PHYLOGENETIC SYSTEMATICS, TAXONOMY, AND BIOGEOGRAPHY OF JELLYFISH (CNIDARIA: MEDUSOZOA)

The coastal shelf inhabiting box jellyfish (Cubozoa) represent the smallest class within Cnidaria with some 50 described species. A robust phylogenetic framework had been missing for Cubozoa. Herein, a molecular phylogeny for Cubozoa is presented. This phylogeny served as the basis for several taxonomic and nomenclatural changes in a reverse taxonomic approach, striving to align the classification scheme for Cubozoa with phylogenetic history. In addition, the revised classification led to a reevaluation of morphological characters used for the delineation and identification of species and higher taxa. This information was condensed into an illustrated taxonomic key to aid the identification of box jellyfish by non-specialists. Furthermore, the utility of ecological niche models for predicting the potential geographic distributions of box jellyfish based on correlations between species occurrences and environmental data was assessed. Since box jellyfish distributions are generally poorly documented, modeling approaches that make use of the limited data available may be of much value for making predictions about species distributions. Similarly, species distributions in the open oceans, in particular in the deep sea, are poorly understood and documented. A new approach to ecological niche and species distribution modeling in three dimensions was developed that has great potential for aiding studies of open ocean fauna. This new approach was used to derive an explicit a priori hypothesis about the population structure of a deep-sea inhabiting jellyfish species. In order to test this hypothesis and better understand the patterns of gene-flow in open ocean environments, population genomic data was used to evaluate population structure for this species on a global scale. The combined approach of ecological niche modeling and population genomics indicated that at least the species investigated here displays panmixia on a global scale

Transcriptomic signatures across a critical sedimentation threshold in a major reef-building coral

Sedimentation is a major cause of global near-shore coral reef decline. Although the negative impacts of sedimentation on coral reef community composition have been well-documented, the effects of sedimentation on coral metabolism in situ have received comparatively little attention. Using transcriptomics, we identified gene expression patterns changing across a previously defined sedimentation threshold that was deemed critical due to changes in coral cover and community composition. We identified genes, pathways, and molecular processes associated with this transition that may allow corals, such as Porites lobata, to tolerate chronic, severe sedimentation and persist in turbid environments. Alternative energy generation pathways may help P. lobata maintain a persistent stress response to survive when the availability of light and oxygen is diminished. We found evidence for the expression of genes linked to increased environmental sensing and cellular communication that likely allow P. lobata to efficiently respond to sedimentation stress and associated pathogen challenges. Cell damage increases under stress; consequently, we found apoptosis pathways over-represented under severe sedimentation, a likely consequence of damaged cell removal to maintain colony integrity. The results presented here provide a framework for the response of P. lobata to sedimentation stress under field conditions. Testing this framework and its related hypotheses using multi-omics approaches can deepen our understanding of the metabolic plasticity and acclimation potential of corals to sedimentation and their resilience in turbid reef systems

Evolution of Linear Mitochondrial Genomes in Medusozoan Cnidarians

In nearly all animals, mitochondrial DNA (mtDNA) consists of a single circular molecule that encodes several subunits of the protein complexes involved in oxidative phosphorylation as well as part of the machinery for their expression. By contrast, mtDNA in species belonging to Medusozoa (one of the two major lineages in the phylum Cnidaria) comprises one to several linear molecules. Many questions remain on the ubiquity of linear mtDNA in medusozoans and the mechanisms responsible for its evolution, replication, and transcription. To address some of these questions, we determined the sequences of nearly complete linear mtDNA from 24 species representing all four medusozoan classes: Cubozoa, Hydrozoa, Scyphozoa, and Staurozoa. All newly determined medusozoan mitochondrial genomes harbor the 17 genes typical for cnidarians and map as linear molecules with a high degree of gene order conservation relative to the anthozoans. In addition, two open reading frames (ORFs), polB and ORF314, are identified in cubozoan, schyphozoan, staurozoan, and trachyline hydrozoan mtDNA. polB belongs to the B-type DNA polymerase gene family, while the product of ORF314 may act as a terminal protein that binds telomeres. We posit that these two ORFs are remnants of a linear plasmid that invaded the mitochondrial genomes of the last common ancestor of Medusozoa and are responsible for its linearity. Hydroidolinan hydrozoans have lost the two ORFs and instead have duplicated cox1 at each end of their mitochondrial chromosome(s). Fragmentation of mtDNA occurred independently in Cubozoa and Hydridae (Hydrozoa, Hydroidolina). Our broad sampling allows us to reconstruct the evolutionary history of linear mtDNA in medusozoans

Cellular plasticity facilitates phenotypic change in a dominant coral’s Symbiodiniaceae assemblage

Coral-associated dinoflagellates (Symbiodiniaceae) are photosynthetic endosymbionts that influence coral acclimation, as indicated by photo-endosymbiotic phenotypic variance across different environmental conditions. Symbiont shuffling (shifts in endosymbiont community composition), changes in endosymbiont cell density, and cellular plasticity have all been proposed as acclimation mechanisms. However, few studies have been able to partition which of the three strategies were responsible for observed phenotypic variance. Using a combination of metabarcoding and flow cytometry, we simultaneously characterized Acropora pulchra-associated Symbiodiniaceae assemblages at the community, population, and individual level under natural environmental conditions to deduce whether seasonal phenotypic change and site-related phenotypic variation of Symbiodiniaceae assemblages is a product of symbiont shuffling or cellular plasticity. Symbiodiniaceae assemblages displayed season-specific phenotypic variance, while Symbiodiniaceae community composition was geographically structured and cell density showed limited data structure. Based on these patterns, we reveal that cellular plasticity of Symbiodiniaceae was the source of a phenotypic variation, thus indicating that cellular plasticity is a mechanism for acclimation to mild environmental change

Ecological interactions and coexistence are predicted by gene expression similarity in freshwater green algae

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136696/1/jec12759_am.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136696/2/jec12759.pd

Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa

Some of the most interesting and enigmatic cnidarians are classified within the hydrozoan subclass Trachylina. Despite being relatively depauperate in species richness, the clade contains four taxa typically accorded ordinal status: Actinulida, Limnomedusae, Narcomedusae and Trachymedusae. We bring molecular data (mitochondrial 16S and nuclear small and large subunit ribosomal genes) to bear on the question of phylogenetic relationships within Trachylina. Surprisingly, we find that a diminutive polyp form, Microhydrula limopsicola (classified within Limnomedusae) is actually a previously unknown life stage of a species of Stauromedusae. Our data confirm that the interstitial form Halammohydra sp. (Actinulida) is derived from holopelagic direct developing ancestors, likely within the trachymedusan family Rhopalonematidae. Trachymedusae is shown to be diphyletic, suggesting that the polyp stage has been lost independently at least two times within trachyline evolution. Narcomedusae is supported as a monophyletic group likely also arising from trachymedusan ancestors. Finally, some data, albeit limited, suggest that some trachyline species names refer to cryptic species that have yet to be sorted taxonomicall

Phylogenetics of Trachylina (Cnidaria: Hydrozoa) with new insights on the evolution of some problematical taxa

This is the published version, also available here: http://dx.doi.org/10.1017/S0025315408001732.Some of the most interesting and enigmatic cnidarians are classified within the hydrozoan subclass Trachylina. Despite being relatively depauperate in species richness, the clade contains four taxa typically accorded ordinal status: Actinulida, Limnomedusae, Narcomedusae and Trachymedusae. We bring molecular data (mitochondrial 16S and nuclear small and large subunit ribosomal genes) to bear on the question of phylogenetic relationships within Trachylina. Surprisingly, we find that a diminutive polyp form, Microhydrula limopsicola (classified within Limnomedusae) is actually a previously unknown life stage of a species of Stauromedusae. Our data confirm that the interstitial form Halammohydra sp. (Actinulida) is derived from holopelagic direct developing ancestors, likely within the trachymedusan family Rhopalonematidae. Trachymedusae is shown to be diphyletic, suggesting that the polyp stage has been lost independently at least two times within trachyline evolution. Narcomedusae is supported as a monophyletic group likely also arising from trachymedusan ancestors. Finally, some data, albeit limited, suggest that some trachyline species names refer to cryptic species that have yet to be sorted taxonomically

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016