History of the database
NSB began as an offline database 'Neptune' in the early 1990s, as a research project headed by Dave Lazarus in Hans Thierstein's group at the ETH in Zürich. It was inspired by the Sepkoski marine families database (1979) which also at a later date inspired the development of the Paleobiology Database (PBDB). Several people contributed to data uploads and taxonomic list development, including Katharina von Salis, Jean Pierre Beckmann, Cathy Nigrini, Jean Pierre Caulet, Connie Sancetta and Cinzia Spencer-Cervato. Lazarus left the group for a position in Berlin in 1994, although data entry by the ETH group and Michael Knappertsbusch (Basel) continued. The initial content was analyzed and described by Spencer-Cervato (1999)- ca 200K occurrence records for Neogene plankton (foraminifera, coccolithophores, diatoms and radiolaria), from ca 100 sections.

The next phase of development took place in the early 2000s under Cervato's leadership as head of the NSF Chronos project (Ames, Iowa) with Patrick Diver (database) and Doug Fils (website front-end). Neptune was ported to standard sql technology, content was extended to ca 500,000 occurrence records and 300 sections by Cervato, Mark Leckie and Kendra Clark, focussing exclusively on calcareous plankon data but including many Paleogene and a few Cretaceous sections. Several simple queries were created for website users. In parallel, John Alroy of the PBDB provided, at the request of the PBDB micropaleo group (Lazarus, Jeremy Young, Huber and several others) a search function at the PBDB website for paleobiology type queries. These access opportunities supported several significant studies by external research groups (see list of selected papers below).

The current phase of development began in 2009 as the Chronos version of Neptune became increasingly unstable as NSF funded technical maintenance had ended. With the support of Niels Stenseth and Lee Hsiang Liow (Oslo), Diver and Lazarus ported Neptune to a simpler, easier to maintain implementation hosted at the MfN in Berlin. Renamed NSB (for Neptune Sandbox Berlin) and with additional support by the EU Earthtime project (in particular Heiko Pälike), Lazarus, Diver and Johan Renaudie extended the content further, to ca 800,000 occurrence records and nearly 500 sections. For the first time since the initial ETH design, NSB data types were significantly extended to include geochronologic data, in particular the event data used to create the age models and their calibrations. Additionally, the taxonomic name lists were substantially updated using the work of ODP's Paleontology Coordination Group (Lazarus, Emanuel Söding, Huber, Young, Masao Iawi, Dave Harwood and Nori Suzuki). NSB access was improved with the development in 2015 of a data link to Young's increasingly popular 'Mikrotax' community online taxonomic catalog for calcareous microfossils.

NSB also provides a data feed for analytic tools at the Geobiodiversity Database (created by Fan Junxuan).

Sepkoski, J., 1979. A kinetic model of Phanerozoic taxonomic diversity. II. Early Phanerozoic families and multiple equilibria. Paleobiology 5, 222–251.



Articles using or citing the Neptune Database
2019

Kocsis, A. T., Reddin, C. J., Alroy, J., and Kiessling, W. The R package divdyn for quantifying diversity dynamics using fossil sampling data. Methods in Ecology and Evolution.

Young, J. R., Bown, P. R., Wade, B. S., Pedder, B. E., Huber, B. T. and Lazarus, D. B. Mikrotax: Developing a Genuinely Effective Platform for Palaeontological Geoinformatics. Acta Geologica Sinica, 93: 70-72.

Jungck, J. R., Wagner, R., van Loo, D., Grossman, B., Khiripet, N., Khiripet, J., Khantuwan, W., and Hagan, M. Art forms in nature: radiolaria from Haeckel and Blaschka to 3D nanotomography, quantitative image analysis, evolution, and contemporary art. Theory in Biosciences, 138(1):159–187.


2018

Fordham, B., Aze, T., Haller, C., Zehady, A. K., Pearson, P. N., Ogg, J. G., and Wade, B. S. Future-proofing the Cenozoic macroperforate planktonic foraminifera phylogeny of Aze & others (2011). PLOS One, 13(10):web.

Lewitus, E., Bittner, L., Malviya, S., Bowler, C., and Morlon, H. Clade-specific diversification dynamics of marine diatoms since the Jurassic. Nature Ecology & Evolution, 2:1715–1723.

Müller, R. D., Cannon, J., Williams, S., and Dutkiewicz, A. PyBacktrack 1.0: a tool for reconstructing paleobathymetry on oceanic and continental crust. Geochemistry, Geophysics, Geosystems, 19:1898–1909.

Nakov, T., Beaulieu, J. M., and Alverson, A. J. Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta). New Phytologist, 219(1):462-473.

Plotnick, R. E. and Wagner, P. J. The greatest hits of all time: the histories of dominant genera in the fossil record. Paleobiology, 44(3):368–384.

Renaudie, J., Drews, E.-L., and Böhne, S. The paleocene record of marine diatoms in deep-sea sediments. Fossil Record, 21(2):183–205.

Witkowski, J. From museum drawers to ocean drilling: Fenneria gen. nov. (Bacillariophyta) offers new insights into Eocene marine diatom biostratigraphy and palaeobiogeography. Acta Geologica Polonica, 68:53–88.


2017

Hannisdal, B., Haaga, K. A., Reitan, T., Diego, D., and Liow, L. H. Common species link global ecosystems to climate change: dynamical evidence in the planktonic fossil record. Proc. R. Society B., 284:1–9 (web).

Intxauspe-Zubiaurre, B., Payros, A., Flores, J. A., and Apellaniz, E. Changes to sea-surface characteristics during the middle Eocene (47.4 Ma) C21r-H6 event: evidence from calcareous nannofossil assemblages of the Gorrondatxe section (western Pyrenees). Newsl. Stratigr., 50(3):245–267.

Lewitus, E. and Morlon, H. Detecting environment-dependent diversification from phylogenies: a simulation study and some empirical illustrations. Systematic Biology, 67(4):576-593.

Pascher, K. M. Paleobiogeography of Eocene Radiolarians in the South-west Pacific. PhD thesis, Victoria University of Wellington.

Powell, M. G. and Glazier, D. S. Asymmetric geographic range expansion explains the latitudinal diversity gradients of four major taxa of marine plankton. Paleobiology, 43(2):196-208.

Yasuhara, M., Tittensor, D. P., Hillebrand, H., and Worm, B. Combining marine macroecology and palaeoecology in understanding biodiversity: microfossils as a model. Biological Reviews, 92(1):199–215.


2016

Cermeño, P. The geological story of marine diatoms and the last generation of fossil fuels. Perspectives in Phycology, 3(2):53-60.

Fenton, I. S., Pearson, P. N., Jones, T. D., Farnsworth, A., Lunt, D., Markwick, P. J., and Purvis, A. The impact of Cenozoic cooling on assemblage diversity in planktonic foraminifera. Phil. Trans. R. Soc. B, 371(1691):20150224.

Fontorbe, G., Frings, P. J., De La Rocha, C. L., Hendry, K. R., and Conley, D. J. A silicon depleted North Atlantic since the Palaeogene: Evidence from sponge and radiolarian silicon isotopes. Earth and Planetary Science Letters, 453:67–77.

Huber, B., Petrizzo, M., Young, J. R., Falzoni, F., Gilardoni, S. E., Bown, P. R., and Wade, B. S. Pforams@microtax: A new online taxonomic database for planktonic foraminifera. Micropaleontology, 62(6):429–438.

Renaudie, J. Quantifying the Cenozoic marine diatom deposition his- tory: links to the C and Si cycles. Biogeosciences, 13(21):6003–6014.

Saraswati, P. K. and Srinivasan, M. S.. Morphology, taxonomy and concepts of species. In Micropaleontology: Principles and Applications, pages 53–65. Springer, Cham, Switzerland.

Suto, I., Iwai, M., and Akiba, F. Some important points when using fossil databases. Fossils, 99:7–14.c

Wiese, R., Renaudie, J., and Lazarus, D. Testing the accuracy of genus-level data to predict species diversity in Cenozoic marine diatoms. Geology, 44(12).


2015

Barron, J. A., Stickley, C. E., and Bukry, D. Paleoceanographic, and paleoclimatic constraints on the global Eocene diatom and silicoflagellate record. Palaeogeography Palaeoclimatology Palaeoecology, 422:85–100.

Cermeño, P., Falkowski, P. G., Romero, O. E., Schaller, M. F., and Vallina, S. M. Continental erosion and the cenozoic rise of marine diatoms. Proceedings of the National Academy of Sciences, 112(14):4239–4244.

Kotrc, B. and Knoll, A. A morphospace of planktonic marine diatoms. I. Two views of disparity through time. Paleobiology, 41(1):45–67.

Kotrc, B. and Knoll, A. A morphospace of planktonic marine diatoms. II. Sampling standardization and spatial disparity partitioning. Paleobiology, 41(1):68–88.

Kotrc, B. and Knoll, A. H. Morphospaces and databases: Diatom diversification through time. In Evolution of Lightweight Structures, pages 17–37. Springer.

Lazarus, D., Suzuki, N., Caulet, J. P., Nigrini, C., Goll, I., Goll, R., Dolven, J. K., Diver, P., and Sanfilippo, A. An evaluated list of Cenozoic-Recent radiolarian species names (Polycystinea), based on those used in the DSDP, ODP and IODP deep-sea drilling programs. Zootaxa, 3999(3):301–333.

Mary, Y. and Knappertsbusch, M. W. Worldwide morphological variability in Mid-Pliocene menardellid globorotalids. Marine Micropaleontology.

Nadim, T., B., M., and Löwe, S. Reconstructions of a historic paleontological collection: Diversity re-created. Earth Sciences History, 34(2):348–366.

Pascher, K. M., Hollis, C. J., Cortese, G., McKay, C., Seebeck, H., Suzuki, N., and Chiba, K. Expansion and diversification of high-latitude radiolarian assemblages in the late Eocene linked to a cooling event in the southwest Pacific. Clim. Past, 11:1599–1620.

Ramkumar, M. Marine Paleobiodiversity: Responses to Sea Level Cycles and Perturbations. Elsevier.

Weiner, A. K. M., Weinkauf, M., Kurasawa, A., Darling, K., and Kucera, M. Genetic and morphometric evidence for parallel evolution of the Globigerinella calida morphotype. Marine Micropalaeontology, 114:19–35.


2014

Lazarus, D. The legacy of early radiolarian taxonomists, with a focus on the species published by early German workers. Journal of Micropalaentology, 33:3–19.

Lazarus, D., Barron, J., Renaudie, J., Diver, P., and Türke, A. Cenozoic diatom diversity and correlation to climate change. PLOS One, 9(1):1–18.


2013

Cermeño, P., Castro-Bugallo, A., and Vallina, S. M. Diversification patterns of planktic foraminifera in the fossil record. Marine Micropalaeontology, 104:38–43.

Ezard, T. H. G., Thomas, G. H., and Purvis, A. Inclusion of a near-complete fossil record reveals speciation-related molecular evolution. Methods in Ecology and Evolution, 4(8):745–753.

Kotrc, B. Evolution of Silica Biomineralizing Plankton. PhD Thesis, Harvard, Cambridge, MA.

Mary, Y. Morphologic, biogeographic and ontogenetic investigation of Mid-Pliocene menardellids (planktonic foraminifera). PhD Thesis, University Basel, Basel, Switzerland.

Mary, Y. and Knappertsbusch, M. W. Morphological variability of menardiform globorotalids in the Atlantic Ocean during Mid-Pliocene. Marine Micropaleontology, 101:180–193.

Renaudie, J. and Lazarus, D. B. On the accuracy of paleodiversity reconstructions: a case study in antarctic neogene radiolarians. Paleobiology, 39(03):491–509.


2012

Andre, A., Weiner, A., Quillevere, F., Aurahs, R., Morard, R., Douady, C. J., de Garidel-Thoron, T., Escarguel, G., de Vargas, C., and Michal Kucera, M. The cryptic and the apparent reversed: lack of genetic differentiation within the morphologically diverse plexus of the planktonic foraminifer Globigerinoides sacculifer. Paleobiology, 39(1):21–39.

Hannisdal, B., Henderiks, J., and Liow, L. H. Long-term evolutionary and ecological responses of calcifying phytoplankton to changes in atmospheric CO2. Global Change Biology, 18(12):3504–3516.

Herrmann, S. and Thierstein, H. R. Cenozoic coccolith size changes— Evolutionary and/or ecological controls? Palaeogeography, Palaeoclimatology, Palaeoecology, 333-334:92–106.

Lazarus, D., Weinkauf, M., and Diver, P. Pacman profiling: a simple procedure to identify stratigraphic outliers in high density deep-sea microfossil data. Paleobiology, 38(1):144–161.

Lloyd, G. T., Pearson, P. N., Young, J. R., and Smith, A. G. Sampling bias and the fossil record of planktonic foraminifera on land and in the deep sea. Paleobiology, 38(4):569–584.

Lloyd, G. T., Young, J. R., and Smith, A. B. Taxonomic structure of the fossil record is shaped by sampling bias. Systematic Biology, 60:1–10.

Renaudie, J. A Synthesis of Antarctic Neogene radiolarians: taxonomy, macroevolution and biostratigraphy. PhD Thesis, Humboldt University, Berlin.

Suto, I., Kawamura, K., Hagimoto, S., Teraishi, A., and Tanaka, Y. Changes in upwelling mechanisms drove the evolution of marine organisms. Palaeogeography Palaeoclimatology Palaeoecology, 339-341:39–51.

van Dam, J. A. Scanning the fossil record: stratophenomics and the generation of primary evolutionary-ecological data. Evolutionary Ecology, 26(3):449–463.


2011

Aze, T., Ezard, T. H. G., Purvis, A., Coxall, H., Stewart, D. R. M., Wade, B. S., and Pearson, P. N. A phylogeny of Cenozoic macroperforate planktonic foraminifera from fossil data. Biological Reviews, 86(4):900–927.

Cermeño, P. Marine planktonic microbes survived climatic stabilities in the past. Proc. R. Society B., 279:474–479.

Ezard, T. H. G., Aze, T., Pearson, P. N., and Purvis, A. Interplay between changing climate and species’ ecology drives macroevolutionary dynamics. Science, 332:349–351.

Lazarus, D. The deep-sea microfossil record of macroevolutionary change in plankton and its study. In Smith, A. and McGowan, A., (Eds), Comparing the Geological and Fossil Records: Implications for Biodiversity Studies, pages 141–166. The Geological Society, London.

Lloyd, G. T., Smith, A. G., and Young, J. R. Quantifying the deep-sea rock and fossil record bias using coccolithophores. In McGowan, A. J. and Smith, A. G., editors, Comparing the Geological and Fossil Records: Implications for Biodiversity Studies, pages 167–178. Geological Society, London.

Powell, M. and MacGregor, J. A geographic test of species selection using planktonic foraminifera during the Cretaceous/Paleogene mass extinction. Paleobiology, 37(3):426–437.

Sadler, P. M. and Cervato, C. Data and tools for geologic timelines and timescales. In Keller, G. R. and Baru, C., editors, Geoinformatics: Cyberinfrastructure for the Solid Earth Sciences, pages 145–165.


2010

Crux, J. A., Gary, A., Gard, G., and Ellington, W. E. Recent advances in the application of biostratigraphy to hydrocarbon exploration and production. In Ratcliffe, K. T. and Zaitlin, B., editors, Application of Modern Stratigraphic Techniques: Theory and Case Histories, pages 57–80. SEPM.

Finkel, Z. V. and Kotrc, B. Silica use through time: macroevolutionary change in the morphology of the diatom frustule. Geomicrobiology Journal, 27:596–608.

Hayward, B., Sabaa, A., Thomas, E., Kawagata, S., Nomura, R., Schröder-Adams, C., Gupta, A., and Johnson, K. Cenozoic record of elongate, cylindrical, deep-sea benthic foraminifera in the Indian Ocean (ODP Sites 722, 738, 744, 758 and 763). Journal of Foraminiferal Research, 40(1):113–133.

Liow, L. H., Skaug, H. J., Ergon, T., and Schweder, T. Global occurrence trajectories of microfossils: environmental volatility and the rise and fall of individual species. Paleobiology, 36(2):224–252.

Marx, F. G. and Uhen, M. D. Climate, critters, and cetaceans: Cenozoic drivers of the evolution of modern whales. Science, 327:993–996.

Renaudie, J., Danelian, T., Saint, M. S., Le, C. L., and Tribovillard, N. Siliceous phytoplankton response to a middle Eocene warming event recorded in the tropical Atlantic (Demerara Rise, ODP Site 1260a). Palaeogeography Palaeoclimatology Palaeoecology, 286(3-4):121–134.


2009

Cermeño, P. and Falkowski, P. G. Controls on diatom biogeography in the ocean. Science, 325:1539–1541.

Fils, D., Cervato, C., Reed, J., Diver, P., Tang, X., Bohling, G., and Greer, D. CHRONOS architecture: Experiences with an open-source services- oriented architecture for geoinformatics. Comp. Geosci., 35(4):774–782.

Frada, M., Percopo, I., Young, J., Zingone, A., de Vargas, C., and Probert, I. First observations of the heterococcolithophore-holococcolithophore life cycle combinations in the family Pontosphaeraceae (Calcihaptophycideae, Haptophyta). Marine Micropalaeontology, 71:20–27.

Lazarus, D. B., Kotrc, B., Wulf, G., and Schmidt, D. N. Radiolarians decreased silicification as an evolutionary response to reduced cenozoic ocean silica availability. Proceedings of the National Academy of Sciences, 106(23):9333–9338.

Rabosky, D. L. and Sorhannus, U. Diversity dynamics of marine planktonic diatoms across the Cenozoic. Nature, 247:183–187.


2008

Cody, R. D., Levy, R. H., Harwood, D. M., and Sadler, P. M. Thinking outside the zone: High-resolution quantitative diatom biochronology for the Antarctic Neogene. Palaeogeography, Palaeoclimatology, Palaeoecology, 260:92–121.

Foote, M., Crampton, J. S., Beu, A. G., and Cooper, R. A. On the bidirectional relationship between geographic range and taxonomic duration. Paleobiology, 34(4):421–433.

Henderiks, J. and Pagani, M. Coccolithophore cell size and the Paleogene decline in atmospheric CO2. Earth and Planetary Science Letters, 269:575– 583.

Lazarus, D., Hollis, C., and Apel, M. Patterns of opal and radiolarian change in the Antarctic mid-Paleogene: clues to the origin of the Southern Ocean. Micropaleontology, 54(1):41–48.


2007

Allen, A. E. and Savage, V. M. Setting the absolute tempo of biodiversity dynamics. Ecology Letters, 10(7):637–646.

Finkel, Z. V., Sebbo, J., Feist-Burkhardt, S., Irwin, A., Katz, M. E., Schofield, O., Young, J., and Falkowski, P. G. A universal driver of macroevolutionary change in the size of marine phytoplankton over the Cenozoic. Proceedings of the National Academy of Sciences of the United States of America, 104(51):20416–20420.

Kucera, M. Planktonic foraminifera as tracers of past oceanic environments. In Hillaire-acel, C. and de Vernal, A., editors, Proxies in Late Cenozoic Paleoceanography, pages 213–262. Elsevier, Amsterdam.

Kucera, M. and Schönfeld, J. The origin of modern oceanic foraminiferal faunas and Neogene climate change. In Williams, M., Haywood, A. M., Gregory, F. J., and Schmidt, D. N., editors, Deep-Time Perspectives on Climate Change: Marrying the Signal from Computer Models and Biological Proxies, pages 409–425. The Geological Society, London.

Liow, L. H. and Stenseth, N. C. The rise and fall of species: implications for macroevolutionary and macroecological studies. Proc. Royal Society B, 274(1626):2745–2752.

McPeek, M. The macroevolutionary consequences of ecological differences among species. Palaeontology, 50(1):111–129.

Muttoni, G. and Kent, D. Widespread formation of cherts during the early Eocene climatic optimum. Palaeogeography, Palaeoclimatology, Palaeoecology, 253(3-4):348–362.


2006

Allen, A. P. and Gillooly, J. F. Assessing latitudinal gradients in speciation rates and biodiversity at the global scale. Ecology Letters, 9(8):947–954.

Allen, A. P., Gillooly, J. F., Savage, V. M., and Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Nat. Acad. Sci. USA, 103(24):9130–9135.

Lazarus, D., Bittniok, B., Diester-Haass, L., Meyers, P., and Billups, K. Comparison of radiolarian and sedimentologic paleoproductivity proxies in the latest Miocene-Recent Benguela Upwelling System. Marine Micropaleontology, 60:269–294.

Lazarus, D. The Micropaleontological Reference Centers network. Scientific Drilling, 3:46–49.


2005

Bohling, G. Chronos Age-Depth Plot: A Java application for stratigraphic data analysis. Geosphere, 1(2):78–84.

Finkel, Z. V., Katz, M. E., Wright, J. D., Schofield, O., and Falkowski, P. Climatically driven macroevolutionary patterns in the size of marine diatoms over the Cenozoic. Proceedings of the National Academy of Sciences of the United States of America, 102(25):8927–8932.

Spezzaferri, S. and Spiegler, D. Fossil planktic foraminifera (an overview). Paläontologische Zeitschrift, 79(1):149–166.


2004

Cortese, G., Gersonde, R., Hillenbrand, C.-D., and Kuhn, G. Opal sedimentation shifts in the World Ocean over the last 15 Myr. Earth and Planetary Science Letters, 224:509–527.

Falkowski, P. G., Katz, M. E., Knoll, A. H., Quigg, A., Raven, J. A., Schofield, O., and Taylor, F. J. R. The evolution of modern eukaryotic phytoplankton. Science, 305:354–360.

Katz, M. E., Finkel, Z. V., Grzebyk, D., Knoll, A., and Falkowski, P. Evolutionary trajectories and biogeochemical impacts of marine eukaryotic phytoplankton. Ann Rev. Ecol. Syst., 35:523–556.

Schmidt, D. N., Thierstein, H., and Bollmann, J. The evolutionary history of size variation of planktic foraminiferal assemblages in the Cenozoic. Palaeogeography, Palaeoclimatology, Palaeoecology, 212:159–180.

Thierstein, H., Cortés, M., and Haidar, A. Plankton community behavior on ecological and evolutionary time-scales: when models confront evidence. In Thierstein, H. and Young, J. R., editors, Coccolithophores: From Molecular Processes to Global Impact, pages 455–480. Springer, Berlin.

Tozzi, S., Schofield, O., and Falkowski, P. Historical climate change and ocean turbulence as selective agents for two key phytoplankton functional groups. Marine Ecology Progress Series, 274:123–132.


pre-2004

Cervato, C. and Burckle, L. (2003). Patten of first and last appearance in diatoms: Oceanic circulation and the position of polar fronts during the Cenozoic. Paleoceanography, 18(2):web.

Lazarus, D. (2002). Environmental control of diversity, evolutionary rates and taxa longevities in Antarctic Neogene radiolaria. Paleontologica Electronica, 5(1):1–30.

Spencer-Cervato, C. (1999). The cenozoic deep sea microfossil record: explorations of the DSDP/ODP sample set using the Neptune database. Palaeontologia electronica, 2(2):270.

Spencer-Cervato, C. (1998). Changing depth distribution of hiatuses during the cenozoic. Paleoceanography, 13(2):178–182.

Spencer-Cervato, C. and Thierstein, H. (1997). First appearance of Globorotalia truncatulinoides: cladogenesis and immigration. Marine Micropalaeontology, 30(4):267–291.

Lazarus, D. B., Spencer-Cervato, C., Pianka-Biolzi, M., Beckmann, J. P., von Salis, K., Hilbrecht, H., and Thierstein, H. R. (1995). Revised chronology of Neogene DSDP holes from the world ocean, volume 24. Ocean Drilling Program, College Station.

Spencer-Cervato, C., Thierstein, H. R., Lazarus, D. B., and Beckmann, J. P. (1994). How synchronous are Neogene marine plankton events? Paleoceanography, 9:739–763.

Lazarus, D. (1994). Neptune: a marine micropaleontology database. Mathematical Geology, 26(7):817–832.

Spencer-Cervato, C., Lazarus, D. B., Beckmann, J. P., Perch-Nielsen, K. v. S., and Biolzi, M. (1993). New calibration of Neogene radiolarian events in the North Pacific. Marine Micropaleontology, 21(4):261–294.