EVOLUTIONARY REDUCTION OF COMPLEX LIFE CYCLES: LOSS OF HOST-ALTERNATION IN PEMPHIGUS (HOMOPTERA: APHIDIDAE)

In a Utah canyon, the aphid, Pemphigus betae, exhibits two life cycles: a cycle involving host-alternation between cottonwood trees and roots of herbaceous plants and a secondarily reduced cycle, in which the cottonwood generations are eliminated so that wingless forms live year round on roots. Relative frequencies of the two life-cycle types vary along a 30-km stretch of the canyon, with the reduced cycle predominating at upper sites. Factors underlying this life-cycle variation were examined with common-garden and transfer experiments. Results showed 1) a facultative increase in production of alternating forms in response to crowding in root colonies, 2) a genetic component to both within- and between-site variation in tendency to produce alternating morphs, and 3) site-specific environmental effects on level of investment in the reduced versus alternating life cycles. Thus, the variation in frequency of life-cycle reduction in this aphid is dependent on a complex of interdependent factors. These include adaptive phenotypic plasticity, microgeographically variable cues affecting mechanisms of morph determination, and genetically based variation in tendency to show reduction versus alternation. Genetic variation between sites corresponds to microgeographic variation in success of life-cycle phases. Where cottonwood hosts are absent (lower elevations) or where the cottonwood phase has low survival (upper elevations), clones tend to produce fewer migrating morphs, as compared to clones from middle elevations, where the cottonwood phase is relatively favorable. Such independence between conditions in alternate phases is a general feature of complex life cycles and can generate strong site-specific selection for permanent life-cycle reduction. Such life-cycle shifts have sometimes been followed by extensive radiations in aphids and other groups.     

Life-cycle associations involving pairs of holococcolithophorid species: intraspecific variation or cryptic speciation?

New holococcolith-heterococcolith life-cycle associations are documented based on observations of combination coccospheres. Daktylethra pirus is shown to be a life-cycle phase of Syracosphaera pulchra and Syracolithus quadriperforatus a life-cycle phase of Calcidiscus leptoporus. In addition, new observations from cultures confirm the life-cycle associations of Crystallolithus braarudii with Coccolithus pelagicus and of Zygosphaera hellenica with Coronosphaera mediterranea. In all four cases previous work has shown that the heterococcolithophorid species is associated with another holococcolithophorid. Two other examples of a heterococcolithophorid being associated with two holococcolithophorids have previously been identified, so this seems to be a common phenomenon. The six examples are reviewed to determine whether a single underlying mechanism is likely to be responsible for all cases. It is concluded that there is no single mechanism but rather that the six examples fall into three categories: (a) in two cases the holococcolith types are probably simply ecophenotypic morphotypes; (b) in two other cases the holococcolith types are discrete and are paralleled by morphometric differences in the heterococcolith types; (c) in the final two cases the holococcolith types are discrete but are not paralleled by any obvious morphological variation in the heterococcolith morphology. We infer that cryptic speciation may be widespread in heterococcolithophorid phases and that study of holococcolithophorid phases can provide key data to elucidate this phenomenon.     

A method for the estimation of parameters for natural stage-structured populations

A relatively simple method is proposed for the estimation of parameters of stage-structured populations from sample data for situation where (a) unit time survival rates may vary with time, and (b) the distribution of entry times to stage 1 is too complicated to be fitted with a simple parametric model such as a normal or gamma distribution. The key aspects of this model are that the entry time distribution is approximated by an exponential function withp parameters, the unit time survival rates in stages are approximated by anr parameter exponential polynomial in the stage number, and the durations of stages are assumed to be the same for all individuals. The new method is applied to four Zooplankton data sets, with parametric bootstrapping used to assess the bias and variation in estimates. It is concluded that good estimates of demographic parameters from stagefrequency data from natural populations will usually only be possible if extra information such as the durations of stages is known.     

The estimation of recruitment from stage frequency data

Summary A general relationship is derived for the area of the sample curve for a given stage in the life-cycle, in terms of the mean survival rate and duration and the number entering the stage. The influence of recruitment, development and mortality patterns on the area of the sample curve is investigated. The results indicate a simple method of analysing stage frequency data to produce a best estimate of the number entering each stage. A test example, using simulated data, is provided with a discussion of the method in relation to other techniques based on the area of the sample curve.     

A Practical Method for Quantifying Eco-efficiency Using Eco-design Support Tools

Eco-efficiency at the product level is defined as product value per unit of environmental impact. In this paper we present a method for quantifying the eco-efficiency using quality function deployment (QFD) and life-cycle impact assessment (LCIA). These well-known tools are widely used in the manufacturing industry.
QFD, which is one of the methods used in product development based on consumer preferences, is introduced to calculate the product value. An index of the product value is calculated as the weighted average of improvement rates of quality characteristics. The importance of customer requirements, derived from the QFD matrix, is applied.
Environmental impacts throughout a product life cycle are calculated based on an LCIA method widely used in Japan. By applying the LCIA method of endpoint type, the endpoint damage caused by various life-cycle inventories is calculated. Willingness to pay is applied to integrate it into a single index.
Eco-design support tools, namely, the life-cycle planning (LCP) tool and the life-cycle assessment (LCA) tool, have already been developed. Using these tools, data required for calculation of the eco-efficiency of products can be collected. The product value is calculated based on QFD data stored in the LCP tool and the environmental impact is calculated using the LCA tool.
Case studies of eco-efficiency are adopted and the adequacy of this method is clarified. Several advantages of this method are characterized.     

Effects of temperature elevation on a field population of Acyrthosiphon svalbardicum (Hemiptera: Aphididae) on Spitsbergen

A manipulation experiment was carried out on a field population of the aphid Acyrthosiphon svalbardicum near Ny Ålesund, on the high arctic island of Spitsbergen, using cloches to raise temperature. An average rise in temperature of 2.8 deg. C over the summer season markedly advanced the phenology of both the host plant Dryas octopetala and the aphid. Advanced aphid phenology, with concomitant increases in reproductive output and survival, and successful completion of the life-cycle led to an eleven-fold increase in the number of overwintering eggs. Thermal budget requirements in day degrees above 0°C were calculated for key life-cycle stages of the aphid. Temperature data from Ny Ålesund over the past 23 years were used to calculate thermal budgets for the field site over the same period and these were compared with the requirements of the aphid. Each estimated thermal budget was then adjusted to simulate the effect of a +2, +4, and –2deg. C change in average temperature on aphid performance. This retrospective analysis (i) confirms that the life-cycle of A. svalbardicum is well suited to exploit higher summer temperatures, (ii) indicates that the annual success of local populations are sensitive to small changes in temperature and (iii) suggests that the aphid is living at the limits of its thermal range at Ny Ålesund based on its summer thermal budget requirements.     

Life-cycle assessment of continuous pad-dyeing technology for cotton fabrics

Purpose

China is the largest producer of textile-dyeing products in the world. The production of these materials consumes high amounts of water and energy and results in the discharge of huge amounts of pollutants. This study aimed at evaluating the life-cycle environmental impacts of the textile-dyeing industry and determining the key processes for mitigating life-cycle environmental impacts efficiently and effectively, which will benefit the application of cleaner production technologies.

Methods

A life-cycle assessment was performed according to the ISO 14040 standard series. The system investigated includes the dyeing process and final disposal and the transportation of raw material, energy production, and transportation. The functional unit is 10,000 m of cotton fabric, which weighs 2,000 kg. Our study encompasses three types of data. The data regarding the production process and the major raw materials, necessary energy, and the source of the energy, as well as the emissions of some pollutants, were provided by a textile-dyeing enterprise in Jiangsu Province. The data regarding transport were generated using the GaBi version 4.3 database. Some emission factor data such as those on CO₂, CH₄, and N₂O emissions were obtained from the literature. Resources, energy consumption, and emissions are quantified, and some of the potential environmental effects were evaluated using the CML2001 method built into the GaBi version 4.3 database.

Results and discussion

Scouring and oxygen bleaching, dyeing, stentering and setting, wastewater treatment, and incineration are the key processes in terms of global warming potential, acidification potential, photochemical ozone creation potential, and eutrophication potential. It will therefore be useful to enhance the recycling of water, control the consumption of additives and dyes, and conserve energy as much as possible. Through scenario analysis, we note that motorized shipment should be used instead of shipment by trucks, when conditions permit.

Conclusions

To promote energy conservation and the clean production of continuous pad-dyeing technology for cotton fabrics, other environmental impact categories besides the impact of the water system should be given focus. Additional work can be performed on the following: considering a consumption-based perspective of the entire process, uncertainty in data on life-cycle inventory, the evaluation methodology employed, temporal and spatial variation, the normalized toxicity of dyes and additives, and weighting methods.     

Extrapolation from Individual-Level Responses to Population Growth Rate Using Population Modeling

Ecological risk assessments of chemicals are often based on simple measurements of toxicity in individuals. However, the protection goals are often set at the population and community levels. Population models may be a useful tool to extrapolate from individual-level measurements to population-level endpoints. In the present study, the population growth rate (λ) was calculated for three sets of full life-cycle data (Tetranychus urticae exposed to agrimek, and Daphnia pulex exposed to spinosad and diazinon). The results were compared to λ from population models, where survival and/or reproduction were adjusted according to 4 d of data from the same life-cycle data. This was done to determine whether truncated demographic data can give results similar to that obtained with full life-cycle data. The resulting correlations were strong when both effects on survival and reproduction were included in the model (p < .001, 0.93 < R₂ < 1.00). There were also strong correlations in several cases when only effects on survival or reproduction were considered, although the total risk to the population tended to be underestimated. The results of the present study show that population models can be useful to extrapolate truncated data on the individual level to more ecologically relevant population-level endpoints.     

Genotype accounts for intraspecific variation in the timing and duration of multiple,sequential life-cycle events in a willow species

Premise

Phenological variation among individuals within populations is common and has a variety of ecological and evolutionary consequences, including forming the basis for population-level responses to environmental change. Although the timing of life-cycle events has genetic underpinnings, whether intraspecific variation in the duration of life-cycle events reflects genetic differences among individuals is poorly understood.

Methods

We used a common garden experiment with 10 genotypes of Salix hookeriana (coastal willow) from northern California, United States to investigate the extent to which genetic variation explains intraspecific variation in the timing and duration of multiple, sequential life-cycle events: flowering, leaf budbreak, leaf expansion, fruiting, and fall leaf coloration. We used seven clones of each genotype, for a total of 70 individual trees.

Results

Genotype affected each sequential life-cycle event independently and explained on average 62% of the variation in the timing and duration of vegetative and reproductive life-cycle events. All events were significantly heritable. A single genotype tended to be “early” or “late” across life-cycle events, but for event durations, there was no consistent response within genotypes.

Conclusions

This research demonstrates that genetic variation can be a major component underlying intraspecific variation in the timing and duration of life-cycle events. It is often assumed that the environment affects durations, but we show that genetic factors also play a role. Because the timing and duration of events are independent of one another, our results suggest that the effects of environmental change on one event will not necessarily cascade to subsequent events.     

Identifying the Genetic Variation of Gene Expression Using Gene Sets: Application of Novel Gene Set eQTL Approach to PharmGKB and KEGG

Genetic variation underlying the regulation of mRNA gene expression in humans may provide key insights into the molecular mechanisms of human traits and complex diseases. Current statistical methods to map genetic variation associated with mRNA gene expression have typically applied standard linkage and/or association methods; however, when genome-wide SNP and mRNA expression data are available performing all pair wise comparisons is computationally burdensome and may not provide optimal power to detect associations. Consideration of different approaches to account for the high dimensionality and multiple testing issues may provide increased efficiency and statistical power. Here we present a novel approach to model and test the association between genetic variation and mRNA gene expression levels in the context of gene sets (GSs) and pathways, referred to as gene set - expression quantitative trait loci analysis (GS-eQTL). The method uses GSs to initially group SNPs and mRNA expression, followed by the application of principal components analysis (PCA) to collapse the variation and reduce the dimensionality within the GSs. We applied GS-eQTL to assess the association between SNP and mRNA expression level data collected from a cell-based model system using PharmGKB and KEGG defined GSs. We observed a large number of significant GS-eQTL associations, in which the most significant associations arose between genetic variation and mRNA expression from the same GS. However, a number of associations involving genetic variation and mRNA expression from different GSs were also identified. Our proposed GS-eQTL method effectively addresses the multiple testing limitations in eQTL studies and provides biological context for SNP-expression associations.     

Environments and evolution: interactions between stress, resource inadequacy and energetic efficiency

Evolutionary change is interpreted in terms of the near-universal ecological scenario of stressful environments. Consequently, there is a premium on the energetically efficient exploitation of resources in a resource-inadequate world. Under this environmental model, fitness can be approximated to energetic efficiency especially towards the limits of survival. Furthermore, fitness at one stage of the life-cycle should correlate with fitness at other stages, especially for development time, survival and longevity; 'good genotypes' under stress should therefore be at a premium. Conservation in the wild depends primarily on adaptation to abiotically changing habitats since towards the limits of survival, genomic variation is rarely restrictive. The balance between energetic costs under variable environments and energy from resources provides a model for interpreting evolutionary stasis, punctuational and gradual change, and specialist diversification. Ultimately, a species should be in an equilibrium between the physiology of an organism and its adaptation to the environment. The primary key to understanding evolutionary change should therefore be ecological, highlighting energy availability in a stressed world; this approach is predictive for various patterns of evolutionary change in the living and fossil biota.     

Enhancing Life-Cycle Inventories via Reconciliation with the Laws of Thermodynamics

Abstract: Obtaining reliable results from life-cycle assessment studies is often quite difficult because life-cycle inventory (LCI) data are usually erroneous, incomplete, and even physically meaningless. The real data must satisfy the laws of thermodynamics, so the quality of LCI data may be enhanced by adjusting them to satisfy these laws. This is not a new idea, but a formal thermodynamically sound and statistically rigorous approach for accomplishing this task is not yet available. This article proposes such an approach based on methods for data rectification developed in process systems engineering. This approach exploits redundancy in the available data and models and solves a constrained optimization problem to remove random errors and estimate some missing values. The quality of the results and presence of gross errors are determined by statistical tests on the constraints and measurements. The accuracy of the rectified data is strongly dependent on the accuracy and completeness of the available models, which should capture information such as the life-cycle network, stream compositions, and reactions. Such models are often not provided in LCI databases, so the proposed approach tackles many new challenges that are not encountered in process data rectification. An iterative approach is developed that relies on increasingly detailed information about the life-cycle processes from the user. A comprehensive application of the method to the chlor-alkali inventory being compiled by the National Renewable Energy Laboratory demonstrates the benefits and challenges of this approach.     

Decision Analysis Utilizing Data from Multiple Life-Cycle Impact Assessment Methods Part I: A Theoretical Basis

Numerous methodologies for the life-cycle impact assessment (LCIA) step of life-cycle assessment (LCA) are currently in popular use. These methods, which are based on a single method or level of analysis, are limited to the environmental fates, impact categories, damage functions, and stressors included in the method or model. Because of this, it has been suggested within the LCA community that LCIA data from multiple methods and/or levels of analysis, that is, end-point and midpoint indicators, be used in LCA-based decision analysis to facilitate better or, at least more informed, decision making. In this (two-part) series of articles, we develop and present a series of LCA-based decision analysis models, based on multiattribute value theory (MAVT), which utilize data from multiple LCIA methods and/or levels of analysis. The key to accomplishing this is the recognition of what LCIA damage indicators represent with respect to decision analysis, namely, decision attributes and, in most cases, proxy attributes. The use of proxy attributes in a decision model, however, poses certain challenges, such as the assessment of decision-maker preferences for actual consequences that are only known imprecisely because of inherent limits of both LCA and scientific knowledge. In this article (part I), we provide a brief overview of MAVT and examine some of the decision-theoretic issues and implications of current LCIA methods. We illustrate the application of MAVT to develop a decision model utilizing damage indicators from a single LCIA methodology; and, we identify the decision-theoretic issues that arise when attempting to combine LCIA indicators from multiple methods and/or levels of analysis in a single decision model. Finally, we introduce the use in our methodology of constructed attributes to combine related end-point damage indicators into single decision attributes and the concept and evaluation of proxy attributes.     

Estimating the annual number of breeding attempts from breeding dates using mixture models

Well-established statistical methods exist to estimate variation in a number of key demographic rates from field data, including life-history transition probabilities and reproductive success per attempt. However, our understanding of the processes underlying population change remains incomplete without knowing the number of reproductive attempts individuals make annually; this is a key demographic rate for which we have no satisfactory method of estimating. Using census data to estimate this parameter from requires disaggregating the overlying temporal distributions of first and subsequent breeding attempts. We describe a Bayesian mixture method to estimate the annual number of reproductive attempts from field data to provide a new tool for demographic inference. We validate our method using comprehensive data on individually-marked song sparrows Melospiza melodia , and then apply it to more typical nest record data collected over 45 years on yellowhammers Emberiza citrinella . We illustrate the utility of our method by testing, and rejecting, the hypothesis that declines in UK yellowhammer populations have occurred concurrently with declines in annual breeding frequency.     

Integrated Multiple “-omics” Data Reveal Subtypes of Hepatocellular Carcinoma

Hepatocellular carcinoma is one of the most heterogeneous cancers, as reflected by its multiple grades and difficulty to subtype. In this study, we integrated copy number variation, DNA methylation, mRNA, and miRNA data with the developed “cluster of cluster” method and classified 256 HCC samples from TCGA (The Cancer Genome Atlas) into five major subgroups (S1-S5). We observed that this classification was associated with specific mutations and protein expression, and we detected that each subgroup had distinct molecular signatures. The subclasses were associated not only with survival but also with clinical observations. S1 was characterized by bulk amplification on 8q24, TP53 mutation, low lipid metabolism, highly expressed onco-proteins, attenuated tumor suppressor proteins and a worse survival rate. S2 and S3 were characterized by telomere hypomethylation and a low expression of TERT and DNMT1/3B. Compared to S2, S3 was associated with less copy number variation and some good prognosis biomarkers, including CRP and CYP2E1. In contrast, the mutation rate of CTNNB1 was higher in S3. S4 was associated with bulk amplification and various molecular characteristics at different biological levels. In summary, we classified the HCC samples into five subgroups using multiple “-omics” data. Each subgroup had a distinct survival rate and molecular signature, which may provide information about the pathogenesis of subtypes in HCC.     

Analysis of inbreeding depression in mixed-mating plants provides evidence for selective interference and stable mixed mating

Hermaphroditic individuals can produce both selfed and outcrossed progeny, termed mixed mating. General theory predicts that mixed-mating populations should evolve quickly toward high rates of selfing, driven by rapid purging of genetic load and loss of inbreeding depression (ID), but the substantial number of mixed-mating species observed in nature calls this prediction into question. Lower average ID reported for selfing than for outcrossing populations is consistent with purging and suggests that mixed-mating taxa in evolutionary transition will have intermediate ID. We compared the magnitude of ID from published estimates for highly selfing (r > 0.8), mixed-mating (0.2 ≤ r ≥ 0.8), and highly outcrossing (r < 0.2) plant populations across 58 species. We found that mixed-mating and outcrossing taxa have equally high average lifetime ID (δ= 0.58 and 0.54, respectively) and similar ID at each of four life-cycle stages. These results are not consistent with evolution toward selfing in most mixed-mating taxa. We suggest that prevention of purging by selective interference could explain stable mixed mating in many natural populations. We identify critical gaps in the empirical data on ID and outline key approaches to filling them.     

Product Environmental Life-Cycle Assessment Using Input-Output Techniques

Life-cycle assessment (LCA) facilitates a systems view in environmental evaluation of products, materials, and processes. Life-cycle assessment attempts to quantify environmental burdens over the entire life-cycle of a product from raw material extraction, manufacturing, and use to ultimate disposal. However, current methods for LCA suffer from problems of subjective boundary definition, inflexibility, high cost, data confidentiality, and aggregation.
This paper proposes alternative models to conduct quick, cost effective, and yet comprehensive life-cycle assessments. The core of the analytical model consists of the 498 sector economic input-output tables for the U.S. economy augmented with various sector-level environmental impact vectors. The environmental impacts covered include global warming, acidification, energy use, non-renewable ores consumption, eutrophication, conventional pollutant emissions and toxic releases to the environment. Alternative models are proposed for environmental assessment of individual products, processes, and life-cycle stages by selective disaggregation of aggregate input-output data or by creation of hypothetical new commodity sectors. To demonstrate the method, a case study comparing the life-cycle environmental performance of steel and plastic automobile fuel tank systems is presented.     

Latitudinal variation in life-cycle characteristics of Potamogeton pectinatus L.: vegetative growth and asexual reproduction

Across latitudinal gradients, environmental conditions that influenceplant growth and reproduction largely change. Here we study clonal variation inlife-cycle characteristics of the cosmopolitan water plantPotamogetonpectinatus L. across a broad latitudinal range.Two consecutive experiments were performed under standardised laboratoryconditions (photoperiod, irradiance and temperature). In the first experimentweinvestigated asexual reproduction among fifteen clones, obtained from latitudesranging from 24 to 68° N. After 90 days of growth, high-latitude clonesproduced more but smaller tubers, while the aboveground biomass was lower ascompared to the clones obtained from low latitudes.In a second experiment we studied inherent differences in early growth,morphology and photosynthesis for eleven clones (obtained from the samelatitudinal range as in experiment 1). We found high among clonal variation formost measured variables, but the number of latitude-correlated traits waslimited. The only trait that correlated with latitude was the number of leavesper plant, which increased in clones from higher latitudes.Our results agree with the hypothesis of a latitude-correlated switch inlife-cycle strategy for this species. For northern clones this results in ashort life-cycle, with an early and high investment in tuber biomass, while forlow latitude clones the length of the life-cycle is prolonged, with a delayedreproduction and increased total plant biomass.     

Effects of water flow on the infection dynamics of Myxobolus cerebralis

Myxobolus cerebralis, the myxozoan parasite responsible for whirling disease in salmonid fishes, has a complex life-cycle involving an invertebrate host and 2 spore stages. Water flow rate is an environmental variable thought to affect the establishment and propagation of M. cerebralis; however, experimental data that separates flow effects from those of other variables are scarce. To compare how this parameter affected parasite infection dynamics and the invertebrate and vertebrate hosts, dead, infected fish were introduced into a naive habitat with susceptible hosts under 2 experimental flow regimes: slow (0 x 02 cm/s) and fast (2 x 0 cm/s). Throughout the 1-year study, uninfected fry were held in both systems, the outflows were screened weekly for spores and the annelid populations were monitored. We found clear differences in prevalence of infection in the worms, prevalence and severity of infection in the fish, and host survival. Both flows provided environments in which M. cerebralis could complete its life-cycle; however, both the parasite and its invertebrate host proliferated to a greater extent in the slow flow environment over the 1-year study period. This finding is of significance for aquatic systems where the flow rate can be manipulated, and should be incorporated into risk analysis assessments.