Climate change is currently one of the biggest threats to biodiversity. Understanding how species respond to climate change, and their capacity to respond to the ever-increasing pace and intensity at which these changes are taking place, is critical for the preservation of ecosystems. Tree species make a case study of particular interest, as they are sedentary, display long generation times, and have high ecological importance. The Mediterranean region has been described as a ‘climate change hotspot’, with increased temperatures and decreased precipitation expected to affect the region in the coming decades. Holm oaks (Quercus genus) are considered keystone tree species of the Mediterranean basin and display several adaptations that award them a high degree of temperature and drought resistance, which helps them deal with the hot, dry summers common to the Mediterranean climate. This work involved samples from two Holm oak species, Quercus ilex and Quercus rotundifolia, collected throughout the Mediterranean basin. Genotyping by Sequencing was used to derive several nuclear Single Nucleotide Polymorphism datasets, which were used (i) to investigate population structure using several complementary approaches, and (ii) to detect evidence of local adaptation through a Landscape Genomics approach involving the detection of Fst outliers and genetic-environmental associations. This was done using samples of Holm oak collected from 18 sampling locations across the western Mediterranean basin. This is, to our knowledge, the first attempt to use genome-wide, nuclear genetic markers to uncover the existence of population structure and signatures of local adaptation in Holm oak. Our results reveal a marked pattern of population structure and differentiation, which supports the status of Q. ilex and Q. rotundifolia as two genetically, morphologically, and ecologically distinct species. A considerable degree of differentiation is also observed between Iberian and Moroccan samples of Q. rotundifolia, indicating their status as distinct populations. On the other hand, Iberian samples and Moroccan samples geographically closer to Iberia show lower levels of differentiation, indicating either the presence of gene flow or incomplete lineage sorting. We also uncover the relatively unstructured nature of the Iberian Q. rotundifolia population. Additionally, we uncover the presence of Q. ilex in Tunisia, where only Q. rotundifolia was thought to inhabit, revealing an incongruity between the known chlorotype distribution and population structure inferred from nuclear DNA, which we hypothesize to be the result of hybridization through long-distance pollen flow. Regarding the detection of local adaptation, we identified a considerable number of putative SNPs under selection in Q. rotundifolia. The majority of these SNPs showed evidence of association with multiple temperature and precipitation-related bioclimatic variables. Annotation of the genomic areas in which the putative SNPs under selection were located, through comparison with the reference genome of Quercus lobata, revealed several genes putatively related to the adaptive process to heat and water stress. In general, these results contribute towards the clarification of the taxonomy of Holm oak, which up until this point has suffered from a lack of consistency, bring new insights into the population structure of Holm oak, and also represent a first step in understanding the capacity of Mediterranean Holm oak populations to respond to future climate change.

Tese de mestrado, Biologia Evolutiva e do Desenvolvimento, 2023, Universidade de Lisboa, Faculdade de Ciências