Lecture 10 - Phylogeny Flashcards
define: molecular study
study of changes in genes and proteins throughout different branches of the tree of life
define: phylogeny
inference of evolutionary relationships (homology)
compare: traditional and current phylogenetic study
traditionally: morphological features
currently: molecular sequence data
molecular clock hypothesis
for every given protein, the rate of molecular evolution is approximately constant in all evolutionary lineages
neutral theory of evolution
the main cause of evolutionary change is a random drift of mutant alleles that selectively neutral; positive Darwinian selection has a limited role
define: topology
branching pattern of tree
how can branch length be scaled
to evolutionary distance or time
define: taxon
a distinct group of organisms, a node on the tree
what do leaves represent in phylogenetic trees
OTUs - operational taxonomic units
what do internal nodes in phylogenetic tree represent
hypothetical ancestors
define: root
a common ancestor of all OTUs under study
what do nodes represent
represent taxa
what are the two types of internal nodes
bifurcating (2 branches) and multifurcating (> 3 branches)
what is an unrooted tree
tree without a common ancestor specified
define: outgroup
a taxon known to be distantly related to all other OTUs, but not expected to be within the target group
what can outgroups be used for
rooting a tree
define: cladogram
tree with branch lengths unscaled
define: phylogram/additive tree
tree with branch lengths that are scaled
define: ultrametric tree
tree with branches that assumes a constant rate of mutation
define: monophyletic group
all taxa are derived from a common ancestor
define: paraphyletic group
group that does not contain all descendants of the same common ancestor
define: polyphyletic group
group that is derived from more than one common ancestor
define: Newick format
text representation of a tree, recorded as a set of nested brackets specifying a hierarchy
draw this tree
((C , (A , B)) , (D , E));
