Molecular phylogeny and new classification of the genera Eulophias and Zoarchias (PISCES, Zoarcoidei)

DNA mini-barcoding reveals the mislabeling rate of canned cat food in Taiwan

Background

Domestic cats are important companion animals in modern society that live closely with their owners. Mislabeling of pet food can not only harm pets but also cause issues in areas such as religious beliefs and natural resource management. Currently, the cat food market is booming. However, despite the risk that mislabeling poses to cats and humans, few studies have focused on species misrepresentation in cat food products.

Methods

To address this issue, we used DNA barcoding, a highly effective identification methodology that can be applied to even highly processed products. We targeted a short segment (~85 basepairs) of the mitochondrial 16S rRNA (16S) gene as a barcode and employed Sanger or next generation sequencing (NGS) to inspect 138 canned cat food products in the Taiwanese market.

Results

We discovered that the majority of mislabeling incidents were related to replacement of tuna with other species. Moreover, our metabarcoding revealed that numerous undeclared ingredients were present in all examined canned products. One product contained CITES Appendix II-listed shortfin mako shark (Isurus oxyrinchus). Overall, we uncovered a mislabeling rate of at least 28.99%. To verify cases of mislabeling, an official standardized list of vernacular names, along with the corresponding scientific species names, as well as a dependable barcoding reference sequence database are necessary.

The first description of larvae and comments on the taxonomy of Stichaeus ochriamkini Taranetz, 1935 (Perciformes: Stichaeidae)

Stichaeus ochriamkini (Stichaeidae) is common in the northern Japan Sea and the southern Okhotsk Sea. Among the five known representatives of the genus Stichaeus, early ontogenesis is the least studied in S. ochriamkini. In this study, the authors provide the first description of all larval stages of this species. In the north-western Japan Sea, larvae are found in plankton from early April to early June. S. ochriamkini larvae can be identified using the following characters: postanal-lateral pigment (PLP) lines present on the sides of the caudal part of the body and run along the anterior edge of hypaxial myomeres; 14-15 abdominal vertebrae; 32-34 rays in the anal fin; larvae disappear from plankton at a body length of L_T > 25.0 mm (L_S > 20 mm). Larvae of S. ochriamkini are very similar to larvae of Stichaeus punctatus. The melanin pigmentation in larvae of both species shows similar patterns of development. In the genus Stichaeus Reinhardt, 1836, two groups of species are distinguished by the presence/absence of PLP lines in larvae, and by significant divergence (clearly exceeding the species level) in the COI mtDNA gene. It is suggested the differences between these species groups is recognized at the generic level. Thus, the genus Stichaeus Reinhardt, 1836 should include S. punctatus and S. ochriamkini, whereas the other three species should be placed in the genus Dinogunellus Herzenstein, 1890: Dinogunellus fuscus, Dinogunellus nozawae and Dinogunellus grigorjewi.

The biogeographic history of eelpouts and related fishes: Linking phylogeny, environmental change, and patterns of dispersal in a globally distributed fish group

Modern genetic data sets present unprecedented opportunities to understand the evolutionary origins of diverse taxonomic groups. When the timing of key events is known, it is possible to investigate biogeographic history in the context of major phenomena (e.g., cooling of a major ocean). In this study, we investigated the biogeographic history of the suborder Zoarcoidei, a globally distributed fish group that includes species inhabiting both poles that produce antifreeze proteins to survive chronic subfreezing temperatures. We first generated a multi-locus, time-calibrated phylogeny for the group. We then used biogeographic modeling to reconstruct ancestral ranges across the tree and to quantify the type and frequency of biogeographic events (e.g., founder, dispersal). With these results, we considered how the cooling of the Southern and Arctic Oceans, which reached their present-day subfreezing temperatures 10-15 million years ago (Mya) and 2-3 Mya, respectively, may have shaped the group's evolutionary history, with an emphasis on the most speciose and widely distributed family, eelpouts (family Zoarcidae). Our phylogenetic results clarified the Zoarcoidei taxonomy and showed that the group began to diversify in the Oligocene ~31-32 Mya, with the center of origin for all families in north temperate waters. Within-area speciation was the most common biogeographic event in the group's history (80% of all events) followed by dispersal (20%). Finally, we only found evidence, albeit limited, for ocean cooling underpinning diversification of eelpouts living in the high Antarctic over the last 10 million years.

Structure, evolution and phylogenetic informativeness of eelpouts (Cottoidei: Zoarcales) mitochondrial control region sequences

Control region (CR) is a major non-coding domain of mitochondrial DNA in vertebrates which contains the promoters for replication and transcription of mitochondrial genome along with the binding sites for metabolic machinery and, hence, is a vital element for the integrity of mitochondrial genome as a biological replicator. The origin and diversity of structural elements within CR have been intensively studied in recent years with the involvement of new diverse taxa. In this paper, we provide new data on the nucleotide and structural patterns of CR evolution and phylogenetic suitability among eelpouts (Cottoidei: Zoarcales). To achieve this, we carried out a comparative phylogenetic and structural analysis of 29 CR sequences belonging to the long shanny Stichaeus grigorjewi together with nine sequences of other eelpouts taxa representing four families in contrast to mitochondrial protein-coding fragments. The CR organization within S. grigorjewi, as well as in all other eelpouts, is consistent with the common three-domain structure known from most vertebrates. We found a hidden CR variation constrains on the landscape level and a lack of nucleotide saturation. Finally, our results demonstrate the advantage of the length variation in CR sequences for phylogenetic reconstructions among eelpouts.

Phylogenetic classification of bony fishes

BACKGROUND

Fish classifications, as those of most other taxonomic groups, are being transformed drastically as new molecular phylogenies provide support for natural groups that were unanticipated by previous studies. A brief review of the main criteria used by ichthyologists to define their classifications during the last 50 years, however, reveals slow progress towards using an explicit phylogenetic framework. Instead, the trend has been to rely, in varying degrees, on deep-rooted anatomical concepts and authority, often mixing taxa with explicit phylogenetic support with arbitrary groupings. Two leading sources in ichthyology frequently used for fish classifications (JS Nelson's volumes of Fishes of the World and W. Eschmeyer's Catalog of Fishes) fail to adopt a global phylogenetic framework despite much recent progress made towards the resolution of the fish Tree of Life. The first explicit phylogenetic classification of bony fishes was published in 2013, based on a comprehensive molecular phylogeny ( www.deepfin.org ). We here update the first version of that classification by incorporating the most recent phylogenetic results.

RESULTS

The updated classification presented here is based on phylogenies inferred using molecular and genomic data for nearly 2000 fishes. A total of 72 orders (and 79 suborders) are recognized in this version, compared with 66 orders in version 1. The phylogeny resolves placement of 410 families, or ~80% of the total of 514 families of bony fishes currently recognized. The ordinal status of 30 percomorph families included in this study, however, remains uncertain (incertae sedis in the series Carangaria, Ovalentaria, or Eupercaria). Comments to support taxonomic decisions and comparisons with conflicting taxonomic groups proposed by others are presented. We also highlight cases were morphological support exist for the groups being classified.

CONCLUSIONS

This version of the phylogenetic classification of bony fishes is substantially improved, providing resolution for more taxa than previous versions, based on more densely sampled phylogenetic trees. The classification presented in this study represents, unlike any other, the most up-to-date hypothesis of the Tree of Life of fishes.

Molecular phylogenetic reconstruction and taxonomic investigation of eelpouts (Cottoidei: Zoarcales) based on Co-1 and Cyt-b mitochondrial genes

The infraorder Zoarcales (Cottoidei), or eelpouts, includes about 400 species of coldwater fishes concentrated mainly in the North Pacific. To date, the molecular phylogenetic methods in combination with morphological data have significantly contributed to understanding the taxonomic composition of this group and made it possible to confirm/refute validity of some families of obscure origin. In spite of the growing amount of new data on taxonomy and evolution of eelpouts, a consideration of the original and independent data is obviously needed to verify the existing knowledge of this taxon. In this study, which is based on concatenated matrix of Co-1 and Cyt-b mitochondrial genes, as well as relying on the samples from seven families and 45 species of eelpouts, we have reconstructed the phylogeny, which is generally consistent with previous inferences. Despite the resolution of the original data matrix is low, we have demonstrated the monophyletic origin of the families Zoarcidae and Anarhichadidae, as well as Neozoarcidae, previously related to Stichaeidae and recently revised Eulophiidae. The polyphyletic patterns amongst some subfamilies in Stichaeidae have been confirmed, whereas Opisthocentrinae and Pholidae seem to constitute a valid family-level taxon. Our results provide new opportunities with respect to taxonomic relationships in the complex and diverse group of eelpouts , whose part in the tree of life is not covered by recently flourishing multilocus phylogeny of teleost fishes. In light of the data obtained, the necessity of more unified and reproducible approaches to resolve the issues of evolution and taxonomy of such a complex group as Zoarcales becomes more evident.

New fossils of Neogene pricklebacks (Actinopterygii: Stichaeidae) from East Asia

Two new findings of fossil pricklebacks (Pisces: Stichaeidae) from the Miocene deposits of Honshu Island (Japan) and Kamchatka Peninsula (Russia) are described. Both specimens are incomplete and cannot be identified below either family or subfamily level. Nevertheless, these findings suggest wide distribution of stichaeids in the North-Western Pacific during the Miocene. The specimen from the deep-sea Bessho Formation of Honshu represents the first fossil record of pricklebacks of the subfamily Lumpeninae.

Osteology and ontogeny of the wrymouths, genus Cryptacanthodes (Cottiformes: Zoarcoidei: Cryptacanthodidae)

The four species included in the family Cryptacanthodidae are eel-like, burrowing fishes distributed in the cold-temperate coastal waters of the North Pacific and the western North Atlantic. This study describes the osteology and aspects of the ontogenetic skeletal development of two species, Cryptacanthodes maculatus from the western North Atlantic and C. aleutensis from the eastern North Pacific. We discuss the relationships of Cryptacanthodidae among other zoarcoid families. The Cryptacanthodidae have been previously included in the Stichaeidae, but removed and classified as a separate family based on the skull, pectoral radial, and cephalic lateral-line morphology. Our observations (similarities in gill arch and pectoral girdle morphology; specifically, a thin sheet-like flange of bone from the posterior margin of the supracleithrum) suggest a close relationship to at least some of the members of the family Stichaeidae.