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Reconstructing Phylogenies

By Levi Clancy for Student Reader on

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Breakdown of the taxons

  1. Select a group of organisms to classify (the ingroup) and an appropriate outgroup.

  2. Choose the characters that will be used in the analysis and identify the possible forms (traits) of the character.

  3. Determine the ancestral and derived traits.

  4. Distinguish homologous from homoplastic traits.

Systematists use many characters to reconstruct phylogenies, including physiological, behavioral, molecular, and structural characters of both living and fossil organisms. The more traits that are measured, the more inferred phylogenies should converge on one another and on the actual evolutionary pattern.

The two most common sources of information for systematists are:

Morphologydescribes the sizes and shapes of body parts. Early developmental stages of many organisms reveal similarities, but these similarities may be lost in adulthood. For example, sea squirt larvae and frog embryos both have a notochord which is lacking in adulthood. Also, the fossil record provides much morphological data and reveals when lineages diverged.
Molecular traits

are also useful for constructing phylogenies. The molecular traits most often used in the construction of phylogenies are the structures of proteins and of nucleic acids such as DNA and RNA.

Comparing proteinsHomologous proteins are obtained and the number of amino acids that have changed since the lineages diverged from a common ancestor are determined.
Comparing nucleic acidsChloroplast DNA (cpDNA) and mitochondrial DNA (mtDNA) have been used extensively to study evolutionary relationships.

Relationships between apes and humans were investigated by sequencing a hemoglobin pseudogene (a nonfunctional DNA sequence derived early in primate evolution by duplication of a hemoglobin gene). The analysis indicated that chimpanzees and humans share a more recent common ancestor with each other than they do with gorillas.

Tips For Reconstructing Phylogenies

The methods used to phylogenize vertebrates are too simplistic – traits can change more than once or undergo evolutionary reversal from fossil records. Systematists use several other methods to sort out the complexities of phylogenetic relationships. The most widely used method is the parsimony principle (extreme care or stinginess). This principle states that one should prefer the simplest hypothesis that explains the observed data. In reconstruction of phylogenies, this means minimizing the number of evolutionary changes that need to be assumed over all characters in all groups in the tree. In other words, the best hypothesis is one that requires fewest homoplasies due to convergent evolution.

The maximum likelihood method is used primarily for phylogenies based on molecular data and requires complex computer programs. Determining the most likely phylogeny for a given group can be difficult. For example, there are 34,459,425 possible phylogenetic trees for a lineage of only 11 species. A consensus tree is the outcome of merging multiple likely phylogenetic trees of approximately equal length. In a consensus tree, groups whose relationships differ among the trees form nodes with more than two branches.