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A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
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Data-driven guidelines for phylogenomic analyses using SNP data
Jacob S Suissa1, Gisel Y De La Cerda2, Leland C Graber3
1Department of Ecology and Evolutionary Biology University of Tennessee at Knoxville Knoxville Tennessee USA.
Applications in Plant Sciences
|December 4, 2024
Summary
Filtering single-nucleotide polymorphisms (SNPs) for phylogenomic analysis should avoid strict thresholds. Using SNPs or locus data impacts branch lengths but not overall tree topology or divergence times.
Area of Science:
- Genomics
- Phylogenetics
- Evolutionary Biology
Background:
- Best practices for filtering single-nucleotide polymorphisms (SNPs) in phylogenomic analyses are debated.
- The choice between using SNPs or entire loci (including flanking regions) for phylogenetic inference remains unclear.
Purpose of the Study:
- To assess the impact of SNP versus locus usage on phylogenomic analyses.
- To evaluate the effects of SNP retention stringency on phylogenetic results.
- To compare branch length, node support, and divergence time estimation under different filtering scenarios.
Main Methods:
- Utilized genotyping-by-sequencing data from 22 *Glycine* species.
- Compared 16 datasets with varying SNP retention stringency and data types (SNP vs. locus).
- Analyzed effects on tree topology, branch length, node support, and divergence time estimation.
Main Results:
- Tree topology remained largely congruent across different datasets.
- Strict SNP filtering (90-100% retention) reduced node support and could alter inferred relationships.
- Absolute branch lengths varied significantly between SNP and locus datasets (by two orders of magnitude).
- Data type and branch length variation had minimal impact on divergence time estimation.
- Phylograms influenced the estimation of ancestral states and morphological evolution rates.
Conclusions:
- SNP or locus datasets yield similar phylogenetic inferences unless absolute branch lengths are critical.
- Excessive filtering thresholds for SNP retention are not recommended due to potential inconsistencies in topology and reduced support.
- Researchers should carefully consider SNP filtering stringency to maintain robust phylogenetic signal.
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