There is substantial interest in uncovering the genetic basis of the traits underlying adaptive responses in tree species, as this information will ultimately aid conservation and industrial endeavors across populations, generations, and environments. Fundamentally, the characterization of such genetic bases is within the context of a genetic architecture, which describes the mutlidimensional relationship between genotype and phenotype through the identification of causative variants, their relative location within a genome, expression, pleiotropic effect, environmental influence, and degree of dominance, epistasis, and additivity.Here, we review theory related to polygenic local adaptation and contextualize these expectations with methods often used to uncover the genetic basis of traits important to tree conservation and industry. A broad literature survey suggests that most tree traits generally exhibit considerable heritability, that underlying quantitative genetic variation (𝑄 "# ) is structured more so across populations than neutral expectations (𝐹 "# ) in 69% of comparisons across the literature, and that single-locus associations often exhibit small estimated per-locus effects.Together, these results suggest differential selection across populations often acts on tree phenotypes underlain by polygenic architectures consisting of numerous small to moderate effect loci. Using this synthesis, we highlight the limits of using solely single-locus approaches to describe underlying genetic architectures and close by addressing hurdles and promising alternatives towards such goals, remark upon the current state of tree genomics, and identify future directions for this field. Importantly, we argue, the success of future endeavors should not be predicated on the shortcomings of past studies and will instead be dependent upon the application of theory to empiricism, standardized reporting, centralized open-access databases, and continual input and review of the community's research.
11There is substantial interest in uncovering the genetic basis of the traits underlying adaptive 12 responses in tree species, as this information will ultimately aid conservation and industrial 13 endeavors across populations, generations, and environments. Fundamentally, the 14 characterization of such genetic bases is within the context of a genetic architecture, which 15 describes the mutlidimensional relationship between genotype and phenotype through the 16 identification of causative variants, their relative location within a genome, expression, 17 pleiotropic effect, environmental influence, and degree of dominance, epistasis, and additivity.
18Here, we review theory related to polygenic local adaptation and contextualize these 19 expectations with methods often used to uncover the genetic basis of traits important to tree 20 conservation and industry. A broad literature survey suggests that most tree traits generally 21 exhibit considerable heritability, that underlying quantitative genetic variation ( "# ) is structured
Long-lived species of trees, especially conifers, often display weak patterns of reproductive isolation, but clear patterns of local adaptation and phenotypic divergence. Discovering the evolutionary history of these patterns is paramount to a generalized understanding of speciation for long-lived plants. We focus on two closely related yet phenotypically divergent pine species, Pinus pungens and P. rigida, that co-exist along high elevation ridgelines of the southern Appalachian Mountains. Based on genome-wide RADseq data, patterns of population structure for each species were uncorrelated to geography and the environment. Signals of admixture, however, were present range-wide. When combined with information from contemporary and historical species distribution models, these patterns are consistent with a complex evolutionary history of speciation. This was confirmed using inferences based on the multidimensional site-frequency spectrum, where demographic modeling inferred recurring gene flow since divergence (9.3 – 15.4 million years ago) and population size reductions that align in timing with the last interglacial period (~120 – 140 thousand years ago). This suggests that phenotypic and genomic divergence, including the evolution of divergent phenological schedules leading to partial reproductive isolation, as previously documented for these two species, can happen rapidly, even between long-lived species of pines.
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