Has molecular data replaced morphological data in phylogeny reconstruction

Essay by katherine.fisher May 2004

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The phylogenetic positioning of taxa within a tree has long been of interest to systematicists such that the evolutionary history of life can be studied. However, due to the timescales involved, direct observation of this phenomenon is not possible and as such, evolutionary history must be inferred from observable characters. Traditionally, morphological features have been used to invoke ancestral and present relationships existent between taxa, but with recent technological advantages in genomics, more weight is being given to molecular data. So, the question arises as to whether this novel method is superior in the results yielded and regarding whether it can potentially replace traditional methods completely.

Morphology has provided the primary source of data throughout the historical study of phylogenetics and has yielded the majority of the trees that are used today. It is rare in the literature to find examples where molecular studies have completely usurped the original tree, albeit examples are found to exist.

This suggests a high degree of congruence between the two applied methods which implies that neither can be considered significantly superior. Where incongruence is found, there are several explanations which can either resolve the problem or contribute to further debate. A simple explanation for incongruence considers the level of support for either estimate in terms of the quantity of information (taxa and/or characters) used in the analysis and this can be quantitatively assessed by means of bootstrap analysis. It is extremely rare to find examples where two conflicting trees are both well supported in terms of their clades. A second explanation centres on the methods of analysis. If a different analysis (e.g. Parsimony, UPGMA) has been applied to the morphological and molecular data sets, different trees may result as an artefact of this, and application of the same method may result in congruence (e.g.