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Ecological and association genetics in two Mediterranean pine species

Isabel Rodríguez Quilón

Published 2017 in Unknown venue

ABSTRACT

ABSTRACT Forests have great ecological, economic and social value, playing also a critical role both as carbon pools and carbon dioxide sinks. Nevertheless, over the last decades, climate change has modified natural forest geographic ranges and ecosystem functioning. Mediterranean forests are especially sensitive to climate change as its consequences are expected to be experienced more abruptly in dry and cool regions, where, in addition, many tree species are found at their adaptive limit. In response, forest trees can adapt, migrate or go extinct. Coping with future environmental conditions in current distributions could be achieved by adaptation processes or via plastic responses. Local adaptation implies a genetic response to selection pressures, while plasticity could enable adapted phenotypes without underlying genetic change. Overall, forest tree populations are genetically very diverse, and local adaptation is expected to rely on such available genetic variability within and among populations. Understanding past and contemporary adaptive process and ecological drivers shaping genetic diversity within species is of key importance to predict the fate of forests and implement effective conservation strategies under the current climate change scenario. However, despite its utmost importance in species persistence and range shifts facing climate change, the genetic basis of local adaptation remains poorly understood. This thesis is framed within the field of ecological genetics, and structured in four chapters, corresponding to already published papers or manuscripts in preparation, and two annexes, with complementary information and also already published studies. The main objective of the thesis was to evaluate past and ongoing evolutionary and ecological processes leading to local adaptation in forest trees. I aimed to disentangle the complex interaction between genotypes, phenotypes and environmental conditions, advancing in the knowledge of the genetic basis of adaptive traits. These research questions were then related to practical issues for dynamic conservation of forest genetic resources. Pinus pinaster Ait. (maritime pine) and P. halepensis Mill. (Aleppo pine) are two ecologically and economically important outcrossing Mediterranean pine species, with different demographic histories and levels of intraspecific genetic diversity. They provide the opportunity to integrate information on population differentiation, genetic architecture, plasticity and ecotypic trends, offering numerous advantages for the study of local adaptation. To do so, here I used genetic data from nuclear microsatellites (12 nuSSRs) and single nucleotide polymorphisms (384 and 6,100 SNPs), and phenotypic data, measured in common gardens replicated in multiple environments. Common garden data allowed to estimate to which extent phenotypic expression is genetically based, and trial replicates under contrasting environments to know whether this expression can also be plastic. Quantitative genetics, population genetics and genotype-phenotype association methods are complementarily used in the four chapters to advance in the understanding of the genetic basis of adaptive traits in maritime and Aleppo pines. Overall, throughout the different studies included in this thesis, I found evidence of intraspecific genetic variation and local adaptation processes in both species. Adaptive traits exhibited a moderate genetic control and were structured across populations. Amongpopulation quantitative genetic differentiation was consistently above among-population molecular marker differentiation across traits and testing environments, at different hierarchical levels, suggesting local adaptation (Chapters 3 and 4). I was also able to identify putatively adaptive loci, underlying important fitness traits (Chapters 2 and 3). Environmental factors influenced genetic variability and the detected genetic architecture of the studied adaptive traits (Chapters 2, 3 and 4). Particularly addressing the relationship between genotype and phenotype, I first approached a traditional evolutionary question: the correlation between heterozygosity and fitness (Chapter 1). I aimed to find out whether inbreeding events, due to increased mating between relatives or genetic drift after a bottleneck, lead to decreased fitness in maritime pine. Genome-wide heterozygosity has little impact on maritime pine fitness, even though variation in inbreeding seems to be associated with survival. This could be explained by maritime pine mating system and evolutionary history. However, heterozygosity at putatively adaptive markers may play a critical role under increased selective pressures, such as the ones that could be derived from climate change. Genotype-phenotype association studies allowed the identification of particular loci underlying different adaptive traits in Aleppo and maritime pines (Chapters 2 and 3). For Aleppo pine, I found 15 SNPs significantly associated with growth traits, wood extractives, lignin content or flowering, explaining a moderate variation in phenotypic traits (<11%). I demonstrate that integrated phenotypes in genotype-phenotype association tests can slightly enhance the proportion of phenotypic variance explained, as well as give the chance of detecting possible pleiotropic effects (Chapter 2). For maritime pine, association tests performed with an increased number of molecular markers (6,100 SNPs) at contrasting environments, allowed the identification of six SNPs associated with survival in trials under mild Atlantic climate, and two SNPs associated with tree height in one of the trials under a harsher Mediterranean climate (Chapter 3). In both cases, future studies would be needed to confirm the identified candidates as functional adaptive genes. As the proportion of phenotypic variance explained remained low (<10%), despite the increased number of molecular markers used for maritime pine, and provided that most adaptive traits are expected to be controlled by a large number of loci with small effect, we moved forward towards a polygenic adaptation approach. For this, I combined population and association genetics, and tested for excess variance in among-population differentiation and signals of excessive correlations with environmental variables, when allele frequencies of a set of candidate adaptive loci were compared to a null model of neutral genetic drift and shared population history. I found an excess of variance among populations for height and survival, consistent with directional selection, mainly driven by covariance among loci (i.e. linkage disequilibrium). I also found signals of excessive correlations with minimum temperatures and mean precipitation, respectively, for height and survival traits, confirming the key role of such environmental variables in local adaptation processes in the species. Our results point to many loci of small effect underlying the studied traits, with local adaptation driven by small allele frequency changes (Chapter 3). In Aleppo pine, I also tested the relationship between ecogeographical variables and different adaptive phenotypes -including growth, reproduction, drought resistance and wood quality traits-, as well as among-trait correlations. Analyses were done trait-by-trait and also for integrated phenotypes. Overall, I found supporting evidence for intraspecific local adaptation and that allocation to adaptive traits related to growth, reproduction and defence trade-off against each other, matching theoretical predictions from allocation and life-history theories in the species (Chapter 2). In maritime pine, I corroborated the existence of clinal variation along temperature and rainfall gradients in the species, and the important role of the environment in maritime pine local adaptation. Consistently higher among-population quantitative genetic differentiation than neutral molecular differentiation, for height and survival under contrasting environments, point to widespread divergent selection too. I found high levels of genetic variation and phenotypic plasticity at different spatial levels, suggesting potential for evolutionary change to cope with new selective pressures, although variable within the species range (Chapter 4). Finally, I show that the acquired knowledge about the genetic variation of adaptive traits can be used to improve dynamic genetic conservation programs for forest trees (Chapter 4). Neutral and adaptive components of genetic diversity, as well as environmental factors, should be accounted for in the identification of conservation units below the species level, especially in species with strong population structure and complex evolutionary histories. The environmental zonation approach currently used by the pan-European genetic conservation strategy for forest trees would be improved by gradually integrating molecular and quantitative trait information, as data become available.

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