Population Genetics And Speciation Of Juniperus Tibetica (Cupressaceae) Complex

One of the long-standing questions in evolutionary biology is to reveal the evolutionary forces shaping genetic variations acted on the natural populations and infer the mechanisms of species divergence between closely related species. Juniperus tibetica and its closely related species, J. convallium, J. saltuaria, and J. przewalskii are the endemic alpine juniper species of the Qinghai-Tibetan Plateau (QTP), and they are subordinate to Cupressaceae family, Juniperus genera, Sabina section. All the four species are characteristic of branch with both scaly and spiny leaf and the cone with only one seed, but the size of cone and the shape of the last branches differentiated between them. J. tibetica, J. convallium, and J. saltuaria have a sympatric or parapatric distribution along the southern part of the QTP and J. przewalskii is mainly occurred at the northeastern plateau. The four junipers constitute a representative species-complex of the modern geographic distribution of juniper on the QTP. This dissertation studied the nucleotide diversity and population genetic structure of the four species inferred from the multiple nuclear loci, and revealed the process of species divergence based on the Isolation-with-Migration (IM) analysis of divergence population genetics.A total of 13 nuclear loci were amplified and sequenced for 219 individuals (megagametophyte) of 53 populations through the entire distribution ranges of J. tibetica complex. Average value of nucleotide diversity across all 13 loci was low in the four species. Juniperus saltuaria had the highest diversity (θwsil= 0.0055,πsil= 0.0042). and J. convallium maintained the lowest (θwsil= 0.00420,πsil=0.00211). These juniper species have a high between-population differentiation based on the AMOVA analysis:J. convallium had the highest average value of FST(0.291), followed by J. przewalskii (0.266), and J. saltuaria had the lowest (0.173). The evolutionary history of species, selective pressures and complex topography of the QTP may have together led to the low level nucleotide variability and significant population genetic differentiation.J.przewalskii and J. convallium have maintained the relative stable population sizes since divergence from their common ancestral species based on the 1M analysis. We got no clear signs about population size of J. tibetica. However, J. saltuaria has the largest effective population size compared to the other three species and this species may have experienced population or range expansion in the past.STRUCTURE analysis revealed two clusters, one composed of the southern QTP species, J. tibetica, J. saltuaria, and J. convallium, and the other one J. przewalskii individuals in the northeastern QTP. Two possibilties may have contributed to the large amount of shared polymorphisms between species. One may be incomplete lineage sorting due to the recently species divergence and the other one the species divergence in the face of gene flow or the introgression after speciation which is supported by IM analysis. Molecular calibration revealved the latest divergence, between J. tibetica and J. convallium, maybe 0.716 Mya while the other species diverged 1.6-2.2 Mya. The Quaternary climatic oscillations and uplift of the QTP may have together drived the speciation or the introgression between juniper species. In summary, we proposed that incomplete lineage sorting and/or species divergence in the face of gene flow have resulted in the shared polymorphisms among the J. tibetica complex.