Center for Organismal Studies (COS) Heidelberg/Botanic Garden and Herbarium Heidelberg (HEID), University of Heidelberg, Im Neuenheimer Feld 345, D-69120, Heidelberg, Germany.
Present address: Department of Environmental Sciences, Botany, University of Basel, Schönbeinstrasse 6, CH-4056, Basel, Switzerland.
BMC Genomics. 2018 Apr 27;19(1):299. doi: 10.1186/s12864-018-4673-2.
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. 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.
Using 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.
Analysis 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.
在上新世末和更新世冰期和冰消期循环结束时，银杏在全球灭绝，仅在中国的遗留地区保留了少数种群，作为第三纪遗留树木的避难所。然而，这些地区作为自然存在种群的避难所的地位直到十年前才得到证实。本文阐述了这样一种假设，即在更新世冷却期间，银杏在中国反复扩大其分布范围。我们对整个质体基因组进行了测序、组装和注释，并在整个裸子植物的系统发育框架中对序列数据进行了分析，为裸子植物，特别是银杏的更新世进化历史建立了一个稳健的时空框架。
利用系统发育方法，我们确定银杏类植物的祖系年龄约为 3.25 亿年，而现存银杏的冠群辐射始于 39 万年前。在反复的变暖阶段，银杏种群因分布范围收缩而被分离和隔离，并退缩到山区，作为温带落叶林的避难所。多样化和系统发育分支与冷却阶段的开始相关，此时银杏扩大了其分布范围，基因库融合。
分析代表野生现存银杏种群整个时空遗传变异的整个质体基因组序列数据，揭示了可追溯到大约 39 万年前的最深时间足迹。目前，西向东的遗传多样性定向混合是最后一个冷却期显著影响的结果。我们的进化框架将作为未来基因组序列数据的概念路线图，为银杏的人口历史提供深入的见解。
