W17 L2 - Phylogenetics: Building Phylogenetic Trees

Flashcards about Phylogenetics lecture covering methods for building phylogenetic trees, including maximum parsimony and UPGMA.

What is a phylogenetic tree?

A hypothesis on how species are related to each other.

Why is finding the best phylogenetic tree a difficult task?

As the number of species increases, the number of possible phylogenetic tree scenarios rapidly scales up, making it a difficult task to find the correct tree.

What are the two main categories of methods to build phylogenetic trees?

Character based methods (maximum parsimony, maximum likelihood) and distance based methods (UPGMA).

What is the starting point for character-based methods in phylogenetics?

Building a character matrix.

What is considered an ancestral character in phylogenetic analysis?

A character found in both the outgroup and the ingroup, indicating it is present in their common ancestor.

What is a derived character in phylogenetic analysis?

A character that arose only once in the ingroup, defining a monophyletic group.

What are the three types of character-based methods for phylogenetic tree construction?

Maximum Parsimony, Maximum Likelihood, and Bayesian Inference

What is the basic assumption of maximum parsimony?

The tree that requires the fewest number of evolutionary changes is the most likely to be correct.

What are the steps to build a maximum parsimony tree?

Identify informative sites, place changes on the three hypotheses, and calculate the number of changes each informative site needs.

What is an informative site in the context of building a phylogenetic tree?

A position in the DNA sequence where at least two different nucleotides are present in at least two different sequences.

What is the role of the outgroup in phylogenetic analysis?

The species that is not within the analysis, but we are using it to identify which is the most ancestral form.

What does UPGMA stand for?

Unweighted Pair Group Method with Arithmetic Mean.

What are the key aspects of the UPGMA method?

UPGMA uses the sequences once to create a table of the number of changes, UPGMA is very fast.

What are the steps in constructing a phylogenetic tree using UPGMA?

Compare sequences by pairs, create a table of the number of differences, identify pairs with the lowest number of differences, and rework the table.