50 whys to look for genes: 41. Depict the Tree of Life

The Tree of Life denotes a range of images or mythologies about the interconnectedness or unity of all things; also, sometimes their fruitfulness (wikipedia).  One form of interconnectedness or unity is the sharing of a common ancestor, which can be seen in the branching diagrams of phylogeny (i.e., evolutionary branching) or classification of taxonomic groups (http://tolweb.org/tree/learn/concepts/whatisphylogeny.html).  In molecular systematics, phylogenies are derived from differences in DNA sequences combined with assumptions about uniform rates of mutation in those sequences, especially in the third base pair of a coding triplet (where differences have little influence over the function of the resulting protein).

(Source: http://www.nature.com/nature/journal/v465/n7300/full/nature09113.html)

In the course of constructing these phylogenies, researchers have learned that organisms as dissimilar as humans and rice share a significant fraction of genes — 25% for humans and rice (schema).

Complications

1. The fraction of genes shared was, when first discovered, interpreted as if the traits were conserved across the diverging branches of the tree or seen as a puzzle, given that some of the genes were involved in traits that did not even exist in the distant common ancestor of the organisms.
2. Soon, however, it was recognized that “[t]he genes we still share we use differently, in the same way you can use a clarinet to play the music of Mozart or Benny Goodman” (National Geographic).  (Perhaps using a cello to play Bach versus harmonic singing might be a better analogy.)
3. Once it is recognized that genes can have different functions in distant lineages, the question arises as to how close the lineages have to be (i.e., how recent the common ancestor) before the function can be treated as the same.  In that spirit, for example, although chimpanzees and bonobos differ from humans in 1.2% of the genome, it does not necessarily follow that the other 98.8% is doing the same thing in the two groups.
4.  The phylogenies produced using molecular data vary according to assumptions made and do not readily allow for horizontal gene transfer among distinct lineages (wikipedia).

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(Introduction to this series of posts)

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