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Molecular phylogeny


The astounding developments in the field of biochemistry and molecular biology, in particular since the 1990's have added a third methodology to the study of relationships between life forms, deriving from three distinct disciplines of science:

  1. The comparison of life forms, in anatomical sense, but also ecologically and behaviorally. (Zoology, Botany)
  2. The anatomical and stratigraphic comparison of fossilized remains of extinct life forms and their traces. (Paleontology)
  3. The comparison of the genetic material of living (or recently extinct) life forms. (Molecular biology, biochemistry)

It is not surprising to find that the results of the various methods are not always in agreement with each other, because each method has its strong and weak points. Both [1] and [3] are essentially limited to extant forms and the geological time axis can only be estimated indirectly. The paleontological method can call upon geological knowledge to provide a better time frame, but like [1] it suffers from a problem called homoplasy: the fact that anatomical similarity can at times be the result of similar adaptation to similar circumstances rather than derive from a same ancestor. Another limitation is that well preserved fossils are a rarity rather than a common occurrence. Soft tissue e.g. is seldom preserved, so that comparisons cannot be made on all aspects of anatomy as in [1].

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The molecular methodology also has its quirks and limitations. Due to the development of advanced sequencing techniques in , it has become feasible to gather large amounts of data (DNA or amino acid sequences) to estimate . For example, it is not rare to find studies with character matrices based on whole . However, it has been proposed that it is more important to increase the number of taxa in the matrix than to increase the number of characters, because the more taxa, the more robust is the resulting . Using simulations, Zwickl and Hillis [1] found that increasing taxon sampling in phylogenetic inference has a positive effect on the accuracy of phylogenetic analyses. This is essentially a statistical and mathematical limitation. It makes no sense to increase the number of rows of a matrix, unless the number of columns is increased as well, because the rank of a matrix is limited by the smaller of the two numbers. This is related to the ability of breaking up of . It has been argued that this is an important reason to incorporate data from fossils into phylogenies where possible. Unfortunately these data are of a rather different nature (anatomical instead of genetic), so that integration is not easy.

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[1] Zwickl, DJ, Hillis DM (2002). "Increased taxon sampling greatly reduces phylogenetic error". Systematic Biology 51: 588-598.


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