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Here, we integrate long\u2010read DNA barcoding, non\u2010target sequence co\u2010amplification, and host plant taxonomy to reconstruct tri\u2010trophic interactions among leaf\u2010mining insects, their host plants, and associated parasitoids in a Mexican tropical dry forest. Using Single Molecule, Real\u2010Time (SMRT) sequencing on the PacBio Sequel IIe platform, we generated high\u2010fidelity barcodes from individual leaf\u2010miner larvae and from parasitoid larvae and pupae recovered from leaf mines. From 253 specimens, we obtained 214 sequences, and identified 83 operational taxonomic units including leaf\u2010mining Lepidoptera, Diptera, Coleoptera, and their hymenopteran parasitoids, plus 31 non\u2010target sequences. Of the 214 sequences, 69 were parasitoid wasps (32.2%). Of these, 40 were obtained from parasitoids dissected directly from leaf mines, while 29 were co\u2010amplified from leaf\u2010miner samples, demonstrating that SMRT\u2010based co\u2010amplification allows detection of parasitism without rearing. Our analysis revealed 156 trophic interaction types and 247 interaction events. Network analyses showed a highly modular tripartite network, with module structure primarily driven by host plant identity and a reduced set of influential leaf\u2010miner and parasitoid taxa. Bipartite networks supported the hypothesis that interactions are more strongly compartmentalized between leafminers and host plants than at higher trophic levels. These results demonstrate that long\u2010read DNA barcoding with co\u2010amplification detection provides a scalable framework for reconstructing multi\u2010trophic interactions from individual specimens, overcoming key limitations of rearing\u2010based methods and enabling robust biodiversity and ecological network assessments in species\u2010rich ecosystems.<\/jats:p>","DOI":"10.1111\/1755-0998.70183","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T13:16:41Z","timestamp":1787750201000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["High\u2010Throughput\n                    <scp>DNA<\/scp>\n                    Barcoding Reveals Multi\u2010Trophic Networks of Plants, Leafminers and Parasitoids in a Tropical Dry Forest"],"prefix":"10.1111","volume":"26","author":[{"given":"Ariel H.","family":"Mu\u00f1oz\u2010S\u00e1nchez","sequence":"first","affiliation":[{"name":"Ciencias Agrogen\u00f3micas, Escuela Nacional de Estudios Superiores Unidad Le\u00f3n Universidad Nacional Aut\u00f3noma de M\u00e9xico  Le\u00f3n Guanajuato Mexico"},{"name":"Posgrado en Ciencias Biol\u00f3gicas Universidad Nacional Aut\u00f3noma de M\u00e9xico  Mexico City Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo","family":"Contreras\u2010Negrete","sequence":"additional","affiliation":[{"name":"Ciencias Agrogen\u00f3micas, Escuela Nacional de Estudios Superiores Unidad Le\u00f3n Universidad Nacional Aut\u00f3noma de M\u00e9xico  Le\u00f3n Guanajuato Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5837-1929","authenticated-orcid":false,"given":"Alejandro","family":"Zald\u00edvar\u2010River\u00f3n","sequence":"additional","affiliation":[{"name":"Colecci\u00f3n Nacional de Insectos, Instituto de Biolog\u00eda Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cd. Universitaria  Ciudad de M\u00e9xico Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rafael Torres","family":"Col\u00edn","sequence":"additional","affiliation":[{"name":"Herbario Nacional, Instituto de Biolog\u00eda Universidad Nacional Aut\u00f3noma de M\u00e9xico, Cd. Universitaria  Ciudad de M\u00e9xico Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Evgeny V.","family":"Zakharov","sequence":"additional","affiliation":[{"name":"Canadian Centre for DNA Barcoding, Centre for Biodiversity Genomics University of Guelph  Guelph Ontario Canada"},{"name":"Department of Integrative Biology University of Guelph  Guelph Ontario Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2278-2368","authenticated-orcid":false,"given":"Carlos","family":"L\u00f3pez\u2010Vaamonde","sequence":"additional","affiliation":[{"name":"Institut de Recherche Sur la Biologie de L'insecte, CNRS UMR 7261, Universit\u00e9 de Tours, UFR Sciences et Techniques  Tours France"},{"name":"INRAE, UR633, Zoologie Foresti\u00e8re  Orl\u00e9ans France"},{"name":"2nd Zoological Department Natural History Museum Vienna  Vienna Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0080-7512","authenticated-orcid":false,"given":"Antonio","family":"Hern\u00e1ndez\u2010L\u00f3pez","sequence":"additional","affiliation":[{"name":"Ciencias Agrogen\u00f3micas, Escuela Nacional de Estudios Superiores Unidad Le\u00f3n Universidad Nacional Aut\u00f3noma de M\u00e9xico  Le\u00f3n Guanajuato Mexico"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"e_1_2_12_2_1","doi-asserted-by":"publisher","DOI":"10.1111\/j.0030-1299.2008.16644.x"},{"key":"e_1_2_12_3_1","volume-title":"Living Planet Report 2022\u2014Building a Nature\u2010Positive Society","author":"Almond R. 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