Phylogeography Of Quercus Franchetii Complex

The Oligocene and Miocene are key periods on the formation of the topography and flora in Southwest China.However,it is still not clear that how geological and climatic factors,especially during the late Paleogene,contributed to the high endemism and species richness in this region.Quercus franchetii complex belongs to Quercus section Ilex(Fagaceae),which is early derived lineage in Quercus section Ilex.The species complex contains four species(Quercus franchetii,Quercus lanata,Quercus leucotricophora,Quercus lodicosa)that is widespread in the SE Himalaya fringe and northern Indo-China with a long evolutionary history.The fossils close related to the complex were widely reported along the Tethys seaway form East Asia to Europe during late Paleogene to Neogene.Therefore,this species complex provides a unique proxy to investigate key factors that boost the high species diversity of evergreen woody lineages and the distribution dynamics of these woody lineages since the Oligocene.In this study,we optimized the protocols to extract the genomic DNA on Fagaceae plants.By integrating geometric morphometric analysis,spatial genetic diversity pattern,and niche simulation methods to analyze the impact of environmental changes in this region on the spatial genetic structure of Quercus franchetii complex.The main research results are as follows:(1)Geometrical morphometric study of Q.franchetii complex groupWe employed genomic morphometric methods to investigate the morphological variation of Q.franchetii complex.We obtained leave image of 878 leaves of 316 individuals of Q.franchetii complex,based on landmarks,we performed Principal component analysis(PCA),discriminant analysis(DA),canonical variable analysis(CVA)and 2B PLS analysis.Our results showed that Q.leucotricophora and Q.lodicosa show little variation on their morphology,but the systematic status of the two species needs further investigation,as very limited samples in this study.(2)Study on population genetics of Q.franchetii complex populationIn this study,we used three chloroplast(cp DNA)sequences and eight nuclear microsatellite loci(n SSRs)to investigate the spatial genetic structure of 33 populations of Q.franchetii complex.Based on comprehensive specimen identification and field collections,145 reliable distribution records and 9 bioclimatic variables were collected to simulate species distribution pattern.The results showed that in a total 33 chloroplast haplotypes were detected based on the combined analysis of the three chloroplast fragments.The genetic diversity among populations was 87%,with significance genetic differentiation among populations.The phylogenetic analysis on cp DNA haplotypes indicated the existence of four lineages corresponding to the geographical distribution ranges.The Nanpan River(NPR)group was firstly derived in the middle Oligocene,followed by the southwestern Lancangjiang group in the late Oligocene,and then the northern Hengduan Mountains(HDM)group and central Yunnan-Guizhou plateau(YGP)group in the early Miocene.The ancestral distribution range reconstruction showed that the Q.franchetii complex was widely distributed in the southern Tibet,the southwest China and the northern Indo-China during Oligocene.The current distribution pattern was established by three disjunction events during the Oligocene to Early Miocene.This divergence pattern might be the outcome of the early capture of the ancient Red River during the Oligocene,as well as the slipping of the Red River fault zone and the uplifts of YGP and HDM during the late Neogene.The geological events restricted seed-mediated gene flow in these geographical regions.Based on n SSR analysis,the genetic variation among the populations was37%,and most of the genetic diversity existed within the populations.The STRUCTURE results revealed two major groups in the populations: the central YGP group and the peripheral distribution group.Neutral detection indicated that the population size of Q.franchetii complex was stable,and there might be obvious biogeographic barrier in the southwest Yunnan.(3)Niche simulation of Q.franchetii complexThe distribution of Q.franchetii complex in the last Glacial Maximum(LGM)largely overlaps with that in the modern era and expanded northwards after LGM.The core YGP groups have exhibited long-term stability.However,the southwest and southeast groups are located in middle-to-low suitability areas under all CO2 emission scenarios,indicating their vulnerability to future climate change.The potential dispersal routes of the Q.franchetii complex in LGM and present periods showed that the northern population had little contact with the core population.Therefore,in situ conservation of the NPR populations and ex situ conservation of the semi-humid evergreen forests in the eastern and southern parts of the YGP should be enforced.This study provides important clues on the early diversification pattern of evergreen broad-leaved forests in SW China and provides important guideline for future forestry conservation in YGP and adjacent regions.