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Methylation of cytosines is a prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms across the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale DNA methylation profiles of multiple organs. Bioinformatic analysis of this large dataset quantified the association of DNA methylation with the underlying genomic DNA sequence throughout vertebrate evolution. We observed a broadly conserved link with two major transitions—once in the first vertebrates and again with the emergence of reptiles. Cross-species comparisons focusing on individual organs supported a deeply conserved association of DNA methylation with tissue type, and cross-mapping analysis of DNA methylation at gene promoters revealed evolutionary changes for orthologous genes. In summary, this study establishes a large resource of vertebrate and invertebrate DNA methylomes, it showcases the power of reference-free epigenome analysis in species for which no reference genomes are available, and it contributes an epigenetic perspective to the study of vertebrate evolution.

Munidopsis species represent some of the dominant macrobenthos in cold seep habitats of the northern South China Sea. Earlier studies documented high abundances of M. verrilli Benedict, 1902 at Site F cold seep and M. lauensis Baba & de Saint Laurent, 1992 at Haima cold seep. However, comparative morphological and genetic analysis of additional materials from the deep waters of California, Manus Basin, and southern Okinawa Trough now indicate that those specimens in the South China Sea require taxonomic revision: the specimens at Site F should be M. longispinosa Cubelio, Tsuchida & Watanabe, 2007 and the specimens at Haima cold seep belong to M. ryukyuensis Cubelio, Tsuchida & Watanabe, 2007. Complementary descriptions of M. ryukyuensis , M. longispinosa and M. verrilli , as well as their geographic distributions, are provided to facilitate future identification.

The methane seeps on the Pacific margin of Costa Rica support extensive animal diversity and offer insights into deep-sea biogeography. During five expeditions between 2009 and 2019, we conducted intensive faunal sampling via 63 submersible dives to 11 localities at depths of 300–3600 m. Based on these expeditions and published literature, we compiled voucher specimens, images, and 274 newly published DNA sequences to present a taxonomic inventory of macrofaunal and megafaunal diversity with a focus on invertebrates. In total 488 morphospecies were identified, representing the highest number of distinct morphospecies published from a single seep or vent region to date. Of these, 131 are described species, at least 58 are undescribed species, and the remainder include some degree of taxonomic uncertainty, likely representing additional undescribed species. Of the described species, 38 are known only from the Costa Rica seeps and their vicinity. Fifteen range extensions are also reported for species known from Mexico, the Galápagos seamounts, Chile, and the western Pacific; as well as 16 new depth records and three new seep records for species known to occur at vents or organic falls. No single evolutionary narrative explains the patterns of biodiversity at these seeps, as even morphologically indistinguishable species can show different biogeographic affinities, biogeographic ranges, or depth ranges. The value of careful molecular taxonomy and comprehensive specimen-based regional inventories is emphasized for biodiversity research and monitoring.

The four named species of Branchipolynoe all live symbiotically in mytilid mussels (Bathymodiolus) that occur at hydrothermal vents or methane seeps. Analyses using mitochondrial (COI and 16S) and nuclear (ITS) genes, as well as morphology, were conducted on a collection of Branchipolynoe from Pacific Costa Rican methane seeps and West Pacific hydrothermal vents. This revealed five new species of Branchipolynoe, and these are formally described. The new species from Costa Rica live in three species of Bathymodiolus mussels (also new) at depths ranging from 1000 to 1800 m. Branchipolynoe kajsae n. sp. and Branchipolynoe halliseyae n. sp. were found in all three undescribed Bathymodiolus species, while Branchipolynoe eliseae n. sp. was found in Bathymodiolus spp. 1 and 2, and Branchipolynoe meridae n. sp. was found in Bathymodiolus spp. 1 and 3. Hence, Bathymodiolus sp. 1 hosted all four of the new species, while the other two Bathymodiolus hosted three each. Most mussels contained only one specimen of Branchipolynoe; where there was more than one, these were often a female and smaller male of the same species. The newly discovered species from the West Pacific, Branchipolynoe tjiasmantoi n. sp., lives in unidentified Bathymodiolus at depths ranging from 674 to 2657 m from hydrothermal vents in the North Fiji (Fiji) and Lau Basins (Tonga) and also from New Zealand, Vanuatu, and the Manus Basin (Papua New Guinea). The phylogenetic and biogeographical implications of this diversity of Branchipolynoe are discussed.

The genus Typhlonida Macpherson & Baba in Machordom et al. 2022 is a group of munidid squat lobsters typically found in deep waters. This study describes and illustrates a new species, Typhlonida cocoensis sp. nov. , from a seamount area in the eastern Pacific. Typhlonida cocoensis sp. nov. is closely related to T. sanctipauli (Henderson, 1885) but can be readily distinguished from the latter by its relatively small eyes, narrow anterior margin of the thoracic sternite 4, lack of granules on the lateral surfaces of sternite 7, and unarmed anterior branchial regions dorsally. In addition to morphological comparisons, genetic distance and phylogenetic analyses were used to support the recognition of this new species. The phylogenetic positions of the Typhlonida and Antillimunida species from the eastern Pacific are discussed.

Midwater ecosystems represent a substantial knowledge gap in baseline biodiversity surveys of the Clarion-Clipperton Zone of the Pacific Ocean, where deep-sea mining of seafloor polymetallic nodules is anticipated to impact the water column via sediment discharge plumes. In the first midwater surveys by remotely operated vehicle of the Nauru Ocean Resources Inc. exploration contract area D (NORI-D), we documented nine annelid species: Poeobius meseres (Flabelligeridae), Tomopteris sp. (Tomopteridae), Tomopteridae sp., Pelagobia sp. (Lopadorrhynchidae), Lopadorrhynchidae sp., and Typhloscolecidae sp. from the mesopelagic oxygen minimum zone and vicinity; and Swima bombiviridis (Acrocirridae), Swima fulgida, and Flota sp. (Flabelligeridae) from greater depths. Five species were vouchered, and the ranges of occurrence for four species were extended substantially, by 1,400–2,900 km across the northeastern Pacific (Swima bombiviridis, Swima fulgida, Flota sp., and Tomopteris sp.). We also report an image of benthopelagic Polynoidae and the first record of parental care of juveniles in Tomopteridae. These specimens, live images, and reference DNA sequences will support the identification of pelagic annelids from video surveys for biodiversity research and environmental impact monitoring.

First described in 2004 off California, Osedax worms are now known from many of the world's oceans, ranging from 10 to over 4000 m in depth. Currently, little is known about species ranges, since most descriptions are from single localities. In this study, we used new sampling in the north-eastern Pacific and available GenBank data from off Japan and Brazil to report expanded ranges for five species: Osedax frankpressi , O. knutei , O. packardorum , O. roseus and O. talkovici . We also provided additional DNA sequences from previously reported localities for two species: Osedax priapus and O. randyi . To assess the distribution of each species, we used cytochrome c oxidase subunit I ( COI ) sequences to generate haplotype networks and assess connectivity amongst localities where sampling permitted. Osedax frankpressi , O. packardorum , O. priapus , O. roseus and O. talkovici all had one or more dominant COI haplotypes shared by individuals at multiple localities, suggesting high connectivity throughout some or all of their ranges. Low Φ ST values amongst populations for O. packardorum , O. roseus and O. talkovici confirmed high levels of gene flow throughout their known ranges. High Φ ST values for O. frankpressi between the eastern Pacific and the Brazilian Atlantic showed little gene flow, reflected by the haplotype network, which had distinct Pacific and Atlantic haplotype clusters. This study greatly expands the ranges and provides insights into the phylogeography for these nine species.

There been increasing interest in polymetallic nodule mining within the Clarion-Clipperton Zone (CCZ). Polymetallic nodule mining within NORI-D will release a sediment plume within the water column and a previous mining collector test within the Nauru Ocean Resources Inc. (NORI-D) contract area released surface pollution from mining tailings. The mid-water plume, as well as accidental surface pollution, indicate that polymetallic nodule mining could impact surface plankton. Although the ichthyoplankton within the eastern tropical Pacific have been well-studied, recent data from within polymetallic nodule mining licence areas is lacking. Environmental Expedition C5e conducted an environmental baseline assessment of both pelagic and benthic fauna within the NORI-D region of the CCZ, which included the opportunistic collection of ichthyoplankton. Ichthyoplankton were collected within NORI-D from November–December 2021 using two plankton nets and a Remotely Operated Vehicle (ROV). Here, we present a checklist of ichthyoplankton within the NORI-D licence area during this winter campaign. Eighteen samples were collected and identified through morphology, with a limited number identified through genetic sequencing. Specimens were from five orders, including Argentiniformes, Stomiiformes, Myctophiformes, Beloniformes and Scombriformes. This checklist will aid contractors and scientists conducting work within the CCZ to examine how wastewater discharge from polymetallic nodule mining could impact fish reproduction and ichthyoplankton survival.

Ecological studies of many pelagic, deep-sea animals are often limited due to their remote habitats and sampling constraints. In the eastern tropical Pacific, numerous studies have been published about the distribution of demersal fishes across the region, yet studies for midwater taxa are lacking. Here, we utilized visual survey transects from an area targeted for polymetallic nodule mining to examine the drivers behind the distribution of two mesopelagic predators, snipe eels (family Nemichthyidae) and sawtooth eels (family Serrivomeridae). Additionally, we compared the vertical distributions of their prey and examined whether the two eels displayed different behaviors in situ. Time of day was not a statistically significant driver of eel distribution, although the shallowest observations were during the night, indicating that some in the populations of Nemichthyidae and Serrivomeridae had migrated weakly to the upper 200 m. Eel distributions were found to be affected by both depth and dissolved oxygen, with Nemichthyidae observed in shallower and lower oxygenated waters and Serrivomeridae in deeper and more oxygenated ones. Two prey taxa (families Euphausiidae and Sergestidae) were abundant at shallower transect depths, which likely drives the distribution of Nemichthyidae, as pelagic crustaceans constitute their primary prey. In terms of behavior, Serrivomeridae were more active and were oriented primarily vertically, suggesting that Nemichthyidae may be less active or under lower predation pressure due to the hypoxic environment in which they occur. This work highlights the importance of visual surveys in obtaining in situ data as a complement to traditional sampling methods, particularly for collecting data on poorly understood animals.