Knowledge gap in vertebrate genetic diversity in a northern remanent of neotropical rainforest

Los Tuxtlas Biosphere Reserve is one of the last remaining areas of primary tropical rainforest in Mexico. This fragile ecosystem heavily reduced by human perturbations is part of the Mesoamerican hotspot. The reserve harbors many endemic species. Thus, identifying, cataloging, and studying the biodiversity of this ecosystem has been of utmost importance. A promising approach for fast species identification to assess biodiversity is the use of DNA barcoding techniques. However, these techniques are limited by reliable DNA databases. Using novel Perl scripts, we generated a barcoding database to assess mitochondrial sequence availability in public databases for 903 vertebrate species that inhabit the reserve. Of these, 39 species had no sequences, 189 had complete mitochondrial genomes sequenced and the rest were partially sequenced. We studied over 80,000 sequences spanning 16 mitochondrial genomic markers and found 5 well-studied markers (COI-5P, CYTB, ND2, 16S rRNA and 12S rRNA) with more than 50% species coverage. The COI-5P region and CYTB were the best studied and most recommended markers for barcoding studies, and 7 additional markers have been preferred for one or more specific taxonomic groups. The remaining markers were almost exclusively sequenced as part of whole mitochondrial genomes. The best-known taxonomic group was mammals while the least known was reptiles. We also evaluated the sequencing frequency distribution for endemic, threatened and trade-restricted species driving interests in ecological research. In general, most species within each group were less sequenced when compared to the mean of all species, skewed by a few highly sequenced species of ecological interest. The most sequenced species are trade-restricted species, especially threatened species. This is driven by ecology-based research in the area. Finally, our results highlight a lack of barcoding research in local and endemic species of the Mesoamerican hotspot focusing on specific species but ignoring the wider range of biodiversity.