Question

1) What are commons errors derived from the phylogenetic analysis? What are the implications of these errors?

5) List two methods to assess the validity of pylogenetic trees.

Answer 1

1) There are thousands of data sets available, for which the "true tree" is known very well from many independent sources of data. For example, in the primates there is fossil data, morphological data etc to show that chimp/human/gorilla shared a common ancestor more recently than those 3 to orangutan etc. For HIV-1 we have many data sets with known history. With deeper branchings, we know that amphibians preceded marsupials which preceded mammals, etc. There are also many ways to generate artificial sequences with known histories, and to retain true ancestors as the sequences are being artificially evolved. And then we can test phylogenetic reconstruction methods on that data.

2)

• By  doing Maximum-Likelihood or Bayesian phylogenetica, and not Neighbour-Joining. They are both more robust inferences
• do more than one type of tree reconstruction (both Likelihood and Bayesian)
• AIC tests or similar are also good ways to test how well your phylogeny holds up compared to an alternative reconstruction.