Expected Preparations:

  [BIN-PHYLO]
Tree_building 		 
  The units listed above are part of this course and contain important preparatory material.  
Keywords: Species trees; gene trees and the importance of naming; Speciation and duplication signatures
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.

Evaluation:

NA: This unit is not evaluated for course marks.

Contents

The analysis of mixed gene trees. NA

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. This ensures that your data and code remain up to date when we update, or fix bugs.
  • 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

osi, Gergely J S et al.. (2015). “Genome-scale phylogenetic analysis finds extensive gene transfer among fungi”. Philosophical Transactions of The Royal Society of London. Series B, Biological Sciences 370(1678):20140335 .
[PMID: 26323765] [DOI: 10.1098/rstb.2014.0335]

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, Ingo et al.. (2012). “A consistent phylogenetic backbone for the fungi”. Molecular Biology and Evolution 29(5):1319–34 .
[PMID: 22114356] [DOI: 10.1093/molbev/msr285]

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, Marina and Toni Gabalda’on. (2009). “The tree versus the forest: the fungal tree of life and the topological diversity within the yeast phylome”. Plos One 4(2):e4357 .
[PMID: 19190756] [DOI: 10.1371/journal.pone.0004357]

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

Questions, comments

If in doubt, ask! If anything about this contents is not clear to you, do not proceed but ask for clarification. If you have ideas about how to make this material better, let’s hear them. We are aiming to compile a list of FAQs for all learning units, and your contributions will count towards your participation marks.

Improve this page! If you have questions or comments, please post them on the Quercus Discussion board with a subject line that includes the name of the unit.

References

Page ID: BIN-PHYLO-Tree_analysis

Author:
Boris Steipe ( <boris.steipe@utoronto.ca> )
Created:
2017-08-05
Last modified:
2022-09-14
Version:
1.1
Version History:
–  1.1 2020 updates; remove iTOL (now using taxize::)
–  1.0 First live version.
–  0.1 First stub
Tagged with:
–  Unit
–  Live
–  Has lecture slides
–  Has R code examples
–  Links to R course project
–  Contains images
–  Has further reading

 

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