A DNA barcode reference library of French Polynesian shore fishes

A new species of Trimma of the T. taylori species group (Teleostei: Gobiidae) from the Red Sea, Indian Ocean

A new species of Trimma is described from the Red Sea along the Saudi Arabian coast. Specimens and/or photographs of this species are available from the Egyptian Red Sea to Eritrea. These specimens, formerly identified as T. taylori, differ from all other samples from the Indo-Pacific currently identified as T. taylori in having 9 and 89 dorsal- and anal-fin rays respectively (vs. usually 10 and 10 rays), 13 pectoral-fin rays (vs. usually 14 rays), and cycloid scales covering the entire predorsal region from the upper base of the pectoral fin anterior to a convex line posterodorsally to just lateral to the base of the sixth first dorsal-fin spine (vs. predorsal region mostly or entirely covered with ctenoid scales). In addition, specimens from the Red Sea form a monophyletic lineage in a Maximum Likelihood analysis of the COI gene. In this tree, the new species is the sister group to a clade composed of three lineages. One is composed of specimens from the Maldives, which is the sister group of a single available specimen from the Seychelles. These two together are the sister group of specimens of a widespread western Pacific clade.

Biodiversity of Philippine marine fishes: A DNA barcode reference library based on voucher specimens

Accurate identification of fishes is essential for understanding their biology and to ensure food safety for consumers. DNA barcoding is an important tool because it can verify identifications of both whole and processed fishes that have had key morphological characters removed (e.g., filets, fish meal); however, DNA reference libraries are incomplete, and public repositories for sequence data contain incorrectly identified sequences. During a nine-year sampling program in the Philippines, a global biodiversity hotspot for marine fishes, we developed a verified reference library of cytochrome c oxidase subunit I (COI) sequences for 2,525 specimens representing 984 species. Specimens were primarily purchased from markets, with additional diversity collected using rotenone or fishing gear. Species identifications were verified based on taxonomic, phenotypic, and genotypic data, and sequences are associated with voucher specimens, live-color photographs, and genetic samples catalogued at Smithsonian Institution, National Museum of Natural History. The Biodiversity of Philippine Marine Fishes dataset is released herein to increase knowledge of species diversity and distributions and to facilitate accurate identification of market fishes.

Maximizing the reliability and the number of species assignments in metabarcoding studies using a curated regional library and a public repository

Biodiversity assessments relying on DNA have increased rapidly over the last decade. However, the reliability of taxonomic assignments in metabarcoding studies is variable and affected by the reference databases and the assignment methods used. Species level assignments are usually considered as reliable using regional libraries but unreliable using public repositories. In this study, we aimed to test this assumption for metazoan species detected in the Gulf of St. Lawrence in the Northwest Atlantic. We first created a regional library (GSL-rl) by data mining COI barcode sequences from BOLD, and included a reliability ranking system for species assignments. We then estimated 1) the accuracy and precision of the public repository NCBI-nt for species assignments using sequences from the regional library and 2) compared the detection and reliability of species assignments of a metabarcoding dataset using either NCBI-nt or the regional library and popular assignment methods. With NCBI-nt and sequences from the regional library, the BLAST-LCA (least common ancestor) method was the most precise method for species assignments, but the accuracy was higher with the BLAST-TopHit method (>80% over all taxa, between 70% and 90% amongst taxonomic groups). With the metabarcoding dataset, the reliability of species assignments was greater using GSL-rl compared to NCBI-nt. However, we also observed that the total number of reliable species assignments could be maximized using both GSL-rl and NCBI-nt with different optimized assignment methods. The use of a two-step approach for species assignments, i.e., using a regional library and a public repository, could improve the reliability and the number of detected species in metabarcoding studies.

Identification of Fish Species and Targeted Genetic Modifications Based on DNA Analysis: State of the Art

Food adulteration is one of the most serious problems regarding food safety and quality worldwide. Besides misleading consumers, it poses a considerable health risk associated with the potential non-labeled allergen content. Fish and fish products are one of the most expensive and widely traded commodities, which predisposes them to being adulterated. Among all fraud types, replacing high-quality or rare fish with a less valuable species predominates. Because fish differ in their allergen content, specifically the main one, parvalbumin, their replacement can endanger consumers. This underlines the need for reliable, robust control systems for fish species identification. Various methods may be used for the aforementioned purpose. DNA-based methods are favored due to the characteristics of the target molecule, DNA, which is heat resistant, and the fact that through its sequencing, several other traits, including the recognition of genetic modifications, can be determined. Thus, they are considered to be powerful tools for identifying cases of food fraud. In this review, the major DNA-based methods applicable for fish meat and product authentication and their commercial applications are discussed, the possibilities of detecting genetic modifications in fish are evaluated, and future trends are highlighted, emphasizing the need for comprehensive and regularly updated online database resources.

A DNA barcode library for katydids, cave crickets, and leaf-rolling crickets (Tettigoniidae, Rhaphidophoridae and Gryllacrididae) from Zhejiang Province, China

Barcode libraries are generally assembled with two main objectives in mind: specimen identification and species discovery/delimitation. In this study, the standard COI barcode region was sequenced from 681 specimens belonging to katydids (Tettigoniidae), cave crickets (Rhaphidophoridae), and leaf-rolling crickets (Gryllacrididae) from Zhejiang Province, China. Of these, four COI-5P sequences were excluded from subsequent analyses because they were likely NUMTs (nuclear mitochondrial pseudogenes). The final dataset consisted of 677 barcode sequences representing 90 putative species-level taxa. Automated cluster delineation using the Barcode of Life Data System (BOLD) revealed 118 BINs (Barcodes Index Numbers). Among these 90 species-level taxa, 68 corresponded with morphospecies, while the remaining 22 were identified based on reverse taxonomy using BIN assignment. Thirteen of these morphospecies were represented by a single barcode (so-called singletons), and each of 19 morphospecies were split into more than one BIN. The consensus delimitation scheme yielded 55 Molecular Operational Taxonomic Units (MOTUs). Only four morphospecies (I _max > DNN) failed to be recovered as monophyletic clades (i.e., Elimaeaterminalis, Phyllomimusklapperichi, Sinochloraszechwanensis and Xizicushowardi), so it is speculated that these may be species complexes. Therefore, the diversity of katydids, cave crickets, and leaf-rolling crickets in Zhejiang Province is probably slightly higher than what current taxonomy would suggest.

Saint Peter and Saint Paul Archipelago barcoded: Fish diversity in the remoteness and DNA barcodes reference library for metabarcoding monitoring

In order to monitor the effects of anthropogenic pressures in ecosystems, molecular techniques can be used to characterize species composition. Among molecular markers capable of identifying species, the cytochrome c oxidase I (COI) is the most used. However, new possibilities of biodiversity profiling have become possible, in which molecular fragments of medium and short-length can now be analyzed in metabarcoding studies. Here, a survey of fishes from the Saint Peter and Saint Paul Archipelago was barcoded using the COI marker, which allowed the identification of 21 species. This paved the way to further investigate the fish biodiversity of the archipelago, transitioning from barcoding to metabarcoding analysis. As preparatory steps for future metabarcoding studies, the first extensive COI library of fishes listed for these islands was constructed and includes new data generated in this survey as well as previously available data, resulting in a final database with 9,183 sequences from 169 species and 63 families of fish. A new primer specifically designed for those fishes was tested in silico to amplify a region of 262 bp. The new approach should guarantee a reliable surveillance of the archipelago and can be used to generate policies that will enhance the archipelago’s protection.

Aquatic Organisms Research with DNA Barcodes

Since their inception, DNA barcodes have become a powerful tool for understanding the biodiversity and biology of aquatic species, with multiple applications in diverse fields such as food security, fisheries, environmental DNA, conservation, and exotic species detection. Nevertheless, most aquatic ecosystems, from marine to freshwater, are understudied, with many species disappearing due to environmental stress, mostly caused by human activities. Here we highlight the progress that has been made in studying aquatic organisms with DNA barcodes, and encourage its further development in assisting sustainable use of aquatic resources and conservation.

Exploring the vertebrate fauna of the Bird's Head Peninsula (Indonesia, West Papua) through DNA barcodes

Biodiversity knowledge is widely heterogeneous across the Earth's biomes. Some areas, due to their remoteness and difficult access, present large taxonomic knowledge gaps. Mostly located in the tropics, these areas have frequently experienced a fast development of anthropogenic activities during the last decades and are therefore of high conservation concerns. The biodiversity hotspots of Southeast Asia exemplify the stakes faced by tropical countries. While the hotspots of Sundaland (Java, Sumatra, Borneo) and Wallacea (Sulawesi, Moluccas) have long attracted the attention of biologists and conservationists alike, extensive parts of the Sahul area, in particular the island of New Guinea, have been much less explored biologically. Here, we describe the results of a DNA-based inventory of aquatic and terrestrial vertebrate communities, which was the objective of a multidisciplinary expedition to the Bird's Head Peninsula (West Papua, Indonesia) conducted between 17 October and 20 November 2014. This expedition resulted in the assembly of 1005 vertebrate DNA barcodes. Based on the use of multiple species-delimitation methods (GMYC, PTP, RESL, ABGD), 264 molecular operational taxonomic units (MOTUs) were delineated, among which 75 were unidentified and an additional 48 were considered cryptic. This study suggests that the diversity of vertebrates of the Bird's Head is severely underestimated and considerations on the evolutionary origin and taxonomic knowledge of these biotas are discussed.

A taxonomic and molecular survey of the pteridophytes of the Nectandra Cloud Forest Reserve, Costa Rica

Floristic surveys are crucial to the conservation of biodiversity, but the vast majority of such surveys are limited to listing species names, and few take into account the evolutionary history of species. Here, we combine classical taxonomic and molecular phylogenetic (DNA barcoding) approaches to catalog the biodiversity of pteridophytes (ferns and lycophytes) of the Nectandra Cloud Forest Reserve, Costa Rica. Surveys were carried out over three field seasons (2008, 2011, and 2013), resulting in 176 species representing 69 genera and 22 families of pteridophytes. Our literature survey of protected areas in Costa Rica shows that Nectandra has an exceptionally diverse pteridophyte flora for its size. Plastid rbcL was selected as a DNA barcode marker and obtained for >95% of pteridophyte taxa at this site. Combined molecular and morphological analyses revealed two previously undescribed taxa that appear to be of hybrid origin. The utility of rbcL for species identification was assessed by calculating minimum interspecific distances and found to have a failure rate of 18%. Finally we compared the distribution of minimum interspecific rbcL distances with two other areas that have been the focus of pteridophyte molecular surveys: Japan and Tahiti. The comparison shows that Nectandra is more similar to Japan than Tahiti, which may reflect the biogeographic history of these floras.

DNA barcoding of commercially important reef fishes in Weh Island, Aceh, Indonesia

Knowledge on the precise identification of fish resources is critical for sustainable fisheries management. This study employs the DNA barcoding approach to generate a molecular taxonomic catalogue of commercially important reef fishes in the waters of Weh Island (Aceh Province), the most northerly inhabited island in the biodiverse Indonesian Archipelago. The waters not only support artisanal fisheries but also a feeder for the industry in the greater island of Aceh. In total, 230 specimens from 72 species belonging to 32 genera and 17 families were DNA barcoded, representing a major segment of the captured reef fish taxa and a quarter of fish species diversity that had previously been recorded. The sequence read lengths were 639 bp revealing 359 conserved sites, 280 variable sites, 269 parsimony informative and 11 singletons. Our molecular findings paralleled the morphological identification with no evidence of cryptic species or new species discovery. This study is a significant contribution to the fisheries statistics of this area, which would facilitate assessment of species catch composition and hence for strategizing management plans. It is an important input to the DNA barcode library of Indonesian marine fishes and to the global DNA barcode entries in general.

Biodiversity inventory of the grey mullets (Actinopterygii: Mugilidae) of the Indo-Australian Archipelago through the iterative use of DNA-based species delimitation and specimen assignment methods

DNA barcoding opens new perspectives on the way we document biodiversity. Initially proposed to circumvent the limits of morphological characters to assign unknown individuals to known species, DNA barcoding has been used in a wide array of studies where collecting species identity constitutes a crucial step. The assignment of unknowns to knowns assumes that species are already well identified and delineated, making the assignment performed reliable. Here, we used DNA-based species delimitation and specimen assignment methods iteratively to tackle the inventory of the Indo-Australian Archipelago grey mullets, a notorious case of taxonomic complexity that requires DNA-based identification methods considering that traditional morphological identifications are usually not repeatable and sequence mislabeling is common in international sequence repositories. We first revisited a DNA barcode reference library available at the global scale for Mugilidae through different DNA-based species delimitation methods to produce a robust consensus scheme of species delineation. We then used this curated library to assign unknown specimens collected throughout the Indo-Australian Archipelago to known species. A second iteration of OTU delimitation and specimen assignment was then performed. We show the benefits of using species delimitation and specimen assignment methods iteratively to improve the accuracy of specimen identification and propose a workflow to do so.

Assessing species diversity of Coral Triangle artisanal fisheries: A DNA barcode reference library for the shore fishes retailed at Ambon harbor (Indonesia)

The Coral Triangle (CT), a region spanning across Indonesia and Philippines, is home to about 4,350 marine fish species and is among the world's most emblematic regions in terms of conservation. Threatened by overfishing and oceans warming, the CT fisheries have faced drastic declines over the last decades. Usually monitored through a biomass-based approach, fisheries trends have rarely been characterized at the species level due to the high number of taxa involved and the difficulty to accurately and routinely identify individuals to the species level. Biomass, however, is a poor proxy of species richness, and automated methods of species identification are required to move beyond biomass-based approaches. Recent meta-analyses have demonstrated that species richness peaks at intermediary levels of biomass. Consequently, preserving biomass is not equal to preserving biodiversity. We present the results of a survey to estimate the shore fish diversity retailed at the harbor of Ambon Island, an island located at the center of the CT that display exceptionally high biomass despite high levels of threat, while building a DNA barcode reference library of CT shore fishes targeted by artisanal fisheries. We sampled 1,187 specimens and successfully barcoded 696 of the 760 selected specimens that represent 202 species. Our results show that DNA barcodes were effective in capturing species boundaries for 96% of the species examined, which opens new perspectives for the routine monitoring of the CT fisheries.

Cirripectes matatakaro, a new species of combtooth blenny from the Central Pacific, illuminates the origins of the Hawaiian fish fauna

Included among the currently recognized 23 species of combtooth blennies of the genus Cirripectes (Blenniiformes: Blenniidae) of the Indo-Pacific are the Hawaiian endemic C. vanderbilti, and the widespread C. variolosus. During the course of a phylogeographic study of these species, a third species was detected, herein described as C. matatakaro. The new species is distinguished primarily by the configuration of the pore structures posterior to the lateral centers of the transverse row of nuchal cirri in addition to 12 meristic characters and nine morphometric characters documented across 72 specimens and ∼4.2% divergence in mtDNA cytochrome oxidase subunit I. The new species is currently known only from the Marquesas, Gambier, Pitcairns, Tuamotus, and Australs in the South Pacific, and the Northern Line Islands and possibly Johnston Atoll south of Hawaiʻi. Previous researchers speculated that the geographically widespread C. variolosus was included in an unresolved trichotomy with the Hawaiian endemic and other species based on a morphological phylogeny. Our molecular-phylogenetic analysis resolves many of the previously unresolved relationships within the genus and reveals C. matatakaro as the sister lineage to the Hawaiian C. vanderbilti. The restricted geographic distribution of Cirripectes matatakaro combines with its status as sister to C. vanderbilti to indicate a southern pathway of colonization into Hawaiʻi.