Background and Aims The genus Allium L., one of the largest monocotyledonous genera and one that includes many economically important crops with nutritional and medicinal value, has been the focus of classification or phylogeny studies for centuries. Recent studies suggested that the genus can be divided into 15 subgenera and 72 sections, which were further classified into three evolutionary lineages. However, the phylogenetic relationships reconstructed by one or two loci showed weaker support, especially for the third evolutionary lineage, which might not show the species relationships very clearly and could hinder further adaptive and evolutionary study. Methods In this study, a total of 39 complete chloroplast genomes of Allium (covering 12 Allium subgenera) were collected, and combining these with 125 species of plastomes from 19 other families of monocots, we reconstructed the phylogeny of the genus Allium, estimated the origin and divergence time of the three evolutionary lineages and investigated the adaptive evolution in this genus and related families. Results Our phylogenetic analysis confirmed the monophyly and three evolutionary lineages of Allium, while new species relationships were detected within the third evolutionary lineage. The divergence time of the three evolutionary lineages was estimated to be in the early Eocene to the middle Miocene, and numerous positive selected genes (PSGs) and PSGs with high average Ka/Ks values were found in Allium species. Conclusions Our results detected a well-supported phylogenetic relationship of Allium. The PSGs and PSGs with high Ka/Ks values, as well as diversified morphologies, complicated chromosome characteristics and unique reproductive modes may play important roles in the adaptation and evolution of Allium species. This is the first study that conducted phylogenetic and evolutionary analyses on the genus Allium combined with the plastome and morphological and cytological data. We hope that this study can contribute to further analysis of Allium for other researchers.

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Urophysa is a Chinese endemic genus with only two species (U. rockii and U. henryi) distributed in Yungui Plateau (Guizhou Province) and adjacent regions (i.e., Provinces of Hunan, Hubei, Chongqing and Sichuan). The aim of this study was to determine the genetic diversity and population differentiation within Urophysa and investigate the effect of the Yungui Plateau uplift and climate oscillations on evolution of Urophysa. In this study, micro-morphological characteristics, nine microsatellite loci (SSR), two nuclear loci (ITS and ETS) and two chloroplast fragments (psbA-trnH and trnL-trnF) were used to analyze the phylogenetic relationships and assess genetic and phylogeographical structure of Urophysa. Isolation by distance (IBD) was performed to research the effects of geographical isolation. We detected high genetic diversity at the species level but low genetic diversity within populations. Striking genetic differentiation (AMOVA) among populations and a significant phylogeographical structure (NST > GST, p < 0.01) were detected among U. henryi populations, along with significant effects of isolation by distance (IBD). Molecular clock estimation using calibration strategy and cpDNA substitution rate indicated that the divergence of U. henryi occurred during late Miocene to early Quaternary, when the orogeny of Yungui Plateau was violent. U. rockii originated at the early Quaternary and further differentiated at early Pleistocene. Our results suggested that habitat fragmentation played an important role in the genetic diversity and population differentiation of U. rockii and U. henryi. Heterogenous geomorphological configuration and complicated environment resulted from rapid uplift of the Yungui Plateau were inferred as important incentives for the modern phylogeograhpical pattern and species divergence of Urophysa. The geographical isolation, limited gene flow, specialized morphologies and the Pleistocene climatic oscillation greatly contributed to the allopatric divergence of U. rockii. Significant genetic drift and inbreeding were detected in these two species, in situ measures should be implemented to protect them.

Based on field investigations, as well as investigation of relevant specimens, Pimpinella rhomboidea var. tenuiloba is shown to be conspecific with Melanosciadium bipinnatum. The distribution and habitat of M. bipinnatum is redescribed and notes on the taxonomy of the species are presented.

A new species, Scrophularia jinii (Scrophulariaceae), from Central China is described and illustrated. This new species was formerly misidentified as S. fargesii, from which it differs in many morphological characters. Moreover, it is distinct with all known Scrophularia species in its unique deeply double serrate leaf margin with 3–7 big teeth on each side. Molecular phylogenetic analysis further supports its species delimitation and suggests a close relationship with several Japanese and North American species.

Ostericum palustre is a critically Endangered species endemic to Europe and was described as the typespecies of the genus Ostericum (Apiaceae). The complete chloroplast genome of O. palustre was reported for the first time, which suggested a circle quadripartite structure of 154923 bp in length comprising the large single-copy region (LSC) of 84750 bp, the small single-copy region (SSC) of 19752 bp, and a pair of inverted regions (IRs) of 25209 bp. There were totally 127 genes including 4 rRNAs, 37 tRNAs, and 82 protein-coding genes. In the phylogenetic analyses, O. palustre was very close to Pterygopleurum neurophyllum but distant from Angelica species, which coincided with the result of ITS sequences analysis. This study provided a significant genetic resource and will be helpful to systematic research and effective conservation.

Angelica muliensis (Apiaceae), a new species from Sichuan Province, southwest China, is described and illustrated. The new species resembles A. biserrata, but differs in the shapes of the leaflets and sheaths, umbel number and size and especially mericarp features. The diagnostic characters of these two species are presented and compared.

Based on fieldwork, literature study and herbarium investigations, the long-term misapplied Pternopetalum botrychioides is clarified and re-illustrated. Pternopetalum latipinnulatum comb. et stat. nov. is proposed based on P. botrychioides var. latipinnulatum, with an amplified and detailed description. On the basis of stereomicroscope, OM and SEM observations, as well as field investigations, a morphological comparison of these two taxa is provided.