The Scripps Institution of Oceanography (SIO) at the University of California, San Diego maintains one of the largest combined oceanographic collections in the world comprising four collections: Geological (sediment cores and dredged rocks), Pelagic Invertebrates, Benthic Invertebrates and Marine Vertebrates. After surviving threats of dissolution, the SIO Collections are now securely funded and have been able to make other collections available to the scientific community. Over the last few years, both the Marine Vertebrate (SIO-MVC) and Benthic Invertebrate (SIO-BIC) Collections have received National Science Foundation (NSF) and institutional funding to integrate important at-risk collections from University of California, Los Angeles (UCLA), the Monterey Bay Aquarium Research Institute (MBARI) and the University of Victoria. The UCLA Ichthyological Collection, around 9000 lots, was at risk of disposal due to hazardous material concerns and lack of institutional support. The collection, accumulated primarily under Boyd Walker (1949-1980) and later Don Buth (1980-), contains material from extensive surveys of the near-shore fishes of Southern California, Baja California and the Tropical Eastern Pacific including remote oceanic islands such as the Revillagigedos, Clipperton and the Galapagos. The UCLA collection also contains over 150 secondary types and over 100 species new to the SIO-MVC. Due to lack of support, the collection records were never digitized and the collection was minimally curated and its holdings were poorly known. For over two years, the collection manager and student employees have physically re-curated and integrated this material into the SIO-MVC. These data are now available online via iDigBio and VertNet and have already been used in numerous studies. The SIO-BIC, holding 45,000 lots, is accepting ownership of two deep-sea animal collections from Verena Tunnicliffe at the University of Victoria and Robert Vrijenhoek at MBARI. These collections include 10,900+ lots, largely from hydrothermal vents across the Pacific. Collected over 35 years from remote deep-sea sites that are difficult and expensive to access, these collections represent a major resource for systematics, genetics, and ecology. With Dr. Vrijenhoek now retired and Dr. Tunnicliffe nearing retirement, their collections were at risk of being lost. This material will be made discoverable online through the SIO-BIC database and iDigBio, and will be available for loan and examination. In the last year, the collection manager and five undergraduate employees have integrated some 3,000 lots. With support from the institution and the NSF, the SIO collections are solidifying their roles as central repositories for deep-sea and Eastern Pacific fauna.

Epizootic shell disease in American lobsters, Homarus americanus H. Milne-Edwards, 1837, has been of special concern since the mid-1990s due to its impact on fisheries. Numerous studies have led to the present understanding that this disease has a polymicrobial etiology. However, lacking in this research is exploration of the potential ways to ameliorate the disease. This is particularly important for public aquariums that have a strong focus on aesthetics and animal health. We performed two experiments to test short-term treatment methods on a laboratory-based model of shell disease on juvenile American lobsters. A preliminary experiment tested the effects of Hikari® Biobandage, a commercially available product used for treating fish lesions, on early- and late-stage shell disease. Another experiment examined resulting shell disease when lobsters were treated with distilled water, 10% povidone-iodine, d-alpha-tocopherol acetate (Vitamin E oil), formalin (100 ppm), and malachite green (5 ppm). We monitored the development of shell disease in both nonfacilitated and facilitated (in which the shell was damaged to induce disease) areas of the shell to determine effectiveness up to ecdysis. Biobandage was not effective at limiting nonfacilitated shell disease or facilitated wounds. Fresh water exacerbated facilitated wounds in comparison to animals treated with povidone-iodine, formalin, and malachite green. Formalin and malachite green treated lobsters showed the lowest severity of nonfacilitated shell disease. The study also showed that frequent handling alone (lobsters in control group) exhibited a higher amount of nonfacilitated shell disease. Identifying effective treatments in captive lobsters may provide unique solutions for studying shell disease.

Background

The unusual holopelagic annelid Poeobius meseres Heath, 1930 (Flabelligeridae) was first collected from Monterey Bay, California and has been subsequently recorded across the northern Pacific from Japan to the Gulf of California. Rare occurrences in the eastern tropical Pacific have extended as far as 7° S off Peru.

New information

Using molecular phylogenetic analysis of a newly-collected specimen from the Salas y Gómez Ridge off Chile, we extend the known geographic range of P. meseres southwards by 2040 km. This subtropical specimen showed higher genetic similarity to a specimen from the type locality (< 1.5% pairwise COI distance) than to representatives from the Aleutian Islands and Japan (5-6%), establishing the first genetically-confirmed occurrence of this species in the Southern Hemisphere. The latitudinal range of P. meseres encompasses the sole collection locality, off Ecuador, of Enigma terwielii Betrem, 1925, a pelagic annelid which has been compared to P. meseres, but is indeterminable due to an inadequate description. We therefore suggest that the earlier sole record of E. terwielii may have been an occurrence of what is known now as P. meseres.

A new caridean shrimp, Alvinocaris costaricensis, is described from methane seeps in the eastern Pacific off Costa Rica. The new species is the 16th described species of the genus, and by molecular analysis appears closest to Alvinocaris komaii from the Lau Basin, southwestern Pacific, but shares certain morphological characters with A. lusca from the Galapagos Rift and A. muricola from the West Florida Escarpment, as well as with A. kexueae from the Manus Basin in the Southwest Pacific.

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: Osedaxfrankpressi, O.knutei, O.packardorum, O.roseus and O.talkovici. We also provided additional DNA sequences from previously reported localities for two species: Osedaxpriapus 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. Osedaxfrankpressi, 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.

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.

Munidopsid squat lobsters are among the most abundant decapods at abyssal depths and the most diverse squat lobster group in the East Pacific region. During recent cruises along the East Pacific, many deep-sea squat lobsters were collected. Among these, we described five new munidopsid species supported both by morphological characters and molecular phylogenetics: Munidopsis girguisi sp. nov., M. nautilus sp. nov., M. testuda sp. nov., M. cortesi sp. nov. and M. hendrickxi sp. nov. We also report new records of several Munidopsis species across the East Pacific that increase the species distribution ranges. Here, we reconstructed the phylogenetic relationships of the East Pacific species in relation to other Galatheoidea using one nuclear and two mitochondrial gene fragment(s); we also performed single locus species delimitation analyses to explore the species status of various East Pacific munidopsid taxa. The new taxa were photographed, illustrated and imaged with micro-computed tomography. The phylogenetic results show that: (1) Janetogalathea californiensis, previously included in the family Galatheidae, nests within Munidopsidae; (2) the phylogenetic position of Phylladiorhynchus and Coralliogalathea as belonging in Galatheidae is not supported; and (3) Munidopsis is paraphyletic, agreeing with recent systematic hypotheses. Short genetic distances and species delimitation analyses suggested that a clade mostly constituted by abyssal species might include fewer species than currently considered, as species show a wider geographic range than previously considered, conforming with traditional hypotheses of cosmopolitanisms in abyssal species. ZooBank: urn:lsid:zoobank.org:pub:CED9EB18-7061-47A7-B2FF-7F1DAFCC7B12.

A new species of the zoarcid genus Pyrolycus Machida & Hashimoto, 2002, Pyrolycus jaco sp. nov., is described from a hydrothermal seep environment named Jacó Scar in the eastern Pacific of Costa Rica. Four specimens were collected in 2018 between 1746-1795 m among tubeworm colonies around the seep. The new species is differentiated from its two western Pacific congeners by having a shorter head, snout, jaw, and pectoral fins. It is further diagnosed by having three postorbital pores and two occipital pores. Molecular sequences of the cytochrome c oxidase I gene are provided and are the first for the genus. The character states indicating miniaturization in this species are discussed. This is the first vertebrate species known from this composite reducing ecosystem and is the fourth hydrothermally-associated zoarcid from the eastern Pacific.

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.

AbstractMethylation of cytosines is the prototypic epigenetic modification of the DNA. It has been implicated in various regulatory mechanisms throughout the animal kingdom and particularly in vertebrates. We mapped DNA methylation in 580 animal species (535 vertebrates, 45 invertebrates), resulting in 2443 genome-scale, base-resolution DNA methylation profiles of primary tissue samples from various organs. Reference-genome independent analysis of this comprehensive 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 with conserved DNA methylation patterns. 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.