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08:57
Using Phylogenetic Analysis to Investigate Eukaryotic Gene Origin
Published on: August 14, 2018
Always look on both sides: phylogenetic information conveyed by simple sequence repeat allele sequences
Stéphanie Barthe1, Felix Gugerli, Noelle A Barkley
1Unité Mixte de Recherche Ecologie des forêts de Guyane, University of French West Indies and French Guiana, Kourou, French Guiana.
Plos One
|July 19, 2012
Summary
Simple sequence repeat (SSR) markers are valuable for genetic studies, but flanking region variations significantly impact evolutionary insights. Understanding both SSR and flanking region diversity is crucial for accurate phylogenetic analysis.
Area of Science:
- Genetics
- Molecular Biology
- Evolutionary Biology
Background:
- Simple sequence repeat (SSR) markers are widely used for genetic diversity and population structure studies.
- Current analyses often assume variation is solely due to repeat number changes, following the stepwise mutation model (SMM).
- The role of polymorphisms in flanking regions (FRs) and their contribution to evolutionary signals is often overlooked.
Purpose of the Study:
- To investigate the types and distribution of polymorphisms within SSR alleles, including SSR and flanking region (FR) sequences.
- To compare the patterns of diversity generated by amplicon size variation, SSR variation, insertions/deletions (indels), and single nucleotide polymorphisms (SNPs) in FRs.
- To assess the contribution of FR polymorphisms to phylogenetic information and population differentiation.
Main Methods:
- Sequencing of SSR alleles across multiple populations of three divergent tree genera.
- Disentangling polymorphisms within SSR and FR sequences.
- Comparative analysis of variation from amplicon size, SSR repeats, indels, and SNPs in FRs.
Main Results:
- Amplicon size variation generally correlated with SSR repeat number.
- The extent of variation in FRs was comparable to that within the SSR itself.
- FR polymorphisms significantly contributed to phylogenetic information and, in some cases, were the primary drivers of individual and population differentiation.
Conclusions:
- SSR marker data interpretation requires caution, as FR polymorphisms significantly influence evolutionary signals.
- The distribution of within-locus polymorphism, including FRs, is critical for understanding evolutionary events across various timescales.
- Incorporating FR variation alongside SSR repeat number provides a more comprehensive phylogenetic and population genetic analysis.
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