Abstract
BackgroundAt the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as sanctuary for Tertiary relict trees. Yet the status of these regions as refuge areas with naturally existing populations has been proven not earlier than one decade ago. Herein we elaborated the hypothesis that during the Pleistocene cooling periods G. biloba expanded its distribution range in China repeatedly. Whole plastid genomes were sequenced, assembled and annotated, and sequence data was analyzed in a phylogenetic framework of the entire gymnosperms to establish a robust spatio-temporal framework for gymnosperms and in particular for G. biloba Pleistocene evolutionary history.ResultsUsing a phylogenetic approach, we identified that Ginkgoatae stem group age is about 325 million years, whereas crown group radiation of extant Ginkgo started not earlier than 390,000 years ago. During repeated warming phases, Gingko populations were separated and isolated by contraction of distribution range and retreated into mountainous regions serving as refuge for warm-temperate deciduous forests. Diversification and phylogenetic splits correlate with the onset of cooling phases when Ginkgo expanded its distribution range and gene pools merged.ConclusionsAnalysis of whole plastid genome sequence data representing the entire spatio-temporal genetic variation of wild extant Ginkgo populations revealed the deepest temporal footprint dating back to approximately 390,000 years ago. Present-day directional West-East admixture of genetic diversity is shown to be the result of pronounced effects of the last cooling period. Our evolutionary framework will serve as a conceptual roadmap for forthcoming genomic sequence data, which can then provide deep insights into the demographic history of Ginkgo.
Highlights
At the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as sanctuary for Tertiary relict trees
For few taxa from EBLF a reverse pattern has been reported with shrinkage of distribution during cooling phases such as during the LGM [21, 22] and postglacial range expansion [23]. To further enlighten these processes, we aimed to unravel a high-resolution temporal maternal evolutionary history of Ginkgo biloba considering our previous knowledge on distribution, refuge areas and demography
The number of missing base pairs was higher for samples with low coverage; most samples with coverage < 50× had uncovered bases, while few of those with coverage > 50× had missing data
Summary
At the end of the Pliocene and the beginning of Pleistocene glaciation and deglaciation cycles Ginkgo biloba went extinct all over the world, and only few populations remained in China in relict areas serving as sanctuary for Tertiary relict trees. During the early Permian, approximately 300 million years ago (mya), Ginkgoatae started to evolve into more than 16 different genera. There is excellent fossil record of Ginkgoatae (see [3, 4] for further references), and it is not surprising that this gymnosperm tree is among the enigmatic “living fossils” fascinating humans for hundreds of years [5]. 1000 to 3000 years old [6] These old Ginkgo trees are often close to human settlements and this is an indication that the tree has always been playing an important role in medicine, food, ornamentation and in culture and religion Since a first draft genome of Ginkgo biloba was published recently [9] more detailed evolutionary and functional studies may be conducted in the near future
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