Literature

The nested hierarchies that emerge from taxonomical studies have often been used as evidence supporting the concept of common descent (i.e. all organisms have evolved from an ancestral single cell). Hierarchies emerge from studies of morphology, from genetic similarities and from other data. However, as has recently been pointed out, "to create an evolutionary tree of relationships, one must make assumptions about the evolutionary process that produced the observed data." This highlights one of the major problems we have in the field of evolutionary biology: the assumptions are so deeply embedded that any alternative approach that seeks to stand outside the conventional paradigm is regarded with suspicion. This research paper has the merit of exploring these issues, although it does so without challenging the evolutionary mindset of phylogenetics. To those who doubt the claim that "No phylogeny estimation is assumption free", this paper deserves their close attention. Once it is recognised that "assumptions" are critical for the production of phylogenies, the evidences against common descent, identified by some (but not all) ID advocates, can then be considered on their merits. This is a scientific issue, worthy of wider debate.

Model use in phylogenetics: nine key questions
Scot A. Kelchner and Michael A. Thomas
Trends in Ecology & Evolution, Volume 22, Issue 2 , February 2007, Pages 87-94

Abstract: Models of character evolution underpin all phylogeny estimations, thus model adequacy remains a crucial issue for phylogenetics and its many applications. Although progress has been made in selecting appropriate models for phylogeny estimation, there is still concern about their purpose and proper use. How do we interpret models in a phylogenetic context? What are their effects on phylogeny estimation? How can we improve confidence in the models that we choose? That the phylogenetics community is asking such questions denotes an important stage in the use of explicit models. Here, we examine these and other common questions and draw conclusions about how the community is using and choosing models, and where this process will take us next.

Models in phylogenetics
No phylogeny estimation (see Glossary) is assumption free. To create an evolutionary tree of relationships, one must make assumptions about the evolutionary process that produced the observed data. Taken as a whole, these assumptions form a 'conceptual model' of character evolution with which estimates of evolutionary relationship are made. The conceptual model could include a mathematically explicit 'formal model' of character change, which is parameterized when applied to nucleotide or amino acid sequence data. It is this formal model that is referred to as the 'model' in phylogenetic literature (as it is here).
Phylogenetics cannot escape the use of conceptual models. Even those methods that do not formalize a model, and thus claim to be model-free (e.g. parsimony), make significant and sometimes incorrect assumptions about character evolution when estimating the amount of change between organisms 1, 2, 3 and 4. The growth of formal model use in phylogenetics, however, has created a noticeable level of concern in the community. In particular, we think that confusion about certain model qualities is contributing to controversies about model 'accuracy', complexity and development.
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