Title: Genomic insights on the contribution of balancing selection and local adaptation to the long-term survival of a widespread living fossil tree, Cercidiphyllum japonicum

Shanshan Zhu, Jun Chen, Jing Zhao, Hans Peter Comes, Pan Li, Chengxin Fu, Xiao Xie, Ruisen  Lu, Wuqin  Xu, Yu  Feng, Wenqing  Ye, Shota  Sakaguchi, Yuji  Isagi, Linfeng  Li, Martin Lascoux, Yingxiong Qiu

First published: 09 July 2020

Summary

‘Living fossils’ are testimonies of long‐term sustained ecological success, but how demographic history and natural selection contributed to their survival, resilience and persistence in the face of Quaternary climate fluctuations remains unclear.

To better understand the interplay between demographic history and selection in shaping genomic diversity and evolution of such organisms, we assembled the whole genome of Cercidiphyllum japonicum , a widespread East Asian Tertiary relict tree, and re‐sequenced 99 individuals of C. japonicum and its sister species, C. magnificum (Central Japan).

We dated this speciation event to the mid‐Miocene, and the intraspecific lineage divergence of C. japonicum (China vs. Japan) to the Early Pliocene. Throughout climatic upheavals of the Late Tertiary/Quaternary, population bottlenecks greatly reduced the genetic diversity of C. japonicum. However, this polymorphism loss was likely counteracted by (1) long‐term balancing selection at multiple chromosomal and heterozygous gene regions, potentially reflecting overdominance; and (2) selective sweeps at stress response and growth‐related genes likely involved in local adaptation.

Our findings contribute to a better understanding of how living fossils have survived climatic upheaval and maintained an extensive geographic range, i.e. both types of selection could be major factors contributing to the species’ survival, resilience and persistence.

Link: https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.16798