The role of weak selection and high mutation rates in nearly neutral evolution

Neutral dynamics occur in evolution if all types are ‘effectively equal’ in their reproductive success, where the definition of ‘effectively equal’ depends on the population size and the details of mutations. Empirically observed neutral genetic evolution in extremely large clonal populations can only be explained under current models if selection is completely absent. Such models typically consider the case where population dynamics occurs on a different timescale to evolution. However, this assumption is invalid when mutations are not rare in a whole population. We show that this has important consequences for the occurrence of neutral evolution in clonal populations. In highly connected type spaces, neutral dynamics can occur for all population sizes despite significant selective differences, via the forming of effectively neutral networks connecting rare neutral types. Biological implications include an explanation for the high diversity of rare types that survive in large clonal populations, and a theoretical justification for the use of neutral null models.     

Bilateral similarity function: A novel and universal method for similarity analysis of biological sequences

Bilateral similarity function is designed for analyzing the similarities of biological sequences such as DNA, RNA secondary structure or protein in this paper. The defined function can perform comprehensive comparison between sequences remarkably well, both in terms of the Hamming distance of two compared sequences and the corresponding location difference. Compared with the existing methods for similarity analysis, the examination of similarities/dissimilarities illustrates that the proposed method with the computational complexity of O(N) is effective for these three kinds of biological sequences, and bears the universality for them.     

A method to describe enzyme-catalyzed reactions by combining steady state and time course enzyme kinetic parameters

Background

Complete analysis of single substrate enzyme-catalyzed reactions has required a separate use of two distinct approaches. Steady state approximations are employed to obtain substrate affinity and initial velocity information. Alternatively, first order exponential decay models permit simulation of the time course data for the reactions. Attempts to use integrals of steady state equations to describe reaction time courses have so far met with little success.

Methods

Here we use equations based on steady state approximations to directly model time course plots.

Results

Testing these expressions with the enzyme β-galactosidase, which adheres to classical Michaelis–Menten kinetics, produced a good fit between observed and calculated values.

General significance

This study indicates that, in addition to providing information on initial kinetic parameters, steady state approximations can be employed to directly model time course kinetics.Integrated forms of the Michaelis–Menten equation have previously been reported in the literature. Here we describe a method to directly apply steady state approximations to time course analysis for predicting product formation and simultaneously obtain multiple kinetic parameters.     

A graphical model of disruptive selection on offspring size and a possible case of speciation in freshwater gobies characterized by egg-size difference

The graphical technique devised bySmith andFretwell (1974) to construct a model of the optimal offspring size was applied to the case where disruptive selection might work on offspring size. On this basis, a possible case of speciation in freshwater gobies characterized by egg-size difference was discussed.     

Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation

We examine properties of adaptive walks on uncorrelated (i.e. random) fitness landscapes starting from moderately fit genotypes under strong selection weak mutation. As an extension of Orr's model for a single step in an adaptive walk under these conditions, we show that the fitness rank of the dominant genotype in a population after the fixation of a beneficial mutation is, on average, (i+6)/4, where i is the fitness rank of the starting genotype. This accounts for the change in rank due to acquiring a new set of single-mutation neighbors after fixing a new allele through natural selection. Under this scenario, adaptive walks can be modeled as a simple Markov chain on the space of possible fitness ranks with an absorbing state at i = 1, from which no beneficial mutations are accessible. We find that these walks are typically short and are often completed in a single step when starting from a moderately fit genotype. As in Orr's original model, these results are insensitive to both the distribution of fitness effects and most biological details of the system under consideration.     

A GIS-based tool for storage,selection and visualization of time series 4D marine datasets

We present an initial attempt for the development of a distributed and scalable GIS-like tool for the storage, selection and visualization of 4D marine datasets. The aim of this tool is to standardize the variety of data available for the water column and support non-technical marine biologists in manipulating 4D marine datasets. The tool is developed towards answering specific environmental and biological questions regarding ocean processes and essential fish habitat mapping in three dimensions. Guest editor: V. D. Valavanis Essential Fish Habitat Mapping in the Mediterranean     

Comparison of identity by descent and identity by state for detecting genetic regions under selection in a sorghum pedigree breeding program

Seventy sorghum inbred lines which formed part of the Queensland Department of Primary Industries (QDPI) sorghum breeding program were screened with 104 previously mapped RFLP markers. The lines were related by pedigree and consisted of ancestral source lines, intermediate lines and recent releases from the program. We compared the effect of defining marker alleles using either identity by state (IBS) or identity by descent (IBD) on our capacity to trace markers through the pedigree and detect evidence of selection for particular alleles. Allelic identities defined using IBD were much more sensitive for detecting non-Mendelian segregation in this pedigree. Only one marker allele showed significant evidence of selection when IBS was used compared with ten regions with particular allelic identities when IBD was used. Regions under selection were compared with the location of QTLs for agronomic traits known to be under selection in the breeding program. Only two of the ten regions were associated with known QTLs that matched with knowledge of the agronomic characteristics of the ancestral lines. Some of the other regions were hypothesised to be associated with genes for particular traits based on the properties of the ancestral source lines.     

A steady state and differential polarised phase fluorimetric study of the liver microsomal and mitochondrial membranes of thermally acclimated green sunfish (Lepomis cyanellus)

The liver mitochondrial and microsomal membranes of green sunfish and rat were examined by steady state polarisation and differential polarised phase fluorimetry to determine the effects of seasonal adaptation of membrane dynamic structure to temperature. Steady state polarisation studies indicated that the liver mitochondria of green sunfish acclimated to different temperatures showed a greater partial compensation of membrane fluidity for the altered acclimation temperature than did liver microsomal membranes. The fatty acid composition of both membrane preparations generally became more unsaturated at lower acclimation temperatures, though the differences between 5°C and 25°C acclimated fish were more pronounced in the mitochondrial fraction than in the microsomal fraction.Differential polarised phase fluorimetric studies indicated that the rotations of diphenylhexatriene in mitochondrial and microsomal membranes were highly hindered, though the hindrance offered by membranes of 25°C acclimated green sunfish was far greater than that offered by the membranes of 5°C acclimated fish, thus supporting the concept of homeoviscous adaptation. The absolute rotational rate was not consistently affected by acclimation treatment.     

Human serum transferrin: a tale of two lobes. Urea gel and steady state fluorescence analysis of recombinant transferrins as a function of pH, time, and the soluble portion of the transferrin receptor

Iron release from human serum transferrin (hTF) has been studied extensively; however, the molecular details of the mechanism(s) remain incomplete. This is in part due to the complexity of this process, which is influenced by lobe–lobe interactions, the transferrin receptor (TFR), the salt effect, the presence of a chelator, and acidification within the endosome, resulting in iron release. The present work brings together many of the concepts and assertions derived from previous studies in a methodical, uniform, and visual manner. Examination of earlier work reveals some uncertainty due to sample and technical limitations. We have used a combination of steady-state fluorescence and urea gels to evaluate the effect of conformation, pH, time, and the soluble portion of the TFR (sTFR) on iron release from each lobe of hTF. The use of authentic recombinant monoferric and locked species removes any possibility of cross-contamination by acquisition of iron. Elimination of detergent by use of the sTFR provides a further technical advantage. We find that iron release from the N-lobe is very sensitive to the conformation of the C-lobe, but is insensitive to the presence of the sTFR or to changes in pH (between 5.6 and 6.4). Specifically, when the cleft of the C-lobe is locked, the urea gels indicate that only about half of the iron is completely removed from the cleft of the N-lobe. Iron release from the C-lobe is most affected by the presence of the sTFR and changes in pH, but is unaffected by the conformation of the N-lobe. A model for iron release from diferric hTF is provided to delineate our findings. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

A comparison of ferric-chelate reductase and chlorophyll and growth ratios as indices of selection of quince,pear and olive genotypes under iron deficiency stress

Quince (Cydonia oblonga Mill.), pear (Pyrus communis L.) and olive (Olea europaea L.) genotypes were evaluated for their tolerance to iron deficiency stress by growing young plants in three types of aerated nutrient solutions: (1) with iron, (2) without iron or (3) low in iron and with 10 mM bicarbonate. Plants were obtained either from rooted softwood cuttings or from germination of seeds. The degree of tolerance was evaluated with several indices: (1) the chlorophyll content, (2) the root Fe³⁺ reducing capacity and (3) the whole plant relative growth. Fifteen hours before Fe³⁺ reducing capacity determination, iron was applied to the roots of plants with iron-stress, since this method resulted in increasing the reductase activity. All quince and pear genotypes increased the root Fe³⁺ reducing capacity when grown in the treatments for iron-stress, in relation to control plants of the same genotypes. In olive cultivars, the Fe³⁺ reducing capacity was lower in the iron-stress treatments than in the control one. Studying the relationship between relative growth and chlorophyll content for each genotype under iron-stress, in relation to both indices in control plants, a classification of species and genotypes was established. According to that, most olive cultivars and some pear rootstocks and cultivars appear more iron-efficient than quince rootstocks. Our study shows that in some woody species, determining root Fe³⁺ reducing capacity is not the best method to establish tolerance to iron deficiency stress.     

Quantifying the habitat structure and spatial pattern of New Jersey (U.S.A.) salt marshes under different management regimes

Mosquito control measures have resulted in majorstructural alterations of many coastal marshes, withrelatively unknown consequences to larger ecosystemfunctioning. Parallel grid ditching and open marshwater management (OMWM) techniques are purposefullydesigned to alter the hydrological regime and therelative availability and/or characteristics ofstanding water on the marsh surface. With the growingrecognition of the important influence that habitatstructure and the configuration of the marsh-edgeboundary has on nekton utilization of salt marshsystems, the impact of mosquito control managementtechniques on the availability and quality of saltmarsh habitat deserves increased scrutiny. Usingdigital image processing techniques, we completed adetailed mapping effort for a 1800 ha study area inTuckerton, New Jersey to provide a picture ofsubtidal and intertidal habitat availability. Spatialanalysis techniques were used to quantify the relativeamount of habitat types and spatial pattern of theland-water interface under different managementregimes: parallel grid-ditched, OMWM and an unalteredreference. The parallel grid-ditched site had a muchlower incidence of marsh ponds which serve asimportant low tide and over-wintering refuge forcertain species of fish. In comparison, the OMWM sitehad a much greater amount of ponded water habitats.The grid-ditched site had a higher density of marshsurface-to-tidal water interface resulting in a lowermedian distance between the marsh interior and theadjacent tidal channel network. This study serves tobenchmark the habitat structure and spatial pattern ofa highly functioning natural marsh for use as areference site in regional wetland creation orrestoration efforts.     

A continent under stress: interactions, feedbacks and risks associated with impact of modified land cover on Australia's climate

Global climate change is the major and most urgent global environmental issue. Australia is already experiencing climate change as evidenced by higher temperatures and more frequent and severe droughts. These impacts are compounded by increasing land use pressures on natural resources and native ecosystems. This paper provides a synthesis of the interactions, feedbacks and risks of natural climate variability, climate change and land use/land cover change (LUCC) impacting on the Australian continent and how they vary regionally. We review evidence of climate change and underlying processes resulting from interactions between global warming caused by increased concentration of atmospheric greenhouse gases and modification of the land surface. The consequences of ignoring the effect of LUCC on current and future droughts in Australia could have catastrophic consequences for the nation's environment, economy and communities. We highlight the need for more integrated, long-term and adaptive policies and regional natural resource management strategies that restore the beneficial feedbacks between native vegetation cover and local-regional climate, to help ameliorate the impact of global warming.