[Molecular dating in the genomic era]

Prospects for building large timetrees using molecular data with incomplete gene coverage among species

Scientists are assembling sequence data sets from increasing numbers of species and genes to build comprehensive timetrees. However, data are often unavailable for some species and gene combinations, and the proportion of missing data is often large for data sets containing many genes and species. Surprisingly, there has not been a systematic analysis of the effect of the degree of sparseness of the species-gene matrix on the accuracy of divergence time estimates. Here, we present results from computer simulations and empirical data analyses to quantify the impact of missing gene data on divergence time estimation in large phylogenies. We found that estimates of divergence times were robust even when sequences from a majority of genes for most of the species were absent. From the analysis of such extremely sparse data sets, we found that the most egregious errors occurred for nodes in the tree that had no common genes for any pair of species in the immediate descendant clades of the node in question. These problematic nodes can be easily detected prior to computational analyses based only on the input sequence alignment and the tree topology. We conclude that it is best to use larger alignments, because adding both genes and species to the alignment augments the number of genes available for estimating divergence events deep in the tree and improves their time estimates.

[Tree thinking: the evolution of vertebrate as a case study]

In the last decades, the reconstruction of phylogenetic relationships and their representation in the form of a phylogenetic tree have become a powerful tool for biology. These methods involve the use of sophisticated computer programs that are unfamiliar to most of biologists. However, our experience as teacher and researcher in evolutionary biology prompted us to realize that the main and most common source of confusion in depicting the evolution of various traits comes from the misunderstanding of the basis of tree reading. We have identified, not only in the work of our students, but also in scientific literature, some common mistakes that reveal the persistency of the concept of the scale of beings that unfortunately maintained as frame of reference to analyse phylogenies.

Signature of a primitive genetic code in ancient protein lineages

The genetic code is the syntactic foundation underlying the structure and function of every protein in the history of the biological world. Its highly ordered degenerate complexity suggests an incremental evolution, the result of a combination of selective, mechanistic, and random processes. These evolutionary processes are still poorly understood and remain an open question in the study of early life on Earth. We perform a compositional analysis of ribosomal proteins and ATPase subunits in bacterial and archaeal lineages, using conserved positions that came and remained under purifying selection before and up to the most recent common ancestor. An observable shift in amino acid usage at these conserved positions likely provides an untapped window into the history of protein sequence space, allowing events of genetic code expansion to be identified. We identify Cys, Glu, Phe, Ile, Lys, Val, Trp, and Tyr as recent additions to the genetic code, with Asn, Gln, Gly, and Leu among the more ancient. Our observations are consistent with a scenario in which genetic code expansion primarily favored amino acids that promoted an increase in polypeptide size and functionality. We propose that this expansion would have been critical in the takeover of many RNA-mediated processes, as well as the addition of novel biological functions inaccessible to an RNA-based physiology, such as crossing lipid membranes. Thus, expansion of the genetic code likely set the stage for the transition from RNA-based to protein-based life.