Abstract
The grass tribe Triticeae (=Hordeeae) comprises only about 300 species, but it is well known for the economically important crop plants wheat, barley, and rye. The group is also recognized as a fascinating example of evolutionary complexity, with a history shaped by numerous events of auto- and allopolyploidy and apparent introgression involving diploids and polyploids. The genus Elymus comprises a heterogeneous collection of allopolyploid genome combinations, all of which include at least one set of homoeologs, designated St, derived from Pseudoroegneria. The current analysis includes a geographically and genomically diverse collection of 21 tetraploid Elymus species, and a single hexaploid species. Diploid and polyploid relationships were estimated using four molecular data sets, including one that combines two regions of the chloroplast genome, and three from unlinked nuclear genes: phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I. Four gene trees were generated using maximum likelihood, and the phylogenetic placement of the polyploid sequences reveals extensive reticulation beyond allopolyploidy alone. The trees were interpreted with reference to numerous phenomena known to complicate allopolyploid phylogenies, and introgression was identified as a major factor in their history. The work illustrates the interpretation of complicated phylogenetic results through the sequential consideration of numerous possible explanations, and the results highlight the value of careful inspection of multiple independent molecular phylogenetic estimates, with particular focus on the differences among them.
Highlights
An allopolyploid genome represents an additive combination of genomes from its contributing diploid species, so the genomic complement of an allopolyploid individual should be identifiable on a gene tree that includes representatives of all of the potential donor species
Unsuspected paralogy coupled with limited within-individual sampling and/or paralog loss can result in a confusing gene tree on which each allopolyploid individual is represented by a random selection of one or more paralogs
This study focuses on Elymus, a diverse, polyphyletic assemblage of allopolyploid species in the wheat tribe, Triticeae Dumort
Summary
An allopolyploid genome represents an additive combination of genomes from its contributing diploid species, so the genomic complement of an allopolyploid individual should be identifiable on a gene tree that includes representatives of all of the potential donor species. The highly repetitive internal transcribed spacers (ITS) of the nuclear ribosomal array have the potential to reveal multiple genome donors [1,2,3,4], but they are subject to concerted evolution in polyploid genomes [5], so that one or more of the progenitors’ arrays might be unrepresented on an ITS gene tree. There are numerous phenomena that can confound the identification of allopolyploid individuals in phylogenetic analyses of low-copy genes. The identification of a polyploid’s progenitors can be further confounded if the relevant diploids are missing from the analysis In these cases, a polyploid will exhibit gene copies with no clear origin among the diploids. The causes for missing diploids include sparse sampling, and the more intractable problem where one or more of a polyploid’s donors are undiscovered or extinct (e.g., [8,20,23,38,39,40,41])
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