Late paleozoic atmospheres and biotic evolution

The latter half of the Paleozoic era is marked by notable evolutionary advances, followed by the greatest of all mass extinctions and the subsequent establishment of Mesozoic‐Cenozoic faunas of very different aspect. Current models suggest marked changes in concentration of oxygen and carbon dioxide in the Paleozoic atmosphere. Atmospheric oxygen is thought to have increased from 15% in the mid‐Devonian to near 35% by the end of the Carboniferous, followed by a decline to 17% near the end of the Permian. Atmospheric carbon dioxide was near 0.5% in the early Paleozoic, declining to less than 0.3% in the Devonian, and then more steeply downward to a minimum near 0.04% at the end of the Carboniferous. The principal causes of these changes were the advent and expansion of land plants, deposition of carbonates and continental weathering. Notwithstanding quantitative uncertainties, it seems clear that a major pulse of high oxygen concentration and associated shifts in carbon dioxide characterized the late Paleozoic atmosphere. Atmospheres with such different compositions have markedly different physical characteristics. These changes have major implications for the physiologies of contemporary organisms. The fossil records of various taxa indicate dramatic changes in the biosphere that coincide in time with the inferred changes in composition of the atmosphere. Major changes in phenotype observed in numerous lineages of animals and plants, including accelerated radiations in fresh water and on the land, are inferred to have occurred in response to these changes in the atmosphere. The morphologies, physiologies, and inferred behavior of many organisms preserved in the fossil record are in good accord with expectations based on hyperoxic, low carbon dioxide conditions of the Carboniferous atmosphere and with a return to lower oxygen levels by the end of the Permian.     

Towards a structured approach to building qualitative reasoning models and simulations

Successful transfer and uptake of qualitative reasoning technology for modelling and simulation in a variety of domains has been hampered by the lack of a structured methodology to support formalisation of ideas. We present a framework that structures and supports the capture of conceptual knowledge about system behaviour using a qualitative reasoning approach. This framework defines a protocol for representing content that supports the development of a conceptual understanding of systems and how they behave. The framework supports modellers in two ways. First, it structures and explicates the work involved in building models. Second, it facilitates easier comparison and evaluation of intermediate and final results of modelling efforts. We show how this framework has been used in developing qualitative reasoning models about three case studies of sustainable development in different river systems.     

Morphological evolution in land plants: new designs with old genes

The colonization and radiation of multicellular plants on land that started over 470 Ma was one of the defining events in the history of this planet. For the first time, large amounts of primary productivity occurred on the continental surface, paving the way for the evolution of complex terrestrial ecosystems and altering global biogeochemical cycles; increased weathering of continental silicates and organic carbon burial resulted in a 90 per cent reduction in atmospheric carbon dioxide levels. The evolution of plants on land was itself characterized by a series of radical transformations of their body plans that included the formation of three-dimensional tissues, de novo evolution of a multicellular diploid sporophyte generation, evolution of multicellular meristems, and the development of specialized tissues and organ systems such as vasculature, roots, leaves, seeds and flowers. In this review, we discuss the evolution of the genes and developmental mechanisms that drove the explosion of plant morphologies on land. Recent studies indicate that many of the gene families which control development in extant plants were already present in the earliest land plants. This suggests that the evolution of novel morphologies was to a large degree driven by the reassembly and reuse of pre-existing genetic mechanisms.     

Carbon benefits from Forest Transitions promoting biomass expansions and thickening

The growth of the global terrestrial sink of carbon dioxide has puzzled scientists for decades. We propose that the role of land management practices—from intensive forestry to allowing passive afforestation of abandoned lands—have played a major role in the growth of the terrestrial carbon sink in the decades since the mid twentieth century. The Forest Transition, a historic transition from shrinking to expanding forests, and from sparser to denser forests, has seen an increase of biomass and carbon across large regions of the globe. We propose that the contribution of Forest Transitions to the terrestrial carbon sink has been underestimated. Because forest growth is slow and incremental, changes in the carbon density in forest biomass and soils often elude detection. Measurement technologies that rely on changes in two‐dimensional ground cover can miss changes in forest density. In contrast, changes from abrupt and total losses of biomass in land clearing, forest fires and clear cuts are easy to measure. Land management improves over time providing important present contributions and future potential to climate change mitigation. Appreciating the contributions of Forest Transitions to the sequestering of atmospheric carbon will enable its potential to aid in climate change mitigation.     

The influence of terrestrial ecosystems on climate

Terrestrial ecosystems influence climate by affecting how much solar energy is absorbed by the land surface and by exchanging climatically important gases with the atmosphere. Recent model analyses show widespread qualitative agreement that terrestrial ecological processes will have a net positive feedback effect on 21st-century global warming, and, therefore, cannot be ignored in climate-change projections. However, the quantitative uncertainty in the net feedback is large. The uncertainty in 21st-century carbon dioxide emissions resulting from terrestrial carbon cycle-climate feedbacks is second in magnitude only to the uncertainty in anthropogenic emissions. We estimate that this translates into an uncertainty in global warming owing to the land surface of 1.5 degrees C by 2100. We also emphasise the need to improve our understanding of terrestrial ecological processes that influence land-atmosphere interactions at relatively long timescales (decadal-century) as well as at shorter intervals (e.g. hourly).     

Green algae to land plants: An evolutionary transition

Studies focused upon the evolutionary transition from ancestral green algae to the earliest land plants are important from a range of ecological, molecular and evolutionary perspectives. A substantial suite of ultrastructural, biochemical and molecular data supports the concept that land plants (embryophytes) are monophyletically derived from an ancestral charophycean alga. However, the details of phylogenetic branching patterns linking extant charophytes and seedless embryophytes are currently unclear. Moreover, the fossil record has so far been mute regarding the algae-land plant transition. Nevertheless, an accurate reflection of major evolutionary events in the history of the earliest land plants can be obtained by comparative paleontological-neontological studies, and comparative molecular, cellular and developmental investigations of extant charophytes and bryophytes. This review focuses upon research progress toward understanding three clade-specific adaptations that were important in the successful colonization of land by plants: the histogenetic apical meristem, the matrotrophic embryo, and decay-resistant cell wall polymers.     

A horizontal gene transfer at the origin of phenylpropanoid metabolism: a key adaptation of plants to land

Background  

The pioneering ancestor of land plants that conquered terrestrial habitats around 500 million years ago had to face dramatic stresses including UV radiation, desiccation, and microbial attack. This drove a number of adaptations, among which the emergence of the phenylpropanoid pathway was crucial, leading to essential compounds such as flavonoids and lignin. However, the origin of this specific land plant secondary metabolism has not been clarified.     

A conceptual model for the development of Phytophthora disease in Quercus robur

Here, a conceptual model is presented for the development of Phytophthora disease in pedunculate oak. The model is presented using the causal loop diagram tool and gives an overview of how various abiotic and biotic factors, such as soil moisture, nutrient availability and mycorrhizal colonization, may affect the reproduction and the infective capacity of soil-borne Phytophthora species, the susceptibility of the host and subsequent disease development. It is suggested that the link between the root damage caused by Phytophthora species and overall tree vitality is in the assimilation and allocation of carbon within the plants. The potential impact of environmental factors on these processes is discussed. The model is presented with reference to scenarios related to variation in soil moisture and nutrient availability. The need for species-specific validation of the model and the implications of the model are discussed.     

Stay by thy neighbor? Social organization determines the efficiency of biodiversity markets with spatial incentives

Market-based conservation instruments, such as payments, auctions or tradable permits, are environmental policies that create financial incentives for landowners to engage in voluntary conservation on their land. But what if ecological processes operate across property boundaries and land use decisions on one property influence ecosystem functions on neighboring sites? This paper examines how to account for such spatial externalities when designing market-based conservation instruments. We use an agent-based model to analyze different spatial metrics and their implications on land use decisions in a dynamic cost environment. The model contains a number of alternative submodels which differ in incentive design and social interactions of agents, the latter including coordinating as well as cooperating behavior of agents. We find that incentive design and social interactions have a strong influence on the spatial allocation and the costs of the conservation market.     

A cognitive neuroscience framework for understanding causal reasoning and the law

Over the past couple of decades, there have been great developments in the fields of psychology and cognitive neuroscience that have allowed the advancement of our understanding of how people make judgements about causality in several domains. We provide a review of some of the contemporary psychological models of causal thinking that are directly relevant to legal reasoning. In addition, we cover some exciting new research using advanced neuroimaging techniques that have helped to uncover the underlying neural signatures of complex causal reasoning. Through the use of functional imaging, we provide a first-hand look at how the brain responds to evidence that is either consistent or inconsistent with one's beliefs and expectations. Based on the data covered in this review, we propose some ideas for how the effectiveness of causal reasoning, especially as it pertains to legal decision-making, may be facilitated.     

Predator effects on aquatic community assembly: disentangling the roles of habitat selection and post-colonization processes

Top predators are known to play an important role in the assembly of communities via two mechanisms: (1) by altering the colonization (or emigration) patterns of prey through behavioral habitat selection, and (2) by altering vital rates (e.g. mortality, birth) of prey after colonization. While both these mechanisms act to determine assembly, research has focused on either their combined overall effects (confounding them), or examined them singly. As a result, it remains unclear how these mechanisms act to sequentially shape community structure. In this study, we experimentally disentangle habitat selection and post‐colonization effects of predaceous fish to test their independent and combined influence on the assembly of insect and larval amphibian communities in experimental freshwater habitats. Specifically, we ask, ‘do the behavioral choices of colonists continue to structure aquatic communities even after post‐colonization processes have occurred?’ Like previous studies, we found that colonization was strongly reduced by the presence of fish cues. More importantly, these effects of fish on prey colonization behavior combined independently with post‐colonization processes to determine the overall effect of predators on community assembly. Although habitat selection and predation both reduced abundance and biomass of most taxa in the post‐colonization communities, these factors had qualitatively different effects on aspects of trophic structure. Habitat selection altered the ratio of secondary to primary consumer abundance and biomass, while post‐colonization predation drove strong trophic cascades not observed in response to habitat selection. Our results suggest that behavioral choices regarding habitat selection can have lasting and unique effects on the structure of aquatic communities.     

Thinking of biology: asteroid impacts, microbes, and the cooling of the atmosphere

The authors examine the cooling of the Earth's surface from 3.75 to 1 billion years ago. Three effects of the bombardment of Earth by asteroids and comets that may have delayed surface cooling include time to form continents, volatilization of carbonate rocks which released carbon dioxide into the atmosphere, and inability of microbes to inhabit land masses during large impact events. Continental microbes may have helped reduce high temperatures from 3.75 to 3.5 billion years ago. If so, the evolutionary sequence of microbes is proposed to be anaerobic heterotrophs, chemoautotrophs, and then photoautotrophs.     

Nitrogen-based symbioses,phosphorus availability,and accounting for a modern world more productive than the Paleozoic

Evolution of high-productivity angiosperms has been regarded as a driver of Mesozoic ecosystem restructuring. However, terrestrial productivity is limited by availability of rock-derived nutrients such as phosphorus for which permanent increases in weathering would violate mass balance requirements of the long-term carbon cycle. The potential reality of productivity increases sustained since the Mesozoic is supported here with documentation of a dramatic increase in the evolution of nitrogen-fixing or nitrogen-scavenging symbioses, including more than 100 lineages of ectomycorrhizal and lichen-forming fungi and plants with specialized microbial associations. Given this evidence of broadly increased nitrogen availability, we explore via carbon cycle modeling how enhanced phosphorus availability might be sustained without violating mass balance requirements. Volcanism is the dominant carbon input, dictating peaks in weathering outputs up to twice modern values. However, times of weathering rate suppression may be more important for setting system behavior, and the late Paleozoic was the only extended period over which rates are expected to have remained lower than modern. Modeling results are consistent with terrestrial organic matter deposition that accompanied Paleozoic vascular plant evolution having suppressed weathering fluxes by providing an alternative sink of atmospheric CO₂. Suppression would have then been progressively lifted as the crustal reservoir's holding capacity for terrestrial organic matter saturated back toward steady state with deposition of new organic matter balanced by erosion of older organic deposits. Although not an absolute increase, weathering fluxes returning to early Paleozoic conditions would represent a novel regime for the complex land biota that evolved in the interim. Volcanism-based peaks in Mesozoic weathering far surpass the modern rates that sustain a complex diversity of nitrogen-based symbioses; only in the late Paleozoic might these ecologies have been suppressed by significantly lower rates. Thus, angiosperms are posited to be another effect rather than proximal cause of Mesozoic upheaval.     

A Highly Social,Land‐Dwelling Fish Defends Territories in a Constantly Fluctuating Environment

The Pacific leaping blenny (Alticus arnoldorum) is a marine fish that has made a highly successful transition to land. We report an extensive field study on the behavior of this remarkable fish and how it has coped with life on land. The fish occurs in great abundance above the waterline along the rocky coastlines of Micronesia. We found them to be terrestrial in all aspects of their adult daily life, but heavily constrained by large fluctuations in both tide and temperature with almost all activity limited to a brief period at mid‐tide. Despite this, the fish were highly social and data were consistent with males defending exclusive territories on land. A variety of metrics – the use of visual displays, the allometry of ornaments, and sexual dimorphism – further imply sexual selection on both sexes was strong. Despite being restricted to an extremely narrow habitable zone in which conditions change constantly, the Pacific leaping blenny is remarkably adapted to life on land and rarely returned to water. The genus is unique among the living fishes in its degree of terrestriality and serves as a useful model of the constraints and adaptations that accompany major ecological transitions.     

The physics and ecology of mining carbon dioxide from the atmosphere by ecosystems

Reforesting and managing ecosystems have been proposed as ways to mitigate global warming and offset anthropogenic carbon emissions. The intent of our opinion piece is to provide a perspective on how well plants and ecosystems sequester carbon. The ability of individual plants and ecosystems to mine carbon dioxide from the atmosphere, as defined by rates and cumulative amounts, is limited by laws of physics and ecological principles. Consequently, the rates and amount of net carbon uptake are slow and low compared to the rates and amounts of carbon dioxide we release by fossil fuels combustion. Managing ecosystems to sequester carbon can also cause unintended consequences to arise. In this paper, we articulate a series of key take‐home points. First, the potential amount of carbon an ecosystem can assimilate on an annual basis scales with absorbed sunlight, which varies with latitude, leaf area index and available water. Second, efforts to improve photosynthesis will come with the cost of more respiration. Third, the rates and amount of net carbon uptake are relatively slow and low, compared to the rates and amounts and rates of carbon dioxide we release by fossil fuels combustion. Fourth, huge amounts of land area for ecosystems will be needed to be an effective carbon sink to mitigate anthropogenic carbon emissions. Fifth, the effectiveness of using this land as a carbon sink will depend on its ability to remain as a permanent carbon sink. Sixth, converting land to forests or wetlands may have unintended costs that warm the local climate, such as changing albedo, increasing surface roughness or releasing other greenhouse gases. We based our analysis on 1,163 site‐years of direct eddy covariance measurements of gross and net carbon fluxes from 155 sites across the globe.     

The influence of disturbance on driving carbon stocks and tree dynamics of riparian forests in Cerrado

Aims Riparian forests in the Brazilian Cerrado, also known as gallery forests, are very heterogeneous in structure, species composition and ecological features due to strong and abrupt variations of soil, hydrological and topographic properties. However, what are the variables driving forest carbon stock and productivity, mortality and recruitment in disturbed gallery forests?Methods We used 36 permanent plots data from a gallery forest in the Brazilian Cerrado. We investigated how tree community dynamics vary in a gallery forest on two contrasting disturbance levels—logged and non-logged—across a topographic gradient intrinsically related to differences in moisture conditions, edge effects, as well as soil fertility and texture.Important findings Soil variables were reduced into principal components and we used structural equation modelling to disentangle covarying variables. We also included carbon stocks as a determinant variable of dynamics rates. Logged forest had 50% higher productivity than non-logged forest and streamside forest had aboveground carbon stocks 70% higher than the forest edge. Both logging and natural disturbance drove variation in the carbon stocks which contributed to shaping productivity and recruitment rates. Distance from the river also drove mortality and carbon stock rates. Areas with high-carbon stocks favoured higher competition and lessened productivity and recruitment rates. Although soil fertility and texture are considered crucial components shaping forest dynamics, there was no clear influence of those variables on the present forest, probably because the strong effects of soil moisture, forest edge and disturbance disrupted the correlation between soil and forest dynamics.     

Extinction patterns in the avifauna of the Hawaiian islands

Through the continuing accumulation of fossil evidence, it is clear that the avifauna of the Hawaiian Islands underwent a large‐scale extinction event around the time of Polynesian arrival. A second wave of extinctions since European colonization has further altered this unique avifauna. Here I present the first systematic analysis of the factors characterizing the species that went extinct in each time period and those that survived in order to provide a clearer picture of the possible causal mechanisms. These analyses were based on mean body size, dietary and ecological information and phylogenetic lineage of all known indigenous, non‐migratory land and freshwater bird species of the five largest Hawaiian Islands. Extinct species were divided into ‘prehistoric’ and ‘historic’ extinction categories based on the timing of their last occurrence. A model of fossil preservation bias was also incorporated. I used regression trees to predict probability of prehistoric and historic extinction based on ecological variables. Prehistoric extinctions showed a strong bias toward larger body sizes and flightless, ground‐nesting species, even after accounting for preservation bias. Many small, specialized species, mostly granivores and frugivores, also disappeared, implicating a wide suite of human impacts including destruction of dry forest habitat. In contrast, the highest extinction rates in the historic period were in medium‐sized nectarivorous and insectivorous species. These differences result from different causal mechanisms underlying the two waves of extinction.     

The temperature dependence of the stimulation of photosynthesis by elevated carbon dioxide in wheat and barley

The temperature dependencies of the solubility of carbon dioxide and oxygen in water and the temperature dependency of the kinetic characteristics of the ribulose-1,5 bisphosphate carboxylase/oxygenase (Rubisco) enzyme result in the short-term stimulation of photosynthesis with a doubling of carbon dioxide from 350 to 700 mol mol^-1 usually decreasing from about 90% at 30C to about 25% at 10C at high photon flux. In field-grown wheat and barley, the expected values at 30°C were observed, but also values as high as 60% at 10°C. The much larger than expected stimulation at cool temperatures in these species also occurred in plants grown at 15°C, but not at 23°C in controlled environment chambers. Gas exchange analysis indicated that an unusually high diffusive limitation was not an explanation for the large response. Assessment of the apparent in vivo specificity of Rubisco by determining the carbon dioxide concentration at which carboxylation equalled carbon dioxide release from oxygenation, indicated that growth at low temperatures altered the apparent enzyme specificity in these species compared to these species grown at the warmer temperature. Inserting the observed specificities into a biochemical model of photosynthesis indicated that altered Rubisco specificity was consistent with the observed rates of assimilation. Whether altered apparent Rubisco specificity is caused by altered stoichiometry of photorespiration or an actual change in enzyme specificity, the results indicate that the temperature dependence of the stimulation of photosynthesis by elevated carbon dioxide may vary greatly with species and with prior exposure to low temperature.Keywords: Barley, carbon dioxide, photosynthesis, temperature, wheat.      

Stomatal conductance, photosynthesis and respiration of temperate deciduous tree seedlings grown outdoors at an elevated concentration of carbon dioxide

Seedlings of temperate deciduous tree species were grown outdoors at ambient and at an elevated concentration of carbon dioxide to examine how aspects of their gas exchange would be altered by growth at elevated carbon dioxide concentration. Leaf conductances to water vapour and net carbon dioxide exchange rates were determined periodically near midday. Whole-plant carbon dioxide efflux rates in darkness were also determined. The stomatal conductance of leaves of plants grown and measured at 700 cm³ m^?3 carbon dioxide did not differ from that of plants grown and measured at 350 cm³ m^?3 in Malus domestica, Quercus prinus and Quercus robur at any measurement time. In Acer saccharinum, lower conductances occurred for plants grown and measured at elevated carbon dioxide concentration only at measurement temperatures above 33°C. Photo-synthetic adjustment to elevated carbon dioxide concentration was evident only in Q. robur. All species examined had lower rates of dark respiration per unit of mass when grown and measured at elevated carbon dioxide concentration.     

Negative arterial-mixed expired PC02 gradient during acute and chronic hypercapnia.

In resting conscious dogs physiological dead space was calculated using the Bohr equation and measurements of arterial and mixed expired carbon dioxide tension. Whenever dogs inhaled carbon dioxide mixtures (5-10%) that had normal or low oxygen concentrations, the calculated dead space became negative. This paradox was based on the fact that the mixed expired carbon dioxide tension in resting hypercapnic dogs. Under these circumstances carbon dioxide was produced from the lung as measured by gas analyses and blood analyses. By the lung as measured by gas analyses and blood analyses. By reasoning this implies that "alveolar" carbon dioxide tension was higher than pulmonary venous carbon dioxide tension. The negative carbon dioxide gradient persisted at 14 days of chronic hypercapnia and reverted to normal within 10 min of breathing air after chronic hypercapnia. These findings suggest that the exchange of carbon dioxide in the lung cannot be explained solely on the basis of passive diffusion.