Classification and Cladistics

• Needed due to the large amount of diversity of species. 

  • Currently 1,200,000 -1, 800,000 cataloged based on binomial nomenclature. 

• A more efficient way to see: 

  • If a species has already been discovered. 

  • Similarities between species 

  • Deduce common ancestry 

  • Predict features that undiscovered but related species should have

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​Why is classification important?

• Classifying organisms in the traditional hierarchy can be difficult

• Challenges:

  • Subjective and arbitrary

  • Doesn’t reflect common ancestry or genetic links

  • Ranked system that must be followed

  • Same genus = same family

  • What if an organism is moved to a different genus?

​Classification Challenges

• Hierarchy system can fail as more organisms are discovered

• Examples:

  • Hybridization in plants:

    • Crossbreeding two species to produce a hybrid

    • If hybrids can reproduce, a new species may form

  • Plant cloning:

    • Should cloned plants be considered a new species?

​Classification Challenges Continued

Introgression - a process by which hybrids form over many generations but , instead of having an equal share of the original two species’ genetic information, there is an unequal contribution from each species.

• Coyote mating with wolf

  • The hybrid is 50% coyote and 50% wolf

  • If hybrid mates with another wolf, offspring would be 75% wolf and 25% coyote (unequal sharing) 

​Backcrossing - the mating of a hybrid organism (offspring of genetically unlike parents) with one of its parents or with an organism genetically similar to the parent.

Why might traditional classification systems based on traits sometimes misgroup organisms?

• Ideal classification system follows evolutionary relationships, grouping species with a common ancestor (as shown in Darwin's tree of life)

• Traditional classification based on traits may not group organisms by common ancestry

• Examples: Birds and Reptiles (feathers vs scales), Sugar gliders and flying squirrels

• Phylogeny: Study of a species' evolutionary history

• Greater similarity = species are more likely related

• Greater differences = species are less likely related

• Comparing genetic profiles creates a phylogenetic tree

• A phylogenetic tree shows evolutionary relationships among organisms

• ​Cladistics - method of classifying organisms into groups called clades, based on shared traits.

• A clade - group of organisms (or viruses) that have all evolved from a common ancestor.

  • Characteristics of organisms can be predicted according to the clades that they are classified into.

• Clades can be organized into cladograms, which are tree diagrams that show the most probably divergence between species.

The most objective evidence for placing organisms in the same clade comes from base sequences of genes or amino acid sequences of proteins. 

Scientists can estimate these relationships by comparing DNA, RNA or protein sequences.

As the organisms evolve and diverge, their DNA sequences accumulate mutations. Scientists compare these mutations using sequence alignments to reconstruct evolutionary history

​Differences in the base sequence of DNA (and therefore proteins) are the result of mutations.

Mutations accumulate gradually over long periods of time at a constant rate, so they can be used as molecular clocks.

​Molecular clocks only allow scientists to estimate when species diverged as the following factors affect mutation rates within a population.

 Limitations of molecular clocks include:

• Generation time - Species with shorter generation times provide more opportunities for mutations to occur, resulting in faster molecular clocks than species with longer generation times.

• Population size - Mutations are more likely to be fixed in small populations, resulting in faster molecular clocks.

• Selective pressure - Under strong selective pressure (high intraspecies competition), mutations are more likely to be fixed in a population.

Cladograms are tree diagrams which show the most probable sequence of divergence between clades.

​Comparing base sequences of genes or amino acid sequences in proteins is the preferred method of constructing cladograms, as the data is objective.

​The fewer differences in the sequence, the more closely related two species are.

node = a split in a cladogram where one branch goes in one direction and the other branch in another direction, representing a hypothetical common ancestor.

​root = the base of the cladogram showing the common ancestor to all the clades in the cladogram.

terminal branch = the end of a branch representing the most recently evolved of the organisms in the clade.

​sister group = a group of the closest relatives.

​outgroup = a group that is less closely related to the others in the cladogram.

Primitive traits (plesiomorphic traits) = characteristics that have evolved early in the history of the organisms being studied.

​Derived traits = characteristics that have evolved more recently.

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A clade is a group of organisms which have evolved from a common ancestor.

A branch on a cladogram that includes a single common ancestor, a node, and all of its descendants represents a clade.