"Choanoflagellates are protists. The other four taxa are animals. Which phylogenetic tree highlights the most recent common ancestor of all animals?"

Using molecular data to build trees

A tool that has revolutionized, and continues to revolutionize, phylogenetic analysis is DNA sequencing. With DNA sequencing, rather than using physical or behavioral features of organisms to build trees, we can instead compare the sequences of their orthologous (evolutionarily related) genes or proteins.

The basic principle of such a comparison is similar to what we went through above: there's an ancestral form of the DNA or protein sequence, and changes may have occurred in it over evolutionary time. However, a gene or protein doesn't just correspond to a single characteristic that exists in two states.

Instead, each nucleotide of a gene or amino acid of a protein can be viewed as a separate feature, one that can flip to multiple states (e.g., A, T, C, or G for a nucleotide) via mutation. So, a gene with 300300300 nucleotides in it could represent 300300300 different features existing in 444 states! The amount of information we get from sequence comparisons—and thus, the resolution we can expect to get in a phylogenetic tree—is much higher than when we're using physical traits.

To analyze sequence data and identify the most probable phylogenetic tree, biologists typically use computer programs and statistical algorithms. In general, though, when we compare the sequences of a gene or protein between species:

A larger number of differences corresponds to less related species

A smaller number of differences corresponds to more related species