Phylogenetics - Back to Basics - Phylogenetic Networks

Michael Charleston

Updated: PURL: gxy.io/GTN:S00119

Tip: press P to view the presenter notes | Use arrow keys to move between slides

1 / 14

Presenter notes contain extra information which might be useful if you intend to use these slides for teaching.

Press P again to switch presenter notes off

Press C to create a new window where the same presentation will be displayed. This window is linked to the main window. Changing slides on one will cause the slide to change on the other.

Useful when presenting.

Requirements

Before diving into this slide deck, we recommend you to have a look at:

Introduction to Galaxy Analyses

2 / 14

About these slides

The following phylogenetic networks of Anolis species were generated in SplitsTree. They represent selected screenshots of networks explored as a live demo in the video associated with these slides.

3 / 14

Uncorrected P model

Phylogenetic network of Anolis species created in SplitsTree using the uncorrected P model. Circular phylogenetic network with many branches splitting outwards from a central point to multiple Anolis species at the periphery. The network is oriented so that the species Diplolaemus darwinii and Phenacosaurus acutirostrus appear on the right hand side.

4 / 14

Exploring splits

Click on the branches of the network to explore different splits. Here A. ahli appears in two different splits highlighted in yellow.

Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the bottom left of the image a split containing A. ahli, A. equestris2 and several other species is highlighted in yellow

Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the top left of the image a split containing A. ahli, A. bimaculatus and several other species is highlighted in yellow

5 / 14

Let's follow a split

This is the network made using the uncorrected p model. We will follow the split containing A. lineatopus and A. limifrons through different models.

Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the bottom left of the image a split containing A. lineatopus and A. limifrons is highlighted in yellow

6 / 14

Jukes Cantor Model

These networks were created using the Jukes Cantor model. Note that the species A. limifrons appears in two alternate splits.

Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the bottom left of the image a split containing A. limifrons and A. humilis is highlighted in yellow

7 / 14

HKY85 Model

This network was created with the HKY85 model. Note that A. limfrons is paired with A. humilis in this split.

Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. At the top left of the image a split containing A. humilis and A. limifrons is highlighted in yellow

8 / 14

Bootstrapped network

Screen shot of a circular phylogenetic network with multiple branches splitting out from a central point. Each branch is annotated with a value between 0-100

9 / 14

Bootstrapped network - a closer look

Let's explore our two splits again

Close up screen shot of a section of a circular phylogenetic network with multiple branches splitting out from a central point. The split containing A. humilis and A. limifrons is highlighted in yellow and is annotated with the value 99.99

Close up screen shot of a section of a circular phylogenetic network with multiple branches splitting out from a central point. The split containing A. lineatopus and A. limifrons is highlighted in yellow and is annotated with the value 38.3

10 / 14

Bootstrapped network - a closer look

This the centre of our bootstrapped network. Note that the values are smaller. Close up screen shot of a section of a circular phylogenetic network with multiple branches splitting out from a central point. The splits form a star like shape and are annotated with numbers

11 / 14

Thank you!

12 / 14

13 / 14

Thank You!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors!

Author(s)	Michael Charleston
Reviewers

Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.

↑, ←, Pg Up, k	Go to previous slide
↓, →, Pg Dn, Space, j	Go to next slide
Home	Go to first slide
End	Go to last slide
Number + Return	Go to specific slide
b / m / f	Toggle blackout / mirrored / fullscreen mode
c	Clone slideshow
p	Toggle presenter mode
t	Restart the presentation timer
?, h	Toggle this help

Phylogenetics - Back to Basics - Phylogenetic Networks

Requirements

About these slides

Uncorrected P model

Exploring splits

Let's follow a split

Jukes Cantor Model

HKY85 Model

Bootstrapped network

Bootstrapped network - a closer look

Bootstrapped network - a closer look

Thank you!

Thank You!

Requirements

Help