Mu, and D. Greenbaum, The real cost of sequencing: higher than you think, Genome Biol, vol.12, p.125, 2011.

M. J. Hamilton and M. J. Sadowsky, DNA Profiling in Ecology. Encyclopedia of Life Sciences. Major Reference Works. Chichester, 2010.

C. Hollands, The animals (scientific procedures) Act, Lancet, vol.328, pp.32-33, 1986.

P. Taberlet and G. Luikart, Non-invasive genetic sampling and individual identification, Biol J Linn Soc, vol.68, pp.41-55, 1999.
URL : https://hal.archives-ouvertes.fr/halsde-00280571

P. Taberlet, L. P. Waits, and G. Luikart, Noninvasive genetic sampling: look before you leap, Trends Ecol Evol, vol.14, pp.323-327, 1999.
URL : https://hal.archives-ouvertes.fr/halsde-00280570

. R-core-team, R: A language and environment for statistical computing. R Foundation for Statistical Computing, 2018.

. Rstudio-;-rstudio, . Inc, M. A. Boston, and . Url, RStudio: Integrated development for R, 2017.

J. Roy, L. Vigilant, M. Gray, E. Wright, and R. Kato, Challenges in the use of genetic mark-recapture to estimate the population size of Bwindi mountain gorillas (Gorilla beringei beringei), Biol Conserv, vol.180, pp.249-261, 2014.

T. Sugimoto, V. V. Aramilev, L. L. Kerley, J. Nagata, and D. G. Miquelle, Noninvasive genetic analyses for estimating population size and genetic diversity of the remaining Far Eastern leopard (Panthera pardus orientalis) population, Conserv Genet, vol.15, pp.521-532, 2014.

D. L. Garshelis, On the allure of noninvasive genetic sampling-putting a face to the name, Ursus, vol.17, p.17, 2006.

T. Waldner and M. Traugott, DNA-based analysis of regurgitates: a noninvasive approach to examine the diet of invertebrate consumers, Mol Ecol Resour, vol.12, pp.669-675, 2012.

J. A. Baumgardt, C. S. Goldberg, K. P. Reese, J. W. Connelly, and D. D. Musil, A method for estimating population sex ratio for sage-grouse using noninvasive genetic samples, Mol Ecol Resour, vol.13, pp.393-402, 2013.

D. A. Williams, C. Leach, A. M. Hale, K. B. Karsten, and E. Mujica, Development of tetranucleotide microsatellite loci and a non-invasive DNA sampling method for Texas horned lizards (Phrynosoma cornutum), Conserv Genet Resour, vol.4, pp.43-45, 2012.

D. Murphy and B. Noon, Coping with uncertainty in wildlife biology, J Wildl Manage, vol.55, pp.773-782, 1991.

K. E. Hodges, Defining the problem: terminology and progress in ecology, Front Ecol Environ, vol.6, pp.311-321, 2008.

A. Rorat, N. Kachamakova-trojanowska, A. Jozkowicz, J. Kruk, and C. Cocquerelle, Coelomocyte-Derived Fluorescence and DNA Markers of Composting Earthworm Species, J Exp Zool PART A-ECOLOGICAL Genet Physiol, vol.321, pp.28-40, 2014.

N. H. Quynh, K. Y. Inn, B. Amaël, and J. Yikweon, Efficient isolation method for high-quality genomic DNA from cicada exuviae, Ecol Evol, vol.7, pp.8161-8169, 2017.

A. Richter, D. Weinhold, G. Robertson, M. Young, and T. Edwards, More than an empty case: a non invasive technique for monitoring the Australian critically endangered golden sun moth, Synemon plana (Lepidoptera: Castniidae), J Insect Conserv, vol.17, pp.529-536, 2013.

M. Lefort, S. Wratten, A. Cusumano, Y. Varennes, and S. Boyer, Disentangling higher trophic level interactions in the cabbage aphid food web using high-throughput DNA sequencing. Metabarcoding and Metagenomics 1: e13709, 2017.
URL : https://hal.archives-ouvertes.fr/hal-01693553

A. A. Madden, A. Barberán, M. A. Bertone, H. L. Menninger, and R. R. Dunn, The diversity of arthropods in homes across the United States as determined by environmental DNA analyses, Mol Ecol, vol.25, pp.6214-6224, 2016.

F. Bienert, D. Danieli, S. , M. C. Coissac, E. Poillot et al., Tracking earthworm communities from soil DNA, Mol Ecol, vol.21, pp.2017-2030, 2012.

E. Mächler, K. Deiner, P. Steinmann, and F. Altermatt, Utility of environmental DNA for monitoring rare and indicator macroinvertebrate species, Freshw Sci, vol.33, pp.1174-1183, 2014.

L. Baillon, F. Pierron, J. Oses, P. Pannetier, and E. Normandeau, Detecting the exposure to Cd and PCBs by means of a non-invasive transcriptomic approach in laboratory and wild contaminated European eels (Anguilla anguilla), Environ Sci Pollut Res, vol.23, pp.5431-5441, 2016.
URL : https://hal.archives-ouvertes.fr/hal-02289127

M. Janse, A. L. Kappe, and B. Van-kuijk, Paternity testing using the poisonous sting in captive white-spotted eagle rays Aetobatus narinari: a non-invasive tool for captive sustainability programmes, J Fish Biol, vol.82, pp.1082-1085, 2013.

A. J. Piaggio, C. A. Cariappa, D. J. Straughan, M. A. Neubaum, and M. Dwire, A noninvasive method to detect Mexican wolves and estimate abundance, Wildl Soc Bull, vol.40, pp.321-330, 2016.

C. R. Stansbury, D. E. Ausband, P. Zager, C. M. Mack, and C. R. Miller, A longterm population monitoring approach for a wide-ranging carnivore: Noninvasive genetic sampling of gray wolf rendezvous sites in Idaho, USA, J Wildl Manage, vol.78, pp.1040-1049, 2014.

C. Wultsch, L. P. Waits, E. M. Hallerman, and M. J. Kelly, Optimizing collection methods for noninvasive genetic sampling of neotropical felids, Wildl Soc Bull, vol.39, pp.403-412, 2015.

D. Tsaparis, N. Karaiskou, Y. Mertzanis, and A. Triantafyllidis, Non-invasive genetic study and population monitoring of the brown bear (Ursus arctos) (Mammalia: Ursidae) in Kastoria region-Greece, J Nat Hist, vol.49, pp.393-410, 2015.

C. R. Stansbury, D. E. Ausband, P. Zager, C. M. Mack, and L. P. Waits, Identifying gray wolf packs and dispersers using noninvasive genetic samples, J Wildl Manage, vol.80, pp.1408-1419, 2016.

A. A. Karamanlidis, A. Stojanov, G. De, M. Hernando, G. Ivanov et al., Distribution and genetic status of brown bears in FYR Macedonia: implications for conservation, Acta Theriol (Warsz), vol.59, pp.119-128, 2014.

T. P. Quinn, A. J. Wirsing, B. Smith, C. J. Cunningham, and J. Ching, Complementary use of motion-activated cameras and unbaited wire snares for DNA sampling reveals diel and seasonal activity patterns of brown bears (Ursus arctos) foraging on adult sockeye salmon (Oncorhynchus nerka), Can J Zool, vol.92, pp.893-903, 2014.

B. L. Godwin, S. E. Albeke, H. L. Bergman, A. Walters, and M. Ben-david, Density of river otters (Lontra canadensis) in relation to energy development in the Green River Basin, Wyoming. Sci Total Environ, vol.532, pp.780-790, 2015.

O. Cohen, A. Barocas, and E. Geffen, Conflicting management policies for the Arabian wolf Canis lupus arabs in the Negev Desert: is this justified?, ORYX, vol.47, pp.228-236, 2013.

S. Anile, C. Arrabito, M. V. Mazzamuto, D. Scornavacca, and B. Ragni, A noninvasive monitoring on European wildcat (Felis silvestris silvestris Schreber, 1777) in Sicily using hair trapping and camera trapping: does scented lure work? HYSTRIX-ITALIAN, J Mammal, vol.23, pp.44-49, 2012.

K. Steyer, O. Simon, R. Kraus, P. Haase, and C. Nowak, Hair trapping with valerian-treated lure sticks as a tool for genetic wildcat monitoring in lowdensity habitats, Eur J Wildl Res, vol.59, pp.39-46, 2013.

G. Yannic, T. Broquet, H. Strøm, A. Aebischer, and C. Dufresnes, Genetic and morphological sex identification methods reveal a male-biased sex ratio in the Ivory Gull Pagophila eburnea, J Ornithol, vol.157, pp.861-873, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01333970

C. I. Cullingham, C. D. Thiessen, A. E. Derocher, P. C. Paquet, and J. M. Miller, Population structure and dispersal of wolves in the Canadian Rocky Mountains, J Mammal, vol.97, pp.839-851, 2016.

Y. Dai, Q. Lin, W. Fang, X. Zhou, and X. Chen, Noninvasive and nondestructive sampling for avian microsatellite genotyping: a case study on the vulnerable Chinese Egret (Egretta eulophotes), Avian Res, vol.6, p.24, 2015.

S. Barbosa, J. Pauperio, J. B. Searle, and P. C. Alves, Genetic identification of Iberian rodent species using both mitochondrial and nuclear loci: application to noninvasive sampling, Mol Ecol Resour, vol.13, pp.43-56, 2013.

M. Malekian, P. Sadeghi, and F. Goudarzi, Assessment of environmental DNA for detection of an imperiled Amphibian, the luristan newt (Neurergus kaiseri, Herpetol Conserv Biol, vol.13, pp.175-182, 1952.

A. Ponjoan, G. Bota, E. De-la-morena, M. B. Morales, and A. Wolff, Adverse effects of capture and handling little bustard, J Wildl Manage, vol.72, pp.315-319, 2008.

R. G. Harcourt, E. Turner, A. Hall, J. R. Waas, and M. Hindell, Effects of capture stress on free-ranging, reproductively active male Weddell seals, J Comp Physiol A, vol.196, pp.147-154, 2010.

M. Seguel, E. Paredes, H. Pavés, and N. L. Gottdenker, Capture-induced stress cardiomyopathy in South American fur seal pups ( Arctophoca australis gracilis ). Mar Mammal Sci, vol.30, pp.1149-1157, 2014.

N. Hollenbeck, D. Scheel, M. C. Gravley, G. K. Sage, and R. Toussaint, Use of Swabs for Sampling Epithelial Cells for Molecular Genetics Analyses in Enteroctopus, Am Malacol Bull, vol.35, pp.145-157, 2017.

G. Fiorito, A. Affuso, J. Basil, A. Cole, and P. De-girolamo, Guidelines for the care and welfare of cephalopods in research -A consensus based on an initiative by cephRes, FELASA and the Boyd Group, Lab Anim, vol.49, pp.1-90, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01578372

J. Li, Y. Cui, J. Jiang, J. Yu, and L. Niu, Applying DNA barcoding to conservation practice: a case study of endangered birds and large mammals in China, Biodivers Conserv, vol.26, pp.653-668, 2017.

D. Porco, R. Rougerie, L. Deharveng, P. Hebert, S. M. Wisely et al., Coupling non-destructive DNA extraction and voucher retrieval for small soft-bodied Arthropods in a high-throughput context: the example of Collembola, Mol Ecol Resour, vol.10, pp.105-107, 2004.

L. M. Koczur, D. Williford, R. W. Deyoung, and B. M. Ballard, Bringing back the dead: Genetic data from avian carcasses, Wildl Soc Bull, vol.41, pp.796-803, 2017.

N. M. Monteiro, R. M. Silva, M. Cunha, A. Antunes, and A. G. Jones, Validating the use of colouration patterns for individual recognition in the worm pipefish using a novel set of microsatellite markers, Mol Ecol Resour, vol.14, pp.150-156, 2014.

E. Ringler, Testing skin swabbing for DNA sampling in dendrobatid frogs, Amphibia-Reptilia, vol.39, pp.245-251, 2018.

D. Player, C. Lausen, B. Zaitlin, J. Harrison, and D. Paetkau, An alternative minimally invasive technique for genetic sampling of bats: Wing swabs yield species identification, Wildl Soc Bull, vol.41, pp.590-596, 2017.

S. P. Jones and S. W. Kennedy, Feathers as a source of RNA for genomic studies in avian species, Ecotoxicology, vol.24, pp.55-60, 2015.

B. Ford, P. Govindarajulu, K. Larsen, and M. Russello, Evaluating the efficacy of non-invasive genetic sampling of the Northern Pacific rattlesnake with implications for other venomous squamates, Conserv Genet Resour, vol.9, pp.13-15, 2017.

S. Barbosa, J. Paupério, J. S. Herman, C. M. Ferreira, and R. Pita, Endemic species may have complex histories: within-refugium phylogeography of an endangered Iberian vole, Mol Ecol, vol.26, pp.951-967, 2017.

Z. Du-toit, J. P. Grobler, A. Kotze, R. Jansen, and D. L. Dalton, Scale samples from Temminck's ground pangolin (Smutsia temminckii): a non-invasive source of DNA, Conserv Genet Resour, vol.9, pp.1-4, 2017.

O. Miller-keane and M. T. 'toole, Encyclopedia and dictionary of medicine, nursing, and allied health. Free Dict, 2005.

L. K. Kauffman, J. K. Bjork, J. M. Gallup, P. M. Boggiatto, and B. H. Bellaire, Early detection of Brucella canis via quantitative polymerase chain reaction analysis, Zoonoses Public Health, vol.61, pp.48-54, 2014.

H. C. Reinardy, E. Skippins, T. B. Henry, and A. N. Jha, Assessment of DNA damage in sperm after repeated non-invasive sampling in zebrafish Danio rerio, J Fish Biol, vol.82, pp.1074-1081, 2013.

A. M. Michael and M. P. Kirsten, Clarifying the effect of toe clipping on frogs with Bayesian statistics, J Appl Ecol, vol.41, pp.780-786, 2004.

. Marschalek-d-a and M. E. Berres, Impact of non-lethal genetic sampling on the survival, longevity and behaviour of the Hermes copper ( Lycaena hermes ) butterfly, Insect Conserv Divers, vol.6, pp.658-662, 2013.

C. A. Oi, M. M. López-uribe, M. Cervini, D. Lama, and M. A. , Non-lethal method of DNA sampling in euglossine bees supported by mark-recapture experiments and microsatellite genotyping, J Insect Conserv, vol.17, pp.1071-1079, 2013.

C. A. Hamm, D. Aggarwal, and D. A. Landis, Evaluating the impact of non-lethal DNA sampling on two butterflies, Vanessa cardui and Satyrodes eurydice, J Insect Conserv, vol.14, pp.11-18, 2010.

M. Vila, . Auger-rozenberg-m-a, F. Goussard, and C. Lopez-vaamonde, Effect of non-lethal sampling on life-history traits of the protected moth Graellsia isabelae (Lepidoptera: Saturniidae), Ecol Entomol, vol.34, pp.356-362, 2009.

L. Doerr, K. Richardson, J. Ewen, and D. Armstrong, Effect of supplementary feeding on reproductive success of hihi (stitchbird, Notiomystis cincta) at a mature forest reintroduction site, N Z J Ecol, vol.41, pp.34-40, 2017.

P. Brekke, P. M. Benner, A. W. Santure, and J. G. Ewen, High genetic diversity in the remnant island population of hihi and the genetic consequences of reintroduction, Mol Ecol, vol.20, pp.29-45, 2011.

G. Bearzi, First report of a common dolphin (Delphinus delphis) death following penetration of a biopsy dart, J Cetacean Res Manag, vol.2, pp.217-221, 2000.

N. Gemmell and P. Majluf, Projectile biopsy sampling of fur seals, Mar Mammal Sci, vol.13, pp.512-516, 1997.

, AMPLING_OF_FUR_SEALS/file/60b7d52273289d686b.pdf. Accessed, 2015.

M. Krützen and L. Barré, A biopsy system for small cetaceans: darting success and wound healing in Tursiops spp, Mar Mammal Sci, vol.18, pp.863-878, 2002.

M. W. Brown, S. D. Kraus, and D. E. , Reaction of North Atlantic right whales (Eubalaena glacialis) to skin biopsy sampling for genetic and pollutant analysis, pp.1381-1389, 1991.

L. Barrett-lennard, A cetacean biopsy system using lightweight pneumatic darts, and its effect on the behavior of killer whales, Mar Mammal Sci, vol.12, pp.14-27, 1996.

J. Gauthier and R. Sears, Behavioral response of four species of balaenopterid whales to biopsy sampling, Mar Mammal Sci, vol.15, pp.85-101, 1999.

K. M. Parris, S. C. Mccall, M. A. Mccarthy, B. A. Minteer, and K. Steele, Assessing ethical trade-offs in ecological field studies, J Appl Ecol, vol.47, pp.227-234, 2010.

A. J. Magoun, C. D. Long, M. K. Schwartz, K. L. Pilgrim, and R. E. Lowell, Integrating motion-detection cameras and hair snags for wolverine identification, J Wildl Manage, vol.75, pp.731-739, 2011.

S. Rovang, S. E. Nielsen, and G. Stenhouse, In the trap: detectability of fixed hair trap DNA methods in grizzly bear population monitoring, Wildlife Biol, vol.21, pp.68-79, 2015.

P. Henry, A. Henry, and M. A. Russello, A noninvasive hair sampling technique to obtain high quality DNA from elusive small mammals, J Vis Exp, 2011.

S. C. Banks, S. D. Hoyle, A. Horsup, P. Sunnucks, and A. C. Taylor, Demographic monitoring of an entire species (the northern hairy-nosed wombat, Lasiorhinus krefftii) by genetic analysis of non-invasively collected material, Anim Conserv, vol.6, pp.101-107, 2003.

L. Dalén and A. Götherström, Recovery of DNA from footprints in the snow, Can Field-Naturalist, vol.121, pp.321-324, 2007.

R. Nichols, H. Königsson, K. Danell, and G. Spong, Browsed twig environmental DNA: diagnostic PCR to identify ungulate species, Mol Ecol Resour, vol.12, pp.983-989, 2012.

J. Prunier, B. Kaufmann, O. Grolet, D. Picard, and F. Pompanon, Skin swabbing as a new efficient DNA sampling technique in amphibians, and 14 new microsatellite markers in the alpine newt (Ichthyosaura alpestris), Mol Ecol Resour, vol.12, pp.524-531, 2012.
URL : https://hal.archives-ouvertes.fr/halsde-00689809

F. Morinha, P. Travassos, D. Carvalho, P. Magalhaes, and J. A. Cabral, DNA sampling from body swabs of terrestrial slugs (Gastropoda: Pulmonata): a simple and non-invasive method for molecular genetics approaches, J Molluscan Stud, vol.80, pp.99-101, 2014.

R. Uno, M. Kondo, T. Yuasa, K. Yamauchi, and H. Tsuruga, Assessment of genotyping accuracy in a non-invasive DNA-based population survey of Asiatic black bears (Ursus thibetanus): lessons from a large-scale pilot study in Iwate prefecture, northern Japan, Popul Ecol, vol.54, pp.509-519, 2012.

. Collins-r-a, K. F. Armstrong, A. J. Holyoake, and S. Keeling, Something in the water: biosecurity monitoring of ornamental fish imports using environmental DNA, Biol Invasions, vol.15, pp.1209-1215, 2012.

K. Kowarski, Effects of remote biopsy sampling on long-finned pilot whales (Globicephala melas) in Nova Scotia, Aquat Mamm, vol.40, pp.117-125, 2014.

A. M. Pagano, E. Peacock, and M. A. Mckinney, Remote biopsy darting and marking of polar bears, Mar Mammal Sci, vol.30, pp.169-183, 2014.

S. Boyer, S. D. Wratten, A. Holyoake, J. Abdelkrim, and R. H. Cruickshank, Using next-generation sequencing to analyse the diet of a highly endangered land snail (Powelliphanta augusta) feeding on endemic earthworms, PLoS One, vol.8, p.75962, 2013.

M. Lefort, S. Boyer, D. Romans, S. Glare, T. Armstrong et al., Invasion success of a scarab beetle within its native range: host range expansion versus host-shift, PeerJ, vol.2, p.262, 2014.

B. R. Waterhouse, S. Boyer, and S. D. Wratten, Pyrosequencing of prey DNA in faeces of carnivorous land snails to facilitate ecological restoration and relocation programmes, Oecologia, vol.175, pp.737-746, 2014.

M. Bateson, Cumulative stress in research animals: Telomere attrition as a biomarker in a welfare context, BioEssays, vol.38, pp.201-212, 2016.

M. Vucicevic, M. Stevanov-pavlovic, J. Stevanovic, J. Bosnjak, and B. Gajic, Sex determination in 58 bird species and evaluation of CHD gene as a universal molecular marker in bird sexing, Zoo Biol, vol.32, pp.269-276, 2013.

P. Hebert, E. H. Penton, J. M. Burns, D. H. Janzen, and W. Hallwachs, Ten species in one: DNA barcoding reveals cryptic species in the neotropical skipper butterfly Astraptes fulgerator, Proc Natl Acad Sci U S A, vol.101, pp.14812-14817, 2004.

B. Fumanal, J. Martin, and M. C. Bon, High through-put characterization of insect morphocryptic entities by a non-invasive method using direct-PCR of fecal DNA, J Biotechnol, vol.119, pp.15-19, 2005.

S. Creel, Social dominance and stress hormones, Trends Ecol Evol, vol.16, pp.491-497, 2001.

M. Suleman and E. Wango, Physiologic manifestations of stress from capture and restraint of free-ranging male African green monkeys (Cercopithecus aethiops), J Zoo Wildl Med, vol.35, pp.20-24, 2004.

J. A. Thomson and M. R. Heithaus, Animal-borne video reveals seasonal activity patterns of green sea turtles and the importance of accounting for capture stress in short-term biologging, J Exp Mar Bio Ecol, vol.450, pp.15-20, 2014.

S. Robinson, L. Waits, and I. Martin, Estimating abundance of American black bears using DNA-based capture-mark-recapture models, Ursus, vol.20, pp.1-11, 2009.

G. Nelson and B. Graves, Anuran population monitoring: comparison of the north American Amphibian monitoring program's calling index with markrecapture estimates for Rana clamitans, J Herpetol, vol.38, pp.355-359, 2004.

J. Boulanger, G. Stenhouse, and R. Munro, Sources of heterogeneity bias when DNA mark-recapture sampling methods are applied to grizzly bear (ursus arctos) populations, J Mammal, vol.85, pp.618-624, 2004.

S. Lampa, K. Henle, R. Klenke, M. Hoehn, and B. Gruber, How to overcome genotyping errors in non-invasive genetic mark-recapture population size estimation-A review of available methods illustrated by a case study, J Wildl Manage, vol.77, pp.1490-1511, 2013.

E. Modave, A. J. Macdonald, and S. D. Sarre, A single mini-barcode test to screen for Australian mammalian predators from environmental samples, Gigascience, vol.6, pp.1-13, 2017.

J. F. Duenas, R. Cruickshank, and J. Ross, Optimisation of a microsatellite panel for the individual identification of brushtail possums using low template DNA, N Z J Ecol, vol.39, pp.93-102, 2015.

H. Huang, H. Wang, L. Li, Z. Wu, and J. Chen, Genetic diversity and population demography of the Chinese crocodile lizard (Shinisaurus crocodilurus) in China, PLoS One, vol.9, 2014.

K. M. Proffitt, J. F. Goldberg, M. Hebblewhite, R. Russell, and B. S. Jimenez, Integrating resource selection into spatial capture-recapture models for large carnivores, vol.6, 2015.

H. López, H. G. Contreras-díaz, P. Oromí, and C. Juan, Delimiting species boundaries for endangered Canary Island grasshoppers based on DNA sequence data, Conserv Genet, vol.8, pp.587-598, 2007.