Resequencing 545 ginkgo genomes across the world reveals the evolutionary history of the living fossil

Yunpeng Zhao ,Jian Wang,Ya-Jun Hao,Simon Ming‐Yuen Lee ,Wenjie Xia,Huanming Yang,Xun Xu,Jiang Chen,Ning Li,Jing-Dan Han,Xiaoning Hong,Xin Liu,Xianwei Yang,Qiwu Xu,Rui Zhang,Dong Kun Lee ,He Zhang,Fu‐Min Zhang ,Shuai Sun,Guangyi Fan,Hanyang Lin ,Yin Pingping ,Chengxin Fu ,K Uehara ,Wenbin Chen,Gang Hu,Xiujue Zheng ,Song Ge

doi:10.1038/s41467-019-12133-5

Abstract

As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Ginkgo (Ginkgo biloba L.) is one of the oldest living plants and a fascinating example of how people have saved a species from extinction and assisted its resurgence. By resequencing 545 genomes of ginkgo trees sampled from 51 populations across the world, we identify three refugia in China and detect multiple cycles of population expansion and reduction along with glacial admixture between relict populations in the southwestern and southern refugia. We demonstrate multiple anthropogenic introductions of ginkgo from eastern China into different continents. Further analyses reveal bioclimatic variables that have affected the geographic distribution of ginkgo and the role of natural selection in ginkgo’s adaptation and resilience. These investigations provide insights into the evolutionary history of ginkgo trees and valuable genomic resources for further addressing various questions involving living fossil species.

Highlights

As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation
Many investigations on the evolutionary history of this mysterious tree have been undertaken, numerous uncertainties and controversies remain, including the identification of relict populations and potential refugia[4,9,10,11], population dynamics in response to Pleistocene climate change[9,12,13], the roles that humans have played in the dispersal of ginkgo trees in China[6,13,14,15] and when and how ginkgo trees were introduced to Japan/Korea, Europe, and North America[4,5,6] as well as the potential factors contributing to the persistence and resilience of the species[1,5,16]
We found that ginkgo populations underwent several cycles of expansion and contraction during the Pleistocene glaciations and revealed a moderate reduction in ginkgo populations in refugia associated with admixture of relict populations in northern and central China

Summary

Introduction

As Charles Darwin anticipated, living fossils provide excellent opportunities to study evolutionary questions related to extinction, competition, and adaptation. Many investigations on the evolutionary history of this mysterious tree have been undertaken, numerous uncertainties and controversies remain, including the identification of relict populations and potential refugia[4,9,10,11], population dynamics in response to Pleistocene climate change[9,12,13], the roles that humans have played in the dispersal of ginkgo trees in China[6,13,14,15] and when and how ginkgo trees were introduced to Japan/Korea, Europe, and North America[4,5,6] as well as the potential factors contributing to the persistence and resilience of the species[1,5,16] Exploration of these questions has been impeded by difficulties in obtaining sufficient samples that represent the entire gene pool of this living fossil and the limited genetic markers available for such an isolated gymnosperm species. These investigations lay an important foundation for further studies of the potential mechanism of ginkgo’s survival and resilience

Methods

Results

Conclusion