Phylogeny of the StH genome species in Triticeae (Poaceae): Evidence from chloroplast trnL-F and mitochondria COXII intron sequences

The StH genome species in Triticeae exhibit different morphological variations and extensive geographic distribution. To estimate the phylogenetic relationship of the StH genome species in Triticeae, mitochondria COXII intron and chloroplast trnL-F sequences of 16 StH genome species were analyzed with those of four Pseudoroegneria species (St) and four Hordeum species (H). Sequence diversity and genealogical analysis suggested that (1) the trnL-F and COXII sequence may evolve faster in the polyploid species than in the diploids; (2) the COXII intron has a high evolutionary rate compared to trnL-F sequence and would provide potentially useful phylogenetic analysis in the StH genome species; (3) different Pseudoroegneria species might serve as the maternal donor during the polyploid speciation of the StH genome species; (4) phylogenetic relationships of the StH genome species may be not linked with the inter-continental disjunction between Eurasian and North American.     

Nucleotide divergence and genetic relationships of Pseudoroegneria species

Nucleotide variation in 8 diploid Pseudoroegneria species was characterized using two single copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and the translation elongation factor G (EF-G), and one chloroplast TrnD/T intergenic region. Among the Pseudoroegneria species studied, the estimates of nucleotide diversity (π) ranged from 0.04577 (RPB2) and 0.00183 (TrnD/T) for Pseudoroegneria tauri to 0.10667 (RPB2), 0.06174 (EF-G) and 0.03743 (TrnD/T) for Pseudoroegneria spicata. The highest nucleotide diversity of the RPB2 data set was found for P. spicata among the taxa analyzed. Our phylogenetic analyses separated the accessions of P. spicata into several groups, with 7 accessions of P. spicata forming a highly supported subclade (BS = 100%, PP = 1.00). The phylogenetic analysis also suggests that P. spicata, Pseudoroegneria gracillima and Pseudoroegneria stipifolia have a closer relationship than the other species within Pseudoroegneria. Pseudoroegneria libanotica and P. tauri were also found to exhibit a high level of sequence homology, however, only nuclear gene data (RPB2 and EF-G) clearly indicated the differentiation between the P. libanotica + P. tauri group with other St genome species.     

Phylogeny and molecular evolution of the rbcL gene of St genome in Elymus sensu lato (Poaceae: Triticeae)

Analysis of the patterns and levels of diversity in duplicate gene not only traces evolutionary history of polyploids, but also provides insight into how the evolutionary process differs between lineages and between homoeologous loci within lineages. Elymus sensu lato is a group of allopolyploid species, which share a common St genome and with the different combinations of H, Y, P, and W genomes. To estimate the evolutionary process of the rbcL gene in species of Elymus s. l. and its putative dioploid relatives, 74 sequences were obtained from 21 species of Elymus s. l. together with 24 diploid taxa representing 19 basic genomes in Triticeae. Phylogeny and sequence diversity pattern analysis suggested that (1) species of Pseudoroegneria (Nevski) Á. Löve might serve as the maternal donor of the species of Elymus s. l; (2) differentiation of St genome were shown in the species of Elymus s. l. following polyploidy event; (3) divergences within the species might associate with geographic diversity and morphological variability; (4) differences in the levels and patterns of nucleotide diversity of the rbcL gene implied that the St genome lineages in the species of Elymus s. l. have differently evolutionary potentials.     

Reticulate Evolutionary History of a Complex Group of Grasses: Phylogeny of Elymus StStHH Allotetraploids Based on Three Nuclear Genes

Background

Elymus (Poaceae) is a large genus of polyploid species in the wheat tribe Triticeae. It is polyphyletic, exhibiting many distinct allopolyploid genome combinations, and its history might be further complicated by introgression and lineage sorting. We focus on a subset of Elymus species with a tetraploid genome complement derived from Pseudoroegneria (genome St) and Hordeum (H). We confirm the species'' allopolyploidy, identify possible genome donors, and pinpoint instances of apparent introgression or incomplete lineage sorting.

Methodology/Principal Findings

We sequenced portions of three unlinked nuclear genes—phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I—from 27 individuals, representing 14 Eurasian and North American StStHH Elymus species. Elymus sequences were combined with existing data from monogenomic representatives of the tribe, and gene trees were estimated separately for each data set using maximum likelihood. Trees were examined for evidence of allopolyploidy and additional reticulate patterns. All trees confirm the StStHH genome configuration of the Elymus species. They suggest that the StStHH group originated in North America, and do not support separate North American and European origins. Our results point to North American Pseudoroegneria and Hordeum species as potential genome donors to Elymus. Diploid P. spicata is a prospective St-genome donor, though conflict among trees involving P. spicata and the Eurasian P. strigosa suggests either introgression of GBSSI sequences from P. strigosa into North American Elymus and Pseudoroegneria, or incomplete lineage sorting of ancestral GBSSI polymorphism. Diploid H. californicum and/or allotetraploid H. jubatum are possible H-genome donors; direct involvement of an allotetraploid Hordeum species would simultaneously introduce two distinct H genomes to Elymus, consistent with some of the relationships among H-genome sequences in Hordeum and Elymus.

Conclusions/Significance

Comparisons among molecular phylogenetic trees confirm allopolyploidy, identify potential genome donors, and highlight cases of apparent introgression or incomplete lineage sorting. The complicated history of this group emphasizes an inherent problem with interpreting conflicts among bifurcating trees—identifying introgression and determining its direction depend on which tree is chosen as a starting point of comparison. In spite of difficulties with interpretation, differences among gene trees allow us to identify reticulate species and develop hypotheses about underlying evolutionary processes.     

Maternal origin,genome constitution and evolutionary relationships of polyploid <Emphasis Type="Italic">Elymus</Emphasis> species and <Emphasis Type="Italic">Hordelymus europaeus</Emphasis>

The trnS/psbC region of chloroplast DNA (cpDNA) was sequenced for 18 Elymus polyploid species, Hordelymus europaeus and their putative diploid ancestors. The objective was to determine the maternal origin and evolutionary relationships of these polyploid taxa. Phylogenetic analysis showed that Elymus and Pseudoroegneria species formed a highly supported monophyletic group (100 % bootstrap values), suggesting that Pseudoroegneria is the maternal genome donor to polyploid Elymus species studied here. The phylogenetic tree based on cpDNA sequence data indicates that E. submuticus contains a St-genome. Taking into consideration of our previously published RPB2 data, we can conclude that hexaploid E. submuticus contains at least one copy of St and Y genomes. Our Neighor-joining analysis of cpDNA data put Psathyrostachys juncea, Hordeum bogdanii and Hordelymus europaeus into one group, suggesting a close relationship among them.     

Genome origin and phylogenetic relationships of Elymus villosus (Triticeae: Poaceae) based on single-copy nuclear Acc1, Pgk1, DMC1 and chloroplast trnL-F sequences

To investigate the genome origin and phylogenetic relationships of Elymus villosus, three single-copy nuclear gene (Acc1, Pgk1 and DMC1) and chloroplast trnL-F gene sequences of two accessions of E. villosus were analyzed with those of eighteen allotetraploids (StH, StY, StP and StE^e genomes) and thirty-five diploid taxa representing eighteen basic genomes in Triticeae. The results revealed that: (1) the genomic constitution of E. villosus is StH as Elymus; (2) North America Pseudoroegneria species served as the maternal donor during the allotetraploid speciation of E. villosus; (3) E. villosus is closely related to North America Elymus species; (4) it is reasonable to recognize the E. villosus as Elymus L. sensu stricto.     

Phylogeny and maternal donor of Kengyilia (Triticeae: Poaceae) based on chloroplast trnT–trnL sequences

The chloroplast DNA regions trnT–trnL was used to analyze to phylogenetic relationships and maternal donor of Kengyilia species and their closely related species. The Neighbor-Joining phylogenetic reconstructions partitioned the species into two reciprocally monophyletic groups. Kengyilia melanthera was related to species of Agropyron, whereas the other species were related to species of Pseudoroegneria and Roegneria. These results indicate that there have been at least two phylogenetically divergent maternal donors within Kengyilia, i.e. Agropyron (P genome) and Pseudoroegneria (St genome). In addition, the St genome of Kengyilia had several origins and diverse species of Pseudoroegneria might have taken part in the formation of polyploid species of Kengyilia.     

Untangling Nucleotide Diversity and Evolution of the H Genome in Polyploid Hordeum and Elymus Species Based on the Single Copy of Nuclear Gene DMC1

Numerous hybrid and polypoid species are found within the Triticeae. It has been suggested that the H subgenome of allopolyploid Elymus (wheatgrass) species originated from diploid Hordeum (barley) species, but the role of hybridization between polyploid Elymus and Hordeum has not been studied. It is not clear whether gene flow across polyploid Hordeum and Elymus species has occurred following polyploid speciation. Answering these questions will provide new insights into the formation of these polyploid species, and the potential role of gene flow among polyploid species during polyploid evolution. In order to address these questions, disrupted meiotic cDNA1 (DMC1) data from the allopolyploid StH Elymus are analyzed together with diploid and polyploid Hordeum species. Phylogenetic analysis revealed that the H copies of DMC1 sequence in some Elymus are very close to the H copies of DMC1 sequence in some polyploid Hordeum species, indicating either that the H genome in theses Elymus and polyploid Hordeum species originated from same diploid donor or that gene flow has occurred among them. Our analysis also suggested that the H genomes in Elymus species originated from limited gene pool, while H genomes in Hordeum polyploids have originated from broad gene pools. Nucleotide diversity (π) of the DMC1 sequences on H genome from polyploid species (π = 0.02083 in Elymus, π = 0.01680 in polyploid Hordeum) is higher than that in diploid Hordeum (π = 0.01488). The estimates of Tajima''s D were significantly departure from the equilibrium neutral model at this locus in diploid Hordeum species (P<0.05), suggesting an excess of rare variants in diploid species which may not contribute to the origination of polyploids. Nucleotide diversity (π) of the DMC1 sequences in Elymus polyploid species (π = 0.02083) is higher than that in polyploid Hordeum (π = 0.01680), suggesting that the degree of relationships between two parents of a polyploid might be a factor affecting nucleotide diversity in allopolyploids.     

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.     

Distinct origin of the Y and St genome in Elymus species: evidence from the analysis of a large sample of St genome species using two nuclear genes

Background

Previous cytological and single copy nuclear genes data suggested the St and Y genome in the StY-genomic Elymus species originated from different donors: the St from a diploid species in Pseudoroegneria and the Y from an unknown diploid species, which are now extinct or undiscovered. However, ITS data suggested that the Y and St genome shared the same progenitor although rather few St genome species were studied. In a recent analysis of many samples of St genome species Pseudoroegneria spicata (Pursh) À. Löve suggested that one accession of P. spicata species was the most likely donor of the Y genome. The present study tested whether intraspecific variation during sampling could affect the outcome of analyses to determining the origin of Y genome in allotetraploid StY species. We also explored the evolutionary dynamics of these species.

Methodology/Principal Findings

Two single copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and the translation elongation factor G (EF-G) sequences from 58 accessions of Pseudoroegneria and Elymus species, together with those from Hordeum (H), Agropyron (P), Australopyrum (W), Lophopyrum (E^e), Thinopyrum (E^a), Thinopyrum (E^b), and Dasypyrum (V) were analyzed using maximum parsimony, maximum likelihood and Bayesian methods. Sequence comparisons among all these genomes revealed that the St and Y genomes are relatively dissimilar. Extensive sequence variations have been detected not only between the sequences from St and Y genome, but also among the sequences from diploid St genome species. Phylogenetic analyses separated the Y sequences from the St sequences.

Conclusions/Significance

Our results confirmed that St and Y genome in Elymus species have originated from different donors, and demonstrated that intraspecific variation does not affect the identification of genome origin in polyploids. Moreover, sequence data showed evidence to support the suggestion of the genome convergent evolution in allopolyploid StY genome species.     

Molecular evolution and nucleotide diversity of nuclear plastid phosphoglycerate kinase (PGK) gene in Triticeae (Poaceae)

Levels of nucleotide divergence provide key evidence in the evolution of polyploids. The nucleotide diversity of 226 sequences of pgk1 gene in Triticeae species was characterized. Phylogenetic analyses based on the pgk1 gene were carried out to determine the diploid origin of polyploids within the tribe in relation to their A^u, B, D, St, Ns, P, and H haplomes. Sequences from the Ns genome represented the highest nucleotide diversity values for both polyploid and diploid species with π = 0.03343 and θ = 0.03536 for polyploid Ns genome sequences and π = 0.03886 and θ = 0.03886 for diploid Psathyrostachys sequences, while Triticum urartu represented the lowest diversity among diploid species at π = 0.0011 and θ = 0.0011. Nucleotide variation of diploid Aegilops speltoides (π = 0.2441, presumed the B genome donor of Triticum species) is five times higher than that (π = 0.00483) of B genome in polyploid species. Significant negative Tajima's D values for the St, A^u, and D genomes along with high rates of polymorphisms and low sequence diversity were observed. Origins of the A^u, B, and D genomes were linked to T. urartu, A. speltoides, and A. tauschii, respectively. Putative St genome donor was Pseudoroegneria, while Ns and P donors were Psathyrostachys and Agropyron. H genome diploid donor is Hordeum.     

Genetic variability and genomic divergence of Elymus repens and related species

Summary In order to study the genetic variation and phylogenetic relationship in Elymus repens, amplified fragment length polymorphism (AFLP) were used, together with sequence data for the nuclear gene phytochrome B, phyB, and the chloroplast ribosomal protein encoding gene rps4. A total of 83 collected E. repens samples, 3 E. repens reference samples and 18 related species accessions were analysed and compared with 13 GenBank sequences. AMOVA analysis revealed a moderate genetic differentiation between the populations of E. repens in the three Swedish provinces investigated, while no differentiation was observed due to landscape type. A moderate genetic differentiation was also found when samples from different fields in one province were compared to samples from a selected field. A common female origin was found in E. repens and seven other Elymus species, Pseudoroegneria spicata, Thinopyrum intermedium, T. junceum, Hordeum bogdanii and H. stenostachys. The latter two both harbour the H genome. Taken together, the data suggest that the Swedish E. repens population is slightly heterogeneous and comprises multiple origins of genome donors; a nuclear genome with contributions from Pseudoroegneria (St), Hordeum (H), Thinopyrum (E) and Y with an unknown donor together with a maternal genome donated from Pseudoroegneria.     

Phylogenetic relationships between Hystrix and its closely related genera (Triticeae; Poaceae) based on nuclear Acc1, DMC1 and chloroplast trnL-F sequences

To estimate the phylogenetic relationship of polyploid Hystrix in Triticeae, two single-copy nuclear genes (Acc1 and DMC1) and chloroplast trnL-F sequences of six Hystrix taxa were analyzed with those of nine Leymus species (NsXm), four Elymus species (StH) and 13 diploid taxa from seven monogenomic genera. Phylogenetic analyses reveal that Hystrix taxa contain two distinct types of genome constitution, despite the overall morphological and ecological similarity among Hystrix taxa. One type of genome constitution is StH (Hy. patula) as Elymus, the other is NsXm (Hy. californica, Hy. coreana, Hy. duthiei, Hy. duthiei ssp. longearistata and Hy. komarovii) as Leymus. The St, H and Ns genomes in Hystrix are donated by Pseudoroegneria, Hordeum and Psathyrostachys, respectively. The donor of the Xm genome is closely related to Agropyron (P). The trnL-F data especially indicate that there has been a maternal haplotype polymorphism in Hystrix species. Based on these results, we suggest that Hy. coreana, Hy. duthiei, Hy. duthiei ssp. longearistata, Hy. komarovii and Hy. californica should be included in the genus Leymus, and Hy. patula in the genus Elymus.     

Phylogenetic relationships in Elymus (Poaceae: Triticeae) based on the nuclear ribosomal internal transcribed spacer and chloroplast trnL-F sequences

To estimate the phylogenetic relationship of polyploid Elymus in Triticeae, nuclear ribosomal internal transcribed spacer (ITS) and chloroplast trnL-F sequences of 45 Elymus accessions containing various genomes were analysed with those of five Pseudoroegneria (St), two Hordeum (H), three Agropyron (P) and two Australopyrum (W) accessions. The ITS sequences revealed a close phylogenetic relationship between the polyploid Elymus and species from the other genera. The ITS and trnL-F trees indicated considerable differentiation of the StY genome species. The trnL-F sequences revealed an especially close relationship of Pseudoroegneria to all Elymus species included. Both the ITS and trnL-F trees suggested multiple origins and recurrent hybridization of Elymus species. The results suggested that: the St, H, P, and W genomes in polyploid Elymus were donated by Pseudoroegneria, Hordeum, Agropyron and Australopyrum, respectively, and the St and Y genomes may have originated from the same ancestor; Pseudoroegneria was the maternal donor of the polyploid Elymus; and some Elymus species showed multiple origin and experienced recurrent hybridization.     

Phylogenetic analysis of North American Elymus and the monogenomic Triticeae (Poaceae) using three chloroplast DNA data sets.

Although the monogenomic genera of the Triticeae have been analyzed in numerous biosystematic studies, the allopolyploid genera have not been as extensively studied within a phylogenetic framework. We focus on North American species of Elymus, which, under the current genomic system of classification, are almost all allotetraploid, combining the St genome of Pseudoroegneria with the H genome of Hordeum. We analyze new and previously published chloroplast DNA data from Elymus and from most of the monogenomic genera of the Triticeae in an attempt to identify the maternal genome donor of Elymus. We also present a cpDNA phylogeny for the monogenomic genera that includes more data than, and thus builds on, those previously published. The chloroplast DNA data indicate that Pseudoroegneria is the maternal genome donor to all but one of the Elymus individuals. There is little divergence among the Elymus and Pseudoroegneria chloroplast genomes, and as a group, they show little divergence from the rest of the Triticeae. Within the monogenomic Triticeae, the problematic group Thinopyrum is resolved as monophyletic on the chloroplast DNA tree. At the intergeneric level, the data reveal several deeper-level relationships that were not resolved by previous cpDNA trees.     

Molecular phylogeny and maternal progenitor implication in the genus Kengyilia (Triticeae: Poaceae): Evidence from COXII intron sequences

Kengyilia is a perennial genus distributing in central and western Asia. Here, the levels of nucleotide diversity for COXII intron were obtained. The estimates of nucleotide diversity for different genome constitution ranged from θ = 0.00082 and π = 0.00082 for St genome species to π = 0.01227 and θ = 0.01229 for P genome species. Employing COXII intron sequences, the phylogenetic relationships within Kengyilia and between Kengyilia genus and its closely related genera were examined. The Maximum Parsimony analysis demonstrated that Kengyilia species were positioned into two clades corresponding to different maternal genomic donor. Kengyilia stenachyra, Kengyilia grandiglumis, Kengyilia hirsuta, Kengyilia melanthera, Kengyilia thoroldiana, Kengyilia alatavica and Kengyilia zhaosuensis were related to species of Agropyron, while Kengyilia kokonorica, Kengyilia rigidula, Kengyilia nana, Kengyilia mutica, Kengyilia longiglumis, Kengyilia laxiflora and Kengyilia gobicola were close to species of Roegneria and Pseudoroegneria. In addition, other three species of Kengyilia, such as Kengyilia batalinii, Kengyilia tahelacana and Kengyilia kaschgarica, were related to Douglasdeweya deweyi, Pseudoroegneria strigosa and Roegneria tibetica. This result indicated that there had been two phylogenetically divergent maternal donors within Kengyilia. Our new finding will help to understand the evolutionary history of the genus Kengyilia.     

披碱草属及其近源属植物种子胚乳细胞多样性研究

披碱草属不仅是小麦、大麦等作物的重要基因库,也是优良牧草的重要组成部分。胚乳是麦类作物种子的重要组成部分,其重量占籽粒重量在90%以上。胚乳特性是一个相对稳定的遗传性状,可以将胚乳特性作为植物分类和系统关系的一个指标。胚乳细胞特征作为植物的一类微形态特征,在麦类植物系统分类与进化研究中具有一定的价值。该研究对小麦族的6个披碱草属(Elymus)物种、2个拟鹅观草属(Pseudoroegneria)物种、1个大麦属(Hordeum)物种和2个冰草属(Agropyron)物种,共4属11份材料的胚乳细胞特征进行解剖观察并测量相关指标。结果表明:(1)不同属、种的植物种子胚乳细胞之间存在丰富的多样性,属间差异大于属内种间差异;(2)同样具有P染色体组的Agropyron cristatum和A.mongolicum与同样具有St染色体组的Pseudoroegneria libanotica和P.spicata各自在细胞形状和大小上的差异很小;(3)不同物种的胚乳细胞在大小、形状和数量上均表现出差异,但不能很好地反映属以及基因组间的差异,研究结果为揭示披碱草属植物的系统关系提供了胚乳细胞方面的证据,同时也为利用该属植物改良麦类作物品质积累资料。     

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, β-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 Elymus Y 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.     

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.     

Phylogenetic relationships between Leymus and related diploid Triticeae species revealed by ISSR markers

To investigate the genetic diversity and phylogenetic relationships between polyploid Leymus and related diploid species of the Triticeae tribe, inter-simple sequence repeats (ISSR) markers was used to analyze 41 Leymus accessions representing 22 species and 2 subspecies, together with Pseudoroegneria stipifolia (St), Psathyrostachys fragilis (Ns), Australopyrum retrofractum (W), Hordeum bogdanii, H. chilense (H) and Lophopyrum elongatum (E^e). A total of 376 clear and reproducible DNA fragments were amplified by 29 ISSR primers, among which 368 (97.87%) fragments were found to be polymorphic. 8–18 polymorphic bands were amplified by each polymorphic primer, with an average of 12.69 bands. The data of 376 ISSR bands were used to generate Nei’s similarity coefficients and to construct a dendrogram by means of UPGMA. The similarity coefficients data suggested great genetic diversity in genus Leymus and related diploid Triticeae species, the genetic diversity among the different species more abundant than that of the different accessions. The dendrogram and principal coordinate analysis showed explicit interspecific relationships and demonstrated close phylogenetic relationships between Leymus species and Psathyrostachys.