Gene duplication plays an important role in plants for diversification and adaptation to new habitats. In this study, we aim to reconstruct the genome‐scale phylogeny and identify large‐scale gene duplication events for the subtribe Gentianinae (Gentianaceae), which is a great symbol of the alpine plants in the Qinghai–Tibet Plateau. We sequenced and assembled 70 transcriptomes from 67 species, representing all six recognized genera in the subtribe Gentianinae plus the closely related outgroups. Using phylogenomic approaches, the backbone relationships of Gentianinae were almost fully resolved with high bootstrap support. Although instances of conflicts were observed between nuclear and plastid phylogenies, six major clades of Gentianinae were consistently recovered in both phylogenies. In addition, we revealed a high occurrence of duplicated genes in our transcriptome assemblies. Using several gene tree reconciliation methods, we collectively identified 10 nodes in the species tree with large concentrations of duplicated genes. Further analysis indicated that many of these duplicated genes likely arose from hybrid polyploidy, which might also account for some of the topological incongruences between nuclear and plastid phylogenies in Gentianinae.

Davidia involucrata Baill, also known as the dove‐tree, is a living fossil and an endangered species currently restricted to the mountains of southwestern and central China. It has a beautiful and innovative trait of high horticultural value: two white bracts covering the flower caputila. Here, we report on the chromosome‐scale genome of this species using single‐molecule real‐time long reads and chromosome conformation capture (Hi‐C) techniques. This species has a larger genome size of 1,169 Mb and contains relatively more genes (42,554) than the closely related species Camptotheca acuminata (397 Mb and 31,825 genes). Both species shared one recent whole genome duplication before their divergence. The expansion of the repetitive elements after their divergence contributed greatly to the increase in the genome size of the dove‐tree. Photosynthesis‐related genes were almost absent or showed reduced expression in the bracts of the dove‐tree, while defence‐ and chemical‐related genes increased greatly, highlighting the important roles of the bracts in protecting flowers and attracting pollinators. The effective population size of the dove‐tree continuously decreased during the climate changes of the Quaternary. Such climate sensitivity should be fully considered in conservation efforts for this relict endangered species in the context of continuous climate warming in the future.

The dynamics of populations and their divergence over time have shaped current levels of biodiversity and in the case of the “sky islands” of mountainous southwest (SW) China have resulted in an area of exceptional botanical diversity. Ficus tikoua is a prostrate fig tree subendemic to the area that displays unique intraspecific diversity, producing figs typical of different pollination modes in different parts of its range. By combining climate models, genetic variation in populations of the tree's obligate fig wasp pollinators and distributions of the different plant phenotypes, we examined how this unusual situation may have developed. We identified three genetically distinct groups of a single Ceratosolen pollinator species that have largely parapatric distributions. The complex topography of the region contributed to genetic divergence among the pollinators by facilitating geographical isolation and providing refugia. Migration along elevations in response to climate oscillations further enhanced genetic differentiation of the three pollinator groups. Their distributions loosely correspond to the distributions of the functionally significant morphological differences in the male figs of their host plants, but postglacial expansion of one group has not been matched by spread of its associated plant phenotype, possibly due to a major river barrier. The results highlight how interplay between the complex topography of the “sky island” complex and climate change has shaped intraspecies differentiation and relationships between the plant and its pollinator. Similar processes may explain the exceptional botanical diversity of SW China.

Most plants are pollinated passively, but active pollination has evolved among insects that depend on ovule fertilization for larval development. Anther‐to‐ovule ratios (A/O ratios, a coarse indicator of pollen‐to‐ovule ratios) are strong indicators of pollination mode in fig trees and are consistent within most species. However, unusually high values and high variation of A/O ratios (0.096–10.0) were detected among male plants from 41 natural populations of Ficus tikoua in China. Higher proportions of male (staminate) flowers were associated with a change in their distribution within the figs, from circum‐ostiolar to scattered. Plants bearing figs with ostiolar or scattered male flowers were geographically separated, with scattered male flowers found mainly on the Yungui Plateau in the southwest of our sample area. The A/O ratios of most F. tikoua figs were indicative of passive pollination, but its Ceratosolen fig wasp pollinator actively loads pollen into its pollen pockets. Additional pollen was also carried on their body surface and pollinators emerging from scattered‐flower figs had more surface pollen. Large amounts of pollen grains on the insects' body surface are usually indicative of a passive pollinator. This is the first recorded case of an actively pollinated Ficus species producing large amounts of pollen. Overall high A/O ratios, particularly in some populations, in combination with actively pollinating pollinators, may reflect a response by the plant to insufficient quantities of pollen transported in the wasps’ pollen pockets, together with geographic variation in this pollen limitation. This suggests an unstable scenario that could lead to eventual loss of wasp active pollination behavior.

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