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Phylogenetics Glossary
Vocab
31
Biology
Undergraduate 4
01/30/2013

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Term
Apomorphy
Definition

derived characteristic of a clade. Any feature novel to a species and its descendants.


Important for feterminind relationshops in cladistic analyses. 


In a character transformation series with more than two states, a particular character state may be apomorphic relative to some states and plesiomorphic relative to other states

Term
Autapomorphy
Definition
An apomorphic character state unique to a single taxon in a cladogram and though to have orgininated within that taxon
Term
Bootstrap analysis
Definition

Technique sometimes used in cladistic analysis to place confidence intervals on the resulting cladograms. 

 

A majority rule concensus tree is created that includes all of the monophyletic taxa that show up in at least 95% of the resulting cladograms

Term
Character
Definition
Any attribute of an organism that can be consistently measured, counted or otherwise defined.
Term
Character State
Definition
One of the expressions of a character (ex. color)
Term
Character Transformation Series
Definition
A hypothesized sequence of changes of states in a character from the most plesiomorphic (primitive) to the most apomorphic (derived). The sequence may be linear or branched
Term
Cladistics
Definition
A type of analysis of phylogenetic relationships in which monophyletic taxa are grouped on the basis of shared derived features (synapomorphies).
Term
Cladogram
Definition
A graphic display of a hypothesis of relationship among a group of taxonomic entities in the form of a branching diagram. The branching sequence is based on the inferred historical connections between the entities. 
Term
Concensus Tree
Definition

A branching diagram that shows the branching patterns shared among a group of alternative cladograms. Areas of disagreement result in polychotomies (unresolved areas in the cladogram where multiple branches arise together). 

 

Term
Strict Consensus Tree
Definition
Includes only those parts of the cladogram that are shared by all of the alternative cladograms
Term
Majority Rule Consensus Tree
Definition
Includes only those parts of the cladogram that are shared by most of the alternative cladograms
Term
Convergent Evolution
Definition
Where two or more kinds of unrelated or distantly related organisms independenly acquire what appears to be the same character state from different preexisting ancestral character states
Term
Data Matrix
Definition
A taxon by character table displaying the character states present in each taxon
Term
Homoplasy
Definition

The result of parallel or convergent evolution in which two or more kinds of organisms independently acquire the same (or apparently the same) character state. 

 

Sometimes also results from reversals  when in a particular lineage a character reverts from an apomorphic to a plesiomorphic state

Term
Ingroup
Definition

The monophyletic group being studied.


It is compared to the outgroup, or the ancestor or otherwise related to the ingroup (double check this. I'm not sure if it has to be an ancestor or can be otherwise related). 

Term
Monophyletic
Definition

In cladistic analyses, a natural taxonomic group composed of an ancestral taxon and all of its descendants. 

 

Some taxonomists may use the use the term monophyletic in the sense of paraphyletic to include taxa derived from a common ancestor but not necessarily including all descendants.

Term
Node
Definition
A branching point in a cladogram, representing a speciation event
Term
Parallel Evolution
Definition
The situation in which two or more kinds of related organisms independently acquire the same character state from the same preexisting ancestral character states
Term
Paraphyletic
Definition
Taxonomic group that includes an ancestral species and some, but not all of its descendants
Term
Parsimony Criterion
Definition

The simplest answer, with the fewest steps is the correct one. 

This is also called Ockham's razor. 

Term
Phylogenetic tree
Definition
A postulated set of relationships among a group of organisms. Often includes a postulated ancestor-descendant relationships and a time scale. 
Term
Phylogeny
Definition
The evolutionary history of a group of organisms
Term
Plesiomorphy
Definition

An evolutionary primitive character state. In a character transformation series the original state is plesiomorphic to all others. 

 

In a character transformation series with more than two states, a particular character state may be apomorphic relative to some states and plesiomorphic relative to others.

Term
Polarization
Definition
Determining which of a pair of character states is plesiomorphic (ancestral) and which is apomorphic (derived)
Term
Polyphyletic
Definition
A nonnatural taxonomic group composed of organsims without a common history, hypothesized to have origins in two or more different evolutionary lines; the most recent common ancestor of the two lineages is excluded from the group
Term
Reversal
Definition
Situation within a monophyletic lineage in which an apomorphic character state reverts to the plesiomorphic condition. Reversals represent a sourse of homoplasy in cladistic analyses
Term
Sister group
Definition
A monophyletic taxon that is hypothesized to be the closest relative of a given taxon. 
Term
Step
Definition
Any hypothesized character state change within the structure of a particular hypothesis of relationship (cladogram)
Term
Symplesiomorphy
Definition
A plesiomorphic character state shared by two or more taxa. In cladistic studies, symplesiomorphies are not considered to be evidence for linking taxa in a cladogram.
Term
Synapomorphy
Definition
An apomorphic (derived) character state shared by two or more taxa, considered in cladistic studies to be evidence of relationship
Term
Tree Length
Definition
The number of steps (hypothesizes character state changes) required by the structure of particular cladogram based on a given set of data. Cladograms of different tree length are judged by the parsimony criterion. 
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