Ancestral character state reconstructions

As mentioned above. Discrete can analyse only binary characters and any multistate character has to be either excluded from the analyses or transformed into binary ones. For some of the characters used in the present analyses, multistate codings are possible. For instance, the presence of dwarf males (character 1 state 1) can be coded as simple and unbranched, as for Garovaglia, or larger and branched, as for Euptychium, Glyphothecium and Cladomnion. It is therefore possible that the uncertainties in ancestral character state reconstructions might be an artifact of the binary... 

Swofford DL, Maddison WP (1987) Reconstructing ancestral character states under Wagner parsimony. Math Biosci 87 199-229... 

Pagel, M. (1999). The maximum likelihood approach to reconstructing ancestral character states of discrete characters on phylogenies. Systematic Biology, 48, 612-622. 

The objectives of this chapter are several first, to resolve phylogenetic relationships within the Ptychomniales using DNA sequence data second, to reconstruct ancestral character states within the Ptychomniales and third, to test whether the presence of dwarf males correlates to morphological characters and the epiphytic habitat. 

Sufficient material of Lepyrodon pseudolagurus and the Chilean specimen for morphological studies was not available and these taxa were pruned from the ML tree. Reconstruction of ancestral character states under MP was accomplished by mapping the morphological characters onto the pruned ML tree using MacClade 4.03 (Maddison and Maddison, 2001). 

Character states were optimized on a topology (the backbone tree) based on the combined analysis of morphology, 18S nrDNA, rbcL and atpB by Doyle and Endress (2000), but also incorporating changes and updates based on more recent analyses (e.g. Doyle et al., 2008 Endress and Doyle, 2009 Doyle and Endress, 2010). Ancestral states were reconstructed using the Ancestral State Reconstruction Package implemented in Mesquite (Maddison and Maddison, 2007) and the... 

Eighteen morphological characters and one habitat character were chosen for reconstruction of ancestral states and correlation studies. The characters included are listed below and the character matrix is presented in Table 18.2. A list of the specimens used for the anatomical and morphological... 

---