Understanding how the environment shapes genetic variation provides critical insight about the evolution of local adaptation in natural populations. At multiple spatial scales and multiple geographic contexts within a single species, such information could address a number of fundamental questions about the scale of local adaptation and whether or not the same loci are involved at different spatial scales or geographic contexts. We used landscape genomic approaches from three local elevational transects and rangewide sampling to (a) identify genetic variation underlying local adaptation to environmental gradients in the California endemic oak,
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Abstract Quercus lobata ; (b) examine whether putatively adaptive SNPs show signatures of selection at multiple spatial scales; and (c) map putatively adaptive variation to assess the scale and pattern of local adaptation. Of over 10 k single‐nucleotide polymorphisms (SNPs) generated with genotyping‐by‐sequencing, we found signatures of natural selection by climate or local environment at over 600 SNPs (536 loci), some at multiple spatial scales across multiple analyses. Candidate SNPs identified with gene–environment tests (LFMM) at the rangewide scale also showed elevated associations with climate variables compared to the background at both rangewide and elevational transect scales with gradient forest analysis. Some loci overlap with those detected in other oak species, raising the question of whether the same loci might be involved in local climate adaptation in different congeneric species that inhabit different geographic contexts. Mapping landscape patterns of adaptive versus background genetic variation identified regions of marked local adaptation and suggests nonlinear association of candidate SNPs and environmental variables. Taken together, our results offer robust evidence for novel candidate genes for local climate adaptation at multiple spatial scales. -
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ABSTRACT Aim The distributions and interactions of co‐occurring species may change if their ranges shift asymmetrically in response to rapid climate change. We aim to test whether two currently interacting taxa, valley oak (
Quercus lobata ) and lace lichen (Ramalina menziesii ), have had a long‐lasting historical association and are likely to continue to associate in the future.Location Central western California, western United States of America
Methods Using population genetic analyses and
MaxEnt software for ecological niche modelling, we estimate species’ distributions during the Last Interglacial, the Last Glacial Maximum, present, and future periods. Mantel and vertex (genetic connection) tests were used to examine the spatial congruence among taxa. To compare the modelled response to climate change, we estimated migration speed between respective time periods using vector analysis.Results We found significant genetic congruence between valley oak and the lichen's green algal photobiont, independent of geographic isolation and habitat isolation, which is consistent with long‐term association. Ecological niche models under past and future climate scenarios indicate that overlap of climatic niche sharing between valley oak and lace lichen might decrease in the future. Our models indicate that the speed of shifts in climate niches between these two taxa differed significantly in past periods from that of the present period.
Main conclusions Our findings reveal that historical interactions between valley oak and lace lichen correlate with long‐term sharing of past climate niches. However, the future association of lace lichen with valley oak may be disrupted in parts of its current distribution due to differential discordance of climate niche shifts, species’ movements and generation times. This study illustrates the processes and patterns that allow long‐term association during historic climate change and how they are likely to change during rapid climate change.
