@article{nokey,

title = {Morphological and dietary changes encoded in the genome of Beroe ovata, a ctenophore-eating ctenophore},

author = {Alexandra M Vargas, Melissa B DeBiasse, Lana L Dykes, Allison Edgar, T Danielle Hayes, Daniel J Gorso, Leslie S Babonis, Mark Q Martindale, Joseph F Ryan},

url = {https://doi.org/10.1093/nargab/lqae069},

year  = {2024},

date = {2024-06-18},

journal = {NAR Genomics and Bioinformatics},

volume = {6},

issue = {2},

keywords = {Beroe ovata, Ctenophora, genome},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor},

author = {Dorothy Mitchell and Allison Edgar and J\'{u}lia Ramon Mateu and Joseph F. Ryan and Mark Q. Martindale},

url = {https://doi.org/10.1038/s42003-024-05901-7},

doi = {10.1038/s42003-024-05901-7},

year  = {2024},

date = {2024-02-19},

urldate = {2024-02-19},

journal = {Communications Biology},

volume = {7},

issue = {203},

keywords = {Ctenophora, gene regulation, regeneration, whole-body regeneration},

pubstate = {published},

tppubtype = {article}

}

@article{nokey,

title = {The ctenophore Mnemiopsis leidyi deploys a rapid injury response dating back to the last common animal ancestor},

author = {Dorothy G. Mitchell and Allison Edgar and J\'{u}lia Ramon Mateu and Joseph F. Ryan and Mark Q. Martindale},

url = {https://doi.org/10.1038/s42003-024-05901-7},

year  = {2024},

date = {2024-02-19},

urldate = {2024-02-19},

journal = {Communications Biology},

volume = {7},

issue = {203},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Rouhana_2023,

title = {Cytoplasmic polyadenylation is an ancestral hallmark of early development in animals},

author = {Labib Rouhana and Allison Edgar and Fredrik Hugosson and Valeria Dountcheva and Mark Q. Martindale and Joseph F. Ryan},

url = {https://doi.org/10.1093/molbev/msad137},

doi = {10.1093/molbev/msad137},

year  = {2023},

date = {2023-05-01},

urldate = {2023-05-01},

journal = {Molecular Biology and Evolution},

volume = {40},

issue = {6},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Differential regulation of gene expression has produced the astonishing diversity of life on Earth. Understanding the origin and evolution of mechanistic innovations for control of gene expression is therefore integral to evolutionary and developmental biology. Cytoplasmic polyadenylation is the biochemical extension of polyadenosine at the 3′-end of cytoplasmic mRNAs. This process regulates the translation of specific maternal transcripts and is mediated by the Cytoplasmic Polyadenylation Element-Binding Protein family (CPEBs). Genes that code for CPEBs are amongst a very few that are present in animals but missing in nonanimal lineages. Whether cytoplasmic polyadenylation is present in non-bilaterian animals (i.e., sponges, ctenophores, placozoans, and cnidarians) remains unknown. We have conducted phylogenetic analyses of CPEBs, and our results show that CPEB1 and CPEB2 subfamilies originated in the animal stem lineage. Our assessment of expression in the sea anemone, Nematostella vectensis (Cnidaria), and the comb jelly, Mnemiopsis leidyi (Ctenophora), demonstrates that maternal expression of CPEB1 and the catalytic subunit of the cytoplasmic polyadenylation machinery (GLD2) is an ancient feature that is conserved across animals. Furthermore, our measurements of poly(A)-tail elongation reveal that key targets of cytoplasmic polyadenylation are shared between vertebrates, cnidarians, and ctenophores, indicating that this mechanism orchestrates a regulatory network that is conserved throughout animal evolution. We postulate that cytoplasmic polyadenylation through CPEBs was a fundamental innovation that contributed to animal evolution from unicellular life.},

keywords = {Cnidaria, Ctenophora, cytoplasmic polyadenylation, Evolution, post-transcriptional regulation},

pubstate = {published},

tppubtype = {article}

}

@article{Edgar_2023,

title = {Reply to Soto-Angel et al.: Is “larva” a natural kind? Phylogenetic thinking provides clarity},

author = {Allison Edgar and Jos\'{e} Miguel Ponciano and Mark Q. Martindale},

url = {https://doi.org/10.1073/pnas.2219704120},

doi = {10.1073/pnas.2219704120},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {120},

number = {4},

publisher = {Proceedings of the National Academy of Sciences},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Edgar_2022,

title = {Ctenophores are direct developers that reproduce continuously beginning very early after hatching},

author = {Allison Edgar and Jos\'{e} Miguel Ponciano and Mark Q. Martindale},

url = {https://doi.org/10.1073/pnas.2122052119},

doi = {10.1073/pnas.2122052119},

year  = {2022},

date = {2022-04-01},

urldate = {2022-04-01},

journal = {Proceedings of the National Academy of Sciences},

volume = {119},

number = {18},

publisher = {Proceedings of the National Academy of Sciences},

abstract = {A substantial body of literature reports that ctenophores exhibit an apparently unique life history characterized by biphasic sexual reproduction, the first phase of which is called larval reproduction or dissogeny. Whether this strategy is plastically deployed or a typical part of these species’ life history was unknown. In contrast to previous reports, we show that the ctenophore Mnemiopsis leidyi does not have separate phases of early and adult reproduction, regardless of the morphological transition to what has been considered the adult form. Rather, these ctenophores begin to reproduce at a small body size and spawn continuously from this point onward under adequate environmental conditions. They do not display a gap in productivity for metamorphosis or other physiological transition at a certain body size. Furthermore, nutritional and environmental constraints on fecundity are similar in both small and large animals. Our results provide critical parameters for understanding resource partitioning between growth and reproduction in this taxon, with implications for management of this species in its invaded range. Finally, we report an observation of similarly small-size spawning in a beroid ctenophore, which is morphologically, ecologically, and phylogenetically distinct from other ctenophores reported to spawn at small sizes. We conclude that spawning at small body size should be considered as the default, on-time developmental trajectory rather than as precocious, stress-induced, or otherwise unusual for ctenophores. The ancestral ctenophore was likely a direct developer, consistent with the hypothesis that multiphasic life cycles were introduced after the divergence of the ctenophore lineage.},

keywords = {Ctenophora, dissogeny, Evolution, larval reproduction, life history, Mnemiopsis leidyi},

pubstate = {published},

tppubtype = {article}

}

@article{Mitchell_2021,

title = {Improved histological fixation of gelatinous marine invertebrates},

author = {Dorothy G. Mitchell and Allison Edgar and Mark Q. Martindale},

url = {https://doi.org/10.1186/s12983-021-00414-z},

doi = {10.1186/s12983-021-00414-z},

year  = {2021},

date = {2021-06-01},

urldate = {2021-06-01},

journal = {Frontiers in Zoology},

volume = {18},

number = {29},

publisher = {Springer Science and Business Media LLC},

abstract = {Background

Gelatinous zooplankton can be difficult to preserve morphologically due to unique physical properties of their cellular and acellular components. The relatively large volume of mesoglea leads to distortion of the delicate morphology and poor sample integrity in specimens prepared with standard aldehyde or alcohol fixation techniques. Similar challenges have made it difficult to extend standard laboratory methods such as in situ hybridization to larger juvenile ctenophores, hampering studies of late development.



Results

We have found that a household water repellant glass treatment product commonly used in laboratories, Rain-X®, alone or in combination with standard aldehyde fixatives, greatly improves morphological preservation of such delicate samples. We present detailed methods for preservation of ctenophores of diverse sizes compatible with long-term storage or detection and localization of target molecules such as with immunohistochemistry and in situ hybridization and show that this fixation might be broadly useful for preservation of other delicate marine specimens.



Conclusion

This new method will enable superior preservation of morphology in gelatinous specimens for a variety of downstream goal. Extending this method may improve the morphological fidelity and durability of museum and laboratory specimens for other delicate sample types.},

keywords = {Ctenophora, fixation, immunohistochemistry, in situ hybridization, Mnemiopsis leidyi, Preservation of zooplankton},

pubstate = {published},

tppubtype = {article}

}

@article{Edgar_2021,

title = {Whole-Body Regeneration in the Lobate Ctenophore Mnemiopsis leidyi},

author = {Allison Edgar and Dorothy G. Mitchell and Mark Q. Martindale},

url = {https://doi.org/10.3390%2Fgenes12060867},

doi = {10.3390/genes12060867},

year  = {2021},

date = {2021-06-01},

urldate = {2021-06-01},

journal = {Genes},

volume = {12},

issue = {6},

pages = {867},

publisher = {MDPI AG},

abstract = {Ctenophores (a.k.a. comb jellies) are one of the earliest branching extant metazoan phyla. Adult regenerative ability varies greatly within the group, with platyctenes undergoing both sexual and asexual reproduction by fission while others in the genus Beroe having completely lost the ability to replace missing body parts. We focus on the unique regenerative aspects of the lobate ctenophore, Mnemiopsis leidyi, which has become a popular model for its rapid wound healing and tissue replacement, optical clarity, and sequenced genome. M. leidyi’s highly mosaic, stereotyped development has been leveraged to reveal the polar coordinate system that directs whole-body regeneration as well as lineage restriction of replacement cells in various regenerating organs. Several cell signaling pathways known to function in regeneration in other animals are absent from the ctenophore’s genome. Further research will either reveal ancient principles of the regenerative process common to all animals or reveal novel solutions to the stability of cell fates and whole-body regeneration.},

keywords = {Ctenophora, Mnemiopsis leidyi, regeneration},

pubstate = {published},

tppubtype = {article}

}

@article{Wang_2020,

title = {Genetic basis for divergence in developmental gene expression in two closely related sea urchins},

author = {Lingyu Wang and Jennifer W. Israel and Allison Edgar and Rudolf A. Raff and Elizabeth C. Raff and Maria Byrne and Gregory A. Wray},

url = {https://doi.org/doi.org/10.1038/s41559-020-1165-y},

doi = {10.1038/s41559-020-1165-y},

year  = {2020},

date = {2020-04-01},

urldate = {2020-04-01},

journal = {Nature Ecology \& Evolution},

volume = {4},

number = {6},

pages = {831\textendash840},

publisher = {Springer Science and Business Media LLC},

abstract = {The genetic basis for divergence in developmental gene expression among species is poorly understood, despite growing evidence that such changes underlie many interesting traits. Here we quantify transcription in hybrids of Heliocidaris tuberculata and Heliocidaris erythrogramma, two closely related sea urchins with highly divergent developmental gene expression and life histories. We find that most expression differences between species result from genetic influences that affect one stage of development, indicating limited pleiotropic consequences for most mutations that contribute to divergence in gene expression. Activation of zygotic transcription is broadly delayed in H. erythrogramma, the species with the derived life history, despite its overall faster premetamorphic development. Altered expression of several terminal differentiation genes associated with the derived larval morphology of H. erythrogramma is based largely on differences in the expression or function of their upstream regulators, providing insights into the genetic basis for the evolution of key life history traits.},

keywords = {developmental biology, Evolution, evolutionary genetics, molecular evolution},

pubstate = {published},

tppubtype = {article}

}

@article{Edgar_2019,

title = {Equalization of Cleavage Is Not Causally Responsible for Specification of Cell Lineage},

author = {Allison Edgar},

url = {https://doi.org/10.1086/705358},

doi = {10.1086/705358},

year  = {2019},

date = {2019-12-01},

urldate = {2019-12-01},

journal = {The Biological Bulletin},

volume = {237},

number = {3},

pages = {250\textendash253},

publisher = {University of Chicago Press},

abstract = {An unequal cleavage gives rise to a dedicated population of larval skeletogenic cells in sea urchins. The timing of this unequal cleavage, associated localization of key lineage markers, and loss of this lineage when embryos are treated with cleavage-equalizing reagents have all suggested that the asymmetry of the daughter cells is causal to the specification of this cell lineage. However, the mechanism by which asymmetric cleavage specifies this cell type remains unidentified. I found that applying a classical cleavage-equalizing reagent (sodium dodecyl sulfate) to embryos of an equally cleaving urchin eliminates its larval skeleton. This result suggests that equalization of cleavage itself is not causally responsible for specification of this cell lineage but coincident.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Edgar_2019b,

title = {Embryo microinjection of the lecithotrophic sea urchin Heliocidaris erythrogramma},

author = {Allison Edgar and Maria Byrne and Gregory A. Wray},

url = {https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6875645/},

year  = {2019},

date = {2019-09-01},

urldate = {2019-09-01},

journal = {Journal of Biological Methods},

volume = {6},

number = {3},

pages = {e119},

publisher = {Journal of Biological Methods},

abstract = {Microinjection is a common embryological technique used for many types of experiments, including lineage tracing, manipulating gene expression, or genome editing. Injectable reagents include mRNA overexpression, mis-expression, or dominant-negative experiments to examine a gene of interest, morpholino antisense oligo to prevent translation of an mRNA or spliceoform of interest and CRISPR-Cas9 reagents. Thus, the technique is broadly useful for basic embryological studies, constructing gene regulatory networks, and directly testing hypotheses about cis-regulatory and coding sequence changes underlying the evolution of development. However, the methods for microinjection in typical planktotrophic marine invertebrates may not work well in the highly modified eggs and embryos of lecithotrophic species. This protocol is optimized for the lecithotrophic sea urchin Heliocidaris erythrogramm},

keywords = {direct development, Heliocidaris erythrogramma, lecithotroph, microinjection, sea urchin},

pubstate = {published},

tppubtype = {article}

}

@article{Edgar_2019c,

title = {Evolution of abbreviated development in Heliocidaris erythrogramma dramatically re-wired the highly conserved sea urchin developmental gene regulatory network to decouple signaling center function from ultimate fate},

author = {Allison Edgar and Maria Byrne and David R McClay and Gregory A Wray},

url = {https://doi.org/10.1101/712216 },

doi = {10.1101/712216},

year  = {2019},

date = {2019-07-01},

urldate = {2019-07-01},

publisher = {Cold Spring Harbor Laboratory},

abstract = {Developmental gene regulatory networks (GRNs) describe the interactions among gene products that drive the differential transcriptional and cell regulatory states that pattern the embryo and specify distinct cell fates. GRNs are often deeply conserved, but whether this is the product of constraint inherent to the network structure or stabilizing selection remains unclear. We have constructed the first formal GRN for early development in Heliocidaris erythrogramma, a species with dramatically accelerated, direct development. This life history switch has important ecological consequences, arose rapidly, and has evolved independently many times in echinoderms, suggesting it is a product of selection. We find that H. erythrogramma exhibits dramatic differences in GRN topology compared with ancestral, indirect-developing sea urchins. In particular, the GRN sub-circuit that directs the early and autonomous commitment of skeletogenic cell precursors in indirect developers appears to be absent in H. erythrogramma, a particularly striking change in relation to both the prior conservation of this sub-circuit and the key role that these cells play ancestrally in early development as the embryonic signaling center. These results show that even highly conserved molecular mechanisms of early development can be substantially reconfigured in a relatively short evolutionary time span, suggesting that selection rather than constraint is responsible for the striking conservation of the GRN among other sea urchins.},

keywords = {developmental biology},

pubstate = {published},

tppubtype = {article}

}

@article{Edgar_2015,

title = {Inaugural meeting of the Pan-American Society for Evolutionary Developmental Biology report: the importance of diversity in a multidisciplinary field},

author = {Allison Edgar and Javiera Chinga},

url = {https://doi.org/10.1186/s13227-015-0035-1},

doi = {10.1186/s13227-015-0035-1},

year  = {2015},

date = {2015-12-01},

urldate = {2015-12-01},

journal = {EvoDevo},

volume = {6},

number = {1},

publisher = {Springer Science and Business Media LLC},

abstract = {We analyze the interdisciplinary state of evolutionary developmental biology based on the diversity of themes, taxa, levels of organization and scientists at the first meeting of the Pan-American Society for Evolutionary Developmental Biology (2015). We first highlight selected presentations representative of three themes: gene regulatory control, developmental patterning mechanisms, and ecological-evolutionary-developmental interactions. We summarize the questions, approaches, and taxonomic sampling of plant and animal research presented at the meeting. Finally, we synthesize themes from the meeting’s panel discussion and workshops on broadening participation, education, and the role of Evolutionary Developmental Biology in the scientific community and its ability to transcend and integrate fields of inquiry.},

keywords = {diversity, Interdisciplinary, Multidisciplinary},

pubstate = {published},

tppubtype = {article}

}

@article{Edgar_2015b,

title = {Gastrulation occurs in multiple phases at two distinct sites in Latrodectus and Cheiracanthium spiders},

author = {Allison Edgar and Christine Bates and Kay Larkin and Steven Black},

url = {http://dx.doi.org/10.1186/s13227-015-0029-z},

doi = {10.1186/s13227-015-0029-z},

year  = {2015},

date = {2015-10-01},

urldate = {2015-10-01},

journal = {EvoDevo},

volume = {6},

number = {33},

issue = {1},

publisher = {Springer Science $mathplus$ Business Media},

abstract = {The longstanding canonical model of spider gastrulation posits that cell internalization occurs only at a unitary central blastopore; and that the cumulus (dorsal organizer) arises from within the early deep layer by cell\textendashcell interaction. Recent work has begun to challenge the canonical model by demonstrating cell internalization at extra-blastoporal sites in two species (Parasteatoda tepidariorum and Zygiella x-notata); and showing in Zygiella that the prospective cumulus internalizes first, before other cells are present in the deep layer. The cell behaviors making up spider gastrulation thus appear to show considerable variation, and a wider sampling of taxa is indicated.},

keywords = {arachnid, arthropod, Chelicerate, gastrulation, morphogenesis, spider},

pubstate = {published},

tppubtype = {article}

}