Abstract
MOTIVATION: Despite the widespread occurrence of polyploids across the Tree of Life, especially in the plant kingdom, very few computational methods have been developed to handle the specific complexities introduced by polyploids in phylogeny estimation. Furthermore, methods that are designed to account for polyploidy often disregard incomplete lineage sorting (ILS), a major source of heterogeneous gene histories, or are computationally very demanding. Therefore, there is a great need for efficient and robust methods to accurately reconstruct polyploid phylogenies. RESULTS: We introduce Polyphest (POLYploid PHylogeny ESTimation), a new method for efficiently and accurately inferring species phylogenies in the presence of both polyploidy and ILS. Polyphest bypasses the need for extensive network space searches by first generating a multilabeled tree based on gene trees, which is then converted into a (uniquely labeled) species phylogeny. We compare the performance of Polyphest to that of two polyploid phylogeny estimation methods, one of which does not account for ILS, namely PADRE, and another that accounts for ILS, namely MPAllopp. Polyphest is more accurate than PADRE and achieves comparable accuracy to MPAllopp, while being significantly faster. We also demonstrate the application of Polyphest to empirical data from the hexaploid bread wheat and confirm the allopolyploid origin of bread wheat along with the closest relatives for each of its subgenomes. AVAILABILITY AND IMPLEMENTATION: Polyphest is available at https://github.com/NakhlehLab/Polyphest.
Abstract from the paper’s OpenAlex record; open copy licensed cc-by. Read at the source ↗
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Claims 6
Claim · model-written summary
Polyphest was more accurate than PADRE.
Not reportedTaxon
Verbatim
e0“Polyphest is more accurate than PADRE”
Claim · model-written summary
Polyphest had comparable accuracy to MPAllopp.
Not reportedTaxon
Verbatim
e0“achieves comparable accuracy to MPAllopp”
Claim · model-written summary
Polyphest was significantly faster than MPAllopp.
Not reportedTaxon
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e0“comparable accuracy to MPAllopp, while being significantly faster”
Claim · model-written summary
Application of Polyphest confirmed the allopolyploid origin of bread wheat.
- Taxon
- bread wheat
Triticum aestivume0 - Outcome
- allopolyploid origin of bread wheate0
- Value
- hexaploide0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“application of Polyphest to empirical data from the hexaploid bread wheat and confirm the allopolyploid origin of bread wheat”
Claim · model-written summary
Polyphest identified closest relatives for each bread wheat subgenome.
- Taxon
- bread wheatTriticum aestivume0
- Outcome
- closest relatives for each of its subgenomese0
- Value
- hexaploide0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“application of Polyphest to empirical data from the hexaploid bread wheat and confirm the allopolyploid origin of bread wheat along with the closest relatives for each of its subgenomes”
Claim · model-written summary
Polyphest software was made available.
Verbatim
e0“Polyphest is available at https://github.com/NakhlehLab/Polyphest”