non-specialist

The evolutionary transition from homo-oligomerism to hetero-oligomerism in multi-meric proteins and its contribution to function innovation and organism complexity remains to be investigated. Here we undertake the challenge of contributing to this theoretical ground by investigating the hetero-oligomerism in the molecular chaperonin CCT from archaea. CCT is amenable to this study because, in contrast to eukaryotic CCTs where sub-functionalisation after gene duplication has been taken to completion, archaeal CCTs present no evidence for subunit functional specialisation. Our analyses yield additional information to previous reports on archaeal CCT paralogy by identifying new duplication events. Analyses of selective constraints show that amino acid sites from one subunit have fixed slightly deleterious mutations at inter-subunit interfaces after gene duplication. These mutations have been followed by compensatory mutations in nearby regions of the same subunit and in the interface contact regions of its paralogous subunit. The strong selective constraints in these regions after speciation support the evolutionary entrapment of CCTs as hetero-

The reduced cost of high throughput sequencing, increasing automation, and the amenability of sequence data for evolutionary analysis are making DNA data (or the corresponding amino acid sequences) the molecular marker of choice for studying microbial population genetics and phylogenetics. Concomitantly, due to the ever-increasing computational power, new, more accurate (and sometimes faster), sequence-based analytical approaches are being developed and applied to these new data. Here we review some commonly used, recently improved, and newly developed methodologies for inferring population dynamics and evolutionary relationships using nucleotide and amino acid sequence data, including: alignment, model selection, bifurcating and network phylogenetic approaches, and methods for estimating demographic history, population structure, and population parameters (recombination, genetic diversity, growth, and natural selection). Because of the extensive literature published on these topics this review cannot be comprehensive in its scope. Instead, for all the methods discussed we introduce the approaches we think are particularly useful for analyses of microbial sequences and where possible, include references to recent and more inclusive reviews.

Research article The complete mitochondrial genome of a basal teleost, the Asian arowana (Scleropages formosus, Osteoglossidae)

Research article Evolutionary history of histone demethylase families: distinct evolutionary patterns suggest functional divergence

Research article The Caenorhabditis globin gene family reveals extensive nematode-specific radiation and diversification

This is an Open Access article distributed under the terms of the Creative Commons Attribution License

Research article Evidence of a chimeric genome in the cyanobacterial ancestor of plastids

Research article The ancestor of the Paulinella chromatophore obtained a carboxysomal operon by horizontal gene transfer from a Nitrococcus-like γ-proteobacterium

PDF corresponds to the article as it appeared upon acceptance. Fully formatted PDF and full text (HTML) versions will be made available soon. Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships