Phylogeographical history of the widespread meadow fescue (Festuca pratensis Huds.) inferred from chloroplast DNA sequences

Aim Here we explore the variation in chloroplast DNA (cpDNA) in a widespread Eurasian diploid forage grass, meadow fescue (Festuca pratensis Huds.), to address its phylogeographical history. In particular, we aim to answer whether the post‐glacial migration routes of meadow fescue are associated with the spread of agriculture or concurrent with well‐documented natural migration pathways from glacial refugia. Location A total of 56 Eurasian accessions of F. pratensis were analysed, representing the entire native distribution area as well as non‐native areas in northernmost Europe. Methods Based on initial sequencing of 10 non‐coding cpDNA regions, three regions were sequenced for all F. pratensis accessions. For reference, three closely related species [the diploid Lolium perenne L. and the polyploids Festuca arundinacea Schreb. and Festuca gigantea (L.) Vill.] were also sequenced, as well as the more distantly related Festuca ovina L. Divergence times were estimated assuming a simple molecular clock, calibrated using a previously published estimate of 9 Myr for the divergence between fine‐leaved (F. ovina) and broad‐leaved fescues (F. pratensis, F. arundinacea and F. gigantea). Results Limited, but geographically structured, cpDNA variation was observed in F. pratensis. Three haplotypes, estimated to have diverged 0.16 Ma, were identified: one western European (A), one with a wide eastern distribution from central‐eastern Europe into Asia (B) and one Caucasian (C). The haplotypes of the polyploids and L. perenne were estimated to have diverged from haplotype A in F. pratensis 0.8–1.3 Ma. Main conclusions We found no definite evidence for migration of the diploid F. pratensis associated with the spread of agriculture from the Fertile Crescent after the last glaciation. The distinct geographical structuring of the present‐day variation in cpDNA can rather be explained by northwards expansion of the western haplotype from an Iberian refugium, expansion of the eastern haplotype from an unlocated (south‐)eastern refugium and glacial survival without subsequent expansion from a Caucasian refugium. The high level of cpDNA divergence observed between this diploid and the polyploids which have probably been derived from it may suggest that the very low level of cpDNA variation in the diploid is caused by a recent bottleneck. Today, F. pratensis is widespread in the open agricultural landscape but appears otherwise confined to naturally open habitats such as river banks, and its populations may have been decimated when dense forests dominated in the previous interglacial.     

Polyploidy associated with altered and broader ecological niches in the Claytonia perfoliata (Portulacaceae) species complex

? Premise of the study: Polyploids are often hypothesized to have distinct and broader niches than their diploid progenitors. Differences in geographic distributions between diploid and polyploids are frequently used to infer niche differentiation and increased breadth, but they are seldom used to test these hypotheses explicitly. ? Methods: Niche overlap and breadth were compared for diploids, tetraploids, and hexaploids of three taxa in the Claytonia perfoliata complex (C. parviflora, C. perfoliata, and C. rubra) with the use of species distribution models. Resampling and randomization approaches were used to test hypotheses of niche differentiation, breadth, and conservatism. ? Key results: Niche differentiation was detected between polyploid and diploid cytotypes assigned to the same taxon (e.g., C. parviflora 2× vs. 4×) but not between hexaploids and tetraploids within a taxon (e.g., C. parviflora 4× vs. 6×). Individual hexaploid cytotypes had broader ecological niches than individual diploid cytotypes. However, as a group the three hexaploid taxa did not exceed the combined niche breadth of the three diploids, suggesting that polyploidy does not result in transgressive niche breadth for this group. Niche overlap was lowest among diploids and was highest among the three hexaploid cytotypes, consistent with introgression associated with polyploidy resulting in greater ecological similarity. Although cytotypes possessed nonidentical niches, after accounting for environmental differences among ranges, cytotypes were more similar than expected, suggesting niche conservatism and similar responses to environmental characteristics. ? Conclusions: These results suggest that polyploids occupy distinct and broader niches relative to diploids but that cytotypes also share fundamentally similar responses to environmental variation across ploidy levels.     

Postglacial colonization history reflects in the genetic structure of natural populations of Festuca rubra in Europe

We conducted a large‐scale population genetic survey of genetic diversity of the host grass Festuca rubra s.l., which fitness can be highly dependent on its symbiotic fungus Epichloë festucae, to evaluate genetic variation and population structure across the European range. The 27 studied populations have previously been found to differ in frequencies of occurrence of the symbiotic fungus E. festucae and ploidy levels. As predicted, we found decreased genetic diversity in previously glaciated areas in comparison with nonglaciated regions and discovered three major maternal genetic groups: southern, northeastern, and northwestern Europe. Interestingly, host populations from Greenland were genetically similar to those from the Faroe Islands and Iceland, suggesting gene flow also between those areas. The level of variation among populations within regions is evidently highly dependent on the postglacial colonization history, in particular on the number of independent long‐distance seed colonization events. Yet, also anthropogenic effects may have affected the population structure in F. rubra. We did not observe higher fungal infection rates in grass populations with lower levels of genetic variability. In fact, the fungal infection rates of E. festucae in relation to genetic variability of the host populations varied widely among geographical areas, which indicate differences in population histories due to colonization events and possible costs of systemic fungi in harsh environmental conditions. We found that the plants of different ploidy levels are genetically closely related within geographic areas indicating independent formation of polyploids in different maternal lineages.     

Photosynthetic characteristics of three ploidy levels of Allium oleraceum L. (Amaryllidaceae) differing in ecological amplitude

To elucidate the mechanisms of the adaptive advantages of polyploidy, there is a need to identify physiological traits that participate in the success of polyploids. We studied selected photosynthetic characteristics, stomatal density, and specific leaf area of three ploidy levels (2n = 4x, 5x, 6x) of the geophyte Allium oleraceum that partially differ in their ecological niches. Although the cytotypes were on average similar with regard to most of the measured photosynthetic traits, the hexaploids showed more rapid initial photosynthetic induction and a tendency for a higher maximum photosynthetic rate per unit area. The stomatal density was not affected by ploidy, though the specific leaf area was reduced for the hexaploids compared to the other cytotypes. A lower intracytotype variation was found for most of the studied photosynthetic and anatomical traits for the hexaploids compared to the large variation found within other cytotypes. A comparison of the photosynthetic traits between the cytotypes showed that the ecological differentiation between cytotypes is only weakly related to the characteristics of their photosynthetic apparatus. However, contrasting ranges of variability in the measured traits between the cytotypes can be related to previously observed differences between cytotypes with regard to the ranges of intracytotype genetic variation, genome size variation, and niche breadth. A higher variability of photosynthetic traits in tetraploids and pentaploids may be related to the existence of a spectrum of types adapted to different environmental conditions. Hexaploids may represent a recently formed cytotype adapted to open environmental conditions.     

Polyploidy: a missing link in the conversation about seed transfer of a commonly seeded native grass in western North America

The use of local, native plant materials is now common in restoration but testing for polyploidy in seed sources is not. Diversity in cytotypes across a landscape can pose special seed transfer challenges, because the methods used to determine genetically appropriate materials for seed transfer do not account for cytotypic variation. This lack of consideration may result in mixing cytotypes through revegetation, which could reduce long‐term population viability. We surveyed nine populations of a native bunchgrass, Pseudoroegneria spicata, in three EPA Level III Ecoregions in the western United States to determine the frequency of polyploidy, whether there are differences in traits (phenotype, fecundity, and mortality) among plants of different cytotypes, and whether cytotype frequency varies among ecoregions. We assessed trait variation over 2 years in a common garden and determined ploidy using flow cytometry. Polyploidy and mixed cytotype populations were common, and polyploids occurred in all ecoregions. Four of the nine populations were diploid. The other five had tetraploids present: three had only tetraploid individuals whereas two had mixed diploid/tetraploid cytotypes. There was significant variation in traits among cytotypes: plants from tetraploid populations were larger than diploid or mixed populations. The frequency and distribution of cytotypes make it likely that seed transfer in the study area will inadvertently mix diploid and polyploid cytotypes in this species. The increasing availability of flow cytometry may allow ploidy to be incorporated into native plant materials sourcing and seed transfer.     

Nucleotide diversity of vernalization and flowering‐time‐related genes in a germplasm collection of meadow fescue (Festuca pratensis Huds. syn. Lolium pratense (Huds.) Darbysh.)

In plant species, control of flowering time is an important factor for adaptation to local natural environments. The Vrn1, CO, FT1 and CK2α genes are key components in the flowering‐specific signaling pathway of grass species. Meadow fescue is an agronomically important forage grass species, which is naturally distributed across Europe and Western Asia. In this study, meadow fescue flowering‐time‐related genes were resequenced to assess nucleotide diversity in European and Western Asian subpopulations. Identified sequence polymorphisms were then converted into PCR‐based molecular genetic markers, and a meadow fescue germplasm collection was genotyped to investigate global allelic variation. Lower nucleotide diversities were observed for the Vrn1 and CO orthologs, while relatively higher values were observed for the FT1 and casein kinase II α‐subunit (CK2α) orthologs. The nucleotide diversity for FT1 orthologs in the Western Asian subpopulation was significantly higher than those of the European subpopulation. Similarly, significant differences in nucleotide diversity for the remaining genes were observed between several combinations of subpopulation. The global allele distribution pattern was consistent with observed level of nucleotide diversity. These results suggested that the degree of purifying selection acting on the genes differs according to geographical location. As previously shown for model plant species, functional specificities of flowering‐time‐related genes may also vary according to environmental conditions.     

Neotyphodium Endophyte Changes Phytoextraction of Zinc in Festuca arundinacea and Lolium perenne

The effect of Neotyphodium endophytes on growth parameters and zinc (Zn) tolerance and uptake was studied in two grass species of Festuca arundinacea and Lolium perenne. Plants were grown under different Zn concentrations (control, 200, 400, 800, and 1800 mg kg^?1) in potted soil for 5 months. The results showed that the number of plant tillers was 85 and 51% greater in endophyte infected Festuca (FaEI) and Lolium (LpEI), respectively, compared to their endophyte free (EF) plants. Roots and shoots dry weights in infected Festuca were 87 and 9% greater than non-infected counterparts but in opposite, EF Lolium had 47 and 8% greater root and shoot dry weights than LpEI. Endophyte infected Festuca and Lolium improved chlorophyll fluorescence as Fv/Fm at high concentrations of Zn, showing their better chlorophyll functions and significant reduction of Zn stress in endophyte infected plants. Shoots of endophyte infectedFestuca had 82% greater concentration of Zn than EF Festuca when grown in soil containing 1800 mg kg^?1 Zn. Festuca and Lolium may tolerate high Zn concentration in soil without reduction in shoot and root growth. Endophyte infection in Festuca may help the grass accumulate and transport more Zn in aboveground parts under Zn-stress, thereby aiding phytoremediation of contaminated soils.     

Flow cytometric and cytogenetic analyses of Iberian Peninsula Festuca spp.

Festuca L. has an important diversification centre in the Iberian Peninsula. We used chromosome counting, fluorescence (FISH) and genomic in situ hybridization (GISH), and DNA flow cytometry (FCM) to clarify the taxonomic position of several taxa, to search for phylogenetic relationships and to assess the extent and pattern of genome variation in fescues. The chromosome number of Festuca duriotagana var. barbata is determined for the first time and new ploidy level estimations are given for F. rothmaleri and F. summilusitana. In the latter species, besides the reported decaploid level, dodecaploidy was found in some populations, which points to the existence of an unrecognized taxon. Moreover, these differences were confirmed by FCM and a high positive correlation was found with the type of substrate where F. summilusitana was growing. For each section, a decrease of genome size with increase of polyploidy was observed. In general, in situ hybridization techniques failed to reveal phylogenetic relationships among the selected species. In FISH, a variation in the number of rDNA sites was observed in some species. GISH results indicate that F. henriquesii is not a progenitor of the studied polyploid species.     

Intergeneric relationships ofLolium,Festuca, andVulpia (Poaceae) and their phylogeny

Morphological and seed protein analyses of 26 species of the generaLolium, Festuca andVulpia confirmed their close systematic affinities. Six inflorescence characters readily differentiatedFestuca fromLolium. Protein similarities betweenFestuca of sect.Bovinae and cross-pollinated species ofLolium, coupled with cytogenetic and crossability data, substantiate that they should be united into one genus.Vulpia had phenetic similarities with sect.Scariosae, Montanae andOvinae ofFestuca. Lolium, Festuca, andVulpia are most likely derived from a common ancestral form which was close toFestuca pratensis andLolium perenne.     

The Microgeographical Patterns of Morphological and Molecular Variation of a Mixed Ploidy Population in the Species Complex Actinidia chinensis

Polyploidy and hybridization are thought to have significant impacts on both the evolution and diversification of the genus Actinidia, but the structure and patterns of morphology and molecular diversity relating to ploidy variation of wild Actinidia plants remain much less understood. Here, we examine the distribution of morphological variation and ploidy levels along geographic and environmental variables of a large mixed-ploidy population of the A. chinensis species complex. We then characterize the extent of both genetic and epigenetic diversity and differentiation exhibited between individuals of different ploidy levels. Our results showed that while there are three ploidy levels in this population, hexaploids were constituted the majority (70.3%). Individuals with different ploidy levels were microgeographically structured in relation to elevation and extent of niche disturbance. The morphological characters examined revealed clear difference between diploids and hexaploids, however tetraploids exhibited intermediate forms. Both genetic and epigenetic diversity were high but the differentiation among cytotypes was weak, suggesting extensive gene flow and/or shared ancestral variation occurred in this population even across ploidy levels. Epigenetic variation was clearly correlated with changes in altitudes, a trend of continuous genetic variation and gradual increase of epigenomic heterogeneities of individuals was also observed. Our results show that complex interactions between the locally microgeographical environment, ploidy and gene flow impact A. chinensis genetic and epigenetic variation. We posit that an increase in ploidy does not broaden the species habitat range, but rather permits A. chinensis adaptation to specific niches.     

Leaf epidermal characteristics and genetic variability in Central European populations of broad-leaved Festuca L. taxa

Leaf epidermal (micromorphological and micromorphometric) features of the leaf blade were examined with light and scanning electron microscopy in 49 Central European natural populations of species belonging to subgenera Schedonorus and Drymanthele within the genus Festuca L. In addition, molecular biological (random amplified polymorphic DNA) studies were conducted on selected populations. The goal of the study was to reveal the degree of anatomical and genetic variability at the taxon and population level, as well as to determine the most important characters that allow differentiation of the taxa in these two subgenera. The anatomical variation was compared with the genetic distance between taxa. Investigated taxa exhibited great anatomic variability in terms of both qualitative (presence or absence, shape and appearance of various cell types) and quantitative characters (frequency and size of cells). Strong correlation was found between the genetic distance of populations and the frequency and size of silica cells in the costal zone of the epidermis, which indicates that silica cells are largely determined by the genetic background, regardless of varying environmental conditions. Our studies highlight that despite the high level of variability in anatomical features and genetic polymorphism, these fescue populations clearly segregate both in terms of epidermal structure and genetic constitution.     

Epichloae infection in a native South African grass,Festuca costata Nees

Fungal endophytes have been documented in almost all terrestrial plant groups. Although the endophyte infection syndrome in agronomic cultivars is well studied, relatively little work addresses questions of spatial ecology and fire effects on epichloae endophyte infection in native grasses, and none, to our knowledge, in sub‐Saharan Africa. We sampled seven populations of the native Festuca costata Nees along the spline of the Drakensberg range in South Africa at several spatial scales, including both recently burned and unburned stands. We tested epichloae presence and prevalence with immunoblot assays, PCR and genetic sequencing. We found epichloae endophytes were present and prevalent (38–98% infection rates depending on location). Variation in infection rates occurred primarily among locations, but also among bunches. There was little evidence that endophyte infection rates varied with fire. Novel evidence of epichloae infection of a native Festuca in South Africa opens the door to several new research questions, from the phylogenetic relationship between epichloae of sub‐Saharan Africa and other continents to the ecological advantages or disadvantages that endophytes confer upon their hosts, especially in a fire‐prone ecosystem vulnerable to global environmental change.     

Inheritance of transgenes in transgenic tall fescue (<Emphasis Type="Italic">Festuca arundinacea</Emphasis> schreb.)

Summary Tall fescue (Festuca arundinacea Schreb.) is the most important forage species worldwide of the Festuca genus. Single genotype-derived embryogenic suspension cultures were established from tall fescue cultivar Kentucky-31, and were used as target cells for biolistic transformation. A chimeric hygromycin phosphotransferase gene (hph) was used as the selectable marker, and a chimeric β-glucuronidase (gusA) gene was co-transformed with hph. Transgenic plants were recovered after microprojectile bombardment of suspension cells and subsequent selection in the presence of a high concentration of hygromycin. Fertile transgenic plants were obtained after vernalization under field conditions. T1 and T2 progenies were obtained after reciprocal crosses between transgenic and untransformed control plants. PCR and Southern hybridization analyses revealed a 1∶1 segregation ratio for both transgenes in the T1 and T2 generations. Southern hybridization patterns were identical for T0, T1, and T2 plants. The results demonstrated for the first time the stable meiotic transmission of transgenes following Mendelian rules in transgenic tall fescue.     

Equilibrium and non‐equilibrium phases in the radiation of Hakea and the drivers of diversity in Mediterranean‐type ecosystems

Mediterranean‐type ecosystems (MTEs) contain exceptional plant diversity. Explanations for this diversity are usually classed as either “equilibrium,” with elevated MTE diversity resulting from greater ecological carrying capacities, or “non‐equilibrium,” with MTEs having a greater accumulation of diversity over time than other types of ecosystems. These models have typically been considered as mutually exclusive. Here, we present a trait‐based explanatory framework that incorporates both equilibrium and non‐equilibrium dynamics. Using a large continental Australian plant radiation (Hakea) as a case study, we identify traits associated with niche partitioning in coexisting species (α‐traits) and with environmental filtering (β‐traits), and reconstruct the mode and relative timing of diversification of these traits. Our results point to a radiation with an early non‐equilibrium phase marked by divergence of β‐traits as Hakea diversified exponentially and expanded from the southwest Australian MTE into biomes across the Australian continent. This was followed from seven million years ago by an equilibrium phase, marked by diversification of α‐traits and a slowdown in lineage diversification as MTE‐niches became saturated. These results suggest that processes consistent with both equilibrium and non‐equilibrium models have been important during different stages of the radiation of Hakea, and together they provide a richer explanation of present‐day diversity patterns.     

Detection of individual ploidy levels with genotyping‐by‐sequencing (GBS) analysis

Ploidy levels sometimes vary among individuals or populations, particularly in plants. When such variation exists, accurate determination of cytotype can inform studies of ecology or trait variation and is required for population genetic analyses. Here, we propose and evaluate a statistical approach for distinguishing low‐level ploidy variants (e.g. diploids, triploids and tetraploids) based on genotyping‐by‐sequencing (GBS) data. The method infers cytotypes based on observed heterozygosity and the ratio of DNA sequences containing different alleles at thousands of heterozygous SNPs (i.e. allelic ratios). Whereas the method does not require prior information on ploidy, a reference set of samples with known ploidy can be included in the analysis if it is available. We explore the power and limitations of this method using simulated data sets and GBS data from natural populations of aspen (Populus tremuloides) known to include both diploid and triploid individuals. The proposed method was able to reliably discriminate among diploids, triploids and tetraploids in simulated data sets, and this was true for different levels of genetic diversity, inbreeding and population structure. Power and accuracy were minimally affected by low coverage (i.e. 2×), but did sometimes suffer when simulated mixtures of diploids, autotetraploids and allotetraploids were analysed. Cytotype assignments based on the proposed method closely matched those from previous microsatellite and flow cytometry data when applied to GBS data from aspen. An R package (gbs2ploidy) implementing the proposed method is available from CRAN.     

Effects of fungal endophytes on the seed and seedling biology of Lolium perenne and Festuca arundinacea

Summary Many grasses are infected by endophytic fungi that grow intercellularly in leaves, stems, and flowers and are transmitted maternally by hyphal growth into ovules and seeds. The seed biology and seedling growth of endophyte-infected and uninfected perennial ryegrass (Lolium perenne) and tall fescue (Festuca arundinacea) were investigated under controlled environmental conditions. The percentage of filled seeds produced by infected tall fescue was over twice of uninfected tall fescue; infected and uninfected perennial reegrass had similar percentages. Weights of seeds from infected and uninfected plants were similar in both species. Seeds from infected plants of both species exhibited a higher rate of germination than seeds from uninfected plants. Shoot growth in the greenhouse was compared by making three sequential harvests of above-ground plant parts from infected and uninfected plants of both species. Infected perennial ryegrass plants produced significantly more biomass and tillers than uninfected plants after 6 and 10 weeks of growth and significantly more biomass after 14 weeks of growth. Infected tall fescue plants produced significantly more biomass and tillers than uninfected plants after 10 and 14 weeks of growth. The physiological mechanism of enhancement of growth is not known. The results of this study suggest that infected plants may have a selective advantage in populations with uninfected members.     

Advances in introgression technologies for precision breeding within the Lolium - Festuca complex

The anticipated complexity of multifunctional grasslands with environment‐friendly and sustainable management practices demands better understanding of traits, their interactions, and their genetic control. Intergeneric hybrids between closely related Lolium and Festuca species are being used to broaden the gene pool and provide the plant breeder with options to combine complementary traits aimed at high quality but more robust grass varieties for the future. New techniques in introgression mapping provide opportunities for precision breeding whereby desirable gene combinations transferred from one species into another are selected preferentially, with the exclusion of deleterious alien genes. The close homology between genomes of Lolium and Festuca species allows high levels of chromosome pairing and recombination. Using genomic in situ hybridisation (GISH) on Lolium/Festuca hybrids and their derivatives, recombination between Lolium and Festuca chromosomes is observed at any point along the chromosome. The system provides unlimited access to any combination of Lolium and Festuca DNA sequence. Moreover, genes transferred between homoeologous chromosome sites are expected to function normally at their new locations. Alien chromosome segments may be reduced in size by further recombination events thereby reducing linkage drag. Molecular markers such as AFLPs, SSRs, SNPs, or RFLPs are being targeted to genes of interest to allow their selection through different generations in plant breeding programmes. Relatively simple PCR‐based marker systems are used for specific traits as breeders' toolkits in plant breeding programmes.     

Novelties in the Festuca valesiaca group (Poaceae) from the central Alps

Due to their ploidy levels, their morphological and anatomical characters and their distribution the central alpine Festuca stricta subsp. bauzanina (2n = 8x = 56) and Festuca ovina var. guinochetii (2n = 10x = 70), both belonging to the Festuca valesiaca group, are raised to the specific level. As a new subspecies Festuca bauzanina subsp. rhaetica is described here. The taxa of the polyploid Festuca valesiaca group are morphologically, anatomically and chorologically characterised and an identification key for these taxa in the central Alps is presented.     

Context-dependent resistance against butterfly herbivory in a polyploid herb

Spatial variation in biotic interactions and natural selection are fundamental parts of natural systems, and can be driven by differences in both trait distributions and the local environmental context of the interaction. Most studies of plant–animal interactions have been performed only in natural settings, making it difficult to disentangle the effects of traits and context. To assess the relative importance of trait differences and environmental context for among-population variation in plant resistance to herbivory, we compared oviposition by the butterfly Anthocharis cardamines on two ploidy types of the herb Cardamine pratensis under experimentally controlled conditions with oviposition in natural populations. Under controlled conditions, plants from octoploid populations were significantly more preferred than plants from tetraploid populations. This difference was largely mediated by differences in flower size. Among natural populations, there was no difference in oviposition rates between the two ploidy types. Our results suggest that differences in oviposition rates among populations of the two cytotypes in the field are caused mainly by differences in environmental context, and that the higher attractiveness of octoploids to herbivores observed under common environmental conditions is balanced by the fact that they occur in habitats which harbor lower densities of butterflies. This illustrates that spatial variation in biotic interactions is the net result of differences in trait distributions of the interacting organisms and differences in environmental context, and that variation in both traits and context are important in understanding species interactions.