Wanted not, wasted not: Searching for non-target taxa in environmental DNA metabarcoding by-catch

Adelino, 2017, Invasive potential of the pied crow (Corvus albus) in eastern Brazil: best to eradicate before it spreads, Perspect. Ecol. Conserv., 15, 227 Alberti, 2017, Viral to metazoan marine plankton nucleotide sequences from the Tara Oceans expedition, Sci. data, 4, 1, 10.1038/sdata.2017.93 Andruszkiewicz, 2017, Biomonitoring of marine vertebrates in Monterey Bay using eDNA metabarcoding, PLoS One, 12, 10.1371/journal.pone.0176343 Andújar, 2018, Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill, Mol. Ecol., 27, 146, 10.1111/mec.14410 Bencke, 2008, Observações ornitológicas relevantes no Parque Nacional do Iguaçu e arredores, incluindo o primeiro registro de Campylorhynchus turdinus para o Paraná, Atualidades Ornitológicas, 145, 6 Benson, 2018, GenBank, Nucleic Acids Res., 46, D41, 10.1093/nar/gkx1094 Blackburn, 2014, A unified classification of alien species based on the magnitude of their environmental impacts, PLoS Biol, 12, 10.1371/journal.pbio.1001850 Brocardo, 2019, Mamíferos do Parque Nacional do Iguaçu, Oecologia Aust, 23 Burgess, 2001, An improved protocol for separating meiofauna from sediments using colloidal silica sols, Mar. Ecol. Prog. Ser., 214, 161, 10.3354/meps214161 Burton, 2002 Callahan, 2016, DADA2: high-resolution sample inference from Illumina amplicon data, Nat. Methods, 13, 581, 10.1038/nmeth.3869 Camacho, 2009, BLAST+: architecture and applications, BMC Bioinformatics, 10, 421, 10.1186/1471-2105-10-421 Closek, 2019, Marine vertebrate biodiversity and distribution within the central California Current using environmental DNA (eDNA) metabarcoding and ecosystem surveys, Front. Mar. Sci., 6, 732, 10.3389/fmars.2019.00732 Collins, 2019, Non-specific amplification compromises environmental DNA metabarcoding with COI, Methods Ecol. Evol., 10, 1985, 10.1111/2041-210X.13276 Corriale, 2014, Patterns of habitat use and selection by the capybara (Hydrochoerus hydrochaeris): a landscape-scale analysis, Ecol. Res., 29, 191, 10.1007/s11284-013-1113-2 Cunningham, 2016, Electric crows: powerlines, climate change and the emergence of a native invader, Divers. Distrib., 22, 17, 10.1111/ddi.12381 Dal Pont, 2021, Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world, Sci. Rep., 11, 1, 10.1038/s41598-021-02593-5 de Oliveira Bueno, 2020, Hydroelectricity water footprint in Parana hydrograph region, Brazil. Renew. Energy, 162, 596, 10.1016/j.renene.2020.08.047 Dias, 2020, Habitat selection in natural and human-modified landscapes by capybaras (Hydrochoerus hydrochaeris), an important host for Amblyomma sculptum ticks, PLoS One, 15, 10.1371/journal.pone.0229277 Duszynski, 2018 Gamage, 2020, Understanding leptospirosis eco-epidemiology by environmental DNA metabarcoding of irrigation water from two agro-ecological regions of Sri Lanka, PLoS Negl. Trop. Dis., 14, 10.1371/journal.pntd.0008437 Harper, 2019, Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals, Biol. Conserv., 238, 10.1016/j.biocon.2019.108225 José, 2021, Environmental DNA metabarcoding as a useful tool for evaluating terrestrial mammal diversity in tropical forests, Ecol. Appl., 31, e02335, 10.1002/eap.2335 Kamel, 2014, Potential impacts of invasive house crows (Corvus splendens) bird species in Ismailia Governorate, Egypt; ecology, control and risk management, J. Life Sci. Technol, 2, 86 Leese, 2021, Improved freshwater macroinvertebrate detection from environmental DNA through minimized nontarget amplification, Environ. DNA, 3, 261, 10.1002/edn3.177 Lima, 2009, Registros de corvo-bicolor Corvus albus (Passeriformes: Corvidae) em território brasileiro, Atualidades Ornitológicas, 150, 10 Macher, 2021, Beyond fish eDNA metabarcoding: Field replicates disproportionately improve the detection of stream associated vertebrate species, Metabarcoding and Metagenomics, 12, e66557, 10.3897/mbmg.5.66557 Mariani, 2021, Estuarine molecular bycatch as a landscape-wide biomonitoring tool, Biol. Conserv., 261, 10.1016/j.biocon.2021.109287 Martin, 2011, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. J., 17, 10, 10.14806/ej.17.1.200 McElroy, 2020, Calibrating environmental DNA metabarcoding to conventional surveys for measuring fish species richness, Front. Ecol. Evol., 8, 276, 10.3389/fevo.2020.00276 McMurdie, 2013, phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data, PLoS One, 8, e61217, 10.1371/journal.pone.0061217 Mikryukov, V., 2019. metagMisc: miscellaneous functions for metagenomic analysis. Miya, 2020, MiFish metabarcoding: a high-throughput approach for simultaneous detection of multiple fish species from environmental DNA and other samples, Fish. Sci., 1 Miya, 2015, MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species, R. Soc. open Sci., 2, 10.1098/rsos.150088 Moreira, 2013, 3 Nowak, 1999 Pedersen, T.L., 2019. Patchwork: The composer of plots. R Packag. version 1. R Core Team, 2021. R: A Language and Environment for Statistical Computing. URL https://www.r-project.org/ [accessed 2020-03-30]. Ryall, 1992, 16, 1 Sales, 2020, Assessing the potential of environmental DNA metabarcoding for monitoring Neotropical mammals: a case study in the Amazon and Atlantic Forest, Brazil. Mamm. Rev., 50, 221, 10.1111/mam.12183 Sales, 2021, Space-time dynamics in monitoring neotropical fish communities using eDNA metabarcoding, Sci. Total Environ., 754, 10.1016/j.scitotenv.2020.142096 Sato, 2019, Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of, Japan. Sci. Rep., 9, 1 Seymour, 2020, Executing multi-taxa eDNA ecological assessment via traditional metrics and interactive networks, Sci. Total Environ., 729, 10.1016/j.scitotenv.2020.138801 Shokralla, 2015, Massively parallel multiplex DNA sequencing for specimen identification using an Illumina MiSeq platform, Sci. Rep., 5, 1, 10.1038/srep09687 Sievert, 2020 Silva e Silva, 2007, Adendas e registros significativos para a avifauna dos manguezais de Santos e Cubatão, SP. Rev. Bras. Ornitol., 15, 551 Stat, 2017, Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment, Sci. Rep., 7, 12240, 10.1038/s41598-017-12501-5 Straube, 2004, Uma revisão crítica sobre o grau de conhecimento da avifauna do Parque Nacional do Iguaçu (Paraná, Brasil) e áreas adjacentes, Atualidades Ornitológicas, 118 Straube, 2004, Novas informações sobre a avifauna do Parque Nacional do Iguaçu (Paraná), Atualidades Ornitológicas, 120, 1 Valdez-Moreno, 2019, Using eDNA to biomonitor the fish community in a tropical oligotrophic lake, PLoS One, 14, 10.1371/journal.pone.0215505 Van Rossum, 2009 Wickham, H., 2017. tidyverse: Easily Install and Load “Tidyverse” Packages (Version R package version 1.1. 1). Wickham, 2016 Yang, 2021, Recent advances in environmental DNA-based biodiversity assessment and conservation, Divers. Distrib., 27, 1876, 10.1111/ddi.13415 Yap, 2004, Southeast Asian invasive birds: ecology, impact and management, Ornithol. Sci., 3, 57, 10.2326/osj.3.57