A possible nitrogen crisis for Archaean life due to reduced nitrogen fixation by lightning.

Nitrogen is an essential element for life and is often the limiting nutrient for terrestrial ecosystems. As most nitrogen is locked in the kinetically stable form, N2, in the Earth's atmosphere, processes that can fix N2 into biologically available forms-such as nitrate and ammonia-control the supply of nitrogen for organisms. On the early Earth, nitrogen is thought to have been fixed abiotically, as nitric oxide formed during lightning discharge. The advent of biological nitrogen fixation suggests that at some point the demand for fixed nitrogen exceeded the supply from abiotic sources, but the timing and causes of the onset of biological nitrogen fixation remain unclear. Here we report an experimental simulation of nitrogen fixation by lightning over a range of Hadean (4.5-3.8 Gyr ago) and Archaean (3.8-2.5 Gyr ago) atmospheric compositions, from predominantly carbon dioxide to predominantly dinitrogen (but always without oxygen). We infer that, as atmospheric CO2 decreased over the Archaean period, the production of nitric oxide from lightning discharge decreased by two orders of magnitude until about 2.2 Gyr. After this time, the rise in oxygen (or methane) concentrations probably initiated other abiotic sources of nitrogen. Although the temporary reduction in nitric oxide production may have lasted for only 100 Myr or less, this was potentially long enough to cause an ecological crisis that triggered the development of biological nitrogen fixation.     

The medaka draft genome and insights into vertebrate genome evolution

Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.     

A complete insect from the Late Devonian period

After terrestrialization, the diversification of arthropods and vertebrates is thought to have occurred in two distinct phases, the first between the Silurian and the Frasnian stages (Late Devonian period) (425-385?million years (Myr) ago), and the second characterized by the emergence of numerous new major taxa, during the Late Carboniferous period (after 345?Myr ago). These two diversification periods bracket the depauperate vertebrate Romer's gap (360-345?Myr ago) and arthropod gap (385-325?Myr ago), which could be due to preservational artefact. Although a recent molecular dating has given an age of 390?Myr for the Holometabola, the record of hexapods during the Early-Middle Devonian (411.5-391?Myr ago, Pragian to Givetian stages) is exceptionally sparse and based on fragmentary remains, which hinders the timing of this diversification. Indeed, although Devonian Archaeognatha are problematic, the Pragian of Scotland has given some Collembola and the incomplete insect Rhyniognatha, with its diagnostic dicondylic, metapterygotan mandibles. The oldest, definitively winged insects are from the Serpukhovian stage (latest Early Carboniferous period). Here we report the first complete Late Devonian insect, which was probably a terrestrial species. Its 'orthopteroid' mandibles are of an omnivorous type, clearly not modified for a solely carnivorous diet. This discovery narrows the 45-Myr gap in the fossil record of Hexapoda, and demonstrates further a first Devonian phase of diversification for the Hexapoda, as in vertebrates, and suggests that the Pterygota diversified before and during Romer's gap.     

Model of carbon fixation in microbial mats from 3,500 Myr ago to the present

Biological carbon fixation is an important part of global carbon cycling and ecology. Fixation that took place 3,500 million years ago is recorded in the laminated sedimentary rock structures known as stromatolites, which are fossilized remains of microbial mat communities. Stromatolites are the most abundant type of fossil found in the Proterozoic (2,500 to 590 Myr ago), but they then declined, possibly because of predation and competition. Using modern microbial mats as analogues for ancient stromatolites, we show that the rate of carbon fixation is higher at the greater levels of atmospheric CO2 that were probably present in the past. We suggest that carbon fixation in microbial mats was not carbon-limited during the early Precambrian, but became carbon-limited as the supply of inorganic carbon decreased. Carbon limitation led to a lower rate of carbon fixation, especially towards the end of the Precambrian. Thus, another reason for the decline of the stromatolites could have been a decrease in available CO2.     

A receptor kinase gene regulating symbiotic nodule development

Leguminous plants are able to establish a nitrogen-fixing symbiosis with soil bacteria generally known as rhizobia. Metabolites exuded by the plant root activate the production of a rhizobial signal molecule, the Nod factor, which is essential for symbiotic nodule development. This lipo-chitooligosaccharide signal is active at femtomolar concentrations, and its structure is correlated with host specificity of symbiosis, suggesting the involvement of a cognate perception system in the plant host. Here we describe the cloning of a gene from Medicago sativa that is essential for Nod-factor perception in alfalfa, and by genetic analogy, in the related legumes Medicago truncatula and Pisum sativum. The identified 'nodulation receptor kinase', NORK, is predicted to function in the Nod-factor perception/transduction system (the NORK system) that initiates a signal cascade leading to nodulation. The family of 'NORK extracellular-sequence-like' (NSL) genes is broadly distributed in the plant kingdom, although their biological function has not been previously ascribed. We suggest that during the evolution of symbiosis an ancestral NSL system was co-opted for transduction of an external ligand, the rhizobial Nod factor, leading to development of the symbiotic root nodule.     

Using the fossil record to estimate the age of the last common ancestor of extant primates

Divergence times estimated from molecular data often considerably predate the earliest known fossil representatives of the groups studied. For the order Primates, molecular data calibrated with various external fossil dates uniformly suggest a mid-Cretaceous divergence from other placental mammals, some 90 million years (Myr) ago, whereas the oldest known fossil primates are from the basal Eocene epoch (54-55 Myr ago). The common ancestor of primates should be earlier than the oldest known fossils, but adequate quantification is needed to interpret possible discrepancies between molecular and palaeontological estimates. Here we present a new statistical method, based on an estimate of species preservation derived from a model of the diversification pattern, that suggests a Cretaceous last common ancestor of primates, approximately 81.5 Myr ago, close to the initial divergence time inferred from molecular data. It also suggests that no more than 7% of all primate species that have ever existed are known from fossils. The approach unites all the available palaeontological methods of timing evolutionary events: the fossil record, extant species and clade diversification models.     

The Cenozoic palaeoenvironment of the Arctic Ocean

The history of the Arctic Ocean during the Cenozoic era (0-65 million years ago) is largely unknown from direct evidence. Here we present a Cenozoic palaeoceanographic record constructed from >400 m of sediment core from a recent drilling expedition to the Lomonosov ridge in the Arctic Ocean. Our record shows a palaeoenvironmental transition from a warm 'greenhouse' world, during the late Palaeocene and early Eocene epochs, to a colder 'icehouse' world influenced by sea ice and icebergs from the middle Eocene epoch to the present. For the most recent approximately 14 Myr, we find sedimentation rates of 1-2 cm per thousand years, in stark contrast to the substantially lower rates proposed in earlier studies; this record of the Neogene reveals cooling of the Arctic that was synchronous with the expansion of Greenland ice (approximately 3.2 Myr ago) and East Antarctic ice (approximately 14 Myr ago). We find evidence for the first occurrence of ice-rafted debris in the middle Eocene epoch (approximately 45 Myr ago), some 35 Myr earlier than previously thought; fresh surface waters were present at approximately 49 Myr ago, before the onset of ice-rafted debris. Also, the temperatures of surface waters during the Palaeocene/Eocene thermal maximum (approximately 55 Myr ago) appear to have been substantially warmer than previously estimated. The revised timing of the earliest Arctic cooling events coincides with those from Antarctica, supporting arguments for bipolar symmetry in climate change.     

A euprimate skull from the early Eocene of China

The debut of undoubted euprimates (primates of modern aspect) was in the early Eocene, about 55 Myr ago. Since their first appearance, the earliest euprimates can be distinguished as Cantius, Donrussellia and Teilhardina. Nonetheless, the earliest euprimates are primarily known from isolated teeth or fragmentary jaws. Here we describe a partially preserved euprimate skull with nearly complete upper and lower dentition, which represents a new species of Teilhardina and constitutes the first discovery of the genus in Asia. The new species is from the upper section of Lingcha Formation, Hunan Province, China, with an estimated age of 54.97 Myr ago. Morphology and phylogeny analyses reveal that the new species is the most primitive species of Teilhardina, positioned near the root of euprimate radiation. This discovery of the earliest euprimate skull known to date casts new light on the debate concerning the adaptive origin of euprimates, and suggests that the last common ancestor of euprimates was probably a small, diurnal, visually oriented predator.     

A new species of great ape from the late Miocene epoch in Ethiopia

With the discovery of Ardipithecus, Orrorin and Sahelanthropus, our knowledge of hominid evolution before the emergence of Pliocene species of Australopithecus has significantly increased, extending the hominid fossil record back to at least 6 million years (Myr) ago. However, because of the dearth of fossil hominoid remains in sub-Saharan Africa spanning the period 12-7 Myr ago, nothing is known of the actual timing and mode of divergence of the African ape and hominid lineages. Most genomic-based studies suggest a late divergence date-5-6 Myr ago and 6-8 Myr ago for the human-chimp and human-gorilla splits, respectively-and some palaeontological and molecular analyses hypothesize a Eurasian origin of the African ape and hominid clade. We report here the discovery and recognition of a new species of great ape, Chororapithecus abyssinicus, from the 10-10.5-Myr-old deposits of the Chorora Formation at the southern margin of the Afar rift. To the best of our knowledge, these are the first fossils of a large-bodied Miocene ape from the African continent north of Kenya. They exhibit a gorilla-sized dentition that combines distinct shearing crests with thick enamel on its 'functional' side cusps. Visualization of the enamel-dentine junction by micro-computed tomography reveals shearing crest features that partly resemble the modern gorilla condition. These features represent genetically based structural modifications probably associated with an initial adaptation to a comparatively fibrous diet. The relatively flat cuspal enamel-dentine junction and thick enamel, however, suggest a concurrent adaptation to hard and/or abrasive food items. The combined evidence suggests that Chororapithecus may be a basal member of the gorilla clade, and that the latter exhibited some amount of adaptive and phyletic diversity at around 10-11 Myr ago.     

生物固氮的研究现状初探

初步探索了生物固氮目前的研究进展,并着重研究了豆科植物根毛与根瘤菌接触到最后形成成熟的可以固氮的根瘤组织的途径,为将来把非豆科植物,特别是禾谷类农作物转变为固氮植物的可行性提供参考。     

An asteroid breakup 160 Myr ago as the probable source of the K/T impactor

The terrestrial and lunar cratering rate is often assumed to have been nearly constant over the past 3 Gyr. Different lines of evidence, however, suggest that the impact flux from kilometre-sized bodies increased by at least a factor of two over the long-term average during the past approximately 100 Myr. Here we argue that this apparent surge was triggered by the catastrophic disruption of the parent body of the asteroid Baptistina, which we infer was a approximately 170-km-diameter body (carbonaceous-chondrite-like) that broke up 160(-20)+30Myr ago in the inner main asteroid belt. Fragments produced by the collision were slowly delivered by dynamical processes to orbits where they could strike the terrestrial planets. We find that this asteroid shower is the most likely source (>90 per cent probability) of the Chicxulub impactor that produced the Cretaceous/Tertiary (K/T) mass extinction event 65 Myr ago.     

Atmospheric carbon dioxide concentrations over the past 60 million years

Knowledge of the evolution of atmospheric carbon dioxide concentrations throughout the Earth's history is important for a reconstruction of the links between climate and radiative forcing of the Earth's surface temperatures. Although atmospheric carbon dioxide concentrations in the early Cenozoic era (about 60 Myr ago) are widely believed to have been higher than at present, there is disagreement regarding the exact carbon dioxide levels, the timing of the decline and the mechanisms that are most important for the control of CO2 concentrations over geological timescales. Here we use the boron-isotope ratios of ancient planktonic foraminifer shells to estimate the pH of surface-layer sea water throughout the past 60 million years, which can be used to reconstruct atmospheric CO2 concentrations. We estimate CO2 concentrations of more than 2,000 p.p.m. for the late Palaeocene and earliest Eocene periods (from about 60 to 52 Myr ago), and find an erratic decline between 55 and 40 Myr ago that may have been caused by reduced CO2 outgassing from ocean ridges, volcanoes and metamorphic belts and increased carbon burial. Since the early Miocene (about 24 Myr ago), atmospheric CO2 concentrations appear to have remained below 500 p.p.m. and were more stable than before, although transient intervals of CO2 reduction may have occurred during periods of rapid cooling approximately 15 and 3 Myr ago.     

Tracing the stepwise oxygenation of the Proterozoic ocean

Biogeochemical signatures preserved in ancient sedimentary rocks provide clues to the nature and timing of the oxygenation of the Earth's atmosphere. Geochemical data suggest that oxygenation proceeded in two broad steps near the beginning and end of the Proterozoic eon (2,500 to 542 million years ago). The oxidation state of the Proterozoic ocean between these two steps and the timing of deep-ocean oxygenation have important implications for the evolutionary course of life on Earth but remain poorly known. Here we present a new perspective on ocean oxygenation based on the authigenic accumulation of the redox-sensitive transition element molybdenum in sulphidic black shales. Accumulation of authigenic molybdenum from sea water is already seen in shales by 2,650 Myr ago; however, the small magnitudes of these enrichments reflect weak or transient sources of dissolved molybdenum before about 2,200 Myr ago, consistent with minimal oxidative weathering of the continents. Enrichments indicative of persistent and vigorous oxidative weathering appear in shales deposited at roughly 2,150 Myr ago, more than 200 million years after the initial rise in atmospheric oxygen. Subsequent expansion of sulphidic conditions after about 1,800 Myr ago (refs 8, 9) maintained a mid-Proterozoic molybdenum reservoir below 20 per cent of the modern inventory, which in turn may have acted as a nutrient feedback limiting the spatiotemporal distribution of euxinic (sulphidic) bottom waters and perhaps the evolutionary and ecological expansion of eukaryotic organisms. By 551 Myr ago, molybdenum contents reflect a greatly expanded oceanic reservoir due to oxygenation of the deep ocean and corresponding decrease in sulphidic conditions in the sediments and water column.     

Plant recognition of symbiotic bacteria requires two LysM receptor-like kinases

Although most higher plants establish a symbiosis with arbuscular mycorrhizal fungi, symbiotic nitrogen fixation with rhizobia is a salient feature of legumes. Despite this host range difference, mycorrhizal and rhizobial invasion shares a common plant-specified genetic programme controlling the early host interaction. One feature distinguishing legumes is their ability to perceive rhizobial-specific signal molecules. We describe here two LysM-type serine/threonine receptor kinase genes, NFR1 and NFR5, enabling the model legume Lotus japonicus to recognize its bacterial microsymbiont Mesorhizobium loti. The extracellular domains of the two transmembrane kinases resemble LysM domains of peptidoglycan- and chitin-binding proteins, suggesting that they may be involved directly in perception of the rhizobial lipochitin-oligosaccharide signal. We show that NFR1 and NFR5 are required for the earliest physiological and cellular responses to this lipochitin-oligosaccharide signal, and demonstrate their role in the mechanism establishing susceptibility of the legume root for bacterial infection.     

豆类植物共生固氮研究近况和展望

<正> 共生固氮作用对农林业生产具有重要的经济意义。近几十年来,人们从生物学、生态学、生理生化和遗传学等各方面对根瘤菌进行了更广泛的研究。虽然由于共生体系的复杂性,有关根瘤菌的许多问题还不十分清楚,特别是根瘤菌遗传学的研究还存在较大的困难,但由于分子遗传学的发展和新技术的采用,加速了这方面的研究工作。可以说,整个生物固氮作用的研究现在已处于一个令人非常振奋的阶段(Postgate,1974)。 本文除介绍豆类树种结瘤固氮的一般情况外,重点讨论有关根瘤菌固氮作用遗传学研究方面近年来进展较大的几个问题。到目前为止,利用根瘤菌作材料研究共生固氮作用的遗传及其调节已经进行了不少工作,70年代以来进展更为迅速。人们企图把固氮基因转入不固氮的高等植物,以扩大共生固氮作用的范围;同时对固氮作用进行有效的调控,以提高固氮效率,促进农林业生产的发展。我们相信这一目的是能够达到的。     

Oligocene mammals from Ethiopia and faunal exchange between Afro-Arabia and Eurasia

Afro-Arabian mammalian communities underwent a marked transition near the Oligocene/Miocene boundary at approximately 24 million years (Myr) ago. Although it is well documented that the endemic paenungulate taxa were replaced by migrants from the Northern Hemisphere, the timing and evolutionary dynamics of this transition have long been a mystery because faunas from about 32 to 24 Myr ago are largely unknown. Here we report a late Oligocene fossil assemblage from Ethiopia, which constrains the migration to postdate 27 Myr ago, and yields new insight into the indigenous faunal dynamics that preceded this event. The fauna is composed of large paenungulate herbivores and reveals not only which earlier taxa persisted into the late Oligocene epoch but also demonstrates that one group, the Proboscidea, underwent a marked diversification. When Eurasian immigrants entered Afro-Arabia, a pattern of winners and losers among the endemics emerged: less diverse taxa such as arsinoitheres became extinct, moderately species-rich groups such as hyracoids continued into the Miocene with reduced diversity, whereas the proboscideans successfully carried their adaptive radiation out of Afro-Arabia and across the world.     

Late Miocene decoupling of oceanic warmth and atmospheric carbon dioxide forcing

Deep-time palaeoclimate studies are vitally important for developing a complete understanding of climate responses to changes in the atmospheric carbon dioxide concentration (that is, the atmospheric partial pressure of CO(2), p(co(2))). Although past studies have explored these responses during portions of the Cenozoic era (the most recent 65.5 million years (Myr) of Earth history), comparatively little is known about the climate of the late Miocene (～12-5 Myr ago), an interval with p(co(2)) values of only 200-350?parts per million by volume but nearly ice-free conditions in the Northern Hemisphere and warmer-than-modern temperatures on the continents. Here we present quantitative geochemical sea surface temperature estimates from the Miocene mid-latitude North Pacific Ocean, and show that oceanic warmth persisted throughout the interval of low p(co(2)) ～12-5 Myr ago. We also present new stable isotope measurements from the western equatorial Pacific that, in conjunction with previously published data, reveal a long-term trend of thermocline shoaling in the equatorial Pacific since ～13?Myr ago. We propose that a relatively deep global thermocline, reductions in low-latitude gradients in sea surface temperature, and cloud and water vapour feedbacks may help to explain the warmth of the late Miocene. Additional shoaling of the thermocline after 5?Myr ago probably explains the stronger coupling between p(co(2)), sea surface temperatures and climate that is characteristic of the more recent Pliocene and Pleistocene epochs.     

Absolute plate motions and true polar wander in the absence of hotspot tracks

The motion of continents relative to the Earth's spin axis may be due either to rotation of the entire Earth relative to its spin axis--true polar wander--or to the motion of individual plates. In order to distinguish between these over the past 320 Myr (since the formation of the Pangaea supercontinent), we present here computations of the global average of continental motion and rotation through time in a palaeomagnetic reference frame. Two components are identified: a steady northward motion and, during certain time intervals, clockwise and anticlockwise rotations, interpreted as evidence for true polar wander. We find approximately 18 degrees anticlockwise rotation about 250-220 Myr ago and the same amount of clockwise rotation about 195-145 Myr ago. In both cases the rotation axis is located at about 10-20 degrees W, 0 degrees N, near the site that became the North American-South American-African triple junction at the break-up of Pangaea. This was followed by approximately 10 degrees clockwise rotation about 145-135 Myr ago, followed again by the same amount of anticlockwise rotation about 110-100 Myr ago, with a rotation axis in both cases approximately 25-50 degrees E in the reconstructed area of North Africa and Arabia. These rotation axes mark the maxima of the degree-two non-hydrostatic geoid during those time intervals, and the fact that the overall net rotation since 320 Myr ago is nearly zero is an indication of long-term stability of the degree-two geoid and related mantle structure. We propose a new reference frame, based on palaeomagnetism, but corrected for the true polar wander identified in this study, appropriate for relating surface to deep mantle processes from 320 Myr ago until hotspot tracks can be used (about 130 Myr ago).     

Sequence and analysis of rice chromosome 4

Rice is the principal food for over half of the population of the world. With its genome size of 430 megabase pairs (Mb), the cultivated rice species Oryza sativa is a model plant for genome research. Here we report the sequence analysis of chromosome 4 of O. sativa, one of the first two rice chromosomes to be sequenced completely. The finished sequence spans 34.6 Mb and represents 97.3% of the chromosome. In addition, we report the longest known sequence for a plant centromere, a completely sequenced contig of 1.16 Mb corresponding to the centromeric region of chromosome 4. We predict 4,658 protein coding genes and 70 transfer RNA genes. A total of 1,681 predicted genes match available unique rice expressed sequence tags. Transposable elements have a pronounced bias towards the euchromatic regions, indicating a close correlation of their distributions to genes along the chromosome. Comparative genome analysis between cultivated rice subspecies shows that there is an overall syntenic relationship between the chromosomes and divergence at the level of single-nucleotide polymorphisms and insertions and deletions. By contrast, there is little conservation in gene order between rice and Arabidopsis.