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.

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.)