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Phylogenetics - Back to Basics - Phylogenetic Networks

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Authors: Michael Charleston avatar Michael Charleston
Published: May 10, 2024
Last Updated: May 10, 2024

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

.pull-left[ 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 ]

.pull-right[ 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 ]

#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

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

.pull-left[ 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 ]

.pull-right[ 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 ]

#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

#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 — #Bootstrapped network - a closer look
Let’s explore our two splits again

.pull-left[ 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 ]

.pull-right[ 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 ]

#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

Thank you!

Thank you!

This material is the result of a collaborative work. Thanks to the Galaxy Training Network and all the contributors! page logo Tutorial Content is licensed under Creative Commons Attribution 4.0 International License.