For maximum-likelihood analysis, we used a generalized time reversible + invariant sites + Γ substitution model as indicated above, nearest-neighbor interchange branch-swapping, and 500 bootstrap replicates to assess node support.
A bootstrap analysis using 1,000 iterations was performed for maximum parsimony and minimum evolution and 100 iterations by using the nearest neighbor interchange branch-swapping algorithm for maximum likelihood.
Each gene tree search was bootstrapped (500 pseudoreplicates) with PhyML using the nearest-neighbor interchange branch-swapping method, and genes supporting strongly conflicting bipartitions were considered LGTs and removed from the analysis.
ML nonparametric bootstrap analyses used 100 heuristic searches with starting trees obtained with NJ based on p distances followed by TBR and nearest-neighbor interchange branch-swapping, saving all optimal trees.
Tree space was searched using Nearest Neighbor Interchange (NNI) branch swapping and local branch length optimization, until convergence.
Heuristic searches were performed with 10 random addition sequences and Closest Neighbour Interchange (CNI) branch swapping.
Maximum parsimony (MP) analysis was performed using a heuristic search, with nearest neighbor interchange (NNI) branch swapping.
Likelihood parameters [base frequencies (A = 0.3300, C = 0.1064, G = 0.1354, T = 0.4282); rate matrix (1.1933, 27.6197, 1.8944, 0.4618, 27.6197, 1); shape of gamma distribution = 1.2494; proportion of invariable sites = 0.5742] found in Modeltest were used and heuristic searches were employed by using a neighbor-joining starting tree and nearest neighbor interchange (NNI) branch swapping.
Each gene tree search was bootstrapped (500 pseudoreplicates) using PhyML with the Nearest-Neighbor Interchange (NNI) branch-swapping method to detect genes that support or conflict with various bipartitions.
At the latter interchange, Highway 12 branches northwest towards Coldwater, where it joins Highway 400 between interchanges 141 and 147; this concurrency is not signed.
The starting tree was generated by Neighbor-Joining (BIONJ) and searched by Nearest Neighbor Interchange (NNI); tree topology, branch lengths, and rate parameters were optimized.
