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Open Access Research article

Widespread and persistent invasions of terrestrial habitats coincident with larval feeding behavior transitions during snail-killing fly evolution (Diptera: Sciomyzidae)

Eric G Chapman1, Andrey A Przhiboro2, James D Harwood1, Benjamin A Foote3 and Walter R Hoeh3*

Author Affiliations

1 Department of Entomology, University of Kentucky, Lexington, KY, 40546, USA

2 Zoological Institute, Russian Academy of Sciences, Universitetskaya nab. I St., Petersburg, 199034, Russia

3 Evolutionary, Population, and Systematic Biology Group, Department of Biological Sciences, Cunningham Hall, Kent State University, Kent, OH, 44242, USA

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BMC Evolutionary Biology 2012, 12:175  doi:10.1186/1471-2148-12-175

Published: 10 September 2012

Additional files

Additional file 1:

Figure S1. Maximum likelihood tree produced by using the partitioning scheme and model assignments in Additional file 1: Table S2 using the default settings in Garli (v. 2.0) except for the following: searchreps = 5, numberofprecreductions = 20, treerejectionthreshold = 100. Drosophila melanogaster sequences were used to root the analysis. Numbers after species names are specimen numbers (Table 1). Figure S2. Bayesian consensus tree produced by using the partitioning scheme and model assignments in Additional file 1: Table S2.Drosophila melanogaster sequences were used to root the analysis. Numbers after species names are specimen numbers (Table 1). Figure S3. Maximum likelihood bootstrap tree (200 replicates) produced by using the partitioning scheme and model assignments in Additional file 1: Table S2 using the default settings in Garli (v. 2.0). Parameter estimates from the non-bootstrap search replicate that obtained the tree with the highest log-likelihood value were fixed. Drosophila melanogaster sequences were used to root the analysis. Numbers after species names are specimen numbers (Table 1). Figure S4. Maximum likelihood optimization of Knutson and Vala's [17] larval feeding groups on the maximum likelihood topology. Additional file 1: Figure S1; pruned to include only one terminal per species) analyzed with Mesquite using the MK1 model of character evolution. Only character states that are statistically significantly better than the others (ancestral character state estimates with a log likelihood two or more units higher than all others) are shown in the pie charts at the nodes. A solid (one color) node indicates that state is significantly better than all other possible states. Grey indicates unknown character states. Numbers after species names are specimen numbers (Table 1). Table S1. Model log-likelihood scores for variations of the ratio of aquatic-terrestrial:terrestrialaquatic transitions using the DEC model in Lagrange with dispersal and extinction rates for each. Bold font indicates significantly better log-likelihoods (i.e., greater than 2 lnL units) than the null (1:1) model. Red font indicates the parameter setting used in the plot of ancestral character states on Figure 3. Figure S5. Lagrange output with ratio of aquatic-to-terrestrial vs. terrestrial-to-aquatic transitions set to 12:1. Only states within 2 log-likelihood units of the best were considered for plotting on Figure 3, and only unambiguous states were plotted. Table S2. Gene information and evolutionary models selected by jModelTest for BI and ML phylogenetic analyses).

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