Success of Alignment-Free Oligonucleotide (k-mer) Analysis Confirms Relative Importance of Genomes not Genes in Speciation and Phylogeny

TL;DR

This paper demonstrates that alignment-free k-mer analysis effectively reflects the biological importance of genomes over genes in speciation and phylogeny, supported by mechanistic and theoretical insights.

Contribution

It provides a mechanistic and theoretical foundation for the biological significance of k-mer based alignment-free methods in phylogenetics and speciation.

Findings

Alignment-free k-mer methods align with chromosomal recombination models.

Genomic differences often drive speciation more than gene differences.

K-mer analysis supports the importance of genomes in evolutionary divergence.

Abstract

The utility of DNA sequence substrings (k-mers) in alignment-free phylogenetic classification, including that of bacteria and viruses, is increasingly recognized. However, its biological basis eludes many twenty-first century practitioners. A path from the nineteenth century recognition of the informational basis of heredity to the modern era can be discerned. Crick's DNA "unpairing postulate" predicted that recombinational pairing of homologous DNAs during meiosis would be mediated by short k-mers in the loops of stem-loop structures extruded from classical duplex helices. The complementary "kissing" duplex loops - like tRNA anticodon-codon k-mer duplexes - would seed a more extensive pairing that would then extend until limited by lack of homology or other factors. Indeed, this became the principle behind alignment-based methods that assessed similarity by degree of DNA-DNA reassociation in vitro. These are now seen as less sensitive than alignment-free methods that are closely consistent, both theoretically and mechanistically, with chromosomal anti-recombination models for the initiation of divergence into new species. The analytical power of k-mer differences supports the theses that evolutionary advance sometimes serves the needs of nucleic acids (genomes) rather than proteins (genes), and that such differences have often played a role in early speciation events.