Additional file 1: of Evolutionary pathways to convergence in plumage patterns
Creators: name: Thanh-Lan Gluckman
name: Mundy, Nicholas
Publisher: name: Figshare
Year: 2016
Subjects: subject: 29999 Physical Sciences not elsewhere classified
subject: FOS: Physical sciences
subject: FOS: Physical sciences
subject: Genetics
subject: FOS: Biological sciences
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subject: Molecular Biology
subject: Evolutionary Biology
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subject: FOS: Earth and related environmental sciences
subject: FOS: Earth and related environmental sciences
subject: Ecology
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subject: 19999 Mathematical Sciences not elsewhere classified
subject: FOS: Mathematics
subject: FOS: Mathematics
subject: Inorganic Chemistry
subject: FOS: Chemical sciences
subject: FOS: Chemical sciences
subject: 110309 Infectious Diseases
subject: FOS: Health sciences
subject: FOS: Health sciences
subject: Computational Biology

description: Figure S1a. The distribution of plumage pattern traits per patch of plumage in Anseriformes. Empty traits indicate that the type of pattern is unknown and/or is mottled plumage. Branches that were collapsed into twigs due to low branch probability are indicated with a red line (see Supplementary Methods above). Each type of plumage pattern is found in extant species and although there is some variation in the most probable ancestral state, where there is support it is for an absence of patterns. Figure S1b. Distribution of plumage pattern traits per patch of plumage in Galliformes. Branches that were collapsed into twigs due to low branch probability are indicated with a red line (see Supplementary Methods above). Empty traits indicate that the type of pattern is unknown and/or is mottled plumage. Each type of plumage pattern is found in extant species and the most probable ancestral state of plumage is an absence of patterns. Figure S2a. Local plumage pattern evolution within individual patches, in Anseriformes and Galliformes using unmodified trees. The width of each evolutionary step is proportional to the average rate per model. Beside each evolutionary step is the marginal probability of each transition not occurring, followed by the marginal probability of it occurring. Where the transition probably does not occur, the transition line is grey. Conversely, where the transition probably does occur, the transition line is black. Equivocal transitions, where the marginal probability is = &lt; 0.05 difference between not occurring and occurring, are indicated by a grey dashed line. Figure S2b. Plumage pattern evolution over the whole body, in Anseriformes and Galliformes using unmodified trees. To examine the effects of uncertainty in the order of plumage pattern evolution in Galliformes we modeled the effect of scales or spots being more derived. The width of each evolutionary step is proportional to the average rate in the top model set. Beside each evolutionary step is the marginal probability of each transition not occurring, followed by the marginal probability of it occurring. Where the transition probably does not occur, the transition line is grey. Conversely, where the transition probably does occur, the transition line is black. Equivocal transitions, where the marginal probability is = &lt; 0.05 difference between not occurring and occurring, are indicated by a grey dashed line. Figure S3a. Local plumage pattern evolution within individual patches, in Anseriformes and Galliformes using trees that only have branches with a high Bayesian probability. The width of each evolutionary step is proportional to the average rate per model. Beside each evolutionary step is the marginal probability of each transition not occurring, followed by the marginal probability of it occurring. Where the transition probably does not occur, the transition line is grey. Conversely, where the transition probably does occur, the transition line is black. Equivocal transitions, where the marginal probability is = &lt; 0.05 difference between not occurring and occurring, are indicated by a grey dashed line. Figure S3b. Plumage pattern evolution over the whole body, in Anseriformes and Galliformes trees that only have branches with a high Bayesian probability. To examine the effects of uncertainty in the order of plumage pattern evolution in Galliformes we modeled the effect of scales or spots being more derived. The width of each evolutionary step is proportional to the average rate in the top model set. Beside each evolutionary step is the marginal probability of each transition not occurring, followed by the marginal probability of it occurring. Where the transition probably does not occur, the transition line is grey. Conversely, where the transition probably does occur, the transition line is black. Equivocal transitions, where the marginal probability is = &lt; 0.05 difference between not occurring and occurring, are indicated by a grey dashed line. Table S1. Prior probability of encountering models of n parameters calculated from binomial for Z (where Z = n parameters that are set to 0 i.e. do not occur) and Bell numbers for models with 12 possible transition rates. Table S2. Prior probability of encountering models of n parameters calculated from binomial for Z (where Z = n parameters that are set to 0 i.e. do not occur) and Bell numbers for models with three pattern states encompassing 6 possible transitions. (DOCX 12836 kb)