References
Ahlstrom, E. H., & Moser, H. G. (1976). Eggs and larvae of fishes and their role in systematic investigations and in fisheries. Revue des Travaux de L’institut des Peches Maritimes40 (3), 379-398.
Aljanabi, S. M., & Martinez, I. (1997). Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques. Nucleic acids research25 (22), 4692-4693.
Alves, C. B. M., Vieira, F., Pompeu, P. S., & Ministério do Meio Ambiente. (2011). Ictiofauna da bacia hidrográfica do rio São Francisco. Diagnóstico do macrozoneamento ecológico-econômico da bacia hidrográfica do rio São Francisco. Ministério do Meio Ambiente, Brasília , 226-241.
Andersen, K., Bird, K. L., Rasmussen, M., Haile, J., Breuning‐Madsen, H., Kjaer, K. H., … Willerslev, E. (2012). Meta‐barcoding of ‘dirt’ DNA from soil reflects vertebrate biodiversity. Molecular Ecology21 (8), 1966-1979.
Baumgartner, G., Nakatani, K., Gomes, L. C., Bialetzki, A., & Sanches, P. V. (2004). Identification of spawning sites and natural nurseries of fishes in the upper Paraná River, Brazil. Environmental Biology of Fishes71 (2), 115-125.
Baumgartner, G., Nakatani, K., Gomes, L. C., Bialetzki, A., Sanches, P. V., & Makrakis, M. C. (2008). Fish larvae from the upper Paraná River: do abiotic factors affect larval density?. Neotropical Ichthyology6 , 551-558.
Becker, R. A., Sales, N. G., Santos, G. M., Santos, G. B., & Carvalho, D. C. (2015). DNA barcoding and morphological identification of neotropical ichthyoplankton from the Upper Paraná and São Francisco. Journal of Fish Biology87 (1), 159-168.
Bialetzki, A., Nakatani, K., Sanches, P. V., Baumgartner, G., & Gomes, L. C. (2005). Larval fish assemblage in the Baía River (Mato Grosso do Sul State, Brazil): temporal and spatial patterns. Environmental Biology of Fishes73 , 37-47.
Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016). DADA2: High-resolution sample inference from Illumina amplicon data. Nature methods13 (7), 581-583.
Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: architecture and applications. BMC bioinformatics10 , 1-9.
Carvalho, D. C. (2022). Ichthyoplankton DNA metabarcoding: Challenges and perspectives. Molecular Ecology31 (6), 1612-1614.
Collins, R. A., Bakker, J., Wangensteen, O. S., Soto, A. Z., Corrigan, L., Sims, D. W., … & Mariani, S. (2019). Non‐specific amplification compromises environmental DNA metabarcoding with COI. Methods in Ecology and Evolution10 (11), 1985-2001.
Da Silva, P. S., Makrakis, M. C., Miranda, L. E., Makrakis, S., Assumpção, L., Paula, S., … & Marques, H. (2015). Importance of reservoir tributaries to spawning of migratory fish in the upper Paraná River. River Research and Applications31 (3), 313-322.
Deagle, B. E., Jarman, S. N., Coissac, E., Pompanon, F., & Taberlet, P. (2014). DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match. Biology letters10 (9), 20140562.
Duke, E. M., & Burton, R. S. (2020). Efficacy of metabarcoding for identification of fish eggs evaluated with mock communities. Ecology and evolution10 (7), 3463-3476.
Fonseca, V. G. (2018). Pitfalls in relative abundance estimation using eDNA metabarcoding. Molecular Ecology Resources . 18 (5), 923-926.
Fonseca, V. G., Carvalho, G. R., Sung, W., Johnson, H. F., Power, D. M., Neill, S. P., … & Creer, S. (2010). Second-generation environmental sequencing unmasks marine metazoan biodiversity. Nature communications1 (1), 98.
Frantine‐Silva, W., Sofia, S. H., Orsi, M. L., & Almeida, F. S. (2015). DNA barcoding of freshwater ichthyoplankton in the Neotropics as a tool for ecological monitoring. Molecular Ecology Resources15 (5), 1226-1237.
Hebert, P. D., Ratnasingham, S., & De Waard, J. R. (2003). Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society of London. Series B: Biological Sciences270 (suppl_1), S96-S99.
Jiang, R., Lusana, J. L., & Chen, Y. (2022). High-Throughput DNA Metabarcoding as an Approach for Ichthyoplankton Survey in Oujiang River Estuary, China. Diversity14 (12), 1111.
Jørgensen, T., Haile, J., Möller, P. E. R., Andreev, A., Boessenkool, S., Rasmussen, M., … Willerslev, E. (2012). A comparative study of ancient sedimentary DNA, pollen and macrofossils from permafrost sediments of northern Siberia reveals long‐term vegetational stability. Molecular Ecology21 (8), 1989-2003.
Kimmerling, N., Zuqert, O., Amitai, G., Gurevich, T., Armoza-Zvuloni, R., Kolesnikov, I., … Sorek, R. (2018). Quantitative species-level ecology of reef fish larvae via metabarcoding. Nature ecology & evolution2 (2), 306-316.
Ko, H. L., Wang, Y. T., Chiu, T. S., Lee, M. A., Leu, M. Y., Chang, K. Z., … & Shao, K. T. (2013). Evaluating the accuracy of morphological identification of larval fishes by applying DNA barcoding. PLoS One8 (1), e53451.
Liu, J., & Zhang, H. (2021). Combining multiple markers in environmental DNA metabarcoding to assess deep-sea benthic biodiversity. Frontiers in Marine Science8 , 684955.
Locatelli, N. S., McIntyre, P. B., Therkildsen, N. O., & Baetscher, D. S. (2020). GenBank’s reliability is uncertain for biodiversity researchers seeking species-level assignment for eDNA. Proceedings of the National Academy of Sciences117 (51), 32211-32212.
Mariac, C., Vigouroux, Y., Duponchelle, F., García-Dávila, C., Núñez, J., Desmarais, E., & Renno, J. F. (2018). Metabarcoding by capture using a single COI probe (MCSP) to identify and quantify fish species in ichthyoplankton swarms. PLoS One13 (9), e0202976.
Martin, M. (2011). Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet. journal17 (1), 10-12.
McMurdie, P. J., & Holmes, S. (2013). phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data. PloS one8 (4), e61217.
Milan, D. T., Mendes, I. S., Damasceno, J. S., Teixeira, D. F., Sales, N. G., & Carvalho, D. C. (2020). New 12S metabarcoding primers for enhanced Neotropical freshwater fish biodiversity assessment. Scientific Reports10 (1), 1-12.
Miya, M., Gotoh, R. O., & Sado, T. (2020). MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples. Fisheries Science86 (6), 939-970.
Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., … 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 science2 (7), 150088.
Nakatani, K., Agostinho, A.A., Baumgartner, G., Bialetzki, A., Sanches, P.V., Makrakis, M.C., Pavanelli, C.S. (2001). Ovos e larvas de peixes de água doce: desenvolvimento e manual de identificação, first ed. EDUEM, Maringá.
Nobile, A. B., Freitas-Souza, D., Ruiz-Ruano, F. J., Nobile, M. L. M., Costa, G. O., De Lima, F. P., … & Oliveira, C. (2019). DNA metabarcoding of Neotropical ichthyoplankton: Enabling high accuracy with lower cost. Metabarcoding and Metagenomics3 , e35060.
R Core Team (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing . Vienna, Austria. https://www.R-project.org/.
Reynalte-Tataje, D. A., Agostinho, A. A., Bialetzki, A., Hermes-Silva, S., Fernandes, R., & Zaniboni-Filho, E. (2012). Spatial and temporal variation of the ichthyoplankton in a subtropical river in Brazil. Environmental Biology of Fishes94 , 403-419.
Sales, N. G., Wangensteen, O. S., Carvalho, D. C., Deiner, K., Præbel, K., Coscia, I., … Mariani, S. (2021). Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding. Science of the Total Environment754 , 142096.
Sayers, E. W., Bolton, E. E., Brister, J. R., Canese, K., Chan, J., Comeau, D. C., … Sherry, S. T. (2023). Database resources of the National Center for Biotechnology Information in 2023. Nucleic Acids Research51 (D1), D29.
Silva, C. B., Dias, J. D., & Bialetzki, A. (2017). Fish larvae diversity in a conservation area of a neotropical floodplain: influence of temporal and spatial scales. Hydrobiologia787 , 141-152.
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., & Willerslev, E. (2012). Towards next‐generation biodiversity assessment using DNA metabarcoding. Molecular Ecology21 (8), 2045-2050.
Van Nynatten, A., Gallage, K. S., Lujan, N. K., Mandrak, N. E., & Lovejoy, N. R. (2023). Ichthyoplankton metabarcoding: An efficient tool for early detection of invasive species establishment. Molecular Ecology Resources .
Ward, R. D. (2009). DNA barcode divergence among species and genera of birds and fishes. Molecular Ecology Resources9 (4), 1077-1085.
Ward, R. D., Zemlak, T. S., Innes, B. H., Last, P. R., & Hebert, P. D. (2005). DNA barcoding Australia’s fish species. Philosophical Transactions of the Royal Society B: Biological Sciences360 (1462), 1847-1857.
Yu, D. W., Ji, Y., Emerson, B. C., Wang, X., Ye, C., Yang, C., & Ding, Z. (2012). Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring. Methods in Ecology and Evolution3 (4), 613-623.
Zhang, G. K., Chain, F. J., Abbott, C. L., & Cristescu, M. E. (2018). Metabarcoding using multiplexed markers increases species detection in complex zooplankton communities. Evolutionary applications11 (10), 1901-1914.
Zhang, S., Zhao, J., & Yao, M. (2020). A comprehensive and comparative evaluation of primers for metabarcoding eDNA from fish. Methods in Ecology and Evolution11 (12), 1609-1625.