Biodeeptime Version 1.0: A New Database of Biodiversity Time Series for the Cenozoic

Smith, Julian F.; Rillo, Marina C.; Kocsis, Ádám T.; Finnegan, Seth; Hull, Pincelli M.; Dornelas, María; Fastovich, David; Huang, Huai-Hsuan May; Kiessling, Wolfgang; Liow, Lee Hsiang; Margulis-Ohnuma, Miranda; Meyers, Stephen R.; Penny, Amelia; Pippenger, Katherine; Renaudie, Johan; Saupe, Erin E.; Steinbauer, Manuel J.; Sugawara, Mauro; Tomášových, Adam; Williams, John R.; Yasuhara, Moriaki

doi:10.1130/abs/2022am-383239

Cited by 4 publications

(14 citation statements)

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“…BioDeepTime is a relational database (Smith et al, 2023b) created through a working group of the Paleosynthesis Project. Taxon records of presence and abundance are linked to additional tables providing diatoms, ostracods, plants (pollen), radiolarians and other invertebrates and vertebrates.…”

Section: Me Thodsmentioning

confidence: 99%

“…Field names (i.e. data table columns) from existing databases were synonymized for inclusion in BioDeepTime (see Appendix S1, Tables S1.1-S1.17 and 'Synonymy of sources' in Smith et al (2023b)).…”

Section: Data Curation and Quality Controlmentioning

confidence: 99%

“…BioDeepTime version 1.0 can be downloaded from Zenodo (Smith et al, 2023b). When a fossil assemblage has accumulated over an extended period of time, the sampled assemblage will be time-averaged and its observed richness and evenness often will be higher than found in a living assemblage observed at any given point during the same period of time (e.g.…”

Section: Usag E Note Smentioning

confidence: 99%

“…The BioDeepTime database and the code to reproduce the data compilation are accessible from the Zenodo repository (Smith et al, 2023b)…”

Section: Co N Fli C T O F I Nter E S T S Tatem Entmentioning

confidence: 99%

“…These additional variables include extended taxonomic information, references to original data sources, types of abundance units and uncertainties in age, among others. A congruence table is included in Appendix S1 to describe differences in variable names and content originating from the source databases (see 'Synonymy of sources' in Smith et al, 2023b).…”

Section: Introductionmentioning

confidence: 99%

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BioDeepTime: A database of biodiversity time series for modern and fossil assemblages

Smith

Rillo

Kocsis

et al. 2023

Global Ecol Biogeogr

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MotivationWe have little understanding of how communities respond to varying magnitudes and rates of environmental perturbations across temporal scales. BioDeepTime harmonizes assemblage time series of presence and abundance data to help facilitate investigations of community dynamics across timescales and the response of communities to natural and anthropogenic stressors. BioDeepTime includes time series of terrestrial and aquatic assemblages of varying spatial and temporal grain and extent from the present‐day to millions of years ago.Main Types of Variables IncludedBioDeepTime currently contains 7,437,847 taxon records from 10,062 assemblage time series, each with a minimum of 10 time steps. Age constraints, sampling method, environment and taxonomic scope are provided for each time series.Spatial Location and GrainThe database includes 8752 unique sampling locations from freshwater, marine and terrestrial ecosystems. Spatial grain represented by individual samples varies from quadrats on the order of several cm2 to grid cells of ~100 km2.Time Period and GrainBioDeepTime in aggregate currently spans the last 451 million years, with the 10,062 modern and fossil assemblage time series ranging in extent from years to millions of years. The median extent of modern time series is 18.7 years and for fossil series is 54,872 years. Temporal grain, the time encompassed by individual samples, ranges from days to tens of thousands of years.Major Taxa and Level of MeasurementThe database contains information on 28,777 unique taxa with 4,769,789 records at the species level and another 271,218 records known to the genus level, including time series of benthic and planktonic foraminifera, coccolithophores, diatoms, ostracods, plants (pollen), radiolarians and other invertebrates and vertebrates. There are to date 7012 modern and 3050 fossil time series in BioDeepTime.Software FormatSQLite, Comma‐separated values.

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Section: Me Thodsmentioning

confidence: 99%

Section: Data Curation and Quality Controlmentioning

confidence: 99%

Section: Usag E Note Smentioning

confidence: 99%

“…The BioDeepTime database and the code to reproduce the data compilation are accessible from the Zenodo repository (Smith et al, 2023b)…”

Section: Co N Fli C T O F I Nter E S T S Tatem Entmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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BioDeepTime: A database of biodiversity time series for modern and fossil assemblages

Smith

Rillo

Kocsis

et al. 2023

Global Ecol Biogeogr

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Increasing the equitability of data citation in paleontology: capacity building for the big data future

Smith,

Raja,

Clements

et al. 2023

Paleobiology

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Data compilations expand the scope of research; however, data citation practice lags behind advances in data use. It remains uncommon for data users to credit data producers in professionally meaningful ways. In paleontology, databases like the Paleobiology Database (PBDB) enable assessment of patterns and processes spanning millions of years, up to global scale. The status quo for data citation creates an imbalance wherein publications drawing data from the PBDB receive significantly more citations (median: 4.3 ± 3.5 citations/year) than the publications producing the data (1.4 ± 1.3 citations/year). By accounting for data reuse where citations were neglected, the projected citation rate for data-provisioning publications approached parity (4.2 ± 2.2 citations/year) and the impact factor of paleontological journals (n = 55) increased by an average of 13.4% (maximum increase = 57.8%) in 2019. Without rebalancing the distribution of scientific credit, emerging “big data” research in paleontology—and science in general—is at risk of undercutting itself through a systematic devaluation of the work that is foundational to the discipline.

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Aligning paleobiological research with conservation priorities using elasmobranchs as a model

Dillon,

Pimiento

2024

Paleobiology

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Humans have dramatically transformed ecosystems over the previous millennia and are potentially causing a mass extinction event comparable to the others that shaped the history of life. However, only a fraction of these impacts has been directly recorded, limiting conservation actions. Conservation paleobiology leverages geohistorical records to offer a long-term perspective on biodiversity change in the face of anthropogenic stressors. Nevertheless, the field's on-the-ground contributions to conservation outcomes are still developing. Here, we present an overview of directions in which paleobiological research could progress to aid conservation in the coming decades using elasmobranchs (sharks, rays, and skates)—a highly threatened group with a rich fossil record—as a model. These research directions are guided by areas of overlap between an expert-led list of current elasmobranch conservation priorities and available fossil and historical records. Four research topics emerged for which paleobiological research could address open questions in elasmobranch science and conservation: (1) baselines, (2) ecological roles, (3) threats, and (4) conservation priorities. Increasingly rich datasets and novel analytical frameworks present exciting opportunities to apply the elasmobranch fossil record to conservation practice. A similar approach could be extended to other clades. Given the synthetic nature of these research topics, we encourage collaboration across timescales and with conservation practitioners to safeguard the future of our planet's rapidly disappearing species.

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Biodeeptime Version 1.0: A New Database of Biodiversity Time Series for the Cenozoic

Cited by 4 publications

References 0 publications

BioDeepTime: A database of biodiversity time series for modern and fossil assemblages

BioDeepTime: A database of biodiversity time series for modern and fossil assemblages

Increasing the equitability of data citation in paleontology: capacity building for the big data future

Aligning paleobiological research with conservation priorities using elasmobranchs as a model

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