Chapter 2 Flashcards
Branching diagram in which 3 or more taxa arise from single hypothetical ancestor
Arise from incomplete or missing data
Polytomy
The hybridization of 2 previously divergent taxa forming a new lineage
Should always be treated as a possibility
Reticulation
Common ancestor plus all descendants of that ancestor
Monophyletic group
2 descendant lineages or clades from a single common ancestor
Sister groups
Includes common ancestor and some but not all known descendants of that ancestor
Paraphyletic group
Contains 2 or more common ancestors
Polyphyletic group
How is monophyly ascertained?
By recognition of one or more unique, shared derived character states that argue for most recent common ancestry of all members of taxon in question
Cladogram derived by combining the features in common between 2 or more cladograms
Consensus tree
Collapses differences in branching pattern between 2 or more cladograms to a polytomy
Strict consensus tree
Only those clades that occur in 50% or more of a given set of trees are retained
50% majority tree
With molecular sequence data, one or more taxa will have a large # of automorphies relative to other taxa in the analysis
Long branch attraction
Grouping taxa in which polarity is not indicated
Unrooted trees
Evaluates alternative trees but considers the probability, based on some selected model of evolution that each tree explains the data
Mostly for molecular sequence data
Helps prevent long branch attraction
Maximum likelihood
Change from one base to another is equivalent to the reverse
GTR general time- reversible model
Based on calculations using posterior probability
Yield the posterior probabilities for each of the branches of a given tree
Rapid
Similar to maximum likelihood
Bayesian inference
Measure of relative amount of homoplasy in cladogram
Close to 1 indicates little to no homoplasy
0 indicates considerable homoplasy
CI - Consistency index
CI + RI
RCI RESCALED CONSISTENCY INDEX
Reanalyzes the data of the original character x taxon matrix by selecting characters at random, such that a given character can be selected more than once
Can give more weight to some characters but total # is the same as original matrix
Bootstrap
Similar to bootstrap but differs in that each randomly selected character may only be resample once and the resultant resample data matrix is smaller than the original
Jackknife
Measure of how many extra steps are needed (beyond the # in most parsimonious cladograms before the original clade is no longer retained
Clade decay
Provides meadure of robustness in calculating posterior probabilities of 95% or greater is statistically well-supported
Bayesian analysis
Devised by naming and ordering monophyletic groups in a sequential, hierarchical classification
Indented method
Sequential listing of derivative lineages from the base to the apex of the cladogram, each derivative lineage receiving the same hierarchical rank
Annotation method
Recognizes common ancestor as the basis if the cladogram and all descendants of that common ancestor as the basis for grouping
Node-based