Lautenschlager, Ulrich and Wagner, Florian and Oberprieler, Christoph (2020) AllCoPol: inferring allele co-ancestry in polyploids. BMC BIOINFORMATICS, 21 (1): 441. ISSN 1471-2105,
Full text not available from this repository. (Request a copy)Abstract
BackgroundInferring phylogenetic relationships of polyploid species and their diploid ancestors (leading to reticulate phylogenies in the case of an allopolyploid origin) based on multi-locus sequence data is complicated by the unknown assignment of alleles found in polyploids to diploid subgenomes. A parsimony-based approach to this problem has been proposed by Oberprieler et al. (Methods Ecol Evol 8:835-849, 2017), however, its implementation is of limited practical value. In addition to previously identified shortcomings, it has been found that in some cases, the obtained results barely satisfy the applied criterion. To be of better use to other researchers, a reimplementation with methodological refinement appears to be indispensable.ResultsWe present the AllCoPol package, which provides a heuristic method for assigning alleles from polyploids to diploid subgenomes based on the Minimizing Deep Coalescences (MDC) criterion in multi-locus sequence datasets. An additional consensus approach further allows to assess the confidence of phylogenetic reconstructions. Simulations of tetra- and hexaploids show that under simplifying assumptions such as completely disomic inheritance, the topological errors of reconstructed phylogenies are similar to those of MDC species trees based on the true allele partition.ConclusionsAllCoPol is a Python package for phylogenetic reconstructions of polyploids offering enhanced functionality as well as improved usability. The included methods are supplied as command line tools without the need for prior programming knowledge.
| Item Type: | Article |
|---|---|
| Uncontrolled Keywords: | GENE TREES; PHYLOGENY; Coalescent theory; Gene tree; Multilocus sequence data; Polyploidy; Python; Reticulate evolution; Simulations; Species tree |
| Subjects: | 500 Science > 580 Botanical sciences |
| Divisions: | Biology, Preclinical Medicine > Institut für Pflanzenwissenschaften > Group Plant Systematics and Evolution (Prof. Dr. Christoph Oberprieler) |
| Depositing User: | Dr. Gernot Deinzer |
| Date Deposited: | 12 Mar 2021 06:37 |
| Last Modified: | 12 Mar 2021 06:37 |
| URI: | https://pred.uni-regensburg.de/id/eprint/43594 |
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