Speciation and the maintenance of species boundaries
Speciation occurs along geographical and genomic continuum and is often mediated by several intrinsic (genomic) and extrinsic factors (environmental). The relative importance of intrinsic and extrinsic factors varies among species and along the speciation continuum. Several species of plants and specifically conifers are known to frequently hybridize, yet maintain species cohesion. As a part of my PhD dissertation, I evaluated the evolutionary trajectory of hybridizing species by characterising the divergence history of Pinus strobiformis and Pinus flexilis and quantifying the relative influence of extrinsic and intrinsic barriers to the maintenance of species boundaries. Here I combined approaches from population genomics and climate predictive modelling to assess whether past climatic conditions have influenced the speciation trajectory and whether the present hybrid zone has experienced niche divergence from both parental species. The primary finding from this work demonstrated a history of ecological speciation with gene flow mediated by divergence along drought and freezing temperatures. Despite 18 My since divergence we could not identify any intrinsic barriers to speciation, yet the hybrid zone exhibited niche divergence from one of the parent species reiterating the relatively higher importance of extrinsic barriers in reinforcing species boundaries.
Relavent manuscript:
Adaptive introgression & species range dynamics
Populations occurring at the geographical margins of a species ranges are often at the fringe of optimal environmental conditions as well as at the epicentre of processes such as range expansions and hybridization with a closely related sister taxon that has abutting range margins. Interspecific gene flow from a closely related species can increase standing genetic diversity and generate novel allelic combinations via introgression, counteracting the expectations from the centre-periphery hypothesis. These novel combinations can act as a conduit for range margin populations to track favourable climatic conditions or facilitate adaptive evolution to on-going and future climate change.
We first evaluated whether hybridization can aid shifts in range margins by assessing spatio-temporal changes in the central location of the P. strobiformis-P. flexilis hybrid zone located on a heavily fragmented landscap. By assessing the coincidence between genomic and morphological cline centres I demonstrated a northward movement of the hybrid zone. Evaluating our empirical findings in the light of individual based landscape simulations we show that the northward shift could not be driven merely by regional differences in population density and likely involved a key contribution from adaptively introgressed variants.
Next, we more intensively sampled the hybrid zone to evaluate the genetic architecture of adaptive evolution. By utilizing genotype-environment association approaches, assessing patterns of linkage disequilibrium and evaluating per loci ancestry, we demonstrate strong signatures of adaptive evolution in the hybrid zone. Introgressed variants (variants from P. flexilis) were primarily adaptive freeze-related gradients while background genetic variants (variants segregating in the hybrid zone) were adaptive along water availability-related gradients.
We are currently combining genome-wide datasets for the hybrid populations with phenotyping assays across three common gardens established as a part of the Southwest Experimental Garden Array (SEGA) to connect all three edges of the genotype-phenotype-environment map. This work is done in collaboration with Amy Whipple & Kristen Warning at Northern Arizona University and aims to assess the architecture of adaptive traits under different environmental conditions. To attain this goal we are currently performing genome-wide association analysis (GWAS) and ancestry based GWAS (aGWAS). To inform conservation practises in the light of changing selective pressures due to climate change, we aim to use the results from GWAS & aGWAS to identify susceptible populations and populations harbouring variants likely adapted to future climatic conditions.
Relavent manuscript:
Evolution of phenotypic plasticity
For long lived sessile organisms such as trees, environment dependent expression of trait values (E effect) and genetic variation for these traits (G x E effect) is critical for survival under rapidly changing climatic conditions. Phenotypic plasticity will likely be a dominant mechanism facilitating response to future climatic conditions in most trees where the rate of environmental change is lower than the generation time of organisms.
The annual growth cycle alternating between period of active growth and dormancy is crucial for the success of most pernnial species and is thought to exhibit strong G*E effects. During my masters, I evaluated among population differentiation for freeze tolerance in a key boreal ecosystem species, Populus balsamifera (Balsam poplar). To assess whether differentiation in key eco-physiological traits and gene expression patterns associated with freeze tolerance varies between bud flush & bud set, this study made use of a common garden establishment in Fairbanks, Alaska. I combined field work with candidate gene analysis to evaluate signatures of selection. Our work demonstrated seasonal fluctuations in the strength of selection on freeze tolerance, indicating that strong among population differentiation is only noted towards the end of the growing season likely as a result of bud set being strongly influenced by source climatic conditions and being under strong genetic control across most plants.
Using the P. strobiformis- P. flexilis hybrid populations growing along two SEGA sites I am presently evaluating global patterns of gene expression plasticity. By treating gene expression as a quantitative trait and comparing it with genome-wide measures of among population differentiation we have identified several transcripts exhibiting signatures of adaptive evolution and that of adaptive plasticity. I am presently working towards assessing trait differentiation at the level of co-expression modules and evaluating whether module topology varies across gardens, likely as a result of differences in the architecture underlying freeze and drought tolerance. Stay tuned for more on this!
Relavent manuscript:
Evolutionary dynamics of Transposable elements (TEs)
Transposable elements (TEs) are stretches of DNA that can move around the genome of an organism and represent more than 50% of the genomic space in several angiosperms. While mostly considered to be under strong purifying selection due to disruption of gene expression and large structural re-organisations, there are now several studies demonstrating the role of TEs towards adaptive evolution. More recently they have also been implicated as key role players in invasion success. As a postdoc at UC Davis my work focuses on evaluating signatures of selection on TEs in maize by accounting for their timing of insertion.
