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Table S1 Species of angiosperms from the Pacific side of Nicaragua and the northern province of Estelí used to construct a local reference psbA-trnH sequence database for automated identification of flora in the Mesoamerican seasonally deciduous tropical forest. Alongside the plant taxonomy, geographical sources, sample voucher numbers (UNAN Herbarium, IBE-JGZ DNA collection) and public sequence database Accession numbers are given

Table S2 Species of Cassidinae (Coleoptera: Chrysomelidae) of known diet used to test the performance of the automated DNA-based identification pipeline. Several individuals for each species were used to retrieve psbA-trnH sequences from whole-specimen DNA extractions, thus likely representing plant tissue remains in the insect gut. The number of specimens tested, of putative diet sequences retrieved and the results obtained with the pipeline are given

Table S3 GenBank psbA-trnH sequences removed a posteriori from the curated database for automated identification due to problematic taxonomic annotations

Table S4 Resuls of BAGpipe automated taxonomic assignment of 104 infertile plant samples based on psbA-trnH sequences and a reference database including GenBank data and a custom Nicaraguan sclerophyll deciduous tropical forest database

Fig. S1 Distribution of minimum p-distances between 114 Nicaraguan SDTF sequences and their conspecifics from GenBank.

Fig. S2 Maximum-likelihood tree with clade support values above 70% produced automatically by the BAGpipe pipeline for a group of 16 putative diet sequences of the cassid Parorectis rugosa. The pipeline isolated a group of closely related sequences from GenBank and our purpose-built SDTF local reference (NPL codes) and placed the diet sequences within a Physalis clade with high confidence.

Fig. S3 Maximum-likelihood tree with clade support values above 70% produced automatically by the BAGpipe pipeline for a group of seven putative diet sequences of the cassid Physonota alutacea. The pipeline isolated a group of closely related sequences from GenBank and our purpose-built SDTF local reference (NPL codes) and placed the diet sequences within a specific clade of Cordia (+Varronia) sequences and with high confidence.

Appendix S1 Examples of GenBank sequences, annotated as psbA-trnH but not retrieved by any of the similarity searches performed.

Appendix S2 BAGpipe manual. The manual for the whole procedure and specific instructions for scripts can be found at http://www.ibe.upf-csic.es/SOFT/Softwareanddata/ and http://sourceforge.net/users/dchesters.

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