Data from: Timing of morphological and ecological innovations in the cyanobacteria – a key to understanding the rise in atmospheric oxygen

When cyanobacteria originated and diversified, and what their ancient traits were, remain critical unresolved problems. Here, we used a phylogenomic approach to construct a well-resolved 'core' cyanobacterial tree. The branching positions of four lineages (Thermosynechococcus elongatus, Synechococcus elongatus, Synechococcus PCC 7335 and Acaryochloris marina) were problematic, probably due to long branch attraction artifacts. A consensus genomic tree was used to study trait evolution using ancestral state reconstruction (ASR). The early cyanobacteria were probably unicellular, freshwater, had small cell diameters, and lacked the traits to form thick microbial mats. Relaxed molecular clock analyses suggested that early cyanobacterial lineages were restricted to freshwater ecosystems until at least 2.4 Ga, before diversifying into coastal brackish and marine environments. The resultant increases in niche space and nutrient availability, and consequent sedimentation of organic carbon into the deep oceans, would have generated large pulses of oxygen into the biosphere, possibly explaining why oxygen rose so rapidly. Rapid atmospheric oxidation could have destroyed the methane-driven greenhouse with simultaneous drawdown in pCO(2), precipitating 'Snowball Earth' conditions. The traits associated with the formation of thick, laminated microbial mats (large cell diameters, filamentous growth, sheaths, motility and nitrogen fixation) were not seen until after diversification of the LPP, SPM and PNT clades, after 2.32 Ga. The appearance of these traits overlaps with a global carbon isotopic excursion between 2.2 and 2.1 Ga. Thus, a massive re-ordering of biogeochemical cycles caused by the appearance of complex laminated microbial communities in marine environments may have caused this excursion. Finally, we show that ASR may provide an explanation for why cyanobacterial microfossils have not been observed until after 2.0 Ga, and make suggestions for how future paleobiological searches for early cyanobacteria might proceed. In summary, key evolutionary events in the microbial world may have triggered some of the key geologic upheavals on the Paleoproterozoic Earth.,Blank&S-B2010.SSURpoCMesquite file containing phylogenetic trees and character matrix.Blank&S-B2010.SSULSUMesquite file containing phylogenetic tree and character matrix.

Data from: Global vegetation patterns of the past 140,000 years

Aim Insight into global biome responses to climatic and other environmental changes is essential to address key questions about past and future impacts of such changes. By simulating global biome patterns 140 ka to present we aimed to address important questions about biome changes during this interval. Location Global. Taxon Plantae. Methods Using the LPJ-GUESS dynamic global vegetation model, we made 89 simulations driven using ice-core atmospheric CO2 concentrations, Earth’s obliquity, and outputs from a pre-industrial and 88 palaeoclimate experiments run using HadCM3. Experiments were run for 81 time slices between 1 ka and 140 ka, seven ‘hosing’ experiments also being run, using a 1 Sv freshwater flux to the North Atlantic, for time slices corresponding to Heinrich Events H0 – H7. Using a rule-based approach, based on carbon mass and leaf area index of the LPJ-GUESS plant functional types, the biome was inferred for each grid cell. Biomes were mapped, and the extent and total vegetation biomass of each biome, and total global vegetation biomass, estimated. Results Substantial changes in biome extents and locations were found on all vegetated continents. Although the largest-magnitude changes were in Eurasia, important changes were seen in tropical latitudes and the Southern Hemisphere. Total global extent of most biomes varied on multi-millennial (orbital) time scales, although some (e.g. Tropical Raingreen Forest) responded principally to the ca. 100 kyr glacial–interglacial cycle and others (e.g. Temperate Broad-leaved Evergreen Forest) mainly to the ca. 20 kyr precession cycle. Many also responded to millennial contrasts between stadial (‘hosing’) and interstadial climates, with some (e.g. Tropical Evergreen Forest) showing stronger responses than to the multi-millennial changes. Main conclusions No two time slices had identical biome patterns. Even equivalent Holocene and last interglacial time slices, and the last and penultimate glacial maxima, showed important differences. Only a small proportion of global land area experienced no biome change since 140 ka; many places experienced multiple biome changes. These modelling experiments provided little evidence for long-term biome stability.,he CMass and LAI files are derived from outputs produced by LPJ-GUESS simulations. These simulations were driven using palaeoclimates derived from a series of GCM runs, along with the associated atmospheric carbon dioxide concentration and orbital obliquity. Full details and relevant citations are given in Allen et al. (2020). The LPJ-GUESS output files were opened (by JRMA) using Microsoft Excel, a header line added and, in the case of the CMass files, columns added giving the grid cell areas and ice-free land fractions, these being copied from the relevant columns of the Ice-free_land_fraction_89_time-slices file. A second worksheet was then added to the CMass files and values for grid cell CMass calculated from the LPJ-GUESS CMass per unit area values output and the product of the grid cell area and ice-free land fraction values. The second worksheet was then saved in comma-delimited (.csv) format. The Biome_assignments_V1.1_89_time-slices.csv file is derived from the primary output file generated by the FORTRAN program BiomiseLPJ_V1.1. This program was written by BH and the source code is provided in the Supplementary Information to Allen et al. (2020). The program output file was opened (by BH) using Microsoft Excel, a header line added, and the resulting worksheet saved in comma-delimited (.csv) format. The Biome_extents_V1.1_89_time-slices and PFT_CMass_by_biome_V1.1_89_time-slices are also derived from output files generated by BiomiseLPJ_V1.1. Minor editing was performed (by BH) using WordPad in order consistently to separate the blocks of data in the files and to ensure that all columns had labels in the header rows, thus rendering the files easier to open using software such as R. The primary data underlying the Ascii grid files are the ETOPO1 1-minute topography and bathymetry dataset, and the ICE-6G 1-degree ice fraction data files, both datasets being downloaded from their respective online locations. In addition, eustatic sea levels prior to 34 ka were estimated using a multiple regression model relating eustatic sea levels 0-34 ka to ocean delta-18O values and a relative sea-level curve, both of which are available extending back to 140 ka and beyond. Fractional ice cover for time slices prior to the Last Glacial Maximum (LGM) was taken to be that of the post-LGM time slice with the closest matching eustatic sea level. These various input sources were processed using FORTRAN programs written by BH for the purpose to generate the 6-minute datasets for land, ocean, ice cover and ice-fraction. Further details are provided in the readme_first.pdf file and in Appendix S2 of the Supplementary Information to Allen et al. (2020). The data in the Ice-free_land_fraction_89_time-slices file was generated from the 1-minute ETOPO1 topography and bathymetry dataset and the ICE-6G data using the same approach as was used for the 6-minute land and ice-fraction datasets, implemented in a FORTRAN program written by BH. In this case the file coverage is only those half-degree grid cells on the current land areas and shelf areas exposed at the LGM, whereas the 6-minute files extend over the entire global surface.,See Readme_first.pdf.

Projected climatic changes lead to biome changes in areas of previously constant biome

Aim: Recent studies in southern Africa identified past biome stability as an important predictor of biodiversity. We aimed to assess the extent to which past biome stability predicts present global biodiversity patterns, and the extent to which projected climatic changes may lead to eventual biome changes in areas with constant past biome. Location: Global. Taxon: Spermatophyta; terrestrial vertebrates. Methods: Biome constancy was assessed and mapped using results from 89 dynamic global vegetation model simulations, driven by outputs of palaeoclimate experiments spanning the past 140 ka. We tested the hypothesis that terrestrial vertebrate diversity is predicted by biome constancy. We also simulated potential future vegetation, and hence potential future biome patterns, and quantified and mapped the extent of projected eventual future biome change in areas of past constant biome. Results: Approximately 11% of global ice-free land had a constant biome since 140 ka. Aside from areas of constant Desert, many areas with constant biome support high species diversity. All terrestrial vertebrate groups show a strong positive relationship between biome constancy and vertebrate diversity in areas of greater diversity, but no relationship in less diverse areas. Climatic change projected by 2100 commits 46–66% of global ice-free land, and 34–52% of areas of past constant biome (excluding areas of constant Desert) to eventual biome change. Main conclusions: Past biome stability strongly predicts vertebrate diversity in areas of higher diversity. Future climatic changes will lead to biome changes in many areas of past constant biome, with profound implications for biodiversity conservation. Some projected biome changes will result in substantial reductions in biospheric carbon sequestration and other ecosystem services.,The CMass and LAI files are derived from outputs produced by LPJ-GUESS simulations. These simulations were driven using climates derived from a GCM run for pre-industrial conditions (000kDV_...) and four GCM runs driven by the changing greenhouse gas concentrations for 2050 (rcp4.55_... & rcp8.55_...) and 2100 (rcp4.57_... & rcp8.57_...) as defined by the RCP 4.5 and RCP 8.5 projections. Full details of the GCM and relevant citations are given in Huntley et al. (2021) and Allen et al. (2020). The LPJ-GUESS output files were opened (by JRMA) using Microsoft Excel, a header line added and, in the case of the CMass files, columns added giving the grid cell areas and ice-free land fractions, these being copied from the relevant columns of the Ice-free_land_fraction_89_time-slices file (see https://doi.org/10.5061/dryad.2fqz612mk for this file). A second worksheet was then added to the CMass files and values for grid cell CMass calculated from the LPJ-GUESS CMass per unit area values output and the product of the grid cell area and ice-free land fraction values. The second worksheet was then saved in comma-delimited (.csv) format. The Biome_assignments_V1.1_present_and_RCPs.csv file is derived from the primary output file generated by the FORTRAN program BiomiseLPJ_V1.1. This program was written by BH and the source code is provided in the Supplementary Information to Allen et al. (2020). The program output file was opened (by BH) using Microsoft Excel, a header line added, and the resulting worksheet saved in comma-delimited (.csv) format. The Biome_extents_V1.1_present_and_RCPs and PFT_CMass_by_biome_V1.1_present_and_RCPs are also derived from output files generated by BiomiseLPJ_V1.1. Minor editing was performed (by BH) using WordPad in order consistently to separate the blocks of data in the files and to ensure that all columns had labels in the header rows, thus rendering the files easier to open using software such as R. The Biome_constancies_89_time-slices_R1_with_0k_ice-free_areas.csv and Biome_counts_89_time-slices_R1_with_number_of_biomes.csv files were derived from the Biome_assignments_V1.1_89_time-slices.csv file (see https://doi.org/10.5061/dryad.2fqz612mk for this file) associated with the results reported by Allen et al. (2020). The latter file was processed using a FORTRAN program written by BH that calculates the % constancy of each biome for each grid cell, including in particular the % constancy of the biome inferred for the 'present', and also counts the number of biomes inferred for that grid cell across the 89 time slices. Output files generated by the program were processed using Excel (by BH) and saved in comma-delimited (.csv) format.,See Readme_first.pdf

Data from: Climatic drivers of latitudinal variation in Late Triassic tetrapod diversity

The latitudinal biodiversity gradient (LBG), the increase in biodiversity from the poles to the equator, is one of the most widely recognised global macroecological patterns, yet its deep time evolution and drivers remain uncertain. The Late Triassic (237–201 million years ago), a critical interval for the early evolution and radiation of modern tetrapod groups (e.g. crocodylomorphs, dinosaurs, mammaliamorphs), offers a unique opportunity to explore the palaeolatitudinal patterns of tetrapod diversity since it is extensively sampled spatially when compared with other pre-Cenozoic intervals, particularly at lower palaeolatitudes. Here, we explore palaeolatitudinal patterns of Late Triassic tetrapod diversity by applying sampling standardisation to comprehensive occurrence data from the Paleobiology Database. We then use palaeoclimatic model simulations to explore the palaeoclimatic ranges occupied by major tetrapod groups, allowing insight into the influence of palaeoclimate on the palaeolatitudinal distribution of these groups. Our results show that Late Triassic tetrapods generally do not conform to a modern-type LBG; instead, sampling-standardised species richness is highest at mid-palaeolatitudes. In contrast, the richness of pseudosuchians (crocodylians and their relatives) is highest at the palaeoequator, a pattern that is retained throughout their subsequent evolutionary history. Pseudosuchians generally occupied a more restricted range of palaeoclimatic conditions than other tetrapod groups, a condition analogous to modern day reptilian ectotherms, while avemetatarsalians (the archosaur group containing dinosaurs and pterosaurs) exhibit comparatively wider ranges, which is more similar to modern endotherms, such as birds and mammals, suggesting important implications for the evolution of thermal physiology in dinosaurs.,Supplementary material & data Additional figures and tables: Supplementary_material.pdf Data file: Late_Triassic_tetrapod_occurrences_cleaned.csv Code for 'cleaning' datasets downloaded from the Paleobiology Database such as the one used in this study (cleaning_code.R). This code and example datasets are also available at: github.com/emmadunne/pbdb_cleaning

Sr isotope-salinity modelling constraints on Quaternary Black Sea connectivity: Datasets and Supplementary Materials

Supplementary file 1: Contains Sr isotopic ratio of modern Black Sea water, its rivers, and Aral Sea, Sr isotopic ratio of biogenic carbonate collected from Black Sea surface sediment, record of Sr isotopic and dinoflagellate assemblages of DSDP Site 379. Supplementary file 2: Contains numerical box model setup and supplementary figures

Data from: Non-random latitudinal gradients in range size and niche breadth predicted by spatial patterns of climate

Aim. Tropical species are thought to experience and be adapted to narrow ranges of abiotic conditions. This idea has been invoked to explain a broad array of biological phenomena, including the latitudinal diversity gradient and differential rates of speciation and extinction. However, debate continues regarding the broad-scale applicability of this pattern and potential processes responsible. Here, we use a simulation approach to test two propositions: (1) strong geographic patterns of variation in realized niche breadth can arise in the absence of variance in the size of fundamental niches, and (2) realized niche breadths can show latitudinal patterns as a consequence of spatio-temporal climate change, even when fundamental niche breadths are unrelated to latitude, and dispersal abilities are held constant. Location. Global. Time period. Simulations were conducted using climate models from over the last 120 Ka, with trait dynamics captured at 95 Ka and present-day. Major taxa studied. We used virtual species with traits based loosely on plants. Methods. We simulated latitudinal trends of niche breadth and range size for virtual species using a cellular automaton algorithm that linked a gridded geographic domain with a three-dimensional environmental landscape. Results. In all simulations, strong spatial patterns in realized niches were obtained in the absence of niche evolution, and realized niches showed geographic patterns deriving only from real-world spatiotemporal variation in climate. We noted contrasting patterns of niche breadth in different environmental dimensions, with temperature breadth increasing with latitude, but precipitation breadth decreasing with latitude. Overall, simulation outcomes mimicked real-world pattern of latitudinal range extent covarying with amount of land area. Main conclusions. Tropical species can have narrower niche breadths for maximum and minimum temperature ranges compared to temperate species solely as the result of the spatial arrangement of environments. We therefore suggest that the complex spatiotemporal distribution of global abiotic environments has strong potential for structuring observed latitudinal gradients of niche breadths.,The data used in the paperdata_tables.zip

Data from: Coupling of palaeontological and neontological reef coral data improves forecasts of biodiversity responses under global climatic change

Reef corals are currently undergoing climatically-driven poleward range expansions, with some evidence for equatorial range retractions. Predicting their response to future climate scenarios is critical to their conservation, but ecological models are based only on short-term observations. The fossil record provides the only empirical evidence for the long-term response of organisms under perturbed climate states. The palaeontological record from the Last Interglacial (LIG; 125,000 years ago), a time of global warming, suggests that reef corals experienced poleward range shifts and an equatorial decline relative to their modern distribution. However, this record is spatiotemporally biased, and existing methods cannot account for data absence. Here, we use ecological niche modelling to estimate reef corals’ realised niche and LIG distribution, based on modern and fossil occurrences. We then make inferences about modelled habitability under two future climate change scenarios (RCP4.5, RCP8.5). Reef coral ranges during the LIG were comparable to the present, with no prominent equatorial decrease in habitability. Reef corals are likely to experience poleward range expansion and large equatorial declines under RCP4.5 and RCP8.5. However, this range expansion is likely optimistic in the face of anthropogenic climate change. Incorporation of fossil data in niche models improves forecasts of biodiversity responses under global climatic change.,Supplementary Material 1Occurrence data for modern and LIG reef corals, as well as the training data for ecological niche modelling. Training data is subsampled to 1.25° x 1.25° and clipped to cells with available environmental data.SM1.xlsxSupplementary Material 2Additional methods and resultsSM2.docxSupplementary Material 3Sum of cells within 5° latitudinal bins for all model classes, binary thresholds and climate scenarios.SM3.xlsx

Data supplement to: Plant proxy evidence for high rainfall and productivity in the eocene of Australia

During the early to middle Eocene, a mid-to-high latitudinal position and enhanced hydrological cycle in Australia would have contributed to a wetter and “greener” Australian continent where today arid to semi-arid climates dominate. Here, we revisit 12 Australian plant megafossil sites from the early to middle Eocene to generate temperature, precipitation and seasonality paleoclimate estimates, as well as net primary productivity (NPP) and vegetation type, based on paleobotanical proxies and compare to early Eocene global climate models. Temperature reconstructions are uniformly subtropical (mean annual, summer, and winter mean temperatures 19–21 °C, 25–27 °C and 14–16 °C, respectively). This indicates that southern Australia was ~5 °C warmer than today, despite a >20° poleward shift from its modern geographic location. Precipitation was less homogeneous than temperature, with mean annual precipitation of ~60 cm over inland sites and >100 cm over coastal sites. Precipitation may have been seasonal with the driest month receiving between 2–7× less precipitation as mean monthly precipitation. Proxy-model comparison is favorable with an 1680 ppm CO2 concentration. However, individual proxy reconstructions can disagree with models as well as with each other. In particular, seasonality reconstructions have systemic offsets. NPP estimates were up to 1000 gC m-2 yr-1 higher than modern, implying a more homogenously “green” Australian continent in the early to middle Eocene and larger carbon fluxes to and from the Australian biosphere. The most similar modern vegetation type is modern-day eastern Australian subtropical forest, although distance from coast and latitude may have led to vegetation heterogeneity

Data from: Early photosynthetic eukaryotes inhabited low-salinity habitats

The early evolutionary history of the chloroplast lineage remains an open question. It is widely accepted that the endosymbiosis that established the chloroplast lineage in eukaryotes can be traced back to a single event, in which a cyanobacterium was incorporated into a protistan host. It is still unclear, however, which Cyanobacteria are most closely related to the chloroplast, when the plastid lineage first evolved, and in what habitats this endosymbiotic event occurred. We present phylogenomic and molecular clock analyses, including data from cyanobacterial and chloroplast genomes using a Bayesian approach, with the aim of estimating the age for the primary endosymbiotic event, the ages of crown groups for photosynthetic eukaryotes, and the independent incorporation of a cyanobacterial endosymbiont by Paulinella. Our analyses include both broad taxon sampling (119 taxa) and 18 fossil calibrations across all Cyanobacteria and photosynthetic eukaryotes. Phylogenomic analyses support the hypothesis that the chloroplast lineage diverged from its closet relative Gloeomargarita, a basal cyanobacterial lineage, ∼2.1 billion y ago (Bya). Our analyses suggest that the Archaeplastida, consisting of glaucophytes, red algae, green algae, and land plants, share a common ancestor that lived ∼1.9 Bya. Whereas crown group Rhodophyta evolved in the Mesoproterozoic Era (1,600–1,000 Mya), crown groups Chlorophyta and Streptophyta began to radiate early in the Neoproterozoic (1,000–542 Mya). Stochastic mapping analyses indicate that the first endosymbiotic event occurred in low-salinity environments. Both red and green algae colonized marine environments early in their histories, with prasinophyte green phytoplankton diversifying 850–650 Mya.,Sanchez-Baracaldo_etal_2017_PNASAlignments for phylogenetic analyses of cyanobacteria and photosynthetic eukaryotes: 26 genes and 119 taxa; 49 cyanobacteria taxa including 136 proteins. Files to perform molecular clock analyses: code, calibration points, alignment including eight genes. Stochastic mapping: files and nexus file with character states for freshwater, marine and brackish.Sanchez-Baracaldo_etal_2017_Data.zip

Data for: Drivers of Holocene Palsa Distribution in North America

Dataset contains supplementary data for the article "Drivers of Holocene palsa distribution in North America" by Fewster et al. Specifically, Dataset S1 contains the catalogue of modern palsas and peat plateaus in North America used to fit our binary logistic regression model; Dataset S2 contains modern climate data extracted from the CRU TS 4.02 climatology for each grid cell in our study area and also presents the presence/absence of peat, the timing of deglaciation, peat initiation, and terrestrial drainage; Dataset S3 contains the palaeoclimate data extracted from equilibrium-type HadCM3 simulations and used to simulate past distributions of the climate envelope; Dataset S4 contains the peatland basal date catalogue used to constrain timings of peat initation in North America; and Dataset S5 contains the Spearman's Rank correlation matrix for each variable included in our final model