Yi Ren’s research while affiliated with Shaanxi Normal University and other places

We have seen an explosive increase of plant plastid genome (plastome) sequences in the last decade, and the view that sequence variation in plastomes is maintained by the mutation‐drift balance has been challenged by new evidence. Although comparative genomic and population‐level studies provided us with evidence for positive evolution of plastid genes at both the macro‐ and micro‐evolution levels, less studies have systematically investigated how plastomes have evolved during the speciation process. We here sequenced 13 plastomes of Actaea purpurea (P.K. Hsiao) J. Compton, and its closest relatives, and conducted a systematic survey of positive selection in their plastid genes using the McDonald‐Kreitman test and codon‐based methods using maximum likelihood to estimate the ratio of nonsynonymous to synonymous substitutions (ω) across a phylogeny. We found that during the speciation of A. purpurea and its relatives, all plastid genes evolved neutrally or were under purifying selection. Genome size, gene order, and number were highly conserved. Comparing to A. purpurea, plastomes of Actaea japonica and Actaea biternata had low genetic diversity, consistent with previous studies. Our work not only sheds important light on the evolutionary history of A. purpurea and its kin, but also on the evolution of plastomes during plant speciation. Thirteen plastomes of 1representative populations of Actaea purpurea and its relatives were conserved with respect to size, structure, gene content, and order, with few variations. Positive selection analysis suggests that all plastid genes evolve neutrally or are subjected to purifying selection. Actaea japonica's low genetic diversity probably results from a recent expansion, not a recent selective sweep on plastid genes.

The amount of plastome sequence data available has soared in the last decade, but the nature of plastome evolution during rapid radiations is largely unknown. Moreover, although there is increasing evidence showing that plastomes may have undergone adaptive evolution in order to allow adaptation to various environments, few studies have systematically investigated the role of the plastome in alpine adaptation. To address these questions, we sequenced and analyzed 12 representative species of Rhodiola, a genus which includes ca. 70 perennial herbs growing in alpine habitats in the Qinghai-Tibet Plateau and the Hengduan Mountains. Rapid radiation in this genus was triggered by the uplift of the Qinghai-Tibet Plateau. We also included nine species of Crassulaceae as the outgroups. All plastomes were conserved with respect to size, structure, and gene content and order, with few variations: each contained 134 genes, including 85 protein-coding genes, 37 tRNAs, 8 rRNAs, and 4 potential pseudogenes. Three types of repeat sequence were detected. Slight contraction and expansion of the inverted repeats were also revealed. Both the genome-wide alignment and sequence polymorphism analyses showed that the inverted repeats and coding regions were more conserved than the single-copy regions and the non-coding regions. Positive selection analyses identified three genes containing sites of positive selection (rpl16, ndhA, ndhH), and one gene with a faster than average rate of evolution (psaA). The products of these genes may be involved in the adaptation of Rhodiola to alpine environments such as low CO2 concentration and high-intensity light.

Morphological adaptations between flowers and pollinators are thought to reflect natural selection by excluding ineffective pollinators and increasing pollination efficiency. Previous studies have reported a variety of tube or spur flower shapes that influence the functional fit between pollinator and plant. However, little is known about the â € open' flower types, which like those of Ranunuculus s.l. are interpreted as â € generalist flowers'. However, petals in Ranunuculus s.l. have nectary scales which vary in shape, and to determine whether their diversity reflects adaptation to different pollinator traits, we compared Ranunculus japonicus with flap-like nectary scales to Halerpestes ruthenica and Batrachium bungei with cup-like and ring-like nectary scales. Visitation rate, visit duration and pollinator efficiency of each group were compared to distinguish true pollinators from visitors. Regression analysis was also used to identify potential correlation between different petal nectary scale shapes and morphological traits of proboscides of pollinators. Our results reveal that flap-like nectary scales exclude hoverflies from accessing nectar and increase both the length of visits by small bees and pollen transfer efficiency. In contrast, cup- and ring-like nectary scales partially allowed nectar access to hoverflies. To our knowledge, this study demonstrates for the first time that pollinator mouthparts are the main driver of nectary shape rather than body and size.

Quaternary climatic oscillations have had tremendous effects on current distribution of species. Previous studies unraveled multiple microrefugia on the Qinghai-Tibetan Plateau (QTP) in two woody plants. Still we know little whether herbs growing in forests responded to climatic oscillations similarly. We herein conducted a phylogeographic study on Rhodiola sect. Trifida, an herbaceous group endemic to the QTP, which mainly growing on the forest floors, using plastid and ITS sequences as well as ecological niche modeling. The origin and divergence of major clades of sect. Trifida were in accordance with the last phase of the QTP uplifts. Mismatch distribution analysis indicated a range expansion dated to ca. 135 thousand years ago. A high frequency and an even distribution of private haplotypes in both plastid and ITS data sets throughout the distribution of sect. Trifida were detected. The ecological niche modeling results showed that there were suitable habitats on the QTP platform during the LGM. Our results found that multiple microrefugia existed on the QTP platform, supporting the hypothesis that species with similar geographic distribution and inhabiting the same community had similar responses to the Quaternary climatic oscillations. Furthermore, species delimitations in sect. Trifida need to be tested based on integrative evidence from morphological, ecological and genetic data.

Recently the genus Aquilegia is emerging as the new model system for plant development, ecology and evolution studies. Previous researches demonstrated that pollinator shift might drive the diversification of North American Aquilegia species and natural selection on the length of spur might play a crucial role. In this genus, A. ecalcarata is the only taxon which has lost spur and nectar on the petal. Previous phylogenetic result indicated that A. ecalcarata, A. yabeana, A. oxysepala var. kansuensis and A. rockii comprised a monophyletic group. However, the genetic diversity pattern of them remains unknown. Besides, little is known about the evolutionary relationship among the four species on population level. Here we carried out a population genetics study with 21 representative populations based on 10 single-copy nuclear gene fragments and found out: 1) A. yabeana conserved the highest genetic diversity (both πsil and θsil) while A. oxysepala var. kansuensis had the lowest level; 2) A. ecalcarata splitted into two groups with one population clustered with A. rockii and the rest five populations clustered with A. oxysepala var. kansuensis; 3) allele frequency spectrum showed an excess of low frequency alleles in all four species, implying that they may undergo the mutation-drift equilibrium. Our findings provide the first investigation of genetic diversity and evolutionary relationship in A. yabeana, A. oxysepala var. kansuensis, A. rockii, A. ecalcarata, and lay foundation for future evolutionary studies like speciation mediated by pollinators.