How to use PhyloLink

Figure 5. When hovering over a terminal the character states appear.

Figure 1.  PhyloJIVE web with application a resizable central view pane for phylogenies with a) with   tabs and controls  hidden  and b) tabs and controls exposed via a button.

​Figure 2.  The web application with tabs which are always visible and a fixed size view pane.​

Figure 3. A portion of the visualization with names aligned. The first column is a quantitative trait colored in a blue heat map with several - indicating missing data. The second column is a qualitative trait with each character state given a different color.  The tree branches are colored according to the character state of the first column character.

Figure 4. Move around screen with the arrows, expand or contract tree or click and drag to move around screen.

Two forms of the PhyloJIVE web application currently exist. They differ primarily in arrangement the graphical user elements such as tabs and styling.  Figure 1(left)  shows the first.  A button placed above the central view pane can be used to reveal and hide tabs which display information as well as a various controls. Figure 2 (right) shows an alternate form of the web application in which information tabs and controls are always visible. Controls and information tabs are otherwise the same.



 



























The visualization shows:

i) the phylogeny to a chosen depth
ii) Pinkish triangles  to indicate unexpanded clades which contain members beyond the selected view depth
iii) branch lengths in proportion
iv) character states for taxa at tips and nodes
v) nodes where selected character sets may be disjoint in daughter taxa



Up to ten characters can be visualized. Their states are indicated by a matrix of coloured icons appearing to the left of taxon names.

Tree branches (and nodes for common ancestors) are coloured according to the predicted value for the first (chosen) character. Taxa are blue where the first character is scored. Same for collapsed clades where all have a value all the first character. Where quantitative characters are chosen and the  taxon names subsequently aligned, the characters are presented as a heat map.





























































Controls and Navigation

Viewers can navigate the screen with the arrow buttons or click and drag with a mouse.  The tree can be expanded with the +/- and home key.

Mousing-over a node or name shows the names of the selected characters and their values. The colored icons next to the scientific names represent different values for the three “characters” selected (these can be changed in the “character” tab), as shown in the legend panel on the right. Tree branches (and nodes for common ancestors) are colored according to the predicted value for the first (chosen) character, as calculated using reverse parsimony. Mousing-over a node or name shows the names of the selected characters and their values. Clicking on a node or name brings up a menu to allow the user to perform a number of tasks.

PhyloJIVE’s screen is in two sections. The left side window holds the phylogenetic tree and the right side controls the options.  By hovering the mouse over the tree, various options become available, by either right or left clicking.  These options can be changed on the right hand widow.

Options appear for the use by either a left or hovering.   A left click over a terminal or a node brings up the popup box above.  After selecting External links a popup window appears and the use links out to a popup window that as currently programmed links to the species information for the chosen terminal at various webservices including ALA. Australian Plant Image Index, Australian Plant Name Index and EOL.  The user can toggle through these window with the arrow buttons on the lower left window and exit by clicking the x in the lower right.  Additional webservices can be accessed by changing the code.  If the user selects View Map a distribution map for that terminal or node is generated in the Map box on the right (see below).
If a clade is condensed to a triangle the clade is expanded by selecting Expand/Collapse.
Hover or click on nodes will fetch taxon specific information pulled from pre-configured webservices. Mousing-over a node or name shows the names of the selected characters and their values (see below). Left clicking on a node or name brings up a menu to allow the user to perform a number of tasks. By left clicking and selecting External Links the user is taken to a webservice with information about the selected taxon.  This a user configurable system which now point to ALA, APNI, APII and EOL but a clever user can configure the viewer to go anywhere.


































Tabs
There are seven tabs which allows the user navigate and configure the tree. Users can change the view scale, collapse or expand select clades, roroot the tree.  In any web browser, viewers can change the presentation of the tree. They can swap the order individual paired branches or sort the whole tree by branch length (ladderise).  They can search the tree for a taxon name – corresponding to a subtree or terminal taxon.
The options tab controls tree viewing options such as expanding/contracting nodes. It is often helpful for viewing character information to check the align names box. This displays all symbols in columns for easier comparisons.

The character tab allows selection of characters, up to ten at a time, to be mapped on the tree. Note that the tree branches are colored based on the characters states, and ancestral state reconstructions, of the first character selected.
 
The Legend tab provides a legend of the character states for all chosen characters.  Quantitative character states are divided into 10 section of equal size and blue heat map is used to color the 10 character states.  Qualitative characters are coded with symbols and colors to differentiate character states.  PhyloJIVE does allow the input of multiple character states however multiple characters states do not reconstruct on the tree. If a terminal has two character states a new colored symbol is produced which is called multiple.  The individual character states are identified on the tree by terminal taxon.

The Map tab will show the distribution map of a selected terminal or nodes. The default is to color the map by terminal name (species), that is each terminal is indicated with a different color. The user has the option of selecting one of the characters to display on the map. For example the A node with ten terminals can be selected and the default will be a map with ten colors one for each species. Alternatively the user can use the colour by toggle box and select habit. Now the map will be colored by the character state tree or shrub.  The trait values come for the coding of the species for that trait.  Double clicking on the map will produce a larger map for easier viewing.
The Search tab allows the use to search for a terminal taxon.  The taxon will be highlighted if found but the use will have to navigate to the terminal branch.



























Characters  tab

Viewers may select up to ten characters for simultaneous display on the tree.  These data can with be from the users upload function of the Input tab or pulled from pre-configured webservices.  The Character tab allows selection of the character from a pull down menu that combines the user uploaded and the webservices derived data.  The data can be a mix of qualitative or quantitative data.  Character 1 is used to color the branches of the phylogenetic tree. When hovering the mouse over a terminal or node the character state is given in a floating box.  The data at the nodes is from an ancestral state reconstruction (see below).  In order to give the viewers a quick overall impression of the distribution of character states for multiple characters colored symbols are used to display the data along with the actual value that is available while hovering over the node or terminal.  Quantitative characters  are shown by a heat map while qualitative characters are mapped with a colored symbol.
Putative differences in the ancestral states qualitative characters are inferred from (Fitch) parsimony. Putative changes in the ancestral states of quantitative characters are inferred from a phylogenetically weighted comparison of means and standard deviations.
The reconstructed ancestral state of the first character is used to determine branch colour. Transitions in any of the three selected characters is indicated by a red box.












































Maps
----Distribution maps of the terminal are available another new feature is the ability to view a map of occurrence records for a given taxon or ancestral node. These data are available through the external links outlined above or can be directly mapped in the Map tab.  Currently PhyloJIOVE is configured to generate the maps by accessing the point data from the Atlas of Living Australia.  This can be configured by the viewer to generate maps of non-Australian taxa by  accessing the data from any other webservice.
The viewer can left click on a terminal and select View Map and the distribution map will appear in the Map tab.  Distribution maps for multiple taxa (up to 32) can also be accessed at nodes by left clicking on the node and selecting View Map.  The default value is to colour dots by species thereby simultaneously mapping multiple taxa each with a different colour.  The user has the option, in the Map tab, “Colour By: pull down menu to colour the map by any character.   For example the user could select a node and map by species and then select the character habit and see the geographic distribution of trees versus shrubs for that node.
Lastly, these maps can be the basis of a spatial analysis by automatically importing the different colour schemes as separate spatial layers in the ALA spatial portal. Clicking the link “View in Spatial Portal” opens the ALA Spatial Portal in a new window (shown below). Layers can be hidden, combined, filtered by other criteria (e.g. collector, institution, etc) and various environmental layers can be overlaid or used as the basis of modelling, etc.









































































 

Figure 6.  Options appear when left clicking on a terminal or node.

Figure 7. These options appear when External Links is clicked.

Figure 8. The right panel has several tabs. These allow the user to select characters to map, view legend, search for a terminal name and see a distribuiotin map

Figures 9 and 10.  Users can map morphological characters on the phylogeny,if characters are available as a .csv file or from a linked webservice such as Identify Life.  Left, up to 10 characters can be selected and mapped at one time in the characters tab and the character state legend is available in the Legend tab, right.

Figures 10 and 11. Distribution maps accessed by left clicking over a node or terminal and selecting view map of single terminals (left) and up to 32 members of a clade (right).  Current source of the map points is the Atlas of Living Australia but this is configurable.

© 2018 by Joe Miller.