Abstract
Ernst Haeckel based his landmark Tree of Life on the supposed ontogenic recapitulation of phylogeny, i.e. that successive embryonic stages during the development of an organism re-trace the morphological forms of its ancestors over the course of evolution. Much of this idea has since been discredited. Today, phylogenies are often based on families of molecular sequences. The standard approach starts with a multiple sequence alignment, in which the sequences are arranged relative to each other in a way that maximises a measure of similarity position-by-position along their entire length. A tree (or sometimes a network) is then inferred. Rigorous multiple sequence alignment is computationally demanding, and evolutionary processes that shape the genomes of many microbes (bacteria, archaea and some morphologically simple eukaryotes) can add further complications. In particular, recombination, genome rearrangement and lateral genetic transfer undermine the assumptions that underlie multiple sequence alignment, and imply that a tree-like structure may be too simplistic. Here, using genome sequences of 143 bacterial and archaeal genomes, we construct a network of phylogenetic relatedness based on the number of shared k-mers (subsequences at fixed length k). Our findings suggest that the network captures not only key aspects of microbial genome evolution as inferred from a tree, but also features that are not treelike. The method is highly scalable, allowing for investigation of genome evolution across a large number of genomes. Instead of using specific regions or sequences from genome sequences, or indeed Haeckel’s idea of ontogeny, we argue that genome phylogenies can be inferred using k-mers from whole-genome sequences. Representing these networks dynamically allows biological questions of interest to be formulated and addressed quickly and in a visually intuitive manner.
Highlights
Ernst Haeckel coined the term Phylogenie to describe the series of morphological stages in the evolutionary history of an organism or group of organisms[1]
Morphologies observed at different developmental stages of an organism resemble and represent the successive stages of its ancestors over the course of evolution. He worked before the advent of genetics and the modern synthesis, and before it was appreciated that information on hereditary is carried by DNA and can be recovered by sequencing and statistical analysis
Using simulated and empirical sequence data, we recently demonstrated that alignment-free approaches can yield phylogenetic trees that are biologically meaningful[25,26,27]
Summary
1. Bernhard Haubold, Max Planck Institute for Evolutionary Biology, Plön, Germany. Any reports and responses or comments on the article can be found at the end of the article. This article is included in the Phylogenetics collection. In this revision, we have rewritten part of the Abstract and Introduction to clarify that (a) phylogenetic approaches based on multiple sequence alignment do not exclude inference of a network, (b) multiple sequence alignment is computationally demanding, and that (c) phylogenetic inference is complicated by non-treelike evolutionary processes that shape microbial genomes. In Results and discussion, we have provided justification for using the 143-genome dataset in this work, and have made explicit the scope of this study. We have cited a number of additional publications in the areas of phylogenetic networks and alignment-free methods
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