Computational phylogenetics uses algorithms and statistical methods to infer evolutionary relationships from biological data. This lesson introduces the kinds of data used, the basic forms of trees and networks, and the challenges of deciding which characters are homologous.
A phylogenetic tree is a model of evolutionary relationships among genes, species, or other taxa. Computational methods search for a tree that describes the observed data well according to an optimality criterion. Common criteria include maximum likelihood, maximum parsimony, Bayesian inference, and minimum evolution.
All flashcards
What is phylogeny search space?
The set of possible tree topologies for a given group of taxa.
What distinguishes a rooted tree from an unrooted tree?
A rooted tree specifies a hypothesized ancestor and direction of descent; an unrooted tree represents relationships without specifying either.
What is an outgroup used for in phylogenetics?
A taxon outside the group of interest that can help locate the root and orient relationships.
Why can a gene tree differ from a species tree?
A gene's evolutionary history can differ from the species history because of processes such as gene transfer or incomplete lineage sorting.
What is a supermatrix?
A concatenated alignment of multiple genes, often partitioned so different genes or data types can be modeled separately.
Quiz questions
What criterion defines maximum-parsimony tree inference?Answer: It selects the tree requiring the fewest or least costly evolutionary changes.
What does Bayesian phylogenetic inference produce?Answer: A posterior distribution of trees based on the data likelihood and prior assumptions.
How are bootstrap replicates commonly generated for phylogenetic support analysis?Answer: Alignment columns are sampled with replacement to form replicate datasets.
Compared with AIC, how does BIC penalize model complexity?Answer: BIC generally applies a stronger penalty for additional model parameters.
What does Bremer support for a clade measure?Answer: The additional evolutionary steps needed before that clade is contradicted.