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

Abstract

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.

Characteristics of the complete mitochondrial genome of Gerres limbatus (Cuvier, 1830) (Perciformes: Gerreidae)

“… 2012 ), Eugerres lineatus (KT067803), Eugerres axillaris (KT067802), Eucinostomus havana (GU225237), Eucinostomus argenteus (GU672692), Ulaema lefroyi (MF999190), Eucinostomus gula (GU225601), Eucinostomus melanopterus (GU225249), Eucinostomus jonesii (GU225238), Eucinostomus harengulus (HM389325), Gerres oyena (JX260872), Gerres simillimus (KT005473), Gerres cinereus (KT005480), Gerres methueni (JF493526), Gerres longirostris (MT076634), Gerres erythrourus (KP194662), Gerres subfasciatus (HQ956559), Gerres shima (OQ386232, Bemis et al. 2023 ), Gerres oblongus (EF607393, Zhang 2011 ), Gerres japonicus (KY371549), Gerres infasciatus (MT076632), Gerres filamentosus (KU179062), Gerres setifer (MK572218, Rahman et al. 2019 ), Gerres microphthalmus (MZ421346), Gerres macracanthus (KF489594).)…”

New species of redbait from the Philippines (Teleostei, Emmelichthyidae, Emmelichthys)

“…All scan data were visualized and segmented using the protocol in Girard et al (2022a) . All other specimen imaging was performed using equipment and protocols listed in Girard et al (2020) and Bemis et al (2023) .…”

“…In 2011, a collaboration among researchers at the National Museum of Natural History, Smithsonian Institution ( NMNH ), the Bureau of Fisheries and Aquatic Resources−National Fisheries Research and Development Institute, Department of Agriculture, Philippines ( BFAR−NFRDI ), and United States Food and Drug Administration ( FDA ) was established to document the diversity of fishes in Philippine markets. The goal of this collaboration was to develop a voucher-based genetic reference library to advance consumer safety and biodiversity research ( Bemis et al 2023 ). The project has yielded descriptions of several new species (e.g., Williams and Carpenter 2015 ; Carpenter et al 2017 ; Matsunuma et al 2018 ) and discovered additional taxa that have yet to be described (see Bemis et al 2023 ).…”

“…The goal of this collaboration was to develop a voucher-based genetic reference library to advance consumer safety and biodiversity research ( Bemis et al 2023 ). The project has yielded descriptions of several new species (e.g., Williams and Carpenter 2015 ; Carpenter et al 2017 ; Matsunuma et al 2018 ) and discovered additional taxa that have yet to be described (see Bemis et al 2023 ). Two emmelichthyid specimens were collected from a fish market on Cebu Island in 2013 that are externally similar to E. struhsakeri , but they have two prominent fleshy papillae associated with the cleithrum, fewer pectoral-fin rays, and fewer gill rakers.…”

Efficient species identification for Pacific salmon genetic monitoring programs

“…Over the past few decades, DNA barcoding using highly conserved mitochondrial gene regions has become the gold standard for genetic species identification used by various federal agencies as a regulatory and enforcement tool (Bemis et al, 2023;GAO, 2009).…”