Farewell to the requirement for character independence: phylogenetic methods to incorporate different types of dependence between characters.

This paper discusses methods to take into account interactions between characters, in the context of parsimony analysis. These interactions can be in the form of some characters becoming inapplicable given certain states of other, primary characters; in the form of only certain states being allowed in some characters when a given state or set of states occurs for other characters; or in the form of transformation costs in some character being higher or lower when other characters have certain states or transformations between states. Character-state reconstructions and evaluation of trees under the assumption of independence may easily lead to ancestral assignments that violate elementary rules of biomechanics, well-established theories relating form and function or ideas about character co-variation.

A reconsideration of inapplicable characters, and an approximation with step-matrix recoding.

Evidence for phylogenetic analysis comes in the form of observed similarities, and trees are selected to minimize the number of similarities that cannot be accounted for by homology (homoplasies). Thus, the classical argument for parsimony directly links homoplasy with explanatory power. When characters are hierarchically related, a first character may represent a primary structure such as tail absence/presence and a secondary (subordinate) character may describe tail colour; this makes tail colour inapplicable when tail is absent.

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.

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.

Testing for effects of climate change on competitive relationships and coexistence between two bird species.

Climate change is expected to have profound ecological effects, yet shifts in competitive abilities among species are rarely studied in this context. Blue tits (Cyanistes caeruleus) and great tits (Parus major) compete for food and roosting sites, yet coexist across much of their range. Climate change might thus change the competitive relationships and coexistence between these two species.