Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow

Abstract

When populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome–environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome‐wide restriction site‐associated single nucleotide polymorphism (SNP) data, we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.

Genomic vulnerability to rapid climate warming in a tree species with a long generation time

“…Even under a moderate future climate scenario including mitigation measures (RCP4.5), the estimated mean AF shift required for the temperature‐associated loci is at least three fold higher than the rate at which populations have shifted their AFs in the past (Figure 4a). Although the AF shift was not specifically related to time, and while climate zones are difficult to compare, previous studies looking at a predictive time‐span of 95–140 years estimated similar RONA values for a projected composite climate measure (0.05–0.48 for Betula nana ; Borrell et al, 2020) or for a projected mean temperature (0.10–0.30 for Eucalyptus microcarpa [RCP8.5; Jordan et al, 2017], 0.09–0.30 for Quercus spp. [scenario A1B; Rellstab et al, 2016], and 0.07–0.38 for Quercus suber [RCP8.5; Pina‐Martins et al, 2018]).…”

Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine

“…This suggests that variable selection in adaptation studies should not be done using a priori knowledge solely based on the power of a variable to predict a species' realised ecological niche. In other words, it is challenging to obtain relevant clues of selective forces at the local scale when habitat characterisation depends on ecological data from the entire species' range (but see, e.g., Borrell, Zohren, Nichols, & Buggs, 2020), especially if the study design consists of a partial sampling at its leading or rear edges (Hampe & Petit, 2005). One reason that might explain this mismatch is the temporal lag involved in the two processes; species presence can reflect rather recent events, while selection signatures are related to an evolutionary time scale, whose dimension depends, among others, on the species' generation time.…”

Intraspecific variation in phenology offers resilience to climate change for Eriophorum vaginatum

“…longevity of tussock forming plants in the arctic, the chances for establishment of southern ecotypes in the north seem unlikely, outside of assisted gene flow or migration (Borrell et al 2020).…”