Difference between revisions of "BIN-PHYLO-Tree analysis"

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<div id="BIO">
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<div id="ABC">
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce; font-size:300%; font-weight:400; color: #000000; width:100%;">
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Title
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Analysing Phylogenetic Trees
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  </div>
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<div style="padding:5px; margin-top:20px; margin-bottom:10px; background-color:#b3dbce; font-size:30%; font-weight:200; color: #000000; ">
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(Species trees, gene trees and the importance of naming, Speciation and duplication signatures)
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</div>
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<div style="padding:5px; border:1px solid #000000; background-color:#b3dbce33; font-size:85%;">
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<div style="font-size:118%;">
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<div class="keywords">
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<b>Abstract:</b><br />
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<b>Keywords:</b>&nbsp;
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<section begin=abstract />
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Species trees, gene trees and the importance of naming, Speciation and duplication signatures
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The analysis of mixed gene trees.
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<section end=abstract />
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</div>
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<!-- ============================  -->
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<hr>
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<table>
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<tr>
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<td style="padding:10px;">
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<b>Objectives:</b><br />
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This unit will ...
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* ... introduce ;
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* ... demonstrate ;
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* ... teach how to fetch a species tree from the NCBI taxonomy page;
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</td>
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<td style="padding:10px;">
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<b>Outcomes:</b><br />
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After working through this unit you ...
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* ... can ;
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* ... are familar with ;
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* ... have begun to.
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</td>
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</tr>
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</table>
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<!-- ============================  -->
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<hr>
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<b>Deliverables:</b><br />
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<section begin=deliverables />
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<li><b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.</li>
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<li><b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.</li>
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<li><b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].</li>
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<section end=deliverables />
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<!-- ============================  -->
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<hr>
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<section begin=prerequisites />
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<b>Prerequisites:</b><br />
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This unit builds on material covered in the following prerequisite units:<br />
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*[[BIN-PHYLO-Tree_building|BIN-PHYLO-Tree_building (Building Phylogenetic Trees)]]
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<section end=prerequisites />
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<!-- ============================  -->
 
</div>
 
</div>
  
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{{DEV}}
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=== Evaluation ===
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<b>Evaluation: NA</b><br />
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<div style="margin-left: 2rem;">This unit is not evaluated for course marks.</div>
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== Contents ==
  
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{{Vspace}}
 
  
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{{Task|1=
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*Read the introductory notes on {{ABC-PDF|BIN-PHYLO-Tree_analysis|analysing phylogenetic trees}}.
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}}
  
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</div>
 
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<div id="ABC-unit-framework">
 
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== Abstract ==
 
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<section begin=abstract />
 
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<!-- included from "../components/BIN-PHYLO-Tree_analysis.components.wtxt", section: "abstract" -->
 
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...
 
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<section end=abstract />
 
  
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{{Vspace}}
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==Analysing your tree==
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{{Smallvspace}}
  
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{{ABC-unit|BIN-PHYLO-Tree_analysis.R}}
  
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== This unit ... ==
 
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=== Prerequisites ===
 
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<!-- included from "../components/BIN-PHYLO-Tree_analysis.components.wtxt", section: "prerequisites" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "notes-prerequisites" -->
 
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You need to complete the following units before beginning this one:
 
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*[[BIN-PHYLO-Tree_building|BIN-PHYLO-Tree_building (Building Phylogenetic Trees)]]
 
  
 
{{Vspace}}
 
{{Vspace}}
  
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<!--
  
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=== Objectives ===
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#Copy the tree-string from the R console.
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<!-- included from "../components/BIN-PHYLO-Tree_analysis.components.wtxt", section: "objectives" -->
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#Visualize the tree online: navigate to the [http://www.trex.uqam.ca/index.php?action=newick&project=trex Trex-online Newick tree viewer]. Visualize the tree as a phylogram. Explore the options.
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...
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# A particularly useful viewer is actually Jalview - although this may be more apparent with the larger alignment of '''all''' sequences we'll produce later.
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##Open Jalview and load your alignment of all APSES domain proteins.
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##Save the Newick-formatted tree.
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##In the alignment window, choose '''File &rarr; Load associated Tree''' and load your tree file. You can click into the tree-window to show which clades branch off at what level - it should be obvious that you can identify three major subclades (plus the outgroup). This view is particularly informative, since you can associate the clades of the tree with the actual sequences in the alignment, and get a good sense what sequence features the tree is based on.
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##Try the '''Calculate &rarr; Sort &rarr; By Tree Order''' option to sort the sequences by their position in the tree. Also note that you can flip the tree around a node by double-clicking on it. This is especially useful: try to rearrange the tree so that the subdivisions into clades are apparent. Clicking into the window "cuts" the tree and colours your sequences according to the clades in which they are found. This is useful to understand what particular sequences contributed to which part of the phylogenetic inference.
  
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{{Vspace}}
 
  
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ANALYSIS
  
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=== Outcomes ===
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* First, the APS and ANK trees should have the same topology, since they are only different parts of the same protein (unless that protein has swapped its domains with another one during evolution). Clearly, that is not the case. The ''basidiomycota'' are reasonably consistent, although their internal ordering is poorly resolved, particularly in the APS tree. The ''ascomycota'' show two major differences, but they are actually consistent between the APS and the ANK tree: SACCE is less similar to all than we would expect from the species tree. And NEUCR is more similar to the ''basidiomycotal'' proteins.
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<!-- included from "../components/BIN-PHYLO-Tree_analysis.components.wtxt", section: "outcomes" -->
 
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...
 
  
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{{Vspace}}
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* Consider the scale bars: ANK domains have evolved at about twice the rate of the APS domains. This alone should tell us to be cautious with our interpretations since this shows there are different degrees of selective pressure on different parts of the protein. Moreover the <u>relative rates</u> differ as well. NEUCR's APSES domain has evolved much faster by comparison to other proteins than its ankyrin domain. Has its biological function changed?
  
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* Secondly, both gene trees should follow the species tree. Again, there are differences. But if we exclude SACCE and NEUCR, the remainder actually turns out relatively consistent.
  
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=== Deliverables ===
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In any case: this is what the data tells us. The big picture is mostly conserved, but there are differences in the details. However: now we know what degree of accuracy we can expect from the analysis.
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<!-- included from "../components/BIN-PHYLO-Tree_analysis.components.wtxt", section: "deliverables" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-time_management" -->
 
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*<b>Time management</b>: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-journal" -->
 
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*<b>Journal</b>: Document your progress in your [[FND-Journal|Course Journal]]. Some tasks may ask you to include specific items in your journal. Don't overlook these.
 
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<!-- included from "ABC-unit_components.wtxt", section: "deliverables-insights" -->
 
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*<b>Insights</b>: If you find something particularly noteworthy about this unit, make a note in your [[ABC-Insights|'''insights!''' page]].
 
  
 
{{Vspace}}
 
{{Vspace}}
  
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==The mixed gene tree==
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{{vspace}}
  
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=== Evaluation ===
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You have now practiced how to calculate, manipulate, plot, annotate and compare trees.
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<!-- included from "../components/BIN-PHYLO-Tree_analysis.components.wtxt", section: "evaluation" -->
 
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<!-- included from "ABC-unit_components.wtxt", section: "eval-none" -->
 
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<b>Evaluation: NA</b><br />
 
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:This unit is not evaluated for course marks.
 
  
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{{Vspace}}
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{{task|1=
  
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* Now use Rproml to calculate a mixed gene tree based on '''all'' APSES domains. You saved it as <code>APSES.mfa</code>. For the fifty or so domains, each run will take about an hour. Thus run as many <code>random.addition</code> cycles as reasonable during a study break, or overnight. Thus the command will be something like:
  
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</div>
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<pre>
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<div id="BIO">
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allApsIn <- read.protein("APSES.mfa")
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== Contents ==
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fullApsTree <- Rproml(allApsIn, path=PROMLPATH, random.addition=3)
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<!-- included from "../components/BIN-PHYLO-Tree_analysis.components.wtxt", section: "contents" -->
 
  
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#... and don't forget:
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save(fullApsTree, file="fullApsTree.rda")
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</pre>
  
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{{Task|1=
 
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*Read the introductory notes on {{ABC-PDF|BIN-PHYLO-Tree_analysis|analysing phylogenetic trees}}.
 
 
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===Analysis===
 
  
 
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== Further reading, links and resources ==
 
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{{#pmid: 26323765}}
 
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{{#pmid: 22114356}}
 
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{{#pmid: 19190756}}
 
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Also: [http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956 Nature-Scitable (2008): '''Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups''']
 
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== Notes ==
 
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<references />
 
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== Self-evaluation ==
 
== Self-evaluation ==
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== Further reading, links and resources ==
  
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{{#pmid: 26323765}}
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{{#pmid: 22114356}}
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{{#pmid: 19190756}}
  
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Also: [http://www.nature.com/scitable/topicpage/reading-a-phylogenetic-tree-the-meaning-of-41956 Nature-Scitable (2008): '''Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups''']
  
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== Notes ==
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<references />
  
 
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<b>If in doubt, ask!</b> If anything about this learning unit is not clear to you, do not proceed blindly but ask for clarification. Post your question on the course mailing list: others are likely to have similar problems. Or send an email to your instructor.
 
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:2017-08-05
 
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<b>Modified:</b><br />
 
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:2020-09-25
 
<b>Version:</b><br />
 
<b>Version:</b><br />
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:0.1
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:1.1
 
<b>Version history:</b><br />
 
<b>Version history:</b><br />
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*1.1 2020 updates; remove iTOL (now using taxize::)
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*1.0 First live version.
 
*0.1 First stub
 
*0.1 First stub
 
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Latest revision as of 11:42, 26 September 2020

Analysing Phylogenetic Trees

(Species trees, gene trees and the importance of naming, Speciation and duplication signatures)


 


Abstract:

The analysis of mixed gene trees.

Objectives:
This unit will ...

  • ... introduce ;
  • ... demonstrate ;
  • ... teach how to fetch a species tree from the NCBI taxonomy page;

Outcomes:
After working through this unit you ...

  • ... can ;
  • ... are familar with ;
  • ... have begun to.

Deliverables:

  • Time management: Before you begin, estimate how long it will take you to complete this unit. Then, record in your course journal: the number of hours you estimated, the number of hours you worked on the unit, and the amount of time that passed between start and completion of this unit.
  • Journal: Document your progress in your Course Journal. Some tasks may ask you to include specific items in your journal. Don't overlook these.
  • Insights: If you find something particularly noteworthy about this unit, make a note in your insights! page.

    • Prerequisites:
    This unit builds on material covered in the following prerequisite units:


     



     



     


    Evaluation

    Evaluation: NA

    This unit is not evaluated for course marks.

    Contents

    Task:


    Analysing your tree

     

    Task:

     
    • Open RStudio and load the ABC-units R project. If you have loaded it before, choose File → Recent projects → ABC-Units. If you have not loaded it before, follow the instructions in the RPR-Introduction unit.
    • Choose Tools → Version Control → Pull Branches to fetch the most recent version of the project from its GitHub repository with all changes and bug fixes included.
    • Type init() if requested.
    • Open the file BIN-PHYLO-Tree_analysis.R and follow the instructions.


     

    Note: take care that you understand all of the code in the script. Evaluation in this course is cumulative and you may be asked to explain any part of code.


     


     

    Further reading, links and resources

    Szöllősi et al. (2015) Genome-scale phylogenetic analysis finds extensive gene transfer among fungi. Philos Trans R Soc Lond., B, Biol Sci 370:20140335. (pmid: 26323765)

    [ PubMed ] [ DOI ] Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis, we compare the dynamics of genome evolution in two groups of organisms: cyanobacteria and fungi. Ancestral genomes are inferred in both clades using two types of methods: first, Count, a gene tree unaware method that models gene duplications, gains and losses to explain the observed numbers of genes present in a genome; second, ALE, a more recent gene tree-aware method that reconciles gene trees with a species tree using a model of gene duplication, loss and transfer. We compare their merits and their ability to quantify the role of transfers, and assess the impact of taxonomic sampling on their inferences. We present what we believe is compelling evidence that gene transfer plays a significant role in the evolution of fungi.

    Ebersberger et al. (2012) A consistent phylogenetic backbone for the fungi. Mol Biol Evol 29:1319-34. (pmid: 22114356)

    [ PubMed ] [ DOI ] The kingdom of fungi provides model organisms for biotechnology, cell biology, genetics, and life sciences in general. Only when their phylogenetic relationships are stably resolved, can individual results from fungal research be integrated into a holistic picture of biology. However, and despite recent progress, many deep relationships within the fungi remain unclear. Here, we present the first phylogenomic study of an entire eukaryotic kingdom that uses a consistency criterion to strengthen phylogenetic conclusions. We reason that branches (splits) recovered with independent data and different tree reconstruction methods are likely to reflect true evolutionary relationships. Two complementary phylogenomic data sets based on 99 fungal genomes and 109 fungal expressed sequence tag (EST) sets analyzed with four different tree reconstruction methods shed light from different angles on the fungal tree of life. Eleven additional data sets address specifically the phylogenetic position of Blastocladiomycota, Ustilaginomycotina, and Dothideomycetes, respectively. The combined evidence from the resulting trees supports the deep-level stability of the fungal groups toward a comprehensive natural system of the fungi. In addition, our analysis reveals methodologically interesting aspects. Enrichment for EST encoded data-a common practice in phylogenomic analyses-introduces a strong bias toward slowly evolving and functionally correlated genes. Consequently, the generalization of phylogenomic data sets as collections of randomly selected genes cannot be taken for granted. A thorough characterization of the data to assess possible influences on the tree reconstruction should therefore become a standard in phylogenomic analyses.

    Marcet-Houben & Gabaldón (2009) The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome. PLoS ONE 4:e4357. (pmid: 19190756)

    [ PubMed ] [ DOI ] A recurrent topic in phylogenomics is the combination of various sequence alignments to reconstruct a tree that describes the evolutionary relationships within a group of species. However, such approach has been criticized for not being able to properly represent the topological diversity found among gene trees. To evaluate the representativeness of species trees based on concatenated alignments, we reconstruct several fungal species trees and compare them with the complete collection of phylogenies of genes encoded in the Saccharomyces cerevisiae genome. We found that, despite high levels of among-gene topological variation, the species trees do represent widely supported phylogenetic relationships. Most topological discrepancies between gene and species trees are concentrated in certain conflicting nodes. We propose to map such information on the species tree so that it accounts for the levels of congruence across the genome. We identified the lack of sufficient accuracy of current alignment and phylogenetic methods as an important source for the topological diversity encountered among gene trees. Finally, we discuss the implications of the high levels of topological variation for phylogeny-based orthology prediction strategies.

    Also: Nature-Scitable (2008): Reading a Phylogenetic Tree: The Meaning of Monophyletic Groups

    Notes


     


    About ...
     
    Author:

    Boris Steipe <boris.steipe@utoronto.ca>

    Created:

    2017-08-05

    Modified:

    2020-09-25

    Version:

    1.1

    Version history:

    • 1.1 2020 updates; remove iTOL (now using taxize::)
    • 1.0 First live version.
    • 0.1 First stub

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