Bibliography
Alberdi, A., Aizpurua, O., Bohmann, K., Gopalakrishnan, S., Lynggaard, C., Nielsen, M., & Gilbert, M. T. P. (2019). Promises and pitfalls of using high-throughput sequencing for diet analysis. Molecular Ecology Resources , 19 (2), 327–348. https://doi.org/10.1111/1755-0998.12960Allard, L., Popée, M., Vigouroux, R., & Brosse, S. (2016). Effect of reduced impact logging and small-scale mining disturbances on Neotropical stream fish assemblages.Aquatic Sciences , 78 (2), 315–325. https://doi.org/10.1007/S00027-015-0433-4/METRICSAraújo, F. G., Pinto, B. C. T., & Teixeira, T. P. (2009). Longitudinal patterns of fish assemblages in a large tropical river in southeastern Brazil: Evaluating environmental influences and some concepts in river ecology.Hydrobiologia , 618 (1), 89–107. https://doi.org/10.1007/S10750-008-9551-5/METRICSBarlow, J., França, F., Gardner, T. A., Hicks, C. C., Lennox, G. D., Berenguer, E., Castello, L., Economo, E. P., Ferreira, J., Guénard, B., Gontijo Leal, C., Isaac, V., Lees, A. C., Parr, C. L., Wilson, S. K., Young, P. J., & Graham, N. A. J. (2018). The future of hyperdiverse tropical ecosystems.Nature , 559 (7715), 517–526. https://doi.org/10.1038/s41586-018-0301-1Blackman, R., Couton, M., Keck, F., Kirschner, D., Carraro, L., Cereghetti, E., Perrelet, K., Bossart, R., Brantschen, J., Zhang, Y., & Altermatt, F. (2024). Environmental DNA: The next chapter. Molecular Ecology , 33 (11). https://doi.org/10.1111/mec.17355Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P., & Coissac, E. (2016). obitools: A unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources , 16 (1), 176–182. https://doi.org/10.1111/1755-0998.12428Boyer, S., Cruickshank, R. H., Wratten, S., & Faeces, S. W. (2015). Faeces of generalist predators as “biodiversity capsules”: A new tool for biodiversity assessment in remote and inaccessible habitats . https://doi.org/10.1016/j.fooweb.2015.02.001ïBrosse S., C. Y., Condachou C. ,. Coutant O. ,. Covain R. ,. Quartarollo G. ,. Vigouroux R. &. Murienne J. (n.d.). Near complete 12S DNA reference library for the freshwater fish of French Guiana, northern Amazonian region .Calvignac-Spencer, S., Merkel, K., Kutzner, N., Kühl, H., Boesch, C., Kappeler, P. M., Metzger, S., Schubert, G., & Leendertz, F. H. (2013). Carrion fly-derived DNA as a tool for comprehensive and cost-effective assessment of mammalian biodiversity. Molecular Ecology , 22 (4), 915–924. https://doi.org/10.1111/MEC.12183Cantera, I., Coutant, O., Jézéquel, C., Decotte, J. B., Dejean, T., Iribar, A., Vigouroux, R., Valentini, A., Murienne, J., & Brosse, S. (2022). Low level of anthropization linked to harsh vertebrate biodiversity declines in Amazonia. Nature Communications , 13 (1). https://doi.org/10.1038/s41467-022-30842-2Cantera, I., Decotte, J. B., Dejean, T., Murienne, J., Vigouroux, R., Valentini, A., & Brosse, S. (2022). Characterizing the spatial signal of environmental DNA in river systems using a community ecology approach. Molecular Ecology Resources , 22 (4), 1274–1283. https://doi.org/10.1111/1755-0998.13544Cantera, I., Jézéquel, C., Dejean, T., Murienne, J., Vigouroux, R., Valentini, A., & Brosse, S. (2023a). Deforestation strengthens environmental filtering and competitive exclusion in Neotropical streams and rivers.Proceedings of the Royal Society B , 290 (2006). https://doi.org/10.1098/RSPB.2023.1130Cantera, I., Jézéquel, C., Dejean, T., Murienne, J., Vigouroux, R., Valentini, A., & Brosse, S. (2023b). Functional responses to deforestation in fish communities inhabiting neotropical streams and rivers. Ecological Processes ,12 (1), 1–17. https://doi.org/10.1186/S13717-023-00463-8/TABLES/2Chao, A., Gotelli, N. J., Hsieh, T. C., Sander, E. L., Ma, K. H., Colwell, R. K., & Ellison, A. M. (2014). Rarefaction and extrapolation with Hill numbers: A framework for sampling and estimation in species diversity studies.Ecological Monographs , 84 (1), 45–67. https://doi.org/10.1890/13-0133.1Collen, B., Whitton, F., Dyer, E. E., Baillie, J. E. M., Cumberlidge, N., Darwall, W. R. T., Pollock, C., Richman, N. I., Soulsby, A. M., & Böhm, M. (2014). Global patterns of freshwater species diversity, threat and endemism. Global Ecology and Biogeography , 23 (1), 40–51. https://doi.org/10.1111/geb.12096Cordone, G., Lozada, M., Vilacoba, E., Thalinger, B., Bigatti, G., Lijtmaer, D. A., Steinke, D., & Galván, D. E. (2022). Metabarcoding, direct stomach observation and stable isotope analysis reveal a highly diverse diet for the invasive green crab in Atlantic Patagonia. Biological Invasions , 24 (2), 505–526. https://doi.org/10.1007/S10530-021-02659-5/METRICSCoutant, O., Jézéquel, C., Mokany, K., Cantera, I., Covain, R., Valentini, A., Dejean, T., Brosse, S., & Murienne, J. (2023). Environmental DNA reveals a mismatch between diversity facets of Amazonian fishes in response to contrasting geographical, environmental and anthropogenic effects. Global Change Biology , 29 (7), 1741–1758. https://doi.org/10.1111/gcb.16533da Cruz, B. R. F., Cunha, M. C., Bueno, A. A. de P., & Jacobucci, G. B. (2021). Natural diet of macrobrachium brasiliense (Crustacea, decapoda) in a cerrado stream. Iheringia - Serie Zoologia , 111 . https://doi.org/10.1590/1678-4766e2021003Deagle, B. E., Thomas, A. C., McInnes, J. C., Clarke, L. J., Vesterinen, E. J., Clare, E. L., Kartzinel, T. R., & Eveson, J. P. (2019). Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data? Molecular Ecology , 28 (2), 391–406. https://doi.org/10.1111/mec.14734Feller, R. J. (2006). Weak meiofaunal trophic linkages in Crangon crangon and Carcinus maenus. Journal of Experimental Marine Biology and Ecology , 330 (1), 274–283. https://doi.org/10.1016/j.jembe.2005.12.033Galan, M., Pons, J. B., Tournayre, O., Pierre, É., Leuchtmann, M., Pontier, D., & Charbonnel, N. (2018). Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis. Molecular Ecology Resources , 18 (3), 474–489. https://doi.org/10.1111/1755-0998.12749Giguet-Covex, C., Pansu, J., Arnaud, F., Rey, P. J., Griggo, C., Gielly, L., Domaizon, I., Coissac, E., David, F., Choler, P., Poulenard, J., & Taberlet, P. (2014). Long livestock farming history and human landscape shaping revealed by lake sediment DNA. Nature Communications , 5 . https://doi.org/10.1038/ncomms4211Hilário, H. O., Mendes, I. S., Guimarães Sales, N., & Carvalho, D. C. (2023). DNA metabarcoding of mock communities highlights potential biases when assessing Neotropical fish diversity. Environmental DNA , 5 (6), 1351–1361. https://doi.org/10.1002/edn3.456Hirt, M. R., Lauermann, T., Brose, U., Noldus, L. P. J. J., & Dell, A. I. (2017). The little things that run: A general scaling of invertebrate exploratory speed with body mass.Ecology , 98 (11), 2751–2757. https://doi.org/10.1002/ecy.2006Hoeinghaus, D. J., Agostinho, A. A., Gomes, L. C., Pelicice, F. M., Okada, E. K., Latini, J. D., Kashiwaqui, E. A. L., & Winemiller, K. O. (2009). Effects of river impoundment on ecosystem services of large tropical rivers: Embodied energy and market value of artisanal fisheries. Conservation Biology , 23 (5), 1222–1231. https://doi.org/10.1111/j.1523-1739.2009.01248.xHsieh, T. C., Ma, K. H., & Chao, A. (2016). iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Methods in Ecology and Evolution , 7 (12), 1451–1456. https://doi.org/10.1111/2041-210X.12613Keck, F., Blackman, R. C., Bossart, R., Brantschen, J., Couton, M., Hürlemann, S., Kirschner, D., Locher, N., Zhang, H., & Altermatt, F. (2022). Meta-analysis shows both congruence and complementarity of DNA and eDNA metabarcoding to traditional methods for biological community assessment. Molecular Ecology , 31 (6), 1820–1835. https://doi.org/10.1111/mec.16364Kocher, A., de Thoisy, B., Catzeflis, F., Valière, S., Bañuls, A. L., & Murienne, J. (2017). iDNA screening: Disease vectors as vertebrate samplers. Molecular Ecology ,26 (22), 6478–6486. https://doi.org/10.1111/mec.14362Le Bail, P.-Y. (2012). Updated checklist of the freshwater and estuarine fishes of French Guiana (Issue 1). Philippe Keith.Lévêque, C., Oberdorff, T., Paugy, D., Stiassny, M. L. J., & Tedesco, P. A. (2008). Global diversity of fish (Pisces) in freshwater. In Freshwater Animal Diversity Assessment (pp. 545–567). Springer Netherlands. https://doi.org/10.1007/978-1-4020-8259-7_53Longin, G., Fontenelle, G., Bonneau de Beaufort, L., Delord, C., Launey, S., Rinaldo, R., Lassalle, G., Le Bail, P. Y., & Roussel, J. M. (2021). When subsistence fishing meets conservation issues: Survey of a small fishery in a neotropical river with high biodiversity value. Fisheries Research ,241 , 105995. https://doi.org/10.1016/J.FISHRES.2021.105995Mariani, S., Baillie, C., Colosimo, G., & Riesgo, A. (2019). Sponges as natural environmental DNA samplers. Current Biology , 29 (11), R401–R402. https://doi.org/10.1016/j.cub.2019.04.031Marques, V., Milhau, T., Albouy, C., Dejean, T., Manel, S., Mouillot, D., & Juhel, J. B. (2021). GAPeDNA: Assessing and mapping global species gaps in genetic databases for eDNA metabarcoding. Diversity and Distributions ,27 (10), 1880–1892. https://doi.org/10.1111/ddi.13142Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads . http://www-huber.embl.de/users/an-Massey, A. L., Bronzoni, R. V. de M., da Silva, D. J. F., Allen, J. M., de Lázari, P. R., dos Santos-Filho, M., Canale, G. R., Bernardo, C. S. S., Peres, C. A., & Levi, T. (2022). Invertebrates for vertebrate biodiversity monitoring: Comparisons using three insect taxa as iDNA samplers.Molecular Ecology Resources , 22 (3), 962–977. https://doi.org/10.1111/1755-0998.13525Miettinen, J., Shi, C., & Liew, S. C. (2011). Deforestation rates in insular Southeast Asia between 2000 and 2010. Global Change Biology , 17 (7), 2261–2270. https://doi.org/10.1111/j.1365-2486.2011.02398.xMiya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., Minamoto, T., Yamamoto, S., Yamanaka, H., Araki, H., Kondoh, M., & Iwasaki, W. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: Detection of more than 230 subtropical marine species. Royal Society Open Science , 2 (7). https://doi.org/10.1098/RSOS.150088Mouillot, D., Bellwood, D. R., Baraloto, C., Chave, J., Galzin, R., Harmelin-Vivien, M., Kulbicki, M., Lavergne, S., Lavorel, S., Mouquet, N., Paine, C. E. T., Renaud, J., & Thuiller, W. (2013). Rare Species Support Vulnerable Functions in High-Diversity Ecosystems. PLoS Biology , 11 (5). https://doi.org/10.1371/journal.pbio.1001569Mouillot, D., Villéger, S., Parravicini, V., Kulbicki, M., Arias-González, J. E., Bender, M., Chabanet, P., Floeter, S. R., Friedlander, A., Vigliola, L., & Bellwood, D. R. (2014). Functional over-redundancy and high functional vulnerability in global fish faunas on tropical reefs. Proceedings of the National Academy of Sciences of the United States of America ,111 (38), 13757–13762. https://doi.org/10.1073/pnas.1317625111Nørgaard, L., Olesen, C. R., Trøjelsgaard, K., Pertoldi, C., Nielsen, J. L., Taberlet, P., Ruiz-González, A., De Barba, M., & Iacolina, L. (2021). eDNA metabarcoding for biodiversity assessment, generalist predators as sampling assistants. Scientific Reports , 11 (1). https://doi.org/10.1038/s41598-021-85488-9Oksanen, J., & Blanchet, F. G. (n.d.). Vegan: Community Ecology Package . https://github.com/vegandevs/veganPapa, Y., Le Bail, P. Y., & Covain, R. (2021). Genetic landscape clustering of a large DNA barcoding data set reveals shared patterns of genetic divergence among freshwater fishes of the Maroni Basin. Molecular Ecology Resources ,21 (6), 2109–2124. https://doi.org/10.1111/1755-0998.13402Pelicice, F. M., Agostinho, A. A., Azevedo-Santos, V. M., Bessa, E., Casatti, L., Garrone-Neto, D., Gomes, L. C., Pavanelli, C. S., Petry, A. C., dos Santos Pompeu, P., Reis, R. E., de Oliveira Roque, F., Sabino, J., de Sousa, L. M., Vilella, F. S., & Zuanon, J. (2023). Ecosystem services generated by Neotropical freshwater fishes. Hydrobiologia , 850 (12–13), 2903–2926. https://doi.org/10.1007/s10750-022-04986-7Pelicice, F. M., Azevedo-Santos, V. M., Vitule, J. R. S., Orsi, M. L., Lima Junior, D. P., Magalhães, A. L. B., Pompeu, P. S., Petrere, M., & Agostinho, A. A. (2017). Neotropical freshwater fishes imperilled by unsustainable policies. Fish and Fisheries , 18 (6), 1119–1133. https://doi.org/10.1111/faf.12228Polanco F., A., Richards, E., Flück, B., Valentini, A., Altermatt, F., Brosse, S., Walser, J. C., Eme, D., Marques, V., Manel, S., Albouy, C., Dejean, T., & Pellissier, L. (2021). Comparing the performance of 12S mitochondrial primers for fish environmental DNA across ecosystems. Environmental DNA ,3 (6), 1113–1127. https://doi.org/10.1002/edn3.232Prog, S., Pihl, L., & Rosenberg, R. (1984). MARINE ECOLOGY-PROGRESS SERIES Crangon crangon in some shallow marine areas in western Sweden .Quéméré, E., Aucourd, M., Troispoux, V., Brosse, S., Murienne, J., Covain, R., Bail, P. Y. L., Olivier, J., Tysklind, N., & Galan, M. (2021). Unraveling the dietary diversity of Neotropical top predators using scat DNA metabarcoding: A case study on the elusive Giant Otter.Environmental DNA , 3 (5), 889–900. https://doi.org/10.1002/edn3.195Ratnasingham, S., & Hebert, P. D. N. (2007). BOLD: The Barcode of Life Data System: Barcoding.Molecular Ecology Notes , 7 (3), 355–364. https://doi.org/10.1111/j.1471-8286.2007.01678.xRobasky, K., Lewis, N. E., & Church, G. M. (2014). The role of replicates for error mitigation in next-generation sequencing. Nature Reviews Genetics ,15 (1), 56–62. https://doi.org/10.1038/nrg3655Sales, N. G., Mariani, S., Salvador, G. N., Pessali, T. C., & Carvalho, D. C. (2018). Hidden Diversity Hampers Conservation Efforts in a Highly Impacted Neotropical River System. Frontiers in Genetics , 9 . https://doi.org/10.3389/fgene.2018.00271Siegenthaler, A., Wangensteen, O. S., Soto, A. Z., Benvenuto, C., Corrigan, L., & Mariani, S. (2019). Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring. Molecular Ecology Resources ,19 (1), 206–220. https://doi.org/10.1111/1755-0998.12956Silveira De Melo, M., & Nakagaki, J. M. (2013). Evaluation of the feeding habits of Macrobrachium brasiliense (Heller, 1862) in the Curral de Arame stream (Dourados/Mato Grosso Do Sul, Brazil). In Nauplius (Vol. 21, Issue 1, pp. 25–33).Su, G., Logez, M., Xu, J., Tao, S., Villéger, S., & Brosse, S. (2021). Human impacts on global freshwater fish biodiversity. Science , 371 (6531), 835–838. https://doi.org/10.1126/SCIENCE.ABD3369/SUPPL_FILE/ABD3369_SU_SM.PDFTakahashi, M., Saccò, M., Kestel, J. H., Nester, G., Campbell, M. A., van der Heyde, M., Heydenrych, M. J., Juszkiewicz, D. J., Nevill, P., Dawkins, K. L., Bessey, C., Fernandes, K., Miller, H., Power, M., Mousavi-Derazmahalleh, M., Newton, J. P., White, N. E., Richards, Z. T., & Allentoft, M. E. (2023). Aquatic environmental DNA: A review of the macro-organismal biomonitoring revolution. Science of the Total Environment , 873 . https://doi.org/10.1016/j.scitotenv.2023.162322Tournayre, O., Leuchtmann, M., Filippi-Codaccioni, O., Trillat, M., Piry, S., Pontier, D., Charbonnel, N., & Galan, M. (2020). In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses. Ecology and Evolution , 10 (13), 6310–6332. https://doi.org/10.1002/ece3.6362Tournayre, O., Tian, H., Lougheed, D. R., Windle, M. J. S., Lambert, S., Carter, J., Sun, Z., Ridal, J., Wang, Y., Cumming, B. F., Arnott, S. E., & Lougheed, S. C. (2024). Enhancing metabarcoding of freshwater biotic communities: A new online tool for primer selection and exploring data from 14 primer pairs.Environmental DNA , 6 (4). https://doi.org/10.1002/edn3.590Toussaint, A., Charpin, N., Brosse, S., & Villéger, S. (2016). Global functional diversity of freshwater fish is concentrated in the Neotropics while functional vulnerability is widespread. Scientific Reports , 6 . https://doi.org/10.1038/srep22125Valentini, A., Taberlet, P., Miaud, C., Civade, R., Herder, J., Thomsen, P. F., Bellemain, E., Besnard, A., Coissac, E., Boyer, F., Gaboriaud, C., Jean, P., Poulet, N., Roset, N., Copp, G. H., Geniez, P., Pont, D., Argillier, C., Baudoin, J. M., … Dejean, T. (2016). Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding. Molecular Ecology , 25 (4), 929–942. https://doi.org/10.1111/mec.13428Vitule, J. R. S., Agostinho, A. A., Azevedo-Santos, V. M., Daga, V. S., Darwall, W. R. T., Fitzgerald, D. B., Frehse, F. A., Hoeinghaus, D. J., Lima-Junior, D. P., Magalhães, A. L. B., Orsi, M. L., Padial, A. A., Pelicice, F. M., Petrere, M., Pompeu, P. S., & Winemiller, K. O. (2017). We need better understanding about functional diversity and vulnerability of tropical freshwater fishes.Biodiversity and Conservation , 26 (3), 757–762. https://doi.org/10.1007/s10531-016-1258-8Weber, S., Junk, I., Brink, L., Wörner, M., Künzel, S., Veith, M., Teubner, D., Klein, R., Paulus, M., & Krehenwinkel, H. (2023). Molecular diet analysis in mussels and other metazoan filter feeders and an assessment of their utility as natural eDNA samplers. Molecular Ecology Resources , 23 (2), 471–485. https://doi.org/10.1111/1755-0998.13710Zinger, L., Donald, J., Brosse, S., Gonzalez, M. A., Iribar, A., Leroy, C., Murienne, J., Orivel, J., Schimann, H., Taberlet, P., & Lopes, C. M. (2020). Advances and prospects of environmental DNA in neotropical rainforests.Advances in Ecological Research , 62 , 331–373. https://doi.org/10.1016/BS.AECR.2020.01.001Zinger, L., Lionnet, C., Benoiston, A. S., Donald, J., Mercier, C., & Boyer, F. (2021). metabaR: An r package for the evaluation and improvement of DNA metabarcoding data quality. Methods in Ecology and Evolution , 12 (4), 586–592. https://doi.org/10.1111/2041-210X.13552