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