The value of updating GenBank accessions for supermatrix phylogeny: The case of the New Guinean marsupial carnivore genus Myoictis

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.

Systematic position of the Clicking Frog (Kassinula Laurent, 1940), the problem of chimeric sequences and the revised classification of the family Hyperoliidae

The systematics of the African frog family Hyperoliidae has undergone turbulent changes in last decades. Representatives of several genera have not been genetically investigated or with only limited data, and their phylogenetic positions are thus still not reliably known. This is the case of the De Witte's Clicking Frog (Kassinula wittei) which belongs to a monotypic genus. This miniature frog occurs in a poorly studied region, southeastern Democratic Republic of the Congo, northern Zambia, Angola. So far it is not settled whether this genus belongs to the subfamily Kassininae as a relative of the genus Kassina, or to the subfamily Hyperoliinae as a relative of the genus Afrixalus. Here we present for the first time a multilocus phylogenetic reconstruction (using five nuclear and one mitochondrial marker) of the family Hyperoliidae, including Kassinula. We demonstrate with high confidence that Kassinula is a member of Hyperoliinae belonging to a clade also containing Afrixalus (sub-Saharan Africa), Heterixalus (Madagascar) and Tachycnemis (Seychelles). We find that Kassinula represents a divergent lineage (17-25 Mya), which supports its separate genus-level status, but its exact systematic position remains uncertain. We propose to name the clade to which the above four genera belong as the tribe Tachycnemini Channing, 1989. A new taxonomy of the family Hyperoliidae was recently proposed by Dubois et al. (2021: Megataxa 5, 1-738). We demonstrate here that the new taxonomy was based on a partially erroneous phylogenetic reconstruction resulting from a supermatrix analysis of chimeric DNA sequences combining data from two families, Hyperoliidae and Arthroleptidae (the case of Cryptothylax). We therefore correct the erroneous part and propose a new, revised suprageneric taxonomy of the family Hyperoliidae. We also emphasize the importance of inspecting individual genetic markers before their concatenation or coalescent-based tree reconstructions to avoid analyses of chimeric DNA sequences producing incorrect phylogenetic reconstructions. Especially when phylogenetic reconstructions are used to propose taxonomies and systematic classifications.

Molecular phylogeny of the threadfin fishes (Polynemidae) using ultraconserved elements

Threadfins (Teleostei: Polynemidae) are a group of fishes named for their elongated and threadlike pectoral-fin rays. These fishes are commonly found in the world's tropical and subtropical waters, and are an economically important group for people living in these regions, with more than 100,000 t harvested in recent years. However, we do not have a detailed understanding of polynemid evolutionary history such that these fishes can be monitored, managed and conserved as an important tropical food source. Recent studies hypothesize at least one genus of threadfins is polyphyletic, and no studies have focused on generating a hypothesis of relationship for the Polynemidae using DNA sequences. In this study, we analyse a genomic dataset of ultraconserved-element and mitochondrial loci to construct a phylogeny of the Polynemidae. We recover the threadfins as a clade sister to flatfishes, with the most taxonomically rich genus, Polydactylus, being resolved as polyphyletic. When comparing our dataset to data from previous studies, we find that a few recent broad-scale phylogenies of fishes have incorporated mislabelled, misidentified or chimeric terminals into their analyses, impacting the relationships of threadfins they recover. We highlight these problematic sequences, providing revised identifications based on the data sequenced in this study. We then discuss the intrarelationships of threadfins, highlighting morphological or ecological characters that support the clades we recover.