Towards a 'natural' time scale for the Precambrian – A proposal

A proposal is put forward to redefine the geological time scale for the Precambrian. Flaws of the present, chronometrically defined, time scale are discussed and illustrated. It is concluded that we need to go back to the rock record to define a “natural” time scale, in which major divisions (eons, eras, etc.) are defined in terms of first-order events and transitions in the observable stratigraphic record. For the earliest part of Earth history, we need a time scale, including a formalized Hadean eon, that is fully consistent with rapidly evolving insights from planetary science.     

The Beothukis/Culmofrons problem and its bearing on Ediacaran macrofossil taxonomy: evidence from an exceptional new fossil locality

The late Ediacaran siliciclastic successions of eastern Newfoundland, Canada, are renowned for their fossils of soft‐bodied macro‐organisms, which may include some of the earliest animals. Despite the potential importance of such fossils for evolutionary understanding, the taxonomic framework within which Ediacaran macrofossils are described is not clearly defined. Rangeomorphs from a newly discovered fossil surface on the Bonavista Peninsula, Newfoundland, require us to reconsider contemporary use of morphological characters to distinguish between genera and species within Ediacaran taxa. The new surface exhibits remarkable preservational fidelity, resolving features smaller than 0.1 mm in dimension in both frondose and non‐frondose taxa. Such preservation permits the recognition of rarely observed fourth‐ and fifth‐order rangeomorph branching, offering unparalleled opportunities to investigate the fine‐scale construction of rangeomorph taxa including Culmofrons plumosa Laflamme et al., 2012. Our observations enable resolution of taxonomic issues relating to rangeomorphs, specifically overlap between the diagnoses of the frondose genera Beothukis Brasier and Antcliffe, 2009 and Culmofrons. We propose a taxonomic framework for all Ediacaran macrofossils whereby gross architecture, the presence/absence of discrete morphological characters and consideration of growth programme are used to distinguish genera, whereas morphometric or continuous characters define taxa at the species level. On the basis of its morphological characters, Culmofrons plumosa is herein synonymized to a species (Beothukis plumosa comb. nov.) within the genus Beothukis. This discussion emphasizes the need to standardize the taxonomic approach used to describe Ediacaran macrofossil taxa at both the genus and species levels, and raises important considerations for future formulation of higher‐level taxonomic groups.     

Elucidating Ernietta: new insights from exceptional specimens in the Ediacaran of Namibia

Exceptionally preserved specimens of Ernietta in a shallow‐marine gutter cast from southern Namibia reveal that all previously figured specimens of this iconic Ediacaran megafossil are incomplete, representing only the base of a larger and more complex organism. The complete organism is interpreted as comprising a buried, sand‐filled anchor exhibiting the classical Ernietta morphology that passes distally into a trunk that is crowned by two facing fans that extended into the overlying water column. All parts of Ernietta, from the base of its buried anchor to the tip of its fans, appear to have been composed of a palisade of tubular elements that have been variably preserved. Similarity of tubule morphology despite the inherent difference in function between these constructions supports the view that these tubes were integral to all anatomical parts and functions of Ernietta. This style of architecture, construction and function is unique to the Erniettomorpha, supporting the view that it represents an extinct Ediacaran clade in the early evolution of multi‐cellular life.     

The Ediacaran emergence of bilaterians: congruence between the genetic and the geological fossil records

Unravelling the timing of the metazoan radiation is crucial for elucidating the macroevolutionary processes associated with the Cambrian explosion. Because estimates of metazoan divergence times derived from molecular clocks range from quite shallow (Ediacaran) to very deep (Mesoproterozoic), it has been difficult to ascertain whether there is concordance or quite dramatic discordance between the genetic and geological fossil records. Here, we show using a range of molecular clock methods that the major pulse of metazoan divergence times was during the Ediacaran, which is consistent with a synoptic reading of the Ediacaran macrobiota. These estimates are robust to changes in priors, and are returned with or without the inclusion of a palaeontologically derived maximal calibration point. Therefore, the two historical records of life both suggest that although the cradle of Metazoa lies in the Cryogenian, and despite the explosion of ecology that occurs in the Cambrian, it is the emergence of bilaterian taxa in the Ediacaran that sets the tempo and mode of macroevolution for the remainder of geological time.     

Rates of evolution on the time scale of the evolutionary process

A generational time scale, involving change from one generation to the next, is the time scale of evolution by natural selection. Microevolutionary and macroevolutionary patterns reflect this process on longer time scales. Rates of evolution are most efficiently expressed in haldane units, H, in standard deviations per generation, indexed by the log of the time interval. Rates from replicated selection experiments and simulations have rate-interval [RI] and log rate-log interval [LRI] scaling relations enabling directional, stationary, and random time series to be distinguished. Empirical microevolutionary and macroevolutionary data exhibit stationary scaling, but point to generational rates of evolution (H ₀) conservatively on the order of 0.2 standard deviations per generation on the time scale of the evolutionary process. This paradox of long-term stationary scaling and short-term high rates of change can be explained by considering the shape of an heuristic time-form evolutionary lattice. Cenozoic mammals occupy a lattice that is about four orders of magnitude longer in time than it has ever been wide in form. The evolutionary process is dynamic but operates within relatively narrow morphological constraints compared to the time available for change.     

Ediacaran acanthomorphic acritarchs from the Outer Krol Belt,Lesser Himalaya,India: Their significance for global correlation

Large acanthomorphic acritarchs have been previously reported from the Ediacaran successions of the Pachmunda and Krol Hill synclines in the Outer Krol Belt of Lesser Himalaya, India. Thin sections of chert from Krol ‘A’ Formation in Khanog and Rajgarh synclines, Outer Krol Belt, record an equally well developed and diversified assemblage of Ediacaran large acanthomorphic acritarchs. This assemblage contains specimens belonging to seven genera and ten species, identified as: Appendisphaera fragilis, A. grandis, Asterocapsoides sp. A, Asterocapsoides sp. B, Cavaspina acuminata, C. basiconica, Eotylotopalla dactylos, Knollisphaeridium sp., Papillomembrana sp., and Weissiella cf. grandistella. It also contains five unnamed forms, viz. A, B, C, D, and E. The Krol acritarch assemblage shows a close resemblance with the Upper Doushantuo or Tanarium anozos–Tanarium conoideum assemblage of China. However, the absence of biostratigraphically important markers such as Tanarium anozos and T. conoideum from the Krol assemblage, so far, makes it difficult to establish a definite biostratigraphic correlation between the two assemblages. The current observations from this new locality provide additional data for regional and global biostratigraphic correlation, and significantly increase the purview of Ediacaran sequences for global biostratigraphic zonation.     

Divergence time of the two regional medaka populations in Japan as a new time scale for comparative genomics of vertebrates

The southern and northern Japanese populations of the medaka fish provide useful tools to gain insights into the comparative genomics and speciation of vertebrates, because they can breed to produce healthy and fertile offspring despite their highly divergent genetic backgrounds compared with those of human–chimpanzee. Comparative genomics analysis has suggested that such large genetic differences between the two populations are caused by higher molecular evolutionary rates among the medakas than those of the hominids. The argument, however, was based on the assumption that the two Japanese populations diverged approximately at the same time (4.0–4.7 Myr ago) as the human–chimpanzee lineage (5.0–6.0 Myr ago). This can be misleading, because the divergence time of the two populations was calculated based on estimated, extremely higher molecular evolutionary rates of other fishes with an implicit assumption of a global molecular clock. Here we show that our estimate, based on a Bayesian relaxed molecular-clock analysis of whole mitogenome sequences from 72 ray-finned fishes (including 14 medakas), is about four times older than that of the previous study (18 Myr). This remarkably older estimate can be reconciled with the vicariant events of the Japanese archipelago, and the resulting rates of molecular evolution are almost identical between the medaka and hominid lineages. Our results further highlight the fact that reproductive isolation may not evolve despite a long period of geographical isolation.     

On the dynamics of flying insects populations controlled by large scale information

We present a diffusion model adapted to an operational control of flying insects. The operational objective entails working with non-homogeneous regions and the corresponding non-uniform diffusion tensors. It the becomes necessary to study the problem of scale in order to justify the diffusion equation. We show that in typical cases, the spatial resolution must be coarser than 20 m and we have specified the appropriated time scales. We propose a method for computing the tensors at the given resolution, in relation to the landscape and the insects' species and a method for the numerical solution of the equations and present two applications.     

FoxO: a new addition to the ESC cartel

The forkhead box O (FoxO) family is involved in diverse cellular processes such as tumor suppression, stress response, and metabolism. In a recent Nature Cell Biology Letter, Zhang et?al. (2011) uncover a novel role for FoxO proteins in regulating the identity of human ESCs.     

Phosphorus in agricultural soils: drivers of its distribution at the global scale

Phosphorus (P) availability in soils limits crop yields in many regions of the World, while excess of soil P triggers aquatic eutrophication in other regions. Numerous processes drive the global spatial distribution of P in agricultural soils, but their relative roles remain unclear. Here, we combined several global data sets describing these drivers with a soil P dynamics model to simulate the distribution of P in agricultural soils and to assess the contributions of the different drivers at the global scale. We analysed both the labile inorganic P (P_ILAB), a proxy of the pool involved in plant nutrition and the total soil P (P_TOT). We found that the soil biogeochemical background corresponding to P inherited from natural soils at the conversion to agriculture (BIOG) and farming practices (FARM) were the main drivers of the spatial variability in cropland soil P content but that their contribution varied between P_TOT vs. P_ILAB. When the spatial variability was computed between grid cells at half‐degree resolution, we found that almost all of the P_TOT spatial variability could be explained by BIOG, while BIOG and FARM explained 38% and 63% of P_ILAB spatial variability, respectively. Our work also showed that the driver contribution was sensitive to the spatial scale characterizing the variability (grid cell vs. continent) and to the region of interest (global vs. tropics for instance). In particular, the heterogeneity of farming practices between continents was large enough to make FARM contribute to the variability in P_TOT at that scale. We thus demonstrated how the different drivers were combined to explain the global distribution of agricultural soil P. Our study is also a promising approach to investigate the potential effect of P as a limiting factor for agroecosystems at the global scale.     

Stochastic and deterministic processes interact in the assembly of desert microbial communities on a global scale

Extreme arid regions in the worlds'' major deserts are typified by quartz pavement terrain. Cryptic hypolithic communities colonize the ventral surface of quartz rocks and this habitat is characterized by a relative lack of environmental and trophic complexity. Combined with readily identifiable major environmental stressors this provides a tractable model system for determining the relative role of stochastic and deterministic drivers in community assembly. Through analyzing an original, worldwide data set of 16S rRNA-gene defined bacterial communities from the most extreme deserts on the Earth, we show that functional assemblages within the communities were subject to different assembly influences. Null models applied to the photosynthetic assemblage revealed that stochastic processes exerted most effect on the assemblage, although the level of community dissimilarity varied between continents in a manner not always consistent with neutral models. The heterotrophic assemblages displayed signatures of niche processes across four continents, whereas in other cases they conformed to neutral predictions. Importantly, for continents where neutrality was either rejected or accepted, assembly drivers differed between the two functional groups. This study demonstrates that multi-trophic microbial systems may not be fully described by a single set of niche or neutral assembly rules and that stochasticity is likely a major determinant of such systems, with significant variation in the influence of these determinants on a global scale.     

Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing

Atomistic simulations of protein folding have the potential to be a great complement to experimental studies, but have been severely limited by the time scales accessible with current computer hardware and algorithms. By employing a worldwide distributed computing network of tens of thousands of PCs and algorithms designed to efficiently utilize this new many-processor, highly heterogeneous, loosely coupled distributed computing paradigm, we have been able to simulate hundreds of microseconds of atomistic molecular dynamics. This has allowed us to directly simulate the folding mechanism and to accurately predict the folding rate of several fast-folding proteins and polymers, including a nonbiological helix, polypeptide alpha-helices, a beta-hairpin, and a three-helix bundle protein from the villin headpiece. Our results demonstrate that one can reach the time scales needed to simulate fast folding using distributed computing, and that potential sets used to describe interatomic interactions are sufficiently accurate to reach the folded state with experimentally validated rates, at least for small proteins.     

大尺度森林碳循环过程模拟模型综述

森林生态系统碳循环是全球陆地生态系统碳循环的重要组成部分,而碳循环模型已经成为研究森林碳循环的必要手段。森林碳循环模型可以分为统计模型和过程模型,其中过程模型以其完整的理论框架、严谨的结构分析和清晰的过程机理,逐渐占据了主导地位。从地球化学过程模型、陆面物理过程模型和生物过程模型等3个方面综述区域尺度到全球尺度(本文称为大尺度)森林碳循环过程模型研究进展,论述了各类模型的主要特征、优缺点以及应用现状,探讨了森林碳循环模拟研究中存在的问题,并讨论了森林碳循环过程模型的主流研究方向。可为不同空间尺度下森林生态系统碳循环模拟模型的选择提供参考,以及为森林碳循环研究提供借鉴。     

The Age of Angels: spiritualism and evolutionary progressionism in a nineteenth-century geologic time chart

The term ‘Anthropocene’ often carries apocalyptic overtones of environmental devastation, but many nineteenth-century iterations of the ‘Age of Humans’ idea were explicitly optimistic. The current time period was framed as a ‘Psychozoic Era’ or ‘Age of Mind’ in which human beings took their predetermined place at the pinnacle of ‘creation’. Hiram Alvin Reid, an amateur scientist in the midwestern United States, took this line of thinking a step further. He drafted a geologic time chart in which the current ‘Age of Man’ was succeeded by a future ‘Age of Angels’, wherein humans will become higher beings. Reid was a Christian spiritualist who thought that evolution drove both physical and spiritual advancement, including the recent development of a ‘sixth sense’ that allowed humans to perceive ghosts and angels. Reid’s views, while idiosyncratic and coloured by his metaphysical beliefs, drew heavily on mainstream concepts in biology and geology. Prominent geologists like James Dana and Joseph Le Conte argued for an Age of Mind in terms that mixed scientific rigor with religious and progressionist ideas. The Psychozoic was also embraced by many progressive-minded individuals outside the natural sciences, paralleling widespread modern interest in the Anthropocene.     

Impacts of biogenic CO2 emissions on human health and terrestrial ecosystems: the case of increased wood extraction for bioenergy production on a global scale

Biofuels are a potentially important source of energy for our society. Common practice in life cycle assessment (LCA) of bioenergy has been to assume that any carbon dioxide (CO₂) emission related to biomass combustion equals the amount absorbed in biomass, thus assuming no climate change impacts. Recent developments show the significance of contributions of biogenic CO₂ emissions during the time they stay in the atmosphere. The goal of this article is to develop a global, spatially explicit method to quantify the potential impact on human health and terrestrial ecosystems of biogenic carbon emissions coming from forest wood extraction for biofuel production. For this purpose, changes in aboveground carbon stock (ΔC_forest) due to an increase in wood extraction via changes in rotation time are simulated worldwide with a 0.5° × 0.5° grid resolution. Our results show that both impacts and benefits can be obtained. When the extraction increase is reached by creating a longer rotation time, new growth is allowed resulting in carbon benefits. In a case study, we assessed the life cycle impacts of heat production via wood to determine the significance of including biogenic CO₂ emissions due to changes in forest management. Impacts of biogenic CO₂ dominate the total climate change impacts from a wood stove. Depending on the wood source country, climate change impacts due to heat production from wood either have an important share in the overall impacts on human health and terrestrial ecosystems, or allow for a large additional CO₂ sink.