@ARTICLE{TreeBASE2Ref23434, author = {Yann J.K. Bertrand and Anne-Cathrine Scheen and Thomas Marcussen and Magnus Lid?n and Bernard Pfeil and Filipe de Sousa and Bengt Oxelman}, title = {Assignment of Homoeologues to Parental Genomes in Allopolyploids for Species Tree Inference, with an Example from Fumaria (Papaveraceae)}, year = {2014}, keywords = {allopolyploidy; homoeologues assignment; genome tree; substitution model error; coalescent stochasticity; coalescent simulation; lineage sorting; NRDP2; Papaveraceae; Fumaria }, doi = {}, url = {http://}, pmid = {}, journal = {Systematic Biology}, volume = {}, number = {}, pages = {}, abstract = {There is a raising awareness that species trees are best inferred from multiple gene loci while taking into account processes affecting individual gene trees such as substitution model error and coalescent stochasticity (presence of lineage sorting). Although much work has focused on dichotomous species trees, these processes are also present in evolutionary histories that are represented by species networks due to presence of multiple hybridizations or, as in the present study, resulting from allopolyploidy events. Recently, methods have been developed that accurately handle incomplete lineage sorting in allopolyploids, but are so far restricted to networks of diploids and tetraploids with no further hybridization (Jones et al. 2013, Syst. Biol. 62:467-478). We propose a procedure that improves on this limitation by designing a workflow that performs assignment of homoeologues to hypothetical diploid ancestral genomes prior to tree construction. Conflicting assignment hypotheses are evaluated against substitution model error and coalescent stochasticity. Incongruence that cannot be explained by stochastic mechanisms needs to be explained by other processes (e.g. homoploid hybridization or paralogy). The data can then be filtered to build multilabeled genome phylogenies using inference methods that can recover species trees either in the face of substitution model error and coalescent stochasticity alone, or while simultaneously accounting for hybridization. Methods are available for folding the resulting multilabeled genome phylogeny into a genome network. The workflow is applied to the reconstruction of the reticulate phylogeny of the plant genus Fumaria (Papaveraceae) with ploidal levels ranging from 2x to 14x. We describe the difficulties in recovering nuclear NRPB2 homoeologues in high ploidy species while combining cloning and direct sequencing techniques. Using parametric bootstrapping simulations we assign nuclear homoeologues to chloroplast sequences (four concatenated loci) that descend from the same hypothetical diploid ancestral genomes. As these assignments hinge on effective population size premises, we investigate how varying these assumptions impacts the recovered genome phylogeny.} }

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