Roberta J. Mason-Gamer

When Genes Tell Different Stories: the Diploid Genera of Triticeae (Gramineae)

Gene trees are generally assumed to reflect the underlying phylogeny of the species, and they are, therefore, generally expected to be congruent with each other. Published gene trees from sequences of three nuclear genes-two 5S DNA arrays and the internal transcribed spacer (ITS) of the ribosomal RNA genes-are known to give somewhat different histories for diploid members of the Triticeae. A phylogeny based on cpDNA restriction sites gives yet another topology. Some discrepancies come from poorly supported nodes. Other differences, however, are statistically significant. The differences among the nuclear gene trees can be ascribed to particular taxa (notably Triticum monococcum and Aegilops tauschii), which have different histories for particular parts of their genomes. We have removed these two taxa, combined the three nuclear loci to produce a well-supported tree, and introduced the two species later as reticulations. The cpDNA tree has no groups in common with any of the nuclear gene trees, and is therefore not combined with them. Multiple reticulations must be introduced to reconcile the cpDNA and combined nuclear trees. Such dramatic differences among gene trees might be expected among populations in a species complex, but are surprising among intersterile genera.

Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass

Recent molecular phylogenetic studies of polyploid plants have successfully clarified complex patterns of reticulate evolution. In this study of Elymus repens, an allohexaploid member of the wheat tribe Triticeae, chloroplast and nuclear DNA data reveal an extreme reticulate pattern, revealing at least five distinct gene lineages coexisting within the species, acquired through a possible combination of allohexaploidy and introgression from both within and beyond the Triticeae. Earlier cytogenetic studies of E. repens suggested that Hordeum (genome H) and Pseudoroegneria (St) were genome donors to E. repens. Chloroplast DNA data presented here (from the rpoA gene and from the region between trnT and trnF) identify three potential maternal genome donors (Pseudoroegneria, Thinopyrum, and Dasypyrum), and information from previous molecular work suggests that, of these, Pseudoroegneria is the most likely maternal donor. Nuclear starch synthase gene data indicate that both Hordeum and Pseudoroegneria have contributed to the nuclear genome of E. repens, in agreement with cytogenetic data. However, these data also show unexpected contributions from Taeniatherum, and from two additional donors of unknown identity. One of the sequences of unknown origin falls within the Triticeae, but is not closely associated with any of the sampled diploid genera. The second falls outside of the clade containing Triticeae and its outgroup Bromus, suggesting the acquisition of genetic material from a surprisingly divergent source. Bias toward the amplification of certain starch synthase variants has complicated attempts to thoroughly sample from within individuals, but the data clearly indicate a complex pattern of reticulate evolution, consistent not only with allohexaploidy, but also with introgression from unexpectedly divergent sources.

Origin of North American Elymus (Poaceae: Triticeae) Allotetraploids Based on Granule-bound Starch Synthase Gene Sequences

Abstract The current circumscription of Elymus based on cytogenetic analyses includes all allopolyploid Triticeae species containing the St (Pseudoroegneria) genome. In North American Elymus, the St genome is combined with H (from Hordeum) in an allotetraploid (StStHH) configuration. The goal of this study is to determine whether molecular phylogenetic analyses support existing cytogenetic data with regard to the evolutionary origin of North American Elymus. Analyses were performed using sequences from the nuclear starch synthase gene, and include multiple species of Elymus, Pseudoroegneria, and Hordeum, along with representatives of most of the other monogenomic genera in the Triticeae. The results support the hypothesis that Pseudoroegneria and Hordeum are the genome donors to the North American Elymus tetraploids. One species currently placed in Elymus (an octoploid, Elymus californicus) appears to be unrelated to the rest. The close relationships among Elymus H-genome sequences, with one exception, are consistent with a single origin of the group. The St-genome group consists of two well-defined clades, but support for the monophyly of the entire St group is weak. There are shortcomings associated with the current dependence on genome pairing data for grouping and ranking in the Triticeae, but molecular phylogenetic data suggest that, in many cases, groups delimited by cytogenetic data do in fact correspond to evolutionary lineages. Communicating Editor: John V. Freudenstein

PHYLOGENY OF ANDROPOGONEAE INFERRED FROM PHYTOCHROME B, GBSSI, AND NDHF

Andropogoneae is a monophyletic tribe of 85 genera that includes Zea and Sorghum. All members exhibit C4 photosynthesis and have inflorescences of paired spikelets. Previous studies of the chloroplast gene ndhF and the nuclear gene GBSSI identified numerous mutations that distinguish genera of the tribe but do not indicate relationships among them; the deep branches of the trees are quite short. Here we add newly collected data from phytochrome B to the data from the other two genes. The same pattern holds, with very short branches along the backbone of the tree indicating that the tribe resulted from rapid radiation. The phylogeny shows a single origin of a disarticulating rachis, which is a synapomorphy for the tribe. We find strong support for a core Andropogoneae that includes Andropogon, Bothriochloa, Capillipedium, Cymbopogon, Dichanthium, Heteropogon, Hyparrhenia, and Schizachyrium and support for its relationship with an expanded Saccharinae that includes Microstegium. The combined data reject the monophyly of subtribes Andropogoninae and Anthistiriinae and provide evidence that subtribes Sorghinae, Saccharinae, and Rottboelliinae are para‐ or polyphyletic, as is the traditional Maydeae. A relationship with Zea and Tripsacum is indicated for Elionurus, while Chionachne and Phacelurus are shown to diverge early in the history of the tribe. Arundinella hirta and Arundinella nepalensis can be included in an expanded Andropogoneae.

Allohexaploidy, introgression, and the complex phylogenetic history of Elymus repens (Poaceae)

The phylogenetic position of hexaploid Elymus repens within the tribe Triticeae (Poaceae) was examined using cloned sequences from the low-copy nuclear genes encoding phosphoenolpyruvate carboxylase (pepC) and beta-amylase. A previous analysis of E. repens using data from the nuclear granule-bound starch synthase I (GBSSI) gene had yielded five phylogenetically distinct gene copies, two more than expected from hexaploidy alone. The three gene trees share three distinct E. repens clades, suggesting that E. repens contains three phylogenetically divergent genomes, contributed by Hordeum, Pseudoroegneria, and an unknown donor. The two additional GBSSI sequences, including one that was apparently derived from outside of the tribe, appear to reflect past introgression of GBSSI sequences into the E. repens genome. On all three trees, the Hordeum-like E. repens sequences are polyphyletic within Hordeum, and the trees are in conflict with regard to the placement of these sequences within Hordeum, highlighting multiple contributions from Hordeum to E. repens.

Is 16S rDNA a reliable phylogenetic marker to characterize relationships below the family level in the enterobacteriaceae

The phylogenetic relationships of multiple enterobacterial species were reconstructed based on 16S rDNA gene sequences to evaluate the robustness of this housekeeping gene in the taxonomic placement of the enteric plant pathogens Erwinia, Brenneria, Pectobacterium, and Pantoea. Four data sets were compiled, two of which consisted of previously published data. The data sets were designed in order to evaluate how 16S rDNA gene phylogenies are affected by the use of different plant pathogen accessions and varying numbers of animal pathogen and outgroup sequences. DNA data matrices were analyzed using maximum likelihood (ML) algorithms, and character support was determined by ML bootstrap and Bayesian analyses. As additional animal pathogen sequences were added to the phylogenetic analyses, taxon placement changed. Further, the phylogenies varied in their placement of the plant pathogen species, and only the genus Pantoea was monophyletic in all four trees. Finally, bootstrap and Bayesian support values were low for most of the nodes, and all nonterminal branches collapsed in strict consensus trees. Inspection of 16S rDNA nucleotide alignments revealed several highly variable blocks punctuated by regions of conserved sequence. These data suggest that 16S rDNA, while effective for both species-level and family-level phylogenetic reconstruction, may underperform for genus-level phylogenetic analyses in the Enterobacteriaceae.

Phylogenetic relationships and reticulation among Asian Elymus (Poaceae) allotetraploids: Analyses of three nuclear gene trees

This phylogenetic study focuses on a subset of the species in Elymus-specifically, the endemic Asian tetraploids presumed to combine the St genome from Pseudoroegneria with the Y genome from an unknown donor. The primary goals were to (1) determine whether the St and Y genomes are derived from phylogenetically distinct donors; (2) identify the closest relative, and potentially the likely donor, of the Y genome; and (3) interpret variation among StStYY species in terms of multiple origins and/or introgression. The goals were addressed using phylogenetic analyses of sequences from three low-copy nuclear genes: phosphoenolpyruvate carboxylase, beta-amylase, and granule-bound starch synthase I. Data sets include 16 StStYY individuals representing nine species, along with a broad sample of representatives from most of the monogenomic (i.e., non-allopolyploid) genera in the tribe. To briefly summarize the results: (1) the data clearly support an allopolyploid origin for the Asian tetraploids, involving two distinct donors; (2) the Y genome was contributed by a single donor, or multiple closely-related donors; (3) the phylogenetic position of the ElymusY genome varies among the three trees and its position is not strongly supported, so the identity of the donor remains a mystery; and (4) conflicts among the gene trees with regard to the St-genome sequences suggest introgression involving both Elymus and Pseudoroegneria.

The Evolution of North American Elymus (Triticeae, Poaceae) Allotetraploids: Evidence from Phosphoenolpyruvate Carboxylase Gene Sequences

Abstract Cytogenetic studies of North American Elymus suggest that the genus is an allopolyploid derivative of Pseudoroegneria (St) and Hordeum (H). To test this, we conducted a phylogenetic analysis of North American Elymus species within a broad sample of diploid Triticeae taxa using cloned sequences from one member of the nuclear gene family encoding phosphoenolpyruvate carboxylase. The phylogeny supports the hypothesis that Pseudoroegneria and Hordeum are the diploid progenitors of the North American Elymus tetraploids. Each tetraploid Elymus individual has two distinct forms of the gene, and each form is in a strongly supported clade with sequences from either Pseudoroegneria or Hordeum, suggesting that these Elymus species have an St + H genomic content. This pattern is consistent with a single (or multiple very similar) polyploid ancestor(s) of the North American tetraploids, confirming earlier results based on granule-bound starch synthase I gene sequence data. We also examined the utility of the phosphoenolpyruvate carboxylase gene to reconstruct the evolutionary history of the Triticeae by comparing it to starch synthase gene sequence data. Both nuclear data sets are phylogenetically informative, but suggest somewhat different evolutionary histories among genera within the tribe.

Phylogenetic Relationships of Asclepias (Apocynaceae) Inferred from Non-Coding Chloroplast DNA Sequences

Abstract Milkweeds (Asclepias s. l., Apocynaceae) are characteristic perennial herbs of grasslands in North America and Africa that have long served as models for studying the evolutionary ecology of plant reproduction and plant defense. Generic circumscription of Asclepias has been long debated with recent workers favoring delimitation on geographic grounds; Asclepias s. s. is limited to the Americas and only segregate genera are recognized for African species. A widely used system introduced by Woodson classifies North American Asclepias into nine subgenera, with the largest subgenus, Asclepias, further divided into eight series. We investigated the phylogeny of Asclepias using three noncoding loci from the plastid genome: rpl16 intron, trnCGCA —rpoB spacer, and the adjacent trnSGCU —trnGuuc spacer and trnGuuc intron. Parsimony, likelihood, and Bayesian analyses were conducted to evaluate hypotheses of continental and taxonomic monophyly. Hypothesis tests were conducted under the parsimony and likelihood criteria. We found moderate support for the monophyly of American Asclepias s. s. and for all but one representative of African Asclepias s. l. Within the Amerian clade, South American species are strongly supported as monophyletic and derived from North American ancestors. Only one of Woodsons 17 infrageneric taxa was found to be monophyletic. Monophyly of more than one half of the remaining 16 taxa could be statistically rejected using a conservative &agr; level. Our results are consistent with taxonomic restriction of Asclepias to American species and single colonization events from Africa to North America and North America to South America. They also point to a need for major restructuring of infrageneric classification and future revsionary work.

Phylogeny of a Genomically Diverse Group of Elymus (Poaceae) Allopolyploids Reveals Multiple Levels of Reticulation

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.