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A long-term record of global mean surface temperature (GMST) provides critical insight into the dynamical limits of Earth’s climate and the complex feedbacks between temperature and the broader Earth system. Here, we present PhanDA, a reconstruction of GMST over the past 485 million years, generated by statistically integrating proxy data with climate model simulations. PhanDA exhibits a large range of GMST, spanning 11° to 36°C. Partitioning the reconstruction into climate states indicates that more time was spent in warmer rather than colder climates and reveals consistent latitudinal temperature gradients within each state. There is a strong correlation between atmospheric carbon dioxide (CO₂) concentrations and GMST, identifying CO₂as the dominant control on variations in Phanerozoic global climate and suggesting an apparent Earth system sensitivity of ~8°C. 

Photorespiration can limit gross primary productivity in terrestrial plants. The rate of photorespiration relative to carbon fixation increases with temperature and decreases with atmospheric [CO₂]. However, the extent to which this rate varies in the environment is unclear. Here, we introduce a proxy for relative photorespiration rate based on the clumped isotopic composition of methoxyl groups (R–O–CH₃) in wood. Most methoxyl C–H bonds are formed either during photorespiration or the Calvin cycle and thus their isotopic composition may be sensitive to the mixing ratio of these pathways. In water-replete growing conditions, we find that the abundance of the clumped isotopologue¹³CH₂D correlates with temperature (18–28 °C) and atmospheric [CO₂] (280–1000 ppm), consistent with a common dependence on relative photorespiration rate. When applied to a global dataset of wood, we observe global trends of isotopic clumping with climate and water availability. Clumped isotopic compositions are similar across environments with temperatures below ~18 °C. Above ~18 °C, clumped isotopic compositions in water-limited and water-replete trees increasingly diverge. We propose that trees from hotter climates photorespire substantially more than trees from cooler climates. How increased photorespiration is managed depends on water availability: water-replete trees export more photorespiratory metabolites to lignin whereas water-limited trees either export fewer overall or direct more to other sinks that mitigate water stress. These disparate trends indicate contrasting responses of photorespiration rate (and thus gross primary productivity) to a future high-[CO₂] world. This work enables reconstructing photorespiration rates in the geologic past using fossil wood. 

Leaves are the most abundant and visible plant organ, both in the modern world and the fossil record. Identifying foliage to the correct plant family based on leaf architecture is a fundamental botanical skill that is also critical for isolated fossil leaves, which often, especially in the Cenozoic, represent extinct genera and species from extant families. Resources focused on leaf identification are remarkably scarce; however, the situation has improved due to the recent proliferation of digitized herbarium material, live-plant identification applications, and online collections of cleared and fossil leaf images. Nevertheless, the need remains for a specialized image dataset for comparative leaf architecture. We address this gap by assembling an open-access database of 30,252 images of vouchered leaf specimens vetted to family level, primarily of angiosperms, including 26,176 images of cleared and x-rayed leaves representing 354 families and 4,076 of fossil leaves from 48 families. The images maintain original resolution, have user-friendly filenames, and are vetted using APG and modern paleobotanical standards. The cleared and x-rayed leaves include the Jack A. Wolfe and Leo J. Hickey contributions to the National Cleared Leaf Collection and a collection of high-resolution scanned x-ray negatives, housed in the Division of Paleobotany, Department of Paleobiology, Smithsonian National Museum of Natural History, Washington D.C.; and the Daniel I. Axelrod Cleared Leaf Collection, housed at the University of California Museum of Paleontology, Berkeley. The fossil images include a sampling of Late Cretaceous to Eocene paleobotanical sites from the Western Hemisphere held at numerous institutions, especially from Florissant Fossil Beds National Monument (late Eocene, Colorado), as well as several other localities from the Late Cretaceous to Eocene of the Western USA and the early Paleogene of Colombia and southern Argentina. The dataset facilitates new research and education opportunities in paleobotany, comparative leaf architecture, systematics, and machine learning. 

While modern forests have their origin in the diversification and expansion of angiosperms in the late Cretaceous and early Cenozoic, it is unclear if the rise of closed-canopy tropical rainforests preceded or followed the end-Cretaceous extinction. The “canopy effect” is a strong vertical gradients in the carbon isotope (δ13C) composition of leaves in modern closed-canopy forests that could serve as a proxy signature for canopy structure in ancient forests. To test this, we report measurements of the carbon isotope composition of nearly 200 fossil angiosperm leaves from two localities in the Paleocene Cerrejón Formation and one locality in the Maastrichtian Guaduas Formation. Leaves from one Cerrejón fossil assemblage deposited in a small fluvial channel exhibited a 6.3‰ range in δ13C, consistent with a closed-canopy forest. Carbon isotope values from lacustrine sediments in the Cerrejón Fm. had a range of 3.3‰, consistent with vegetation along a lake edge. An even narrower range of δ13C values (2.7‰) was observed for a leaf assemblage recovered from the Cretaceous Guaduas Fm., and suggests vegetation with an open canopy structure. Carbon isotope fractionation by late Cretaceous and early Paleogene leaves was in all cases similar to modern relatives, consistent with estimates of low atmospheric CO2 during this time period. This study confirms other lines of evidence suggesting closed-canopy forests in tropical South America existed by the late Paleocene, and fails to find isotopic evidence for a closed-canopy forest in the Cretaceous. 

Leguminosae are one of the most diverse flowering-plant groups today, but the evolutionary history of the family remains obscure because of the scarce early fossil record, particularly from lowland tropics. Here, we report ~500 compression or impression specimens with distinctive legume features collected from the Cerrejón and Bogotá Formations, Middle to Late Paleocene of Colombia. The specimens were segregated into eight fruit and six leaf morphotypes. Two bipinnate leaf morphotypes are confidently placed in the Caesalpinioideae and are the earliest record of this subfamily. Two of the fruit morphotypes are placed in the Detarioideae and Dialioideae. All other fruit and leaf morphotypes show similarities with more than one subfamily or their affinities remain uncertain. The abundant fossil fruits and leaves described here show that Leguminosae was the most important component of the earliest rainforests in northern South America c. 60–58 million years ago. 

Summary Stomata regulate important physiological processes in plants and are often phenotyped by researchers in diverse fields of plant biology. Currently, there are no user‐friendly, fully automated methods to perform the task of identifying and counting stomata, and stomata density is generally estimated by manually counting stomata.We introduce StomataCounter, an automated stomata counting system using a deep convolutional neural network to identify stomata in a variety of different microscopic images. We use a human‐in‐the‐loop approach to train and refine a neural network on a taxonomically diverse collection of microscopic images.Our network achieves 98.1% identification accuracy onGinkgoscanning electron microscropy micrographs, and 94.2% transfer accuracy when tested on untrained species.To facilitate adoption of the method, we provide the method in a publicly available website athttp://www.stomata.science/.