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10:08
Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis
Published on: August 12, 2019
Addressing inter-gene heterogeneity in maximum likelihood phylogenomic analysis: yeasts revisited
1Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, United States of America. jhess@oeb.harvard.edu
Plos One
|August 19, 2011
Summary
Phylogenomic analysis of 18 yeast species reveals that using sophisticated evolutionary models improves accuracy. These advanced methods, accounting for gene-specific evolutionary processes, are crucial for reliable species tree reconstruction.
Area of Science:
- Evolutionary Biology
- Genomics
- Mycology
Background:
- Phylogenomic methods using concatenated genes are common for species relationship studies.
- However, data heterogeneity and model violations can lead to inaccurate phylogenetic trees despite high support.
Purpose of the Study:
- To reconstruct an accurate species tree for 18 ascomycetous yeasts.
- To investigate appropriate evolutionary models for phylogenomic data, addressing inter-gene heterogeneity.
- To assess the scalability and validity of supermatrix analysis with increasing gene numbers.
Main Methods:
- Extended a previous yeast phylogenomic study by adding species and genes.
- Employed sophisticated maximum likelihood analyses, including concatenated and partitioned models.
- Partitioned models allowed evolutionary parameters to vary across different genes (loci).
Main Results:
- Significant increases in phylogenetic likelihood were observed with complex, partitioned models.
- These models effectively accounted for variations in evolutionary processes across different genes.
- A well-supported species tree for 18 ascomycetous yeasts was reconstructed.
Conclusions:
- Appropriate evolutionary models are essential for accurate phylogenomic data analysis.
- Partitioned models offer a more robust approach to handling inter-gene heterogeneities.
- The study provides a reliable evolutionary framework for ascomycetous yeasts over 250 million years.
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