Evolution of gene sequence and gene expression are not correlated in yeast

We show that, in yeast, the divergence rate of gene expression is not correlated with that of its associated coding sequence. Gene essentiality influences both modes of evolution, but other properties related to protein structure or promoter composition are only correlated with coding-sequence divergence or gene expression divergence, respectively. Based on these findings, we discuss the possibilities of neutral evolution of gene expression and of different modes of evolution in unicellular versus multicellular organisms.     

Sequence-based linkage analysis

The rapid decrease in the cost of DNA sequencing will enable its use for novel applications. Here, we investigate the use of DNA sequencing for simultaneous discovery and genotyping of polymorphisms in family linkage studies. In the proposed approach, short contiguous segments of genomic DNA, regularly spaced across the genome, are resequenced in each pedigree member, and all sequence polymorphisms discovered within a pedigree are used as genetic markers. We use computer simulations consistent with observed human sequence diversity to show that segments of 500-1,000 base pairs, spaced at intervals of 1-2 Mb across the genome, provide linkage information that equals or exceeds that of traditional marker-based approaches. We validate these results experimentally by implementing the sequence-based linkage approach for chromosome 19 in CEPH pedigrees.     

Computational verification of protein-protein interactions by orthologous co-expression

Background  

High-throughput methods identify an overwhelming number of protein-protein interactions. However, the limited accuracy of these methods results in the false identification of many spurious interactions. Accordingly, the resulting interactions are regarded as hypothetical and computational methods are needed to increase their confidence. Several methods have recently been suggested for this purpose including co-expression as a confidence measure for interacting proteins, but their performance is still quite poor.     

Site-Specific Evolutionary Rate Inference: Taking Phylogenetic Uncertainty into Account

The evolutionary rate at an amino acid site is indicative of how conserved this site is and, in turn, allows evaluating the importance of this site in maintaining the structure/function of the protein. When evolutionary rates are estimated, one must reconstruct the phylogenetic tree describing the evolutionary relationship among the sequences under study. However, if the inferred phylogenetic tree is incorrect, it can lead to erroneous site-specific rate estimates. Here we describe a novel Bayesian method that uses Markov chain Monte Carlo methodology to integrate over the space of all possible trees and model parameters. By doing so, the method considers alternative evolutionary scenarios weighted by their posterior probabilities. We show that this comprehensive evolutionary approach is superior over methods that are based on only a single tree. We illustrate the potential of our algorithm by analyzing the conservation pattern of the potassium channel protein family.Itay Mayrose, Amir Mitchell contributed equal. Reviewing Editor : Dr. Nicolas Galtier     

Scaling vs. nonscaling methods of assessing autonomic tone in streptozotocin-induced diabetic rats

We studied heart rate variability in rats by power scaling spectral analysis (PSSA), autoregressive modeling (AR), and detrended fluctuation analysis (DFA), assessed stability by coefficient of variation between consecutive 6-h epochs, and then compared cross-correlation among techniques. These same parameters were checked from baseline conditions through acute and chronic disease states (streptozotocin-induced diabetes) followed by therapeutic intervention (insulin). Cross-correlation between methods over the entire time period was r = 0.94 (DFA and PSSA), r = 0.81 (DFA and AR), and r = 0.77 (AR and PSSA). Under baseline conditions the scaling parameter measured by DFA and PSSA and the high-frequency (HF) component measured by AR fluctuated around an average value, but these fluctuations were different for the three methods. After diabetes induction, a strong correlation was found between the HF power and the short-term scaling parameter. Despite their differences in methodology, DFA and PSSA assess changes in parasympathetic tone as detected by autoregressive modeling.     

Sex determination,longevity, and the birth and death of reptilian species

Vertebrate sex‐determining mechanisms (SDMs) are triggered by the genotype (GSD), by temperature (TSD), or occasionally, by both. The causes and consequences of SDM diversity remain enigmatic. Theory predicts SDM effects on species diversification, and life‐span effects on SDM evolutionary turnover. Yet, evidence is conflicting in clades with labile SDMs, such as reptiles. Here, we investigate whether SDM is associated with diversification in turtles and lizards, and whether alterative factors, such as lifespan's effect on transition rates, could explain the relative prevalence of SDMs in turtles and lizards (including and excluding snakes). We assembled a comprehensive dataset of SDM states for squamates and turtles and leveraged large phylogenies for these two groups. We found no evidence that SDMs affect turtle, squamate, or lizard diversification. However, SDM transition rates differ between groups. In lizards TSD‐to‐GSD surpass GSD‐to‐TSD transitions, explaining the predominance of GSD lizards in nature. SDM transitions are fewer in turtles and the rates are similar to each other (TSD‐to‐GSD equals GSD‐to‐TSD), which, coupled with TSD ancestry, could explain TSD's predominance in turtles. These contrasting patterns can be explained by differences in life history. Namely, our data support the notion that in general, shorter lizard lifespan renders TSD detrimental favoring GSD evolution in squamates, whereas turtle longevity permits TSD retention. Thus, based on the macro‐evolutionary evidence we uncovered, we hypothesize that turtles and lizards followed different evolutionary trajectories with respect to SDM, likely mediated by differences in lifespan. Combined, our findings revealed a complex evolutionary interplay between SDMs and life histories that warrants further research that should make use of expanded datasets on unexamined taxa to enable more conclusive analyses.