MEGA6: Molecular Evolutionary Genetics Analysis version 6.0

F ig . 2.

( A ) Timetree inferred in MEGA6 and shown in the Tree Explorer

(A) Timetree inferred in MEGA6 and shown in the Tree Explorer, where it is displayed with divergence times and their respective 95% confidence intervals. A scale bar for absolute divergence times is shown. (B) An information panel that can be made visible by pressing the icon marked with an i. When focused on a tree node (left side), it shows the internal node identifier, and absolute or relative divergence time as appropriate; when focused on a branch (right side), it displays the local clock rate as well as the relative branch length. (C) A timetable exported using the displayed timetree, which shows the ancestordescendant relationship along with relative node times, relative branch rates, absolute divergence times, and confidence intervals. Users can display internal node identifiers in the Tree Explorer as well as internal node names, which can be provided in the input topology file. On pressing the Caption in the Tree Explorer menu bar, MEGA produces the following text to inform the user about the methods, choices, and data used. Caption: The timetree shown was generated using the RelTime method. Divergence times for all branching points in the user-supplied topology were calculated using the Maximum Likelihood method based on the General Time Reversible model. Relative times were optimized and converted to absolute divergence times (shown next to branching points) based on user-supplied calibration constraints. Bars around each node represent 95% confidence intervals which were computed using the method described in Tamura et al. (2013). The estimated log likelihood value of the topology shown is 247671.60. A discrete Gamma distribution was used to model evolutionary rate differences among sites (4 categories, +G, parameter = 38.07). The tree is drawn to scale, with branch lengths measured in the relative number of substitutions per site. The analysis involved 446 nucleotide sequences. All positions with less than 95% site coverage were eliminated. That is, fewer than 5% alignment gaps, missing data, and ambiguous bases were allowed at any position. There were a total of 1,048 positions in the final data set. Evolutionary analyses were conducted in MEGA6 (Tamura et al. 2013).

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MEGA6: Molecular Evolutionary Genetics Analysis version 6.0