The use of genome-level characters for phylogenetic reconstruction

Now that large-scale genome-sequencing projects are sampling many organismal lineages, it is becoming possible to compare large data sets of not only DNA and protein sequences, but also genome-level features, such as gene arrangements and the positions of mobile genetic elements. Although it is unlikely that comparisons of such features will address a large number of evolutionary branch points across the broad tree of life owing to the infeasibility of such sampling, they have great potential for resolving many crucial, contested relationships for which no other data seem promising. Here, I discuss the advancements, advantages, methods, and problems of the use of genome-level characters for reconstructing evolutionary relationships. Now that large-scale genome-sequencing projects are sampling many organismal lineages, it is becoming possible to compare large data sets of not only DNA and protein sequences, but also genome-level features, such as gene arrangements and the positions of mobile genetic elements. Although it is unlikely that comparisons of such features will address a large number of evolutionary branch points across the broad tree of life owing to the infeasibility of such sampling, they have great potential for resolving many crucial, contested relationships for which no other data seem promising. Here, I discuss the advancements, advantages, methods, and problems of the use of genome-level characters for reconstructing evolutionary relationships. Bacterial Artificial Chromosomes, a type of vector for cloning large inserts of DNA, typically 100–200 kb. any trait being considered for phylogenetic analysis (e.g. ‘type of limb’). the condition of the character for a particular taxon (e.g. ‘branched limbs’). a group of organisms that shares a common ancestor to the exclusion of the other considered taxa. a school of thought that emphasizes reconstructing evolutionary relationships solely through recognizing clades by a set of specific criteria for inference. changes to an identical character state occurring independently in separate lineages. the change of a character state back into an earlier occurring state. a type of vector for cloning DNA, typically in fragments of approximately 40 kb. features of a genome or its products other than the linear sequences of nucleotides or amino acids that can be assessed for phylogenetic analysis. a pattern of character states that supports an alternative to the true, accepted or most parsimonious evolutionary tree that is generally caused by evolutionary convergence or reversion. the parts of an evolutionary tree that connect one internal node to the next (i.e. not terminal branches). portions of a gene between the coding exons that are also transcribed, but are enzymatically removed from the mRNA before its translation into a protein. mitochondrial DNA that is incorporated into the nuclear genome as a pseudogene. homologous genes in two of more organisms that are related only by lineage splitting and not by gene duplication. one or more taxa assumed for the purpose of analysis to be less closely related to the other organisms being considered than they are to one another. phylogenetic reconstruction based on measures of overall similarity. mobile genetic elements that use an RNA intermediate in their transposition. a character state that can be inferred by outgroup comparison or other methods to be derived specifically for a particular clade. the parts of an evolutionary tree that lead only to the taxon considered (i.e. not internode branches). a misnomer based on an earlier, incorrect belief that all genomes share the same code for specifying amino acids from triplets of nucleotides (although it is nearly universal).