Standing genomic variation within coding and regulatory regions contributes to the adaptive capacity to climate in a foundation tree species

Abstract

Global climate is rapidly changing, and the ability for tree species to adapt is dependent on standing genomic variation; however, the distribution and abundance of functional and adaptive variants are poorly understood in natural systems. We test key hypotheses regarding the genetics of adaptive variation in a foundation tree: genomic variation is associated with climate, and genomic variation is more likely to be associated with temperature than precipitation or aridity. To test these hypotheses, we used 9,593 independent, genomic single‐nucleotide polymorphisms (SNPs) from 270 individuals sampled from Corymbia calophylla's entire distribution in south‐western Western Australia, spanning orthogonal temperature and precipitation gradients. Environmental association analyses returned 537 unique SNPs putatively adaptive to climate. We identified SNPs associated with climatic variation (i.e., temperature [458], precipitation [75] and aridity [78]) across the landscape. Of these, 78 SNPs were nonsynonymous (NS), while 26 SNPs were found within gene regulatory regions. The NS and regulatory candidate SNPs associated with temperature explained more deviance (27.35%) than precipitation (5.93%) and aridity (4.77%), suggesting that temperature provides stronger adaptive signals than precipitation. Genes associated with adaptive variants include functions important in stress responses to temperature and precipitation. Patterns of allelic turnover of NS and regulatory SNPs show small patterns of change through climate space with the exception of an aldehyde dehydrogenase gene variant with 80% allelic turnover with temperature. Together, these findings provide evidence for the presence of adaptive variation to climate in a foundation species and provide critical information to guide adaptive management practices.

Plant functional traits differ in adaptability and are predicted to be differentially affected by climate change

“…We found evidence to support adaptation of functional traits in C. calophylla across populations in southwest Western Australia. These patterns of adaptation are consistent with previous studies of genetics, growth, and physiology of C. calophylla (Ahrens, Byrne, et al, ; Ahrens, Mazanec, et al, ; Aspinwall et al, ; Blackman et al, ). This study builds upon previous research by focusing on the genetic determination of functional traits, elucidating the relationship between functional traits, determining the relationship between functional traits and climate, and predicting genetically determined trait distributions under current and future climates.…”

“…It is considered a foundation species because its characteristics are critical for forest structure and ecological processes (Ellison et al, 2005). This species is an ideal candidate in which to study adaptation of functional traits because its distribution traverses strong environmental gradients over short distances, it has recently experienced mortality events attributed to climate change (Matusick, Ruthrof, Brouwers, Dell, & Hardy, 2013;Ruthrof, Matusick, & Hardy, 2015), and evidence of adaptation to climate has been identified in physiological experiments and genome-environment investigations (Ahrens, Byrne, & Rymer, 2019;Ahrens, Mazanec, et al, 2019;Aspinwall et al, 2017;Blackman, Aspinwall, Tissue, & Rymer, 2017).…”

Spatial, climate, and ploidy factors drive genomic diversity and resilience in the widespread grassThemeda triandra

“…common garden experiments – Sork, 2017), our results are consistent with the idea that signals of adaptation are ubiquitous throughout genomes (Kern & Hahn, 2018). Maximum temperature of the warmest month or week (T MAX ) has been found to be an important driving force of selection in other Australian plants (Steane et al , 2017a,b; Jordan et al , 2017; Ahrens et al , 2019). Interestingly, evidence suggests that climatic factors can have different impacts on patterns of genetic diversity and adaptation in different grass species.…”

“…In Australia, research efforts have mostly focused on Eucalyptus species, finding that eucalypt populations are often connected by high levels of gene flow and adapted to local climates (e.g. Steane et al , 2015; Jordan et al , 2017; Supple et al , 2018; Ahrens et al , 2019). In one of the first landscape-scale genomic studies in Australia for an understory species, we show that the iconic grass T. triandra has very different patterns of connectivity and adaptation compared with its Eucalyptus counterparts.…”

The impact of biological invasion and genomic local adaptation on the geographical distribution of Aedes aegypti in Panama

“…The few studies that have assessed adaptive allele frequency change across geographical space support the role that local adaptation plays across a wide range of organisms with varying dispersal abilities (41)(42)(43)(44)(45)(46)(47). Thus, the emerging data are demonstrating that even well-connected populations can adapt to environmental differences and habitat heterogeneity across narrow spatial scales.…”