Detecting and mapping repulsion-phase linkage in polyploids with polysomic inheritance

It has been suggested that ratios of coupling- to repulsion-phase linked markers can be used to distinguish between allopolyploids and autopolyploids, because repulsion-phase linkages are much more difficult to detect in autopolyploids with polysomic inheritance than allopolyploids with disomic inheritance. In this report, we analyze the segregation pattern of repulsion-phase linked markers in polyploids without complete preferential pairing. The observed repulsion-phase recombination fraction (R) in such polyploids is composed of a fraction due to crossing-over (R_c) and another fraction due to independent assortment (R_i). R_i is the minimum distance that can be detected between repulsion-phase linked markers. Because R_i is high in autopolyploids (0.3373, 0.4000, 0.4286 and 0.4444) for autopolyploids of 2n=4x, 6x, 8x and 10x), large population sizes are required to reliably detect repulsion linkages. In addition, the default linkage used in mapping-programs must be greater than the corresponding R_i to determine whether a polyploid is a true autopolyploid. Unfortunately, much lower default linkages than the R_is have been used in recent polyploid studies to determine polyploid type, and markers have been incorporated into polyploid maps based on the R values. Herein, we describe how mapping repulsion linkages can result in spurious results, and present methods to accurately detect the degree of preferential pairing in polyploids using repulsion linkage analysis. Received: 29 February 2000 / Accepted: 17 July 2000     

Autopolyploidy leads to rapid genomic changes in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Polyploidy is a widespread feature of plant genomes. As a typical model of polyploidy, autopolyploidy has been postulated evolutionary dead ends and received little attention compared with allopolyploidy. For the limited data available so far, the evolutionary outcome of genome diversity in autopolyploids remains controversial in comparison with its diploid ancestors. In the present study, the effects of autopolyploidy on genome diversity were revealed at a genome-wide scale by comparative analyses of polymorphism between Arabidopsis autopolyploids (autotetraploids and autotriploids) and related diploids within the first ten successive inbred generations using amplified fragment length polymorphism. The results showed that in contrast with diploids, the rapid genomic changes (including gain and loss of DNA sequences) in autopolyploids were definitely found within the first generations after autopolyploidization, but slow down and probably stabilized in the higher generations as a source of genetic diversity in the long term. The sequencing of these DNA fragments indicated that these changes occurred both on genic and inter-genic (or intronic) regions, and quantitative PCR showed that the expression of some corresponding genes in the genic regions was obviously affected (including upregulation, downregulation and silencing) in autopolyploids. Therefore, this study demonstrated that autopolyploidy could lead to rapid genomic changes and probably influence expression and function of certain genes within the first generations, giving rising to genetic diversification after polyploidization.     

Computational characterization of double reduction in autotetraploid natural populations

Population genetic theory has been well developed for diploid species, but its extension to study genetic diversity, variation and evolution in autopolyploids, a class of polyploids derived from the genome doubling of a single ancestral species, requires the incorporation of multisomic inheritance. Double reduction, which is characteristic of autopolyploidy, has long been believed to shape the evolutionary consequence of organisms in changing environments. Here, we develop a computational model for testing and estimating double reduction and its genomic distribution in autotetraploids. The model is implemented with the expectation–maximization (EM) algorithm to dissect unobservable allelic recombinations among multiple chromosomes, enabling the simultaneous estimation of allele frequencies and double reduction in natural populations. The framework fills an important gap in the population genetic theory of autopolyploids.     

Phenotypic and gene expression analyses of a ploidy series of maize inbred Oh43

Polyploidization has repeatedly occurred during plant evolution. Although autopolyploidy is the best model to characterize the polyploidization effects in a highly controlled manner, there are limited studies on autopolyploids compared to allopolyploids. To improve our understanding of autopolyploidy effects in maize, we developed an inbred Oh43 ploidy series consisting of the diploid (2X), tetraploid (4X) and hexaploid (6X) lines and compared their phenotypes and gene expression in the mature adult leaf tissue. Our phenotypic study showed that plants of higher ploidy exhibit increased cell size but slower growth rate, later flowering, fewer tassel branches, reduced stature and fertility. Two-dimensional difference gel electrophoresis (2D DIGE) and gel electrophoresis followed by liquid chromatography and mass spectrometry (GeLC-MS) assays of the leaf proteomes revealed ~40 and 26% quantitative differentially expressed (DE) proteins, respectively, at the per genome level. A small number of qualitative DE proteins were also identified in the GeLC-MS assay. The majority of the quantitative DE proteins found in the 2D DIGE assay were present in either the 4X versus 6X or the 2X versus 6X comparison but not the 2X versus 4X comparison. Aneuploidy in some 6X plants might contribute to the more extensive changes of gene expression per genome in the 6X. Most changes of the protein expression per genome are less than twofold. Less than 5% of the DE genes exhibit a positive or negative continuous correlation through the ploidy series between their protein expression per genome, and the genome copy number. Hence, in the Oh43 ploidy series, expression for most proteins in a cell increases linearly with ploidy.     

Size matters in Triticeae polyploids: larger genomes have higher remodeling

Polyploidization is one of the major driving forces in plant evolution and is extremely relevant to speciation and diversity creation. Polyploidization leads to a myriad of genetic and epigenetic alterations that ultimately generate plants and species with increased genome plasticity. Polyploids are the result of the fusion of two or more genomes into the same nucleus and can be classified as allopolyploids (different genomes) or autopolyploids (same genome). Triticeae synthetic allopolyploid species are excellent models to study polyploids evolution, particularly the wheat-rye hybrid triticale, which includes various ploidy levels and genome combinations. In this review, we reanalyze data concerning genomic analysis of octoploid and hexaploid triticale and different synthetic wheat hybrids, in comparison with other polyploid species. This analysis reveals high levels of genomic restructuring events in triticale and wheat hybrids, namely major parental band disappearance and the appearance of novel bands. Furthermore, the data shows that restructuring depends on parental genomes, ploidy level, and sequence type (repetitive, low copy, and (or) coding); is markedly different after wide hybridization or genome doubling; and affects preferentially the larger parental genome. The shared role of genetic and epigenetic modifications in parental genome size homogenization, diploidization establishment, and stabilization of polyploid species is discussed.     

Genetic Relationships between Haploid and Triploid Targionia (Targioniaceae, Hepaticae)

The species complex Targionia hypophylla-Targionia lorbeeriana includes a haploid and a triploid cytotype in Europe and the Atlantic islands. As shown by isozyme analysis, high levels of fixed heterozygosity and duplication of one of the chromosome sets characterize the triploids that are fertile. Hybridization between two haploids, followed by chromosome doubling and meiotic nondisjunction can explain triploidy. Both allopolyploidy and autopolyploidy are invoked for the origin of the triploid. The duplicated chromosome set most likely comes from the existing haploid that could be one of the putative parents. The morphological intergradation between the two cytotypes, their identical ecological requirements and sympatric distribution can be understood in the light of these data. A haploid Texan colony analyzed for comparison can be discarded as the other putative parent, which remains unknown. Moreover, three triploid African and Australasian colonies do not share the same duplicated genome as the triploids from Europe and the Atlantic islands. Electrophoretic data indicate independent origins of the European-Atlantic and African-Australasian polyploids.     

Ecological studies of polyploidy in the 100 years following its discovery

Polyploidy is a mutation with profound phenotypic consequences and thus hypothesized to have transformative effects in plant ecology. This is most often considered in the context of geographical and environmental distributions—as achieved from divergence of physiological and life-history traits—but may also include species interactions and biological invasion. This paper presents a historical overview of hypotheses and empirical data regarding the ecology of polyploids. Early researchers of polyploidy (1910s–1930s) were geneticists by training but nonetheless savvy to its phenotypic effects, and speculated on the importance of genome duplication to adaptation and crop improvement. Cytogenetic studies in the 1930s–1950s indicated that polyploids are larger (sturdier foliage, thicker stems and taller stature) than diploids while cytogeographic surveys suggested that polyploids and diploids have allopatric or parapatric distributions. Although autopolyploidy was initially regarded as common, influential writings by North American botanists in the 1940s and 1950s argued for the principle role of allopolyploidy; according to this view, genome duplication was significant for providing a broader canvas for hybridization rather than for its phenotypic effects per se. The emphasis on allopolyploidy had a chilling effect on nascent ecological work, in part due to taxonomic challenges posed by interspecific hybridization. Nonetheless, biosystematic efforts over the next few decades (1950s–1970s) laid the foundation for ecological research by documenting cytotype distributions and identifying phenotypic correlates of polyploidy. Rigorous investigation of polyploid ecology was achieved in the 1980s and 1990s by population biologists who leveraged flow cytometry for comparative work in autopolyploid complexes. These efforts revealed multi-faceted ecological and phenotypic differences, some of which may be direct consequences of genome duplication. Several classical hypotheses about the ecology of polyploids remain untested, however, and allopolyploidy—regarded by most botanists as the primary mode of genome duplication—is largely unstudied in an ecological context.     

Retrotransposons and genomic stability in populations of the young allopolyploid species Spartina anglica C.E. Hubbard (Poaceae)

Spartina x townsendii arose during the end of the 19th century in England by hybridization between the indigenous Spartina maritima and the introduced Spartina alterniflora, native to the eastern seaboard of North America. Duplication of the hybrid genome gave rise to Spartina anglica, a vigorous allopolyploid involved in natural and artificial invasions on several continents. This system allows investigation of the early evolutionary changes that accompany stabilization of new allopolyploid species. Because allopolyploidy may be a genomic shock, eliciting retroelement insertional activity, we examined whether retrotransposons present in the parental species have been activated in the genome of S. anglica. For this purpose we used inter-retrotransposon amplified polymorphism (IRAP) and retrotransposons-microsatellite amplified polymorphism (REMAP) markers, which are multilocus PCR-based methods detecting retrotransposon integration events in the genome. IRAP and REMAP allowed the screening of insertional polymorphisms in populations of S. anglica. The populations are composed mainly of one major multilocus genotype, identical to the first-generation hybrid S. x townsendii. Few new integration sites were encountered in the young allopolyploid genome. We also found strict additivity of the parental subgenomes in the allopolyploid. Both these findings indicate that the genome of S. anglica has not undergone extensive changes since its formation. This contrasts with previous results from the literature, which report rapid structural changes in experimentally resynthesized allopolyploids.     

Molecular Data and the Dynamic Nature of Polyploidy

During the past decade, molecular techniques have provided a wealth of data that have facilitated the resolution of several controversial questions in polyploid evolution. Herein we have focused on several of these issues: (1) the frequency of recurrent formation of polyploid species; (2) the genetic consequences of multiple polyploidizations within a species; (3) the prevalence and genetic attributes of autopolyploids; and (4) the genetic changes that occur in polyploid genomes following their formation.

Molecular data provide a more dynamic picture of polyploid evolution than has been traditionally espoused. Numerous studies have demonstrated multiple origins of both allopolyploids and autopolyploids. In several polyploid species studied in detail, multiple origins were found to be frequent on a local geographic scale, as well as during a short span of time. Molecular data strongly suggest that recurrent formation of polyploid species is the rule, rather than the exception. In addition, molecular data indicate that recurrent formation of polyploids has important genetic consequences, introducing considerable genetic variation from diploid progenitors into polyploid derivatives.

Molecular data also suggest a much more important role for natural autopolyploids than has been historically envisioned. In contrast to the longstanding view of autopolyploidy as being rare, molecular data continue to reveal steadily increasing numbers of well-documented autoploids having tetrasomic or higher-level polysomic inheritance. Although autopolyploidy undoubtedly occurs much less frequently than allopolyploidy in natural populations, it nonetheless has been a significant evolutionary mechanism. Molecular data also provide compelling genetic evidence that contradicts the traditional view of autopolyploidy as being maladaptive. Electrophoretic studies have revealed three important attributes of autopolyploids compared to their diploid progenitors: (1) enzyme multiplicity, (2) increased heterozygosity, and (3) increased allelic diversity. Genetic variability is, in fact, typically substantially higher in autopoloids than in their diploid progenitors. These genetic attributes of autopolyploids are due to polysomic inheritance and provide strong genetic arguments for the potential success of autopolyploids in nature.

In addition to providing numerous important insights into the formation of polyploids and the immediate genetic consequences of polyploidy, molecular data also have been used to study the subsequent evolution of polyploid genomes. Common hypotheses on the subsequent evolution of polyploid genomes include (1) gene silencing, eventually leading to extensively diploidized polyploid genomes; (2) gene diversification, resulting in regulatory or functional divergence of duplicate genes; and (3) genome diversification, resulting in chromosomal repatterning. Compelling, but limited, genetic evidence for all of these factors has been obtained in molecular analyses of polyploid species. The occurrence of these processes in polyploid genomes indicates that polyploid genomes are plastic and susceptible to evolutionary change.

In summary, molecular data continue to demonstrate that polyploidization and the subsequent evolution of polyploid genomes are very dynamic processes.     

Genetic diversity patterns in Curcuma reflect differences in genome size

The relationships between genome size and the systematic and evolutionary patterns in vascular plants are equivocal, although a close relationship between genome size and evolutionary patterns has been previously reported. However, several studies have also revealed the dynamic nature of genome size evolution and its considerable ‘ups’ and ‘downs’. Thus, in this study, the phylogenetic relationships among three previously revealed genome size groups and among species of the highly polyploid genus Curcuma were evaluated using AFLP. Our results suggest two main lineages within Indian Curcuma reflecting evolution of genome size. The first one includes hexaploids and higher polyploids of the previously recognized genome size group I, and the second one includes mainly hexaploids of genome size groups II and III. Within genome size group I, relationships among species seem to be influenced by reticulate evolution and higher polyploids are likely to be of allopolyploid origin. Reproductive systems in Indian Curcuma vary considerably among ploidy levels and these differences considerably affect morphological and genetic variation. In general, clonally reproducing species are expected to exhibit low genotypic diversity, but, at the same time, species of allopolyploid origin are expected to maintain higher levels of heterozygosity compared with their progenitors. We investigated intra‐populational genetic variability in Curcuma spp. to evaluate whether mode of reproduction or ploidy represent the main factor influencing the degree of genetic diversity. We found that hexaploid species exhibited significantly higher genetic diversity than higher polyploids (9x, 15x). Our results suggest that this genetic diversity pattern is largely influenced by the mode of reproduction, as higher polyploids reproduce exclusively vegetatively, whereas hexaploids reproduce mainly sexually. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 388–401.     

Estimation of preferential pairing rates in second-generation autotetraploid pacific oysters (Crassostrea gigas)

Although previously disregarded, polyploidy, and in particular autopolyploidy, is now believed to have played a prominent role in the evolution of plants and animals. We estimated the rate of preferential pairing in second-generation autotetraploid Pacific oysters from gametic frequencies. We found significant levels of preferential pairing in these recently generated autopolyploids, suggesting that genetic variation in standing populations may play a role in meiotic mechanisms of polyploids derived from these populations.     

Genome evolution in Oryza allopolyploids of various ages: Insights into the process of diploidization

The prevalence and recurrence of whole-genome duplication in plants and its major role in evolution have been well recognized. Despite great efforts, many aspects of genome evolution, particularly the temporal progression of genomic responses to allopolyploidy and the underlying mechanisms, remain poorly understood. The rice genus Oryza consists of both recently formed and older allopolyploid species, representing an attractive system for studying the genome evolution after allopolyploidy. In this study, through screening BAC libraries and sequencing and annotating the targeted BAC clones, we generated orthologous genomic sequences surrounding the DEP1 locus, a major grain yield QTL in cultivated rice, from four Oryza polyploids of various ages and their likely diploid genome donors or close relatives. Based on sequenced DEP1 region and published data from three other genomic regions, we investigated the temporal evolutionary dynamics of four polyploid genomes at both genetic and expression levels. In the recently formed BBCC polyploid, Oryza minuta, genome dominance was not observed and its short-term responses to allopolyploidy are mainly manifested as a high proportion of homoeologous gene pairs showing unequal expression. This could partly be explained by parental legacy, rewiring of divergent regulatory networks and epigenetic modulation. Moreover, we detected an ongoing diploidization process in this genus, and suggest that the expression divergence driven by changes of selective constraint probably plays a big role in the long-term diploidization. These findings add novel insights into our understanding of genome evolution after allopolyploidy, and could facilitate crop improvements through hybridization and polyploidization.     

The BOY NAMED SUE Quantitative Trait Locus Confers Increased Meiotic Stability to an Adapted Natural Allopolyploid of Arabidopsis

Whole-genome duplication resulting from polyploidy is ubiquitous in the evolutionary history of plant species. Yet, polyploids must overcome the meiotic challenge of pairing, recombining, and segregating more than two sets of chromosomes. Using genomic sequencing of synthetic and natural allopolyploids of Arabidopsis thaliana and Arabidopsis arenosa, we determined that dosage variation and chromosomal translocations consistent with homoeologous pairing were more frequent in the synthetic allopolyploids. To test the role of structural chromosomal differentiation versus genetic regulation of meiotic pairing, we performed sequenced-based, high-density genetic mapping in F2 hybrids between synthetic and natural lines. This F2 population displayed frequent dosage variation and deleterious homoeologous recombination. The genetic map derived from this population provided no indication of structural evolution of the genome of the natural allopolyploid Arabidopsis suecica, compared with its predicted parents. The F2 population displayed variation in meiotic regularity and pollen viability that correlated with a single quantitative trait locus, which we named BOY NAMED SUE, and whose beneficial allele was contributed by A. suecica. This demonstrates that an additive, gain-of-function allele contributes to meiotic stability and fertility in a recently established allopolyploid and provides an Arabidopsis system to decipher evolutionary and molecular mechanisms of meiotic regularity in polyploids.     

Autopolyploidy differentially influences body size in plants, but facilitates enhanced accumulation of secondary metabolites, causing increased cytosine methylation

Whole genome duplication leads to autopolyploidy and brings about an increase in cell size, concentration of secondary metabolites and enhanced cytosine methylation. The increased cell size offers a positive advantage to polyploids for cell-surface-related activities, but there is a differential response to change in body size across species and taxonomic groups. Although polyploidy has been very extensively studied, having genetic, ecological and evolutionary implications, there is no report that underscores the significance of native secondary metabolites vis-à-vis body size with ploidy change. To address this problem we targeted unique diploid-autotetraploid paired sets of eight diverse clones of six species of Cymbopogon- a species complex of aromatic grasses that accumulate qualitatively different monoterpene essential oils (secondary metabolite) in their vegetative biomass. Based on the qualitative composition of essential oils and the plant body size relationship between the diploid versus autotetraploid paired sets, we show that polyploidy brings about enhanced accumulation of secondary metabolites in all cases, but exerts differential effects on body size in various species. It is observed that the accumulation of alcohol-type metabolites (e.g. geraniol) does not inhibit increase in body size with ploidy change from 2× to 4× (r = 0.854, P < 0.01), but aldehyde-type metabolites (e.g. citral) appear to drastically impede body development (r = -0.895). Such a differential response may be correlated to the metabolic steps involved in the synthesis of essential oil components. When changed to tetraploidy, the progenitor diploids requiring longer metabolic steps in production of their secondary metabolites are stressed, and those having shorter metabolite routes better utilize their resources for growth and vigour. In situ immunodetection of 5-methylcytosine sites reveals enhanced DNA methylation in autopolyploids. It is underpinned that the qualitative composition of secondary metabolites found in the vegetative biomass of the progenitor diploid has a decisive bearing on the body size of the derived autotetraploids and brings about an enhancement in genome-wide cytosine methylation.     

Partial preferential chromosome pairing is genotype dependent in tetraploid rose

It has long been recognised that polyploid species do not always neatly fall into the categories of auto‐ or allopolyploid, leading to the term ‘segmental allopolyploid’ to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra‐high‐density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re‐mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion‐phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra‐dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co‐linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.     

Nonadditive changes in genome size during allopolyploidization in the wheat (aegilops-triticum) group

Interspecific or intergeneric hybridization, followed by chromosome doubling, can lead to the formation of new allopolyploid species. Recent studies indicate that allopolyploid formation is associated with genetic and epigenetic changes. Despite these studies, it is not yet clear whether the C value of an allopolyploid is the sum of its diploid parents. To address this question, six newly synthesized wheat allopolyploids and their parental plants were investigated. It was found that allopolyploids have a genome size significantly smaller than the expected value. The reduction of the nuclear genome size in the synthetic allotetraploids and allohexaploids was 2 pg DNA at 2C. It was also found that changes in the genome size already existed in the first generation amphiploids, indicating that the change was a rapid event. There was no difference in the reduction of nuclear genome size between the allotetraploid and the allohexaploid. These data clearly show that genome differentiation in allopolyploids was not related to the ploidy level. The data obtained clearly suggested that the nonadditive change in genome size that occurred during allopolyploidization may represent a preprogrammed adaptive response to genomic stress caused by hybridization and allopolyploidy, which serves to stabilize polyploid genomes.     

Contrasted histories of organelle and nuclear genomes underlying physiological diversification in a grass species

C₄ photosynthesis evolved multiple times independently in angiosperms, but most origins are relatively old so that the early events linked to photosynthetic diversification are blurred. The grass Alloteropsis semialata is an exception, as this species encompasses C₄ and non-C₄ populations. Using phylogenomics and population genomics, we infer the history of dispersal and secondary gene flow before, during and after photosynthetic divergence in A. semialata. We further analyse the genome composition of individuals with varied ploidy levels to establish the origins of polyploids in this species. Detailed organelle phylogenies indicate limited seed dispersal within the mountainous region of origin and the emergence of a C₄ lineage after dispersal to warmer areas of lower elevation. Nuclear genome analyses highlight repeated secondary gene flow. In particular, the nuclear genome associated with the C₄ phenotype was swept into a distantly related maternal lineage probably via unidirectional pollen flow. Multiple intraspecific allopolyploidy events mediated additional secondary genetic exchanges between photosynthetic types. Overall, our results show that limited dispersal and isolation allowed lineage divergence, with photosynthetic innovation happening after migration to new environments, and pollen-mediated gene flow led to the rapid spread of the derived C₄ physiology away from its region of origin.     

Evolutionary dynamics of retrotransposons following autopolyploidy in the Buckler Mustard species complex

Long terminal repeat retrotransposons (LTR‐RTs) represent a major fraction of plant genomes, but processes leading to transposition bursts remain elusive. Polyploidy expectedly leads to LTR‐RT proliferation, as the merging of divergent diploids provokes a genome shock activating LTR‐RTs and/or genetic redundancy supports the accumulation of active LTR‐RTs through relaxation of selective constraints. Available evidence supports interspecific hybridization as the main trigger of genome dynamics, but few studies have addressed the consequences of intraspecific polyploidy (i.e. autopolyploidy), where the genome shock is expectedly minimized. The dynamics of LTR‐RTs was thus here evaluated through low coverage 454 sequencing of three closely related diploid progenitors and three independent autotetraploids from the young Biscutella laevigata species complex. Genomes from this early diverging Brassicaceae lineage presented a minimum of 40% repeats and a large diversity of transposable elements. Differential abundances and patterns of sequence divergence among genomes for 37 LTR‐RT families revealed contrasted dynamics during species diversification. Quiescent LTR‐RT families with limited genetic variation among genomes were distinguished from active families (37.8%) having proliferated in specific taxa. Specific families proliferated in autopolyploids only, but most transpositionally active families in polyploids were also differentiated among diploids. Low expression levels of transpositionally active LTR‐RT families in autopolyploids further supported that genome shock and redundancy are non‐mutually exclusive triggers of LTR‐RT proliferation. Although reputed stable, autopolyploid genomes show LTR‐RT fractions presenting analogies with polyploids between widely divergent genomes.     

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.