Define phylogeny and give the name of the branching diagram that represents phylogeny.

Phylogeny refers to the evolutionary history or pattern of descent of a group of organisms.

A phylogeny is visually represtented in the form of a  cladogram

What is phylogenetic systematics and what are its goals?

Phylogenetic systematics, or cladistics, is that branch of systematics concerned with inferring phylogeny. Its primary goal is the determination of life’s history of descent.

What are the lines of a cladogram called and what do they represent?

The lines of a cladogram are known as lineages, often referred to simply as “branches.” Lineages represent the sequence of ancestral-descendant populations through time, ultimately denoting descent.

What does a split, from one lineage to two, represent?

A split represents lineage divergence or diversification, the formation of two separate lineages from one common ancestor. (The two lineages could diverge into what would be designated separate species, the process of forming two species from one termed speciation.)

Name the term for both a preexisting feature and a new feature.

Preexisting feature: ancestral (also called plesiomorphic or primitive) condition. New feature: derived (also called apomorphic or advanced) condition.

What is the difference between an autapomorphy and a synapomorphy?

An autapomorphy occurs within a single lineage. A synapomorphy unites two or more lineages.

What does topology refer to and what is its significance in displaying cladograms?

Topology is the structure of the branching diagram, i.e., how lineages, including those terminating in taxa, are connected together. Cladograms can be displayed in different ways, yet still have the same topology.

What is a “phylogram” and how does it differ from a typical cladogram?

The term phylogram is often used for a cladogram that has an absolute time scale, such that nodes and branch lengths are calibrated and correspond more closely to real elapsed time.

What names are given to both the group as a whole and the individual component taxa in a cladistic analysis?

Group as a whole: ingroup. Individual components: operational taxonomic units (OTUs).

What precautions must be taken in taxon selection?

At a minimum, OTUs must be well-circumscribed and delimited from one another, and the study group itself should be large enough so that all probable closely related OTUs are included in the analysis. More specifically, both OTUs and ingroup should be deemed monophyletic before the analysis is begun.

What criteria are used in the selection and definition of characters and character states?

Generally, characters and their states should be: (1) genetically determined and heritable (termed “intrinsic”), (2) relatively invariable within an OTU, and (3) denote clear discontinuities from other similar characters and character states.

Why and how are characters assessed for character state discreteness?

Character states should be discrete or discontinuous from one another because phylogenetic systematics entails the recognition of an evolutionary transformation from one state discrete state to another.

Molecular characters and their states are usually discrete, although polymorphism of nucleotide base sites can occur.

For some morphological, qualitative characters, discontinuity of states is clear.  But for other features, such as quantitative characters, states may be evaluated for discontinuity by various statistical analyses, such as by comparing the means, ranges, and standard deviations or tests such as ANOVAS, t-tests, or multivariate statistics.

How might characters be correlated, and what should be done in a cladistic analysis if they are?

Characters may be correlated if what are defined as separate characters are actually components of a common structure, the manifestation of a single evolutionary novelty.

If characters are deemed to be correlated, they should either be combined into a single character or scaled, such that each component character gets a reduced weight in a phylogenetic analysis.

What is homology and how may it be assessed?

Homology is similarity resulting from common ancestry.

Homology is generally hypothesized based on some evidence of similarity, either direct similarity (e.g., of structure, position, or development) or similarity via a gradation series (e.g., intermediate forms between character states).

Hypotheses of homology are tested by means of a cladistic analysis.

What is homoplasy?

Homoplasy is similarity that is not the result of homology.

Name and define the two types of homoplasy and give an example of each.

1) Convergence is the independent evolution of a similar feature in two or more lineages.
2) Reversal is the loss of a derived feature with the reestablishment of an ancestral feature.

What is a transformation series or morphocline?

The hypothesized sequence of evolutionary change, from one character state to another, in terms of direction and probability.

What is character state polarity and what is the most common method for establishing polarity?

Polarity is the designation of relative ancestry to the character states of a morphocline.

Name, define, and discuss the rationale for the two basic types of transformation series.

An unordered transformation series allows for each character state to evolve into every other character state with equal probability, i.e., in a single evolutionary step.

An ordered transformation series places the character states in a predetermined sequence.

What is character weighting? Scaling? Why is either done?

Character weighting is the assignment of greater or lesser taxonomic importance to certain characters over other characters in determining phylogenetic relationships. Characters may be given greater weight in cases for which the designation of homology is considered relatively certain.

Character scaling is assignment of a weight that is the inverse of the number of characters. It may be done to prevent excess weighting of correlated characters.

What is a character step matrix? A character x taxon matrix?

a) A listing of character states in a top row and left column; intersecting numbers within the matrix indicate the number of steps required, going from states in the left column to states in the top row.

b) A tabulation of taxa and their corresponding characters and character states, in numerical form.

STOPPED AT 21 OF 55 REVIEW QUESTIONS!

I am assuming we do not need to know the rest since we did not cover them in lecture (and they are EXTREMELY boring).