Genome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot

Jiahui Chen ,Hang Sun,Mingming Shi ,Jun He,Yongping Yang ,Xudong Sun ,Guang-Yan Wang,Kaiyun Chen ,Richard J Abbott,Quanzheng Yun ,Wei Lü ,Ren-Gang Zhang,Benjamin Brachi,Z Zhou ,Hongna Li ,Yuan Huang,Wei Zhang,Yunheng Ji ,Weibang Sun ,Wenqing Li

doi:10.1038/s41467-019-13128-y

Abstract

The Hengduan Mountains (HDM) biodiversity hotspot exhibits exceptional alpine plant diversity. Here, we investigate factors driving intraspecific divergence within a HDM alpine species Salix brachista (Cushion willow), a common component of subnival assemblages. We produce a high-quality genome assembly for this species and characterize its genetic diversity, population structure and pattern of evolution by resequencing individuals collected across its distribution. We detect population divergence that has been shaped by a landscape of isolated sky island-like habitats displaying strong environmental heterogeneity across elevational gradients, combined with population size fluctuations that have occurred since approximately the late Miocene. These factors are likely important drivers of intraspecific divergence within Cushion willow and possibly other alpine plants with a similar distribution. Since intraspecific divergence is often the first step toward speciation, the same factors can be important contributors to the high alpine species diversity in the HDM.

Highlights

The Hengduan Mountains (HDM) biodiversity hotspot exhibits exceptional alpine plant diversity
Our results suggest that the species generally coped well with environmental changes caused by HDM uplift and the glacial-interglacial cycles that have occurred since the late Miocene, and that the HDM has been a long-term refugium for Cushion willow
Whole-genome resequencing-based population genetic analyses revealed that sky island populations of Cushion willow in the HDM located on high mountains isolated from others were genetically divergent and poorly connected by gene flow, despite occasional longdistance dispersal events

Summary

Introduction

The Hengduan Mountains (HDM) biodiversity hotspot exhibits exceptional alpine plant diversity. We detect population divergence that has been shaped by a landscape of isolated sky island-like habitats displaying strong environmental heterogeneity across elevational gradients, combined with population size fluctuations that have occurred since approximately the late Miocene These factors are likely important drivers of intraspecific divergence within Cushion willow and possibly other alpine plants with a similar distribution. Salix brachista Schneid is a typical alpine willow mainly distributed in the subnival zones of mountains in the HDM, and occasionally in neighboring areas (i.e., the eastern Himalaya and middle Yunnan Plateau), where it is a dominant component of many subnival assemblages It is a cushion plant (hereafter referred to as Cushion willow) with a creeping stem and lateral branches growing to a height of usually no more than 5 cm (Fig. 1a–d).

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Conclusion