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Peer Review

Phylogeny and Reconstructing Phylogenetic Trees



Overall Numeric Rating:

4 stars
Content Quality: 4 stars
Effectiveness: 4 stars
Ease of Use: 4 stars
Reviewed: Jul 23, 2002 by Biology Editorial Board
Overview: Phylogenetic trees and Reconstructing Phylogeny uses Java applets that can
create random phylogenies to illustrate and teach some of the basic principles
behind phylogeny reconstruction. The author has taken a single concept and
concentrated on presenting it well. It starts with an introduction to phylogeny
and the concept of phylogenetic trees. An interactive section allows students to
see the many possible configurations a tree may take with any specified number
of species. The second page discusses the use of mutations as a measure of
genetic relatedness, along with what type of mutations work best for this
purpose. An interactive section includes the random trees from the first page
but also shows a distance matrix for the species, generated from random
mutations in a set of arbitrary characters. The number of characters, the
mutation rate and the number of alternative states for each character can all be
varied independently and a new distance matrix consistent with the current tree
is produced. Then, the site covers how to reconstruct a phylogenetic tree from
the genetic information; in other words, how to determine the best of the
possible trees shown in the introduction using the mutation information. The
student can also change the mutation information and see how that impacts the
tree. The last page puts all of the parts together into a unified concept. Each
page contains a java-based simulation where numbers of organisms, number of
characteristics, mutation rate, and the reconstruction method can be varied.
Finally, there is a very nice description of how the applet actually works.
Throughout the site, students can alter the parameters of the model and
immediately see how that affects the result. Perhaps more important, they can
see how the same set of data can support more than one interpretation
Type of Material: Simulation
Technical Requirements: Java enabled browser
Identify Major Learning Goals: A basic understanding of how phylogeny reconstruction is done
Target Student Population: College/University students in an evolution course

Evaluation and Observation

Content Quality

Rating: 4 stars

Quality of Content: (4.5) (4) = 4.25

Feature(s) of Excellence

  • Text is well written
  • Material is clearly organized
  • Graphics appropriate to the topic
  • Applet is accurate and clearly demonstrates some key points in phylogeny
  • Applet is very flexible, with several different presentation modes and
    numerous independent variables

  • The text does not mention any other reconstruction methods, in particular,
    there is no mention of cladistics

Potential Effectiveness as a Teaching Tool

Rating: 4 stars

Potential Effectiveness: (4) (4) = 4.0

Feature(s) of Excellence

  • A very interactive and visual demonstration of the important point that
    phylogeny reconstructions are only estimates of the true phylogeny
  • Clearly demonstrates relationships
  • Effectively builds up concepts over several pages
  • Would be possible to write assignments based on using the applet.

  • Does not encourage or stress the importance of varying the parameters to
    observe the effects
  • Does not have any suggested experiments or assignments for students that
    would lead them into a deeper investigation
  • An actual example (real-world) of the use of this process would be helpful

Ease of Use for Both Students and Faculty

Rating: 4 stars

Ease of Use: (4.5) (4) = 4.25

Feature(s) of Excellence

  • The controls are all well labeled and easy to use
  • The applet runs very fast

Other Issues and Comments:

Overall rating: 4.25