Web site User Guide:
There are 4 elements to the Chondrichthyan Tree of Life website:
Each can be accessed from the opening page.
(1) Phylogeny: Exploring evolutionary relationships among extant sharks, rays, skates and chimaeras.
· A linear evolutionary tree of relationships is presented on the left of the opening page. Species are depicted with their scientific names. Illustrations for each species appear when the cursor is place over the name. You can scroll to the bottom of the tree using the scroll bar on the right of the panel. To search for a particular species, enter the scientific name in the search field above the tree.
· The interactive circular tree in the centre of the screen depicts 14 major lineages that correspond to the ordinal level divisions of the current taxonomy. The tree can be rotated by holding the cursor on a branch and moving it. Clicking on an internal node (blue circle) will collapse the descendent nodes. Clicking on a terminal node will expand the node to reveal the family level lineages contained in the parent node. Clicking on a “family level” node will reveal all of the species the family contains. Shift-clicking will restrict the operation to the set of taxa contained in the node, excluding all other taxa from the screen display.
(2) Atlas: Species ranges.
· The interactive Orthographic (globe) is rotated using the cursor. You can also zoom in to focus on any region of interest. To see a species range, place the cursor on the name of the species in the tree, and click. The selected species range will appear on the globe. Multiple species can be shown at the same time. Intersections between species ranges are shown in a different colour. Clicking on an internal branch will select the ranges of all of the species descended from that branch.
· Equal Area (rectangular) projection shows species ranges as for the interactive globe but on a static projection. The “select a range” radio button allows the user to draw a rectangular box anywhere on the map by clicking and dragging the cursor. The ranges of all the species occurring in the box are returned. The number of species present in the box is shown next to the “select a range” radio button. This function can be useful to find out which species occur in a particular part of the world.
(3) DNA: Single copy gene sequences.
· 1077 single copy gene exons are shown in the column on the left. Species are shown on the right. Any subset of taxa and exons can be selected using the radio buttons. The “download” button will download an aligned data set for the taxa and genes in a nexus formatted file for subsequent phylogenetic analysis. This function is currently password protected.
(4) Anatomy: Interactive comparison of skeletal data.
· Segmented CT scan data of representative specimens are available for most the major lineages of extant chondrichthyans. (i.e. those for which material was available that would fit in the scanner) The skeletal anatomy can be examined and compared across species.
· Species are selected from the tree. The corresponding CT scan subsequently appears in the interaction window. The cursor is used to manipulate and rotate the image. The anatomical components associated with the specimen are listed to the left of the window.
Note: Several specimens include a “skin layer” which prevents the user from seeing the underlying skeletal anatomy. This “skin layer” can be removed by first selecting the “ delete” radio button (which will turn blue with a check mark, when selected) and then placing the cursor anywhere on the skin and clicking.
· Selecting the “colours” radio button facilitates distinction of different parts of the anatomy by colour.
· The “focus” radio button allows the user to select a structure in the main anatomy window to serve as the focal element in the skeleton. Zooming and rotating will subsequently center around the mid point of the focal structure . This feature is especially useful for examining the association of structures in a particular part of the anatomy.
· Clicking on any one of the skeletal elements will delete it. If the “delete “ radio button in not checked then clicking on a skeletal element will open up a new window beneath the primary window to allow for the examination of the selected element in isolation. Multiple elements from a single specimen can be examined (such as the chondrocranium and the jaws) as well as elements from different specimens. This feature facilitates comparison of homologous elements across species.
· Selecting the “lock” button, locks all of the sub-windows such that the rotation of a skeletal element in one window causes the elements in the others to be rotated by an equivalent amount in an equivalent direction