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Published on: August 14, 2018
General functions to transform associate data to host data, and their use in phylogenetic inference from sequences
1Organismic Botany, Eberhard-Karls-University, Auf der Morgenstelle 1, Tübingen, Germany. markus.goeker@uni-tuebingen.de
BMC Evolutionary Biology
|March 28, 2008
Summary
This study introduces transformation functions to analyze plant phylogenetic data, specifically nuclear ribosomal internal transcribed spacers (ITS), addressing intra-individual variability. These functions accurately reflect evolutionary relationships and identify hybrids and ancestral taxa in angiosperm genera.
Area of Science:
- Molecular Biology
- Phylogenetics
- Bioinformatics
Background:
- Nuclear ribosomal internal transcribed spacers (ITS) are common molecular markers for plant phylogenetic studies.
- Intra-individual variability in ITS regions poses challenges for accurate phylogenetic reconstruction.
- This study frames the problem as inferring host (plant individual) characteristics from associate (sequence) features.
Purpose of the Study:
- To develop and validate general transformation functions for analyzing sequence data with intra-individual variability.
- To establish a distance-based framework for phylogenetic reconstruction using these functions.
- To assess the utility of these functions in reflecting evolutionary relationships and identifying hybrids/ancestral taxa.
Main Methods:
- Introduced six general transformation functions for associate-to-host character and distance transformations.
- Applied functions to ITS sequences from Acer, Fagus, and Zelkova, and allelic data from Rosa spp.
- Validated functions using phylogeny-independent treelikeness measures, correlation with independent host characters, and splits graph visualization.
Main Results:
- High-quality distance matrices were obtained with four of the six transformation formulae.
- One formula was identified as a generalization of the Sørensen coefficient, widely used in ecology.
- Results showed good agreement with validation measures, datasets, theoretical predictions, and existing literature.
Conclusions:
- The general transformation functions have broad applicability to host-associate biological problems.
- These functions accurately reflect evolutionary relationships within angiosperm genera and can identify hybrids and ancestral taxa.
- Treelikeness measures are valuable tools for comparative studies of biological distance functions.
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