Biology Reference
In-Depth Information
developed further: one can reconstruct a phylogenetic tree not only of
organisms, but also of biological molecules such as proteins or genes.
3. Molecular Phylogenetics
Until the mid-20th century, the classification of organisms was based
exclusively on anatomy and morphology. In the language of genetics,
only phenotypic characters (i.e. visible ones) could be compared. Today,
with the large amount of genetic sequence data available in public data-
bases and the relatively low cost of sequencing and computing technol-
ogy, numerical phylogenetics has shifted strongly towards molecular
characters.
Such a shift has its advantages and its disadvantages. While it is very
tricky to study molecular characters of fossils (extracting intact DNA
from fossils without contaminating it is quite challenging), their mor-
phological and anatomical characters can readily be compared to those of
modern-day organisms. Paleontology may give a phylogeneticist direct
information on whether a phenotypic character's state is ancestral or
derived. On the other hand, the information content of molecular data
and the sheer number of characters available for comparison make the
molecular approach very attractive.
Since 1966, it is known that genes are basically sequences of molec-
ular characters: four nucleic bases constitute the four possible states for
each nucleotide in the sequence (a gap in an alignment may be consid-
ered as a special kind of fifth state). Notwithstanding the technical diffi-
culties of a multiple alignment, comparisons are straightforward with
molecular sequences: when comparing two bases, these are identical or
not; quantification problems typical of morphological data, such as where
to draw the line between long legs and short legs, are avoided.
3.1. Gene Duplication vs.Speciation,
Paralogy vs.Orthology
As we have seen in Sec. 1, evolutionary processes tend to increase the
complexity of the tree of life. Not only does the number of living
