Parsimony analysis of unaligned sequence data: maximization of homology and minimization of homoplasy, not minimization of operationally defined total cost or minimization of equally weighted transformations

Abstract

Wheeler (2012) stated that minimization of ad hoc hypotheses as emphasized by Farris (1983) always leads to a preference for trivial optimizations when analysing unaligned sequence data, leaving no basis for tree choice. That is not correct. Farris's framework can be expressed as maximization of homology, a formulation that has been used to overcome the problems with inapplicables (it leads to the notion of subcharacters as a quantity to be co‐minimized in parsimony analysis) and that is known not to lead to a preference for trivial optimizations when analysing unaligned sequence data. Maximization of homology, in turn, can be formulated as a minimization of ad hoc hypotheses of homoplasy in the sense of Farris, as shown here. These issues are not just theoretical but have empirical relevance. It is therefore also discussed how maximization of homology can be approximated under various weighting schemes in heuristic tree alignment programs, such as POY, that do not take into account subcharacters. Empirical analyses that use the so‐called 3221 cost set (gap opening cost three, transversion and transition costs two, and gap extension cost one), the cost set that is known to be an optimal approximation under equally weighted homology in POY, are briefly reviewed. From a theoretical point of view, maximization of homology provides the general framework to understand such cost sets in terms that are biologically relevant and meaningful. Whether or not embedded in a sensitivity analysis, this is not the case for minimization of a cost that is defined in operational terms only. Neither is it the case for minimization of equally weighted transformations, a known problem that is not addressed by Kluge and Grant's (2006) proposal to invoke the anti‐superfluity principle as a rationale for this minimization.

Sensitive phylogenetics ofClematisand its position in Ranunculaceae

“…Equal weight parsimony is often supported on philosophical grounds (e.g. Frost et al ., ; Grant & Kluge, ), but, in practice, is not applicable to all transformations (De Laet, , ; Giribet & Wheeler, ) and may not be well founded (Goloboff et al ., ,b). Transitions are generally considered to be more homoplasious than transversions and, for this reason, are often given lower weight (but see Broughton, Stanley & Durrett, ).…”

“…Gap characters of varying lengths are especially problematic because they may compromise the assumption of base‐to‐base homology. De Laet (, ) introduced a transformation cost regime of a substitution cost 2, gap opening cost 2 + 1 and gap extension cost 1 (usually referred to as ‘3221’, but, because of different usage of gap opening cost in POY5, expressed here as 2:2:2:1) to maximize total sequence homology. Indeed, several studies have supported low gap extension cost as logically and practically superior to equal transformation costs (Aagesen, ; Aagesen, Petersen & Seberg, ; Pons & Vogler, ; Spagna & Álvarez‐Padilla, ; Liu et al ., ).…”

Molecular homology and multiple-sequence alignment: an analysis of concepts and practice

“…In this sense, they are sometimes seen as maximising homology in sequence data (e.g. De Laet 2014). Programs that use iterative refinement of the alignment and guide tree also use congruence (Mindell 1991).…”

Influence of different modes of morphological character correlation on phylogenetic tree inference

“…Logical dependence, however, is easily distinguished prior to phylogenetic inference, while the two other ones (intra-organismal and evolutionary) are much harder. However, the development of algorithms and software has not yet caught up with the need to deal with these interdependencies (De Laet, 2015; Brazeau et al, 2017). Intra-organismal dependence requires more detailed, often extremely time-consuming studies (and possibly beyond the limits of available technology).…”