Taxonomy and phylogeny

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What is the point?

  1. To be able to define "Taxonomy" and "phylogeny"
  2. To be able to describe the differences between these
  3. To be able to describe why this distinction is important

A taxonomy is a classification scheme for species (or any other collection of objects, for that matter). There are three related components of a biological taxonomy:

  1. Grouping : The organization of organisms into groups based on similarity
  2. Naming : Labeling organisms & groups of organisms with names
  3. Identifying : The identification of organisms when they're found

Taxonomies are artificial constructions, methods created by and used by humans to organize species. Any self-consistent taxonomy is valid, whether it reflects the natural relationships of the organisms or not.

For example, wildflower field guides organize species by features that are readily observed in the field. The first division might be by flower color, a trivial feature of the plants in evolutionary terms, but perfectly reasonable for a taxonomy. There is no implication that plants with the same color flower are actually related genetically, nor that plants with different colored flowers are not related. The field guide is designed for grouping, naming, and identifying species, and are useful taxonomies.

A phylogeny is the evolutionary pathway relating species. Think of a phylogeny as a large-scale genealogy of species. Phylogenies represent the actual natural relationships between organisms. Phylogenies are most commonly displayed graphically in the form of phylogenetic trees.

Unfortunately, their aren't natural delineations between groups in a phylogenetic tree. However, taxonomists can start with a phylogenetic tree, and try to divide the tree into reasonable groups based on the branches of the tree and the phenotypes of the organisms. In doing so, they attempt to devise a taxonomy that reflects (or at least is consistent with) the phylogenetic relationships between the species as closely as possible.

The classical taxonomies of plants and animals are fairly good representations of the phylogenetic relationships between their members because the intricate morphology of these organisms reveals their ancestry. This is not true for microbes. There was no way to determine evolutionary relationships between Bacteria, Archaea, or even protists, algae or fungi, until the development of molecular phylogenetics, in which phylogenetic relationships are inferred on the basis of gene sequences.

Why is an understanding of phylogeny important?

  1. To predict the properties of organisms based on the properties of their relatives.

    Think about how much insight you can get into a person by getting to know their family - this is why meeting the family of someone you’re dating is so important! Understanding an organisms relationships to other species is the key to understanding it’s properties.

  2. To prevent inappropriate comparisons based on nonexistent relationships.

    For example, Euglena was used for years as a unicellular model system to study photosynthesis in green plants. However, it turns out that Euglena isn't related to plants, but to trypanosomes! It's chloroplast is not like those of plant chloroplasts, and was acquired independently. Chlamydomonas is a better system - because it is phylogenetically a unicellular green plant.