One of the basic ideas of biology is Darwin’s notion that all life on this planet is related through common ancestors at some time. It is only though the passage of ‘deep’ time, the infidelity of genetic machinery (among other processes) leading to variation and the separation of species by physical (or other) boundaries that has led to divergence into the great variety of species we see today. Constructing phylogenetic trees is a simple graphical way of communicating this concept.
The Animal Tree of Life, published in the 15 Feb 2013 Science magazine <LINK>discusses the construction of a phylogenetic tree over the past 25 years since molecular evidence was admitted as a means of establishing relationships with greater accuracy, and with less subjectivity than ever before. “ For the past century, the use of detailed descriptions of animal adult morphology and embryology has been at the heart of the study of evolutionary relationships among distant groups such as phyla. However the methodology can have both implicit problems and practical difficulties.” 1
This early paper used 18S rRNA sequences extensively to derive phylogenies because it was thought that this gene was required for life of many (all?) organisms and that sequence was highly critical to an organism’s survival, and would suffer fewer modifications over time than other, less crucial genes.
The earlier disagreements derived from varying interpretations of the morphological and embryological characteristics of animals. Many of these characters have evolved repeatedly in unrelated lineages as adaptations to similar selective pressures or have been lost from certain groups through disuse. Today’s strengthening consensus is almost entirely thanks to the use of molecular genetic data in reconstructing trees. Heritable changes in nucleotides and amino acids are abundant and generally much less prone to the problems of convergent evolution and loss than are morphological characters.2
More recently, sequencing of mitochondrial and chloroplast DNA has revealed these organelles’ relationship to free-living bacteria, providing an interesting challenge for illustrators of these genetic trees and establishing solid data supporting the endosymbiotic theory.
Using the great wealth of DNA data we have today, relationships can be determined using similarities found in a number of different genes, providing a high degree of statistical assurance that the conclusions are unbiased and accurate.
1. K. G. Fieldet al., Science 239, 748 (1988).
2. M. J. Telford, R. R. Copley, Trends Genet. 27, 186 (2011).