Rare Genomic Changes

Abstract

Sequence-based phylogenetic analyses can be biased by different sources of errors. Rare genomic changes constitute an interesting additional phylogenetic marker to test or propose hypotheses of evolutionary relationships. In difference to amino acid or nucleotide substitutions, these characters do not evolve clocklike. Several different marker systems have been explored in their value to provide additional synapomorphies for the support of monophyletic groups. Genome-level characters used include absence/presence patterns of mobile elements, microRNAs and introns. Moreover, gene order rearrangement and changes in the genetic code have been analysed to solve phylogenetic problems. Most promising has been a type of mobile elements known as retrotransposons, as due to their copy-and-paste mechanism and their nearly neutral evolution, they are close to a perfect phylogenetic marker. Only low levels of true convergency are reported for retrotransposons; however, in case of rapid radiations, high levels of lineage sorting can become apparent. These markers were successfully used in reconstructing bird or mammalian phylogenies, even though deeper relationships with divergences beyond an age of 50 million years might be only difficult or impossible to tackle. MicroRNAs showed a bigger potential to resolve deep phylogenies. These small RNAs involved in the regulation of gene expression are highly conserved across taxa and can be found in plants and animals. Especially, deep animal phylogeny has been investigated using microRNAs. However, convergent loss seems to be more frequent than previously assumed, thereby complicating analyses, which can be alleviated by using explicit evolutionary models. The usefulness of absence/presence patterns of introns, which are typically interrupting the coding sequences in eukaryotic genomes, has been established for some phylogenetic problems. Even though intron positions across eukaryotes are conserved, high levels of intron gain and intron loss are biasing analyses. A special case of intron markers are so-called near intron pairs, which seem to be more promising as a phylogenetic character. The historically oldest genome-level character used to unravel evolutionary relationships is the order of genes in the genome. Genes are coded on both strands of the DNA molecule, and several mechanisms (inversion, transposition, tandem duplication random loss, translocation, fusion, fission) can result in the rearrangement of the ancestral order. Most phylogenetic studies concentrated on gene order changes in unichromosomal organellar genomes, which due to their limited size were easier to access, even without next-generation sequencing. Gene order can be analysed either using distance methods or by coding all adjacent pairs into a character matrix to be analysed by parsimony or likelihood methods.