An independent base composition of each rate class for improved likelihood-based phylogeny estimation; the 5rf model.

The combination of a ime eversible Markov process with a "hidden" mixture of amma distributed relative site rates plus nvariant sites have become the most favoured options for likelihood and other probabilistic models of nucleotide evolution (e.g., tr4gi which approximates a gamma with four rate classes).

Visible light-induced palladium-carbon bond weakening in catalytically relevant T-shaped complexes.

Triggering one-electron redox processes during palladium catalysis holds the potential to unlock new reaction mechanisms and synthetic methods not previously accessible in the typical two-electron reaction manifolds that dominate palladium catalysis. We report that T-shaped organopalladium(ii) complexes coordinated by a bulky monophosphine, a class of organometallic intermediate featured in a range of contemporary catalytic reactions, undergo blue light-promoted bond weakening leading to mild and efficient homolytic cleavage of strong Pd(ii)-C(sp) bonds under ambient conditions. The origin of light-triggered radical formation in these systems, which lack an obvious ligand-based chromophore (, π-systems), was investigated using a combination of DFT calculations, photoactinometry, and transient absorption spectroscopy.

Widespread introgression across a phylogeny of 155 Drosophila genomes.

Genome-scale sequence data have invigorated the study of hybridization and introgression, particularly in animals. However, outside of a few notable cases, we lack systematic tests for introgression at a larger phylogenetic scale across entire clades. Here, we leverage 155 genome assemblies from 149 species to generate a fossil-calibrated phylogeny and conduct multilocus tests for introgression across 9 monophyletic radiations within the genus Drosophila.

Electron-Rich Metal Cations Enable Synthesis of High Molecular Weight, Linear Functional Polyethylenes.

Group 10 metal catalysts have shown much promise for the copolymerization of nonpolar with polar alkenes to directly generate functional materials, but access to high copolymer molecular weights nevertheless remains a key challenge toward practical applications in this field. In the context of identifying new strategies for molecular weight control, we report a series of highly polarized P(V)-P(III) chelating ligands that manifest unique space filling and electrostatic effects within the coordination sphere of single component Pd polymerization catalysts and exert important influences on (co)polymer molecular weights. Single component, cationic phosphonic diamide-phosphine (PDAP) Pd catalysts are competent to generate linear, functional polyethylenes with M up to ca.

Potential Mechanisms for Cancer Resistance in Elephants and Comparative Cellular Response to DNA Damage in Humans.

Importance: Evolutionary medicine may provide insights into human physiology and pathophysiology, including tumor biology.

Objective: To identify mechanisms for cancer resistance in elephants and compare cellular response to DNA damage among elephants, healthy human controls, and cancer-prone patients with Li-Fraumeni syndrome (LFS).

Design, Setting, And Participants: A comprehensive survey of necropsy data was performed across 36 mammalian species to validate cancer resistance in large and long-lived organisms, including elephants (n = 644).

Effects of DNA methylation on nucleosome stability.

Methylation of DNA at CpG dinucleotides represents one of the most important epigenetic mechanisms involved in the control of gene expression in vertebrate cells. In this report, we conducted nucleosome reconstitution experiments in conjunction with high-throughput sequencing on 572 KB of human DNA and 668 KB of mouse DNA that was unmethylated or methylated in order to investigate the effects of this epigenetic modification on the positioning and stability of nucleosomes. The results demonstrated that a subset of nucleosomes positioned by nucleotide sequence was sensitive to methylation where the modification increased the affinity of these sequences for the histone octamer.

Structure of Penaeus stylirostris densovirus, a shrimp pathogen.

Penaeus stylirostris densovirus (PstDNV), a pathogen of penaeid shrimp, causes significant damage to farmed and wild shrimp populations. In contrast to other parvoviruses, PstDNV probably has only one type of capsid protein that lacks the phospholipase A2 activity that has been implicated as a requirement during parvoviral host cell infection. The structure of recombinant virus-like particles, composed of 60 copies of the 37.

Measuring fit of sequence data to phylogenetic model: gain of power using marginal tests.

Testing fit of data to model is fundamentally important to any science, but publications in the field of phylogenetics rarely do this. Such analyses discard fundamental aspects of science as prescribed by Karl Popper. Indeed, not without cause, Popper (Unended quest: an intellectual autobiography.

LINE-1 elements: analysis by fluorescence in-situ hybridization and nucleotide sequences.

Long-interspersed nuclear element-1 (LINE-1) is a non-terminal repeat transposon that constitutes a major component of the mammalian genome. LINE-1 has a dynamic evolutionary history characterized by the rise, fall, and replacement of subfamilies. The distribution of LINE-1 elements can be viewed from a chromosomal perspective using fluorescence in-situ hybridization (FISH), as well as at the sequence level.

TALI: local alignment of protein structures using backbone torsion angles.

Unlabelled: Torsion angle alignment (TALI) is a novel approach to local structural motif alignment, based on backbone torsion angles (phi, psi) rather than the more traditional atomic distance matrices. Representation of a protein structure in the form of a sequence of torsion angles enables easy integration of sequence and structural information, and adopts mature techniques in sequence alignment to improve performance and alignment quality. We show that TALI is able to match local structural motifs as well as identify global structural similarity.

Robust time estimation reconciles views of the antiquity of placental mammals.

Background: Molecular studies have reported divergence times of modern placental orders long before the Cretaceous-Tertiary boundary and far older than paleontological data. However, this discrepancy may not be real, but rather appear because of the violation of implicit assumptions in the estimation procedures, such as non-gradual change of evolutionary rate and failure to correct for convergent evolution.

Methodology/principal Findings: New procedures for divergence-time estimation robust to abrupt changes in the rate of molecular evolution are described.

Evolutionary history of LINE-1 in the major clades of placental mammals.

Background: LINE-1 constitutes an important component of mammalian genomes. It has a dynamic evolutionary history characterized by the rise, fall and replacement of subfamilies. Most data concerning LINE-1 biology and evolution are derived from the human and mouse genomes and are often assumed to hold for all placentals.

Phylogenetic methodology for detecting protein interactions.

Detecting protein-protein interactions and assigning proteins to functional complexes are key challenges of modern biology. The rise of genomics has lead to evidence that correlated patterns of presence/absence and/or fusing of proteins in any organism suggest these proteins interact. Unfortunately, methods based on such data work best with divergent genomes, whereas major sequencing efforts in vertebrates, for example, are yielding alignments of the same set of proteins sampled from the same set of taxa (species).

Measuring the fit of sequence data to phylogenetic model: allowing for missing data.

It is fundamentally important to assess the fit of data to model in phylogenetic and evolutionary studies. Phylogenetic methods using molecular sequences typically start with a multiple alignment. It is possible to measure the fit of data to model expectations of data, for example, via the likelihood-ratio (G) test or the X(2) test, if all sites in all sequences have an unambiguous residue.

Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data.

Evolutionary trees sit at the core of all realistic models describing a set of related sequences, including alignment, homology search, ancestral protein reconstruction and 2D/3D structural change. It is important to assess the stochastic error when estimating a tree, including models using the most realistic likelihood-based optimizations, yet computation times may be many days or weeks. If so, the bootstrap is computationally prohibitive.

Molecular systematics of primary reptilian lineages and the tuatara mitochondrial genome.

We provide phylogenetic analyses for primary Reptilia lineages including, for the first time, Sphenodon punctatus (tuatara) using data from whole mitochondrial genomes. Our analyses firmly support a sister relationship between Sphenodon and Squamata, which includes lizards and snakes. Using Sphenodon as an outgroup for select squamates, we found evidence indicating a sister relationship, among our study taxa, between Serpentes (represented by Dinodon) and Varanidae.

Evaluating placental inter-ordinal phylogenies with novel sequences including RAG1, gamma-fibrinogen, ND6, and mt-tRNA, plus MCMC-driven nucleotide, amino acid, and codon models.

It is essential to test a priori scientific hypotheses with independent data, not least to partly negate factors such as gene-specific base composition biases misleading our models. Seven new gene segments and sequences plus Bayesian likelihood phylogenetic methods were used to compare and test five recent placental phylogenies. These five phylogenies are similar to each other, yet quite different from Fthose of previously proposed trees, and span Waddell et al.

Pika and vole mitochondrial genomes increase support for both rodent monophyly and glires.

Complete mitochondrial genomes are reported for a pika (Ochotona collaris) and a vole (Volemys kikuchii) then analysed together with 35 other mitochondrial genomes from mammals. With standard phylogenetic methods the pika joins with the other lagomorph (rabbit) and the vole with the other murid rodents (rat and mouse). In addition, with hedgehog excluded, the seven rodent genomes consistently form a homogeneous group in the unrooted placental tree.