13.1 : Evolutionary Relationships through Genome Comparisons

Linnaeus's traditional classification of organisms is called cladistics, which is based on the differences in organism's physical characteristics, and scientists have commonly constructed trees, called dendrograms, to give visual representations of these splits and groups.

However, with the advent of modern technology, comparing DNA has become a common way to build such trees. If sequence data is examined across a single species, like humans, there is a very high degree of similarity in the genetic code, around 99.9%  because the genetic code of an organism is passed from parent to offspring.

Humans also share much of this DNA code with other species, like chimpanzees and mice, but the degree of overall similarity between human DNA and theirs is significantly different. This means that trees can be created for groups of species based on the similarities or differences between their genetic codes. This field of analysis, combining statistics, mathematical modeling, and computer science, is part of a field known as bioinformatics.

The genetic data used to create these trees can take many forms. For example, in molecular phylogeny one or two key genetic loci are sequenced and then compared across the species of interest.

However, as individual genes or genetic regions may evolve at vastly different rates in different species or even be exchanged between different species through horizontal gene transfer, these small-scale genetic surveys may not always provide accurate phylogenies.

In bacterial phylogenies, a technique called multi-locus sequence typing, or MLST, is often used. This method generates sequences across multiple genetic regions - typically housekeeping genes which are essential to cellular function and so are conserved across species.

However, the housekeeping genes may evolve slowly, hence, with MLST it is difficult to obtain strain-level resolution.

Finally, whole-genome sequencing, or WGS, can be used to elucidate evolutionary relationships. This method involves the sequencing of the complete genome of an organism, including mitochondrial DNA in eukaryotes, and even chloroplast DNA in plants.

WGS aligns the whole genomes at fine-scale resolution and can identify mutations or species specific markers, branching points, and even strains or populations of a single species. Such fine details may be missed in more targeted sequencing.