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Competition among species and entire clades can impact species diversification and extinction, which can shape macroevolutionary patterns. The fossil record shows successive biotic turnovers such that a dominant group is replaced by another. One striking example involves the decline of gymnosperms and the rapid diversification and ecological dominance of angiosperms in the Cretaceous. It is generally believed that angiosperms outcompeted gymnosperms, but the macroevolutionary processes and alternative drivers explaining this pattern remain elusive. Using extant time trees and vetted fossil occurrences for conifers, we tested the hypotheses that clade competition or climate change led to the decline of conifers at the expense of angiosperms. Here, we find that both fossil and molecular data show high congruence in revealing 1) low diversification rates, punctuated by speciation pulses, during warming events throughout the Phanerozoic and 2) that conifer extinction increased significantly in the Mid- Cretaceous (100 to 110 Ma) and remained high ever since. Their extinction rates are best explained by the rise of angiosperms, rejecting alternative models based on either climate change or time alone. Our results support the hypothesis of an active clade replacement, implying that direct competition with angiosperms increased the extinction of conifers by pushing their remaining species diversity and dominance out of the warm tropics. This study illustrates how entire branches on the Tree of Life may actively compete for ecological dominance under changing climates.

Sedimentary ancient DNA (sedaDNA) has been established as a viable biomolecular proxy for tracking taxon presence through time in a local environment, even in the total absence of surviving tissues. SedaDNA is thought to survive through mineral binding, facilitating long-term biomolecular preservation, but also challenging DNA isolation. Two common limitations in sedaDNA extraction are the carryover of other substances that inhibit enzymatic reactions, and the loss of authentic sedaDNA when attempting to reduce inhibitor co-elution. Here, we present a sedaDNA extraction procedure paired with targeted enrichment intended to maximize DNA recovery. Our procedure exhibits a 7.7–19.3x increase in on-target plant and animal sedaDNA compared to a commercial soil extraction kit, and a 1.2–59.9x increase compared to a metabarcoding approach. To illustrate the effectiveness of our cold spin extraction and PalaeoChip capture enrichment approach, we present results for the diachronic presence of plants and animals from Yukon permafrost samples dating to the Pleistocene-Holocene transition, and discuss new potential evidence for the late survival (~9700 years ago) of mammoth (Mammuthus sp.) and horse (Equus sp.) in the Klondike region of Yukon, Canada. This enrichment approach translates to a more taxonomically diverse dataset and improved on-target sequencing.

The oxygenation of Earth’s surface fundamentally altered global biogeochemical cycles and ultimately paved the way for the rise of metazoans at the end of the Proterozoic. However, current estimates for atmospheric oxygen (O₂) levels during the billion years leading up to this time vary widely. On the basis of chromium (Cr) isotope data from a suite of Proterozoic sediments from China, Australia, and North America, interpreted in the context of data from similar depositional environments from Phanerozoic time, we find evidence for inhibited oxidation of Cr at Earth’s surface in the mid-Proterozoic (1.8 to 0.8 billion years ago). These data suggest that atmospheric O₂ levels were at most 0.1% of present atmospheric levels. Direct evidence for such low O₂ concentrations in the Proterozoic helps explain the late emergence and diversification of metazoans.

Polar temperatures over the last several million years have, at times, been slightly warmer than today, yet global mean sea level has been 6–9 metres higher as recently as the Last Interglacial (130,000 to 115,000 years ago) and possibly higher during the Pliocene epoch (about three million years ago). In both cases the Antarctic ice sheet has been implicated as the primary contributor, hinting at its future vulnerability. Here we use a model coupling ice sheet and climate dynamics—including previously underappreciated processes linking atmospheric warming with hydrofracturing of buttressing ice shelves and structural collapse of marine-terminating ice cliffs—that is calibrated against Pliocene and Last Interglacial sea-level estimates and applied to future greenhouse gas emission scenarios. Antarctica has the potential to contribute more than a metre of sea-level rise by 2100 and more than 15 metres by 2500, if emissions continue unabated. In this case atmospheric warming will soon become the dominant driver of ice loss, but prolonged ocean warming will delay its recovery for thousands of years. Climate and ice-sheet modelling that includes ice fracture dynamics reveals that Antarctica could contribute more than a metre of sea-level rise by 2100 and more than 13 metres by 2500, if greenhouse gas emissions continue unabated. A 500-year model of Antarctica's contribution to future sea-level rise Robert DeConto and David Pollard use a newly improved numerical ice-sheet model calibrated to Pliocene and Last Interglacial sea-level estimates to develop projections of Antarctica's evolution over the next five centuries, driven by a range of greenhouse gas scenarios. The modelling shows that the Antarctic ice sheet has the potential to contribute between almost nothing, to contributing more than a metre of sea-level rise by 2100 and more than 15 metres by 2500. The startling high-end estimate arises from unabated emissions and previously underappreciated mechanisms: ice-fracturing by surface meltwater and collapse of large ice cliffs. The low end shows that a scenario of strong climate mitigation can radically reduce societal exposure to higher sea levels.

Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago 1 had climates resembling those forecasted under future warming 2 . Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11–19 °C above contemporary values 3 , 4 . The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare 5 . Here we report an ancient environmental DNA 6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA. Analysis of two-million-year-old ancient environmental DNA from the Kap København Formation in North Greenland shows there was an open boreal forest with diverse plant and animal species, of which several taxa have not previously been detected at the site, representing an ecosystem that has no present-day analogue.

A dated phylogeny and spatial distribution data for Chinese angiosperms show that eastern China has tended to act as a refugium for older taxa whereas western China has acted as a centre for their evolutionary diversification. A blossoming history of Chinese flora China is home to a vast range of flowering plants and has been seen as both a refuge for ancient lineages and a cradle for recent ones. Zhi-Duan Chen and colleagues examine the evolutionary history of Chinese flora and conclude that it is indeed both refuge and birthplace, but with a geographical twist. They find that 66% of Chinese flowering plant genera did not originate until the early Miocene (23 million years ago), but also uncover a distinct split between western and eastern China. Whereas lush, lowland eastern China tends to offer refuge for older genera, the rugged heights and harsh deserts of the west tend to be cradles for new evolutionary diversity. High species diversity may result from recent rapid speciation in a ‘cradle’ and/or the gradual accumulation and preservation of species over time in a ‘museum’ 1 , 2 . China harbours nearly 10% of angiosperm species worldwide and has long been considered as both a museum, owing to the presence of many species with hypothesized ancient origins 3 , 4 , and a cradle, as many lineages have originated as recent topographic changes and climatic shifts—such as the formation of the Qinghai–Tibetan Plateau and the development of the monsoon—provided new habitats that promoted remarkable radiation 5 . However, no detailed phylogenetic study has addressed when and how the major components of the Chinese angiosperm flora assembled to form the present-day vegetation. Here we investigate the spatio-temporal divergence patterns of the Chinese flora using a dated phylogeny of 92% of the angiosperm genera for the region, a nearly complete species-level tree comprising 26,978 species and detailed spatial distribution data. We found that 66% of the angiosperm genera in China did not originate until early in the Miocene epoch (23 million years ago (Mya)). The flora of eastern China bears a signature of older divergence (mean divergence times of 22.04–25.39 Mya), phylogenetic overdispersion (spatial co-occurrence of distant relatives) and higher phylogenetic diversity. In western China, the flora shows more recent divergence (mean divergence times of 15.29–18.86 Mya), pronounced phylogenetic clustering (co-occurrence of close relatives) and lower phylogenetic diversity. Analyses of species-level phylogenetic diversity using simulated branch lengths yielded results similar to genus-level patterns. Our analyses indicate that eastern China represents a floristic museum, and western China an evolutionary cradle, for herbaceous genera; eastern China has served as both a museum and a cradle for woody genera. These results identify areas of high species richness and phylogenetic diversity, and provide a foundation on which to build conservation efforts in China.

Paleogeographic reconstructions are important to understand Earth's tectonic evolution, past eustatic and regional sea level change, paleoclimate and ocean circulation, deep Earth resources and to constrain and interpret the dynamic topography predicted by mantle convection models. Global paleogeographic maps have been compiled and published, but they are generally presented as static maps with varying map projections, different time intervals represented by the maps and different plate motion models that underlie the paleogeographic reconstructions. This makes it difficult to convert the maps into a digital form and link them to alternative digital plate tectonic reconstructions. To address this limitation, we develop a workflow to restore global paleogeographic maps to their present-day coordinates and enable them to be linked to a different tectonic reconstruction. We use marine fossil collections from the Paleobiology Database to identify inconsistencies between their indicative paleoenvironments and published paleogeographic maps, and revise the locations of inferred paleo-coastlines that represent the estimated maximum transgression surfaces by resolving these inconsistencies. As a result, the consistency ratio between the paleogeography and the paleoenvironments indicated by the marine fossil collections is increased from an average of 75 % to nearly full consistency (100 %). The paleogeography in the main regions of North America, South America, Europe and Africa is significantly revised, especially in the Late Carboniferous, Middle Permian, Triassic, Jurassic, Late Cretaceous and most of the Cenozoic. The global flooded continental areas since the Early Devonian calculated from the revised paleogeography in this study are generally consistent with results derived from other paleoenvironment and paleo-lithofacies data and with the strontium isotope record in marine carbonates. We also estimate the terrestrial areal change over time associated with transferring reconstruction, filling gaps and modifying the paleogeographic geometries based on the paleobiology test. This indicates that the variation of the underlying plate reconstruction is the main factor that contributes to the terrestrial areal change, and the effect of revising paleogeographic geometries based on paleobiology is secondary.

During the late Miocene epoch, about seven million years ago, large areas of the continents experienced drying, enhanced seasonality, and a restructuring of terrestrial plant and animal communities. These changes are seen throughout the subtropics, but have typically been attributed to regional tectonic forcing. Here we present a set of globally distributed sea surface temperature records spanning the past 12 million years based on the alkenone unsaturation method. We find that a sustained late Miocene cooling occurred synchronously in both hemispheres, and culminated with ocean temperatures dipping to near-modern values between about 7 and 5.4 million years ago. The period of maximum cooling coincides with evidence for transient glaciations in the Northern Hemisphere and with a steepening of the pole-to-equator temperature gradient, as well. We thus infer that late Miocene aridity and terrestrial ecosystem changes occurred in a global context of increasing meridional temperature gradients. We conclude that a global forcing mechanism, such as the previously hypothesized decline in atmospheric CO 2 levels between eight and six million years ago, is required to explain the late Miocene changes in temperature, climate and ecosystems. A period of continental aridification and ecosystem change occurred about seven million years ago. A global sea surface temperature reconstruction identifies cooling temperatures and a strengthened meridional temperature gradient at this time.