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To date, five ctenophore species’ mitochondrial genomes have been sequenced, and each contains open reading frames (ORFs) that if translated have no identifiable orthologs. ORFs with no identifiable orthologs are called unidentified reading frames (URFs). If truly protein-coding, ctenophore mitochondrial URFs represent a little understood path in early-diverging metazoan mitochondrial evolution and metabolism. We sequenced and annotated the mitochondrial genomes of three individuals of the beroid ctenophore Beroe forskalii and found that in addition to sharing the same canonical mitochondrial genes as other ctenophores, the B. forskalii mitochondrial genome contains two URFs. These URFs are conserved among the three individuals but not found in other sequenced species. We developed computational tools called pauvre and cuttlery to determine the likelihood that URFs are protein coding. There is evidence that the two URFs are under negative selection, and a novel Bayesian hypothesis test of trinucleotide frequency shows that the URFs are more similar to known coding genes than noncoding intergenic sequence. Protein structure and function prediction of all ctenophore URFs suggests that they all code for transmembrane transport proteins. These findings, along with the presence of URFs in other sequenced ctenophore mitochondrial genomes, suggest that ctenophores may have uncharacterized transmembrane proteins present in their mitochondria.

  [...]many are unaware of tools and practices that would allow them to write more reliable and maintainable code with less effort. [...]recent studies have found that scientists typically spend 30% or more of their time developing software [1],[2]. None of these practices will guarantee efficient, error-free software development, but used in concert they will reduce the number of errors in scientific software, make it easier to reuse, and save the authors of the software time and effort that can used for focusing on the underlying scientific questions.

The squid Sthenoteuthis oualaniensis , formerly Symplectoteuthis oualaniensis , generates light using the luciferin coelenterazine and a unique enzyme, symplectin. Genetic information is limited for bioluminescent cephalopod species, so many proteins, including symplectin, occur in public databases only as sequence isolates with few identifiable homologs. As the distribution of the symplectin/pantetheinase protein family in Metazoa remains mostly unexplored, we have sequenced the transcriptomes of four additional luminous squid, and make use of publicly available but unanalyzed data of other cephalopods, to examine the occurrence and evolution of this protein family. While the majority of spiralians have one or two copies of this protein family, four well-supported groups of proteins are found in cephalopods, one of which corresponds to symplectin. A cysteine that is critical for symplectin functioning is conserved across essentially all members of the protein family, even those unlikely to be used for bioluminescence. Conversely, active site residues involved in pantetheinase catalysis are also conserved across essentially all of these proteins, suggesting that symplectin may have multiple functions including hydrolase activity, and that the evolution of the luminous phenotype required other changes in the protein outside of the main binding pocket.

Improved relations The accumulation of molecular data is reshaping our understanding of the evolutionary relationships between the major groups of animals. Early work in the field relied upon data from a small number of genes, but the availability of fully sequenced genomes and expressed sequence tags (ESTs, short sub-sequences obtained from large numbers of complementary DNA clones), means that huge swathes of the animal kingdom can now be subjected to such analysis. A new study describes and discusses almost 40 megabases-worth of ESTs from animals of 21 phyla, including 11 animals for which no genomic or EST data were previously available. The conclusions confirm ideas long established by anatomy, including the monophyletic nature of the molluscs, deriving from a common ancestor despite their remarkable variety. New and interesting evolutionary relationships are also uncovered, including a single origin for spiral cleavage of the early embryo. The cover illustrates animal diversity, including acorn, ribbon, arrow and velvet worms, jellyfish and sea spider. This paper describes and discusses almost 40 megabases of expressed sequence tags (EST) clones from the DNA of animals from 21 phyla, including 11 animals for which genomic or EST data were previously lacking. The conclusions confirm ideas long established by anatomy, but raise new and interesting evolutionary relationships. Long-held ideas regarding the evolutionary relationships among animals have recently been upended by sometimes controversial hypotheses based largely on insights from molecular data 1 , 2 . These new hypotheses include a clade of moulting animals (Ecdysozoa) 3 and the close relationship of the lophophorates to molluscs and annelids (Lophotrochozoa) 4 . Many relationships remain disputed, including those that are required to polarize key features of character evolution, and support for deep nodes is often low. Phylogenomic approaches, which use data from many genes, have shown promise for resolving deep animal relationships, but are hindered by a lack of data from many important groups. Here we report a total of 39.9 Mb of expressed sequence tags from 29 animals belonging to 21 phyla, including 11 phyla previously lacking genomic or expressed-sequence-tag data. Analysed in combination with existing sequences, our data reinforce several previously identified clades that split deeply in the animal tree (including Protostomia, Ecdysozoa and Lophotrochozoa), unambiguously resolve multiple long-standing issues for which there was strong conflicting support in earlier studies with less data (such as velvet worms rather than tardigrades as the sister group of arthropods 5 ), and provide molecular support for the monophyly of molluscs, a group long recognized by morphologists. In addition, we find strong support for several new hypotheses. These include a clade that unites annelids (including sipunculans and echiurans) with nemerteans, phoronids and brachiopods, molluscs as sister to that assemblage, and the placement of ctenophores as the earliest diverging extant multicellular animals. A single origin of spiral cleavage (with subsequent losses) is inferred from well-supported nodes. Many relationships between a stable subset of taxa find strong support, and a diminishing number of lineages remain recalcitrant to placement on the tree.

During the past several decades, high numbers of gelatinous Zooplankton species have been reported in many estuarine and coastal ecosystems. Coupled with media-driven public perception, a paradigm has evolved in which the global ocean ecosystems are thought to he heading toward being dominated by “nuisance” jellyfish. We question this current paradigm by presenting a broad overview of gelatinous Zooplankton in a historical context to develop the hypothesis that population changes reflect the human-mediated alteration of global ocean ecosystems. To this end, we synthesize information related to the evolutionary context of contemporary gelatinous Zooplankton blooms, the human frame of reference for changes in gelatinous Zooplankton populations, and whether sufficient data are available to have established the paradigm. We conclude that the current paradigm in which it is believed that there has been a global increase in gelatinous Zooplankton is unsubstantiated, and we develop a strategy for addressing the critical questions about long-term, human-related changes in the sea as they relate to gelatinous Zooplankton blooms.

A central question in evolutionary biology is whether sponges or ctenophores (comb jellies) are the sister group to all other animals. These alternative phylogenetic hypotheses imply different scenarios for the evolution of complex neural systems and other animal-specific traits 1 – 6 . Conventional phylogenetic approaches based on morphological characters and increasingly extensive gene sequence collections have not been able to definitively answer this question 7 – 11 . Here we develop chromosome-scale gene linkage, also known as synteny, as a phylogenetic character for resolving this question 12 . We report new chromosome-scale genomes for a ctenophore and two marine sponges, and for three unicellular relatives of animals (a choanoflagellate, a filasterean amoeba and an ichthyosporean) that serve as outgroups for phylogenetic analysis. We find ancient syntenies that are conserved between animals and their close unicellular relatives. Ctenophores and unicellular eukaryotes share ancestral metazoan patterns, whereas sponges, bilaterians, and cnidarians share derived chromosomal rearrangements. Conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of ctenophores, placing ctenophores as the sister group to all other animals. The patterns of synteny shared by sponges, bilaterians, and cnidarians are the result of rare and irreversible chromosome fusion-and-mixing events that provide robust and unambiguous phylogenetic support for the ctenophore-sister hypothesis. These findings provide a new framework for resolving deep, recalcitrant phylogenetic problems and have implications for our understanding of animal evolution. Deeply conserved syntenic characters unite sponges with bilaterians, cnidarians, and placozoans in a monophyletic clade to the exclusion of the comb jellies (ctenophores)—placing ctenophores as the sister group to all other animals.

Background Siphonophores (Hydrozoa) have unparalleled colony-level complexity, precision of colony organization, and functional specialization between zooids (i.e., the units that make up colonies). Previous work has shown that, unlike other colonial animals, most growth in siphonophores is restricted to one or two well-defined growth zones that are the sites of both elongation and zooid budding. It remained unknown, however, how this unique colony growth and development is realized at the cellular level. Results To understand the colony-level growth and development of siphonophores at the cellular level, we characterize the distribution of proliferating cells and interstitial stem cells (i-cells) in the siphonophore Nanomia bijuga . Within the colony, we find evidence that i-cells are present at the tip of the horn, the structure within the growth zone that gives rise to new zooids. Co-localized gene expression of vasa-1 , pl10 , piwi , nanos-1 , and nanos-2 suggests that i-cells persist in the youngest zooid buds and that i-cells become progressively restricted to specific regions within the zooids until they are mostly absent from the oldest zooids. The examined genes remain expressed in gametogenic regions. No evidence for i-cells is found in the stem between maturing zooids. Domains of high cell proliferation include regions where the examined genes are expressed, but also include some areas in which the examined genes were not expressed such as the stem within the growth zones. Cell proliferation in regions devoid of vasa-1 , pl10 , piwi , nanos-1 , and nanos-2 expression indicates the presence of mitotically active epithelial cell lineages and, potentially, progenitor cell populations. Conclusions We provide the first evidence for i-cells in a siphonophore. Our findings suggest maintenance of i-cell populations at the sites of growth zones and that these sites are the main source of i-cells. This restriction of stem cells to particular regions in the colony, in combination with localized budding and spatial patterning during pro-bud subdivision, may play a major role in facilitating the precision of siphonophore growth. Spatially restricted maintenance of i-cells in mature zooids and absence of i-cells along the stem may explain the reduced developmental plasticity in older parts of the colony.

Bioluminescence (light production) and fluorescence (re-emission of absorbed radiation as light) are found in an unaccountably diverse array of marine organisms, where their functions are largely unknown. Here we report a deep-sea siphonophore that twitches glowing lures to attract fish. This is rare evidence of bioluminescence used for prey attraction among nonvisual marine organisms. The lures also contain red fluorescent material that shifts the wavelength of emitted light. The existence of a red-luminescent invertebrate suggests that long-wavelength light plays a greater role in marine interactions than previously suspected.

The jumbo or Humboldt squid, Dosidicus gigas, is an important fisheries resource and a significant participant in regional ecologies as both predator and prey. It is the largest species in the oceanic squid family Ommastrephidae and has the largest known potential fecundity of any cephalopod, yet little is understood about its reproductive biology. We report the first discovery of a naturally deposited egg mass of Dosidicus gigas, as well as the first spawning of eggs in captivity. The egg mass was found in warm water (25–27°C) at a depth of 16 m and was far larger than the egg masses of any squid species previously reported. Eggs were embedded in a watery, gelatinous matrix and were individually surrounded by a unique envelope external to the chorion. This envelope was present in both wild and captive-spawned egg masses, but it was not present in artificially fertilized eggs. The wild egg mass appeared to be resistant to microbial infection, unlike the incomplete and damaged egg masses spawned in captivity, suggesting that the intact egg mass protects the eggs within. Chorion expansion was also more extensive in the wild egg mass. Hatchling behaviours included proboscis extension, chromatophore activity, and a range of swimming speeds that may allow them to exercise some control over their distribution in the wild.

Food web linkages, or the feeding relationships between species inhabiting a shared ecosystem, are an ecological lens through which ecosystem structure and function can be assessed, and thus are fundamental to informing sustainable resource management. Empirical feeding datasets have traditionally been painstakingly generated from stomach content analysis, direct observations and from biochemical trophic markers (stable isotopes, fatty acids, molecular tools). Each approach carries inherent biases and limitations, as well as advantages. Here, using 27 years (1991–2016) of in situ feeding observations collected by remotely operated vehicles (ROVs), we quantitatively characterize the deep pelagic food web of central California within the California Current, complementing existing studies of diet and trophic interactions with a unique perspective. Seven hundred and forty-three independent feeding events were observed with ROVs from near-surface waters down to depths approaching 4000 m, involving an assemblage of 84 different predators and 82 different prey types, for a total of 242 unique feeding relationships. The greatest diversity of prey was consumed by narcomedusae, followed by physonect siphonophores, ctenophores and cephalopods. We highlight key interactions within the poorly understood ‘jelly web’, showing the importance of medusae, ctenophores and siphonophores as key predators, whose ecological significance is comparable to large fish and squid species within the central California deep pelagic food web. Gelatinous predators are often thought to comprise relatively inefficient trophic pathways within marine communities, but we build upon previous findings to document their substantial and integral roles in deep pelagic food webs.