Plant Phylogenetic

• Phylogeny


  The study of the evolutionary development of groups of organisms. The relationships are hypothesized based on the idea that all life is derived from a common ancestor.
• TWO TYPES OF CLASSIFICATION

  • PHENETICS
  • PHYLOGENETICS
• Phylogenetics Systematics


  From the Greek work "klados" which means "branch", first developed by German entomologist Willi Hennig
• Cladistics or Phylogenetic Systematics


  The method that groups organisms that share derived characters
• Cladogram or Phylogenetic Tree


  A branching diagram that conceptually represents the best estimate of phylogeny
• Cladogram


  • Used by a scientist studying phylogenetic systematics to visualize the groups of organisms being compared, how they are related, and their most common ancestors
  • Can be simple, comparing only two or three groups of organisms, or it can be enormously complex and contain all the known forms of life
• Parts of a Cladogram

  • Root represents the first common ancestor of all species
  • Nodes represent the separating stem point of origin, each node represents a possible ancestor who gave birth to two or more offspring species
  • Clade consists of an origin and all of its descendants, contains a certain node and all of its related branches
  • Lines represent evolutionary time, or a series of organisms that lead to the population it connects to
  • Taxon or outgroup is the most distantly related organism in the entire chart
• Orientation of a Cladogram
• Taxon Selection


  Includes both the group as a whole, called the study group or ingroup, and the individual unit taxa, termed Operational Taxonomic Units, or OTUs
• Outgroup


  A taxon that is closely related to but not a member of the ingroup, used to root a tree
• Cautions in Taxa Selection

  • The OTUs have to be clearly defined and distinguished from one another
  • The size of the study group itself needs to be sufficient to include in the analysis all likely closely related OTUs
  • Monophyly must be determined for both OTUs and the group as a whole before any analysis is conducted
• Monophyletic


  A valid clade that consists of the ancestor species and all its descendants
• Paraphyletic


  A grouping that consists of an ancestral species and some, but not all, of the descendants
• Polyphyletic


  A grouping that includes numerous types of organisms that lack a common ancestor
• Outgroup


  A species or group of species that is closely related to the ingroup, the various species being studied
• Homologies


  Shared characteristics that originated in an ancestor of the taxon
• Character Selection and Definition

  • Characters that are genetically determined and heritable (termed intrinsic)
  • Characters that are relatively invariable within an OTU
  • Characters that denote clear discontinuities from other similar characters and character states
• Shared Ancestral Character


  A character that originated in an ancestor of the taxon
• Shared Derived Character


  An evolutionary novelty unique to a particular clade
• In cladistics, only shared derived characters are considered informative about evolutionary relationships
• Shared Ancestral Characters


  • Chloroplast
  • Anchors or roots
• Derived Characteristic


  Unique to that clade, e.g. flower
• Discrete Characters


  A particular type of data, which contain information on how the species should be grouped together
• Character Correlation


  An interaction between what are defined as separate characters, but which are actually components of a common structure, the manifestation of a single evolutionary novelty
• Homologous Characters or Character States


  Identical traits present in the common ancestor of two or more taxa
• Homologous Taxa


  Thought to have similar or identical DNA sequences or gene groups through common ancestry, which could influence the evolution of a shared structure
• Homology


  Traits have common ancestry, may/may not share function, may/may not look alike
• Analogy


  Traits with common function evolved separately, do not share ancestry
• Homoplasy


  Traits are similar because of convergent evolution, parallel evolution or character reversal
• Types of Transformation Series

  • Binary character - a character with only two character states where only one transformation series exists
  • Multistate characters - characters having three or more character states which can be arranged in transformation series that are either ordered or unordered
  • Unordered transformation series - allows for each character state to evolve into every other character state with equal probability, in a single evolutionary step
  • Ordered transformation series - places the character states in a predetermined sequence that may be linear or branched
• Character Weighting


  The assignment of greater or lesser taxonomic importance to certain characters over other characters in determining phylogenetic relationships
• Character Polarity


  The designation of relative ancestry to the character states of a morphocline - are they ancestral or derived?
• Character Matrix


  A table that lists terminal taxa as rows and the characters as columns, with each cell coded with the character state applicable for each taxon-character combination
• Three Basic Assumptions in Cladistics

  • Change in characteristics occurs in lineages over time
  • Any group of organisms are related by descent from a common ancestor
  • There is a bifurcating pattern of cladogenesis
• Plesiomorphic


  The "original" state of a characteristic
• Apomorphic


  The "changed" state of a characteristic
• Bifurcating Pattern of Cladogenesis


  New kinds of organisms may arise when existing species or populations divide into exactly two groups
• How to Construct a Cladogram

  1. Compile a table of characters being compared

  2. Use the data to construct a Venn diagram

  3. Convert the Venn diagram into a Cladogram
• Principle of Parsimony


  The cladogram that is the shortest has the fewest number of steps, as character state changes are accepted as most probable because it minimizes the number of ad hoc hypotheses
• Maximum Likelihood


  The principle that given certain rules about how DNA changes over time, a tree can be found that reflects the most likely sequence of evolutionary events