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Biology 2108 Lecture
Phylogeny and Systematics
Chapter 26


What are systematics and phylogeny?

'Taxon' - group of similar and related invidividuals

The hierarchical system of classification:


      Phylum or Division
                Species -a group of organisms that can potentially breed with one another

 The basis of modern classification was developed by Carl Linnaeus (1707-1778).    Why classify organisms? 

Jean Baptiste Lamarck and others recognized that this nested, hierarchical  pattern would be produce if organisms evolved from common ancestors.

Systematics is the study of the diversity and relationship of organisms (how these organisms are named and classified is the discipline of taxonomy).
From similarity and differences of morphological, biochemical, cellular characteristics, biologist have constructed 'phylogenetic (evolutionary) trees'  (who is most closely related to who, analogous to a family tree)
  (click here for a good review of this subject)

'Phylogeny' is the evolutionary relationships among organisms; the patterns of lineage branching produced by the true evolutionary history of the organisms being considered.

Phylogentic trees link classification with phylogeny:

Phylogenetic trees generally show divergence of lineages through time  (i.e. the evolutionary relationship of taxa)

Some trees merely express order of divergence (cladograms):   
All 3 of these trees shown above express the exact same information.
  Some trees can indicate estimated time since divergence or the amount of evolutionary change:

In the tree shown on the above left:

What taxon is most closely related to birds?
Which taxon is least closely related to humans?
Which taxon diverged first (longest ago) from the lineage that gave rise to humans?
Which taxon has the least recent shared ancestors with humans?
Trees that show the same patterns of divergence can be arranged differently:

In terms of order of divergence,
which of these trees
is not like the others?


In terms of order of divergence,
which of these trees is
not like the others?
Given four hypothetical taxa, construct a tree in which Taxon G is more closely related to Taxon L than to Taxon A, but all three of these taxa are more closely related to each other than Taxon F.

The most obvious way to determine the evolutionary relationship of organisms (i.e. their phylogenetic tree) is compare morphological similarities

For example:

However, it is not easy to construct phylogenetic trees and there is often controversy among systematists (a phylogenetic tree is a hypothesis on how a group of organisms might be related).  Some organisms that appeared closely related in some respects, may seem more distantly related in other respects.


Why doesn't morphological similarity always reflect the evolutionary relationship of organism?

1) Closely related organisms are not always similar in appearance:



2) Organisms that appear similar are not always closely related:

analogous structures - structures that are independently similar between two species that are not closely related; attributable to convergent evolution.

(As opposed to homologous structures - structures in different species that are similar because of common ancestry; such structures are helpful in determining evolutionary relatedness)


So when attempting to determine phylogenetic relationships among a group of organisms, should analogous or homologous structures be compared?

Evolution sometimes results in structures becoming less complex rather than more complex.


If shared primitive characteristics are used, for example cellularity:
(a primitive (or ancestral) characteristic is one that is present in the common ancestor of the group being considered)


Where did multicellularity  evolve and how many times?
Which of the two trees above is a simpler explanation?
If shared derived characteristics are used, for example development of organelles:
(a derived characteristic is one that has evolved and therefore not present in the common ancestor)


Where did a the eukaryotic condition evolve and how many times?
Which of the two trees above is a simpler explanation? 
Therefore, which is better to use, shared primitive or shared derived characteristics?  The decision is based on the principle of maximum parsimony ("Occam's razor").  (The principle of maximum likelihood is also used to support certain trees over others.)

This assumes that we are sure the prokaryotic condition is truly primitive.  How do we know this?

Another example:


Birds and mammals share the derived characteristic of a four-chambered heart.  Which of the above trees is the more simple evolutionary explanation?   Which is more simple if we consider the shared primitive characteristic of no hair?

One school of systematics, Cladistics (phylogenetic systematics), demands adherence to using only homologous, shared derived characteristics.  Strict rules are applied (multiple trees are calculated with sophisticated computer algorithms and the one that uses the least number of convergent evolutions is considered best). 

Cladists insist that boundaries for groupings be based strictly on evolutionary sequence of divergence produced by cladistic analysis.

Fig. 26.16

A clade (or monophyletic group) is a group of species that includes an ancestral species and all of its descendants (i.e. members within the clade are all more closely related to each other than any members outside the clade).

A cladistic classification system attempts to group organisms together only into monophyletic taxa.   Even though lizards and crocs share a lot of primitive characteristics, shared derived characteristics indicate a more recent common ancestor between crocs and birds.  “Reptiles” as a group are paraphyletic in that some members have a more recent shared ancestor with a group outside that taxon than with some members within that group.  A cladist would object to such a taxonomic grouping.

Do species 1 and 2 make up a distinct clade (is it a monophyletic group)?
Do species 1, 2, and 3 make up a distinct clade?
Do species 1, 2, 3,and 4 make up a distinct clade?
If a grouping excludes a taxon (or taxa) that has a more recent common ancestor with some members but not all of that grouping, then it is said to be paraphyletic.  What would be an example of this in the above diagram?


In the tree below:
Are reptiles (which include lizards, crocodiles, and dinosaurs) a monophyletic group?
Of the organisms represented in this tree, do humans, whales, and demitrodons form a monophyletic group?


What other types of evidence can be used to elucidate the evolutionary relationship of organisms? (i.e. how do we get around some  of the problems discussed above?)

  1. Examine paleontological (fossil) evidence of ancestors
Primitive characteristics should be  more common in older fossils
Re-examination and new discoveries have improved interpretation of fossil data
For example, two fossil beds (Burgess Shale and the Chengjiang) from the early Cambrian  have preserved soft bodied animals.  Only very specialized conditions lead to fossilization of soft-bodied organisms.

2. Concentrate on early developmental characteristics.

3. Genetic data

Molecular phylogeny is based on comparing the sequence of molecular subunits (e.g. nucleotides of RNA or DNA)


Molecular phylogenetics is no different in principle from inferring phylogeny from the similarities in morphology. 

Advantages of molecular phylogeny:

An examples of shared problems with other phylogentic methods
Numerous mutations are possible (reversals, substitutions, insertions, and deletions of bases) make alignment difficult.  What might initially appear as two very different sequences may be the result of a single mutation.

“Molecular phylogenetics does not necessarily provide the correct phylogeny, but it can help eliminate incorrect ones and can suggest alternative hypotheses that otherwise might not have been considered.”  - C. Leon Harris, Department of Biological Sciences, State University of New York
Phylogenies can also be reconstructed at the level of the gene.

Exceptions to divergence in phylogenetic "trees"  - horizontal gene transfer
Bottom line when constructing phylogenies: 
All available evidence must be considered and weighed.  Confidence comes when there is significant agreement among independent evidence for a particular phylogenetic scheme.  Using multiple techniques reveals a preponderance of homologous structures in some taxa (indicating relatedness), and scattering of analogous structures that are 'built' differently (indicating the importance of certain adaptations to solve certain environmental problems in a limited number of ways).

The study of phylogeny has disspelled misconception of evolution as a sequence of linear progress.  Instead the tree of life on Earth is an extremely complex array of branches, some that are been severely pruned during periods of mass extinction, some that have yielded a great diversity of smaller branches, and other that are spindly and bizarrely different than other forms of life.


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