Phylogenetic Trees & Cladograms (College Board AP Biology)

• Evolutionary relationships between species can be represented visually using a diagram called a cladogram
• Cladograms are evolutionary trees that show probable order of divergence from ancestral species and therefore probable relationships between species
• Analysis of a cladogram can provide several pieces of information
• The point at which two branches separate is known as a node, and represents common ancestor species
  • A node immediately adjacent to a pair of clades indicates that these two clades share a recent common ancestor
  • This shows that the two clades are more closely related to each other than they are to any other clade in the cladogram
  • If several nodes need to be traced back before two clades can be joined, this indicates a more distant relationship between two clades

Cladogram Example

A cladogram with notes to indicate some of the conclusions that can be drawn from it.  A cladogram like this one contains no numbers or time scale, so it does not show the number of base or amino acid changes that have occurred between one node and the next, or how much time has passed between nodes

Phylogenetic Tree

• A phylogenetic tree looks rather similar to a cladogram, with some subtle but important differences
• Sometimes, the terms are used interchangeably despite the differences in meaning
• The layout of each diagram is similar
  • With a branching structure
  • Though phylogenetic trees display branches whose lengths indicate the amount of evolutionary change between organisms
• Phylogenetic trees are thought to be an account of proven scientific fact, whereas cladograms represent hypotheses about ancestry relationships between species that are as yet not fully accepted
  • Phylogenetic trees show data that is calibrated against other data sources such as the fossil record or the molecular clock (see below)
• However, there is no overall consensus in the scientific community about the differences between cladograms and phylogenetic trees
  • Therefore, the two terms are often used interchangeably to refer to a branched diagram that shows ancestral relationships

The Molecular Clock

• The evolutionary relationships between species can be determined by analyzing sequence data from, e.g. DNA bases, mRNA bases, or amino acids in polypeptides
• The number of differences between sets of sequence data provides information on how closely related two species are
  
  • The more differences there are between the sequences, the longer ago the species diverged, and vice versa
  • The number of differences between sequences can be determined using a method known as DNA hybridization
    
    • Sections of single stranded DNA from corresponding parts of the genome are taken from two species
    • The two complementary strands are allowed to bind to each other, or hybridize
    • The points on the DNA strand that do not bind show where bases are different to each other
    • The number of differences is recorded
• The differences between sequence data can also be used to produce a quantitative estimate for how long ago two species diverged from each other
  
  • Differences in sequence data come about due to mutations in the DNA
  • Evidence suggests that mutations occur at a fairly constant rate
  • This means that the number of mutations that have occurred gives an indication of the amount of time that has passed since two species diverged
  • Scientists refer to the constant rate of mutation as the molecular clock
    
    • It is worth noting that the assumed rate of mutations does not always match with the actual rate at which mutations occur, so the molecular clock provides estimates rather than exact time periods
• The rate at which mutations accumulate can be affected by, eg.
  
  • Generation time
  • Population size
  • Selection pressures
• Analyzing the differences in sequence data allows evolutionary biologists to determine the order in which different species diverged from a common ancestor, and therefore how closely related species are

Phylogenetic Tree Example

A phylogenetic tree includes a timescale that shows the evolutionary distance between different species

Interpretation of Phylogenetic Trees & Cladograms

• Phylogenetic trees and cladograms both show evolutionary relationships among lineages
• Phylogenetic trees and cladograms both show relationships between lineages, but phylogenetic trees show the amount of change over time calibrated by fossils or a molecular clock
• Traits that are either gained or lost during evolution can be used to construct phylogenetic trees and cladograms
  • Shared characters are present in more than one lineage
  • Shared, derived characters indicate common ancestry and are informative for the construction of phylogenetic trees and cladograms
  • The  most remote group in the diagram represents the lineage that is least closely related to the remainder of the organisms in the phylogenetic tree or cladogram
• Molecular data (from DNA or protein sequences, for example) typically provide more accurate and reliable evidence than morphological traits in the construction of phylogenetic trees or cladograms
• Both types of diagram can be used to illustrate the extent to which speciation has occurred (next topic)
• Both types of diagram represent hypotheses that are constantly being revised as new evidence emerges from research and scientific debate

• Cladograms sometimes show numbers along the branches; these indicate the number of base or amino acid changes that have occurred between one node and the next or between a node and an emerging clade or species
• The constant rate at which mutations accumulate means that these numbers can be used as a molecular clock to calculate how much time has passed

• • Some cladograms have a time scale to show how many millions have years have passed
• Computers use the information from sequence data to build the most likely cladogram
  • This is done using the principle of parsimony which states that the simplest explanation is preferred
    • The computer builds the shortest possible cladogram with the smallest number of divergence events to fit the available data

• Cladograms provide the most likely estimate of the evolutionary progress of organisms
  • The reliability of a cladogram may vary depending on the amount of sequence data used to construct it
    • A cladogram based on the sequencing of one gene will be less reliable than a cladogram based on the sequencing of several genes

  • Cladograms are subject to change when new sequence data becomes available