Knowledge gap in vertebrate genetic diversity in a northern remanent of neotropical rainforest
4 affiliations
- 1Departamento de Ciencias de la Sustentabilidad, Unidad Tapachula, El Colegio de la Frontera Sur, Tapachula, Chiapas, México
- 2Departamento de Zoología/Pabellón Nacional de la Biodiversidad, Instituto de Biología, Universidad Nacional Autónoma de México, Ciudad de México, México
- 3Sceretaría de Ciencias, Humanidades, Tecnología e Innovación-Dirección de Innovación y Transferencia de Conocimiento, Benemérita Universidad Autónoma de Puebla, Puebla, México
- 4Secretaría de Ciencia, Humanidades, Tecnología e Innovación, Ciudad de México, México
Abstract
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.
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BibTeX
@article{cano2026knowledge,
title = {{Knowledge gap in vertebrate genetic diversity in a northern remanent of neotropical rainforest}},
author = {David José Martínez Cano and Víctor Hugo Reynoso and María de Lourdes Vázquez-Cruz and Edyciel Jordán Alvarado-Robledo and Yesenia Ithaí Ángeles-López and Eugenia Zarza},
journal = {PLOS One},
year = {2026},
month = nov,
doi = {10.1371/journal.pone.0357894},
url = {https://doi.org/10.1371/journal.pone.0357894},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Knowledge gap in vertebrate genetic diversity in a northern remanent of neotropical rainforest
AU - David José Martínez Cano
AU - Víctor Hugo Reynoso
AU - María de Lourdes Vázquez-Cruz
AU - Edyciel Jordán Alvarado-Robledo
AU - Yesenia Ithaí Ángeles-López
AU - Eugenia Zarza
PY - 2026
DA - 2026/11/03
JO - PLOS One
DO - 10.1371/journal.pone.0357894
UR - https://doi.org/10.1371/journal.pone.0357894
AB - 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.
SN - 1932-6203
ER -