Preservation Obscures Pelagic Deep-Sea Fish Diversity: Doubling the Number of Sole-Bearing Opisthoproctids and Resurrection of the Genus Monacoa (Opisthoproctidae, Argentiniformes)

recolorize: An R package for flexible colour segmentation of biological images

Colour pattern variation provides biological information in fields ranging from disease ecology to speciation dynamics. Comparing colour pattern geometries across images requires colour segmentation, where pixels in an image are assigned to one of a set of colour classes shared by all images. Manual methods for colour segmentation are slow and subjective, while automated methods can struggle with high technical variation in aggregate image sets. We present recolorize, an R package toolbox for human-subjective colour segmentation with functions for batch-processing low-variation image sets and additional tools for handling images from diverse (high-variation) sources. The package also includes export options for a variety of formats and colour analysis packages. This paper illustrates recolorize for three example datasets, including high variation, batch processing and combining with reflectance spectra, and demonstrates the downstream use of methods that rely on this output.

Diversity and evolution of optically complex eyes in a family of deep-sea fish: Ocular diverticula in barreleye spookfish (Opisthoproctidae)

Several families of mesopelagic fish have tubular eyes that are usually upwardly directed. These maximise sensitivity to dim downwelling sunlight and dorsal bioluminescence, as well as facilitating the detection of dark silhouettes above the animal. Such eyes, however, have a much-reduced field of view and will not be sensitive to, for example, lateral and ventral bioluminescent stimuli. All mesopelagic Opisthoproctidae so far examined have evolved mechanisms for extending the limited visual field of their eyes using approximately ventrolaterally directed, light-sensitive, diverticula. Some genera have small rudimentary lateral retinal areas capable of detecting only unfocussed illumination. Others have more extensive structures resulting in eyes that simultaneously focus light from above onto the main retina of the tubular eye using a lens, while diverticula produce focussed images of ventrolateral illumination using either reflection or possibly refraction. These bipartite structures represent perhaps the most optically complex of all vertebrate eyes. Here we extend the limited previous data on the ocular morphology of five Opisthoproctidae (Opisthoproctus soleatus, Winteria telescopa, Dolichopteryx longipes, Rhynchohyalus natalensis, and Bathylychnops exilis) using a combination of histology and magnetic resonance imaging and provide a preliminary description of the eyes of Macropinna microstoma. We note an increase in diverticular complexity over the life span of some species and quantify the contribution of the diverticulum to the eye’s total neural output in D. longipes and R. natalensis (25 and 20%, respectively). To help understand the evolution of Opisthoproctidae ocular diversity, a phylogeny, including all the species whose eye types are known, was reconstructed using DNA sequences from 15 mitochondrial and four nuclear genes. Mapping the different types of diverticula onto this phylogeny suggests a process of repeated evolution of complex ocular morphology from more rudimentary diverticula.

Anatomy and evolution of bioluminescent organs in the slimeheads (Teleostei: Trachichthyidae)

Bacterial bioluminescent organs in fishes have a diverse range of tissues of origin, patterns of compartmentalization, and associated light-conducting structures. The morphology of the perianal, bacterial bioluminescent organ of Aulotrachichthys prosthemius was described previously, but the light organ in other species of slimeheads, family Trachichthyidae, is poorly known. Here, we describe the anatomy of the bioluminescent organs in trachichthyids and places the evolution of this light-producing system in the context of a new phylogeny of the Trachichthyoidei to test the hypothesis that bioluminescence evolved twice in the suborder and that the light-producing component derives from the perianal ectoderm. We use gross and histological examination to provide the first description of the bioluminescent organ of Paratrachichthys and four additional species of Aulotrachichthys. Observations also strongly suggest the presence of a perianal bioluminescent organ in Sorosichthys ananasa. The updated phylogeny of the Trachichthyoidei is the first to combine morphological and DNA-sequence (11-gene fragments) evidence, and supports a monophyletic Trachichthyidae with component subfamilies Hoplostethinae and Trachichthyinae, supporting continued recognition of the family Anoplogastridae. All bioluminescent trachichthyoids share a similar bioluminescent-organ structure with elongate chambers filled with bacteria and connected to collecting ducts that, in turn, connect to superficial ducts that lead to and have lining epithelia continuous with the epidermis. In the context of the phylogeny, the bioluminescent organ of trachichthyids is inferred to have evolved as an elaboration of the proctodeum in the ancestor of Aulotrachichthys, Paratrachichthys, and Sorosichthys independently from the structurally similar cephalic bioluminescent organs in Anomalopidae and Monocentridae.

Discovery of a colossal slickhead (Alepocephaliformes: Alepocephalidae): an active-swimming top predator in the deep waters of Suruga Bay, Japan

A novel species of the family Alepocephalidae (slickheads), Narcetes shonanmaruae, is described based on four specimens collected at depths greater than 2171 m in Suruga Bay, Japan. Compared to other alepocephalids, this species is colossal (reaching ca. 140 cm in total length and 25 kg in body weight) and possesses a unique combination of morphological characters comprising anal fin entirely behind the dorsal fin, multiserial teeth on jaws, more scale rows than congeners, precaudal vertebrae less than 30, seven branchiostegal rays, two epurals, and head smaller than those of relatives. Mitogenomic analyses also support the novelty of this large deep-sea slickhead. Although most slickheads are benthopelagic or mesopelagic feeders of gelatinous zooplankton, behavioural observations and dietary analyses indicate that the new species is piscivorous. In addition, a stable nitrogen isotope analysis of specific amino acids showed that N. shonanmaruae occupies one of the highest trophic positions reported from marine environments to date. Video footage recorded using a baited camera deployed at a depth of 2572 m in Suruga Bay revealed the active swimming behaviour of this slickhead. The scavenging ability and broad gape of N. shonanmaruae might be correlated with its colossal body size and relatively high trophic position.

The first evidence of intrinsic epidermal bioluminescence within ray-finned fishes in the linebelly swallower Pseudoscopelus sagamianus (Chiasmodontidae)

External and histological examination of the photophores of the linebelly swallower Pseudoscopelus sagamianus reveal three epidermal layers of cells that form the light-producing and light-transmitting components of the photophores. Photophores among the examined photophore tracts are not significantly different in structure but the presence of mucous cells in the superficial layers of the photophore suggest continued function of the epidermal photophore in contributing to the mucous coat. This is the first evidence of intrinsic bioluminescence in primarily epidermal photophores reported in ray-finned fishes.

Resolving deep-sea pelagic saccopharyngiform eel mysteries: Identification of Neocyema and Monognathidae leptocephali and establishment of a new fish family "Neocyematidae" based on larvae, adults and mitogenomic gene orders

Deep-sea midwater "saccopharyngiform" eels of the families Cyematidae, Monognathidae, Eurypharyngidae and Saccopharyngidae (order Anguilliformes) are extraordinary fishes having major skeletal reductions and modifications compared to the general anguilliform body structure. Little is known about most aspects of the systematics, phylogeny, and ecology of these families, and few of the approximately 30 species described from adult specimens have been matched with their leptotocephalus larvae. Based on mitogenomic sequence data from rare new specimens, we show that the long-speculated-about larval form referred to as "Leptocephalus holti", which was thought to possibly be the larva of the rare orange-colored eels of Neocyema (5 known specimens; speculated to belong to the Cyematidae) are actually the larvae of the one-jaw eels of the family Monognathidae. One of the 5 types of L. holti larvae that were collected in the Pacific is genetically matched with Monognathus jesperseni, but multiple species exist based on larval sequence data and the morphology of adult specimens. A rare leptocephalus from the Sargasso Sea, with unique morphological characteristics including many small orange spots on the gut, was found to be the larva of Neocyema, which is presently only known from the Atlantic Ocean. We demonstrate that Neocyema constitutes a separate family being most closely related to Eurypharyngidae and Saccopharyngidae based on mitogenomic DNA sequences and unique mitochondrial gene orders.