Evidence of genomic adaptation to climate in Eucalyptus microcarpa: Implications for adaptive potential to projected climate change

Abstract

Understanding whether populations can adapt in situ or whether interventions are required is of key importance for biodiversity management under climate change. Landscape genomics is becoming an increasingly important and powerful tool for rapid assessments of climate adaptation, especially in long-lived species such as trees. We investigated climate adaptation in Eucalyptus microcarpa using the DArTseq genomic approach. A combination of F outlier and environmental association analyses were performed using >4200 genomewide single nucleotide polymorphisms (SNPs) from 26 populations spanning climate gradients in southeastern Australia. Eighty-one SNPs were identified as putatively adaptive, based on significance in F outlier tests and significant associations with one or more climate variables related to temperature (70/81), aridity (37/81) or precipitation (35/81). Adaptive SNPs were located on all 11 chromosomes, with no particular region associated with individual climate variables. Climate adaptation appeared to be characterized by subtle shifts in allele frequencies, with no consistent fixed differences identified. Based on these associations, we predict adaptation under projected changes in climate will include a suite of shifts in allele frequencies. Whether this can occur sufficiently rapidly through natural selection within populations, or would benefit from assisted gene migration, requires further evaluation. In some populations, the absence or predicted increases to near fixation of particular adaptive alleles hint at potential limits to adaptive capacity. Together, these results reinforce the importance of standing genetic variation at the geographic level for maintaining species' evolutionary potential.

Independent genetic control of drought resistance, recovery, and growth of Eucalyptus globulus seedlings

“…These include the first QTL to be detected in eucalypts underlying direct measurements of drought damage and recovery, as well as those for relative lignotuber size, which has been implicated as playing important roles in recovery (Borzak et al, ; Lloret et al, ; Paula & Pausas, ; Walters, Bell, & Read, ). Our results argue that these traits are under multigenic control, with up to four independent QTL detected per trait in this mapping family, consistent with genomic studies that suggest that adaptation to aridity is a genome‐wide phenomenon in eucalypts (Jordan, Hoffmann, Dillon, & Prober, ; Steane et al, ) and other taxa (Eckert et al, ). Although seedling size prior to drought did impact susceptibility to drought damage, as suggested in our first hypothesis, this was mainly evident in the correlations, and the majority of QTL we detected for drought damage and recovery were independent of those for growth (HT1, HT2, and TL).…”

“…These include the first QTL to be detected in eucalypts underlying direct measurements of drought damage and recovery, as well as those for relative lignotuber size, which has been implicated as playing important roles in recovery (Borzak et al, 2017;Lloret et al, 1999;Paula & Pausas, 2006;Walters, Bell, & Read, 2005). Our results argue that these traits are under multigenic control, with up to four independent QTL detected per trait in this mapping family, consistent with genomic studies that suggest that adaptation to aridity is a genomewide phenomenon in eucalypts (Jordan, Hoffmann, Dillon, & Prober, 2017;Steane et al, 2017) and other taxa (Eckert et al, 2010).…”

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

“…Our study identified patterns between genotype and climate similar to those identified in other studies on eucalypts, where temperature was found to identify a greater number of adaptive variants (Dillon et al, 2014;Jordan, Dillon, & SK, Prober SM, 2017;Steane et al, 2017Steane et al, , 2014. These associations indicate that climate is shaping patterns of genetic variation, possibly creating locally adapted populations, supporting our first hypothesis.…”

Understanding managers’ and scientists’ perspectives on opportunities to achieve more evolutionarily enlightened management in conservation

“…Where connectivity has been disrupted, managed gene flow through translations can act to restore genetic diversity and reverse the impacts of inbreeding depression (e.g., genetic rescue; Weeks et al, 2017) Sourcing seed from populations that occur along an environmental gradient can maximize the adaptive capacity and resilience of restoration effects (Prober et al, 2016). Maximizing connectivity along an environmental gradient can enable the movement of adaptive alleles (Jordan, Hoffmann, Dillon, & Prober, 2017) Restrict gene flow between populations to limit genetic diversity and adaptive potential (Hendry et al, 2011).…”