Speciation and phylogeography in the cosmopolitan marine moon jelly, Aurelia sp

The microbiome of a Pacific moon jellyfish Aurelia coerulea

The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.

Long-term dynamics, population structure and connectivity of the helmet jellyfish Periphylla periphylla in a Norwegian fjord and adjacent waters

Mass occurrences of Periphylla periphylla in Norwegian fjords cause major concerns related to potential regime shifts that could affect ecosystem stability. 15 years of trawl data (2006-2015), complemented with comprehensive sampling in different areas and seasons (2018-2021) allowed new insights on the dynamics, structure and connectivity of P. periphylla populations within and beyond Trondheimsfjorden. Despite assumed population bursts, no clear trend on P. periphylla population size in Trondheimsfjorden were identified. Sampling frequency and population size suggest a local reproduction of P. periphylla, especially in the inner part of the fjord where young-of-the-year (YOY) individuals occur. Size variations occurred in relation to sampling month, thus pointing at seasonal patterns in growth and reproduction. No distinct population structure of P. periphylla populations within Trondheimsfjorden and over larger spatial scales (> 100 km) along the Norwegian coast was observed. Such poor geographic population structure provides evidence for a strong dispersal of P. periphylla, potentially triggered by frequent deep-water renewals of the fjords' basins that enable a high gene flow. Data on P. periphylla long-term dynamics, population structure and connectivity provide valuable information for ecosystem state assessments and enable the advancement of ecosystem management approaches, thus accounting for both stakeholder and ecosystem demands.

Non-Bilaterians as Model Systems for Tissue Mechanics

In animals, epithelial tissues are barriers against the external environment, providing protection against biological, chemical, and physical damage. Depending on the organism's physiology and behavior, these tissues encounter different types of mechanical forces and need to provide a suitable adaptive response to ensure success. Therefore, understanding tissue mechanics in different contexts is an important research area. Here, we review recent tissue mechanics discoveries in three early divergent non-bilaterian systems-Trichoplax adhaerens, Hydra vulgaris, and Aurelia aurita. We highlight each animal's simple body plan and biology and unique, rapid tissue remodeling phenomena that play a crucial role in its physiology. We also discuss the emergent large-scale mechanics in these systems that arise from small-scale phenomena. Finally, we emphasize the potential of these non-bilaterian animals to be model systems in a bottom-up approach for further investigation in tissue mechanics.

Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations

BACKGROUND

Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method.

RESULTS

We reconstructed the FST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors.

CONCLUSION

Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.

The Life Cycle of Aurelia aurita Depends on the Presence of a Microbiome in Polyps Prior to Onset of Strobilation

Aurelia aurita's intricate life cycle alternates between benthic polyp and pelagic medusa stages. The strobilation process, a critical asexual reproduction mechanism in this jellyfish, is severely compromised in the absence of the natural polyp microbiome, with limited production and release of ephyrae. Yet, the recolonization of sterile polyps with a native polyp microbiome can correct this defect. Here, we investigated the precise timing necessary for recolonization as well as the host-associated molecular processes involved. We deciphered that a natural microbiota had to be present in polyps prior to the onset of strobilation to ensure normal asexual reproduction and a successful polyp-to-medusa transition. Providing the native microbiota to sterile polyps after the onset of strobilation failed to restore the normal strobilation process. The absence of a microbiome was associated with decreased transcription of developmental and strobilation genes as monitored by reverse transcription-quantitative PCR. Transcription of these genes was exclusively observed for native polyps and sterile polyps that were recolonized before the initiation of strobilation. We further propose that direct cell contact between the host and its associated bacteria is required for the normal production of offspring. Overall, our findings indicate that the presence of a native microbiome at the polyp stage prior to the onset of strobilation is essential to ensure a normal polyp-to-medusa transition. IMPORTANCE All multicellular organisms are associated with microorganisms that play fundamental roles in the health and fitness of the host. Notably, the native microbiome of the Cnidarian Aurelia aurita is crucial for the asexual reproduction by strobilation. Sterile polyps display malformed strobilae and a halt of ephyrae release, which is restored by recolonizing sterile polyps with a native microbiota. Despite that, little is known about the microbial impact on the strobilation process's timing and molecular consequences. The present study shows that A. aurita's life cycle depends on the presence of the native microbiome at the polyp stage prior to the onset of strobilation to ensure the polyp-to-medusa transition. Moreover, sterile individuals correlate with reduced transcription levels of developmental and strobilation genes, evidencing the microbiome's impact on strobilation on the molecular level. Transcription of strobilation genes was exclusively detected in native polyps and those recolonized before initiating strobilation, suggesting microbiota-dependent gene regulation.

Exceptional population genomic homogeneity in the black brittle star Ophiocomina nigra (Ophiuroidea, Echinodermata) along the Atlantic-Mediterranean coast

The Atlantic-Mediterranean marine transition is characterised by strong oceanographic barriers and steep environmental gradients that generally result in connectivity breaks between populations from both basins and may lead to local adaptation. Here, we performed a population genomic study of the black brittle star, Ophiocomina nigra, covering most of its distribution range along the Atlantic-Mediterranean region. Interestingly, O. nigra is extremely variable in its coloration, with individuals ranging from black to yellow-orange, and different colour morphs inhabiting different depths and habitats. In this work, we used a fragment of the mitochondrial COI gene and 2,374 genome-wide ddRADseq-derived SNPs to explore: (a) whether the different colour morphs of O. nigra represent different evolutionary units; (b) the disruptive effects of major oceanographic fronts on its population structure; and (c) genomic signals of local adaptation to divergent environments. Our results revealed exceptional population homogeneity, barely affected by oceanographic fronts, with no signals of local adaptation nor genetic differentiation between colour morphs. This remarkable panmixia likely results from a long pelagic larval duration, a large effective population size and recent demographic expansions. Our study unveils an extraordinary phenotypic plasticity in O. nigra, opening further research questions on the ecological and molecular mechanisms underpinning coloration in Ophiuroidea.

Artemisia herba-alba sesquiterpenes: in silico inhibition in the ATP-binding pocket

To identify antimicrobial leads for medical applications, metabolites from the aerial part of Artemisia herba-alba were extracted and chromatographically purified. Two new sesquiterpenes, 1β,8α-dihydroxyeudesm-4-en-6β,7α,11βH-12,6-olide (1) and 1β,6α,8α-trihydroxy, 11α-methyl-eudesma-4(15)-en-13-propanoate (2) along with a known eudesmanolide 11-epi-artapshin (3) were identified. Structures were determined by spectroscopic methods including 1D- and 2D-NMR as well as mass spectroscopy. Compound 3 inhibited Gram-positive bacteria Bacillus subtilis, Lactobacillus cereus and Staphylococcus aureus and exhibited antifungal activity against the pathogenic fungus F. solani. The mode-of-action of these antimicrobial sesquiterpenes as bacterial type II DNA topoisomerase and/or DNA gyrase B inhibitors were examined via in silico studies. Such molecular-docking studies were also employed to examine antifungal activity against an N-myristoyl transferase (NMT) target. Compound 3 had the greatest gyrase B binding affinity in the ATP-binding pocket and was found to possess an inhibitory action against non-invasive micro-test technology (NMT).

DNA Barcoding of Moon Jellyfish (Cnidaria, Scyphozoa, Ulmaridae, Aurelia): Two Cryptic Species from the Azores (NE Atlantic, Macaronesia), and Evaluation of the Non-Indigenous Species (NIS)

Moon jellies are some of the most popular, widely distributed, and best-studied marine jellyfish. By the end of the past century only two or three Aurelia species were recognized, but with the rise of DNA barcoding studies, around thirty Aurelia species are presently accepted. Most of the species are morphologically indistinguishable and have restricted biogeography. We reveal, with COI, 16S, and ITS1-5.8S sequence data, two (pseudo-)cryptic species of Aurelia, potentially endemic to the Azores ecoregion, herein provisionally classified as A. “cf. pseudosolida” and A. “misteriosa”. These species are closely related to the Mediterranean lineages of A. pseudosolida and A. persea, respectively. In the Azores, the shape of the campanula and oral arms readily distinguishes the two species: the former with folded oral arms and globose campanula, and the latter with flattened campanula and thick and long oral arms. Previous reports of A. solida and A. aurita in the Azores should generally correspond to A. “misteriosa” and A. cf. pseudosolida, respectively. The phylogenetic (re-)examination of the available DNA barcodes of Aurelia only evidenced human-mediated dispersal for A. coerulea, A. relicta, and A. aurita. Aurelia solida cannot be yet considered NIS in the Mediterranean. More jellyfish DNA (meta)barcoding should reveal further cryptic diversity, biological invasions, and phylogeographic inferences.

Asexual reproduction strategies in the moon jellyfish Aurelia (Cnidaria: Scyphozoa)

The genus Aurelia is one of the major contributors to jellyfish blooms in coastal waters, possibly due to its adaptive reproduction strategies. Different Aurelia lineages have adapted their reproduction modes to varying environmental conditions in their respective habitats. To understand the successful adaptation strategies, three strains of Aurelia coerulea and two strains of Aurelia solida polyps from different geographical areas were exposed to a range of temperatures and two food regimes, and the effects on reproduction rates were assessed. Asexual reproduction was significantly affected by the changes in these factors. The highest reproduction rate under sufficient food conditions was observed in the United States strain and the lowest was observed in the Israel strain, regardless of temperature, indicating the differences in the blooming potential. Six asexual reproduction modes were observed, of which lateral budding, lateral budding by means of stolons, and reproduction from parts of stolons were the main modes used by all Aurelia strains, except Aurelia solidaISR, for which reproduction by stolons was the main mode. The capability to switch reproductive strategies in response to environmental cues depending on the lineage predetermines the highly frequent blooming events of Aurelia.

YMLA: A comparative platform to carry out functional enrichment analysis for multiple gene lists in yeast

Comparative analysis among multiple gene lists on their functional features is now a routine task due to the advancement of high-throughput experiments. Several enrichment analysis tools were developed in the past. However, these tools mainly focus on one gene list and contain only gene ontology or interaction features. What makes it worse, comparative investigation and customized feature set reanalysis are still unavailable. Therefore, we constructed the YMLA (Yeast Multiple List Analyzer) platform in this research. YMLA includes 39 yeast features and facilitates comparative analysis among multiple gene lists via tabular views, heatmaps, and network plots. Moreover, the customized feature set reanalysis function was implemented in YMLA to help form mechanism hypotheses based on a selected enriched feature subset. We demonstrated the biological applicability of YMLA via example lists consisting of genes with top/bottom translation efficiency values. The analysis results provided by YMLA reveal novel facts consistent with previous experiments. YMLA is available at https://cosbi7.ee.ncku.edu.tw/YMLA/.

Insight into the cryptic diversity and phylogeography of the peculiar fried egg jellyfish Phacellophora (Cnidaria, Scyphozoa, Ulmaridae)

The fried egg jellyfish Phacellophora camtschatica (senso lato) is a morphologically peculiar and conspicuous species occurring mostly in the cold waters of the North Pacific. It is less common in the cold waters of the NW Atlantic, and occasionally has been reported in the Mediterranean, Arctic, East and South Pacific, and E, SW and NE Atlantic. However, sightings of this scyphozoan jellyfish have intensified during the past two to three decades in Macaronesia, the Iberian Peninsula and the Mediterranean. These jellyfish are known to be voracious predators of other jellies, but also of other taxa, including fish of commercial interest. Therefore, Phacellophora aggregations may threaten local fisheries, aquaculture, and local biodiversity structuring. We report the first known occurrences of Phacellophora in the Azores Islands, which apparently become more frequent in recent years of the past decade. We confirm, through DNA barcoding of COI and 16S mitochondrial markers, the genetic identity of Phacellophora occurring in the Azores (NE Atlantic). We reveal, with COI sequence data, three (potentially four) cryptic species within the Phacellophora camtschatica complex. Two Phacellophora species co-occur in the North Pacific. In the North Atlantic (and possibly in the Mediterranean) one or two distinct species exist. Three nominal species of the genus that are currently synonymized, with type localities in the N Pacific, NW Atlantic, and the Mediterranean, need reassessment. The morphotypes previously defined for the four putative species names given for Phacellophora might be eventually differentiated by the number and disposition of the marginal lappets of umbrellae. This morphologic character has to be further inspected in vouchers of the four genetic lineages of Phacellophora, to decide between the description of new species, and the resurrection of junior synonyms through the designation of neotypes with DNA Barcodes, to validate the identity of the cryptic taxa detected. More haplotype sampling is necessary across the distribution of the genus to further investigate the genetic diversity and phylogeographic history of Phacellophora. The high genetic relatedness of Phacellophora from the cold NW Atlantic and the sub-tropical shores of the Azores, revealed by 16S and COI sequence data, suggests a recent invasion, in terms of geologic time, of the temperate waters of the NE Atlantic (and possibly of the Mediterranean). The medusivorous habits of Phacellophora, and especially its predation on the mauve stinger (Pelagia spp.) which frequently blooms in Macaronesia and Mediterranean waters, could relate to the recent reports of Phacellophora in the Azores, Madeira, Canary Islands, and the Mediterranean. More investment, including on scientific staff, is necessary to catalog, DNA barcode and monitor jellyfish dynamics more accurately worldwide.

Description of Aurelia pseudosolida sp. nov. (Scyphozoa, Ulmaridae) from the Adriatic Sea

Until 2021, the genus Aurelia contained eleven described species (WoRMS, 2020), with many genetic species still awaiting a formal description. In 2021, ten new species of Aurelia were described almost solely from genetic data in a novel attempt to use genetic characters as diagnostic characters for species descriptions, leaving seven genetic species still undescribed. Here we present the description of a new Aurelia species from the Adriatic Sea using an integrative taxonomy approach, i.e., employing molecular as well as morphological characteristics in order to describe this new Aurelia species. The species is described based on a single medusa sampled from the town of Rovinj (Croatia), North Adriatic, amidst combined blooms of the ctenophore Mnemiopsis leidy and cnidarian Aurelia solida in the summer of 2020. Based on genetic data, the newly described Aurelia pseudosolida sp. nov. has never been sequenced in any of the previous investigations of the molecular diversity of Aurelia. This is the second species belonging to Discomedusae described from the North Adriatic in little more than half a decade, which could be yet another indication of the susceptibility of the North Adriatic to proliferation of non-indigenous gelatinous species, especially if we take into account historical as well as recent blooms of suspected non-indigenous gelatinous species such as Muggiaea atlantica, Aurelia solida, Mawia benovici and Mnemiopsis leidy.

A Parachlorella kessleri (Trebouxiophyceae, Chlorophyta) strain tolerant to high concentration of calcium chloride

Members of coccoid green algae have been documented in various extreme environments. In this article, a unicellular green alga was found to slowly grow in high concentration (3.6 g/L) and pure calcium chloride solution in the laboratory. It was successfully cultured and a taxonomic study combined approaches of morphological and molecular methods was conducted to determine its classification attribution, which was followed by a preliminary physiology research to explore its unique tolerance characteristics against calcium chloride stress. The strain was identified as Parachlorella kessleri by very similar morphology and the same phylogenetic position. The morphological differences among the three species in genus Parachlorella were then discussed and the characteristic traits of absent or thin mucilaginous envelop and mantel-shaped chloroplast for P. kessleri were supported. In addition, the almost strictly spherical shape of adult cells could further distinguish the P. kessleri from the other two species. The tolerant characteristics to CaCl₂  stress for this strain were confirmed and the limit concentration was revealed as between 2000 and 4000 times than the standard BG11 culture concentration. Therefore, this P. kessleri strain is expected to be a good material to explore the mechanism of resistance to calcium ions stress for eukaryotic microbiology.

The importance of molecular characters when morphological variability hinders diagnosability: systematics of the moon jellyfish genus Aurelia (Cnidaria: Scyphozoa)

Cryptic species have been detected across Metazoa, and while no apparent morphological features distinguish them, it should not impede taxonomists from formal descriptions. We accepted this challenge for the jellyfish genus Aurelia, which has a long and confusing taxonomic history. We demonstrate that morphological variability in Aurelia medusae overlaps across very distant geographic localities. Even though some morphological features seem responsible for most of the variation, regional geographic patterns of dissimilarities are lacking. This is further emphasized by morphological differences found when comparing lab-cultured Aurelia coerulea medusae with the diagnostic features in its recent redescription. Previous studies have also highlighted the difficulties in distinguishing Aurelia polyps and ephyrae, and their morphological plasticity. Therefore, mostly based on genetic data, we recognize 28 species of Aurelia, of which seven were already described, 10 are formally described herein, four are resurrected and seven remain undescribed. We present diagnostic genetic characters for all species and designate type materials for newly described and some resurrected species. Recognizing moon jellyfish diversity with formal names is vital for conservation efforts and other studies. This work clarifies the practical implications of molecular genetic data as diagnostic characters, and sheds light on the patterns and processes that generate crypsis.

Comparative genetics of scyphozoan species reveals the geological history and contemporary processes of the Mediterranean Sea

Jellyfish are useful genetic indicators for aquatic ecosystems as they have limited mobility and are highly exposed to the water column. By using comparative genomics and the molecular clock (timetree) of Rhizostoma pulmo, we revealed a divergence point between the East and West Mediterranean Sea (MS) populations that occurred 4.59 million years ago (mya). It is suggested that the two distinct ecological environments we know today were formed at this time. We propose that before this divergence, the highly mixed Atlantic and Mediterranean waters led to the wide dispersal of different species including R. pulmo. At 4.59 mya, the Western and Eastern MS were formed, indicating the possibility of a dramatic environmental event. For the first time, we find that for the jellyfish we examined, the division of the MS in east and west is not at the Straits of Sicily as generally thought, but significantly to the east. Using genomics of the Aurelia species, we examined contemporary anthropogenic impacts with a focus on migration of scyphozoa across the Suez Canal (Lessepsian migration). Aurelia sp. is among the few scyphozoa we find in both the MS and the Red Sea, but our DNA analysis revealed that the Red Sea Aurelia sp. did not migrate or mix with MS species. Phyllorhiza punctata results showed that this species was only recently introduced to the MS as a result of anthropogenic transportation activity, such as ballast water discharge, and revealed a migration vector from Australia to the MS. Our findings demonstrate that jellyfish genomes can be used as a phylogeographic molecular tool to trace past events across large temporal scales and reveal invasive species introduction due to human activity.

Speciation across the Tree of Life

Much of what we know about speciation comes from detailed studies of well-known model systems. Although there have been several important syntheses on speciation, few (if any) have explicitly compared speciation among major groups across the Tree of Life. Here, we synthesize and compare what is known about key aspects of speciation across taxa, including bacteria, protists, fungi, plants, and major animal groups. We focus on three main questions. Is allopatric speciation predominant across groups? How common is ecological divergence of sister species (a requirement for ecological speciation), and on what niche axes do species diverge in each group? What are the reproductive isolating barriers in each group? Our review suggests the following patterns. (i) Based on our survey and projected species numbers, the most frequent speciation process across the Tree of Life may be co-speciation between endosymbiotic bacteria and their insect hosts. (ii) Allopatric speciation appears to be present in all major groups, and may be the most common mode in both animals and plants, based on non-overlapping ranges of sister species. (iii) Full sympatry of sister species is also widespread, and may be more common in fungi than allopatry. (iv) Full sympatry of sister species is more common in some marine animals than in terrestrial and freshwater ones. (v) Ecological divergence of sister species is widespread in all groups, including ~70% of surveyed species pairs of plants and insects. (vi) Major axes of ecological divergence involve species interactions (e.g. host-switching) and habitat divergence. (vii) Prezygotic isolation appears to be generally more widespread and important than postzygotic isolation. (viii) Rates of diversification (and presumably speciation) are strikingly different across groups, with the fastest rates in plants, and successively slower rates in animals, fungi, and protists, with the slowest rates in prokaryotes. Overall, our study represents an initial step towards understanding general patterns in speciation across all organisms.

Genetic diversity and novel lineages in the cosmopolitan copepod Pleuromamma abdominalis in the Southeast Pacific

Across boundary currents, zooplankton are subject to strong oceanographic gradients and hence strong selective pressures. How such gradients interact with the speciation process of pelagic organisms is still poorly understood in the open ocean realm. Here we report on genetic diversity within the pelagic copepod Pleuromamma abdominalis in the poorly known Southeast Pacific region, with samples spanning an ocean gradient from coastal upwelling to the oligotrophic South Pacific Subtropical Gyre. We assessed variation in fragments of the mitochondrial (mt) genes cytochrome c oxidase subunit I (COI) and Cytochrome b as well as in the nuclear internal transcribed spacer (ITS) region and 28 S rRNA. Phylogenetic analyses revealed the presence of 8 divergent lineages occurring across the gradient with genetic distances in the range of 0.036 and 0.44 (mt genes), and GMYC species delimitation methods support their inference as distinct (undescribed) species. Genetic lineages occurring across the zonal gradient showed strong genetic structuring, with the presence of at least two new lineages within the coastal upwelling zone, revealing an unexpectedly high level of endemism within the Humboldt Current System. Multivariate analyses found strong correlation between genetic variation and surface chlorophyll-a and salinity, suggesting an important role for hydrographic gradients in maintaining genetic diversity. However, the presence of cryptic lineages within the upwelling zone cannot be easily accounted for by environmental heterogeneity and poses challenging questions for understanding the speciation process for oceanic zooplankton.

Global phylogeography of toxic cyanobacteria Moorea producens reveals distinct genetic partitioning influenced by Proterozoic glacial cycles

Lyngbya majuscula is a marine filamentous cyanobacteria belonging to the family Oscillatoriaceae. Recent phylogenetic analyses of L. majuscula have reclassified a subset of this species into various genera such as Moorea, Okeania and Dapis. From the genus Moorea, Moorea producens is a toxic invasive cyanobacterium that produces bioactive secondary metabolites that can cause severe inflammation and blistering. Despite the global distribution of M. producens, little information is available on their origin, patterns of dispersal and population structure. In this study, the spatial population structure of M. producens was investigated using near-complete 16S rRNA sequences. Analysis of the global population of M. producens by Isolation by Distance and STRUCTURE revealed two significantly distinct cosmopolitan populations that were separated by a genetic break. Lineage-specific divergence estimates of 147 cyanobacterial taxa, based on a relaxed molecular clock indicated the first global emergence of M. producens during the Mesoarchean and a subsequent global recolonization during the Mesoproterozoic period. We conclude that the genetic discontinuity between both cosmopolitan populations is attributed to refugia associated with Proterozoic glacial cycles.

Medusozoan genomes inform the evolution of the jellyfish body plan

Cnidarians are astonishingly diverse in body form and lifestyle, including the presence of a jellyfish stage in medusozoans and its absence in anthozoans. Here, we sequence the genomes of Aurelia aurita (a scyphozoan) and Morbakka virulenta (a cubozoan) to understand the molecular mechanisms responsible for the origin of the jellyfish body plan. We show that the magnitude of genetic differences between the two jellyfish types is equivalent, on average, to the level of genetic differences between humans and sea urchins in the bilaterian lineage. About one-third of Aurelia genes with jellyfish-specific expression have no matches in the genomes of the coral and sea anemone, indicating that the polyp-to-jellyfish transition requires a combination of conserved and novel, medusozoa-specific genes. While no genomic region is specifically associated with the ability to produce a jellyfish stage, the arrangement of genes involved in the development of a nematocyte-a phylum-specific cell type-is highly structured and conserved in cnidarian genomes; thus, it represents a phylotypic gene cluster.

Comprehensive Analysis of the Jellyfish Chrysaora pacifica (Goette, 1886) (Semaeostomeae: Pelagiidae) with Description of the Complete rDNA Sequence

Jinho Chae, Yoseph Seo, Won Bae Yu, Won Duk Yoon, Hye Eun Lee, Soo-Jung Chang, and Jang-Seu Ki (2018) The Scyphomedusae genus Chrysaora consists of highly diversified jellyfishes. Although morphological systematics of the genus has been documented over the past century, characterization of molecular taxonomy has been attempted only recently. In the present study, we sequenced an 8,167 bp region, encompassing a single ribosomal DNA (rDNA) repeat unit, from Chrysaora pacifica, and used it for phylogenetic analyses. The tandemly repeated rDNA units turned out to consist of both coding and noncoding regions, whose arrangement was found to be the same as that of a typical eukaryote. None of the 5S rRNA sequences were found among the repeat units. Comparative analyses of jellyfish rDNA sequences showed that the 28S locus is highly informative and divergent compared to the 18S locus. Phylogenetic analyses of the 18S and 28S loci revealed that the Semaeostomeae order of jellyfish is separated into taxonomic groups by families and genera, with a few exceptions. The family Pelagiidae was in a clade separate from other groups, thus forming a monophyletic lineage. All Chrysaora included here formed a strongly supported clade within the family Pelagiidae, and Pelagiidae manifested a sister relationship with Cyanea. Nonetheless, Chrysaora was found to be paraphyletic in both 18S and 28S phylogenies. Chrysaora pacifica was clearly distinct from close relatives C. melanaster and C. quinquecirrha. These results provide a special reference for the DNA taxonomy of Pelagiidae jellyfishes in terms of nuclear cistron rDNA sequences and improve our understanding of the molecular phylogenetic relationships among Semaeostomeae jellyfishes.

Medusa: A Review of an Ancient Cnidarian Body Form

Medusae (aka jellyfish) have multiphasic life cycles and a propensity to adapt to, and proliferate in, a plethora of aquatic habitats, connecting them to a number of ecological and societal issues. Now, in the midst of the genomics era, affordable next-generation sequencing (NGS) platforms coupled with publically available bioinformatics tools present the much-anticipated opportunity to explore medusa taxa as potential model systems. Genome-wide studies of medusae would provide a remarkable opportunity to address long-standing questions related to the biology, physiology, and nervous system of some of the earliest pelagic animals. Furthermore, medusae have become key targets in the exploration of marine natural products, in the development of marine biomarkers, and for their application to the biomedical and robotics fields. Presented here is a synopsis of the current state of medusa research, highlighting insights provided by multi-omics studies, as well as existing knowledge gaps, calling upon the scientific community to adopt a number of medusa taxa as model systems in forthcoming research endeavors.

Multigene phylogeny of the scyphozoan jellyfish family Pelagiidae reveals that the common U.S. Atlantic sea nettle comprises two distinct species (Chrysaora quinquecirrha and C. chesapeakei)

BACKGROUND

Species of the scyphozoan family Pelagiidae (e.g., Pelagia noctiluca, Chrysaora quinquecirrha) are well-known for impacting fisheries, aquaculture, and tourism, especially for the painful sting they can inflict on swimmers. However, historical taxonomic uncertainty at the genus (e.g., new genus Mawia) and species levels hinders progress in studying their biology and evolutionary adaptations that make them nuisance species, as well as ability to understand and/or mitigate their ecological and economic impacts.

METHODS

We collected nuclear (28S rDNA) and mitochondrial (cytochrome c oxidase I and 16S rDNA) sequence data from individuals of all four pelagiid genera, including 11 of 13 currently recognized species of Chrysaora. To examine species boundaries in the U.S. Atlantic sea nettle Chrysaora quinquecirrha, specimens were included from its entire range along the U.S. Atlantic and Gulf of Mexico coasts, with representatives also examined morphologically (macromorphology and cnidome).

RESULTS

Phylogenetic analyses show that the genus Chrysaora is paraphyletic with respect to other pelagiid genera. In combined analyses, Mawia, sampled from the coast of Senegal, is most closely related to Sanderia malayensis, and Pelagia forms a close relationship to a clade of Pacific Chrysaora species (Chrysaora achlyos, Chrysaora colorata, Chrysaora fuscescens, and Chrysaora melanaster). Chrysaora quinquecirrha is polyphyletic, with one clade from the U.S. coastal Atlantic and another in U.S. Atlantic estuaries and Gulf of Mexico. These genetic differences are reflected in morphology, e.g., tentacle and lappet number, oral arm length, and nematocyst dimensions. Caribbean sea nettles (Jamaica and Panama) are genetically similar to the U.S. Atlantic estuaries and Gulf of Mexico clade of Chrysaora quinquecirrha.

DISCUSSION

Our phylogenetic hypothesis for Pelagiidae contradicts current generic definitions, revealing major disagreements between DNA-based and morphology-based phylogenies. A paraphyletic Chrysaora raises systematic questions at the genus level for Pelagiidae; accepting the validity of the recently erected genus Mawia, as well as past genera, will require the creation of additional pelagiid genera. Historical review of the species-delineating genetic and morphological differences indicates that Chrysaora quinquecirrha Desor 1848 applies to the U.S. Coastal Atlantic Chrysaora species (U.S. Atlantic sea nettle), while the name C. chesapeakei Papenfuss 1936 applies to the U.S. Atlantic estuarine and Gulf of Mexico Chrysaora species (Atlantic bay nettle). We provide a detailed redescription, with designation of a neotype for Chrysaora chesapeakei, and clarify the description of Chrysaora quinquecirrha. Since Caribbean Chrysaora are genetically similar to Chrysaora chesapeakei, we provisionally term them Chrysaora c.f. chesapeakei. The presence of Mawia benovici off the coast of Western Africa provides a potential source region for jellyfish introduced into the Adriatic Sea in 2013.

Environmental control of asexual reproduction and somatic growth of Aurelia spp. (Cnidaria, Scyphozoa) polyps from the Adriatic Sea

Polyps of two moon jellyfish species, Aurelia coerulea and A. relicta, from two Adriatic Sea coastal habitats were incubated under multiple combinations of temperature (14, 21°C), salinity (24, 37 ppt) and food regime (9.3, 18.6, 27.9 μg C ind-1 week-1) to comparatively assess how these factors may influence major asexual reproduction processes in the two species. Both species exhibited a shared pattern of budding mode (Directly Budded Polyps: DBP; Stolonal Budded Polyps: SBP), with DBP favoured under low food supply (9.3 μg C ind -1 week-1) and low temperature (14°C), and SBP dominant under high temperature (21°C). However, A. coerulea showed an overall higher productivity than A. relicta, in terms of budding and podocyst production rates. Further, A. coerulea exhibited a wide physiological plasticity across different temperatures and salinities as typical adaptation to ecological features of transitional coastal habitats. This may support the hypothesis that the invasion of A. coerulea across coastal habitats worldwide has been driven by shellfish aquaculture, with scyphistoma polyps and resting stages commonly found on bivalve shells. On the contrary, A. relicta appears to be strongly stenovalent, with cold, marine environmental optimal preferences (salinity 37 ppt, T ranging 14-19°C), corroborating the hypothesis of endemicity within the highly peculiar habitat of the Mljet lake. By exposing A. relicta polyps to slightly higher temperature (21°C), a previously unknown developmental mode was observed, by the sessile polyp regressing into a dispersive, temporarily unattached and tentacle-less, non-feeding stage. This may allow A. relicta polyps to escape climatic anomalies associated to warming of surface layers and deepening of isotherms, by moving into deeper, colder layers. Overall, investigations on species-specific eco-physiological and ontogenetic potentials of polyp stages may contribute to clarify the biogeographic distribution of jellyfish and the phylogenetic relationships among evolutionary related sister clades.

Description and experimental transmission of Tetracapsuloides vermiformis n. sp. (Cnidaria: Myxozoa) and guidelines for describing malacosporean species including reinstatement of Buddenbrockia bryozoides n. comb. (syn. Tetracapsula bryozoides)

This paper provides the first detailed description of a Tetracapsuloides species, Tetracapsuloides vermiformis n. sp., with vermiform stages in the bryozoan host, Fredericella sultana, and its experimental transmission from F. sultana to Cyprinus carpio. The suitability of morphological, biological and 18S rDNA sequence data for discrimination between malacosporean species is reviewed and recommendations are given for future descriptions. Presently, malacosporean species cannot be differentiated morphologically due to their cryptic nature and the lack of differential characters of spores and spore-forming stages in both hosts. We examined biological, morphological and molecular characters for the present description and for revising malacosporean taxonomy in general. As a result, Buddenbrockia plumatellae was split into two species, with its sac-like stages being ascribed to Buddenbrockia bryozoides n. comb. In addition to ribosomal DNA sequences multiple biological features rather than morphological characters are considered essential tools to improve malacosporean taxonomy in the future according to our analysis of the limited traits presently available.

Preliminary Taxonomic Survey and Molecular Documentation of Jellyfish Species (Cnidaria: Scyphozoa and Cubozoa) in Malaysia

Mohammed Rizman-Idid, Abu Bakar Farrah-Azwa, and Ving Ching Chong (2016) Scientific enquiries into jellyfish blooms and associated problems are often deterred by the lack of taxonomical and ecological studies worldwide. Taxonomic difficulty is attributed to the high degree of morphological variations among and within species. To date, only two scyphozoan jellyfish species have been documented from field surveys in Malaysian waters, whereas another four Malaysian scyphozoan and two cubozoan jellyfish species have been mentioned in toxicological studies. None of these species have; however, been verified. This study thus aimed to document and resolves the uncertainty of earlier identified species in the region using morphology and molecular DNA sequencing. Jellyfish specimens were collected from Malaysian waters in the Straits of Malacca, South-China Sea and the Sulu-Sulawesi Sea over two years (June 2008 to October 2010), and their DNA sequences were compared with those from the Atlantic and Pacific regions. Ten scyphozoan and two cubozoan species were recorded in Malaysian waters (South China Sea and Straits of Malacca). These jellyfish included eight species from the order Rhizostomeae (Rhizostomatidae, Lobonematidae, Mastigiidae, Catostylidae and Cepheidae), two species from Semaestomeae (Pelagiidae and Cyaneidae) and two species from class Cubozoa; one from order Carybdeida (family Carukiidae) and another from order Chirodropida (family Chiropsalmidae). Molecular identification of species using phylogenetic approaches was based on DNA sequences of partial cytochrome oxidase I (COI), 16S and internal transcribed spacer (ITS1) regions. The COI phylogenetic tree of Cubozoa and Scyphozoa species from the Atlantic and Pacific regions showed distinct clustering of six Malaysian jellyfish species. However, most of the deeper divergences and relationships between the families were unresolved, which were also observed in the 16S and ITS1 phylogenetic trees. The Malaysian edible species Lobonemoides robustus, Rhopilema hispidum and Rhopilema esculentum were grouped within Rhizostomeae, whereas other scyphozoans showed phylogenetic affinities to Semaestomeae and Kolpophorae. Chrysaora and Cyanea appeared non-monophyletic; however their paraphyly was not confirmed. This study has provided the much needed baseline information on the taxonomy of Malaysian jellyfish species which have been substantiated by partial COI, 16S and ITS1 sequences. A total of 12 putative species of jellyfish were identified, which encompassed 12 genera.

Local versus Generalized Phenotypes in Two Sympatric Aurelia Species: Understanding Jellyfish Ecology Using Genetics and Morphometrics

For individuals living in environmentally heterogeneous environments, a key component for adaptation and persistence is the extent of phenotypic differentiation in response to local environmental conditions. In order to determine the extent of environmentally induced morphological variation in a natural population distributed along environmental gradients, it is necessary to account for potential genetic differences contributing to morphological differentiation. In this study, we set out to quantify geographic morphological variation in the moon jellyfish Aurelia exposed at the extremes of a latitudinal environmental gradient in the Gulf of Mexico (GoM). We used morphological data based on 28 characters, and genetic data taken from mitochondrial cytochrome oxidase I (COI) and nuclear internal transcribed spacer 1 (ITS-1). Molecular analyses revealed the presence of two genetically distinct species of Aurelia co-occurring in the GoM: Aurelia sp. 9 and Aurelia c.f. sp. 2, named for its divergence from (for COI) and similarity to (for ITS-1) Aurelia sp. 2 (Brazil). Neither species exhibited significant population genetic structure between the Northern and the Southeastern Gulf of Mexico; however, they differed greatly in the degree of geographic morphological variation. The morphology of Aurelia sp. 9 exhibited ecophenotypic plasticity and varied significantly between locations, while morphology of Aurelia c.f. sp. 2 was geographically invariant (i.e., canalized). The plastic, generalist medusae of Aurelia sp. 9 are likely able to produce environmentally-induced, “optimal” phenotypes that confer high relative fitness in different environments. In contrast, the non-plastic generalist individuals of Aurelia c.f. sp. 2 likely produce environmentally-independent phenotypes that provide the highest fitness across environments. These findings suggest the two Aurelia lineages co-occurring in the GoM were likely exposed to different past environmental conditions (i.e., different selective pressures) and evolved different strategies to cope with environmental variation. This study highlights the importance of using genetics and morphometric data to understand jellyfish ecology, evolution and systematics.

Transoceanic dispersal and cryptic diversity in a cosmopolitan rafting nudibranch

The aeolid nudibranch Fiona pinnata (Eschscholtz, 1831) is an obligate rafter that occurs exclusively on macroalgal rafts and other floating substrata, and has a seemingly cosmopolitan marine distribution. Mitochondrial (mtDNA) and nuclear DNA sequence data were generated from specimens collected worldwide to test for global connectivity in this species. Phylogeographic analyses revealed three divergent mtDNA lineages, two of which were abundant and widespread. One of these lineages has an apparent circumequatorial distribution, whereas the other may have an antitropical distribution within the Pacific Ocean. Low genetic divergences within each lineage suggest that rafting can mediate dispersal across transoceanic scales. A third, highly divergent, lineage was detected in a single Indonesian specimen. Broadly concordant phylogeographic relationships were detected for the nuclear ITS1 region, with distinct tropical versus antitropical lineages observed. The substantial genetic divergences and largely allopatric distributions observed among the F. pinnata lineages suggest that they represent a species complex.

Redescription of Pelagia benovici into a new jellyfish genus, Mawia, gen. nov., and its phylogenetic position within Pelagiidae (Cnidaria : Scyphozoa : Semaeostomeae)

This study provides new and additional data on morphology and a phylogenetic analysis of the recently described species Pelagia benovici Piraino, Aglieri, Scorrano & Boero, 2014 from the Northern Adriatic (Mediterranean Sea). Comprehensive morphological analyses of diagnostic characters, of which the most significant are marginal tentacles anatomy, basal pillars, gonad pattern, subgenital ostia and exumbrellar sensory pits, revealed significant differences from the currently known genera Sanderia, Chrysaora and Pelagia in the family Pelagiidae. A phylogenetic analysis of mitochondrial genes (COI, 16S rRNA, 12S rRNA) and nuclear ribosomal genes (28S rRNA, ITS1/ITS2 regions), together with cladistic analysis of morphological characters, positioned Pelagia benovici as a sister taxon with Sanderia malayensis, and both share a common ancestor with Chrysaora hysoscella. Pelagia benovici does not share a direct common ancestor with the genus Pelagia, and thus we propose it should not belong to this genus. Therefore, a new genus Mawia, gen. nov. (Semaeostomeae : Pelagiidae) is described, and Pelagia benovici is renamed as Mawia benovici, comb, nov.

Multilocus evidence for globally distributed cryptic species and distinct populations across ocean gyres in a mesopelagic copepod

Zooplanktonic taxa have a greater number of distinct populations and species than might be predicted based on their large population sizes and open-ocean habitat, which lacks obvious physical barriers to dispersal and gene flow. To gain insight into the evolutionary mechanisms driving genetic diversification in zooplankton, we developed eight microsatellite markers to examine the population structure of an abundant, globally distributed mesopelagic copepod, Haloptilus longicornis, at 18 sample sites across the Atlantic and Pacific Oceans (n = 761). When comparing our microsatellite results with those of a prior study that used a mtDNA marker (mtCOII, n = 1059, 43 sample sites), we unexpectedly found evidence for the presence of a cryptic species pair. These species were globally distributed and apparently sympatric, and were separated by relatively weak genetic divergence (reciprocally monophyletic mtCOII lineages 1.6% divergent; microsatellite FST ranging from 0.28 to 0.88 across loci, P < 0.00001). Using both mtDNA and microsatellite data for the most common of the two species (n = 669 for microsatellites, n = 572 for mtDNA), we also found evidence for allopatric barriers to gene flow within species, with distinct populations separated by continental landmasses and equatorial waters in both the Atlantic and Pacific Ocean basins. Our study shows that oceanic barriers to gene flow can act as a mechanism promoting allopatric diversification in holoplanktonic taxa, despite the high potential dispersal abilities and pelagic habitat for these species.

Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population

The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle.

Self-repairing symmetry in jellyfish through mechanically driven reorganization

What happens when an animal is injured and loses important structures? Some animals simply heal the wound, whereas others are able to regenerate lost parts. In this study, we report a previously unidentified strategy of self-repair, where moon jellyfish respond to injuries by reorganizing existing parts, and rebuilding essential body symmetry, without regenerating what is lost. Specifically, in response to arm amputation, the young jellyfish of Aurelia aurita rearrange their remaining arms, recenter their manubria, and rebuild their muscular networks, all completed within 12 hours to 4 days. We call this process symmetrization. We find that symmetrization is not driven by external cues, cell proliferation, cell death, and proceeded even when foreign arms were grafted on. Instead, we find that forces generated by the muscular network are essential. Inhibiting pulsation using muscle relaxants completely, and reversibly, blocked symmetrization. Furthermore, we observed that decreasing pulse frequency using muscle relaxants slowed symmetrization, whereas increasing pulse frequency by lowering the magnesium concentration in seawater accelerated symmetrization. A mathematical model that describes the compressive forces from the muscle contraction, within the context of the elastic response from the mesoglea and the ephyra geometry, can recapitulate the recovery of global symmetry. Thus, self-repair in Aurelia proceeds through the reorganization of existing parts, and is driven by forces generated by its own propulsion machinery. We find evidence for symmetrization across species of jellyfish (Chrysaora pacifica, Mastigias sp., and Cotylorhiza tuberculata).

Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts

Bacterial symbionts are important fitness determinants of insects. Some hosts have independently acquired taxonomically related microbes to meet similar challenges, but whether distantly related hosts that live in tight symbiosis can maintain similar microbial communities has not been investigated. Varying degrees of nest sharing between Megalomyrmex social parasites (Solenopsidini) and their fungus-growing ant hosts (Attini) from the genera Cyphomyrmex, Trachymyrmex and Sericomyrmex allowed us to address this question, as both ant lineages rely on the same fungal diet, interact in varying intensities and are distantly related. We used tag-encoded FLX 454 pyrosequencing and diagnostic PCR to map bacterial symbiont diversity across the Megalomyrmex phylogenetic tree, which also contains free-living generalist predators. We show that social parasites and hosts share a subset of bacterial symbionts, primarily consisting of Entomoplasmatales, Bartonellaceae, Acinetobacter, Wolbachia and Pseudonocardia and that Entomoplasmatales and Bartonellaceae can co-infect specifically associated combinations of hosts and social parasites with identical 16S rRNA genotypes. We reconstructed in more detail the population-level infection dynamics for Entomoplasmatales and Bartonellaceae in Megalomyrmex symmetochus guest ants and their Sericomyrmex amabilis hosts. We further assessed the stability of the bacterial communities through a diet manipulation experiment and evaluated possible transmission modes in shared nests such as consumption of the same fungus garden food, eating of host brood by social parasites, trophallaxis and grooming interactions between the ants, or parallel acquisition from the same nest environment. Our results imply that cohabiting ant social parasites and hosts may obtain functional benefits from bacterial symbiont transfer even when they are not closely related.

Reassessment of morphological diagnostic characters and species boundaries requires taxonomical changes for the genus orthopyxis L. Agassiz, 1862 (campanulariidae, hydrozoa) and some related campanulariids

The genus Orthopyxis is widely known for its morphological variability, making species identification particularly difficult. A number of nominal species have been recorded in the southwestern Atlantic, although most of these records are doubtful. The goal of this study was to infer species boundaries in the genus Orthopyxis from the southwestern Atlantic using an integrative approach. Intergeneric limits were also tested using comparisons with specimens of the genus Campanularia. We performed DNA analyses using the mitochondrial genes 16S and COI and the nuclear ITS1 and ITS2 regions. Orthopyxis was monophyletic in maximum likelihood analyses using the combined dataset and in analyses with 16S alone. Four lineages of Orthopyxis were retrieved for all analyses, corresponding morphologically to the species Orthopyxis sargassicola (previously known in the area), Orthopyxis crenata (first recorded for the southwestern Atlantic), Orthopyxis caliculata (= Orthopyxis minuta Vannucci, 1949 and considered a synonym of O. integra by some authors), and Orthopyxis mianzani sp. nov. A re-evaluation of the traditional morphological diagnostic characters, guided by our molecular analyses, revealed that O. integra does not occur in the study area, and O. caliculata is the correct identification of one of the lineages occurring in this region, corroborating the validity of that species. Orthopyxis mianzani sp. nov. resembles O. caliculata with respect to gonothecae morphology and a smooth hydrothecae rim, although it shows significant differences for other characters, such as perisarc thickness, which has traditionally been thought to have wide intraspecific variation. The species O. sargassicola is morphologically similar to O. crenata, although they differ in gonothecae morphology, and these species can only be reliably identified when this structure is present.

Transcriptome profiling of the dynamic life cycle of the scypohozoan jellyfish Aurelia aurita

Background

The moon jellyfish Aurelia aurita is a widespread scyphozoan species that forms large seasonal blooms. Here we provide the first comprehensive view of the entire complex life of the Aurelia Red Sea strain by employing transcriptomic profiling of each stage from planula to mature medusa.

Results

A de novo transcriptome was assembled from Illumina RNA-Seq data generated from six stages throughout the Aurelia life cycle. Transcript expression profiling yielded clusters of annotated transcripts with functions related to each specific life-cycle stage. Free-swimming planulae were found highly enriched for functions related to cilia and microtubules, and the drastic morphogenetic process undergone by the planula while establishing the future body of the polyp may be mediated by specifically expressed Wnt ligands. Specific transcripts related to sensory functions were found in the strobila and the ephyra, whereas extracellular matrix functions were enriched in the medusa due to high expression of transcripts such as collagen, fibrillin and laminin, presumably involved in mesoglea development. The CL390-like gene, suggested to act as a strobilation hormone, was also highly expressed in the advanced strobila of the Red Sea species, and in the medusa stage we identified betaine-homocysteine methyltransferase, an enzyme that may play an important part in maintaining equilibrium of the medusa’s bell. Finally, we identified the transcription factors participating in the Aurelia life-cycle and found that 70% of these 487 identified transcription factors were expressed in a developmental-stage-specific manner.

Conclusions

This study provides the first scyphozoan transcriptome covering the entire developmental trajectory of the life cycle of Aurelia. It highlights the importance of numerous stage-specific transcription factors in driving morphological and functional changes throughout this complex metamorphosis, and is expected to be a valuable resource to the community.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1320-z) contains supplementary material, which is available to authorized users.

Fast-evolving mitochondrial DNA in Ceriantharia: a reflection of hexacorallia paraphyly?

The low evolutionary rate of mitochondrial genes in Anthozoa has challenged their utility for phylogenetic and systematic purposes, especially for DNA barcoding. However, the evolutionary rate of Ceriantharia, one of the most enigmatic "orders" within Anthozoa, has never been specifically examined. In this study, the divergence of mitochondrial DNA of Ceriantharia was compared to members of other Anthozoa and Medusozoa groups. In addition, nuclear markers were used to check the relative phylogenetic position of Ceriantharia in relation to other Cnidaria members. The results demonstrated a pattern of divergence of mitochondrial DNA completely different from those estimated for other anthozoans, and phylogenetic analyses indicate that Ceriantharia is not included within hexacorallians in most performed analyses. Thus, we propose that the Ceriantharia should be addressed as a separate clade.

Regulation of polyp-to-jellyfish transition in Aurelia aurita

BACKGROUND

The life cycle of scyphozoan cnidarians alternates between sessile asexual polyps and pelagic medusa. Transition from one life form to another is triggered by environmental signals, but the molecular cascades involved in the drastic morphological and physiological changes remain unknown.

RESULTS

We show in the moon jelly Aurelia aurita that the molecular machinery controlling transition of the sessile polyp into a free-swimming jellyfish consists of two parts. One is conserved and relies on retinoic acid signaling. The second, novel part is based on secreted proteins that are strongly upregulated prior to metamorphosis in response to the seasonal temperature changes. One of these proteins functions as a temperature-sensitive "timer" and encodes the precursor of the strobilation hormone of Aurelia.

CONCLUSIONS

Our findings uncover the molecule framework controlling the polyp-to-jellyfish transition in a basal metazoan and provide insights into the evolution of complex life cycles in the animal kingdom.

Long-term fluctuations in circalunar Beach aggregations of the box jellyfish Alatina moseri in Hawaii, with links to environmental variability

The box jellyfish Alatina moseri forms monthly aggregations at Waikiki Beach 8-12 days after each full moon, posing a recurrent hazard to swimmers due to painful stings. We present an analysis of long-term (14 years: Jan 1998- Dec 2011) changes in box jellyfish abundance at Waikiki Beach. We tested the relationship of beach counts to climate and biogeochemical variables over time in the North Pacific Sub-tropical Gyre (NPSG). Generalized Additive Models (GAM), Change-Point Analysis (CPA), and General Regression Models (GRM) were used to characterize patterns in box jellyfish arrival at Waikiki Beach 8-12 days following 173 consecutive full moons. Variation in box jellyfish abundance lacked seasonality, but exhibited dramatic differences among months and among years, and followed an oscillating pattern with significant periods of increase (1998-2001; 2006-2011) and decrease (2001-2006). Of three climatic and 12 biogeochemical variables examined, box jellyfish showed a strong, positive relationship with primary production, >2 mm zooplankton biomass, and the North Pacific Gyre Oscillation (NPGO) index. It is clear that that the moon cycle plays a key role in synchronizing timing of the arrival of Alatina moseri medusae to shore. We propose that bottom-up processes, likely initiated by inter-annual regional climatic fluctuations influence primary production, secondary production, and ultimately regulate food availability, and are therefore important in controlling the inter-annual changes in box jellyfish abundance observed at Waikiki Beach.

High cryptic diversity across the global range of the migratory planktonic copepods Pleuromamma piseki and P. gracilis

Although holoplankton are ocean drifters and exhibit high dispersal potential, a number of studies on single species are finding highly divergent genetic clades. These cryptic species complexes are important to discover and describe, as identification of common marine species is fundamental to understanding ecosystem dynamics. Here we investigate the global diversity within Pleuromamma piseki and P. gracilis, two dominant members of the migratory zooplankton assemblage in subtropical and tropical waters worldwide. Using DNA sequence data from the mitochondrial gene cytochrome c oxidase subunit II (mtCOII) from 522 specimens collected across the Pacific, Atlantic and Indian Oceans, we discover twelve well-resolved genetically distinct clades in this species complex (Bayesian posterior probabilities >0.7; 6.3–17% genetic divergence between clades). The morphologically described species P. piseki and P. gracilis did not form monophyletic groups, rather they were distributed throughout the phylogeny and sometimes co-occurred within well-resolved clades: this result suggests that morphological characters currently used for taxonomic identification of P. gracilis and P. piseki may be inaccurate as indicators of species’ boundaries. Cryptic clades within the species complex ranged from being common to rare, and from cosmopolitan to highly restricted in distribution across the global ocean. These novel lineages appear to be ecologically divergent, with distinct biogeographic distributions across varied pelagic habitats. We hypothesize that these mtDNA lineages are distinct species and suggest that resolving their systematic status is important, given the ecological significance of the genus Pleuromamma in subtropical-tropical waters worldwide.

Mitogenomics at the base of Metazoa

Unraveling the base of metazoan evolution is of crucial importance for rooting the metazoan Tree of Life. This subject has attracted substantial attention for more than a century and recently fueled a burst of modern phylogenetic studies. Conflicting scenarios from different studies and incongruent results from nuclear versus mitochondrial markers challenge current molecular phylogenetic approaches. Here we analyze the presently most comprehensive data sets of mitochondrial genomes from non-bilaterian animals to illuminate the phylogenetic relationships among early branching metazoan phyla. The results of our analyses illustrate the value of mitogenomics and support previously known topologies between animal phyla but also identify several problematic taxa, which are sensitive to long branch artifacts or missing data.