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Updated: Jul 11, 2026
08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Maximum likelihood analysis of gene-based and structure-based process partitions, using mammalian mitochondrial
1Department of Biological Sciences, Box 210006, University of Cincinnati, Cincinnati, Ohio 45221-0006, USA. ron.debry@uc.edu
Systematic Biology
|June 18, 2002
Summary
Phylogenetic analysis of mammalian mitochondrial genomes suggests gene-based data partitions are more reliable than structure-based ones for inferring evolutionary relationships. This impacts our understanding of mammalian evolution.
Area of Science:
- Evolutionary Biology
- Genomics
- Bioinformatics
Background:
- Mammalian mitochondrial genomes contain protein-coding genes crucial for evolutionary studies.
- Phylogenetic analyses rely on accurate data partitioning for robust evolutionary inferences.
- Understanding relationships between mammalian orders like Artiodactyla, Cetacea, Perissodactyla, and Carnivora is an ongoing challenge.
Purpose of the Study:
- To compare the effectiveness of gene-based versus structure-based data partitions in phylogenetic analyses of mammalian mitochondrial genomes.
- To investigate different partitioning schemes for inferring mammalian evolutionary history.
- To resolve conflicting phylogenetic hypotheses regarding the relationships between major mammalian clades.
Main Methods:
- Phylogenetic analyses using parsimony and maximum likelihood methods.
- Examination of aligned protein-coding genes from 19 mammalian mitochondrial genomes.
- Development and testing of three surrogate structure-based partitioning schemes using consensus amino acid identities.
- Comparison of gene-based partitioning with structure-based approaches.
Main Results:
- Gene-based partitioning schemes yielded significantly higher likelihoods than the tested structure-based scheme.
- One amino-acid-based scheme showed the highest likelihood but relied on prior phylogenetic assumptions.
- Phylogenetic analyses supported two contrasting evolutionary trees depending on branch length constraints.
Conclusions:
- Gene-based data partitioning is a more reliable method for inferring mammalian mitochondrial phylogeny.
- The study provides evidence for a specific evolutionary arrangement: (((Artiodactyla, Cetacea) Carnivora) Perissodactyla).
- This research refines our understanding of mammalian evolutionary relationships using genomic data.
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