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
Internode plus all descendants of that stem
Stem-based
All members of a monophyletic group that share a given, unique evolutionary event are grouped together
Apomorphy-based
Grouped by overall similarity, represented in the form of a branching diagram called phonogram
Grouped by ancestral and shared derived traits
Phenetic classification
Ancestral features
Symplesiomorphies
Derived character states
Synapomorphies
Characters representation (plotting) on a cladogram in the most parsimonious way, such that the minimal # of character state changes occur between nodes
Minimizes tree length
Parsimony optimization
Optimization hypothesis an earlier initial state change w/ a later reversal of the same character
Acctran accelerated transformation
Optimization hypothesizes two later, convergent state changes
Deltran delayed transformation
Emphasizes determining the character condition at each ancestral node rather than changes between nodes
Ancestral state reconstruction
Movement of an organism or propalogue from one region to another, such as the transport of a seed or fruit by wind, bird, water from a continent to an island
Dispersal
Splitting of one population into two or more
Vicariance
Mature structures end
Ontogeny
Evolutionary change in the rate or timing of development
Heterochrony
Derived type of heterochrony in which ontogeny passes through and goes beyond the stages trajectory of the ancestral condition
Peramorphosis
Type of heterochrony in which the mature or adult stage of the derived ontogenetic sequence resembles a juvenile ontogenetic stage if the ancestral condition
Paedomorphosis
Type of paedomorphosis that is caused by a decrease in the rate of development of a structure
Neotony
