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

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.

The Tetracentron genome provides insight into the early evolution of eudicots and the formation of vessel elements

“…Hence, our results suggested that in addition to the Southwestern China refuge [31], there were three refugia in central China: one in the Sichuan Basin corresponding to the area covered by the Jinfo and Emei Mountains, one in the east part including the Shennong Mountains, and one in the Qinling Mountains. These areas have long been regarded as important global Pleistocene glacial refugia and the areas around the Sichuan Basin of central China and the Shennong Mountains in the east of central China were also likely refugia for many other relict tree species such as Cathaya, Cercidiphyllum, Ginkgo, and Taxus [68][69][70].…”

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

“…As shown by a recent study in G . biloba (Zhao et al ., 2019), the advance of whole‐genome sequencing technologies has dramatically increased our ability to understand the joint effects of demography and selection on the genetic polymorphisms of a Tertiary relict tree. By taking advantage of Ginkgo 's reference genome, these authors inferred multiple population declines but also recoveries of the species in China over late Tertiary/Quaternary timescales.…”

“…climate) and biotic (e.g. pathogen defence) stresses (Zhao et al ., 2019). Together, these results suggest that both demographic history and natural selection contributed to the species' long‐term persistence and resilience.…”

Number and distribution of large old ginkgos in east China: Implications for regional conservation

“…Both ecological and molecular evidence indicate that Tianmu Mountains, Zhejiang Province, hold wild populations of ginkgos (Tredici et al 1992;Li et al 2011). Zhao et al (2019) identified three refugia in China by re-sequencing Ginkgo genomes across the world and pointed out that anthropogenic introductions resulted in the spread of ginkgos from eastern China to other countries. A multi-feature analysis of ginkgo vascular cambial cells found that old ginkgos include a high expression of disease resistance-related genes, which may lead to its longevity (Wang et al 2020).…”