Genetic Structure And Evolutionary History Of Chinese Oak Species In Quercus Section Cerris

Quercus acutissima Carruth.,Q.chenii Nakai,and Q.variabilis Bl.constitute the East Asian clade of Quercus section Cerris.These three closely related oak species have an overlapping distribution,with Q.acutissima and Q.variabilis widely distributed in the East Asian warm-temperate deciduous forests,and Q.chenii narrowly confined to the East China flora.The early Neogene fossils of section Cerris in northern and southwestern China implies that these three species may have experienced a long and complicated evolutionary history underlying the pre-Quaternary geological and climate dynamics.Varieties characterized by intermediate morphology among those suggest that hybrids may have occurred in the overlapping region.Thus,Q.acutissima,Q.chenii,and Q.variabilis may provide a useful model to investigate the impacts of palaeoenvironmental changes since the Miocene on multiple evolutionary processes,such as speciation,introgression,lineage diversification and range dynamics for plants in East Asia.Furthermore,these three oak species are main forest species used in afforestation in China,which are traditionally planted for producing timber,fuelwood,and hardwood logs for shiitake cultivation.Previous studies have described the genetic variation of these three species in China,South Korea,and Japan.However,the information on the genetic structure and evolutionary history was limited by small sample size and a narrow sampling range.Thus,more genetic investigations at a much larger geographic scale are expected to provide better guidance for germplasm resource management of those oaks in China.In this thesis,we used both nuclear microsatellite(nSSR)markers and chloroplast(cp)DNA sequences to evaluate the genetic variation of Q.acutissima,Q.chenii,and Q.variabilis.Multiple methods of phylogeography,population genetics,landscape genetics,phylogenetics,and ecological modeling were combined to evaluate how topography and climate have interacted over time and space to influence the genetic structure and evolutionary history of the three species.The main conclusions are as follows:(1)Q.acutissima exhibits a significant east-west divergence along the boundary separating the mountainous West China and the lowland East China.Western populations of the species present much stronger differentiation and lower genetic diversity than eastern populations.The divergence between the groups of Southwest China and East China was estimated to have occurred 3.55–2.37 million years ago(Ma),closely associated with the recent uplift of the Qinghai-Tibetan Plateau(QTP)and climate changes during the late Pliocene to the early Pleistocene.The Central China group may arise from the admixture of these two groups,which was dated to 0.83–0.55 Ma,a period covering several interglacial intervals with unusually warm and wet climate in Central China.(2)The genetic structure of Q.chenii was strongly influenced by both topography and climatic heterogeneity in East China.Multiple intraspecific genetic boundaries were identified well associated with persistent landscape barriers(e.g.,the Tianmu Mountain,the Dabie Mountain,and the Mufu Mountain)of East China.Lowland populations present a higher level of genetic diversity and genetic admixture,while a lower level of genetic differentiation than highland populations.Environmental differences along elevation and temperature gradients strengthen the divergence between highlands and lowlands.By contrast,post-glacial range shifts along plains and basins may have increased the genetic connectivity among lowland populations via admixture.(3)Q.acutissima and Q.chenii can be delimited by nSSR markers.Speciation between the two species was estimated to have occurred during the early Miocene,together with the onset or intensification of East Asian monsoons.During this period,subtropical aridity disappeared and humidification increased in southern China.Divergent climatic conditions may have promoted speciation via climatic niche divergence.Global climatic cooling after the Middle Miocene Climatic Optimum and phased enhancement of East Asian monsoon intensity may also have triggered the lineage diversification of the chloroplast haplotypes.(4)Introgression between Q.acutissima and Q.chenii was supported by evidence of both nSSR makers and cpDNA sequences.More than 80% of the hybrids inferred from nSSR makers and more than 90% of the individuals with regionally shared haplotypes were concentrated in a putative introgression zone along the northern distribution edge of Q.chenii.The two species may have experienced historical introgression during glacial-interglacial cycles of the Pleistocene.Both long-term coexistence or secondary contact may explain the origin of putative hybrids.(5)Extensive sharing of chloroplast haplotypes occurs among Q.acutissima,Q.chenii,and Q.variabilis.A much lower level of interspecific differentiation at the chloroplast genome was detected than at the nuclear genome.Incomplete lineage sorting may explain the occurrence of shared haplotypes that occupied the interior position in the network and exhibited a random geographic distribution,while interspecific introgression may better explain the occurrence of shared haplotypes that located at the tips of the network and presented a regional distribution.Most regionally shared haplotypes were concentrated in the western Yunnan Province,the Liaoning-Shandong Peninsula,and the mountainous areas of Central China.Long-term coexistence in shared refugia and secondary contact triggered by climatic fluctuations may result in the cpDNA introgression among these three oak species.