Molecular data

Molecular data (DNA or protein sequences) can be edited, manipulated, simulated and analyzed in various ways in Mesquite. Most of the features discussed elsewhere concerning editing and analysis of general categorical data also apply to molecular data; here we focus on features specifically designed for sequence data.

Contents

• Editing molecular data
• Simulating DNA sequence evolution
• Statistics for DNA sequences
• Statistics for Protein sequences
• Visualizing tertiary structure
• Sequence Data within populations
• Reconstructing ancestral states

Editing molecular data

Molecular data can be imported from files of NBRF format, PHYLIP format, and simple table format. It can also be exported to these formats.

The Character Matrix Editor can be used to edit a molecular sequence matrix. Standard ambiguity codes are allowed.

The following can be applied to all or the selected portions of a molecular sequence matrix in the Character Matrix Editor. These are available under the Alter/Transform submenu of the Matrix menu:

• Nucleotide complement (DNA matrix only) — enters the complementar sequence into the selected cells
• Reverse sequence — reverses the order of contiguously selected blocks of sequence

Other options may appear; see the page on characters for standard choices in this submenu. You can also apply the other editing tools described for character matrices.

Statistics for DNA sequences

Calculations for categorical characters in general can be applied to DNA sequences. For example, Parsimony calculations can be made for DNA sequences, as can basic descriptive statistics such as the percent of a sequence or character that is missing data or gaps. In addition, there are several modules specifically designed for DNA data, illustrated by examples in Mesquite_Folder/examples/Molecular. These calculate compositional bias:

• ACGT Compositional Bias — This module supplies the compositional bias of taxa, measured over the taxon's sequence. The bias is treated as a continuous character, and thus can be used wherever characters are used, as for instance in the reconstruction of the evolution of compositional bias as shown in the image below. It can return either the proportion G+C, or separately A, C, G, and T proportions.

• Character Compositional Bias — This module supplies the compositional bias for characters. It calculates the percent of taxa with particular nucleotides (GC bias, or individual frequency of A, C, G or T) for a character. The image below shows a moving window analysis of compositional bias along a sequence; the instructions for generating the chart are given here.

• GC bias coloring of matrices — The cells of the Character Matrix Editor may be colored according to a moving window of GC bias along the sequence, as shown below, by selecting Matrix>Color Cells>Color By Cell Value, then once shown the colors can be smoothed by a moving window analysis by selecting Matrix>Moving Window (for colors).

Statistics for Protein Data

• Site hydrophobicity — This module supplies the average amino acid hydrophobicity, averaged across taxa, for each site. It can be used in charts, for instance to see the relationship between a phylogenetic statistic for the site (character) and it average hydrophobicity. This chart, for example, shows parsimony character steps as a function of hydrophobicity:

• Amino Acid hydrophobicity — The cells of the Character Matrix Editor may be colored according to a moving window of hydrophobicity along the sequence, as shown below, by selecting Matrix>Color Cells>Color By Cell Value, then once shown the colors can be smoothed by a moving window analysis by selecting Matrix>Moving Window (for colors).

Visualizing tertiary structure

Although there are not yet dedicated windows for visualizing phylogenetic statistics in the context of molecular structure, features have been added to the Scattergram chart to allow it to be adapted for this purpose. For instance, in this image cytochrome B is shown, with the amino acids colored according to a simple phylogenetic statistic: the number of parsimony steps on a phylogeny. The colors are smoothed by a moving window, and show that several coils of the molecule, a few at the left and one deep at the right, evolve more rapidly than others. This example is illustrated in the data file at Mesquite_Folder/examples/Molecular/06-cytochromeB.nex

To build such a chart, begin with a file with a matrix of protein sequences. The procedure is also described in the example files 08-cytochromeBlinked.nex and 09-cytochromeBscatter.nex.

• Select New Linked Matrix from the Characters menu. When a matrix is made to be linked to a second matrix, the two matrices are constrained to have the same number of characters.
• Indicate that you want the linked matrix to be a Continuous matrix, and link it to your protein matrix. Then, turn it into a three dimensional matrix (Taxa X Characters X Coordinates [x, y and z]) by using Add Item and Rename Item in the Utilities submenu of the Matrix menu of the Character Matrix Editor. The x,y,z coordinates could be added for all taxa if known, but otherwise only one taxon needs to be filled out (because we will use the average x,y,z coordinates for the amino acids).
• Once the linked matrix of xyz amino acid positions is entered, select Analysis>New Scattergram for> Characters. Indicate you want the scattergram to be for Stored Characters, and indicate Same value for the two axes. In the dialog box "Values for axes", choose Mean Value of Character (Linked Matrix). In response to "Use characters from which matrix? (for Character Source)" choose the protein sequence matrix as the matrix to be used. This will plot the sites (amino acids, characters) in their correct places, but as a series of round spots.
• To change the appearance of the plot, select Join the Dots in the Special Effects submenu of the Scattergram menu. Then select Thick Joints, deselect Show Dots, deselect Join First to Last, and set the marker size larger (e.g., 8). This will result in a plot as shown above, but without the colors.
• Next, choose Color by Third Value from the Colors menu and choose the value by which to color the amino acids. For parsimony steps, for instance, choose Character Value with current tree.
• Finally, to use a moving window to smooth the colors, select Moving Window for Colors from the Colors menu and indicate the window size (e.g., 5).

Sequence data within populations

See the page on population genetics.

Reconstructing ancestral states

Ancestral states of continuous characters can be reconstructed as described in the page on reconstructing ancestral states. Likelihood methods are not yet available for molecular characters.