Environmental mutagenesis during the end-Permian ecological crisis

Repeated pulses of volcanism drove the end-Permian terrestrial crisis in northwest China

The Permo-Triassic mass extinction was linked to catastrophic environmental changes and large igneous province (LIP) volcanism. In addition to the widespread marine losses, the Permo-Triassic event was the most severe terrestrial ecological crisis in Earth's history and the only known mass extinction among insects, but the cause of extinction on land remains unclear. In this study, high-resolution Hg concentration records and multiple-archive S-isotope analyses of sediments from the Junggar Basin (China) provide evidence of repeated pulses of volcanic-S (acid rain) and increased Hg loading culminating in a crisis of terrestrial biota in the Junggar Basin coeval with the interval of LIP emplacement. Minor S-isotope analyses are, however, inconsistent with total ozone layer collapse. Our data suggest that LIP volcanism repeatedly stressed end-Permian terrestrial environments in the ~300 kyr preceding the marine extinction locally via S-driven acidification and deposition of Hg, and globally via pulsed addition of CO2.

The Possible Earliest Allopolyploidization in Tracheophytes Revealed by Phylotranscriptomics and Morphology of Selaginellaceae

Selaginellaceae, originated in the Carboniferous and survived the Permian-Triassic mass extinction, is the largest family of lycophyte, which is sister to other tracheophytes. It stands out from tracheophytes by exhibiting extraordinary habitat diversity and lacking polyploidization. The organelle genome-based phylogenies confirmed the monophyly of Selaginella, with six or seven subgenera grouped into two superclades, but the phylogenetic positions of the enigmatic Selaginella sanguinolenta clade remained problematic. Here, we conducted a phylogenomic study on Selaginellaceae utilizing large-scale nuclear gene data from RNA-seq to elucidate the phylogeny and explore the causes of the phylogenetic incongruence of the S. sanguinolenta clade. Our phylogenetic analyses resolved three different positions of the S. sanguinolenta clade, which were supported by the sorted three nuclear gene sets, respectively. The results from the gene flow test, species network inference, and plastome-based phylogeny congruently suggested a probable hybrid origin of the S. sanguinolenta clade involving each common ancestor of the two superclades in Selaginellaceae. The hybrid hypothesis is corroborated by the evidence from rhizophore morphology and spore micromorphology. The chromosome observation and Ks distributions further suggested hybridization accompanied by polyploidization. Divergence time estimation based on independent datasets from nuclear gene sets and plastid genome data congruently inferred that allopolyploidization occurred in the Early Triassic. To our best knowledge, the allopolyploidization in the Mesozoic reported here represents the earliest record of tracheophytes. Our study revealed a unique triad of phylogenetic positions for a hybrid-originated group with comprehensive evidence and proposed a hypothesis for retaining both parental alleles through gene conversion.

Climate-forced Hg-remobilization associated with fern mutagenesis in the aftermath of the end-Triassic extinction

The long-term effects of the Central Atlantic Magmatic Province, a large igneous province connected to the end-Triassic mass-extinction (201.5 Ma), remain largely elusive. Here, we document the persistence of volcanic-induced mercury (Hg) pollution and its effects on the biosphere for ~1.3 million years after the extinction event. In sediments recovered in Germany (Schandelah-1 core), we record not only high abundances of malformed fern spores at the Triassic-Jurassic boundary, but also during the lower Jurassic Hettangian, indicating repeated vegetation disturbance and stress that was eccentricity-forced. Crucially, these abundances correspond to increases in sedimentary Hg-concentrations. Hg-isotope ratios (δ202Hg, Δ199Hg) suggest a volcanic source of Hg-enrichment at the Triassic-Jurassic boundary but a terrestrial source for the early Jurassic peaks. We conclude that volcanically injected Hg across the extinction was repeatedly remobilized from coastal wetlands and hinterland areas during eccentricity-forced phases of severe hydrological upheaval and erosion, focusing Hg-pollution in the Central European Basin.

The terrestrial end-Permian mass extinction in the paleotropics postdates the marine extinction

The end-Permian mass extinction was the most severe ecological event during the Phanerozoic and has long been presumed contemporaneous across terrestrial and marine realms with global environmental deterioration triggered by the Siberian Traps Large Igneous Province. We present high-precision zircon U-Pb geochronology by the chemical abrasion-isotope dilution-thermal ionization mass spectrometry technique on tuffs from terrestrial to transitional coastal settings in Southwest China, which reveals a protracted collapse of the Cathaysian rainforest beginning after the onset of the end-Permian marine extinction. Integrated with high-resolution geochronology from coeval successions, our results suggest that the terrestrial extinction occurred diachronously with latitude, beginning at high latitudes during the late Changhsingian and progressing to the tropics by the early Induan, spanning a duration of nearly 1 million years. This latitudinal age gradient may have been related to variations in surface warming with more degraded environmental conditions at higher latitudes contributing to higher extinction rates.

The Cenomanian/Turonian boundary in light of new developments in terrestrial palynology

The Cenomanian/Turonian boundary interval is associated with an oceanic anoxic event (OAE 2,  94.0 Ma) during one of the warmest episodes in the Mesozoic. To date, plant responses to these climatic conditions are known only from the northern mid-latitudinal succession in Cassis, France. There, conifer-dominated and angiosperm-dominated vegetation types alternate. However, whether the exceptional environmental conditions had an impact on plant reproduction is unknown to date. We applied a new environmental proxy based on spore and pollen teratology on palynological samples from the Cassis succession, to explore if this phenomenon also occurs across the OAE 2. The observed frequencies of<1% malformed spores and pollen grains suggest that plant reproduction was not affected during the Cenomanian/Turonian boundary interval. While the effects of continental Large Igneous Province(s) on plant reproduction have shown to produce abnormal spore or pollen morphologies as evidence for severe environmental pollution, by contrast the effects of oceanic LIP(s) seems to be inconsequential.

Dying in the Sun: Direct evidence for elevated UV-B radiation at the end-Permian mass extinction

Land plants can adjust the concentration of protective ultraviolet B (UV-B)-absorbing compounds (UACs) in the outer wall of their reproductive propagules in response to ambient UV-B flux. To infer changes in UV-B radiation flux at Earth's surface during the end-Permian mass extinction, we analyze UAC abundances in ca. 800 pollen grains from an independently dated Permian-Triassic boundary section in Tibet. Our data reveal an excursion in UACs that coincide with a spike in mercury concentration and a negative carbon-isotope excursion in the latest Permian deposits, suggesting a close temporal link between large-scale volcanic eruptions, global carbon and mercury cycle perturbations, and ozone layer disruption. Because enhanced UV-B radiation can exacerbate the environmental deterioration induced by massive magmatism, ozone depletion is considered a compelling ecological driver for the terrestrial mass extinction.

The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution

The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.

The biogeochemical cycling of chlorine

Chlorine has important roles in the Earth's systems. In different forms, it helps balance the charge and osmotic potential of cells, provides energy for microorganisms, mobilizes metals in geologic fluids, alters the salinity of waters, and degrades atmospheric ozone. Despite this importance, there has not been a comprehensive summary of chlorine's geobiology. Here, we unite different areas of recent research to describe a biogeochemical cycle for chlorine. Chlorine enters the biosphere through volcanism and weathering of rocks and is sequestered by subduction and the formation of evaporite sediments from inland seas. In the biosphere, chlorine is converted between solid, dissolved, and gaseous states and in oxidation states ranging from -1 to +7, with the soluble, reduced chloride ion as its most common form. Living organisms and chemical reactions change chlorine's form through oxidation and reduction and the addition and removal of chlorine from organic molecules. Chlorine can be transported through the atmosphere, and the highest oxidation states of chlorine are produced by reactions between sunlight and trace chlorine gases. Partial oxidation of chlorine occurs across the biosphere and creates reactive chlorine species that contribute to the oxidative stress experienced by living cells. A unified view of this chlorine cycle demonstrates connections between chlorine biology, chemistry, and geology that affect life on the Earth.

Polyploidy: an evolutionary and ecological force in stressful times

Polyploidy has been hypothesized to be both an evolutionary dead-end and a source for evolutionary innovation and species diversification. Although polyploid organisms, especially plants, abound, the apparent nonrandom long-term establishment of genome duplications suggests a link with environmental conditions. Whole-genome duplications seem to correlate with periods of extinction or global change, while polyploids often thrive in harsh or disturbed environments. Evidence is also accumulating that biotic interactions, for instance, with pathogens or mutualists, affect polyploids differently than nonpolyploids. Here, we review recent findings and insights on the effect of both abiotic and biotic stress on polyploids versus nonpolyploids and propose that stress response in general is an important and even determining factor in the establishment and success of polyploidy.

Mercury spikes as evidence of extended arc-volcanism around the Devonian-Carboniferous boundary in the South Tian Shan (southern Uzbekistan)

Recently, the end-Devonian mass extinction (Hangenberg Crisis, 359 Ma) was identified as a first-order mass extinction, albeit not one of the “Big Five” events. Many marine and terrestrial organisms were affected by this crisis. The cause of this mass extinction is still conjectural and widely discussed. Here we report anomalously high mercury (Hg) concentrations from the South Tian Shan (Uzbekistan), together with correlation using conodont biostratigraphic data. Hg enrichment (to 5825 ppb) was detected in marine deposits encompassing the Hangenberg Crisis. In the Novchomok section, the Hangenberg Crisis interval does not contain typical Hangenberg Black Shales; however, by means of inorganic geochemistry (enrichment of redox-sensitive elements such as Mo, V, and U) we detected an equivalent level despite the lack of marked facies changes. This is the first record of Hg and Hg/total organic carbon anomalies in marly shales, marls and carbonates that are totally independent of facies changes, implying that volcanism was the most probable cause of the Hangenberg Crisis. This conclusion is confirmed by the presence of a negative δ¹³C excursion, which may reflect massive release of isotopically light carbon from volcanogenic and thermogenic devolatilization likely combined with increased arc-volcanism activity worldwide at the end of the Devonian.

Permo-Triassic boundary carbon and mercury cycling linked to terrestrial ecosystem collapse

Records suggest that the Permo-Triassic mass extinction (PTME) involved one of the most severe terrestrial ecosystem collapses of the Phanerozoic. However, it has proved difficult to constrain the extent of the primary productivity loss on land, hindering our understanding of the effects on global biogeochemistry. We build a new biogeochemical model that couples the global Hg and C cycles to evaluate the distinct terrestrial contribution to atmosphere-ocean biogeochemistry separated from coeval volcanic fluxes. We show that the large short-lived Hg spike, and nadirs in δ²⁰²Hg and δ¹³C values at the marine PTME are best explained by a sudden, massive pulse of terrestrial biomass oxidation, while volcanism remains an adequate explanation for the longer-term geochemical changes. Our modelling shows that a massive collapse of terrestrial ecosystems linked to volcanism-driven environmental change triggered significant biogeochemical changes, and cascaded organic matter, nutrients, Hg and other organically-bound species into the marine system.

UV-B radiation was the Devonian-Carboniferous boundary terrestrial extinction kill mechanism

There is an unexplained terrestrial mass extinction at the Devonian-Carboniferous boundary (359 million years ago). The discovery in east Greenland of malformed land plant spores demonstrates that the extinction was coincident with elevated UV-B radiation demonstrating ozone layer reduction. Mercury data through the extinction level prove that, unlike other mass extinctions, there were no planetary scale volcanic eruptions. Importantly, the Devonian-Carboniferous boundary terrestrial mass extinction was coincident with a major climatic warming that ended the intense final glacial cycle of the latest Devonian ice age. A mechanism for ozone layer reduction during rapid warming is increased convective transport of ClO. Hence, ozone loss during rapid warming is an inherent Earth system process with the unavoidable conclusion that we should be alert for such an eventuality in the future warming world.

Volcanic mercury and mutagenesis in land plants during the end-Triassic mass extinction

During the past 600 million years of Earth history, four of five major extinction events were synchronous with volcanism in large igneous provinces. Despite improved temporal frameworks for these events, the mechanisms causing extinctions remain unclear. Volcanic emissions of greenhouse gases, SO₂, and halocarbons are generally considered as major factors in the biotic crises, resulting in global warming, acid deposition, and ozone layer depletion. Here, we show that pulsed elevated concentrations of mercury in marine and terrestrial sediments across the Triassic-Jurassic boundary in southern Scandinavia and northern Germany correlate with intense volcanic activity in the Central Atlantic Magmatic Province. The increased levels of mercury-the most genotoxic element on Earth-also correlate with high occurrences of abnormal fern spores, indicating severe environmental stress and genetic disturbance in the parent plants. We conclude that this offers compelling evidence that emissions of toxic volcanogenic substances contributed to the end-Triassic biotic crisis.

Fossil pollen and spores as a tool for reconstructing ancient solar-ultraviolet irradiance received by plants: an assessment of prospects and challenges using proxy-system modelling

Ultraviolet-B radiation (UV-B, 280-315 nm) constitutes less than 1% of the total solar radiation that reaches the Earth's surface but has a disproportional impact on biological and ecological processes from the individual to the ecosystem level. Absorption of UV-B by ozone is also one of the primary heat sources to the stratosphere, so variations in UV-B have important relationships to the Earth's radiation budget. Yet despite its importance for understanding atmospheric and ecological processes, there is limited understanding about the changes in UV-B radiation in the geological past. This is because systematic measurements of total ozone and surface UV-B only exist since the 1970s, so biological or geochemical proxies from sediment archives are needed to reconstruct UV-B irradiance received at the Earth surface beyond the experimental record. Recent developments have shown that the quantification of UV-B-absorbing compounds in pollen and spores have the potential to provide a continuous record of the solar-ultraviolet radiation received by plants. There is increasing interest in developing this proxy in palaeoclimatic and palaeoecological research. However, differences in interpretation exist between palaeoecologists, who are beginning to apply the proxy under various geological settings, and UV-B ecologists, who question whether a causal dose-response relationship of pollen and spore chemistry to UV-B irradiance has really been established. Here, we use a proxy-system modelling approach to systematically assess components of the pollen- and spore-based UV-B-irradiance proxy to ask how these differences can be resolved. We identify key unknowns and uncertainties in making inferences about past UV-B irradiance, from the pollen sensor, the sedimentary archive, and through the laboratory and experimental procedures in order to target priority areas of future work. We argue that an interdisciplinary approach, modifying methods used by plant ecologists studying contemporary responses to solar-UV-B radiation specifically to suit the needs of palaeoecological analyses, provides a way forward in developing the most reliable reconstructions for the UV-B irradiance received by plants across a range of timescales.

Widespread ancient whole-genome duplications in Malpighiales coincide with Eocene global climatic upheaval

Whole-genome duplications (WGDs) are widespread and prevalent in vascular plants and frequently coincide with major episodes of global and climatic upheaval, including the mass extinction at the Cretaceous-Tertiary boundary (c. 65 Ma) and during more recent periods of global aridification in the Miocene (c. 10-5 Ma). Here, we explore WGDs in the diverse flowering plant clade Malpighiales. Using transcriptomes and complete genomes from 42 species, we applied a multipronged phylogenomic pipeline to identify, locate, and determine the age of WGDs in Malpighiales using three means of inference: distributions of synonymous substitutions per synonymous site (Ks ) among paralogs, phylogenomic (gene tree) reconciliation, and a likelihood-based gene-count method. We conservatively identify 22 ancient WGDs, widely distributed across Malpighiales subclades. Importantly, these events are clustered around the Eocene-Paleocene transition (c. 54 Ma), during which time the planet was warmer and wetter than any period in the Cenozoic. These results establish that the Eocene Climatic Optimum likely represents a previously unrecognized period of prolific WGDs in plants, and lends further support to the hypothesis that polyploidization promotes adaptation and enhances plant survival during episodes of global change, especially for tropical organisms like Malpighiales, which have tight thermal tolerances.

Linkages between stratospheric ozone, UV radiation and climate change and their implications for terrestrial ecosystems

Linkages between stratospheric ozone, UV radiation and climate change: terrestrial ecosystems.

Climate change and marine mass extinction

The end of the Permian Period was catastrophic for life in high-latitude regions

Why does the magnitude of genotype-by-environment interaction vary?

Genotype-by-environment interaction (G × E), that is, genetic variation in phenotypic plasticity, is a central concept in ecology and evolutionary biology. G×E has wide-ranging implications for trait development and for understanding how organisms will respond to environmental change. Although G × E has been extensively documented, its presence and magnitude vary dramatically across populations and traits. Despite this, we still know little about why G × E is so evident in some traits and populations, but minimal or absent in others. To encourage synthetic research in this area, we review diverse hypotheses for the underlying biological causes of variation in G × E. We extract common themes from these hypotheses to develop a more synthetic understanding of variation in G × E and suggest some important next steps.

UV-B-induced forest sterility: Implications of ozone shield failure in Earth's largest extinction

Although Siberian Trap volcanism is considered a primary driver of the largest extinction in Earth history, the end-Permian crisis, the relationship between these events remains unclear. However, malformations in fossilized gymnosperm pollen from the extinction interval suggest biological stress coinciding with pulsed forest decline. These grains are hypothesized to have been caused by enhanced ultraviolet-B (UV-B) irradiation from volcanism-induced ozone shield deterioration. We tested this proposed mechanism by observing the effects of inferred end-Permian UV-B regimes on pollen development and reproductive success in living conifers. We find that pollen malformation frequencies increase fivefold under high UV-B intensities. Surprisingly, all trees survived but were sterilized under enhanced UV-B. These results support the hypothesis that heightened UV-B stress could have contributed not only to pollen malformation production but also to deforestation during Permian-Triassic crisis intervals. By reducing the fertility of several widespread gymnosperm lineages, pulsed ozone shield weakening could have induced repeated terrestrial biosphere destabilization and food web collapse without exerting a direct "kill" mechanism on land plants or animals. These findings challenge the paradigm that mass extinctions require kill mechanisms and suggest that modern conifer forests may be considerably more vulnerable to anthropogenic ozone layer depletion than expected.

A tree of life based on ninety-eight expressed genes conserved across diverse eukaryotic species

Rapid advances in DNA sequencing technologies have resulted in the accumulation of large data sets in the public domain, facilitating comparative studies to provide novel insights into the evolution of life. Phylogenetic studies across the eukaryotic taxa have been reported but on the basis of a limited number of genes. Here we present a genome-wide analysis across different plant, fungal, protist, and animal species, with reference to the 36,002 expressed genes of the rice genome. Our analysis revealed 9831 genes unique to rice and 98 genes conserved across all 49 eukaryotic species analysed. The 98 genes conserved across diverse eukaryotes mostly exhibited binding and catalytic activities and shared common sequence motifs; and hence appeared to have a common origin. The 98 conserved genes belonged to 22 functional gene families including 26S protease, actin, ADP–ribosylation factor, ATP synthase, casein kinase, DEAD-box protein, DnaK, elongation factor 2, glyceraldehyde 3-phosphate, phosphatase 2A, ras-related protein, Ser/Thr protein phosphatase family protein, tubulin, ubiquitin and others. The consensus Bayesian eukaryotic tree of life developed in this study demonstrated widely separated clades of plants, fungi, and animals. Musa acuminata provided an evolutionary link between monocotyledons and dicotyledons, and Salpingoeca rosetta provided an evolutionary link between fungi and animals, which indicating that protozoan species are close relatives of fungi and animals. The divergence times for 1176 species pairs were estimated accurately by integrating fossil information with synonymous substitution rates in the comprehensive set of 98 genes. The present study provides valuable insight into the evolution of eukaryotes.

On transient climate change at the Cretaceous-Paleogene boundary due to atmospheric soot injections

Climate simulations that consider injection into the atmosphere of 15,000 Tg of soot, the amount estimated to be present at the Cretaceous-Paleogene boundary, produce what might have been one of the largest episodes of transient climate change in Earth history. The observed soot is believed to originate from global wildfires ignited after the impact of a 10-km-diameter asteroid on the Yucatán Peninsula 66 million y ago. Following injection into the atmosphere, the soot is heated by sunlight and lofted to great heights, resulting in a worldwide soot aerosol layer that lasts several years. As a result, little or no sunlight reaches the surface for over a year, such that photosynthesis is impossible and continents and oceans cool by as much as 28 °C and 11 °C, respectively. The absorption of light by the soot heats the upper atmosphere by hundreds of degrees. These high temperatures, together with a massive injection of water, which is a source of odd-hydrogen radicals, destroy the stratospheric ozone layer, such that Earth's surface receives high doses of UV radiation for about a year once the soot clears, five years after the impact. Temperatures remain above freezing in the oceans, coastal areas, and parts of the Tropics, but photosynthesis is severely inhibited for the first 1 y to 2 y, and freezing temperatures persist at middle latitudes for 3 y to 4 y. Refugia from these effects would have been very limited. The transient climate perturbation ends abruptly as the stratosphere cools and becomes supersaturated, causing rapid dehydration that removes all remaining soot via wet deposition.

The evolutionary significance of polyploidy

Polyploidy, or the duplication of entire genomes, has been observed in prokaryotic and eukaryotic organisms, and in somatic and germ cells. The consequences of polyploidization are complex and variable, and they differ greatly between systems (clonal or non-clonal) and species, but the process has often been considered to be an evolutionary 'dead end'. Here, we review the accumulating evidence that correlates polyploidization with environmental change or stress, and that has led to an increased recognition of its short-term adaptive potential. In addition, we discuss how, once polyploidy has been established, the unique retention profile of duplicated genes following whole-genome duplication might explain key longer-term evolutionary transitions and a general increase in biological complexity.

Pollen and spores as biological recorders of past ultraviolet irradiance

Solar ultraviolet (UV) irradiance is a key driver of climatic and biotic change. Ultraviolet irradiance modulates stratospheric warming and ozone production, and influences the biosphere from ecosystem-level processes through to the largest scale patterns of diversification and extinction. Yet our understanding of ultraviolet irradiance is limited because no method has been validated to reconstruct its flux over timescales relevant to climatic or biotic processes. Here, we show that a recently developed proxy for ultraviolet irradiance based on spore and pollen chemistry can be used over long (10⁵ years) timescales. Firstly we demonstrate that spatial variations in spore and pollen chemistry correlate with known latitudinal solar irradiance gradients. Using this relationship we provide a reconstruction of past changes in solar irradiance based on the pollen record from Lake Bosumtwi in Ghana. As anticipated, variations in the chemistry of grass pollen from the Lake Bosumtwi record show a link to multiple orbital precessional cycles (19–21 thousand years). By providing a unique, local proxy for broad spectrum solar irradiance, the chemical analysis of spores and pollen offers unprecedented opportunities to decouple solar variability, climate and vegetation change through geologic time and a new proxy with which to probe the Earth system.

Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta)

The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses. RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (Ks ) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome. Both Ks frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation. Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.

Severest crisis overlooked-Worst disruption of terrestrial environments postdates the Permian-Triassic mass extinction

Generally Early Triassic floras are believed to be depauperate, suffering from protracted recovery following the Permian–Triassic extinction event. Here we present palynological data of an expanded East Greenland section documenting recovered floras in the basal Triassic (Griesbachian) and a subsequent fundamental floral turnover, postdating the Permian–Triassic boundary extinction by about 500 kyrs. This event is marked by a swap in dominating floral elements, changing from gymnosperm pollen-dominated associations in the Griesbachian to lycopsid spore-dominated assemblages in the Dienerian. This turnover coincides with an extreme δ¹³C_org negative shift revealing a severe environmental crisis, probably induced by volcanic outbursts of the Siberian Traps, accompanied by a climatic turnover, changing from cool and dry in the Griesbachian to hot and humid in the Dienerian. Estimates of sedimentation rates suggest that this environmental alteration took place within some 1000 years. Similar, coeval changes documented on the North Indian Margin (Pakistan) and the Bowen Basin (Australia) indicate the global extent of this crisis. Our results evidence the first profound disruption of the recovery of terrestrial environments about 500kyrs after the Permian–Triassic extinction event. It was followed by another crisis, about 1myrs later thus, the Early Triassic can be characterised as a time of successive environmental crises.

Of dups and dinos: evolution at the K/Pg boundary

Fifteen years into sequencing entire plant genomes, more than 30 paleopolyploidy events could be mapped on the tree of flowering plants (and many more when also transcriptome data sets are considered). While some genome duplications are very old and have occurred early in the evolution of dicots and monocots, or even before, others are more recent and seem to have occurred independently in many different plant lineages. Strikingly, a majority of these duplications date somewhere between 55 and 75 million years ago (mya), and thus likely correlate with the K/Pg boundary. If true, this would suggest that plants that had their genome duplicated at that time, had an increased chance to survive the most recent mass extinction event, at 66mya, which wiped out a majority of plant and animal life, including all non-avian dinosaurs. Here, we review several processes, both neutral and adaptive, that might explain the establishment of polyploid plants, following the K/Pg mass extinction.

Polyploidy and genome evolution in plants

Plant genomes vary in size and complexity, fueled in part by processes of whole-genome duplication (WGD; polyploidy) and subsequent genome evolution. Despite repeated episodes of WGD throughout the evolutionary history of angiosperms in particular, the genomes are not uniformly large, and even plants with very small genomes carry the signatures of ancient duplication events. The processes governing the evolution of plant genomes following these ancient events are largely unknown. Here, we consider mechanisms of diploidization, evidence of genome reorganization in recently formed polyploid species, and macroevolutionary patterns of WGD in plant genomes and propose that the ongoing genomic changes observed in recent polyploids may illustrate the diploidization processes that result in ancient signatures of WGD over geological timescales.

Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution

Genome sequencing has demonstrated that besides frequent small-scale duplications, large-scale duplication events such as whole genome duplications (WGDs) are found on many branches of the evolutionary tree of life. Especially in the plant lineage, there is evidence for recurrent WGDs, and the ancestor of all angiosperms was in fact most likely a polyploid species. The number of WGDs found in sequenced plant genomes allows us to investigate questions about the roles of WGDs that were hitherto impossible to address. An intriguing observation is that many plant WGDs seem associated with periods of increased environmental stress and/or fluctuations, a trend that is evident for both present-day polyploids and palaeopolyploids formed around the Cretaceous–Palaeogene (K–Pg) extinction at 66 Ma. Here, we revisit the WGDs in plants that mark the K–Pg boundary, and discuss some specific examples of biological innovations and/or diversifications that may be linked to these WGDs. We review evidence for the processes that could have contributed to increased polyploid establishment at the K–Pg boundary, and discuss the implications on subsequent plant evolution in the Cenozoic.

Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary

Ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their attributed role remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates. Previously, based on dating WGDs in a limited number of plant species, we found a clustering of angiosperm paleopolyploidizations around the Cretaceous-Paleogene (K-Pg) extinction event about 66 million years ago. Here we revisit this finding, which has proven controversial, by combining genome sequence information for many more plant lineages and using more sophisticated analyses. We include 38 full genome sequences and three transcriptome assemblies in a Bayesian evolutionary analysis framework that incorporates uncorrelated relaxed clock methods and fossil uncertainty. In accordance with earlier findings, we demonstrate a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the K-Pg boundary. We interpret these results in the context of recent studies on invasive polyploid plant species, and suggest that polyploid establishment is promoted during times of environmental stress. We argue that considering the evolutionary potential of polyploids in light of the environmental and ecological conditions present around the time of polyploidization could mitigate the stark contrast in the proposed evolutionary fates of polyploids.

Cryptospores and cryptophytes reveal hidden diversity in early land floras

Cryptospores, recovered from Ordovician through Devonian rocks, differ from trilete spores in possessing distinctive configurations (i.e. hilate monads, dyads, and permanent tetrads). Their affinities are contentious, but knowledge of their relationships is essential to understanding the nature of the earliest land flora. This review brings together evidence about the source plants, mostly obtained from spores extracted from minute, fragmented, yet exceptionally anatomically preserved fossils. We coin the term 'cryptophytes' for plants that produced the cryptospores and show them to have been simple terrestrial organisms of short stature (i.e. millimetres high). Two lineages are currently recognized. Partitatheca shows a combination of characters (e.g. spo-rophyte bifurcation, stomata, and dyads) unknown in plants today. Lenticulatheca encompasses discoidal sporangia containing monads formed from dyads with ultrastructure closer to that of higher plants, as exemplified by Cooksonia. Other emerging groupings are less well characterized, and their precise affinities to living clades remain unclear. Some may be stem group embryophytes or tracheophytes. Others are more closely related to the bryophytes, but they are not bryophytes as defined by extant representatives. Cryptophytes encompass a pool of diversity from which modern bryophytes and vascular plants emerged, but were competitively replaced by early tracheophytes. Sporogenesis always produced either dyads or tetrads, indicating strict genetic control. The long-held consensus that tetrads were the archetypal condition in land plants is challenged.

Aberrant Classopollis pollen reveals evidence for unreduced (2n) pollen in the conifer family Cheirolepidiaceae during the Triassic-Jurassic transition

Polyploidy (or whole-genome doubling) is a key mechanism for plant speciation leading to new evolutionary lineages. Several lines of evidence show that most species among flowering plants had polyploidy ancestry, but it is virtually unknown for conifers. Here, we study variability in pollen tetrad morphology and the size of the conifer pollen type Classopollis extracted from sediments of the Triassic-Jurassic transition, 200 Ma. Classopollis producing Cheirolepidiaceae were one of the most dominant and diverse groups of conifers during the Mesozoic. We show that aberrant pollen Classopollis tetrads, triads and dyads, and the large variation in pollen size indicates the presence of unreduced (2n) pollen, which is one of the main mechanisms in modern polyploid formation. Polyploid speciation may explain the high variability of growth forms and adaptation of these conifers to different environments and their resistance to extreme growth conditions. We suggest that polyploidy may have also reduced the extinction risk of these conifers during the End-Triassic biotic crisis.

Quantification of UV-B flux through time using UV-B-absorbing compounds contained in fossil Pinus sporopollenin

UV-B radiation currently represents c. 1.5% of incoming solar radiation. However, significant changes are known to have occurred in the amount of incoming radiation both on recent and on geological timescales. Until now it has not been possible to reconstruct a detailed measure of UV-B radiation beyond c. 150 yr ago. Here, we studied the suitability of fossil Pinus spp. pollen to record variations in UV-B flux through time. In view of the large size of the grain and its long fossil history, we hypothesized that this grain could provide a good proxy for recording past variations in UV-B flux. Two key objectives were addressed: to determine whether there was, similar to other studied species, a clear relationship between UV-B-absorbing compounds in the sporopollenin of extant pollen and the magnitude of UV-B radiation to which it had been exposed; and to determine whether these compounds could be extracted from a small enough sample size of fossil pollen to make reconstruction of a continuous record through time a realistic prospect. Preliminary results indicate the excellent potential of this species for providing a quantitative record of UV-B through time. Using this technique, we present the first record of UV-B flux during the last 9500 yr from a site near Bergen, Norway.

Metabolomic and physiological responses reveal multi-phasic acclimation of Arabidopsis thaliana to chronic UV radiation

Biochemical changes in vivo and pathway interactions were investigated using integrated physiological and metabolic responses of Arabidopsis thaliana L. to ultraviolet (UV) radiation (280-400 nm) at 9.96 kJ m(-2) d(-1) over the entire life cycle from seed to seed (8 weeks). Columbia-0 (Col-0) and a UV-B sensitive accession (fah-1) showed significant (P < 0.001) reductions in leaf growth after 6 weeks. Col-0 recovered growth after 8 weeks, with recovery corresponding to a switch from production of phenylpropanoids to flavonoids. fah-1 failed to recover, indicating that sinapate production is an essential component of recovery. Epidermal features show that UV radiation caused significant (P < 0.001) increases in trichome density, which may act as a structural defence response. Stomatal indices showed a significant (P < 0.0001) reduction in Col-0 and a significant (P < 0.001) increase in fah-1. Epidermal cell density was significantly increased under UV radiation on the abaxial leaf surface, suggesting that that a fully functioning phenylpropanoid pathway is a requirement for cell expansion and leaf development. Despite wild-type acclimation, the costs of adaptation lead to reduced plant fitness by decreasing flower numbers and total seed biomass. A multi-phasic acclimation to UV radiation and the induction of specific metabolites link stress-induced biochemical responses to enhanced acclimation.

Selaginella and 400 million years of separation

Selaginella (spikemoss) is an enigma in the plant kingdom. Although a fascination to botanists at the turn of the twentieth century, members of this genus are unremarkable in appearance, never flower, and are of no agronomic value. However, members of this genus are relicts from ancient times, and one has to marvel at how this genus has survived virtually unchanged in appearance for hundreds of millions of years. In light of the recent completion of the Selaginella moellendorffii genome sequence, this review is intended to survey what is known about Selaginella, with a special emphasis on recent inquiries into its unique biology and importance in understanding the early evolution of vascular plants.

Genome size as a predictor of guard cell length in Arabidopsis thaliana is independent of environmental conditions

The recent discovery of a strong positive relationship between angiosperm genome size and stomatal guard cell length (GCL) opens the possibility of using plant fossil guard cell size as a proxy for changes in angiosperm genome size over periods of environmental change. The responses of GCL to environmental stimuli are currently unknown and may obscure this predictive relationship. Here, we investigated the effects of environmental variables (atmospheric CO2, drought, relative humidity, irradiance, ultraviolet radiation and pathogen attack) on GCL in the model plant Arabidopsis thaliana to quantify environmentally induced variation. GCL responded to all variables tested, but the changes incurred did not significantly impinge on the predictive capability of the relationship.

Mass extinction events and the plant fossil record

Five mass extinction events have punctuated the geological record of marine invertebrate life. They are characterized by faunal extinction rates and magnitudes that far exceed those observed elsewhere in the geological record. Despite compelling evidence that these extinction events were probably driven by dramatic global environmental change, they were originally thought to have little macroecological or evolutionary consequence for terrestrial plants. New high-resolution regional palaeoecological studies are beginning to challenge this orthodoxy, providing evidence for extensive ecological upheaval, high species-level turnover and recovery intervals lasting millions of years. The challenge ahead is to establish the geographical extent of the ecological upheaval, because reconstructing the vegetation dynamics associated with these events will elucidate the role of floral change in faunal mass extinction and provide a better understanding of how plants have historically responded to global environmental change similar to that anticipated for our future.

The stability of the stratospheric ozone layer during the end-Permian eruption of the Siberian Traps

The discovery of mutated palynomorphs in end-Permian rocks led to the hypothesis that the eruption of the Siberian Traps through older organic-rich sediments synthesized and released massive quantities of organohalogens, which caused widespread O3 depletion and allowed increased terrestrial incidence of harmful ultraviolet-B radiation (UV-B, 280-315nm; Visscher et al. 2004 Proc. Natl Acad. Sci. USA 101, 12952-12956). Here, we use an extended version of the Cambridge two-dimensional chemistry-transport model to evaluate quantitatively this possibility along with two other potential causes of O3 loss at this time: (i) direct effects of HCl release by the Siberian Traps and (ii) the indirect release of organohalogens from dispersed organic matter. According to our simulations, CH3Cl released from the heating of coals alone caused comparatively minor O3 depletion (5-20% maximum) because this mechanism fails to deliver sufficiently large amounts of Cl into the stratosphere. The unusual explosive nature of the Siberian Traps, combined with the direct release of large quantities of HCl, depleted the model O3 layer in the high northern latitudes by 33-55%, given a main eruptive phase of less than or equal to 200kyr. Nevertheless, O3 depletion was most extensive when HCl release from the Siberian Traps was combined with massive CH3Cl release synthesized from a large reservoir of dispersed organic matter in Siberian rocks. This suite of model experiments produced column O3 depletion of 70-85% and 55-80% in the high northern and southern latitudes, respectively, given eruption durations of 100-200kyr. On longer eruption time scales of 400-600kyr, corresponding O3 depletion was 30-40% and 20-30%, respectively. Calculated year-round increases in total near-surface biologically effective (BE) UV-B radiation following these reductions in O3 layer range from 30-60 (kJm(-2)d(-1))BE up to 50-100 (kJm(-2)d(-1))BE. These ranges of daily UV-B doses appear sufficient to exert mutagenic effects on plants, especially if sustained over tens of thousands of years, unlike either rising temperatures or SO2 concentrations.

Critical issues in trace gas biogeochemistry and global change

The atmospheric composition of trace gases and aerosols is determined by the emission of compounds from the marine and terrestrial biospheres, anthropogenic sources and their chemistry and deposition processes. Biogenic emissions depend upon physiological processes and climate, and the atmospheric chemistry is governed by climate and feedbacks involving greenhouse gases themselves. Understanding and predicting the biogeochemistry of trace gases in past, present and future climates therefore demands an interdisciplinary approach integrating across physiology, atmospheric chemistry, physics and meteorology. Here, we highlight critical issues raised by recent findings in all of these key areas to provide a framework for better understanding the past and possible future evolution of the atmosphere. Incorporating recent experimental and observational findings, especially the influence of CO2 on trace gas emissions from marine algae and terrestrial plants, into earth system models remains a major research priority. As we move towards this goal, archives of the concentration and isotopes of N2O and CH4 from polar ice cores extending back over 650,000 years will provide a valuable benchmark for evaluating such models. In the Pre-Quaternary, synthesis of theoretical modelling with geochemical and palaeontological evidence is also uncovering the roles played by trace gases in episodes of abrupt climatic warming and ozone depletion. Finally, observations and palaeorecords across a range of timescales allow assessment of the Earth's climate sensitivity, a metric influencing our ability to decide what constitutes 'dangerous' climate change.

Attempts to probe the ozone layer and the ultraviolet-B levels of the past

To get a proper perspective on the current status of atmospheric ozone, which protects the biosphere from ultraviolet-B (UV-B; 280-315 nm) radiation, it would be of value to know how ozone and UV-B radiation have varied in the past. The record of worldwide ozone monitoring goes back only a few decades, and the record of reliable UV-B measurements is even shorter. Here we review indirect methods to assess their status further back in time. These include variations in the Sun's emission and how these affect the atmosphere, changes in the Earth's orbit, geologic imprints of atmospheric ozone, effects of catastrophic events such as volcanic eruptions, biological proxies of UV-B radiation, the spectral signature of terrestrial ozone in old recordings of star spectra, and the modeling of UV-B irradiance from ozone data and meteorological recordings. Although reliable reconstructions do not yet extend far into the past, there is some hope for future progress.

Changes in biologically-active ultraviolet radiation reaching the Earth's surface

The Montreal Protocol is working. Concentrations of major ozone-depleting substances in the atmosphere are now decreasing, and the decline in total column amounts seen in the 1980s and 1990s at mid-latitudes has not continued. In polar regions, there is much greater natural variability. Each spring, large ozone holes continue to occur in Antarctica and less severe regions of depleted ozone continue to occur in the Arctic. There is evidence that some of these changes are driven by changes in atmospheric circulation rather than being solely attributable to reductions in ozone-depleting substances, which may indicate a linkage to climate change. Global ozone is still lower than in the 1970s and a return to that state is not expected for several decades. As changes in ozone impinge directly on UV radiation, elevated UV radiation due to reduced ozone is expected to continue over that period. Long-term changes in UV-B due to ozone depletion are difficult to verify through direct measurement, but there is strong evidence that UV-B irradiance increased over the period of ozone depletion. At unpolluted sites in the southern hemisphere, there is some evidence that UV-B irradiance has diminished since the late 1990s. The availability and temporal extent of UV data have improved, and we are now able to evaluate the changes in recent times compared with those estimated since the late 1920s, when ozone measurements first became available. The increases in UV-B irradiance over the latter part of the 20th century have been larger than the natural variability. There is increased evidence that aerosols have a larger effect on surface UV-B radiation than previously thought. At some sites in the Northern Hemisphere, UV-B irradiance may continue to increase because of continuing reductions in aerosol extinctions since the 1990s. Interactions between ozone depletion and climate change are complex and can be mediated through changes in chemistry, radiation, and atmospheric circulation patterns. The changes can be in both directions: ozone changes can affect climate, and climate change can affect ozone. The observational evidence suggests that stratospheric ozone (and therefore UV-B) has responded relatively quickly to changes in ozone-depleting substances, implying that climate interactions have not delayed this process. Model calculations predict that at mid-latitudes a return of ozone to pre-1980 levels is expected by the mid 21st century. However, it may take a decade or two longer in polar regions. Climate change can also affect UV radiation through changes in cloudiness and albedo, without involving ozone and since temperature changes over the 21st century are likely to be about 5 times greater than in the past century. This is likely to have significant effects on future cloud, aerosol and surface reflectivity. Consequently, unless strong mitigation measures are undertaken with respect to climate change, profound effects on the biosphere and on the solar UV radiation received at the Earth's surface can be anticipated. The future remains uncertain. Ozone is expected to increase slowly over the decades ahead, but it is not known whether ozone will return to higher levels, or lower levels, than those present prior to the onset of ozone depletion in the 1970s. There is even greater uncertainty about future UV radiation, since it will be additionally influenced by changes in aerosols and clouds.

Mass extinctions

Factors influencing the evolution of complex traits such as body size are notoriously difficult to study but a new review of work on marine iguanas in the Galapagos islands suggests an answer may lie in the interplay of natural and sexual selection.