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Understanding processes that generate and maintain large disjunctions within plant species can provide valuable insights into plant diversity and speciation. The butterfly bush Buddleja alternifolia has an unusual disjunct distribution, occurring in the Himalaya, Hengduan Mountains (HDM) and the Loess Plateau (LP) in China. We generated a high-quality, chromosome-level genome assembly of B. alternifolia, the first within the family Scrophulariaceae. Whole-genome re-sequencing data from 48 populations plus morphological and petal colour reflectance data covering its full distribution range were collected. Three distinct genetic lineages of B. alternifolia were uncovered, corresponding to Himalayan, HDM and LP populations, with the last also differentiated morphologically and phenologically, indicating occurrence of allopatric speciation likely to be facilitated by geographic isolation and divergent adaptation to distinct ecological niches. Moreover, speciation with gene flow between populations from either side of a mountain barrier could be under way within LP. The current disjunctions within B. alternifolia might result from vicariance of a once widespread distribution, followed by several past contraction and expansion events, possibly linked to climate fluctuations promoted by the Kunlun-Yellow river tectonic movement. Several adaptive genes are likely to be either uniformly or diversely selected among regions, providing a footprint of local adaptations. These findings provide new insights into plant biogeography, adaptation and different processes of allopatric speciation.

Buddleja alternifolia is China’s specialty, and scattered in northwest China. Here, we assembled and characterized the complete chloroplast (cp) genome of B. alternifolia using Illumina sequencing data for the first time. The complete cp genome was 154,280 bp in length, consisting of a pair of inverted repeats of 25,440 bp, a large single-copy (LSC) region of 85,330 bp, and a small single-copy (SSC) region of 18,070 bp. The genome encoded 115 unique genes, including 80 protein-coding genes, 31 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 16 complete cp genome sequences indicated that B. alternifolia is closely related to Buddleja colvilei.

Hierarchical clustering method was applied for division of stages of old-field succession of loess area of Northern Shaanxi, and the similarity among different communities in abandoned field of different abandoned year and site condition can be learnt quantitatively, and stages or sequence of old-filed succession can be determined. The result revealed that the stages of old-field succession are: polydominant association of annual weed artemisia scoparia and other perennial herbage→Lespedeza davurica and perennial herbage association→artemisia vestita and perennial herbage association→tuft grass bothriochloa ischaemum and perennial herbage association→undershrub Buddleja alternifolia association. Among them, the appearance of shrub association (undershrub Buddleja alternifolia) contrasts results in former studies that it was impossible to form shrub association in loess area of Northern Shaanxi. Thus, this study is not only a complement of former studies, but also a new discovery and innovation.