The Fungal Tree of Life and Yeast Phylogeny
Author Information
Author(s): Marcet-Houben Marina, Gabaldón Toni
Primary Institution: Centro de Investigación Príncipe Felipe, València, Spain
Hypothesis
Do species trees constructed with standard alignment concatenation approaches fairly represent the topologies found in gene phylogenies across a genome?
Conclusion
Despite high levels of topological variation, species trees reconstructed from concatenated alignments generally represent widely supported phylogenetic relationships.
Supporting Evidence
- Most nodes in the species tree represent genome-wide supported evolutionary relationships.
- Some conflicting nodes concentrate most of the topological variations found between gene and species trees.
- The lack of sufficient accuracy of current alignment and phylogenetic methods is an important source for the topological diversity.
Takeaway
Scientists studied how well trees showing relationships between different fungi match up with trees made from individual genes, and found that most of the time they do match, even if there are some differences.
Methodology
The study reconstructed several fungal species trees using concatenated alignments of widespread proteins and compared them with gene phylogenies from the Saccharomyces cerevisiae genome.
Potential Biases
The choice of different parameters or methodologies may introduce topological variations in phylogenies.
Limitations
The analysis only reflects the topological variation found in the yeast phylome and does not account for phylogenies of genes not present in S. cerevisiae.
Digital Object Identifier (DOI)
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