Confronting Sources of Systematic Error to Resolve Historically Contentious Relationships: A Case Study Using Gadiform Fishes (Teleostei, Paracanthopterygii, Gadiformes)

Evolution and genetic adaptation of fishes to the deep sea

The deep sea, especially hadal zones, characterized by high-hydrostatic pressure, low temperatures, and near-total darkness, present some of the most challenging environments for life on Earth. However, teleost fish have successfully colonized these extreme habitats through complex adaptations. We generated genome assemblies of 12 species, including 11 deep-sea fishes. Our findings reconstructed the teleost deep-sea colonization history and revealed the overall impact of the deep-sea environment on fishes. Interestingly, our results question the previously assumed linear correlation between trimethylamine oxide (TMAO) content and depth. By contrast, we observed a convergent aa replacement in the rtf1 gene in most deep-sea fishes under 3,000 m, and in vitro experiments suggest that this mutation can influence transcriptional efficiency, which is likely to be advantageous in the deep-sea environment. Moreover, our study underlines the pervasive impact of human activities, as we detected the presence of persistent organic pollutants in species from the Mariana Trench.

Gaidropsarus mauritanicus (Gadiformes, Gaidropsaridae) a new three-bearded rockling from a deep-water coral ecosystem with a genetically verified biogeographical distribution of the genus and notes to its ecology and behavior

Gaidropsarus mauritanicus sp. nov. is described from one specimen collected using a grab sample from the Tanoûdêrt Canyon (ca. 20° N) off Mauritania at a depth of 595 m. The new species was further observed during eight remotely operated vehicle (ROV) dives along the Mauritanian slope southwards down to the Tiguent Coral Mound Complex (~17° N) in a bathymetric range between 613 and 416 m. It can be distinguished from congeners by a combination of characteristics, including large eyes (38.1% head length [HL]), large head (25.8% standard length [SL]), elongated pelvic fins (35.7% SL), low number of vertebrae (44), and coloration (pinkish with a dorsal darker brownish hue and bright blotches along the dorsal-fin base). A species-delimitation analysis performed with available cytochrome c oxidase subunit 1 (COI) sequences affiliated to the genus Gaidropsarus additionally supported the validity of the new species. Video analyses showed a deep-water coral-associated and protection-seeking behavior, which may explain why the species has remained undescribed until now. Additional ROV footage from separate deep-water coral sites in the North Atlantic and Mediterranean Sea further highlights the ecological behavior and hidden diversity of bathyal three-bearded rocklings. Here, we additionally discuss the biogeographical distribution of all genetically verified Gaidropsarus spp. in combination with genetic data and morphological characters. G. mauritanicus sp. nov. is closely related to a species from Tasmania (43° S), a geographical point furthest among the studied samples, which may hint to an important influence of (paleo-) oceanography on the distributions of Gaidropsarus species.

Whole-genome-based phylogenetic analyses provide new insights into the evolution of springtails (Hexapoda: Collembola)

Springtails (Collembola) stand as one of the most abundant, widespread, and ancient terrestrial arthropods on earth. However, their evolutionary history and deep phylogenetic relationships remain elusive. In this study, we employed phylogenomic approaches to elucidate the basal relationships among Collembola. We sampled whole-genome data representing all major collembolan lineages in proportion to their known diversity. To account for potential phylogenomic biases, we implemented various data extraction, locus sampling, and signal filtering strategies to generate matrices. Subsequently, we applied a diverse array of tree-searching and rate-modelling methods to reconstruct the phylogeny. Our analyses, utilizing different matrices and methods, converged on the same unrooted relationships among collembolan ingroups, supporting the current ordinal classification and challenging the monophyly of Arthropleona and Symphypleona s.l. However, discrepancies across analyses existed in the root of Collembola. Among various root positions, those based on more informative matrices and biologically realistic models, favoring a basal topology of Entomobryomorpha + (Symphypleona s.s. + (Neelipleona + Poduromorpha)), were supported by subsequent methodological assessment, topology tests, and rooting analyses. This optimal topology suggests multiple independent reduction of the pronotum in non-poduromorph orders and aligns with the plesiomorphic status of neuroendocrine organs and epicuticular structure of Entomobryomorpha. Fossil-calibrated dating analyses based on the optimal topology indicated late-Paleozoic to mid-Mesozoic origins of the crown Collembola and four orders. In addition, our results questioned the monophyly of Isotomidae and Neanuridae, underscoring the need for further attention to the systematics of these families. Overall, this study provides novel insights into the phylogenetic backbone of Collembola, which will inform future studies on the systematics, ecology, and evolution of this significant arthropod lineage.

The Palaeozoic assembly of the holocephalan body plan far preceded post-Cretaceous radiations into the ocean depths

Among cartilaginous fishes, Holocephali represents the species-depauperate, morphologically conservative sister to sharks, rays and skates and the last survivor of a once far greater Palaeozoic and Mesozoic diversity. Currently, holocephalan diversity is concentrated in deep-sea species, suggesting that this lineage might contain relictual diversity that now persists in the ocean depths. However, the relationships of living holocephalans to their extinct relatives and the timescale of their diversification remain unclear. Here, we reconstruct the evolutionary history of holocephalans using comprehensive morphological and DNA sequence datasets. Our results suggest that crown holocephalans entered and diversified in deep (below 1000 m) ocean waters after the Cretaceous-Palaeogene mass extinction, contrasting with the hypothesis that this ecosystem has acted as a refugium of ancient cartilaginous fishes. These invasions were decoupled from the evolution of key features of the holocephalan body plan, including crushing dentition, a single frontal clasper, and holostylic jaw suspension, during the Palaeozoic Era. However, these invasions considerably postdated the appearance of extant holocephalan families 150 million years ago during a major period of biotic turnover in oceans termed the Mesozoic Marine Revolution. These results clarify the origins of living holocephalans as the recent diversification of a single surviving clade among numerous Palaeozoic lineages.

On the occurrence of a post-larval specimen of Brosme brosme (Gadiformes: Lotidae) on Porcupine Bank (west Ireland)

The occurrence of a small specimen of Brosme brosme (Gadiformes: Lotidae) from the Porcupine Bank is reported. A single specimen with a total length of 73.2 mm was caught with bottom trawl at a depth of 322 m depth in 2017. The specimen was identified morphologically and confirmed by molecular taxonomy using DNA barcoding. Based on the size and ontogenetic characters found, the specimen was identified as a post-larval individual, and a pelagic habitat of the specimen seems more likely.

A new species of Bregmaceros (Gadiformes: Bregmacerotidae) from the eastern Pacific Ocean, with comments on B. atlanticus and B. japonicus

A new species of Bregmaceros is described based on a series of specimens from the eastern Pacific Ocean from near the Hawaiian Islands eastward to the California Current region. The new species bears considerable similarity in body shape and pigmentation to other overall darkly pigmented species with moderately high anal-fin counts (5159 in B. moseri) and modified prehaemal anal-fin pterygiophores (B. atlanticus and B. japonicus). The form and occurrence of these modified pterygiophores among Bregmaceros species is discussed. The new species is distinguished from B. atlanticus and B. japonicus and other undescribed forms in the historical literature commonly referred to Bregmaceros mcclellandi based on its high precaudal (prehaemal) vertebral counts (15 or 16 vs. 1315, typically 14) and associated elongation of the anterior portion of the body, and dark pigmentation concentrated dorsally on body and on head dorsal to nares anteriorly and operculum posteriorly but little or no pigment on lateral and ventral surfaces of head. The new species uniquely shares with these other species the modified prehaemal anal-fin pterygiophores and a lack of posterior bifurcation of the coelomic space otherwise present in the remaining species in the genus.

Delimitation and species discovery in the Profundulidae fish family: Using genetic, environmental and morphologic data to address taxonomic uncertainty

The family Profundulidae includes some one of the most enigmatic freshwater fishes of Mesoamerica: despite many attempts, a robust phylogenetic framework to delimit species is lacking, mainly due to limited morphological variation within the group. The accumulation of molecular data of profundulid fishes has led to advances in the description of new taxa, but relatively less progress has been made estimating evolutionary and phylogenetic relationships for this fish family. Here, we adopt an integrative taxonomy approach including the use of nuclear and mitochondrial DNA sequences, morphometric and ecological data, to test species boundaries in profundulid fishes in the westernmost area of their known distribution range in the states of Guerrero and Oaxaca, Mexico. Using a combination of methods for species discovery and validation based on Bayesian gene tree topologies, our analyses support the delimitation of 15 valid species of profundulid fishes - a combination of previously described species validated by this study, the synonymy of unsupported taxa, and the description of two new species. Using species delimitation methods, examination of phenotypic variation, and ecological niche characterization, we also identify five potentially new lineages which require further evidence to be erected as new species. We demonstrate that the use of an integrative taxonomy approach provides a robust methodology to delimit species in a taxonomically complex group like Profundulidae. Accurate taxonomic and ecological information is crucial for the conservation of these microendemic fishes, as several species are endangered.

Molecular phylogeny and phylogeography of ricefishes (Teleostei: Adrianichthyidae: Oryzias) in Sri Lanka

Ricefishes of the genus Oryzias occur commonly in the fresh and brackish waters in coastal lowlands ranging from India across Southeast Asia and on to Japan. Among the three species of Oryzias recorded from peninsular India, two widespread species, O. carnaticus and O. dancena, have previously been reported from Sri Lanka based on museum specimens derived from a few scattered localities. However, members of the genus are widespread in the coastal lowlands of Sri Lanka, a continental island separated from India by the shallow Palk Strait. Although recent molecular phylogenies of Adrianichthyidae represent near-complete taxon representation, they lack samples from Sri Lanka. Here, based on sampling at 13 locations representative of the entire geographic and climatic regions of the island's coastal lowlands, we investigate for the first time the molecular phylogenetic relationships and phylogeography of Sri Lankan Oryzias based on one nuclear and two mitochondrial markers. Sri Lankan Oryzias comprise two distinct non-sister lineages within the javanicus species group. One of these is represented by samples exclusively from the northern parts of the island; it is recognized as O. dancena. This lineage is recovered as the sister group to the remaining species in the javanicus group. The second lineage represents a species that is widespread across the island's coastal lowlands. It is recovered as the sister group of O. javanicus and is identified as O. cf. carnaticus. Ancestral-range estimates suggest two independent colonizations of Indian subcontinent and Sri Lanka by widespread ancestral species of Oryzias during two discrete temporal windows: late Miocene and Plio-Pleistocene. No phylogeographic structure is apparent in Sri Lankan Oryzias, suggesting that there are no strong barriers to gene flow and dispersal along the coastal floodplains, as is the case also for other generalist freshwater fishes in the island.

Gaidropsarus gallaeciae (Gadiformes: Gaidropsaridae), a New Northeast Atlantic Rockling Fish, with Commentary on the Taxonomy of the Genus

A new species of rockling fish genus Gaidropsarus is described based on six specimens collected in Galicia and Porcupine Banks, in Atlantic European waters. An analysis of morphological characters has confirmed the specific status of specimens of a previously described clade by comparison of DNA sequences. Gaidropsarus gallaeciae sp. nov. it is distinguished from congeners by the following combination of characters: 43–44 vertebrae; 54–60 third dorsal fin rays; 44–52 anal fin rays; 21–23 pectoral fin rays; head length 21.1–25.2% of standard length (SL); length of the pelvic fin 16.2–19% SL; length of the first dorsal fin ray 15.8–27% of head length (%HL); eye diameter 15.8–20.5% HL; and interorbital space 21.7–28% HL. Using the nucleotide sequence of the 5’ end of the mitochondrial COI gene as a molecular marker, the genetic p-distance between the new species and its congeners far exceeds the usual 2%, granting the former the status of an independent taxon, which is in accordance with the morphological identification. A comparison with the other 12 valid species of the genus is presented. The study also highlights the morphological diversity resulting from the meristic and biometric variability of Gaidropsarus species and lays the groundwork for future taxonomic studies on this genus.

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.

The Complete Genome Sequences of 18 Species of Gadiformes (Actinopterygii, Chordata)

We present the complete genome sequences of 18 species of Gadiformes from 9 genera. Illumina sequencing was performed on genetic material from single wild-caught individuals. The reads were assembled using a de novo method followed by a finishing step. The raw and assembled data is publicly available via Genbank.

Propagation of a De Novo Gene under Natural Selection: Antifreeze Glycoprotein Genes and Their Evolutionary History in Codfishes

The de novo birth of functional genes from non-coding DNA as an important contributor to new gene formation is increasingly supported by evidence from diverse eukaryotic lineages. However, many uncertainties remain, including how the incipient de novo genes would continue to evolve and the molecular mechanisms underlying their evolutionary trajectory. Here we address these questions by investigating evolutionary history of the de novo antifreeze glycoprotein (AFGP) gene and gene family in gadid (codfish) lineages. We examined AFGP phenotype on a phylogenetic framework encompassing a broad sampling of gadids from freezing and non-freezing habitats. In three select species representing different AFGP-bearing clades, we analyzed all AFGP gene family members and the broader scale AFGP genomic regions in detail. Codon usage analyses suggest that motif duplication produced the intragenic AFGP tripeptide coding repeats, and rapid sequence divergence post-duplication stabilized the recombination-prone long repetitive coding region. Genomic loci analyses support AFGP originated once from a single ancestral genomic origin, and shed light on how the de novo gene proliferated into a gene family. Results also show the processes of gene duplication and gene loss are distinctive in separate clades, and both genotype and phenotype are commensurate with differential local selective pressures.