Adaptation of Arabidopsis thaliana to the Yangtze River basin

Yu-Pan Zou,Dunyan Tan,Ya-Long Guo,Ting-Shen Han,Li Yang,Jie Zhang,Qiong Wu,Zi-Wen Li,Xing-Hui Hou,Xiao-Min Niu,Jia-Fu Chen,Hongya Gu,Zhixi Tian,Yong-Chao Xu,Fu-Min Zhang

doi:10.1186/s13059-017-1378-9

Abstract

BackgroundOrganisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. However, how organisms adapt to climate changes is a crucial biological question that is still largely unanswered. The plant Arabidopsis thaliana is an excellent system to study this fundamental question. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different.ResultsWe sequenced 118 A. thaliana strains from the region surrounding the Yangtze River basin. We found that the Yangtze River basin population is a unique population and diverged about 61,409 years ago, with gene flows occurring at two different time points, followed by a population dispersion into the Yangtze River basin in the last few thousands of years. Positive selection analyses revealed that biological regulation processes, such as flowering time, immune and defense response processes could be correlated with the adaptation event. In particular, we found that the flowering time gene SVP has contributed to A. thaliana adaptation to the Yangtze River basin based on genetic mapping.ConclusionsA. thaliana adapted to the Yangtze River basin habitat by promoting the onset of flowering, a finding that sheds light on how a species can adapt to locales with very different climates.

Highlights

Organisms need to adapt to keep pace with a changing environment
To explore the relationship among samples, admixture analysis, phylogenetic analysis, and principal component analysis (PCA) were conducted. These analyses suggested that these 221 strains, with some intermediate strains, could be divided into three major groups, roughly consistent with their geographical origin (Fig. 1b–d)
Phylogenetic analyses using two close relatives, Arabidopsis lyrata and Capsella rubella, as outgroups suggested that the Iberian Peninsula and North Africa strains are located at the basal position of the phylogenetic tree and confirmed that they are relicts [7, 9] (Additional file 2: Figure S3)

Summary

Introduction

Organisms need to adapt to keep pace with a changing environment. Examining recent range expansion aids our understanding of how organisms evolve to overcome environmental constraints. How organisms adapt to climate changes is a crucial biological question that is still largely unanswered. Its origin is in the Iberian Peninsula and North Africa, but it has spread to the Far East, including the most south-eastern edge of its native habitats, the Yangtze River basin, where the climate is very different. Global climate change has a profound influence on human health, food security, and biological diversity as it greatly taxes the ability of organisms to adapt to new environments [1,2,3]. A fundamental biological question that has recently emerged concerns how best to resolve the mismatch between organisms and human-altered environments. We use the plant model species Arabidopsis thaliana to address this fundamental question in the context of its adaptation in natural environments. A. thaliana is a good model system to understand the mechanism of adaptation in natural environments at a global level [13, 16,17,18,19]

Methods

Results

Conclusion