Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taedaL., Pinaceae)

Abstract

Natural populations of forest trees exhibit striking phenotypic adaptations to diverse environmental gradients, thereby making them appealing subjects for the study of genes underlying ecologically relevant phenotypes. Here, we use a genome-wide data set of single nucleotide polymorphisms genotyped across 3059 functional genes to study patterns of population structure and identify loci associated with aridity across the natural range of loblolly pine (Pinus taeda L.). Overall patterns of population structure, as inferred using principal components and Bayesian cluster analyses, were consistent with three genetic clusters likely resulting from expansions out of Pleistocene refugia located in Mexico and Florida. A novel application of association analysis, which removes the confounding effects of shared ancestry on correlations between genetic and environmental variation, identified five loci correlated with aridity. These loci were primarily involved with abiotic stress response to temperature and drought. A unique set of 24 loci was identified as F ST outliers on the basis of the genetic clusters identified previously and after accounting for expansions out of Pleistocene refugia. These loci were involved with a diversity of physiological processes. Identification of nonoverlapping sets of loci highlights the fundamental differences implicit in the use of either method and suggests a pluralistic, yet complementary, approach to the identification of genes underlying ecologically relevant phenotypes. E NVIRONMENTAL heterogeneity at multiple spatial scales influences the distribution of genetic variation across plant populations. Correlations between genetic variation and environmental gradients have been identified in a variety of plant species

Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

“…Quaternary climate changes have also been hypothesized to have driven the decline of a now-extinct species of Picea in the southeastern United State, far outside of the ice sheet distribution (Jackson and Weng, 1999). Thus, current P. angustifolia genetic subdivision likely reveals the existence of multiple Pleistocene populations, similar to hypotheses about P. trichocarpa (Slavov et al, 2012), P. balsamifera (Breen et al, 2012) and Pinus taeda (Eckert et al, 2010). Among these P. angustifolia subpopulations, however, N e changes in the recent past reflect drastically different impacts of western North America climate.…”

“…Ingvarsson (2008) and Ma et al (2010) found support for models of population bottlenecks and expansion in P. tremula, as did Keller et al (2010) in a sample of P. balsamifera, and Zhou et al (2014) in P. trichocarpa. Outside of regions covered by Pleistocene ice, Eckert et al (2010) found evidence of expansion from multiple refugia for Pinus taeda based on patterns of population structure. Although these studies have found evidence of expansion since the LGM, warming and drying of southern range portions could reduce regional suitability for some species, leading to population contraction.…”

Signatures of volcanism and aridity in the evolution of an insular pine (Pinus canariensis Chr. Sm. Ex DC in Buch)

“…Local adaptation to arid environments despite high levels of gene flow Weak patterns of population structure and high historical gene flow estimates between distant populations were found for P. canariensis, consistent with high contemporary gene flow by pollen and seed (Ló pez de Heredia et al, 2010) and for other coniferous species Eckert et al, 2010b). Molecular studies based on chloroplast DNA variation have revealed that gene flow is significant along elevational transects (Navascués and Emerson, 2007) but that some level of genetic differentiation, suggested by the presence of private chloroplast DNA haplotypes, was maintained among valleys (Gó mez et al, 2003).…”

Historical connectivity, contemporary isolation and local adaptation in a widespread but discontinuously distributed species endemic to Taiwan, Rhododendron oldhamii (Ericaceae)

“…Our results suggest that ecologically relevant selective forces were involved in population adaptive divergence of R. oldhamii. Spatial heterogeneity in environmental variables, revealed by the multivariate analysis of variance, is expected to cause genetic divergence among populations, which may create sufficient variations in fitness-related traits and the consequent formation of local adaptations (for example, Eckert et al, 2010).…”