Here we illustrate and discuss the major challenges involved in reticulate phylogenetic reconstruction, with special reference to single- and low-copy nuclear data (the RNA polymerase genes) produced for the polyploid Cerastium alpinum group and close relatives. The dynamic nature of polyploid genomes paves the way for evolutionary novelty, and is obviously an important clue for the evolutionary success of polyploid plants, but at the same time it also creates problems in reconstruct- ing the evolutionary history of polyploids. Nascent allopolyploids will hold two homoeologous copies of every gene that is initially single-copy in the parental species; however, immediately after the polyploidization event, modification of the polyploid genome starts, involving gene silencing, pseudogenization and divergence of duplicated genes. Identifying the signatures of reticulation, especially when dealing with old polyploids, may thus be a huge challenge. Sorting of ancestral/diploid variation in the polyploids and additional gene losses and duplications not associated with polyploidy may further complicate the case. Besides these general problems related to incongruent gene and organism lineage phylogenies, there are also several method- ological challenges connected with retrieving sequence information from polyploids, such as polymerase errors, differential amplification of homoeologs (PCR selection), generation of chimeric sequences during PCR, and selection of shorter and more common fragments and insertion of incorrect fragments during the cloning reaction
Brysting, A. K., Mathiesen, C., & Marcussen, T. (2011). Challenges in polyploid phylogenetic reconstruction: A case story from the arctic-alpine Cerastium alpinum complex. Taxon, 60(2), 333–347.