Genomic Data Reveals Profound Genetic Structure and Multiple Glacial Refugia in Lonicera oblata (Caprifoliaceae), a Threatened Montane Shrub Endemic to North China.

Characterizing genetic diversity and structure and identifying conservation units are both crucial for the conservation and management of threatened species. The development of high-throughput sequencing technology provides exciting opportunities for conservation genetics. Here, we employed the powerful SuperGBS method to identify 33, 758 high-quality single-nucleotide polymorphisms (SNP) from 134 individuals of a critically endangered montane shrub endemic to North China, Lonicera oblata. A low level of genetic diversity and a high degree of genetic differentiation among populations were observed based on the SNP data. Both principal component and phylogenetic analyses detected seven clusters, which correspond exactly to the seven geographic populations. Under the optimal K = 7, Admixture suggested the combination of the two small and geographically neighboring populations in the Taihang Mountains, Dongling Mountains, and Lijiazhuang, while the division of the big population of Jiankou Great Wall in the Yan Mountains into two clusters. High population genetic diversity and a large number of private alleles were detected in the four large populations, while low diversity and non-private alleles were observed for the remaining three small populations, implying the importance of these large populations as conservation units in priority. Demographic history inference suggested two drastic contractions of population size events that occurred after the Middle Pleistocene Transition and the Last Glacial Maximum, respectively. Combining our previous ecological niche modeling results with the present genomic data, there was a possible presence of glacial refugia in the Taihang and Yan Mountains, North China. This study provides valuable data for the conservation and management of L. oblata and broadens the understanding of the high biodiversity in the Taihang and Yan Mountains.

Reproductive biology of an endangered lithophytic shrub and implications for its conservation.

BACKGROUND: Plants in cliff habitats may evolve specific reproductive strategies to cope with harsh environments, and unraveling these reproductive characteristics can improve our understanding of survival strategies and lithophyte evolution. This understanding is especially important for efforts to protect rare and endemic plants. Here, we investigated the reproductive biology of Lonicera oblata, an endangered lithophytic shrub that is scattered in highly fragmented and isolated cliff habitats of the Taihang and Yan mountains in North China. RESULTS: Flowers of L. oblata are herkogamous and protandrous, characteristics that can prevent autogamy at the single-flower level, and insects are necessary for pollination. The outcrossing index, pollen/ovule ratio, and the results of hand pollination were measured and all revealed a mixed mating system for L. oblata, that combines cross-fertilization and partial self-fertilization. The floral traits of L. oblata of zygomorphic and brightly yellowish corolla, heavy fragrance, and rich nectar, suggest an entomophilous pollination system. Sweat bees were observed as the most effective pollinators but their visiting frequencies were not high. Pollen limitation may limit the reproductive success of L. oblata. CONCLUSIONS: We determined the reproductive characteristics of L. oblata, a critically endangered species endemic to cliffs in North China, providing insight into its endangerment and suggesting conservation strategies. L. oblata has highly pollinator-dependent self-fertilization as part of a mixed mating system. Floral features such as low-flowering synchrony, asynchronous anthers dehiscence, and high duration of stigma receptivity, improve pollination efficiency in the case of low pollinator service. Our work provides reference information to understand the survival strategies and conservation of L. oblata and other lithophytes.

Plastid phylogenomics and biogeography of the medicinal plant lineage Hyoscyameae (Solanaceae).

The cosmopolitan family Solanaceae, which originated and first diversified in South America, is economically important. The tribe Hyoscyameae is one of the three clades in Solanaceae that occurs outside of the New World; Hyoscyameae genera are distributed mainly in Europe and Asia, and have centers of species diversity in the Qinghai-Tibet Plateau and adjacent regions. Although many phylogenetic studies have focused on Solanaceae, the phylogenetic relationships within the tribe Hyoscyameae and its biogeographic history remain obscure. In this study, we reconstructed the phylogeny of Hyoscyameae based on whole chloroplast genome data, and estimated lineage divergence times according to the newly reported fruit fossil from the Eocene Patagonia, Physalis infinemundi, the earliest known fossil of Solanaceae. We reconstructed a robust phylogeny of Hyoscyameae that reveals the berry fruit-type Atropa is sister to the six capsule-bearing genera (Hyoscyameae sensu stricto), Atropanthe is sister to the clade (Scopolia, Physochlaina, Przewalskia), and together they are sister to the robustly supported Anisodus-Hyoscyamus clade. The stem age of Hyoscyameae was inferred to be in the Eocene (47.11 Ma, 95% HPD: 36.75-57.86 Ma), and the crown ages of Hyoscyameae sensu stricto were estimated as the early Miocene (22.52 Ma, 95% HPD: 15.19-30.53 Ma), which shows a close correlation with the rapid uplift of the Qinghai-Tibet Plateau at the Paleogene/Neogene boundary. Our results provide insights into the phylogenetic relationships and the history of the biogeographic diversification of the tribe Hyoscyameae, as well as plant diversification on the Qinghai-Tibet Plateau.

The complete chloroplast genome of Physochlaina physaloides (Solanaceae), an important medicinal plant.

Physochlaina is an important perennial herbaceous genus with significant medicinal value, while the phylogeny of Physochlaina and tribe Hyoscyameae is not well resolved yet. In this study, we report the complete chloroplast genome sequences of Ph. physaloides, its complete chloroplast genome is 156,413 bp in length, which is a typical quadripartite structure that includes a large single-copy region of 86,659 bp, a small single-copy region of 18,012 bp, and its GC content was 37.7%. A total of 132 genes were identified, including 87 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Furthermore, a phylogenetic tree of the tribe Hyoscyameae was constructed based the complete chloroplast genome sequence, and a new topology of the tribe was obtained. This study provides valuable genetic information for the conservation and utilization of Ph. physaloides and also provide the potential for better understanding of the phylogeny of Hyoscyameae and Solanaceae.