The accuracy of several multiple sequence alignment programs for proteins

MAFFT multiple sequence alignment software version 7: improvements in performance and usability

We report a major update of the MAFFT multiple sequence alignment program. This version has several new features, including options for adding unaligned sequences into an existing alignment, adjustment of direction in nucleotide alignment, constrained alignment and parallel processing, which were implemented after the previous major update. This report shows actual examples to explain how these features work, alone and in combination. Some examples incorrectly aligned by MAFFT are also shown to clarify its limitations. We discuss how to avoid misalignments, and our ongoing efforts to overcome such limitations.

Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes

The present review focuses on the evolution of proteins and the impact of amino acid mutations on function from a structural perspective. Proteins evolve under the law of natural selection and undergo alternating periods of conservative evolution and of relatively rapid change. The likelihood of mutations being fixed in the genome depends on various factors, such as the fitness of the phenotype or the position of the residues in the three-dimensional structure. For example, co-evolution of residues located close together in three-dimensional space can occur to preserve global stability. Whereas point mutations can fine-tune the protein function, residue insertions and deletions (‘decorations’ at the structural level) can sometimes modify functional sites and protein interactions more dramatically. We discuss recent developments and tools to identify such episodic mutations, and examine their applications in medical research. Such tools have been tested on simulated data and applied to real data such as viruses or animal sequences. Traditionally, there has been little if any cross-talk between the fields of protein biophysics, protein structure–function and molecular evolution. However, the last several years have seen some exciting developments in combining these approaches to obtain an in-depth understanding of how proteins evolve. For example, a better understanding of how structural constraints affect protein evolution will greatly help us to optimize our models of sequence evolution. The present review explores this new synthesis of perspectives.

Building megaphylogenies for macroecology: taking up the challenge

The last decades have seen an upsurge in ecological studies incorporating phylogenetic information with increasing species samples, motivated by the common conjecture that species with common ancestors should share some ecological characteristics due to niche conservatism. This has been carried out using various methods of increasing complexity and reliability: using only taxonomical classification; constructing supertrees that incorporate only topological information from previously published phylogenies; or building supermatrices of molecular data that are used to estimate phylogenies with evolutionary meaningful branch lengths. Although the latter option is more informative than the others, it remains under-used in ecology because ecologists are generally unaware of or unfamiliar with modern molecular phylogenetic methods. However, a solid phylogenetic hypothesis is necessary to conduct reliable ecological analysis integrating evolutive aspects. Our aim here is to clarify the concepts and methodological issues associated with the reconstruction of dated megaphylogenies, and to show that it is nowadays possible to obtain accurate and well sampled megaphylogenies with informative branch-lengths on large species samples. This is possible thanks to improved phylogenetic methods, vast amounts of molecular data available from databases such as Genbank, and consensus knowledge on deep phylogenetic relationships for an increasing number of groups of organisms. Finally, we include a detailed step-by-step workflow pipeline (Supplementary material), from data acquisition to phylogenetic inference, mainly based on the R environment (widely used by ecologists) and the use of free web-servers, that has been applied to the reconstruction of a species-level phylogeny of all breeding birds of Europe.