Recognizing ancestors: analogies and homologies
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It was on the basis of structural and anatomical similarities that Carl Linnaeus (1707-1778) proposed his hierarchical system for the unambiguous naming of all plants and animals.  

In this scheme, each type of organism is given a unique genus and a species name, such as Homo sapiens or Homo floresiensis or Escherichia coli (both names are italicized and the species name is lower case).

Organisms are also placed within a classification hierarchy - in an order, within a class, in a phylum.

Kingdom
. . Phylum
. . . Class
. . . . Order
. . . . . Genus
. . . . . . Species
. . .. . . . . Variety

The anatomical similarities between living, and later fossil, organisms, makes sense if they are related.  

Such an ordering of organisms is difficult to understand if each organism originated independently - if each were created de novo.

The concept of a species is complex, in large part because populations vary and evolve.  The biological species concept was defined by Mayr in 1942.  		 

"Species are groups of actually (or potentially) interbreeding natural populations which are reproductively isolated from other such groups." - Ernst Mayr (1953)

This definition is not completely unambiguous.  For example, when during the course of time does one species become distinct from its progenitor?   How do you define a species when individuals do not interbreed. 

A particularly interesting example is known as a ring species.  

Imagine populations of the species A.  Over the geographic range of A there are a number of subpopulations. 

These subpopulations (A1-A5) and (Aa-Ae) have limited regions of over-lap with one another, but in those regions, they interbreed successfully.

But, populations A5 and Ae no longer interbreed successfully – are these populations separate species?  

 

  • How would you go about determining whether an organism, identified through fossil evidence, was part of a new or a living species?  
  • How would you determine whether two species are part of the same genus?
  • How does a species differ from a genus or an order, are both equally "natural" groupings? 

Defining relationships between species:

The linnean classification system suggests a tree-like organization to the relationships between organisms. 

How do we arrange organisms on such a phylogenic tree?

One approach is known as cladistics.  In this approach, each type of organism is analyzed in terms of primitive and derived (that is, more specialized) characteristics. 

Based on these traits, organisms can be arranged into trees.


Of course, exactly how such a tree is structured depends upon which traits are considered to be primitive (and so present in ancestral forms) and which traits are considered to represent recent specializations.

The traits used in such studies were originally anatomical, but more recently DNA sequence data has become increasingly important.  

For example, such a molecular analysis indicates that the primates share a common requirement for vitamin C. 

This requirement is due to a mutation in the gene required for the synthesis of vitamin C; all primates have mutations in this gene (known as GULO or 1-gulono-gamma-lactone oxidase); this mutation appears to have occurred ~40 million years ago.

Most other mammals have a functional copy of this gene; transferring the mouse GULO gene to human cells "cures" them of their need for exogenous vitamin C.

Phylogenetic trees are generally compared based on the principle of parsimony, often known as Occam's razor. 

This principle states that, all else being equal, the simplest model that explains the data is preferable to a more complex one.  When two models produce the same predictions and explain the same set of data, we should prefer the simpler of the two. 

 

 
  • Do non-scientific ideas about life make predictions about phylogenic relationships?
  • Why is the need of primates for vitamin C evidence that they have a common ancestor? 
  • What types of traits are likely to be primitive?   How can you decide whether a trait is primitive or derived? Is it always unambiguous?
  • What is Occam's razor?  In your day to day decision making processes, do you use Occam's razor?
  • Does Occam's razor always lead to the correct conclusion?  How does one decide that a simpler explanation is incorrect?

Homologs and Analogs

A major problem in classifying organisms is deciding whether similar traits were inherited from a common ancestor or whether they represent independent solutions to a particular problem.

For example, an anatomical analysis of the forelimb of the mammals suggests that they are homologous structures.

To say that two structures are homologous means that they are derived from a common ancestor and that the feature was present in that common ancestor.

This type of reasoning leads to the prediction that fossils of the last common ancestor of the mammals will be found to have a forelimb with a structure similar to that of modern mammals.

Not all similar structures are homologous, however.  The alternative is that the structures are analogous.   When two structures are analogous, it means that they evolved independently, but perform the same functions.

Their common form was determined by their common function.

Consider the wing of a pterodactyl, a flying reptile, a bird, and a bat, a mammal.

Analysis of these structures indicates that they are distinctly different from one another.

In the pterodactyl, the wing membrane is supported by the 5th finger of the forelimb, in the bird by the 2nd finger, and in the bat, by the 3rd, 4th and 5th fingers.

The last common ancestor of flying reptiles,birds and mammals did not have wings, although it certainly had forelimbs.

While wings of pterodactyls, birds, and bats are analogous structures, their forelimbs are homologous.

The physics of flight are constant. Organisms of similar size face the same aerodynamic and thermodynamic constraints. In general there are only a limited number of physically workable solutions to deal with these constraints.


Under these conditions different populations will, through the process of variation and selection, end up with structurally similar solutions. This process is known as convergent evolution. 

Convergent evolution occurs when only certain solutions to a particular problem are possible.

As another example, the use of a dagger is an effective solution to the problem of killing another organism.

Variations of this solution has been "discovered" or invented independently many times.

Marsupial and placental mammals diverged from a common ancestor ~100Myr ago.

Since then, they have converged on a number of similar adaptations.

 

 

 
  • What type of evidence would convince you that structures in two different organisms are homologous?   
  • Why doesn't convergent evolution produce exactly the same solution in different organisms? Why is a bat's wing not exactly the same as a bird's wing?
  • How does the presence of convergent evolution complicate a cladistic analyses? 

The loss of traits

Another process that can confuse or complicate cladistic analysis is the loss of traits. 

As organisms adapt to a specific environment and life style, traits once useful can be lost.

A classic example is the reduction of hind limbs during the evolution of whales. 

 
 
 

Another common loss is that of eyes, which is often seen as populations adapt to environments in which light is absent.  The loss of traits can itself be an adaptation if it provides an advantage to organisms living in a particular environment. 

This fact can make it difficult to determine whether an organism is primitive (that is retains ancestral features) or is highly evolved. 

 

  • What other mammalian traits have whales lost during their evolution?  which have they retained?
  • What types of conditions might lead to a highly evolved organism appearing primitive?  what advantages might it provide?
  • What possible benefit could be linked to the loss of eyesight or other "advanced" traits? 
  • How does the loss of a trait complicate a cladistic analysis? 

Evidence for a common ancestor:

Similar structures may arise independently, while apparently different structures, such as a human hand and a whale's flipper, are related.

How do we distinguish between these two possibilities?  In general, we carry out a detailed comparative analysis of the development and final form of the structure. 

In the modern world of molecular biology, this involves the genes that are active as the structure forms. 

The more details two structures share, the more likely they are homologous.

  


Detailed analyses of many different types of organisms reveals the presence of a common "molecular signature" that strongly suggests that all living organisms are closely related; that is, that they share a common ancestor.

What are these similarities?   They range from the basic structure of cells to the molecular machinery involved in energy capture and transduction, information storage and utilization. 

For example, all extant organisms ...

  • use the nucleic acid DNA as their genetic material
  • use the same molecular systems, transcription and translation, to access the information stored in DNA
  • use a common genetic code, with few variations, to specify the sequence of polypeptides (proteins)
  • use a common set of 20 amino acids (out of thousands of possible amino acids) to build polypeptides
  • use a common set of 4 ribonucleotides  and 4 deoxyribonucleotide to build nucleic acids
  • use adenosine triphosphate (ATP) to store energy
  • they share common enzymatic pathways, such as fermentation

As an example, all organisms use ribosomes (composed of similar proteins and RNAs) to translate the information stored in messenger RNAs into polypeptides.

The ribosomes of bacteria, archea (not shown), and humans are quite similar in shape and molecular organization; they appear to be homologous. roll over →

  
 
  • As we go back in time, it gets harder to be completely sure about the relationships between organisms – why is that?
  • Does the premise of "intelligent design" make any clear or testable predictions about the apparent relatedness of different species? is it useful for understanding homologous and analogous structures?
  • Is convergent evolution possible at the molecular level?  
  • If all organisms are descended from a common ancestor, what can we say about the diversity of pre-biogenic systems that existed before that ancestor?
  • What can we say about the this "last common universal ancestor" (luca)? 
Use Wikipedia | revised 25-Aug-2008