The geological timings used in this paper are from Geological Time Scale (GTS) 202051.
Plant macrofossil and palynology data normalization steps
Plant macrofossils are typically fragmented into different parts (organs) prior to fossilization, with each part typically named separately using Linnean binomials23. We normalized the dataset to correct for potential duplications in which different parts of the same plant may be included under different species or genus names. In normalization, organs such as species or genera of seeds, trunks, roots and leaves are removed from the dataset if another, more identifiable or morphological diverse organ produced by the same plant is present, so that each whole plant is counted only once. For diverse leaf groups, for example ferns and sphenophytes, leaf species or genera are used, as these fossils typically lack more distinctive organs with suitable preservation. An example is the diverse trunk group of tree lycopods, where species of Lepidodendron are used as they are abundant and systematically informative23,52, rather than other organs produced by the same plant, including cones, sporophylls (fertile leaves) or roots (see ref. 21 for detail). Indeterminate species denoted as “sp.” of an existing genus are regarded as poorly preserved examples of the existing species of that genus, and are deleted. If the indeterminate species is the only species in that genus, they are counted as a single, unnamed species of that genus. Normalized macro plant fossil species data is listed in Table S4. In strata lacking plant macrofossils, palynological occurrences are taken into account.
Macro fossil plant species extinction magnitude
All the species occurrences presented are based on the normalized data (Table S4). Longitude and latitude for each fossil location are listed in Table S5. The high latitude area is defined to be >45 degrees north and south of the equator, while low-middle latitude area is <45 degrees north or south. The range of plant fossils in each stage was checked and extended for calculating the extinction magnitude over a global high-latitude and low–middle latitude area. The extinction magnitude for each stage is the extinct species number compared to a later stage, minus the total normalized species number of this stage. See the extinction rate results in Supplementary Information Table S1.
Flora characterization by clustering and morphological group
To analyze the character of floras from the end Permian (Changhsingian) to Middle Triassic (Anisian), family level clustering was used with the normalized plant fossil data. The clustering result is based on the Euclidean method. The plant systematic information comes from the Global Biodiversity Information Facility (GBIF) https://www.gbif.org/ database, with additions from the literature listed in the Supplementary Information. The taxonomic affinity of most spores and pollens are unknown, and so only plant macrofossil data was used in clustering, and the palynology data was only used in the morphological group diversity analysis. To show the uncertainty of the clustering results, we list the plant species number after each flora in Figure 1-A. Unsurprisingly, the clustering results for flora with fewer taxa were less reliable and more crowded together. As an auxiliary method to clustering, we counted the plant species number in each morphological group (see the fourteen morphological group classifications below), then calculated the proportion of the species number in each morphological group within floras to directly show the character and to construct a representative pie chart for each flora. For flora with fewer taxa, we adjusted the location of each flora in the clustering tree manually, according to the character shown by the morphological group diversity.
Plants were divided into six habitats and fourteen groups, including four arid types: conifer, gymnosperm (for seed plants where systematic class/group is uncertain), peltasperm and seed fern; three humid high-land types: cordaites, ginkgophyte, cycadophyte; one rainforest type: gigantopterid; two humid types: fern and ‘fern2’ (for taxa that could be either ferns or seed fern); two marsh types: sphenophyte and lycopod; one cold type: glossopterid – normally reported in boreal Gondwana; and one coastal type: herbaceous lycopod. Flora dominated by one habitat group was classified into the corresponding climate zone, and flora with more than one habitat group was defined as a mixture. In this step, we also took flora without a macrofossil record but with palynology data into account. The group information of the in-situ spore and pollen producing plant were counted53. For flora with both plant macrofossil and palynology data, we chose the dataset which contains more information. In Figure 1-A, flora with more than 150 taxa, such as the Changhsingian South China flora, have the biggest pie chart area, while flora with less than 10 taxa, like the German flora, have the smallest pie chart. After the clustering and morphological group counting analysis, the character of the flora from the End Permian to the Middle Triassic was systematically studied and classified into climate zones as shown in Table S2.
Vegetation biomass reconstruction
Terrestrial tetrapod data was used to infer the occurrence of plants on regions without a plant fossil record. Generally terrestrial tetrapod occurrences in our study coincided with the occurrences in the plant fossils, except for the Olenekian record in America and Canada. Therefore, vegetation type in those areas at this time was inferred from the tetrapod information alone (Supplementary Information Table S6).
Global vegetation was reconstructed by extension of fossil flora data across appropriate climate zones indicated by a sedimentary climate map31. In arid and polar areas, plant fossil extrapolation is restricted12,54. Extrapolation was not carried out at the boundaries of humid and arid environments in places that lacked supporting mineralogical data. For example, the Early and Middle Triassic low-latitude inner Pangean continent is inferred to have been arid savanna or steppe, based on the available fossil record and lithological climatic indicators. Fossils from more productive biomes which are found nearer the coast are therefore not extrapolated far into the continental interior where climate is arid, but are restricted to the coastline (Fig. 2).
Three principles are used for functional comparison between ancient and recent floras to estimate palaeo-biomass: firstly, recent floras must have a similar physiology or function to the ancient flora we wish to imitate, so we prefer C3 plants and not angiosperms. Secondly, the recent and ancient floras should be in the same climate zone and similar geographic location, for example, the latest Permian South China tropical forest was a low-latitude island, and so present-day, large tropical islands like Indonesia and Thailand were chosen over (for example) continental Brazil. Thirdly, the chosen flora should fit in the global diversity and NPP gradient at a similar place to the ancient flora. For instance, the end Permian (Changhsingian) tropical South China flora has the highest diversity, and is matched with a present day high-diversity, high-productivity biome, that of present day Thailand. The NPP of each ancient flora is listed in Table S2 and details of corresponding recent flora are in Table S3.
Palaeogeographic reconstruction
To reconstruct the spatial vegetation map, we assembled a database of fossil locations, plant macrofossil, palynology and terrestrial tetrapod data for our time periods (Table S5). The fossil locations were then reconstructed to their time of deposition using GPlates55. Because the palaeogeographic reconstruction used in SCION56 has no available set of reconstruction files, we used the reconstruction files of Macdonald57, whose reconstruction at ~250 Ma is similar to that of ref. 56. This allowed us to place fossil locations in an internally correct position at 250 Ma. However, minor manual manipulation was needed to then map some of these locations to their correct corresponding positions in the SCION land-sea maps.
Plant latitudinal diversity calculation
To investigate the influence of plant fossil sampling completeness on our estimates of diversity, squares and interpolation methods were applied to our normalized plant macrofossil occurrence data. As for the raw data, squares and interpolation were applied to 15° latitude bins for the Late Permian (Changhsingian) to Middle Triassic (Anisian). Coverage-based interpolation uses the abundance structure present within samples, to either subsample or extrapolate diversity estimates to particular levels of sampling completeness, known as quorum levels26,58,59. This was applied using the R package iNEXT58. Squares is an extrapolator based on the proportion of singletons in a sample, and is thought to be more robust to biases associated with small sample sizes and uneven abundance distributions60,61.
Throughout the interval, the raw, squares and interpolated diversity estimates generally show similar latitudinal patterns, suggesting that sampling is not particularly uneven across space in our dataset (Figure 1-B). However, many of the points in the interpolated curves were removed due to over-extrapolation, which indicates that many of the spatio-temporal bins may be under-sampled. Our results indicate that during the Induan, the highest plant diversity was found in the high latitudes, particularly in the northern hemisphere. However, during the Changhsingian, Olenekian and Anisian, we see higher diversity levels at tropical latitudes, suggesting that the latitudinal diversity gradient had reverted to a situation similar to that of the present day.
Climate-biogeochemical modelling
To investigate the effects of vegetation change on Early Triassic climate, we ran the SCION Earth Evolution Model18. We removed the equation which calculates terrestrial vegetation biomass (as a single global number) and replaced this with our reconstruction, mapped onto the model continental surface. We altered the model parameter fbiota, which represents the biotic enhancement of continental weathering (again a single number in SCION), to make this dependent on the local vegetation biomass in the following way:
Functionally, this returns tending towards 0.25 when biomass is very low, and a linear scaling with NPP when biomass rises. The choice of 0.25 relates to the four-fold enhancement between simple ground covers and higher plants used in first-generation long-term carbon cycle models such as GEOCARB62,63, and based on field and laboratory studies37. We vary this ‘preplant’ factor between 0.15 – 1 in the SI and modify the linear scaling to account for this. In all formulations, the scaling factor for NPP is chosen to return present day global weathering rates.
We defined land-derived organic carbon burial as:
where klocb is the present-day rate of land-derived organic carbon burial, Pland is the phosphorus delivery to land, Pland0 is the present-day phosphorus delivery, and kpreservation is an arbitrary multiplier set to 2 in the Palaeozoic and 1 in the Mesozoic, to represent better preservation of Palaeozoic organic matter (see text), and allowing the model to replicate high Permian carbonate δ13C.
Data availability
The normalized plant and land tetrapod data taxa list and occurrence are provided in Supplementary Information Tables S4–S6. The normalization details are available from Zhen Xu on request.
Code availability
Full SCION model code and documentation is available at https://github.com/bjwmills/SCION. Open access preprints for papers describing all model versions and derivations are available at bjwmills.com.
[the model code version used for this work is attached to this paper submission and will be available online if the paper is published]
Further References
51. Gradstein, F.M., Ogg, J.G., Schmitz, M.D., & Ogg, G.M. (Eds.) Geological time scale 2020 (Elsevier, Netherlands, 2020).
52. Bateman, R.M., DiMichele, W.A. Escaping the voluntary constraints of “tyre‐track” taxonomy. Taxon 70, 1062–1077 (2021).
53. Balme, B.A., Fossil in situ spores and pollen grains: an annotated catalogue. Rev. Palaeobot. Palynol. 87, 81–323 (1995).
54. Berdugo, M. et al. Global ecosystem thresholds driven by aridity. Science 367(6479), 787–790 (2020).
55. Müller, R.D., Cannon, J., Qin, X.D., Watson, R.J., Gurnis, M., Williams, S., Pfaffelmoser, T., Seton, M., Russell, S.H.J., Zahirovic, S. GPlates: building a virtual Earth through deep time. Geochem. Geophys. Geosys. 19, 2243–2261 (2018).
56. Blakey, R.C., Fielding, C.R. Gondwana paleogeography from assembly to breakup―A 500 my odyssey. Geol. Soc. Am. Spec. Pap. 441, 1–28 (2008).
57. Macdonald, F.A., Swanson-Hysell, N.L., Park, Y., Lisiecki, L., &Jagoutz, O. Arc-continent collisions in the tropics set Earth’s climate state. Science 364, 181–184 (2019).
58. Hsieh, T.C., Ma, K.H., & Chao, A. iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers). Meth. Ecol. Evol. 7, 1451–1456 (2016).
59. Dunne, E.M. et al. Diversity change during the rise of tetrapods and the impact of the ‘Carboniferous rainforest collapse’. Proc. R. Soc. B. 285, 20172730 (2018).
60. Alroy, J. Limits to species richness in terrestrial communities. Ecol. Lett. 21, 1781–1789 (2018).
61. Alroy, J. On four measures of taxonomic richness. Paleobiology 1–18 (2020).
62. Berner, R.A. A model for atmospheric CO sub 2 over phanerozoic time. Am. J. Sci. 291 (1991).
63. Berner, R.A. GEOCARB II: A revised model of atmospheric CO2 over phanerozoic time. Am. J. Sci. 294 (1994).