Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA

RESEARCH ARTICLE Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA Ce´ dric MariacID1,2*, Fabrice Duponchelle2,3☯, Guido MirandaID2,4,5☯, Camila Ramallo4, Robert Wallace4, Gabriel Tarifa4, Carmen Garcia-Davila2,6, Herna´ n Ortega7, Julio Pinto5, Jean-Franc¸ ois Renno1,2 1 DIADE, Univ Montpellier, CIRAD, IRD, Montpellier, France, 2 Laboratoire Mixte International—Evolution et Domestication de l’Ichtyofaune Amazonienne (LMI—EDIA), IIAP, UAGRM, IRD, Paris, France, 3 MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France, 4 Wildlife Conservation Society, Bolivia Program, La Paz, Bolivia, 5 Unidad de Limnologı´a, Instituto de Ecologı´a, Universidad Mayor de San Andre´ s, La Paz, Bolivia, 6 Instituto de Investigaciones de la Amazonı´a Peruana (IIAP), Laboratorio de Biologı´a y Gene´tica Molecular (LBGM), Iquitos, Peru´, 7 Departamento de Ictiologı´a, Museo de Historia Natural, Universidad Nacional Mayor San Marcos, Lima, Peru ☯ These authors contributed equally to this work. * cedric.mariac@ird.fr Abstract To date, more than 2400 valid fish species have been recorded in the Amazon basin. How- ever, some regions remain poorly documented. This is the case in the Beni basin and in partic- ular in one of its main sub-basins, the Tuichi, an Andean foothills rivers flowing through the Madidi National Park in the Bolivian Amazonia. The knowledge of its ichthyological diversity is, however, essential for the management and protection of aquatic ecosystems, which are

threatened by the development of infrastructures (dams, factories and cities), mining and deforestation. Environmental DNA (eDNA) has been relatively little used so far in the Amazon basin. We sampled eDNA from water in 34 sites in lakes and rivers in the Beni basin including 22 sites in the Tuichi sub-basin, during the dry season. To assess the biogeographical patterns of the amazonian ichthyofauna, we implemented a metabarcoding approach using two pairs of specific primers designed and developed in our laboratory to amplify two partially overlap- ping CO1 fragments, one of 185bp and another of 285bp. We detected 252 fish taxa (207 at species level) among which 57 are newly identified for the Beni watershed. Species composi- tions are significantly different between lakes and rivers but also between rivers according to their hydrographic rank and altitude. Furthermore, the diversity patterns are related to the dif- ferent hydro-ecoregions through which the Tuichi flows. The eDNA approach makes it possi- ble to identify and complete the inventory of the ichthyofauna in this still poorly documented Amazon basin. However, taxonomic identification remains constrained by the lack of reference barcodes in public databases and does not allow the assignment of all OTUs. Our results can be taken into account in conservation and management strategies and could serve as a base- line for future studies, including on other Andean tributaries. PLOS ONE PLOS ONE | https://doi.org/10.1371/journal.pone.0262357 January 4, 2022 1 / 25 a1111111111 a1111111111 a1111111111 a1111111111

a1111111111 OPEN ACCESS Citation: Mariac C, Duponchelle F, Miranda G, Ramallo C, Wallace R, Tarifa G, et al. (2022) Unveiling biogeographical patterns of the ichthyofauna in the Tuichi basin, a biodiversity hotspot in the Bolivian Amazon, using environmental DNA. PLoS ONE 17(1): e0262357. https://doi.org/10.1371/journal.pone.0262357 Editor: Hideyuki Doi, University of Hyogo, JAPAN Received: June 16, 2021 Accepted: December 21, 2021 Published: January 4, 2022 Peer Review History: PLOS recognizes the benefits of transparency in the peer review process; therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. The editorial history of this article is available here: https://doi.org/10.1371/journal.pone.0262357 Copyright: © 2022 Mariac et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Data Availability Statement: Sequencing reads were deposited in the National Center for Biotechnology Information Sequence Read Archive