Taxa
Taxa are the fundamental entities in Mesquite: they represent
the species or gene copies whose characteristics are recorded
in character matrices, whose relationships are summarized in trees.
Our use of the word "taxa" isn't the traditional one,
which views a taxon as a formally recognized group at any level
(e.g., genus, family, order) in a taxonomic classification. Rather,
as with other computer programs, Mesquite uses "taxon"
as a shorthand for "terminal taxon" (the smallest unit
of analysis of relationships, equivalent to "Operational
Taxonomic Unit" or "Evolutionary Unit"). Higher
level groups are refered to as clades.
Taxa in Mesquite currently must belong to taxa blocks, which
are collections of taxa. Thus, the taxon "Homo sapiens"
would belong to a taxa block, for instance one called "Mammalia"
which may also contain other taxa such as "Mus musculus"
and "Ornithorhynchus anatinus".
Creating and managing taxa blocks
To add taxa to a data file, a taxa block must first be created
to contain them. Mesquite automatically asks you to create a taxa
block when you make a new file. You can later create a new taxa
block by selecting Taxa&Trees>New Block
of Taxa... A dialog box will ask you the name of the
taxa block and the initial number of taxa (you can add or delete
taxa later). You will be then shown the List of Taxa window, in
which you can rename the taxa (you can also rename them in the
Character Matrix Editor).
Mesquite allows more than one taxa block to exist in a file.
Thus, there is a List of Taxa Blocks window which shows you all
of the taxa blocks defined. To rename a taxa block, edit its name
directly in tis window. To delete a taxa block, select its row
in this window and choose List>Delete Selected
Taxa Blocks. Deleting a taxa block may cause character
matrices and tree blocks that depend on it to be deleted.
Managing taxa
You can add and delete taxa in the List of Taxa window and in
the Character Matrix editor. In the List of Taxa window, taxa
can be added by selecting List>Add Taxa....
In the Character Matrix Editor, taxa can be added either by using
the Add Taxa tool or by selecting Matrix>Add
Taxa...
Taxa can be deleted in the List of Taxa window by selecting their
rows and choosing List>Delete Selected Taxa.
Taxa can be deleted in the Character Matrix Editor by selecting
their rows and choosing Matrix>Delete Selected.
Taxa can be renamed by editing their names directly in the List
of Taxa window or in the Character Matrix editor, or by using
the Name tool in the Tree Window.
To change the order of taxa, you can select and drag entire taxa
in the List of Taxa Window or the Character Matrix Editor. You
can also us the sort tool (
)
to sort taxa automatically in alphabetical or numerical order
of the column on which you touch in these windows.
Taxa can be merged, with their character states merged, using
Merge Taxa of the Taxon
Utilities submenu.
Different blocks of taxa can be merged during file
import or file
export. Otherwise there are not yet methods to merge taxa
blocks within Mesquite.
Renaming taxa
Taxa can be renamed by editing their names directly in the List
of Taxa window or in the Character Matrix editor, or by using
the Name tool in the Tree Window.
In the List of Taxa window and Character Matrix Editor, the Taxon
Names submenu permits you to make changes to taxon names. Condense
Taxon Names, for instance, assigns shorter names with
punctuation removed. This may be useful for converting names to
a format for other programs.
There is also a feature to archive
current taxon names for later recovery.
Assigning group membership
Taxa can be assigned to groups to form a partition of the taxa.
Thus, taxa could be assigned to groups according to a traditional
taxonomic scheme (some taxa in the group "Vertebrates",
others "Invertebrates"), or according to some quality
such as distribution ("Neotropical", "Holarctic").
The reason to assign taxa to groups is not to constrain trees
or do formal analyses (these groups in most circumstances don't
get involved in formal analyses) but rather for reasons of graphics
and interface. Groups can be assigned colors, and thus taxa can
be highlighed by their group's color wherever they appear (e.g.,
in charts, in the Tree Window). (One analytical advantage is in
multivariate analysis, where Canonical Variates uses the assigned
groups as the prior grouping.)
To assign taxa to groups, go to the List of Taxa window. Select
Columns>Group Membership (Taxa)
to show the column indicating group membership. If you click on
the column heading "Group", a menu will drop down with
menu items to manage group membership. You must first create groups
using New Group. For instance, you could create a group Neotropical
and another group Holarctic. Then, you can assign taxa to the group
using the Set Group submenu. You can also edit the color of the
group, and rename the group.
Associating two taxa blocks
Associating the taxa in one block with taxa in another block is
useful in two contexts. First, you may want to indicate how genes
are assigned to species or parasites to hosts for studies of gene
tree/species tree or parasite tree/host tree relationships.
Second, you may want to indicate equivalence of taxa in different
blocks, e.g., sequence matrices of different gene loci with slightly
different taxon names but pertaining to the same set of specimens
or species. This can be helpful for fused
export into a single matrix.
To set up an association between two taxa blocks, follow the instructions here.
