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  • Frontiers Media  (56)
  • National Academy of Sciences  (18)
  • 2020-2023  (74)
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  • 1
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    The Earth BioGenome Project 2020: starting the clock (2022)
    National Academy of Sciences
    Details
    Publication Date: 2022-05-27
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Lewin, H. A., Richards, S., Lieberman Aiden, E., Allende, M. L., Archibald, J. M., Bálint, M., Barker, K. B., Baumgartner, B., Belov, K., Bertorelle, G., Blaxter, Mark L., Cai, J., Caperello, N. D., Carlson, K., Castilla-Rubio, J. C., Chaw, S-M., Chen, L., Childers, A. K., Coddington, J. A., Conde, D. A., Corominas, M., Crandall, K. A., Crawford, A. J., DiPalma, F., Durbin, R., Ebenezer, T. E., Edwards, S. V., Fedrigo, O., Flicek, P., Formenti, G., Gibbs, R. A., Gilbert, M. Thomas P., Goldstein, M. M., Graves, J. M., Greely, H. T., Grigoriev, I. V., Hackett, K. J., Hall, N., Haussler, D., Helgen, K. M., Hogg, C. J., Isobe, S., Jakobsen, K. S., Janke, A., Jarvis, E. D., Johnson, W. E., Jones, S. J. M., Karlsson, E. K., Kersey, P. J., Kim, J-H., Kress, W. J., Kuraku, S., Lawniczak, M. K. N., Leebens-Mack, J. H., Li, X., Lindblad-Toh, K., Liu, X., Lopez, J. V., Marques-Bonet, T., Mazard, S., Mazet, J. A. K., Mazzoni, C. J., Myers, E. W., O’Neill, R. J., Paez, S., Park, H., Robinson, G. E., Roquet, C., Ryder, O. A., Sabir, J. S. M., Shaffer, H. B., Shank, T. M., Sherkow, J. S., Soltis, P. S., Tang, B., Tedersoo, L., Uliano-Silva, M., Wang, K., Wei, X., Wetzer, R., Wilson, J. L., Xu, X., Yang, H., Yoder, A. D., Zhang, G. The Earth BioGenome Project 2020: starting the clock. Proceedings of the National Academy of Sciences of the United States of America, 119(4), (2022): e2115635118, https://doi.org/10.1073/pnas.2115635118.
    Description: November 2020 marked 2 y since the launch of the Earth BioGenome Project (EBP), which aims to sequence all known eukaryotic species in a 10-y timeframe. Since then, significant progress has been made across all aspects of the EBP roadmap, as outlined in the 2018 article describing the project’s goals, strategies, and challenges (1). The launch phase has ended and the clock has started on reaching the EBP’s major milestones. This Special Feature explores the many facets of the EBP, including a review of progress, a description of major scientific goals, exemplar projects, ethical legal and social issues, and applications of biodiversity genomics. In this Introduction, we summarize the current status of the EBP, held virtually October 5 to 9, 2020, including recent updates through February 2021. References to the nine Perspective articles included in this Special Feature are cited to guide the reader toward deeper understanding of the goals and challenges facing the EBP.
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  • 2
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    Argo data 1999-2019: two million temperature-salinity profiles and subsurface velocity observations from a global array of profiling floats. (2020)
    Frontiers Media
    Details
    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Wong, A. P. S., Wijffels, S. E., Riser, S. C., Pouliquen, S., Hosoda, S., Roemmich, D., Gilson, J., Johnson, G. C., Martini, K., Murphy, D. J., Scanderbeg, M., Bhaskar, T. V. S. U., Buck, J. J. H., Merceur, F., Carval, T., Maze, G., Cabanes, C., Andre, X., Poffa, N., Yashayaev, I., Barker, P. M., Guinehut, S., Belbeoch, M., Ignaszewski, M., Baringer, M. O., Schmid, C., Lyman, J. M., McTaggart, K. E., Purkey, S. G., Zilberman, N., Alkire, M. B., Swift, D., Owens, W. B., Jayne, S. R., Hersh, C., Robbins, P., West-Mack, D., Bahr, F., Yoshida, S., Sutton, P. J. H., Cancouet, R., Coatanoan, C., Dobbler, D., Juan, A. G., Gourrion, J., Kolodziejczyk, N., Bernard, V., Bourles, B., Claustre, H., D'Ortenzio, F., Le Reste, S., Le Traon, P., Rannou, J., Saout-Grit, C., Speich, S., Thierry, V., Verbrugge, N., Angel-Benavides, I. M., Klein, B., Notarstefano, G., Poulain, P., Velez-Belchi, P., Suga, T., Ando, K., Iwasaska, N., Kobayashi, T., Masuda, S., Oka, E., Sato, K., Nakamura, T., Sato, K., Takatsuki, Y., Yoshida, T., Cowley, R., Lovell, J. L., Oke, P. R., van Wijk, E. M., Carse, F., Donnelly, M., Gould, W. J., Gowers, K., King, B. A., Loch, S. G., Mowat, M., Turton, J., Rama Rao, E. P., Ravichandran, M., Freeland, H. J., Gaboury, I., Gilbert, D., Greenan, B. J. W., Ouellet, M., Ross, T., Tran, A., Dong, M., Liu, Z., Xu, J., Kang, K., Jo, H., Kim, S., & Park, H. Argo data 1999-2019: two million temperature-salinity profiles and subsurface velocity observations from a global array of profiling floats. Frontiers in Marine Science, 7, (2020): 700, doi:10.3389/fmars.2020.00700.
    Description: In the past two decades, the Argo Program has collected, processed, and distributed over two million vertical profiles of temperature and salinity from the upper two kilometers of the global ocean. A similar number of subsurface velocity observations near 1,000 dbar have also been collected. This paper recounts the history of the global Argo Program, from its aspiration arising out of the World Ocean Circulation Experiment, to the development and implementation of its instrumentation and telecommunication systems, and the various technical problems encountered. We describe the Argo data system and its quality control procedures, and the gradual changes in the vertical resolution and spatial coverage of Argo data from 1999 to 2019. The accuracies of the float data have been assessed by comparison with high-quality shipboard measurements, and are concluded to be 0.002°C for temperature, 2.4 dbar for pressure, and 0.01 PSS-78 for salinity, after delayed-mode adjustments. Finally, the challenges faced by the vision of an expanding Argo Program beyond 2020 are discussed.
    Description: AW, SR, and other scientists at the University of Washington (UW) were supported by the US Argo Program through the NOAA Grant NA15OAR4320063 to the Joint Institute for the Study of the Atmosphere and Ocean (JISAO) at the UW. SW and other scientists at the Woods Hole Oceanographic Institution (WHOI) were supported by the US Argo Program through the NOAA Grant NA19OAR4320074 (CINAR/WHOI Argo). The Scripps Institution of Oceanography's role in Argo was supported by the US Argo Program through the NOAA Grant NA15OAR4320071 (CIMEC). Euro-Argo scientists were supported by the Monitoring the Oceans and Climate Change with Argo (MOCCA) project, under the Grant Agreement EASME/EMFF/2015/1.2.1.1/SI2.709624 for the European Commission.
    Keywords: global ; ocean ; pressure ; temperature ; salinity ; Argo ; profiling ; floats
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  • 3
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    The helium and carbon isotope characteristics of the Andean Convergent Margin (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Barry, P. H., De Moor, J. M., Chiodi, A., Aguilera, F., Hudak, M. R., Bekaert, D. V., Turner, S. J., Curtice, J., Seltzer, A. M., Jessen, G. L., Osses, E., Blamey, J. M., Amenabar, M. J., Selci, M., Cascone, M., Bastianoni, A., Nakagawa, M., Filipovich, R., Bustos, E., Schrenk, M. O. , Buongiorno, J., Ramírez, C. J., Rogers, T. J., Lloyd, K. G. & Giovannelli, D. The helium and carbon isotope characteristics of the Andean Convergent Margin. Frontiers in Earth Science, 10, (2022): 897267, https://doi.org/10.3389/feart.2022.897267.
    Description: Subduction zones represent the interface between Earth’s interior (crust and mantle) and exterior (atmosphere and oceans), where carbon and other volatile elements are actively cycled between Earth reservoirs by plate tectonics. Helium is a sensitive tracer of volatile sources and can be used to deconvolute mantle and crustal sources in arcs; however it is not thought to be recycled into the mantle by subduction processes. In contrast, carbon is readily recycled, mostly in the form of carbon-rich sediments, and can thus be used to understand volatile delivery via subduction. Further, carbon is chemically-reactive and isotope fractionation can be used to determine the main processes controlling volatile movements within arc systems. Here, we report helium isotope and abundance data for 42 deeply-sourced fluid and gas samples from the Central Volcanic Zone (CVZ) and Southern Volcanic Zone (SVZ) of the Andean Convergent Margin (ACM). Data are used to assess the influence of subduction parameters (e.g., crustal thickness, subduction inputs, and convergence rate) on the composition of volatiles in surface volcanic fluid and gas emissions. He isotopes from the CVZ backarc range from 0.1 to 2.6 RA (n = 23), with the highest values in the Puna and the lowest in the Sub-Andean foreland fold-and-thrust belt. Atmosphere-corrected He isotopes from the SVZ range from 0.7 to 5.0 RA (n = 19). Taken together, these data reveal a clear southeastward increase in 3He/4He, with the highest values (in the SVZ) falling below the nominal range associated with pure upper mantle helium (8 ± 1 RA), approaching the mean He isotope value for arc gases of (5.4 ± 1.9 RA). Notably, the lowest values are found in the CVZ, suggesting more significant crustal inputs (i.e., assimilation of 4He) to the helium budget. The crustal thickness in the CVZ (up to 70 km) is significantly larger than in the SVZ, where it is just ∼40 km. We suggest that crustal thickness exerts a primary control on the extent of fluid-crust interaction, as helium and other volatiles rise through the upper plate in the ACM. We also report carbon isotopes from (n = 11) sites in the CVZ, where δ13C varies between −15.3‰ and −1.2‰ [vs. Vienna Pee Dee Belemnite (VPDB)] and CO2/3He values that vary by over two orders of magnitude (6.9 × 108–1.7 × 1011). In the SVZ, carbon isotope ratios are also reported from (n = 13) sites and vary between −17.2‰ and −4.1‰. CO2/3He values vary by over four orders of magnitude (4.7 × 107–1.7 × 1012). Low δ13C and CO2/3He values are consistent with CO2 removal (e.g., calcite precipitation and gas dissolution) in shallow hydrothermal systems. Carbon isotope fractionation modeling suggests that calcite precipitation occurs at temperatures coincident with the upper temperature limit for life (122°C), suggesting that biology may play a role in C-He systematics of arc-related volcanic fluid and gas emissions.
    Description: This work was principally supported by the NSF-FRES award 2121637 to PB, KL, and JM. Field work was also supported by award G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to PB, KL, DG, and JM. Additional support came from The National Fund for Scientific and Technological Development of Chile (FONDECYT) Grant 11191138 (The National Research and Development Agency of Chile, ANID Chile), and COPAS COASTAL ANID FB210021 to GJ. DG was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG.
    Keywords: Helium ; Carbon ; SVZ ; CVZ ; Andes (Argentina and Chile)
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  • 4
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    The possession of coccoliths fails to deter microzooplankton grazers (2021)
    Frontiers Media
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    Publication Date: 2022-05-26
    Description: © The Author(s), 2020. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Mayers, K. M. J., Poulton, A. J., Bidle, K., Thamatrakoln, K., Schieler, B., Giering, S. L. C., Wells, S. R., Tarran, G. A., Mayor, D., Johnson, M., Riebesell, U., Larsen, A., Vardi, A., & Harvey, E. L. The possession of coccoliths fails to deter microzooplankton grazers. Frontiers in Marine Science, 7, (2020): 562020, doi:10.3389/fmars.2020.569896.
    Description: Phytoplankton play a central role in the regulation of global carbon and nutrient cycles, forming the basis of the marine food webs. A group of biogeochemically important phytoplankton, the coccolithophores, produce calcium carbonate scales that have been hypothesized to deter or reduce grazing by microzooplankton. Here, a meta-analysis of mesocosm-based experiments demonstrates that calcification of the cosmopolitan coccolithophore, Emiliania huxleyi, fails to deter microzooplankton grazing. The median grazing to growth ratio for E. huxleyi (0.56 ± 0.40) was not significantly different among non-calcified nano- or picoeukaryotes (0.71 ± 0.31 and 0.55 ± 0.34, respectively). Additionally, the environmental concentration of E. huxleyi did not drive preferential grazing of non-calcified groups. These results strongly suggest that the possession of coccoliths does not provide E. huxleyi effective protection from microzooplankton grazing. Such indiscriminate consumption has implications for the dissolution and fate of CaCO3 in the ocean, and the evolution of coccoliths.
    Description: Mesocosm experiments in 2015 were supported by the Kiel Excellence Cluster “The Future Ocean” (CP1540) and the Leibniz Award to UR, in 2017 the MESOHUX experiment was supported by NSF (OCE-1559179) to KT and KB, NSF (OCE-1537951 and OCE-1459200) to KB, NSF (OCE-1459190, 1657808, and DBI-1624593) to EH, and in 2018 by AQUACOSM (EU H2020-INFRAIA-project No 731065). KM was supported by a NERC Doctoral Training Partnership (DTP) studentship as part of the Southampton Partnership for Innovative Training of Future Investigators Researching the Environment (SPITFIRE, grant number NE/L002531/1) and Research Council of Norway project (#280414) MIXsTRUCT.
    Keywords: coccolithophore ; phytoplankton ; microzooplankton ; biomineralisation ; predation ; evolution
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  • 5
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    Linkages among dissolved organic matter export, dissolved metabolites, and associated microbial community structure response in the northwestern Sargasso Sea on a seasonal scale (2022)
    Frontiers Media
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Liu, S., Longnecker, K., Kujawinski, E., Vergin, K., Bolaños, L., Giovannoni, S., Parsons, R., Opalk, K., Halewood, E., Hansell, D., Johnson, R., Curry, R., & Carlson, C. Linkages among dissolved organic matter export, dissolved metabolites, and associated microbial community structure response in the northwestern Sargasso Sea on a seasonal scale. Frontiers in Microbiology, 13, (2022): 833252, https://doi.org/10.3389/fmicb.2022.833252.
    Description: Deep convective mixing of dissolved and suspended organic matter from the surface to depth can represent an important export pathway of the biological carbon pump. The seasonally oligotrophic Sargasso Sea experiences annual winter convective mixing to as deep as 300 m, providing a unique model system to examine dissolved organic matter (DOM) export and its subsequent compositional transformation by microbial oxidation. We analyzed biogeochemical and microbial parameters collected from the northwestern Sargasso Sea, including bulk dissolved organic carbon (DOC), total dissolved amino acids (TDAA), dissolved metabolites, bacterial abundance and production, and bacterial community structure, to assess the fate and compositional transformation of DOM by microbes on a seasonal time-scale in 2016–2017. DOM dynamics at the Bermuda Atlantic Time-series Study site followed a general annual trend of DOC accumulation in the surface during stratified periods followed by downward flux during winter convective mixing. Changes in the amino acid concentrations and compositions provide useful indices of diagenetic alteration of DOM. TDAA concentrations and degradation indices increased in the mesopelagic zone during mixing, indicating the export of a relatively less diagenetically altered (i.e., more labile) DOM. During periods of deep mixing, a unique subset of dissolved metabolites, such as amino acids, vitamins, and benzoic acids, was produced or lost. DOM export and compositional change were accompanied by mesopelagic bacterial growth and response of specific bacterial lineages in the SAR11, SAR202, and SAR86 clades, Acidimicrobiales, and Flavobacteria, during and shortly following deep mixing. Complementary DOM biogeochemistry and microbial measurements revealed seasonal changes in DOM composition and diagenetic state, highlighting microbial alteration of the quantity and quality of DOM in the ocean.
    Description: This project was funded by the Simons Foundation International’s BIOS-SCOPE program and US National Science Foundation (NSF OCE-1756105 for BATS cruises).
    Keywords: Dissolved organic matter ; Amino acids ; Metabolites ; Bacterioplankton ; Sargasso Sea ; Seasonal ; Mixing
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  • 6
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    A decade of incorporating social sciences in the Integrated Marine Biosphere Research Project (IMBeR): much done, much to do? (2021)
    Frontiers Media
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    Publication Date: 2022-05-27
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in van Putten, I., Kelly, R., Cavanagh, R. D., Murphy, E. J., Breckwoldt, A., Brodie, S., Cvitanovic, C., Dickey-Collas, M., Maddison, L., Melbourne-Thomas, J., Arrizabalaga, H., Azetsu-Scott, K., Beckley, L. E., Bellerby, R., Constable, A. J., Cowie, G., Evans, K., Glaser, M., Hall, J., Hobday, A. J., Johnston, N. M., Llopiz, J. K., Mueter, F., Muller-Karger, F. E., Weng, K. C., Wolf-Gladrow, D., Xavier, J. C. A decade of incorporating social sciences in the Integrated Marine Biosphere Research Project (IMBeR): much done, much to do? Frontiers in Marine Science, 8, (2021): 662350, https://doi.org/10.3389/fmars.2021.662350.
    Description: Successful management and mitigation of marine challenges depends on cooperation and knowledge sharing which often occurs across culturally diverse geographic regions. Global ocean science collaboration is therefore essential for developing global solutions. Building effective global research networks that can enable collaboration also need to ensure inter- and transdisciplinary research approaches to tackle complex marine socio-ecological challenges. To understand the contribution of interdisciplinary global research networks to solving these complex challenges, we use the Integrated Marine Biosphere Research (IMBeR) project as a case study. We investigated the diversity and characteristics of 1,827 scientists from 11 global regions who were attendees at different IMBeR global science engagement opportunities since 2009. We also determined the role of social science engagement in natural science based regional programmes (using key informants) and identified the potential for enhanced collaboration in the future. Event attendees were predominantly from western Europe, North America, and East Asia. But overall, in the global network, there was growing participation by females, students and early career researchers, and social scientists, thus assisting in moving toward interdisciplinarity in IMBeR research. The mainly natural science oriented regional programmes showed mixed success in engaging and collaborating with social scientists. This was mostly attributed to the largely natural science (i.e., biological, physical) goals and agendas of the programmes, and the lack of institutional support and push to initiate connections with social science. Recognising that social science research may not be relevant to all the aims and activities of all regional programmes, all researchers however, recognised the (potential) benefits of interdisciplinarity, which included broadening scientists’ understanding and perspectives, developing connections and interlinkages, and making science more useful. Pathways to achieve progress in regional programmes fell into four groups: specific funding, events to come together, within-programme-reflections, and social science champions. Future research programmes should have a strategic plan to be truly interdisciplinary, engaging natural and social sciences, as well as aiding early career professionals to actively engage in such programmes.
    Description: This publication resulted in part from support from the U.S. National Science Foundation (Grant OCE-1840868) to the Scientific Committee on Oceanic Research (SCOR).
    Keywords: marine science ; research networks ; disciplines ; global ; regional programmes
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  • 7
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    Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark (2022)
    National Academy of Sciences
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    Publication Date: 2022-08-15
    Description: © The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Womersley, F. C., Humphries, N. E., Queiroz, N., Vedor, M., da Costa, I., Furtado, M., Tyminski, J. P., Abrantes, K., Araujo, G., Bach, S. S., Barnett, A., Berumen, M. L., Bessudo Lion, S., Braun, C. D., Clingham, E., Cochran, J. E. M., de la Parra, R., Diamant, S., Dove, A. D. M., Dudgeon, C. L., Erdmann, M. V., Espinoza, E., Fitzpatrick, R., González Cano, J., Green, J. R., Guzman, H. M., Hardenstine, R., Hasan, A., Hazin, F. H. V., Hearn, A. R., Hueter, R. E., Jaidah, M. Y., Labaja, J., Ladinol, F., Macena, B. C. L., Morris Jr., J. J., Norman, B. M., Peñaherrera-Palmav, C., Pierce, S. J., Quintero, L. M., Ramırez-Macías, D., Reynolds, S. D., Richardson, A. J., Robinson, D. P., Rohner, C. A., Rowat, D. R. L., Sheaves, M., Shivji, M. S., Sianipar, A. B., Skomal, G. B., Soler, G., Syakurachman, I., Thorrold, S. R., Webb, D. H., Wetherbee, B. M., White, T. D., Clavelle, T., Kroodsma, D. A., Thums, M., Ferreira, L. C., Meekan, M. G., Arrowsmith, L. M., Lester, E. K., Meyers, M. M., Peel, L. R., Sequeira, A. M. M., Eguıluz, V. M., Duarte, C. M., & Sims, D. W. Global collision-risk hotspots of marine traffic and the world’s largest fish, the whale shark. Proceedings of the National Academy of Sciences of the United States of America, 119(20), (2022): e2117440119, https://doi.org/10.1073/pnas.2117440119.
    Description: Marine traffic is increasing globally yet collisions with endangered megafauna such as whales, sea turtles, and planktivorous sharks go largely undetected or unreported. Collisions leading to mortality can have population-level consequences for endangered species. Hence, identifying simultaneous space use of megafauna and shipping throughout ranges may reveal as-yet-unknown spatial targets requiring conservation. However, global studies tracking megafauna and shipping occurrences are lacking. Here we combine satellite-tracked movements of the whale shark, Rhincodon typus, and vessel activity to show that 92% of sharks’ horizontal space use and nearly 50% of vertical space use overlap with persistent large vessel (〉300 gross tons) traffic. Collision-risk estimates correlated with reported whale shark mortality from ship strikes, indicating higher mortality in areas with greatest overlap. Hotspots of potential collision risk were evident in all major oceans, predominantly from overlap with cargo and tanker vessels, and were concentrated in gulf regions, where dense traffic co-occurred with seasonal shark movements. Nearly a third of whale shark hotspots overlapped with the highest collision-risk areas, with the last known locations of tracked sharks coinciding with busier shipping routes more often than expected. Depth-recording tags provided evidence for sinking, likely dead, whale sharks, suggesting substantial “cryptic” lethal ship strikes are possible, which could explain why whale shark population declines continue despite international protection and low fishing-induced mortality. Mitigation measures to reduce ship-strike risk should be considered to conserve this species and other ocean giants that are likely experiencing similar impacts from growing global vessel traffic.
    Description: Funding for data analysis was provided by the UK Natural Environment Research Council (NERC) through a University of Southampton INSPIRE DTP PhD Studentship to F.C.W. Additional funding for data analysis was provided by NERC Discovery Science (NE/R00997/X/1) and the European Research Council (ERC-AdG-2019 883583 OCEAN DEOXYFISH) to D.W.S., Fundação para a Ciência e a Tecnologia (FCT) under PTDC/BIA/28855/2017 and COMPETE POCI-01–0145-FEDER-028855, and MARINFO–NORTE-01–0145-FEDER-000031 (funded by Norte Portugal Regional Operational Program [NORTE2020] under the PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund–ERDF) to N.Q. FCT also supported N.Q. (CEECIND/02857/2018) and M.V. (PTDC/BIA-COM/28855/2017). D.W.S. was supported by a Marine Biological Association Senior Research Fellowship. All tagging procedures were approved by institutional ethical review bodies and complied with all relevant ethical regulations in the jurisdictions in which they were performed. Details for individual research teams are given in SI Appendix, section 8. Full acknowledgments for tagging and field research are given in SI Appendix, section 7. This research is part of the Global Shark Movement Project (https://www.globalsharkmovement.org).
    Keywords: ship strike ; marine megafauna ; conservation ; movement ecology ; human impact
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  • 8
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    High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume (2022)
    National Academy of Sciences
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    Publication Date: 2022-10-26
    Description: © The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Bekaert, D. V., Gazel, E., Turner, S., Behn, M. D., de Moor, J. M., Zahirovic, S., Manea, V. C., Hoernle, K., Fischer, T. P., Hammerstrom, A., Seltzer, A. M., Kulongoski, J. T., Patel, B. S., Schrenk, M. O., Halldórsson, S. A., Nakagawa, M., Ramírez, C. J., Krantz, J. A., Yücel, M., Ballentine, C. J., Giovannelli, D., Lloyd, K. G., Barry, P. H. High (3)He/(4)He in central Panama reveals a distal connection to the Galápagos plume. Proceedings of the National Academy of Sciences of the United States of America, 118(47), (2021): e2110997118, https://doi.org/10.1073/pnas.2110997118.
    Description: It is well established that mantle plumes are the main conduits for upwelling geochemically enriched material from Earth's deep interior. The fashion and extent to which lateral flow processes at shallow depths may disperse enriched mantle material far (〉1,000 km) from vertical plume conduits, however, remain poorly constrained. Here, we report He and C isotope data from 65 hydrothermal fluids from the southern Central America Margin (CAM) which reveal strikingly high 3He/4He (up to 8.9RA) in low-temperature (≤50 °C) geothermal springs of central Panama that are not associated with active volcanism. Following radiogenic correction, these data imply a mantle source 3He/4He 〉10.3RA (and potentially up to 26RA, similar to Galápagos hotspot lavas) markedly greater than the upper mantle range (8 ± 1RA). Lava geochemistry (Pb isotopes, Nb/U, and Ce/Pb) and geophysical constraints show that high 3He/4He values in central Panama are likely derived from the infiltration of a Galápagos plume–like mantle through a slab window that opened ∼8 Mya. Two potential transport mechanisms can explain the connection between the Galápagos plume and the slab window: 1) sublithospheric transport of Galápagos plume material channeled by lithosphere thinning along the Panama Fracture Zone or 2) active upwelling of Galápagos plume material blown by a “mantle wind” toward the CAM. We present a model of global mantle flow that supports the second mechanism, whereby most of the eastward transport of Galápagos plume material occurs in the shallow asthenosphere. These findings underscore the potential for lateral mantle flow to transport mantle geochemical heterogeneities thousands of kilometers away from plume conduits.
    Description: This work was principally supported by Grant G-2016-7206 from the Alfred P. Sloan Foundation and the Deep Carbon Observatory to P.H.B. We also acknowledge the NSF awards (1144559, 1923915, and 2015789) to P.H.B., which partially supported this work. S.Z. was supported by the Australian Research Council Grant DE210100084 and a University of Sydney Robinson Fellowship. D.G. was partially supported by funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program Grant Agreement No. 948972—COEVOLVE—ERC-2020-STG. This study was also supported in part by NSF award No. EAR 1826673 to E.G. Folkmar Hauff is acknowledged for contributing to the analysis of the La Providencia samples at GEOMAR.
    Keywords: Helium ; Mantle plume ; Slab window ; Mantle flow ; Geochemistry
    Repository Name: Woods Hole Open Access Server
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    Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea (2022)
    National Academy of Sciences
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    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 Criswell, K. E., Roberts, L. E., Koo, E. T., Head, J. J., & Gillis, J. A. Hox gene expression predicts tetrapod-like axial regionalization in the skate, Leucoraja erinacea. Proceedings of the National Academy of Sciences of the United States of America, 118(51), (2021): e2114563118, https://doi.org/10.1073/pnas.2114563118.
    Description: The axial skeleton of tetrapods is organized into distinct anteroposterior regions of the vertebral column (cervical, trunk, sacral, and caudal), and transitions between these regions are determined by colinear anterior expression boundaries of Hox5/6, -9, -10, and -11 paralogy group genes within embryonic paraxial mesoderm. Fishes, conversely, exhibit little in the way of discrete axial regionalization, and this has led to scenarios of an origin of Hox-mediated axial skeletal complexity with the evolutionary transition to land in tetrapods. Here, combining geometric morphometric analysis of vertebral column morphology with cell lineage tracing of hox gene expression boundaries in developing embryos, we recover evidence of at least five distinct regions in the vertebral skeleton of a cartilaginous fish, the little skate (Leucoraja erinacea). We find that skate embryos exhibit tetrapod-like anteroposterior nesting of hox gene expression in their paraxial mesoderm, and we show that anterior expression boundaries of hox5/6, hox9, hox10, and hox11 paralogy group genes predict regional transitions in the differentiated skate axial skeleton. Our findings suggest that hox-based axial skeletal regionalization did not originate with tetrapods but rather has a much deeper evolutionary history than was previously appreciated.
    Description: This research was funded by a Natural Environment Research Council Grant (to J.J.H., J.A.G., and K.E.C.: NE/S000739/1) and a Royal Society University Research Fellowship (UF130182 and URF\R\191007), Royal Society Research Grant (RG140377), and University of Cambridge Sir Isaac Newton Trust Grant (14.23z) (to J.A.G.).
    Keywords: Hox genes ; Regionalization ; Chondrichthyan ; Vertebral column
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  • 10
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    Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis (2020)
    National Academy of Sciences
    Details
    Publication Date: 2022-10-31
    Description: © The Author(s), 2019. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Northcutt, A. J., Kick, D. R., Otopalik, A. G., Goetz, B. M., Harris, R. M., Santin, J. M., Hofmann, H. A., Marder, E., & Schulz, D. J. Molecular profiling of single neurons of known identity in two ganglia from the crab Cancer borealis. Proceedings of the National Academy of Sciences of the United States of America, 116 (52) (2019): 26980-26990, doi: 10.1073/pnas.1911413116.
    Description: Understanding circuit organization depends on identification of cell types. Recent advances in transcriptional profiling methods have enabled classification of cell types by their gene expression. While exceptionally powerful and high throughput, the ground-truth validation of these methods is difficult: If cell type is unknown, how does one assess whether a given analysis accurately captures neuronal identity? To shed light on the capabilities and limitations of solely using transcriptional profiling for cell-type classification, we performed 2 forms of transcriptional profiling—RNA-seq and quantitative RT-PCR, in single, unambiguously identified neurons from 2 small crustacean neuronal networks: The stomatogastric and cardiac ganglia. We then combined our knowledge of cell type with unbiased clustering analyses and supervised machine learning to determine how accurately functionally defined neuron types can be classified by expression profile alone. The results demonstrate that expression profile is able to capture neuronal identity most accurately when combined with multimodal information that allows for post hoc grouping, so analysis can proceed from a supervised perspective. Solely unsupervised clustering can lead to misidentification and an inability to distinguish between 2 or more cell types. Therefore, this study supports the general utility of cell identification by transcriptional profiling, but adds a caution: It is difficult or impossible to know under what conditions transcriptional profiling alone is capable of assigning cell identity. Only by combining multiple modalities of information such as physiology, morphology, or innervation target can neuronal identity be unambiguously determined.
    Description: We thank members of the D.J.S., H.A.H., and E.M. laboratories for helpful discussions. We thank the Genomic Sequencing and Analysis Facility (The University of Texas [UT] at Austin) for library preparation and sequencing and the bioinformatics consulting team at the UT Austin Center for Computational Biology and Bioinformatics for helpful advice. This work was supported by National Institutes of Health grant R01MH046742-29 (to E.M. and D.J.S.) and the National Institute of General Medical Sciences T32GM008396 (support for A.J.N.) and National Institute of Mental Health grant 5R25MH059472-18 and the Grass Foundation (support for Neural Systems and Behavior Course at the Marine Biological Laboratory).
    Keywords: qPCR ; RNA-seq ; Stomatogastric ; Expression profiling
    Repository Name: Woods Hole Open Access Server
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