Phylogenetics #16 Flashcards
What is a phylogeny?
A phylogeny is the history of species birth and death, depicting the two major processes of anagenesis (evolutionary change of features within a single lineage) and cladogenesis (branching of a lineage into two or more descendant lineages).
How are phylogenies inferred?
Phylogenies are inferred from similarities and differences in homologous characters (inherited from common ancestors), which include morphology, phenotypes, and DNA sequences.
What are the methods for inferring phylogenies?
The methods include distance methods (UPGMA, NJ, LS, ME), sequence methods (maximum parsimony, maximum likelihood, Bayesian), and evaluation of the tree using pairwise distance, pathway of least resistance, or maximum likelihood.
How do we read a tree?
Time is usually implicit and relative, and closely related species do not necessarily have similar morphologies. Phylogenies can also contain polytomies and can differ depending on the marker and gene trees used.
What are the issues with phylogenies?
Inferring a phylogeny is difficult when many characters evolve repeatedly, mutations occur frequently, and gene trees and species trees are incongruent. Additionally, paralogues (resulting from ancestral gene duplication) can have different phylogenetic histories.
