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Existing studies of root/shoot ratios (R/S) in the field show large differences among environments, from high values in unproductive environments to low values in productive environments. However, virtually, all such studies are community‐wide, that is compare biomasses of roots and shoots summed over all coexisting species. Therefore, we do not know to what extent this is due to innate interspecific differences in the R/S ratios or to plastic response to nutrient limitations. This is due to methodological difficulties in assigning roots into species, which preclude the contribution of species‐specific differences to the community‐wide R/S ratio. These limitations can be overcome by DNA analyses. We used qPCR to determine species‐specific R/S ratios in a montane grassland and compared these values to R/S ratios from a two‐season long single‐species pot experiment. To translate the qPCR data to root biomass units, we extracted DNA from the experimental plants to perform calibration for each species and to take into account potential change during the ontogeny of root systems. We used these calibration relationships to recalculate gene copies estimated in a set of field samples to species‐specific root biomass values. All species except one showed fairly high correlation between above‐ground biomass (determined by weighing) and below‐ground biomass (determined by qPCR) across all studied plots in the field. Root/shoot ratios determined from the field were for most species slightly lower than the aggregate values of the whole community determined by weighing both roots and above‐ground biomass. They showed significant correlation with the R/S ratios from the pot experiment, indicating innate differences among species that persist across two very different sets of conditions (multispecies community in the field, single species culture in pots). The field R/S ratios based on qPCR root estimation are informative on the true field patterns. This is supported by their correlation with the pot‐derived values. While the values seem to be slightly underestimated, they are well in the reasonable range of values. This opens a new field of study, namely examination how R/S ratios in the field respond to changed nutrient availability and diversity and species composition of neighbouring species. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

Abstract Background Hieracium s.str. is a complex species-rich group of perennial herbs composed of few sexual diploids and numerous apomictic polyploids. The existence of reticulation and the near-continuity of morphological characters across taxa seriously affect species determination, making Hieracium one of the best examples of a 'botanist's nightmare'. Consequently, its species relationships have not previously been addressed by molecular methods. Concentrating on the supposed major evolutionary units, we used nuclear ribosomal (ETS) and chloroplast (trnT-trnL) sequences in order to disentangle the phylogenetic relationships and to infer the origins of the polyploids. Results Despite relatively low interspecific variation, the nuclear data revealed the existence of two major groups roughly corresponding to species with a Western or Eastern European origin. Extensive reticulation was mainly inferred from the character additivity of parental ETS variants. Surprisingly, many diploid species were of hybrid origin whilst several polyploid taxa showed no evidence of reticulation. Intra-individual ETS sequence polymorphism generally exceeded interspecific variation and was either independent of, or additional to, additive patterns accounted for by hybrid origin. Several ETS ribotypes occurred in different hybrid taxa, but never as the only variant in any species analyzed. Conclusion The high level of intra-individual ETS polymorphism prevented straightforward phylogenetic analysis. Characterization of this variation as additive, shared informative, homoplasious, or unique made it possible to uncover the phylogenetic signal and to reveal the hybrid origin of 29 out of 60 accessions. Contrary to expectation, diploid sexuals and polyploid apomicts did not differ in their molecular patterns. The basic division of the genus into two major clades had not previously been intimated on morphological grounds. Both major groups are thought to have survived in different glacial refugia and to have hybridized as a result of secondary contact. Several lines of evidence suggest the data is best explained by the presence of an extinct range of variation and a larger diversity of ancestral diploids in former times rather than by unsampled variation. Extinct diversity and extensive reticulation are thought to have largely obscured the species relationships. Our study illustrates how multigene sequences can be used to disentangle the evolutionary history of agamic complexes or similarly difficult datasets.

Summary: Intra‐specific variability is a cornerstone of evolutionary success of species. Acquiring genetic material from distant sources is an important adaptive mechanism in bacteria, but it can also play a role in eukaryotes. In this paper, we investigate the nature and evolution of a chromosomal segment of panicoid (Poaceae, Panicoideae) origin occurring in the nuclear genomes of species of the barley genus Hordeum (Pooideae). The segment, spanning over 440 kb in the Asian Hordeumbogdanii and 219 kb in the South American Hordeumpubiflorum, resides on a pair of nucleolar organizer region (NOR)‐bearing chromosomes. Conserved synteny and micro‐collinearity of the segment in both species indicate a common origin of the segment, which was acquired before the split of the respective barley lineages 5–1.7 million years ago. A major part of the foreign DNA consists of several approximately 68 kb long repeated blocks containing five stress‐related protein‐coding genes and transposable elements (TEs). Whereas outside these repeats, the locus was invaded by multiple TEs from the host genome, the repeated blocks are rather intact and appear to be preserved. The protein‐coding genes remained partly functional, as indicated by conserved reading frames, a low amount of non‐synonymous mutations, and expression of mRNA. A screen across Hordeum species targeting the panicoid protein‐coding genes revealed the presence of the genes in all species of the section Stenostachys. In summary, our study shows that grass genomes can contain large genomic segments obtained from distantly related species. These segments usually remain undetected, but they may play an important role in the evolution and adaptation of species. [ABSTRACT FROM AUTHOR]