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

We describe a new species of redbait in the genus Emmelichthys collected from fish markets on Panay and Cebu islands in the Visayas region of the Philippines. The species is externally similar to E.struhsakeri but is diagnosable by two prominent fleshy papillae associated with the cleithrum and fewer pectoral-fin rays (18-19 vs. 19-21) and gill rakers (30-33 vs. 34-41). Additionally, mitochondrial DNA differentiates this taxon from other species of Emmelichthys. We generate mitochondrial genomes for two of the three type specimens and several other emmelichthyids to place the new taxon in a phylogenetic context. Analysis of the protein-coding mitochondrial loci calls into question the monophyly of two emmelichthyid genera (Emmelichthys and Erythrocles) and highlights the need for subsequent analyses targeting the intrarelationships of the Emmelichthyidae.

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.

New species of Monomitopus (Ophidiidae) from Hawaii, with the description of a larval coiling behavior.

In 1985, Carter and Cohen noted that there are several yet-to-be described species of Monomitopus (Ophidiidae), including one from Hawaii. Recently, blackwater divers collected a larval fish off Kona, Hawaii, similar to the previously described larvae of M. kumae, but DNA sequence data from the larva does not match any of the six previously sequenced species within the genus. Within the Smithsonian Institutions National Museum of Natural History Ichthyology Collection, we find a single unidentified adult specimen of Monomitopus collected North of Maui, Hawaii in 1972 whose fin-ray and vertebral/myomere counts overlap those of the larval specimen. We describe this new Hawaiian species of Monomitopus based on larval and adult characters. Additionally, blackwater photographs of several species of Monomitopus show the larvae coiled into a tight ball, a novel behavior to be observed in cusk-eels. We describe this behavior, highlighting the importance of blackwater photography in advancing our understanding of marine larval fish biology.

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.

Getting somewhere with the Red Queen: chasing a biologically modern definition of the hypothesis.

The Red Queen hypothesis (RQH) is both familiar and murky, with a scope and range that has broadened beyond its original focus. Although originally developed in the palaeontological arena, it now encompasses many evolutionary theories that champion biotic interactions as significant mechanisms for evolutionary change. As such it de-emphasizes the important role of abiotic drivers in evolution, even though such a role is frequently posited to be pivotal. Concomitant with this shift in focus, several studies challenged the validity of the RQH and downplayed its propriety. Herein, we examine in detail the assumptions that underpin the RQH in the hopes of furthering conceptual understanding and promoting appropriate application of the hypothesis. We identify issues and inconsistencies with the assumptions of the RQH, and propose a redefinition where the Red Queen's reign is restricted to certain types of biotic interactions and evolutionary patterns occurring at the population level.

Light in the darkness: New perspective on lanternfish relationships and classification using genomic and morphological data.

Massive parallel sequencing allows scientists to gather DNA sequences composed of millions of base pairs that can be combined into large datasets and analyzed to infer organismal relationships at a genome-wide scale in non-model organisms. Although the use of these large datasets is becoming more widespread, little to no work has been done in estimating phylogenetic relationships using UCEs in deep-sea fishes. Among deep-sea animals, the 257 species of lanternfishes (Myctophiformes) are among the most important open-ocean lineages, representing half of all mesopelagic vertebrate biomass. With this relative abundance, they are key members of the midwater food web where they feed on smaller invertebrates and fishes in addition to being a primary prey item for other open-ocean animals. Understanding the evolution and relationships of midwater organisms generally, and this dominant group of fishes in particular, is necessary for understanding and preserving the underexplored deep-sea ecosystem. Despite substantial congruence in the evolutionary relationships among deep-sea lanternfishes at higher classification levels in previous studies, the relationships among tribes, genera, and species within Myctophidae often conflict across phylogenetic studies or lack resolution and support. Herein we provide the first genome-scale phylogenetic analysis of lanternfishes, and we integrate these data from across the nuclear genome with additional protein-coding gene sequences and morphological data to further test evolutionary relationships among lanternfishes. Our phylogenetic hypotheses of relationships among lanternfishes are entirely congruent across a diversity of analyses that vary in methods, taxonomic sampling, and data analyzed. Within the Myctophiformes, the Neoscopelidae is inferred to be monophyletic and sister to a monophyletic Myctophidae. The current classification of lanternfishes is incongruent with our phylogenetic tree, so we recommend revisions that retain much of the traditional tribal structure and recognize five subfamilies instead of the traditional two subfamilies. The revised monophyletic taxonomy of myctophids includes the elevation of three former lampanyctine tribes to subfamilies. A restricted Lampanyctinae was recovered sister to Notolychninae. These two clades together were recovered as the sister group to the Gymnoscopelinae. Combined, these three subfamilies were recovered as the sister group to a clade composed of a monophyletic Diaphinae sister to the traditional Myctophinae. Our results corroborate recent multilocus molecular studies that infer a polyphyletic Myctophum in Myctophinae, and a para- or polyphyletic Lampanyctus and Nannobrachium within Lampanyctinae. We resurrect Dasyscopelus and Ctenoscopelus for the independent clades traditionally classified as species of Myctophum, and we place Nannobrachium into the synonymy of Lampanyctus.

Phylogenetic relationships of weaverbirds (Aves: Ploceidae): A first robust phylogeny based on mitochondrial and nuclear markers.

Weaverbirds are a diverse passerine group with species diversity concentrated in sub-Saharan Africa. No comprehensive phylogenetic hypothesis regarding relationships of weaverbirds has been produced, however, so we developed a first extensive phylogeny for the family Ploceidae, based on a multilocus dataset of three mitochondrial loci and four nuclear markers. Analysis of these data offered strong support for monophyly of the family and revealed seven distinct clades within Ploceidae. A major feature of our results is broad polyphyly of Ploceus: Asian Ploceus species should retain the generic name, whereas African Ploceus, together with Anaplectes, should be placed in Malimbus. In light of deep divergence, we assign the Malagasy Ploceus species to their own genus, Nelicurvius. Divergence time analysis based on DNA substitution rates suggests a mid-Miocene origin of the family. This study lays a foundation for an array of future studies of character evolution, biogeography, and evolutionary history of the family.

The phylogeny of marine sculpins of the genus Icelinus with comments on the evolution and biogeography of the Pseudoblenninae.

The marine sculpins (Psychrolutidae) are a diverse percomorph family with notable morphological variation and repeated biogeographic patterns within the group. The psychrolutid genus Icelinus is unusual because it is one of the few near-shore members of the family that exhibits a trans-Pacific distribution; it has two species in the western Pacific and nine species in the eastern Pacific. Furthermore, the placement of Icelinus has been more inconsistent across molecular and morphological analyses than many genera. Previous phylogenetic studies have hypothesized sister taxa to Icelinus ranging from Antipodocottus, Chitonotus, and Stlengis, to a mixed clade of psychrolutids. The varied placements across these studies may be due to limited taxon sampling within Icelinus, and previous authors have never included western Pacific species of Icelinus in their analyses. This study tests the monophyly of the genus, examines the relationships between eastern and western Pacific species of Icelinus, and explores the relationships of Icelinus within Psychrolutidae. Our results show that the traditional grouping of Icelinus is polyphyletic. The eastern Pacific species of Icelinus are restricted to a clade sister to Furcina and Antipodocottus. The western Pacific species of Icelinus are recovered sister to the genus Stlengis. Given the polyphyly of Icelinus, the sister-group pairing of western Pacific species of Icelinus and Stlengis, as well as morphological similarity between the two groups, we recommend treating the western Pacific species of Icelinus as members of the genus Stlengis. With this taxonomic change, species in the genus Icelinus are now limited to the eastern Pacific, ranging from Alaska to Mexico.

Evolution of Venomous Cartilaginous and Ray-Finned Fishes.

Venom and its associated delivery systems have evolved in numerous animal groups ranging from jellyfishes to spiders, lizards, shrews, and the male platypus. Building off new data and previously published anatomical and molecular studies, we explore the evolution of and variation within venomous fishes. We show the results of the first multi-locus, ordinal-level phylogenetic analysis of cartilaginous (Chondrichthyes) and ray-finned (Actinopterygii) fishes that hypothesizes 18 independent evolutions of this specialization. Ancestral-states reconstruction indicates that among the 2386-2962 extant venomous fishes, envenomed structures have evolved four times in cartilaginous fishes, once in eels (Anguilliformes), once in catfishes (Siluriformes), and 12 times in spiny-rayed fishes (Acanthomorpha). From our anatomical studies and phylogenetic reconstruction, we show that dorsal spines are the most common envenomed structures (∼95% of venomous fish species and 15 independent evolutions). In addition to envenomed spines, fishes have also evolved venomous fangs (2% of venomous fish species, two independent evolutions), cleithral spines (2% of venomous fish species, one independent evolution), and opercular or subopercular spines (1% of venomous fish species, three independent evolutions).