Question

Describe TWO advantages of phylogenomic methods over traditional single-gene phylogenetics and provide examples to justify answer.

Answer 1

Phylogenetics is the study of reconstructing the evolutionary history of life on Earth. Traditionally, phylogentics were constructed using morphological data only, but the introduction of Sanger sequencing and PCR in the late 1970s enabled genetic information to be incorporated into phylogenetic analyses.Traditional Sanger sequencing studies include relatively few loci and are therefore limited by stochastic error. As there is a relatively small number of phylogenetically informative characters available in one or a few genes, this random noise influences the inference of backbone nodes, potentially leading to poorly resolved or poorly supported phylogenetic trees. This problem can be addressed successfully by using much larger amounts of sequence data

When molecular data were used, a single experiment can provide information on lot of different characters: in a DNA sequence, for example, every nucleotide position is a character with four character states, A, C, G and T. Large molecular datasets can therefore be generated relatively quickly.Molecular character states are unambiguous: A, C, G and T are easily recognizable and one cannot be confused with another. Some morphological characters, such as those based on the shape of a structure, can be less easy to distinguish because of overlaps between different character states.Molecular data are easily converted to numerical form and hence are amenable to mathematical and statistical analysis.This operation is repeated until all the possible pairs have been examined, enabling the combination that gives the tree with the shortest total branch length to be identified. This pair of sequences will be neighbors in the final tree; in the interim, they are combined into a single unit, creating a new star with one branch fewer than the original one. The whole process of pair selection and tree-length calculation is now repeated so that a second pair of neighboring sequences is identified, and then repeated again so that a third pair is located, and so on. The result is a complete reconstructed tree