Cladistics

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Cladistics

• Making a Phylogenetic Tree

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The Discovery of Cells

• In the 1600s, biology was changed forever by the
  discovery and refining of lenses.
• This led to the discovery of cells.
• The discovery of cells caused naturalists to
  realize that at the microscopic level, all
  organisms are related.

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The Need to Classify

• This realization that organisms are all more
  closely related than people thought, along with
  the constant discovery of new life in the
  Americas, led scientists to want a disciplined
  unit of naming and classifying life.
• The first system of classification was only
  interested in naming and organizing life.
• It was not interested in showing that life was
  relatedWhy not?

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Taxonomy

• Taxonomy is the original system created by
  Carolus Linnaeus for classifying life.
• Much of Linnaeus system is still used today.

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Whats in a Name

• The common names of organisms have no rules.
• In the United States, we call both black vultures
  and turkey vultures buzzards.
• But in the United Kingdom, what they call
  buzzards are all the broad-winged hawks.   

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Whats in a Name

• Another problem was that scientists would change
  the name of species based on a whim, not on a set
  of rules.
• Inconsistencies like these led to the creation of
  a system of naming things that allows scientists
  all over the world to communicate more precisely.
  

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Binomial Nomenclature

• The system that Linnaeus created names species
  according to their genus and species.
• The genus name is capitalized.
• The species name is not.
• Both the genus and species name should be
  italicized.

Homo sapien Pan troglodytes Musa acuminata
Write your first and last name as if you were
classifying yourself as a species.
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Taxon (Plural Taxa)

• A taxon can represent an organism or a group of
  organisms.
• In the Linnaean system organisms were organized
  into taxa based on similarities.
• However, Linnaeus thought these taxa appeared
  because life was created in a hierarchy from the
  simplest organisms to humans.

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Cladistics

• Linnaeus did not think that the similarities of
  life were because more complex life came from a
  simpler ancestral life.
• Darwin and Wallace changed that!
• As evolution became more and more accepted, the
  Linnaean system had to be revised.
• A new system called cladistics was born.

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Terminology

• Phylogeny
• Evolutionary Tree
• Phylogenetic Tree
• Cladogram
• Although these terms are sometimes used
  differently, for our purposes they all mean
  basically the same thing.

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Phylogeny

• A phylogeny, evolutionary tree, or phylogenetic
  tree represents the evolutionary relationships
  among a taxa or a group of taxon.

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Clade

• Once Biologists realized that taxa were all
  related, they came up with a new term called a
  clade.
• A clade is a group of taxa that are all related.
  
• A clade includes an ancestor and all descendents
  of that ancestor.
• You can think of a clade as a branch on the tree
  of life.

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The Tips and Nodes

• The tips of the tree represent groups of
  descendent taxa (often species).
• The nodes on the tree represent the common
  ancestors of those descendents.

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Sister Groups

• Two descendents that split from the same node are
  called sister groups. In the tree below, species
  A B are sister groups they are each other's
  closest relatives.

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The Outgroup

• Many phylogenies also include an outgroup a
  taxon outside the group of interest.
• All the members of the group of interest are more
  closely related to each other than they are to
  the outgroup.

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The Outgroup

• An outgroup can give you a sense of where on the
  bigger tree of life the main group of organisms
  falls.
• It is also useful when constructing evolutionary
  trees.

Which taxon is the outgroup?
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Cladistics

• Cladistics is a method of hypothesizing
  relationships among organisms in other words, a
  method of reconstructing evolutionary trees.

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Cladistic Analysis

• The basis of a cladistic analysis is data on the
  morphologies (characters, or traits), of the
  organisms in which we are interested.
• These characters could be
• Anatomical characteristics
• Physiological characteristics,
• Behavioral characteristics
• Genetic sequence similarities
• Amino acid sequence similarities

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3 Cladistic Assumptions

• AssumptionsThere are three basic assumptions in
  cladistics
• 1. Change in characteristics occurs in lineages
  over time.The assumption that characteristics of
  organisms change over time is the most important
  one in cladistics.

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• We call the "original" state of the
  characteristic plesiomorphic (primitive) and the
  "changed" state apomorphic (derived).

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3 Cladistic Assumptions

• 2. Any group of organisms is related by descent
  from a common ancestor.This assumption is
  supported by many lines of evidence and
  essentially means that all life on Earth today is
  related and shares a common ancestor.

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3 Cladistic Assumptions

• There is a bifurcating, or branching, pattern of
  lineage-splitting.This assumption suggests that
  when a lineage splits, it divides into exactly
  two groups.
• There are some situations that violate this
  assumption.