In the Mexican Caribbean, the exotic lionfish Pterois volitans has become a species of great concern because of their predatory habits and rapid expansion onto the Mesoamerican coral reef, the second largest continuous reef system in the world. This is the first report of DNA identification of stomach contents of lionfish using the barcode of life reference database (BOLD). We confirm with barcoding that only Pterois volitans is apparently present in the Mexican Caribbean. We analyzed the stomach contents of 157 specimens of P. volitans from various locations in the region. Based on DNA matches in the Barcode of Life Database (BOLD) and GenBank, we identified fishes from five orders, 14 families, 22 genera and 34 species in the stomach contents. The families with the most species represented were Gobiidae and Apogonidae. Some prey taxa are commercially important species. Seven species were new records for the Mexican Caribbean: Apogon mosavi, Coryphopterus venezuelae, C. thrix, C. tortugae, Lythrypnus minimus, Starksia langi and S. ocellata. DNA matches, as well as the presence of intact lionfish in the stomach contents, indicate some degree of cannibalism, a behavior confirmed in this species by the first time. We obtained 45 distinct crustacean prey sequences, from which only 20 taxa could be identified from the BOLD and GenBank databases. The matches were primarily to Decapoda but only a single taxon could be identified to the species level, Euphausia americana. This technique proved to be an efficient and useful method, especially since prey species could be identified from partially-digested remains. The primary limitation is the lack of comprehensive coverage of potential prey species in the region in the BOLD and GenBank databases, especially among invertebrates.

Barcoding has proven a useful tool in the rapid identification of all life stages of fish species. Such information is of critical importance for fisheries management and conservation, especially in high-diversity regions, such as Mexico’s marine waters, where more than 2200 species occur. The present study reports the barcode analysis of 1392 specimens from the Yucatan Peninsula, corresponding to 610 adults and juveniles, 757 larvae and 25 eggs, representing 181 species (179 teleosts and 2 rays), 136 genera and 74 families. Barcoding results revealed major range extensions and overlooked taxa, including three sympatric species of Albula (one likely undescribed) and a new taxon of Floridichthys. In total, six species of eggs and 34 species of larvae were identified through their barcode match with adults. These cases enabled the first discrimination of the larvae of four species of Eucinostomus, and new information about spawning locality and time was obtained from egg records for the hogfish, Lachnolaimus maximus, which is one of the most commercially important species in the Mexican Caribbean. Also, barcodes revealed mistakes in species recognition during a sport-fish contest. In the future, barcodes will help avoid similar errors and protect rare or endangered species, and will aid regulation of fisheries quotas.

In the waters surrounding Banco Chinchorro in the Mexican Caribbean are spawning and nursery areas for many types of fish. In this natural environment, as opposed to under controlled laboratory conditions, it is almost impossible to link an individual egg to the adult that laid it. This makes identifying the species of the eggs difficult. However, DNA barcodes have made this easier. In the present study, 300 eggs were processed for molecular analysis, from which 139 sequences were obtained. We identified 42 taxa (33 species with their binomial names), 35 genera, and 24 families. The identified eggs included those from Ariomma melanum, which is the first recording of this species in the Mexican Caribbean. Eggs from economically important fish species were also identified, including frigate tuna (Auxis thazard), crevalle jack (Caranx hippos), common dolphinfish (Coryphaena hippurus), sailfish (Istiophorus platypterus), white marlin (Kajikia albida), skipjack tuna (Katsuwonus pelamis), blackfin tuna (Thunnus atlanticus), and swordfish (Xiphias gladius). We have also described new morphological characteristics and captured photographs for 21 species, as well as obtained new information about spawning locality and time for 16 species. This valuable information will provide the basis to develop more effective conservation measures for sustainable fisheries and protection of the Mesoamerican Barrier Reef System.

Decapods include species of economic importance, such as Achelata (lobsters) and Brachyura (true crabs), since they have aesthetic, commercial, gastronomic, and biomedical value. These groups exhibit a great variety of shapes, larval stages, habits, and sizes, making them difficult to recognize. In the Southern Mexican Caribbean (SMC), no taxonomic list or analysis of the biological diversity for the Achelata and Brachyura has been performed. Herein, the biological diversity of these groups was analyzed by reviewing the literature and collecting specimens in the SMC to obtain morphological, ecological, and molecular data. These results showed a total of 29 families, 67 genera, and 98 species recorded, of which, one is considered as a potentially new species, six are new records for the SMC, 12 expanded their distribution range, and 14 species names were updated. In addition, the BOLD system assigned 21 BINs supported with morphological identification. This work contributes positively to the knowledge of the marine and coastal decapods from the SCM as it represents the first effort to recognize their current biological diversity. This information will be used to develop adequate strategies for the conservation and management of marine and coastal natural resources of the SMC.

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).

Our work shows the efficacy of DNA barcoding for recognizing the early stages of freshwater fish. We collected 3195 larvae and juveniles. Of them, we identified 43 different morphotypes. After DNA barcodes of 350 specimens, we ascertained 7 orders, 12 families, 19 genera, 20 species, and 20 Barcode Index Numbers, corresponding to putative species. For the first time, we reported the presence of the brackish species, Gobiosoma yucatanum in Lake Bacalar. Specimens of the genus Atherinella sp. and Anchoa sp. are possibly new species. Using both methods, morphology, and DNA barcodes, we identified 95% of the total larvae collected (2953 to species, and 78 to genus), and all of them were native. From them, the order Gobiiformes represented 87%. The most abundant species were Lophogobius cyprinoides and Dormitator maculatus, followed by Gobiosoma yucatanum and Ctenobius fasciatus. The Muyil and Chuyanché lagoons have the highest number of species. We present for the first time a short description of Cyprinodon artifrons and Floridichthys polyommus. This information conforms an indispensable baseline for ecological monitoring, to evaluate impacts, and developing management and conservation plans of biodiversity, principally in areas under human pressure such as Sian Ka’an, and Lake Bacalar, where tourism is high and growing in disorder.