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When is enough, enough in phylogenetics? A case in point from Hordeum (Poaceae)
Gitte Petersen1, Lone Aagesen2, Ole Seberg1
1Botanical Garden and Museum, Natural History Museum of Denmark, University of Copenhagen, Sølvgade 83 opg. S, DK-1307 Copenhagen, Denmark.
Cladistics : the International Journal of the Willi Hennig Society
|December 8, 2021
Summary
Phylogenetic analysis of the Hordeum genus using nuclear and plastid DNA revealed a robust evolutionary tree. However, plastid DNA can mislead phylogenetic reconstruction, necessitating caution.
Area of Science:
- Evolutionary Biology
- Genomics
- Phylogenetics
Background:
- The study reconstructs the phylogeny of 26 diploid taxa within the genus Hordeum.
- A comprehensive dataset of 16 nucleotide sequence regions from both nuclear and plastid genomes was utilized.
- Nuclear data included nine single-copy, protein-coding genes from six chromosome pairs of Hordeum vulgare, while plastid data comprised seven protein-coding and intergenic regions.
Discussion:
- Character congruence analysis revealed no correlation between chromosomal location and congruence in nuclear sequences.
- Congruence levels among plastid sequences were comparable to those among nuclear sequences.
- Combined analysis of all data provided a fully resolved phylogeny with well-supported clades, though some relationships remain ambiguously inferred due to data partition incongruence.
Key Insights:
- The combined analysis of nuclear and plastid DNA resolved the Hordeum phylogeny, yielding robust and well-supported clades.
- Incongruence among data partitions indicates that some relationships may remain ambiguously inferred.
- Plastid data, in some instances, appeared misleading, highlighting the risks of relying solely on it for phylogenetic reconstruction.
Outlook:
- Future phylogenetic analyses could benefit from exploring incongruence patterns by incorporating data from multiple specimens per taxon, rather than solely adding more genes.
- Caution is advised when using plastid data as the sole or dominant source for phylogenetic reconstruction and subsequent re-classification.
- Further research may refine understanding of Hordeum evolution by addressing data incongruence and exploring alternative data sources.
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