Phylogenetic trees
Phylogenetic trees represent the branching history of descent
linking taxa, whether these taxa are species or genes. In Mesquite,
a tree refers to the taxa in a particular taxa
block and once created cannot be transfered to refer a different
taxa block. (As explained in the page on taxa,
"taxon" here is used as shorthand for "terminal
taxon" or "OTU".)
Characteristics of trees
Mesquite typically treats trees as rooted, although it is possible
to de-root trees. Trees may contain polytomies (multifurcations)
and also unbranched internal nodes. A tree in Mesqite does not
need to contain all of the taxa in the taxa block, and indeed
can contain as few as one taxon. Unlike MacClade, Mesquite does
not support trees with observed taxa fixed in ancestral position.
Mesquite can read, edit and write branch lengths in trees. In
addition to length, a branch may have various other attributes
such as width (e.g. for effective population size in population
genetics) and color (for display purposes).
Polytomies in trees are interpreted either as "soft"
(uncertainty in resolution) or "hard" (simultaneous
divergence). The default interpetation is specified in the Defaults
menu of the Startup Window, the Project and Files window, or the
Log window. A change in this default applies to all projects and
files. Individual trees can be marked as using a specific assumption,
thus overriding the default (e.g., by using the Set Polytomy Assumption
menu items in the Alter/Transform Tree submenu of the Tree menu
of the Tree Window). The appropriate assumption for most phylogenetic
studies is "soft", but calculations using soft polytomies
are extremely difficult, and most Mesquite calculations yield
results only with dichotomous trees and those with hard polytomies.
Analyzing trees
Trees can be visualized in various tree windows, and statistics
about them presented in tree windows,
the List of Trees window, and in charts.
We will not attempt to summarize all of the options here, which
are discussed elsewhere, in particular in the analysis links at
left.
Tree comparison methods include the following:
- Tree to tree similarity measures —
The Shared Partitions module measures the number of partitions
between taxa shared by two trees. The separately-available TSV
package includes other measures such as the Robinson-Foulds
metric.
- Consensus trees — This is not available
standardly in Mesquite, but can be added with the TSV package,
which includes strict consensus trees.
- Fits of trees into trees — The fit
of a contained tree (e.g. gene or parasite) into a containing
tree (e.g. species or host) can be measured by Deep
Coalescence in the coalesce package.
- Taxon instability among trees — This
module measures for each taxon how variable are its relationships
among a set of trees. Taxa that are particulary unstable, i.e.
whose placement is especially variable from tree to tree, score
high on this index. Taxon instability calculations are illustrated
in the example file at Mesquite_Folder/examples/Basic_Examples/tree_manipulation/13-instability.nex
Stored trees and tree blocks
Trees may exist within tree blocks that are
stored in the data file. A tree block is a collection of trees
stored as a unit. A single data file may contain more than one
tree block, each containing from one to many trees.
Mesquite calculations can use trees other than those stored in
tree blocks in a data file. Most calculations can use trees that
are temporarily created using simulations or randomizations specifically
for the purpose of the calculation and then discarded. Also, a
recently edited tree in the Tree Window might not be stored in
the file if the user has not explicitly stored it in the file
using "Store Tree" or "Store Tree As". More
details on storing trees in tree blocks in the file are given
below.
To create a new, empty tree block into which to store trees,
select Taxa&Trees>New Empty Block of
Trees... A new block of trees is automatically created
if you ask in the Tree Window to store a tree and no block has
yet been created to receive trees.
It is also possible to create tree blocks that are already filled
with trees. For instance, if you want to make a duplicate of an
existing tree block, select Taxa&Trees>Make
New Trees Block from>Stored Trees. Other choices
under Taxa&Trees>Make New Trees Block
from> allow you to create tree blocks filled with
trees resulting from simulations or randomizations, or other tree
sources.
Trees stored in a tree block can be
renamed or deleted in the List of Trees window
(available in the Taxa&Trees menu). To rename, edit the tree's
name in the list directly. To delete a tree, select the tree's
row in the list window and choose List>Delete
Selected Trees. Statistics about trees can also be
viewed in the List of Trees window by adding the appropriate columns
using the List menu.
Tree blocks stored in a file can be renamed or deleted in the
List of Tree Blocks window (available in the Taxa&Trees menu).
To rename, edit the tree block's name in the list directly. To
delete a tree block, select the tree block's row in the list window
and choose List>Delete Selected Tree Blocks.
For tree files with too many trees to be held in memory simultaneously,
Mesquite can read the trees in directly from the file, one at
a time, and discard each from memory after it is used (for instance,
in charts or in the Tree Window). To do this use Trees Directly
from File as your tree source.
Filtering Trees
Trees used in charts, the tree window or to make a new tree block
can be filtered. To do this, select Filter Trees from Other source
as your source of trees. You will be asked for the original source
of trees, and the filtering method. There are currently three
filtering methods:
- Selected Taxa Form Clade - retains only those trees in which
the currently selected set of taxa form a clade on the tree
- Selected Taxa Convex in Tree - retains only those trees
in which the currently selected set of taxa can be form a
clade by rerooting the tree
- Tree Value Satisfies Criterion - retains only those trees
whose value is greater than, less than or equal to a particular
target value. For "value", one can use any of the
available calculations that assign numbers to trees, such
as treelength, tree depth, likelihood in character, tree asymmetry,
and so on. The user is also asked what is the target value,
and whether the criterion is to be greater than, less than or equal to the target.
Modifying trees automatically
Trees can be edited by hand, as described below,
or the user can request Mesquite to automatically modify trees
using the "Alter/Transform" modules. These modules can
be used:
- in the Tree menu of the Tree Window, under the Alter/Transform
Tree submenu, or the Alter/Tranform Branch Lengths submenu.
Selecting an item in these submenus performs the transformation
on the tree in the Tree Window.
- in the List menu of the List of Trees window, in the Utilities
submenu, in the Alter Trees or Alter Branch Lengths submenus.
Selecting an item in these submenus performs the transformation
on all selected trees, or on all trees if none is selected.
- to transform trees on the fly that are being supplied for
a chart or tree window or making a new tree block for a file.
To do this, select "Transform Trees from Other Source"
whenever a source of trees is required. You will be asked for
a source of trees to be transformed or filtered, and then for
a means by which to transform the trees.
The Alter/Transform modules include:
- Root tree with selected taxa as outgroup
- Resolve Polytomies (to 0-length branches)
- Collapse Zero-length Branches
- Convert Negative Branch Lengths to Zero
- All Branch Lengths to 1
- Scale All Branch Lengths
- Ultrametricize
To use "Root tree with selected taxa as outgroup",
you first must select the outgroup taxa in, for example, the Taxa
List window. Then, choose the menu item "Root tree with selected
taxa as outgroup" in the Alter/Transform Tree submenu of
the Tree menu of the tree window, and in the Alter Trees submenu
of the Utilities submenu of the List menu of the List of Trees
window. This module will reroot the taxa in between the selected
outgroups and the remaining taxa, if this is possible. If the
tree cannot be rerooted so that the remaining taxa form a clade,
then the tree will not be rerooted, and a warning will be given
(perhaps visible only in the log). If the tree can be rerooted,
then both the outgroup and ingroup will be monophyletic on the
rerooted tree. In addition, if the tree has branch lengths specified,
the root will be positioned at the midway point along the branch
on which it is placed. That is, the length of the branch from
the root to the ingroup will be equal to the length of the branch
from the root to the outgroup. Future versions may allow user-choice
of the branch length distribution. Adjusting of the length of
the two basal branches is NOT done if the tree is already rooted
between the chosen outgroups and ingroup.
Editing trees: The Basic Tree Window
The Tree Window shows a tree that can be edited and used in analyses.
A new Tree Window can be requested by selecting Taxa&Trees>New
Tree Window. (Mesquite allows multple tree windows,
and so if you select this menu item a second time, you'll get
a new tree window.) Many of the Tree Window's fundamental functions
are controlled by its Tree menu. This menu contains items to select
the tree source, store trees, and alter the tree. A second important
menu is the Drawing menu, which controls the appearance of the
tree. Additional menu items related to the Tree Window are found
in the Analysis menu.
Tree source
The Tree Window shows trees from a particular source (although
the tree being shown could differ from those in the tree source,
if you've recently modified the tree using the tools). The source
of trees might be a tree block in the data file. In this case,
as you used the blue arrows at the upper portion of the tool palette,
you would be browsing through the stored trees, scrolling from
one stored tree to another. Alternatively, the source of trees
might be a coalescent simulation, in which case you would be browsing
through gene trees representing replicate simulations of the coalescent
process. Other tree sources may be available, and can be selected
when you request the Tree Window for the first time or by using
the submenu Tree>Tree Source>.
One tree source, "Default Trees", offers a simple pectinate
tree ("Default Ladder"), a full polytomy ("Default
Bush"), and a symmetrical tree. It is available merely as
a last resort, in case other tree sources are unavailable.
We expect a common confusion will be that users will be unable
to find the trees that they recently stored in the file. For example,
when a new file is created, there are no stored trees, and hence
the Tree Window would be forced to use another tree source (for
example, "Default Trees"). If a user then stores a tree
in the file (see next section), he or she might hit the blue scroll
arrows of the Tree Window expecting to browse the stored trees,
only to be shown one of the Default Trees. The problem is that
the Tree Window is using Default Trees as the tree source, not
Stored Trees. To see the trees stored in the file, select Tree>Tree
Source>Stored Trees to change the tree source to
Stored Trees.
Moving from Tree to Tree
To select which tree to view, use the tree scroll at the upper
left of the Tree Window:
The left and right blue arrows take you to the previous and next
trees, respectively, in the tree source. The Go To button takes
you to the tree whose number is entered in the text area. The
Recent Editings button offers you a drop down menu by which you
can return to recently edited trees. The menu lists only trees
that you have edited; it does not list the trees that came directly
from the tree source, and is therefore not a complete history
of recent trees. The number of little white triangles in the button
indicates the number of recently edited trees stored.
Storing trees
Although the Tree Window can be used merely to browse existing
trees, it will commonly be used as a tree editor, allowing the
user to build a tree according to some prior hypothesis, or to
modify trees to explore the effect of changes in the tree.
Once a tree has been edited, the user may want to store this
new tree in the file. Exactly how that is done depends on the
tree source being used by the Tree Window:
- If the tree source is Stored Trees, then two menu items are
available in the Tree menu to store trees, "Store Tree"
and "Store Tree As...". For instance, imagine that
you scroll through the stored trees until you get to tree number
5. If you edit it using the tools of the tool palette, then
you select Store Tree, your newly modified tree will replace
the original tree number 5 in the tree block. If instead you
choose Store Tree As, you will add your modified tree as a new
tree at the end of the tree block, leaving the original tree
number 5 untouched. Thus, Mesquite assumes that you are potentially
editing the original tree in the tree block whenever you edit
the tree. However, the original copy is not replaced by your
edited version until you select "Store Tree". Until
you select this, your modified tree is maintained as a temporary
tree associated with the tree window, and not stored in the
tree block.
- If the tree source is not Stored Trees then you can't modify
the original trees, because they are merely temporary trees,
produced by something like a simulation. Thus, in this case
there is no Store Tree menu item available. Instead, there is
a "Store Copy of Tree As" menu item. This acts more
or less like Store Tree As, in that the tree is added to a tree
block.
You can tell that a tree has been edited to be different from
that in the tree source when a black diamond appears in the message
area at the lower left side of the Tree Window. The message area
turns green when the tree is an unsaved, edited tree and the tree
source is not Stored Trees.
Tools
At the left side of the Tree Window is a tool palette,
containing tools that you can use to interact with the tree. Exactly
which tools are available will depend on the modules installed
and loaded. In the description of tools below, it will be assumed
that a basic set of modules is installed and loaded.
Some tools act when they are touched on a branch of the tree;
others act when a branch is touched then dragged and dropped.
Some tools behave differently if a key such as shift or control
is held down when the tool is used. These details are explained
below. Some explanation of the tool is also given in the window's
Explanation Area when the tool is selected in the palette. The
currently selected tool has its button darker than the rest in
the tool palette. If you are running Java version 1.2 or above
(e.g., on Linux, Windows or Mac OS X) then the cursor will change
to reflect the tool when it is over the tree. If you ware running
Java version 1.1.8 or below (e.g. on Mac OS 9) then the cursor
will remain an arrow.
Some tools have options that can be set. If so, then the button
for the tool in the tool palette will have a small black triangle
indicating the availability of a drop down menu. If you touch
the button and hold down the mouse for a moment, the menu will
appear to allow you to make choices.
The following tools change the topology of the
tree (the fundamental relationships among taxa implied by the
tree). Some of these tools might not be available if their controlling
modules are not installed or loaded.
The following tools change the branch lengths or widths
of the tree.
The following tools affect the appearance of
the tree, or change attributes of its branches, but do not change
the topology or branch lengths. Thus the changes these tools make
will not affect most calculations.
Alter/Transform menu items
In the Tree menu of the Tree Window are two submenus by which
you can change the tree, "Alter/Transform Tree" and
"Alter/Transform Branch Lengths". These provide various
utilities to change the tree, including its branch lengths. Some,
such as "Scale All Branch Lengths", affect all branches of the
tree simultaneously. See the section on automatic
modification for more details.
Analyses
The Tree Window has, in its Analysis menu, menu
items that yield analyses using the current tree in the Tree Window.
Which analyses are available depends on what modules are installed
and loaded. Typically the following will be available at least:
- Trace Character History - Illustrates a history of character
evolution on the tree. Described in detail in the chapter on
reconstructing
ancestral states.
- Tree Legend - adds a small legend to the Tree Window. The
legend can describe information about the tree, including the
results of calculations done using the tree. When the legend
is in the Tree Window, an additional menu appears, the Legend
menu, by which you can choose to show or hide lines of information.
- Values at Nodes - shows values associated with nodes, either
by coloring the nodes or labeling them. These values describe
information about the nodes, such as a statistic calculated
over the clade above the node. At the moment there are few such
values available (notably, the reconstructed character state
in a continuous character, also available through Trace Character
History).
How trees are drawn
There are many options for the appearance of trees as drawn in
the Tree Window and other windows displaying trees. Trees may
have diagonal, square or circular branches; they may be drawn
black on white or green on blue; they may be drawn so that apparent
branch length is proportional to assigned branch length. These
options are controlled by the Drawing menu.
Some of the menu items in the Drawing menu are:
- Tree Form - Chooses general form of the tree. Some are merely
graphical, others involve analyses such as PlotTree and PlotTree3D
(which plot the tree in a 2D or 3D space) and Contained Associates
(which shows gene trees within species trees, or parasites within
hosts).
- Set Current Form As Default - Sets as default the tree drawing
style currently in use (e.g. Diagonal Tree, Balls & Sticks
etc.). It does not capture all of the current parameters chosen
for that drawing form (background color, spot sizes, etc.).
- Background Color - Sets the color of the field on which the
tree is shown.
- Branch Color - Sets the color of the branches. These color
are not retained with the tree, but are for graphical purposes
only. In this regard it is different from the Color Branch tool,
whose colors are retained with the tree.
- Size to Window (Only in the basic Tree Window) - Shrinks the
tree to fit into the window. If this is turned off, then the
tree exists in a panel that may be much bigger than the tree
window itself. To see various parts of this panel, you can use
the scroll bars or the Bird's Eye View box that appears at the
lower left corner of the Tree Window.
- Drawing Size (Only in the basic Tree Window) - When Size to
Window is turned off, this item allows you to set the size of
the panel in which the tree is drawn.
- Float Legends (Only in the basic Tree Window) - When Size
to Window is turned off, this item allows you to choose whether
the legends such as the Tree Legend and Trace Character Legend
are anchored to the panel in which the tree is drawn or, anchored
to the window itself.
- Font, Font Size, Font Color - Sets the font characteristics
of the taxon names and node names.
- Names - Determines what names are shown and whether taxon
names are colored by the taxon group.
- Orientation (Only for some tree forms) - Chooses whether the
root to terminal orientation is up (classic phylogeneticist
or paleontologist), to the right (molecular evolutionist), bottom
(population geneticist or mathematician) or left (?)
- Branches Proportional to Length - Determines if the drawn
lengths of branches are proportional to their assigned lengths.
Otherwise, the tree drawing routine chooses node positions at
its own convenience.
- Save Macro for Tree Drawing - Saves the current tree drawing
specifications (form, color, orientation, etc.) as a macro.
The macro will then appear under the Macros For Tree Drawing
submenu, and can be used later to set other tree windows to
use the same specifications.
Printing trees and saving graphics files
Mesquite's Tree Window offers two menu items for printing trees:
Print Tree and Print Tree to Fit Page. The former prints the tree
in its current size, even if that requires it to be placed over
multiple pages. The latter automatically reduces or enlarges to
tree image to fit a single printed page. It attempts to choose landscape
or portrait mode to maximize the size of the fitted image.
There is as yet no direct way to save graphics files of tree
images, but satisfactory results can be obtained if you ask to
print the tree image, then you use your operating system's Print
dialog box to direct the output to a file (e.g., postscript or
pdf) instead of a printer. These files may be editable by programs
such as Adobe Illustrator.
Dependent Tree Window
This window shows the same tree as in the Tree Window (hence it
is "dependent"). It is available in the Tree menu
of the Tree Window. It is useful when analyses or graphics are desired
for the Tree Window, but which would conflict visually with currently
running analyses or graphics. Thus, the Dependent Tree Window gives
additional space on which to display graphics and analyses. As the
tree in the Tree Window is changed, the tree in the Dependent Tree
Window is also changed. Note: If the Tree Window is closed, the
Dependent Tree Window will close also.
Users may find the menus of the Tree Window and Dependent Tree
Window somewhat confusing when the latter is in use, as both windows
include some menus of the other. This is a consequence of Mesquite's
automatic menu arrangement; we realize it is not optimal in this
case.
Mirror Tree Window
This window, like the Dependent Tree Window, shows the same tree
as in the Tree Window. However, the Mirror Tree Window shows it
twice, in mirror image. This allows you to compare, for instance,
two different traced characters visually, as in this
example. The analysis shown on the left side is controlled by
the Left side submenu; that on the right by the Right side submenu.
Users may find menus confusing when this window is in use; see
comments under Dependent Tree Window.
Multi Tree Window
This window, available in the Taxa & Trees
menu, shows multiple trees simultaneously. It is not dependent on
a Tree Window, but gets its trees from an available tree source.
