Correlates of substitution rate variation in mammalian protein-coding sequences

BACKGROUND: Rates of molecular evolution in different lineages can vary widely, and some of this variation might be predictable from aspects of species' biology. Investigating such predictable rate variation can help us to understand the causes of molecular evolution, and could also help to improve molecular dating methods. Here we present a comprehensive study of the life history correlates of substitution rate variation across the mammals, comparing results for mitochondrial and nuclear loci, and for synonymous and non-synonymous sites. We use phylogenetic comparative methods, refined to take into account the special nature of substitution rate data. Particular attention is paid to the widespread correlations between the components of mammalian life history, which can complicate the interpretation of results. RESULTS: We find that mitochondrial synonymous substitution rates, estimated from the 9 longest mitochondrial genes, show strong negative correlations with body mass and with maximum recorded lifespan. But lifespan is the sole variable to remain after multiple regression and model simplification. Nuclear synonymous substitution rates, estimated from 6 genes, show strong negative correlations with body mass and generation time, and a strong positive correlation with fecundity. In contrast to the mitochondrial results, the same trends are evident in rates of nonsynonymous substitution. CONCLUSION: A substantial proportion of variation in mammalian substitution rates can be explained by aspects of their life history, implying that molecular and life history evolution are closely interlinked in this group. The strength and consistency of the nuclear body mass effect suggests that molecular dating studies may have been systematically misled, but also that methods could be improved by incorporating the finding as a priori information. Mitochondrial synonymous rates also show the body mass effect, but for apparently quite different reasons, and the strength of the relationship with maximum lifespan provides support for the hypothesis that mtDNA damage is causally linked to aging

The “Island Rule” and Deep-Sea Gastropods: Re-Examining the Evidence

Background: One of the most intriguing patterns in mammalian biogeography is the ‘‘island rule’’, which states that colonising species have a tendency to converge in body size, with larger species evolving decreased sizes and smaller species increased sizes. It has recently been suggested that an analogous pattern holds for the colonisation of the deep-sea benthos by marine Gastropoda. In particular, a pioneering study showed that gastropods from the Western Atlantic showed the same graded trend from dwarfism to gigantism that is evident in island endemic mammals. However, subsequent to the publication of the gastropod study, the standard tests of the island rule have been shown to yield false positives at a very high rate, leaving the result open to doubt. Methodology/Principal Findings: The evolution of gastropod body size in the deep sea is reexamined. Using an extended and updated data set, and improved statistical methods, it is shown that some results of the previous study may have been artifactual, but that its central conclusion is robust. It is further shown that the effect is not restricted to a single gastropod clade, that its strength increases markedly with depth, but that it applies even in the mesopelagic zone. Conclusions/Significance: The replication of the island rule in a distant taxonomic group and a partially analogous ecological situation could help to uncover the causes of the patterns observed—which are currently much disputed. Th

The distribution of epistasis on simple fitness landscapes.

Fitness interactions between mutations can influence a population's evolution in many different ways. While epistatic effects are difficult to measure precisely, important information is captured by the mean and variance of log fitnesses for individuals carrying different numbers of mutations. We derive predictions for these quantities from a class of simple fitness landscapes, based on models of optimizing selection on quantitative traits. We also explore extensions to the models, including modular pleiotropy, variable effect sizes, mutational bias and maladaptation of the wild type. We illustrate our approach by reanalysing a large dataset of mutant effects in a yeast snoRNA (small nucleolar RNA). Though characterized by some large epistatic effects, these data give a good overall fit to the non-epistatic null model, suggesting that epistasis might have limited influence on the evolutionary dynamics in this system. We also show how the amount of epistasis depends on both the underlying fitness landscape and the distribution of mutations, and so is expected to vary in consistent ways between new mutations, standing variation and fixed mutations.N

Why Might Bacterial Pathogens Have Small Genomes?

Bacteria that cause serious disease often have smaller genomes, and fewer genes, than their nonpathogenic, or less pathogenic relatives. Here, we review evidence for the generality of this association, and summarise the various reasons why the association might hold. We focus on the population genetic processes that might lead to reductive genome evolution, and show how several of these could be connected to pathogenicity. We find some evidence for most of the processes having acted in bacterial pathogens, including several different modes of genome reduction acting in the same lineage. We argue that predictable processes of genome evolution might not reflect any common underlying process

On the use of drift bottle and seabed drifter data in coastal management

The use of drift bottle and seabed drifter information for use in coastal management is discussed. The drift bottle/seabed drifter portion of VIMS project MACONS (Mid Atlantic Continental Shelf) is described as an example of how a comprehensive survey using drift bottles and seabed drifters provides data useful for coastal management. The data from MACONS are analyzed to answer specific questions of interest to several different coastal managers: a manager siting a deep oil port, one siting a sewage outfall, a manager responsible for setting up emergency beach protection procedures before an accident occurs, and a manager responsible for the environmental quality of a particular small section of coastline

Single-Scattering Optical Tomography: Simultaneous Reconstruction of Scattering and Absorption

We demonstrate that simultaneous reconstruction of scattering and absorption of a mesoscopic system using angularly-resolved measurements of scattered light intensity is possible. Image reconstruction is realized based on the algebraic inversion of a generalized Radon transform relating the scattering and absorption coefficients of the medium to the measured light intensity and derived using the single-scattering approximation to the radiative transport equation.Comment: This is a sequel to physics/070311

Alternative model for the administration and analysis of research-based assessments

Research-based assessments represent a valuable tool for both instructors and researchers interested in improving undergraduate physics education. However, the historical model for disseminating and propagating conceptual and attitudinal assessments developed by the physics education research (PER) community has not resulted in widespread adoption of these assessments within the broader community of physics instructors. Within this historical model, assessment developers create high quality, validated assessments, make them available for a wide range of instructors to use, and provide minimal (if any) support to assist with administration or analysis of the results. Here, we present and discuss an alternative model for assessment dissemination, which is characterized by centralized data collection and analysis. This model provides a greater degree of support for both researchers and instructors in order to more explicitly support adoption of research-based assessments. Specifically, we describe our experiences developing a centralized, automated system for an attitudinal assessment we previously created to examine students' epistemologies and expectations about experimental physics. This system provides a proof-of-concept that we use to discuss the advantages associated with centralized administration and data collection for research-based assessments in PER. We also discuss the challenges that we encountered while developing, maintaining, and automating this system. Ultimately, we argue that centralized administration and data collection for standardized assessments is a viable and potentially advantageous alternative to the default model characterized by decentralized administration and analysis. Moreover, with the help of online administration and automation, this model can support the long-term sustainability of centralized assessment systems.Comment: 7 pages, 1 figure, accepted in Phys. Rev. PE

Analysis of the Space Shuttle main engine simulation

This is a final report on an analysis of the Space Shuttle Main Engine Program, a digital simulator code written in Fortran. The research was undertaken in ultimate support of future design studies of a shuttle life-extending Intelligent Control System (ICS). These studies are to be conducted by NASA Lewis Space Research Center. The primary purpose of the analysis was to define the means to achieve a faster running simulation, and to determine if additional hardware would be necessary for speeding up simulations for the ICS project. In particular, the analysis was to consider the use of custom integrators based on the Matrix Stability Region Placement (MSRP) method. In addition to speed of execution, other qualities of the software were to be examined. Among these are the accuracy of computations, the useability of the simulation system, and the maintainability of the program and data files. Accuracy involves control of truncation error of the methods, and roundoff error induced by floating point operations. It also involves the requirement that the user be fully aware of the model that the simulator is implementing

Correlates of substitution rate variation in mammalian protein-coding sequences

<p>Abstract</p> <p>Background</p> <p>Rates of molecular evolution in different lineages can vary widely, and some of this variation might be predictable from aspects of species' biology. Investigating such predictable rate variation can help us to understand the causes of molecular evolution, and could also help to improve molecular dating methods. Here we present a comprehensive study of the life history correlates of substitution rate variation across the mammals, comparing results for mitochondrial and nuclear loci, and for synonymous and non-synonymous sites. We use phylogenetic comparative methods, refined to take into account the special nature of substitution rate data. Particular attention is paid to the widespread correlations between the components of mammalian life history, which can complicate the interpretation of results.</p> <p>Results</p> <p>We find that mitochondrial synonymous substitution rates, estimated from the 9 longest mitochondrial genes, show strong negative correlations with body mass and with maximum recorded lifespan. But lifespan is the sole variable to remain after multiple regression and model simplification. Nuclear synonymous substitution rates, estimated from 6 genes, show strong negative correlations with body mass and generation time, and a strong positive correlation with fecundity. In contrast to the mitochondrial results, the same trends are evident in rates of nonsynonymous substitution.</p> <p>Conclusion</p> <p>A substantial proportion of variation in mammalian substitution rates can be explained by aspects of their life history, implying that molecular and life history evolution are closely interlinked in this group. The strength and consistency of the nuclear body mass effect suggests that molecular dating studies may have been systematically misled, but also that methods could be improved by incorporating the finding as <it>a priori </it>information. Mitochondrial synonymous rates also show the body mass effect, but for apparently quite different reasons, and the strength of the relationship with maximum lifespan provides support for the hypothesis that mtDNA damage is causally linked to aging.</p