DNA Barcodes Applied to a Rapid Baseline Construction in Biodiversity Monitoring for the Conservation of Aquatic Ecosystems in the Sian Ka’an Reserve (Mexico) and Adjacent Areas

Abstract

This study is focused on the aquatic environments of the Sian Ka’an reserve, a World Heritage Site. We applied recently developed protocols for the rapid assessment of most animal taxa inhabiting any freshwater system using light traps and DNA barcodes, represented by the mitochondrial gene Cytochrome Oxidase I (COI). We DNA barcoded 1037 specimens comprising mites, crustaceans, insects, and fish larvae from 13 aquatic environments close or inside the reserve, with a success rate of 99.8%. In total, 167 barcode index numbers (BINs) were detected. From them, we identified 43 species. All others remain as a BIN. Besides, we applied the non-invasive method of environmental DNA (eDNA) to analyze the adult fish communities and identified the sequences obtained with the Barcode of Life Database (BOLD). All round, we found 25 fish species and other terrestrial vertebrates from this region. No alien species was found. After comparing the BINs from all systems, we found that each water body was unique with respect to the communities observed. The reference library presented here represents the first step for future programs to detect any change in these ecosystems, including invasive species, and to improve the knowledge of freshwater zooplankton, enhancing the task of compiling the species barcodes not yet stored in databases (such as BOLD or GenBank).

Identifying Early Stages of Freshwater Fish with DNA Barcodes in Several Sinkholes and Lagoons from the East of Yucatan Peninsula, Mexico

“…Most of the fish species found in this study have been reported in different aquatic systems in Yucatán and the Quintana Roo state [22,24]. Valdez Moreno et al [25], using metabarcoding in the same places as us (except Minicenote), corroborated the presence of all the species found by us in these sites [24,25]. However, we found some interesting cases, explained in the following paragraphs.…”

“…Although Cocalitos has the highest number of species, it is necessary to consider that this place was sampled six times compared to the others, which were visited once or twice (Table 1). Based on our results and previous studies [25], Muyil and Chuyanché lagoons have the highest number of species. The differences among the richness reported can be associated with several factors such as vegetation, shore area, and collecting method [54,56].…”

“…For the morphological identification of the larvae, we used different identification keys as Richards [9], Fahay [20], and studies of freshwater fishes where their larval stages are described [21]. For information about what species could be found in the study area, we used Miller et al [22], Schmitter-Soto [23], and Valdez-Moreno [24,25].…”

“…pers.) and using environmental DNA [24,25,57]. These differences are most likely due to different collection methods and objectives (minnow traps, dip, cast nets, hanging nets, DNA in water, and none of them collected larvae).…”

Mesozooplankton biodiversity, vertical assemblages, and diel migration in the western tropical Pacific Ocean revealed by eDNA metabarcoding and morphological methods

“…The eDNA method has been used to assess the biodiversity and distribution of medusae (Takasu et al, 2019;Ames et al, 2021). Therefore, this method is becoming a research priority, and it has great application potential in ecological monitoring and assessment (Valdez-Moreno et al, 2021;Xie et al, 2021). However, limited metabarcoding studies were conducted in the open sea with high biodiversity and complex community structure relative to coastal waters and continental shelf areas (Suter et al, 2021).…”