Abstract
Several approaches have been developed to estimate both the relative and absolute rates of speciation and extinction within clades based on molecular phylogenetic reconstructions of evolutionary relationships, according to an underlying model of diversification. However, the macroevolutionary models established for eukaryotes have scarcely been used with prokaryotes. We have investigated the rate and pattern of cladogenesis in the genus Aeromonas (γ-Proteobacteria, Proteobacteria, Bacteria) using the sequences of five housekeeping genes and an uncorrelated relaxed-clock approach. To our knowledge, until now this analysis has never been applied to all the species described in a bacterial genus and thus opens up the possibility of establishing models of speciation from sequence data commonly used in phylogenetic studies of prokaryotes. Our results suggest that the genus Aeromonas began to diverge between 248 and 266 million years ago, exhibiting a constant divergence rate through the Phanerozoic, which could be described as a pure birth process.
Highlights
Speciation is a central topic in evolutionary science and has been the focus of an enormous amount of research, especially during the last 20 years [1,2,3]
Phylogenetic trees inferred from molecular sequences, those including all the living species in a higher taxonomic group, provide an indirect record of speciation events that have led to present day species [1]
Since Nee et al [4] proposed a method to estimate both speciation and extinction rates of a lineage from phylogenies reconstructed from contemporary taxa, several other methods mainly based on birth-death models have been developed [5]–[7]
Summary
Speciation is a central topic in evolutionary science and has been the focus of an enormous amount of research, especially during the last 20 years [1,2,3]. The recent expansion of molecular phylogenetics has provided a useful approach to overcoming this problem As tools such as DNA sequencing, genomics and proteomics become feasible for larger samples, it has been possible to analyse diversification patterns from molecular data. Several authors have developed methods to estimate changes in diversification rates through time and across lineages from phylogenetic data of extant species [4], [10], [11]. All these methods have potential applications in the study of speciation and extinction processes in organisms with few or no existent fossil records, such as prokaryotes, a major problem is the difficulty in estimating divergence times. Phylogenetic trees derived from DNA sequences only contain information about the relative timing of reconstructed speciation events (i.e. branch lengths of these trees represent the evolution rate multiplied by the elapsed time)
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