Re-evaluation and typification of Foeniculum piperitum (Apiaceae), an underknown medicinal plant and crop wild relative

Foeniculum piperitum was described as Anethum piperitum based on plants collected in Sicily, Italy. Currently it is treated either as a synonym of Foeniculum vulgare, or as one of two subspecies within that taxon. Here we show that F. vulgare and F. piperitum are two different, sometimes co-occurring, taxa and that given clear morphological and ecological separation, they should be treated as distinct species. Anethum piperitum is typified. Owing to misapplication of names and wrong synonymizations, the ecology and chorology of F. vulgare and F. piperitum have to be better defined.

Comparative Transcriptomic Profiling ofYersinia enterocoliticaO:3 and O:8 Reveals Major Expression Differences of Fitness- and Virulence-Relevant Genes Indicating Ecological Separation

ABSTRACTYersinia enterocoliticais a zoonotic pathogen and an important cause of bacterial gastrointestinal infections in humans. Large-scale population genomic analyses revealed genetic and phenotypic diversity of this bacterial species, but little is known about the differences in the transcriptome organization, small RNA (sRNA) repertoire, and transcriptional output. Here, we present the first comparative high-resolution transcriptome analysis ofY. enterocoliticastrains representing highly pathogenic phylogroup 2 (serotype O:8) and moderately pathogenic phylogroup 3 (serotype O:3) grown under four infection-relevant conditions. Our transcriptome sequencing (RNA-seq) approach revealed 1,299 and 1,076 transcriptional start sites and identified strain-specific sRNAs that could contribute to differential regulation among the phylogroups. Comparative transcriptomics further uncovered major gene expression differences, in particular, in the temperature-responsive regulon. Multiple virulence-relevant genes are differentially regulated between the two strains, supporting an ecological separation of phylogroups with certain niche-adapted properties. Strong upregulation of theystAenterotoxin gene in combination with constitutive high expression of cell invasion factor InvA further showed that the toxicity of recent outbreak O:3 strains has increased. Overall, our report provides new insights into the specific transcriptome organization of phylogroups 2 and 3 and reveals gene expression differences contributing to the substantial phenotypic differences that exist between the lineages.IMPORTANCEYersinia enterocoliticais a major diarrheal pathogen and is associated with a large range of gut-associated diseases. Members of this species have evolved into different phylogroups with genotypic variations. We performed the first characterization of theY. enterocoliticatranscriptional landscape and tracked the consequences of the genomic variations between two different pathogenic phylogroups by comparing their RNA repertoire, promoter usage, and expression profiles under four different virulence-relevant conditions. Our analysis revealed major differences in the transcriptional outputs of the closely related strains, pointing to an ecological separation in which one is more adapted to an environmental lifestyle and the other to a mostly mammal-associated lifestyle. Moreover, a variety of pathoadaptive alterations, including alterations in acid resistance genes, colonization factors, and toxins, were identified which affect virulence and host specificity. This illustrates that comparative transcriptomics is an excellent approach to discover differences in the functional output from closely related genomes affecting niche adaptation and virulence, which cannot be directly inferred from DNA sequences.

Morphospaces of functionally analogous traits show ecological separation between birds and pterosaurs

Birds originated and radiated in the presence of another group of flying vertebrates, the pterosaurs. Opinion is divided as to whether birds competitively displaced pterosaurs from small-body size niches or whether the two groups coexisted with little competition. Previous studies of Mesozoic birds and pterosaurs compared measurements of homologous limb bones to test these hypotheses. However, these characters probably reflect differing ancestries rather than ecologies. Here, competition and ecological separation were tested for using multivariate analyses of functionally equivalent morphological characters. As well as using characters from the fore- and hindlimbs, these analyses also included measurements of the lower jaw. The results of this study indicate that pterosaurs had relatively longer jaws, shorter metatarsals and shorter brachial regions compared with birds of similar size. Contrary to the results of previous studies, the distal wing was not important for separating the two clades in morphospace owing to the inclusion of the primary feathers in this unit. The differences found here indicate ecological separation based on differences in size, locomotory features and feeding adaptations. Thus, instead of one group displacing the other, birds and pterosaurs appear to have adopted distinctive ecological strategies throughout their period of coexistence.