A Genomic Perspective on the Evolutionary Diversification of Turtles

To examine phylogenetic heterogeneity in turtle evolution, we collected thousands of high-confidence single-copy orthologs from 19 genome assemblies representative of extant turtle diversity and estimated a phylogeny with multispecies coalescent and concatenated partitioned methods. We also collected next-generation sequences from 26 turtle species and assembled millions of biallelic markers to reconstruct phylogenies from annotated regions (coding regions, introns, untranslated regions, intergenic, and others) of the western painted turtle (Chrysemys picta bellii) genome. We then measured gene tree-species tree discordance, as well as gene and site heterogeneity at each node in the inferred trees, and tested for incomplete lineage sorting and temporal patterns in phylogenomic heterogeneity across turtle evolution. We found 100% support for all bifurcations in the inferred turtle species phylogenies. However, a number of genes, sites, and genomic features supported alternate relationships between turtle taxa, and some nodes in the turtle phylogeny were well-explained by incomplete lineage sorting. There was no clear pattern between site concordance, node age, and DNA substitution rate across most annotated genomic regions, suggesting a relatively uniform proportion of informative sites drive phylogenetic inference across the evolution of turtles. We found more gene concordance at older nodes in the turtle phylogeny, and suggest that, in addition to incomplete lineage sorting, an overall lack of gene informativeness stemming from a slow rate of evolution can confound inferred patterns in turtle phylogenomics, particularly at more recent divergences. Our study demonstrates that heterogeneity is to be expected even in well resolved clades such as turtles, and that future phylogenomic studies should aim to sample as much of the genome as possible.

Context dependency of nucleotide probabilities and variants in human DNA

Background: Genomic DNA has been shaped by mutational processes through evolution. The cellular machinery for error correction and repair has left its marks in the nucleotide composition along with structural and functional constraints. Therefore, the probability of observing a base in a certain position in the human genome is highly context-dependent. Mutations are also known to depend on the genomic context, but in previous work, the nucleotide distribution and the mutability have not been combined. Results: Here we use a context-dependent nucleotide model as the basis for a mutability model for the human genome. We first investigate simple models of nucleotides conditioned on sequence context and develop a bidirectional Markov model that depends on up to 14 nucleotides to each side. We show how the genome predictability varies across different types of genomic regions. Surprisingly, this model can predict a base from its context with an average of more than 50% accuracy. Inspired by DNA substitution models, we develop a model of mutability that estimates a mutation matrix (called the alpha matrix) on top of the nucleotide distribution. The advantage of this separation into two terms is that the alpha matrix can be estimated from a much smaller context than the nucleotide model, but the final model will still depend on the full context of the nucleotide model. With the bidirectional Markov model of order 14 and an alpha matrix dependent on just one base to each side, we obtain a model that compares well with a model of mutability that estimates mutation probabilities directly conditioned on three nucleotides to each side. For high-probability population variants, which are mainly CpG sites, the simple model fits better than our hybrid model, but for somatic variants it is opposite. Interestingly, the model is not very sensitive to the size of the context for the alpha matrix. Conclusions: Our study found strong context dependencies of nucleotides in the human genome. The best model can estimate the nucleotide probabilities depending on contexts up to 14 nucleotides to each side. Based on these models, a substitution model was constructed that separates into the context model and an alpha matrix dependent in a small context. These models fit variants very well.

An efficient data masking for securing medical data using DNA encoding and chaotic system

Data security is utmost important for ubiquitous computing of medical/diagnostic data or images. Along with must consider preserving privacy of patients. Recently, deoxyribose nucleic acid (DNA) sequences and chaotic sequence are jointly used for building efficient data masking model. However, the state-of-art model are not robust against noise and cropping attack (CA). Since in existing model most digits of each pixel are not altered. This work present efficient data masking (EDM) method using chaos and DNA based encryption method for securing health care data. For overcoming research challenges effective bit scrambling method is required. Firstly, this work present an efficient bit scrambling using logistic sine map and pseudorandom sequence using chaotic system. Then, DNA substitution is performed among them to resist against differential attack (DA), statistical attack (SA) and CA. Experiment are conducted on standard considering diverse images. The outcome achieved shows proposed model efficient when compared to existing models.

Evolutionary dynamics of neutral phenotypes under DNA substitution models

We study the evolution of quantitative molecular traits in the absence of selection. Using a simple theory based on Felsenstein’s 1981 DNA substitution model, we predict a linear restoring force on the mean of an additive phenotype. Remarkably, the mean dynamics are independent of the effect sizes and genotype and are similar to the widely-used OU model for stabilizing selection. We confirm the predictions empirically using additive molecular phenotypes calculated from ancestral reconstructions of putatively unconstrained DNA sequences in primate genomes. We show that the OU model is favoured by inference software even when applied to GC content of unconstrained sequences or simulations of DNA evolution. We predict and confirm empirically that the dynamics of the variance are more complicated than those predicted by the OU model, and show that our results for the restoring force of mutation hold even for non-additive phenotypes, such as number of transcription factor binding sites, longest encoded peptide and folding propensity of the encoded peptide. Our results have implications for efforts to infer selection based on quantitative phenotype dynamics as well as to understand long-term trends in evolution of quantitative molecular traits.

Alternative analyses of compensatory base changes in an ITS2 phylogeny of Corydalis (Papaveraceae)

Background and Aims Compensatory base changes (CBCs) that occur in stems of ribosomal internal transcribed spacer 2 (ITS2) can have important phylogenetic implications because they are not expected to occur within a single species and also affect selection of appropriate DNA substitution models. These effects have been demonstrated when studying ancient lineages. Here we examine these effects to quantify their importance within a more recent lineage by using both DNA- and RNA-specific models. Methods We examined the phylogenetic implications of the CBC process by using a comprehensive sampling of ITS2 from ten closely related species of Corydalis. We predicted ITS2 secondary structures by using homology modelling, which was then used for a structure-based alignment. Paired and unpaired regions were analysed separately and in combination by using both RNA-specific substitution models and conventional DNA models. We mapped all base-pair states of CBCs on the phylogenetic tree to infer their evolution and relative timing. Key Results Our results indicate that selection acted to increase the thermodynamic stability of the secondary structure. Thus, the unpaired and paired regions did not evolve under a common substitution model. Only two CBCs occurred within the lineage sampled and no striking differences in topology or support for the shared clades were found between trees constructed using DNA- or RNA-specific substitution models. Conclusions Although application of RNA-specific substitution models remains preferred over more conventional DNA models, we infer that application of conventional DNA models is unlikely to be problematic when conducting phylogenetic analyses of ITS2 within closely related lineages wherein few CBCs are observed. Each of the two CBCs was found within the same lineages but was not observed within a given species, which supports application of the CBC species concept.