Metabarcoding de comunidades de eucariontes
  • Sesiones
  • Lecturas recomendadas
  1. Lecturas recomendadas
  2. Referencias
  • Día 1
    • Conexión a Zoom
    • Conexión al servidor
  • Día 2
    • Introducción a Linux y R
    • Introducción al pipeline DADA2
    • Nuestros datos: eDNA de peces del Golfo de California
    • Clonación de repositorio Github
    • Preparación del entorno
  • Día 3
    • Archivos FASTQ: estructura y organización
    • Control de calidad y recorte de primers con Cutadapt
    • DADA2 — Filtrado inicial
  • Día 4
    • Dada2 - Dereplicación e Inferencia de Errores
    • Dada2 - Unión de lecturas paired-end
    • Dada2 - Remoción de quimeras y seguimiento de lecturas
    • Dada2 - Asignación taxonómica y guardado de resultados
  • Día 5
    • Análisis ecológico de comunidades de peces
    • OTUs: agrupamiento por similitud con VSEARCH
    • Detección y remoción de contaminantes con decontam
    • Bases de datos de referencia personalizadas
  • Lecturas recomendadas
    • Referencias
  1. Lecturas recomendadas
  2. Referencias

Referencias

Referencias

Allen, M. C., Kwait, R., Vastano, A., Kisurin, A., Zoccolo, I., Jaffe, B. D., Angle, J. C., Maslo, B., & Lockwood, J. L. (2023). Sampling environmental DNA from trees and soil to detect cryptic arboreal mammals. Sci. Rep., 13(1), 180.
Antich, A., Palacin, C., Wangensteen, O. S., & Turon, X. (2021). To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography. BMC Bioinformatics, 22(1), 177.
Antich, A., Palacín, C., Cebrian, E., Golo, R., Wangensteen, O. S., & Turon, X. (2021). Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities? Mol. Ecol., 30(13), 3175-3188.
Bang-Andreasen, T., Schostag, M., Priemé, A., Elberling, B., & Jacobsen, C. S. (2017). Potential microbial contamination during sampling of permafrost soil assessed by tracers. Sci. Rep., 7(1), 43338.
Beng, K. C., & Corlett, R. T. (2020). Applications of environmental DNA (eDNA) in ecology and conservation: opportunities, challenges and prospects. Biodivers. Conserv., 29(7), 2089-2121.
Blischak, J. D., Davenport, E. R., & Wilson, G. (2016). A quick introduction to version control with git and GitHub. PLoS Comput. Biol., 12(1), e1004668.
Bowers, H. A., Pochon, X., Ammon, U. von, Gemmell, N., Stanton, J.-A. L., Jeunen, G.-J., Sherman, C. D. H., & Zaiko, A. (s. f.). Towards the Optimization of eDNA/eRNA Sampling Technologies for Marine Biosecurity Surveillance.
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. Nat. Methods, 13(7), 581-583.
Capo, E., Giguet-Covex, C., Rouillard, A., Nota, K., Heintzman, P. D., Vuillemin, A., Ariztegui, D., Arnaud, F., Belle, S., Bertilsson, S., Bigler, C., Bindler, R., Brown, A. G., Clarke, C. L., Crump, S. E., Debroas, D., Englund, G., Ficetola, G. F., Garner, R. E., … Parducci, L. (2021). Lake sedimentary DNA research on past terrestrial and aquatic biodiversity: Overview and recommendations. Quaternary, 4(1), 6.
Capo, E., Monchamp, M.-E., Coolen, M. J. L., Domaizon, I., Armbrecht, L., & Bertilsson, S. (2022). Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential. Environ. Microbiol., 24(5), 2201-2209.
Çevik, T., & Çevik, N. (2025). Environmental DNA (eDNA): A review of ecosystem biodiversity detection and applications. Biodivers. Conserv., 34(9), 2999-3035.
Cruz-Cano, R., Kolb, M., Saldaña-Vázquez, R. A., Bretón-Deval, L., Cruz-Cano, N., & Aldama-Cervantes, A. (2024). Existing evidence on the use of environmental DNA as an operational method for studying rivers: a systematic map and thematic synthesis. Environ. Evid., 13(1), 2.
Dickie, I. A., Boyer, S., Buckley, H. L., Duncan, R. P., Gardner, P. P., Hogg, I. D., Holdaway, R. J., Lear, G., Makiola, A., Morales, S. E., Powell, J. R., & Weaver, L. (2018). Towards robust and repeatable sampling methods in eDNA-based studies. Mol. Ecol. Resour., 18(5), 940-952.
Elbrecht, V., & Leese, F. (2017). Validation and Development of COI Metabarcoding Primers for Freshwater Macroinvertebrate Bioassessment. Front. Environ. Sci. Eng. China, 5.
Francioli, D., Lentendu, G., Lewin, S., & Kolb, S. (2021). DNA metabarcoding for the characterization of terrestrial Microbiota-pitfalls and solutions. Microorganisms, 9(2), 361.
Gold, Z., Wall, A. R., Schweizer, T. M., Pentcheff, N. D., Curd, E. E., Barber, P. H., Meyer, R. S., Wayne, R., Stolzenbach, K., Prickett, K., Luedy, J., & Wetzer, R. (2022). A manager’s guide to using eDNA metabarcoding in marine ecosystems. PeerJ, 10(e14071), e14071.
Hakimzadeh, A., Abdala Asbun, A., Albanese, D., Bernard, M., Buchner, D., Callahan, B., Caporaso, J. G., Curd, E., Djemiel, C., Brandström Durling, M., Elbrecht, V., Gold, Z., Gweon, H. S., Hajibabaei, M., Hildebrand, F., Mikryukov, V., Normandeau, E., Özkurt, E., M Palmer, J., … Anslan, S. (2024). A pile of pipelines: An overview of the bioinformatics software for metabarcoding data analyses. Mol. Ecol. Resour., 24(5), e13847.
Hoshino, T., & Inagaki, F. (2024). Distribution of eukaryotic environmental DNA in global subseafloor sediments. Prog. Earth Planet. Sci., 11(1), 19.
Howell, L., LaRue, M., & Flanagan, S. P. (2021). Environmental DNA as a tool for monitoring Antarctic vertebrates. N. Z. J. Zool., 48(3-4), 245-262.
Jaquier, M., Albouy, C., Bach, W., Waldock, C., Marques, V., Maire, E., Juhel, J. B., Andrello, M., Valentini, A., Manel, S., Dejean, T., Mouillot, D., & Pellissier, L. (2024). Environmental DNA recovers fish composition turnover of the coral reefs of West Indian Ocean islands. Ecol. Evol., 14(5), e11337.
Jeunen, G.-J., Lamare, M., Cummings, V., Treece, J., Ferreira, S., Massuger, J., Pryor Rodgers, L., Tait, L., Lust, B., Wilkinson, S., Mariani, S., Mills, S., & Gemmell, N. (2023). Unveiling the hidden diversity of marine eukaryotes in the Ross Sea: A comparative analysis of seawater and sponge eDNA surveys. Environ. DNA, 5(6), 1780-1792.
Jo, T. S. (2023). Utilizing the state of environmental DNA (eDNA) to incorporate time-scale information into eDNA analysis. Proc. Biol. Sci., 290(1999), 20230979.
Kamoroff, C., & Goldberg, C. S. (2018). An issue of life or death: using eDNA to detect viable individuals in wilderness restoration. Freshw. Sci., 000-000.
Kumar, G., Eble, J. E., & Gaither, M. R. (2020). A practical guide to sample preservation and pre-PCR processing of aquatic environmental DNA. Mol. Ecol. Resour., 20(1), 29-39.
Kuo, L.-Y., Tang, S.-K., Huang, Y.-H., Xie, P.-J., Chen, C.-W., Chang, Z.-X., Hsu, T.-C., Chang, Y.-H., Chao, Y.-S., Chen, C.-W., Fawcett, S., Nitta, J. H., Sundue, M., Kao, T.-T., Luu, H. T., Mustapeng, A. M. A., Coritico, F. P., Amoroso, V. B., & Thai, Y. K. (2024). A DNA barcode reference of Asian ferns with expert-identified voucher specimens and DNA samples. Sci. Data, 11(1), 1314.
Lamy, T., Pitz, K. J., Chavez, F. P., Yorke, C. E., & Miller, R. J. (2021). Environmental DNA reveals the fine-grained and hierarchical spatial structure of kelp forest fish communities. Sci. Rep., 11(1), 14439.
Macher, T.-H., Arle, J., Beermann, A. J., Frank, L., Hupało, K., Koschorreck, J., Schütz, R., & Leese, F. (2024). Is it worth the extra mile? Comparing environmental DNA and RNA metabarcoding for vertebrate and invertebrate biodiversity surveys in a lowland stream. PeerJ, 12, e18016.
Marchesi, J. R., & Ravel, J. (2015). The vocabulary of microbiome research: a proposal. Microbiome, 3(1), 31.
Massilani, D., Morley, M. W., Mentzer, S. M., Aldeias, V., Vernot, B., Miller, C., Stahlschmidt, M., Kozlikin, M. B., Shunkov, M. V., Derevianko, A. P., Conard, N. J., Wurz, S., Henshilwood, C. S., Vasquez, J., Essel, E., Nagel, S., Richter, J., Nickel, B., Roberts, R. G., … Meyer, M. (2022). Microstratigraphic preservation of ancient faunal and hominin DNA in Pleistocene cave sediments. Proc. Natl. Acad. Sci. U. S. A., 119(1), e2113666118.
Mauvisseau, Q., Harper, L. R., Sander, M., Hanner, R. H., Kleyer, H., & Deiner, K. (2022). The multiple states of environmental DNA and what is known about their persistence in aquatic environments. Environ. Sci. Technol., 56(9), 5322-5333.
McClenaghan, B., Compson, Z. G., & Hajibabaei, M. (2020). Validating metabarcoding-based biodiversity assessments with multi-species occupancy models: A case study using coastal marine eDNA. PLoS One, 15(3), e0224119.
Morey, K. C., Myler, E., Hanner, R., & Tetreault, G. (2024). Taxonomic blind spots: A limitation of environmental DNA metabarcoding‐based detection for Canadian freshwater fishes. Environ. DNA, 6(6), e70054.
Nichols, P. K., Fraiola, K. M. S., Sherwood, A. R., Hauk, B. B., Lopes, K. H., Jr, Davis, C. A., Fumo, J. T., Counsell, C. W. W., Williams, T. M., Spalding, H. L., & Marko, P. B. (2025). Navigating uncertainty in environmental DNA detection of a nuisance marine macroalga. PLoS One, 20(2), e0318414.
Patin, N. V., & Goodwin, K. D. (2022). Capturing marine microbiomes and environmental DNA: A field sampling guide. Front. Microbiol., 13, 1026596.
Pawlowski, J., Apothéloz-Perret-Gentil, L., & Altermatt, F. (2020). Environmental DNA: What’s behind the term? Clarifying the terminology and recommendations for its future use in biomonitoring. Mol. Ecol., 29(22), 4258-4264.
Pawlowski, J., Bruce, K., Panksep, K., Aguirre, F. I., Amalfitano, S., Apothéloz-Perret-Gentil, L., Baussant, T., Bouchez, A., Carugati, L., Cermakova, K., Cordier, T., Corinaldesi, C., Costa, F. O., Danovaro, R., Dell’Anno, A., Duarte, S., Eisendle, U., Ferrari, B. J. D., Frontalini, F., … Fazi, S. (2022). Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods. Sci. Total Environ., 818(151783), 151783.
(PDF) Taxonomic Blind Spots: A Limitation of Environmental DNA Metabarcoding‐Based Detection for Canadian Freshwater Fishes. (s. f.). https://www.researchgate.net/publication/387445076_Taxonomic_Blind_Spots_A_Limitation_of_Environmental_DNA_Metabarcoding-Based_Detection_for_Canadian_Freshwater_Fishes.
Rishan, S. T., Kline, R. J., & Rahman, M. S. (2025). Environmental DNA (eDNA) collection techniques across diverse ecosystems: a mini-review of promising new tools for eDNA metabarcoding. Environ. Sci. Pollut. Res. Int., 32(23), 13566-13577.
Rodriguez-Ezpeleta, N., Morissette, O., Bean, C. W., Manu, S., Banerjee, P., Lacoursière-Roussel, A., Beng, K. C., Alter, S. E., Roger, F., Holman, L. E., Stewart, K. A., Monaghan, M. T., Mauvisseau, Q., Mirimin, L., Wangensteen, O. S., Antognazza, C. M., Helyar, S. J., Boer, H. de, Monchamp, M.-E., … Deiner, K. (2021). Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA: Comment on «Environmental DNA: What’s behind the term?» by Pawlowski et al., (2020). Mol. Ecol., 30(19), 4601-4605.
Ruppert, K. M., Kline, R. J., & Rahman, M. S. (2019). Past, present, and future perspectives of environmental DNA (eDNA) metabarcoding: A systematic review in methods, monitoring, and applications of global eDNA. Global Ecology and Conservation, 17, e00547.
Sahu, A., Singh, M., Amin, A., Malik, M. M., Qadri, S. N., Abubakr, A., Teja, S. S., Dar, S. A., & Ahmad, I. (2025). A systematic review on environmental DNA (eDNA) Science: An eco-friendly survey method for conservation and restoration of fragile ecosystems. Ecol. Indic., 173(113441), 113441.
Santos, R. A. dos, & Blabolil, P. (2025). Comparison of bioinformatic pipelines for eDNA metabarcoding data analysis of fish populations. G., 10(5), 214.
Taberlet, P., Coissac, E., Pompanon, F., Brochmann, C., & Willerslev, E. (2012). Towards next-generation biodiversity assessment using DNA metabarcoding. Mol. Ecol., 21(8), 2045-2050.
Tournayre, O., Littlefair, J. E., Garrett, N. R., Allerton, J. J., Brown, A. S., Cristescu, M. E., & Clare, E. L. (2025). First national survey of terrestrial biodiversity using airborne eDNA. Sci. Rep., 15(1), 19247.
Varotto, C., Pindo, M., Bertoni, E., Casarotto, C., Camin, F., Girardi, M., Maggi, V., & Cristofori, A. (2021). A pilot study of eDNA metabarcoding to estimate plant biodiversity by an alpine glacier core (Adamello glacier, North Italy). Sci. Rep., 11(1), 1208.
View of Is it really there? Addressing inadequate sampling and false detection in environmental DNA metabarcoding. (s. f.). https://journals.uplb.edu.ph/index.php/JESAM/article/view/1276/1003.
Walker, S. J., Boilard, A., Henriksen, M., Lord, E., Robu, M., Buylaert, J.-P., Beijersbergen, L. M. T., Halvorsen, L. S., Cintrón-Santiago, A. M., Onshuus, E. K., Cockerill, C. A., Ujvari, G., Palcsu, L., Temovski, M., Maccali, J., Linge, H., Olsen, J., Aksnes, S., Bertheussen, A., … Boessenkool, S. (2025). A 75,000-y-old Scandinavian Arctic cave deposit reveals past faunal diversity and paleoenvironment. Proc. Natl. Acad. Sci. U. S. A., 122(32), e2415008122.
Weigand, H., Beermann, A. J., Čiampor, F., Costa, F. O., Csabai, Z., Duarte, S., Geiger, M. F., Grabowski, M., Rimet, F., Rulik, B., Strand, M., Szucsich, N., Weigand, A. M., Willassen, E., Wyler, S. A., Bouchez, A., Borja, A., Čiamporová-Zaťovičová, Z., Ferreira, S., … Ekrem, T. (2019). DNA barcode reference libraries for the monitoring of aquatic biota in Europe: Gap-analysis and recommendations for future work. Sci. Total Environ., 678, 499-524.
Weingarten, A., Häusler, M., Serangeli, J., Verheijen, I., Reiter, E., Radzevičiūtė, R., Stoessel, A., Krause, J., Spyrou, M. A., Conard, N. J., Nieselt, K., & Posth, C. (2025). Mitochondrial genomes of Middle Pleistocene horses from the open-air site complex of Schöningen. Nat. Ecol. Evol., 9(12), 2248-2258.
Williams, J., Pettorelli, N., Dowell, R., Macdonald, K., Meyer, C., Steyaert, M., Tweedt, S., & Ransome, E. (2024). SimpleMetaPipeline: Breaking the bioinformatics bottleneck in metabarcoding. Methods Ecol. Evol., 15(11), 1949-1957.
Zainal Abidin, D. H., Mohd Nor, S. A., Lavoué, S., A Rahim, M., & Mohammed Akib, N. A. (2022). Assessing a megadiverse but poorly known community of fishes in a tropical mangrove estuary through environmental DNA (eDNA) metabarcoding. Sci. Rep., 12(1), 16346.
Zarcero, J., Antich, A., Rius, M., Wangensteen, O. S., & Turon, X. (2024). A new sampling device for metabarcoding surveillance of port communities and detection of non-indigenous species. iScience, 27(1), 108588.
Zemmer, F., Cristofori, A., Cristofolini, F., & Gottardini, E. (2024). Aerobiology in alpine environments: Exploring pollen biodiversity and its impacts on human health. Sci. Total Environ., 955(176908), 176908.
Bases de datos de referencia personalizadas

© Dra. Tania Valdivia Carrillo — Todos los derechos reservados