How sex shapes transcriptome evolution in the songbird brain.

Sex differences have captivated scientists for a long time, yet the evolutionary rate of change in sex-biased gene expression has not been directly quantified. To address this issue, we leverage brain gene expression data from male and female songbirds. To do this, we introduce new options for unbounded Brownian motion and variable evolutionary rates among genes in the software package CAGEE (Computational Analysis of Gene Expression Evolution).

Human deleterious mutation rate slows adaptation and implies high fitness variance.

Each new human has an expected new deleterious mutations. Using a novel approach to capture complex linkage disequilibria from high using genome-wide simulations, we confirm that fitness decline due to the fixation of many slightly deleterious mutations can be compensated by rarer beneficial mutations of larger effect. The evolution of increased genome size and complexity have previously been attributed to a similarly asymmetric pattern of fixations, but we propose that the cause might be high rather than the small population size posited as causal by drift barrier theory.

CAGEE: Computational Analysis of Gene Expression Evolution.

Despite the increasing abundance of whole transcriptome data, few methods are available to analyze global gene expression across phylogenies. Here, we present a new software package (Computational Analysis of Gene Expression Evolution [CAGEE]) for inferring patterns of increases and decreases in gene expression across a phylogenetic tree, as well as the rate at which these changes occur. In contrast to previous methods that treat each gene independently, CAGEE can calculate genome-wide rates of gene expression, along with ancestral states for each gene.

Allele frequency divergence reveals ubiquitous influence of positive selection in Drosophila.

Resolving the role of natural selection is a basic objective of evolutionary biology. It is generally difficult to detect the influence of selection because ubiquitous non-selective stochastic change in allele frequencies (genetic drift) degrades evidence of selection. As a result, selection scans typically only identify genomic regions that have undergone episodes of intense selection.

Mutation bias can shape adaptation in large asexual populations experiencing clonal interference.

The extended evolutionary synthesis invokes a role for development in shaping adaptive evolution, which in population genetics terms corresponds to mutation-biased adaptation. Critics have claimed that clonal interference makes mutation-biased adaptation rare. We consider the behaviour of two simultaneously adapting traits, one with larger mutation rate , the other with larger selection coefficient , using asexual travelling wave models.

Evolution Rapidly Optimizes Stability and Aggregation in Lattice Proteins Despite Pervasive Landscape Valleys and Mazes.

The "fitness" landscapes of genetic sequences are characterized by high dimensionality and "ruggedness" due to sign epistasis. Ascending from low to high fitness on such landscapes can be difficult because adaptive trajectories get stuck at low-fitness local peaks. Compounding matters, recent theoretical arguments have proposed that extremely long, winding adaptive paths may be required to reach even local peaks: a "maze-like" landscape topography.

Poly(d,l-Lactic acid) Composite Foams Containing Phosphate Glass Particles Produced via Solid-State Foaming Using CO for Bone Tissue Engineering Applications.

This study reports on the production and characterization of highly porous (up to 91%) composite foams for potential bone tissue engineering (BTE) applications. A calcium phosphate-based glass particulate (PGP) filler of the formulation 50PO-40CaO-10TiO mol.%, was incorporated into biodegradable poly(d,l-lactic acid) (PDLLA) at 5, 10, 20, and 30 vol.

Different mechanisms drive the maintenance of polymorphism at loci subject to strong versus weak fluctuating selection.

The long-running debate about the role of selection in maintaining genetic variation has been given new impetus by the discovery of hundreds of seasonally oscillating polymorphisms in wild Drosophila, possibly stabilized by an alternating summer-winter selection regime. Historically, there has been skepticism about the potential of temporal variation to balance polymorphism, because selection must be strong to have a meaningful stabilizing effect-unless dominance also varies over time ("reversal of dominance"). Here, we develop a simplified model of seasonally variable selection that simultaneously incorporates four different stabilizing mechanisms, including two genetic mechanisms ("cumulative overdominance" and reversal of dominance), as well as ecological "storage" ("protection from selection" and boom-bust demography).

A Shift in Aggregation Avoidance Strategy Marks a Long-Term Direction to Protein Evolution.

To detect a direction to evolution, without the pitfalls of reconstructing ancestral states, we need to compare "more evolved" to "less evolved" entities. But because all extant species have the same common ancestor, none are chronologically more evolved than any other. However, different gene families were born at different times, allowing us to compare young protein-coding genes to those that are older and hence have been evolving for longer.

Density-dependent selection and the limits of relative fitness.

Selection is commonly described by assigning constant relative fitness values to genotypes. Yet population density is often regulated by crowding. Relative fitness may then depend on density, and selection can change density when it acts on a density-regulating trait.

Directional Selection Rather Than Functional Constraints Can Shape the G Matrix in Rapidly Adapting Asexuals.

Genetic covariances represent a combination of pleiotropy and linkage disequilibrium, shaped by the population's history. Observed genetic covariance is most often interpreted in pleiotropic terms. In particular, functional constraints restricting which phenotypes are physically possible can lead to a stable matrix with high genetic variance in fitness-associated traits, and high pleiotropic negative covariance along the phenotypic curve of constraint.

Statistical patterns in tropical tree cover explained by the different water demand of individual trees and grasses.

Tree cover varies enormously across tropical ecosystems-from arid savannas to closed rain forests-and yet a general predictive theory of tropical tree cover remains elusive. Here we use the maximum-entropy method to predict the most likely sample frequency distribution of ecosystems with different tree and grass fractional cover if balance between water supply and demand were the dominant constraint on community assembly. Assuming a hierarchy of individual plant water demand in which trees require more water than grasses, we reproduce observed trends in the means and the upper and lower limits of tropical tree and grass cover across the entire spectrum of tropical ecosystem water supply.

Sry delivery to the adrenal medulla increases blood pressure and adrenal medullary tyrosine hydroxylase of normotensive WKY rats.

Background: Our laboratory has shown that a locus on the SHR Y chromosome increases blood pressure (BP) in the SHR rat and in WKY rats that had the SHR Y chromosome locus crossed into their genome (SHR/y rat). A potential candidate for this Y chromosome hypertension locus is Sry, a gene that encodes a transcription factor that is responsible for testes development and the Sry protein may affect other target genes.

Methods: The following study examined if exogenous Sry would elevate adrenal Th, adrenal catecholamines, plasma catecholamines and blood pressure.