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  • 1
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    Organized and quality-controlled CalCOFI data for CTD casts and bottle measurements from CalCOFI stations between La Jolla, California to Point Conception between 1984-2019 (2022)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-11-09
    Description: Dataset: Luminoxyscape environmental
    Description: In this dataset, we analyzed daytime casts (09:00-16:00) of both discrete bottle data and continuous CTD casts from CalCOFI stations restricted to an area from La Jolla, California to Point Conception and 215 km maximum offshore. This dataset has combined bottle and CTD casts to represent the date range 1984-2019. We used the oxygen and irradiance measurements to determine the visual luminoxyscape for each of the larval species. This range was bounded by the oxygen (partial pressure) where the pO2 would permit 50% minimum retinal function (V50; 13, 7.2, 10.2, and 6.8 kPa for larvae of 'Doryteuthis opalescens', 'Octopus bimaculatus', 'Metacarcinus gracilis', and 'Pleuroncodes planipes', respectively), and where there is sufficient irradiance for a visual response (0.0311 µmol photons m-2 s-1) for each species. Additionally, oxygen limits for metabolism were used to determine the depth of occurrence of the Pcrit (the oxygen below which the animal cannot maintain a constant metabolic rate). The depths of occurrence for metabolic limits were determined for larvae of 'D. opalescens' and 'O. bimaculatus'. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/860397
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1829623
    Description: 2022-12-31
    Keywords: Vision ; Marine invertebrate ; Larvae ; Crustacean ; Cephalopod
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 2
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    Maximum depths of the visual luminoxyscape for four species of marine invertebrate larvae from CalCOFI stations between La Jolla, California to Point Conception between 1984-2019 (2022)
    Biological and Chemical Oceanography Data Management Office (BCO-DMO). Contact: bco-dmo-data@whoi.edu
    Details
    Publication Date: 2022-11-09
    Description: Dataset: Luminoxyscape maximum depth
    Description: In this dataset, the maximum depths of the visual luminoxyscape for four species of marine invertebrate larvae were recorded. Data in this study are from CalCOFI stations restricted to an area from La Jolla, California to Point Conception and 215 kilometers maximum offshore (Station 60). We analyzed daytime casts (09:00-16:00) of both discrete bottle data and continuous CTD casts to represent the date range of 1984-2019 and used the oxygen and irradiance measurements to determine the visual luminoxyscape for each of the larval species. This range was bounded by the oxygen (partial pressure) where the pO2 would permit 50% minimum retinal function (V50; 13, 7.2, 10.2, and 6.8 kPa for larvae of 'Doryteuthis opalescens', 'Octopus bimaculatus', 'Metacarcinus gracilis', and 'Pleuroncodes planipes', respectively), and where there is sufficient irradiance for a visual response (0.0311 µmol photons m-2 s-1) for each species. Additionally, oxygen limits for metabolism were used to determine the depth of occurrence of the Pcrit (the oxygen below which the animal cannot maintain a constant metabolic rate). The depths of occurrence for metabolic limits were determined for larvae of 'D. opalescens' and 'O. bimaculatus'. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/859867
    Description: NSF Division of Ocean Sciences (NSF OCE) OCE-1829623
    Keywords: Vision ; Marine invertebrate ; Larvae ; Crustacean ; Cephalopod
    Repository Name: Woods Hole Open Access Server
    Type: Dataset
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  • 3
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    The lesser Pacific Striped Octopus, Octopus chierchiae: an emerging laboratory model (2022)
    Frontiers Media
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Grearson, A. G., Dugan, A., Sakmar, T., Sivitilli, D. M., Gire, D. H., Caldwell, R. L., Niell, C. M., Doelen, G., Wang, Z. Y., & Grasse, B. The lesser Pacific Striped Octopus, Octopus chierchiae: an emerging laboratory model. Frontiers in Marine Science, 8, (2021): 753483, https://doi.org/10.3389/fmars.2021.753483.
    Description: Cephalopods have the potential to become useful experimental models in various fields of science, particularly in neuroscience, physiology, and behavior. Their complex nervous systems, intricate color- and texture-changing body patterns, and problem-solving abilities have attracted the attention of the biological research community, while the high growth rates and short life cycles of some species render them suitable for laboratory culture. Octopus chierchiae is a small octopus native to the central Pacific coast of North America whose predictable reproduction, short time to maturity, small adult size, and ability to lay multiple egg clutches (iteroparity) make this species ideally suited to laboratory culture. Here we describe novel methods for multigenerational culture of O. chierchiae, with emphasis on enclosure designs, feeding regimes, and breeding management. O. chierchiae bred in the laboratory grow from a 3.5 mm mantle length at hatching to an adult mantle length of approximately 20–30 mm in 250–300 days, with 15 and 14% survivorship to over 400 days of age in first and second generations, respectively. O. chierchiae sexually matures at around 6 months of age and, unlike most octopus species, can lay multiple clutches of large, direct-developing eggs every ∼30–90 days. Based on these results, we propose that O. chierchiae possesses both the practical and biological features needed for a model octopus that can be cultured repeatedly to address a wide range of biological questions.
    Description: The cephalopod program at the Marine Biological Laboratory (MBL) was supported by NSF 1827509 and NSF 1723141 grants. CN received funding from HFSP RGP0042. DG and DS received funding and research support from the University of Washington Friday Harbor Laboratories. ZYW was supported by funds from the Whitman Center at the MBL.
    Keywords: Iteroparity ; Cephalopod ; Model organism ; Aquaculture ; Reproduction – mollusk ; Developmental biology ; Neurobiology
    Repository Name: Woods Hole Open Access Server
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  • 4
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    An experimental method for evoking and characterizing dynamic color patterning of cuttlefish during prey capture (2022)
    POL Scientific
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kim, D., Buresch, K. C., Hanlon, R. T., & Kampff, A. R. An experimental method for evoking and characterizing dynamic color patterning of cuttlefish during prey capture. Journal of Biological Methods, 9(2), (2022): e161, https://doi.org/10.14440/jbm.2022.386.
    Description: Cuttlefish are active carnivores that possess a wide repertoire of body patterns that can be changed within milliseconds for many types of camouflage and communication. The forms and functions of many body patterns are well known from ethological studies in the field and laboratory. Yet one aspect has not been reported in detail: the category of rapid, brief and high-contrast changes in body coloration (“Tentacle Shot Patterns” or TSPs) that always occur with the ejection of two ballistic tentacles to strike live moving prey (“Tentacles Go Ballistic” or TGB moment). We designed and tested a mechanical device that presented prey in a controlled manner, taking advantage of a key stimulus for feeding: motion of the prey. High-speed video recordings show a rapid transition into TSPs starting 114 ms before TGB (N = 114). TSPs are then suppressed as early as 470–500 ms after TGB (P 〈 0.05) in unsuccessful hunts, while persisting for at least 3 s after TGB in successful hunts. A granularity analysis revealed significant differences in the large-scale high-contrast body patterning present in TSPs compared to the camouflage body pattern deployed beforehand. TSPs best fit the category of secondary defense called deimatic displaying, meant to briefly startle predators and interrupt their attack sequence while cuttlefish are distracted by striking prey. We characterize TSPs as a pattern category for which the main distinguishing feature is a high-contrast signaling pattern with aspects of Acute Conflict Mottle or Acute Disruptive Pattern. The data and methodology presented here open opportunities for quantifying the rapid neural responses in this visual sensorimotor set of behaviors.
    Description: KCB and RTH acknowledge partial support from the Sholley Foundation.
    Keywords: Deimatic behavior ; Secondary defense ; Cephalopod ; Body patterning ; Sepia officinalis
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 5
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    A draft genome sequence of the elusive giant squid, Architeuthis dux (2020)
    Oxford University Press
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in da Fonseca, R. R., Couto, A., Machado, A. M., Brejova, B., Albertin, C. B., Silva, F., Gardner, P., Baril, T., Hayward, A., Campos, A., Ribeiro, A. M., Barrio-Hernandez, I., Hoving, H. J., Tafur-Jimenez, R., Chu, C., Frazao, B., Petersen, B., Penaloza, F., Musacchia, F., Alexander, G. C., Osorio, H., Winkelmann, I., Simakov, O., Rasmussen, S., Rahman, M. Z., Pisani, D., Vinther, J., Jarvis, E., Zhang, G., Strugnell, J. M., Castro, L. F. C., Fedrigo, O., Patricio, M., Li, Q., Rocha, S., Antunes, A., Wu, Y., Ma, B., Sanges, R., Vinar, T., Blagoev, B., Sicheritz-Ponten, T., Nielsen, R., & Gilbert, M. T. P. A draft genome sequence of the elusive giant squid, Architeuthis dux. Gigascience, 9(1), (2020): giz152. doi: 10.1093/gigascience/giz152.
    Description: Background: The giant squid (Architeuthis dux; Steenstrup, 1857) is an enigmatic giant mollusc with a circumglobal distribution in the deep ocean, except in the high Arctic and Antarctic waters. The elusiveness of the species makes it difficult to study. Thus, having a genome assembled for this deep-sea–dwelling species will allow several pending evolutionary questions to be unlocked. Findings: We present a draft genome assembly that includes 200 Gb of Illumina reads, 4 Gb of Moleculo synthetic long reads, and 108 Gb of Chicago libraries, with a final size matching the estimated genome size of 2.7 Gb, and a scaffold N50 of 4.8 Mb. We also present an alternative assembly including 27 Gb raw reads generated using the Pacific Biosciences platform. In addition, we sequenced the proteome of the same individual and RNA from 3 different tissue types from 3 other species of squid (Onychoteuthis banksii, Dosidicus gigas, and Sthenoteuthis oualaniensis) to assist genome annotation. We annotated 33,406 protein-coding genes supported by evidence, and the genome completeness estimated by BUSCO reached 92%. Repetitive regions cover 49.17% of the genome. Conclusions: This annotated draft genome of A. dux provides a critical resource to investigate the unique traits of this species, including its gigantism and key adaptations to deep-sea environments.
    Description: R.R.F. thanks the Villum Fonden for grant VKR023446 (Villum Fonden Young Investigator Grant), the Portuguese Science Foundation (FCT) for grant PTDC/MAR/115347/2009; COMPETE-FCOMP-01-012; FEDER-015453, Marie Curie Actions (FP7-PEOPLE-2010-IEF, Proposal 272927), and the Danish National Research Foundation (DNRF96) for its funding of the Center for Macroecology, Evolution, and Climate. H.O. thanks the Rede Nacional de Espectrometria de Massa, ROTEIRO/0028/2013, ref. LISBOA-01-0145-FEDER-022125, supported by COMPETE and North Portugal Regional Operational Programme (Norte2020), under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). A.C. thanks FCT for project UID/Multi/04423/2019. M.P. acknowledges the support from the Wellcome Trust (grant number WT108749/Z/15/Z) and the European Molecular Biology Laboratory. M.P.T.G. thanks the Danish National Research Foundation for its funding of the Center for GeoGenetics (grant DNRF94) and Lundbeck Foundation for grant R52–5062 on Pathogen Palaeogenomics. S.R. was supported by the Novo Nordisk Foundation grant NNF14CC0001. A.H. is supported by a Biotechnology and Biological Sciences Research Council David Phillips Fellowship (fellowship reference: BB/N020146/1). T.B. is supported by the Biotechnology and Biological Sciences Research Council-funded South West Biosciences Doctoral Training Partnership (training grant reference BB/M009122/1). This work was partially funded by the Lundbeck Foundation (R52-A4895 to B.B.). H.J.T.H. was supported by the David and Lucile Packard Foundation, the Netherlands Organization for Scientific Research (#825.09.016), and currently by the Deutsche Forschungsgemeinschaft (DFG) under grant HO 5569/2-1 (Emmy Noether Junior Research Group). T.V. and B. Brejova were supported by grants from the Slovak grant agency VEGA (1/0684/16, 1/0458/18). F.S. was supported by a PhD grant (SFRH/BD/126560/2016) from FCT. A.A. was partly supported by the FCT project PTDC/CTA-AMB/31774/2017. C.C. and Y.W. are partly supported by grant IIS-1526415 from the US National Science Foundation. Computation for the work described in this article was partially supported by the DeiC National Life Science Supercomputer at DTU.
    Keywords: Cephalopod ; Invertebrate ; Genome assembly
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 6
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    Coupled genomic evolutionary histories as signatures of organismal innovations in cephalopods: co-evolutionary signatures across levels of genome organization may shed light on functional linkage and origin of cephalopod novelties (2020)
    Wiley
    Details
    Publication Date: 2022-10-27
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Ritschard, E. A., Whitelaw, B., Albertin, C. B., Cooke, I. R., Strugnell, J. M., & Simakov, O. Coupled genomic evolutionary histories as signatures of organismal innovations in cephalopods: co-evolutionary signatures across levels of genome organization may shed light on functional linkage and origin of cephalopod novelties. BioEssays, 41, (2019): 1900073, doi: 10.1002/bies.201900073.
    Description: How genomic innovation translates into organismal organization remains largely unanswered. Possessing the largest invertebrate nervous system, in conjunction with many species‐specific organs, coleoid cephalopods (octopuses, squids, cuttlefishes) provide exciting model systems to investigate how organismal novelties evolve. However, dissecting these processes requires novel approaches that enable deeper interrogation of genome evolution. Here, the existence of specific sets of genomic co‐evolutionary signatures between expanded gene families, genome reorganization, and novel genes is posited. It is reasoned that their co‐evolution has contributed to the complex organization of cephalopod nervous systems and the emergence of ecologically unique organs. In the course of reviewing this field, how the first cephalopod genomic studies have begun to shed light on the molecular underpinnings of morphological novelty is illustrated and their impact on directing future research is described. It is argued that the application and evolutionary profiling of evolutionary signatures from these studies will help identify and dissect the organismal principles of cephalopod innovations. By providing specific examples, the implications of this approach both within and beyond cephalopod biology are discussed.
    Description: E.A.R. and O.S. are supported by the Austrian Science Fund (Grant No. P30686‐B29). E.A.R. is supported by Stazione Zoologica Anton Dohrn (Naples, Italy) PhD Program. The authors wish to thank Graziano Fiorito (SZN, Italy), Hannah Schmidbaur (University of Vienna, Austria), Thomas Hummel (University of Vienna, Austria) for many insightful comments and reading of the draft manuscript. The authors would like to apologize to all colleagues whose work has been omitted due to space constraints.
    Keywords: Cephalopod ; Gene duplication ; Genome rearrangement ; Novel gene ; Organismal innovation
    Repository Name: Woods Hole Open Access Server
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  • 7
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    Assessing anthropogenic noise impacts and relevant soundscape cues for marine invertebrates: leveraging squid and coral reefs as model systems (2021)
    Massachusetts Institute of Technology and Woods Hole Oceanographic Institution
    Details
    Publication Date: 2022-10-20
    Description: Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Biological Oceanography at the Massachusetts Institute of Technology and the Woods Hole Oceanographic Institution September 2021.
    Description: Sound is utilized by marine animal taxa for many ecologically important functions, and these taxa are vulnerable to adverse effects of anthropogenic noise on hearing and behavior. However, little is known about marine invertebrates’ responses to anthropogenic noise, and the ambient environmental sounds (“soundscapes”) they detect and respond to. Most acoustic studies report sound pressure (detected by mammals and some fish), but few report particle motion, the back-and-forth vibratory component of sound detected by marine invertebrates. I investigated invertebrate use of and response to sounds in two facets: 1) behavioral responses of longfin squid, Doryteuthis pealeii to anthropogenic noise, and 2) particle motion of coral reef soundscapes in the U.S. Virgin Islands. In laboratory-based experiments I exposed D. pealeii to construction noise originally recorded from an offshore wind farm. I found significant increases in squids’ alarm responses and in failed prey capture attempts during noise. Conversely, noise exposure had no significant effects on reproductive behaviors of groups of D. pealeii, indicating high motivation of these squid to reproduce during this stressor. Collectively, these experiments revealed the importance of considering behavioral context in studies and regulatory decisions regarding invertebrates’ susceptibility to anthropogenic noise impacts. In studying coral reef soundscapes, I reported particle motion trends over several months for coral reefs varying in habitat quality, including coral cover and fish abundance. I found acoustic properties over which particle motion closely scaled with pressure, and others over which it did not. I compared soundscape data with particle motion hearing thresholds, and found that invertebrates may only detect high amplitude and low frequency transient sound cues on reefs, such as those produced by fishes. My research bring new insights on natural and anthropogenic sound cues detectable by marine invertebrates, and how and when invertebrates will be vulnerable to anthropogenic noise pollution.
    Description: My graduate work was funded in part by the US Department of Interior, Bureau of Ocean Energy Management Environmental Studies Program through Interagency Agreement Number M17PG00029 with the U.S. Department of Commerce, National Oceanic and Atmospheric Administration (funding to Aran Mooney and Jenni Stanley). My work was also supported by the NSF Biological Oceanography award OCE-1536782 (funding to Aran Mooney). I received tuition and stipend support from the National Science Foundation Graduate Research Fellowship Program [Grant No. 2388357]. The Academic Program Office at the Woods Hole Oceanographic Institution provided tuition and stipend support as well as travel support. The MIT Student Assistance Fund, the Aquatic Noise 2019 Organizing Committee, and the Acoustical Society of America also provided travel support.
    Keywords: Cephalopod ; Renewable energy ; Ecoacoustics
    Repository Name: Woods Hole Open Access Server
    Type: Thesis
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