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Biodiversity data from: The mass extinction debt of the Anthropocene

Citation

Spalding, Christopher; Hull, Pincelli (2021), Biodiversity data from: The mass extinction debt of the Anthropocene, Dryad, Dataset, https://doi.org/10.5061/dryad.tdz08kpzt

Abstract

To make sense of our present biodiversity crises, the modern rate of species extinctions is commonly compared to a benchmark, or “background,” rate derived from the fossil record. These estimates are critical for bounding the scale of modern diversity loss, but have yet to account for the fundamental structure of extinction rates through time. Namely, a substantial fraction of extinctions within the fossil record occur within relatively short-lived extinction pulses, and not during intervals characterized by background rates of extinction. Accordingly, it is more appropriate to compare the modern event to these pulses than to the long-term average rate. Unfortunately, neither the duration of extinction pulses in the geological record nor the ultimate magnitude of the extinction pulse today is resolved, making assessments of their relative sizes difficult. In addition, the common metric used to compare current and past extinction rates does not correct for large differences in observation duration. Here we propose a new predictive metric that may be used to ascertain the ultimate extent of the ongoing extinction threat, building on the observation that extinction magnitude in the marine fossil record is correlated to the magnitude of sedimentary turnover. Thus, we propose that the ultimate number of species destined for extinction today can be predicted by way of a quantitative appraisal of humanity’s modification of ecosystems as recorded in sediments –that is, by comparing our future rock record with that of the past. The ubiquity of habitat disruption worldwide suggests that a profound mass extinction debt exists today, but one that might yet be averted by preserving and restoring ecosystems and their geological traces.

Methods

Data associated with “Towards Quantifying the Mass Extinction Debt of the Anthropocene” by C. Spalding & P. M. Hull. In Section 3.1 of the main text, we introduced our data, which was drawn from the paleobiology database (PBDB), the compilation of Barnosky et al. (2011), the IUCN Red List (as of 2019) and the publication of Heim & Peters (2011). Descriptions of this data are included below.

1. Data from the paleobiology database (PBDB) was downloaded from the following URL’s:

1.1:This data includes all animal genera at stage level during the Phanerozoic. This data was downloaded from the Paleobiology Database on Tue 2021-03-02 19:46:14 GMT, using the parameters: count=genera_ time_reso=stage, base_name=animalia, interval = Cambrian,Holocene, timerule=major. Used in Figure 2. Data URL: http://paleobiodb.org/data1.2/occs/diversity.tsv?datainfo&rowcount&base_name=animalia&count=genera&interval=Cambrian,holocene.

1.2: This data includes all animal genera at stage level during the Cenozoic. This data was downloaded from the Paleobiology Database on Mon 2021-01-25 15:40:44 GMT, using the parameters: count=genera, time_reso=stage, base_name=animalia, interval Cenozoic,Holocene, timerule=major. Used in Figure 3. Data URL: http://paleobiodb.org/data1.2/occs/diversity.tsv?datainfo&rowcount&base_name=Animalia&count=genera&interval=Cenozoic,Holocene

1.3: This data includes all animal genera at epoch level across the Phanerozoic. This data was downloaded from the Paleobiology Database on Mon 2021-01-25 15:08:54 GMT, using the parameters: count=genera, time_reso=epoch, base_name=animalia, interval Cambrian,Holocene, timerule=major. Used in Figure 2. Data URL: http://paleobiodb.org/data1.2/occs/diversity.tsv?datainfo&rowcount&base_name=Animalia&count=genera&interval=Cambrian,Holocene&time_reso=epoch

1.4: This data includes all animal genera at period level across the Phanerozoic. This data was downloaded from the Paleobiology Database on Mon 2021-01-25 15:09:02 GMT, using the parameters: count=genera, time_reso=period, base_name=animalia, interval Cambrian,Holocene, timerule=major. Used in Figure 2. Data URL: http://paleobiodb.org/data1.2/occs/diversity.tsv?datainfo&rowcount&base_name=Animalia&count=genera&interval=Cambrian,Holocene&time_reso=period

1.5: This data includes all mammalian genera at stage level during the Cenozoic. This data was downloaded from the Paleobiology Database on Mon 2021-01-25 15:04:46 GMT, using the parameters: count=genera, time_reso=stage, base_name=mammalia, interval Cenozoic,Holocene, timerule=major. Used in Figure 3. Data URL: http://paleobiodb.org/data1.2/occs/diversity.tsv?datainfo&rowcount&base_name=Mammalia&count=genera&interval=Cenozoic,Holocene

2. Data from the compilation of Barnosky et al. (2011) (B11), described in the publication is found in the following files:

Barnosky, A. D., Matzke, N., Tomiya, S., Wogan, G. O., Swartz, B., Quental, T. B., ... & Ferrer, E. A. (2011). Has the Earth’s sixth mass extinction already arrived?. Nature, 471(7336), 51-57

2.1.Barnosky_Genus_Recents. This data compiles the extinction rates, in terms of fraction of genus extinctions per million years, occurring over the most recent 100,000 years across a range of time intervals. Plotted in Figure 3. 

2.2.Barnosky_Species_Recents. This data compiles the extinction rates, in terms of fraction of species extinctions per million years, occurring over the most recent 100,000 years across a range of time intervals. Plotted in Figure 3.

2. Data from the compilation of Barnosky et al. (2011) (B11)

As described in publication:

Barnosky, A. D., Matzke, N., Tomiya, S., Wogan, G. O., Swartz, B., Quental, T. B., ... & Ferrer, E. A. (2011). Has the Earth’s sixth mass extinction already arrived?. Nature, 471(7336), 51-57, the data provided were derived from a collection of previous works. These include the publications:

1. Barnosky, A. D. Megafauna biomass tradeoff as a driver of Quaternary and future extinctions. Proc. Natl Acad. Sci. USA 105, 11543–11548 (2008).

2. Koch, P. L.& Barnosky, A. D. Late Quaternary extinctions: state of the debate. Annu. Rev. Ecol. Evol. Syst. 37, 215–250 (2006).

3. IUCN. International Union for Conservation of Nature Red List http://www.iucn.org/ about/work/programmes/species/red_list/ (2010).

4. Barnosky, A. D. & Lindsey, E. L. Timing of Quaternary megafaunal extinction in South America in relation to human arrival and climate change. Quat. Int. 217, 10–29 (2010).

5. Turvey, S. T. Holocene Extinctions (Oxford University Press, 2009).

6. Faith, J. T. & Surovell, T. A. Synchronous extinction of North America’s Pleistocene mammals. Proc. Natl Acad. Sci. USA 106, 20641–20645 (2009).

7. Surovell, T., Waguespack, N. & Brantingham, P. J. Global archaeological evidence for proboscidean overkill. Proc. Natl Acad. Sci. USA 102, 6231–6236 (2005).

8. Finlayson, C. et al. Late survival of Neanderthals at the southernmost extreme of Europe. Nature 443, 850–853 (2006).

9. Morwood, M. J. et al. Archaeology and age of a new hominin fromFlores in eastern Indonesia. Nature 431, 1087–1091 (2004).

10. Orlova, L.A., Vasil’ev, S. K.,Kuz’min, Y. V.&Kosintsev, P. A.Newdata onthe timeand place of extinction of the woolly rhinoceros Coelodonta antiquitatis Blumenbach, 1799. Dokl. Akad. Nauk 423, 133–135 (2008).

11. Reumer, J. W. F. et al. Late Pleistocene survival of the saber-toothed cat Homotherium in Northwestern Europe. J. Vertebr. Paleontol. 23, 260–262 (2003).

12. MacPhee, R. D. E. Extinctions in Near Time: Causes, Contexts, and Consequences (Kluwer Academic/Plenum Publishers, 1999).

This dataset is found in the following two files:

2.1: Barnosky_Genus_Recents.tsv. This data compiles the extinction rates, in terms of fraction of genus extinctions per million years, occurring over the most recent 100,000 years across a range of time intervals. Plotted in Figure 3.

2.2: Barnosky_Species_Recents.tsv. This data compiles the extinction rates, in terms of fraction of species extinctions per million years, occurring over the most recent 100,000 years across a range of time intervals. Plotted in Figure 3.

3. Data from the publication of Heim & Peters (2011). This data is also stored online at the repository:

Heim, N.; Peters, S. (2010): Supplemental material: Covariation in macrostratigraphic and macroevolutionary patterns in the marine record of North America. Geological Society of America. Journal contribution. https://doi.org/10.1130/2010183

Tables reproduced here include:

3.1. Heim_Peters_Data2_PBDB.xlsx. This data represents the stage-level turnover in sedimentary packages and hiatuses. 

3.2. Heim_Peters_Data_Strat.xlsx. This data represents the stage-level turnover in biodiversity. 

3.3.Heim_Peters_Data3_Timescale.xlsx. The bottom and top boundary times of the intervals recorded in datasets 3.1 and 3.2.

Figures:

Figures 2, 3 and 4 in the publication use the data described above. Figures were generated using Mathematica files F2.nb, F3.nband F4.nb respectively.