Ancient introgression drives adaptation to cooler and drier mountain habitats in a cypress species complex

Yazhen Ma,Kangshan Mao,Yongshuai Sun,Jialiang Li,Lei Zhang,Jianquan Liu,Richard J Abbott,Ji Wang,Quanjun Hu

doi:10.1038/s42003-019-0445-z

Abstract

Introgression may act as an important source of new genetic variation to facilitate the adaptation of organisms to new environments, yet how introgression might enable tree species to adapt to higher latitudes and elevations remains unclear. Applying whole-transcriptome sequencing and population genetic analyses, we present an example of ancient introgression from a cypress species (Cupressus gigantea) that occurs at higher latitude and elevation on the Qinghai-Tibet Plateau into a related species (C. duclouxiana), which has likely aided the latter species to extend its range by colonizing cooler and drier mountain habitats during postglacial periods. We show that 16 introgressed candidate adaptive loci could have played pivotal roles in response to diverse stresses experienced in a high-elevation environment. Our findings provide new insights into the evolutionary history of Qinghai-Tibet Plateau plants and the importance of introgression in the adaptation of species to climate change.

Highlights

Introgression may act as an important source of new genetic variation to facilitate the adaptation of organisms to new environments, yet how introgression might enable tree species to adapt to higher latitudes and elevations remains unclear
We analysed RNA-sequences from leaf samples representing both Cupressus species to address the following questions: What is the genetic affinity of northern to southern populations of C. duclouxiana and to populations of C. gigantea? What is the level and direction of gene flow between the different genetic groups detected? What role might adaptive introgression have played in shaping the distribution pattern of genetic variation in this complex, enabling C. duclouxiana to grow over a wide range of elevations? Our results suggest that both C. duclouxiana and C. gigantea are monophyletic; genetic introgression from C. gigantea to northern C. duclouxiana is supported by multiple lines of evidence
After aligning transcriptome reads from all individuals to the reference transcriptome and undertaking stringent quality filtering, we identified a total of 878,614 single nucleotide polymorphisms (SNPs) across all 65 individuals of C. duclouxiana and C. gigantea examined

Summary

Introduction

Introgression may act as an important source of new genetic variation to facilitate the adaptation of organisms to new environments, yet how introgression might enable tree species to adapt to higher latitudes and elevations remains unclear. Dogs, cattle, sunflowers, poplars, and oaks suggest that introgression from other species can be a very important source of new genetic variation in the adaptation of species to new environments[7,8,9,10,11,12]. A major challenge to detecting introgression between species with long generation times and large effective population sizes, such as trees, is to distinguish between the causes of shared polymorphisms due to incomplete lineage sorting or introgression[24,25] Notwithstanding this difficulty, a growing number of studies have shown that introgression occurs in at least some tree genera Populations of C. duclouxiana in the northern and southern parts of its range are genetically divergent, forming two separate groups based on microsatellite variation[44]

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Conclusion