Evolutionary genetics of adaptation in Tasmanian blue gum

Abstract

© 2016 Dr. Hossein Valipour KahroodObjectives The main aim of this thesis was to understand the role of Darwinian positive selection in Eucalyptus evolution and provide persuasive indications of adaptive evolution for forest trees. Background The species-rich genus Eucalyptus L’Héritier De Brutelle (Eucalyptus) forms the dominant canopy species of the Australian landscape and plays an essential role in diverse ecological aspects of its ecosystems including micro and macroclimates, biodiversity, fire spread, and water resources. Species of this genus for their outstanding growth and wood quality constitute the majority of Australian hardwood plantations and are among the major commercial plantation hardwoods in tropical and temperate regions of the world. Understanding evolutionary processes contributing genetic variation of Eucalyptus would aid in deriving more sustainable management strategies of conservation biology and forest tree breeding in Australia and worldwide. In conservation genetics it can help inform public policy directed at the conservation and the short- and long-term adaptability of the species. In breeding programs using association or genomic selection methods, identification of elite trees is influenced by demographic and selective histories of the species. Approach and results The wealth of nucleotide diversity in Eucalyptus, existence of numerous repetitive features of its DNA sequences coupled with the lack of a sophisticated NGS data pipeline at the time hindered obtaining good-quality, long stretch nuclear DNA. This thesis used a significant number of entire chloroplast genomes carrying both divergence and diversity information. In the first study, a phylogeny-based analysis was applied to measure rates of evolution and detect molecular signatures of positive selection of 85 plastid-encoded orthologous genes from 39 Myrtaceae species (interspecific set). Amino acid residues of several genes showed rate acceleration consistent with strong directional selection. The Eucalyptus clade showed elevated substitution rates when compared to its sister Corymbia+Angophora clade, indicating the role of natural selection in adaptation, radiation and/or speciation of the Eucalyptus species when inhabiting new environments. In the second study, a similar analysis was carried out on the same set of genes in 136 individuals from seven populations of Eucalyptus globulus Labill. ssp globulus (E. globulus) to pinpoint its genetic variation in an intraspecific approach. Tasmanian blue gum was used since the species is widely distributed across elevation and annual rainfall classes between southern Victoria and south of Tasmania, encouraging speculation about potential variation. In this study, a smaller number of genes (intraspecific set) were identified as showing similar signature consistent with those identified in the previous study. These included accD, ccsA, matK, ndhD, ndhF, ndhH, rbcL and ycf1, and within those five sites including ndhD-454, ndhF-230, matK-252, rbcL-142 and rbcL-251 were shared between the two datasets. The dataset in this study also enabled for the first time analysis of the phylogeography of E. globulus ssp. globulus as well as studying demographic history of the species using the whole cp genomes. Two distinct origins of E. globulus were confirmed with one lineage being differentiated in mainland Australia and the other one in Tasmania. These two major lineages diverged approximately 5 7 Ma with the second split between the western and eastern mainland sub-lineages taking place around 2 2.5 Ma. The split times of these lineages and sub-lineages coincided with major cooling and/or drying periods in the distant past. It was also shown that the above lineages had expanded their territory from the Mid-Pleistocene onwards, and thus genetic drift has principally affected Eucalyptus genetic variation, in comparison to which natural selection appears to have had local influence. In the last section of this thesis, it is hypothesised that sites with similar signatures between the two datasets are of functional importance. Among those, rbcL, the large subunit of RuBisCo - the most abundant enzyme on Earth and the most critical enzyme in the process of carbon fixation - appeared most amenable for physiological experiments in order to phenotypically validate its putative signatures of selection. A functional link was found between the rbcL haplotypes (PI, PM, TM) and net assimilation rate of CO2, providing an insight into the process of natural selection in deriving adaptive evolution of the species. The glasshouse experiment was followed by protein modelling and the higher photosynthetic rates of the PM and PI haplotypes over TM haplotype was explained. Conclusions The readily hybridising closely-related species of Eucalyptus occur across a large range of contrasting climates, making them an excellent model to explore naturally-occurring genetic variation that is under selection. This thesis reports how genetic variation of a key enzyme in photosynthesis with signatures consistent with having been subject to positive selection can be advantageous under future climate change where higher temperatures and/or prolonged drought are predicted. Apart from the availability of naturally-occurring genetic variations in chloroplast genomes for tree adaption, breeding programs and forest health monitoring, this research also proves that the haploid nature of the chloroplast genome is appropriate for studying phylogeography and evolutionary history of the species. Using the entire chloroplast genome for both interspecific and intraspecific data, a comprehensive demographic history of Tasmanian blue gum, a worldwide commercially important forest tree species, is illustrated. This thesis therefore provides a unique perspective in studying evolutionary genetics of a plant species