Local Adaptation To Climate In Pinus Densata Complex

Global climate change has been challenging the world. Animals can adopt migration and climatic adaptation while plants mainly depend on local adaptation to face climate change. Coniferous species have experienced past climate oscillations since the Carboniferous Period (360-286million years ago, MYA). During this time, they have adapted to different climatic conditions and have given rise to new species while undergoing many demographic events, such as range and population size expansions, bottlenecks and variable gene flow. Conifers is therefore becoming a great study system for investigating how plants adapt to climate change. Moreover, conifers play a dominant role in global carbon fixation. Investigations of climatic adaptation in conifers have its potential to shed light on how people will act on future global warming.I used Pinus densata from the Qinghai-Tibetan Plateau (QTP) and its potential parental species Pinus tabulaeformis and Pinus yunnanensis as a system to detect molecular signals of climatic adaptation in the species complex. Previuos investigations suggested that P. densata might be a result of homoploid hybrid speciation between P. tabulaeformis and P. yunnanensis, using cytoplasmic and nuclear genetic varaiton. However, reproductive barriers between the species are still incomplete. As the species are distributed in parapatry, lineage sorting in the speciation continuum is complicated by introgression. The processes of speciation in P. densata complex might be more complicated than what previously known. The species have adapted to different environmental conditions by divergent selection shaping underlying genes. The genomic islands under local selection can extend gradually to the whole genome by linkage disequilibrium. This process is also in line with ecological speciation. Anyway, there is another interesting question about how P. densata can have better fitness than its parental species and can adapt to the drought and cold enviromental conditions at the QTP. Physiological and ecological studies have suggested that P. densata had better fitness for drought stress and clod tolerance at some pysiological traits than its parental species, but by far the genetic basis of the possible hybrid vigor is poorly known. Both recent local selection and ancient balancing selection contribute to climatic adaptation. In model organisms, climatic adaptation have been studied using population genetic analyses on genome-wide data sets, which suggested that recent local selection played a major role. However, as conifers have a rich experience of past climate change, ancient balancing selection might also favored climate change adaptation in the species, but previous studies have been mainly focused on detecting molecular footprints of recent selection. Local selection for adaption use either new mutations or alleles from standing genetic variation, It is hard to distinguish between the two when the investigation is only based on single species. However, in the P. densata complex, we can detect whether the adaptive allele is presented in its parental species (standing genetic variation) or only specific in P. densata (new mutation). Heterosis or hybrid vigor might explain P. densata adapting to the drought and cold enviroments in the QTP, interactions between the alleles or gene regulations from both parental species may enable the species to harbor better fitness compared to its parental species.We sampled68natural populations across the ranges of the three species,10-15individual for each population. We sequenced all the individuals using four cp and two mt gene fragments. We also sequenced25climate-related candidate genes and12reference loci for27populations chosen across the species’ranges. Using population genetic, landscape genetic and biogeographic approaches, we detected signals of ancient at the lineages of the species and the outgroup belonging to strobus, and recent selection within species especially for marginal populations. We then compared patterns of intra-and interspecific distribution of cp, mt, neutral nuclear and adaptive nuclear genetic variation to distinguish selection on new mutations and standing genetic variation, and to detect possible adaptive introgression, as well as to investigate the roles of cp and mt gene flow in adaptive evolution.Our results showed that1) both recent local selection and ancient balancing selection contribute to climatic adaptation in the species;2) climate-related candidate genes, such as agp4, aqua-MIP, dhn7, dhn9and lp3-1were found to be under recent positive selection in P. densata;3) recent differential selection but ancient shared selection signals were detected because of the shared evolutionary history between the species;4) in line with conditional neutrality, different sets of SNPs were detect under local selection at the southern and northern marginal populations in P. tabulaeformis; 5) both new mutations and standing genetic variation have contributed to local climatic adaptation in P. densata;6) adaptive introgression or benificial ancestral polymorphisms from both parental species favors climatic adaptation of P. densata to the QTP;7) co-specific populations have been linked by cp gene flow which might have also transferred adaptive alleles across populations. Shared alleles for climatic adaption between the species might have been caused by mt gene flow or incomplete lineage sorting.The results in this thesis are valuable for understanding evolution in general, especially for forest genetics. The results can also be used for other applied purposes such as tree breeding and climate change adaptation.