Signatures of natural selection in a foundation tree along Mediterranean climatic gradients

Abstract

Temperature and precipitation regimes are rapidly changing, resulting in forest dieback and extinction events, particularly in Mediterranean-type climates (MTC). Forest management that enhance forests' resilience is urgently required, however adaptation to climates in heterogeneous landscapes with multiple selection pressures is complex.For widespread trees in MTC we hypothesized that: patterns of local adaptation are associated with climate; precipitation is a stronger factor of adaptation than temperature; functionally related genes show similar signatures of adaptation; and adaptive variants are independently sorting across the landscape. We sampled 28 populations across the geographic distribution of Eucalyptus marginata (jarrah), in South-west Western Australia, and obtained 13,534 independent single nucleotide polymorphic (SNP) markers across the genome. Three genotype-association analyses that employ different ways of correcting population structure were used to identify putatively adapted SNPs associated with independent climate variables. While overall levels of population differentiation were low (F ST = 0.04), environmental association analyses found a total of 2336 unique SNPs associated with temperature and precipitation variables, with 1440 SNPs annotated to genic regions. Considerable allelic turnover was identified for SNPs associated with temperature seasonality and mean precipitation of the warmest quarter, suggesting that both temperature and precipitation are important factors in adaptation. SNPs with similar gene functions had analogous allelic turnover along climate gradients, while SNPs among temperature and precipitation variables had uncorrelated patterns of adaptation. These contrasting patterns provide evidence that there may be standing genomic variation adapted to current climate gradients, providing the basis for adaptive management strategies to bolster forest resilience in the future.

Leaf Economic and Hydraulic Traits Signal Disparate Climate Adaptation Patterns in Two Co-Occurring Woodland Eucalypts

“…However, as the two species are widespread throughout Tasmania and are likely to have been subject to similar distributional changes during and following the last Pleistocene glaciation of the island [ 59 ], we expected a positive association of patterns of population variation. Further, the Tasmanian populations of both species exhibit very low differentiation in SNP and microsatellite markers [ 60 ] (reports of species-wide F ST values include: microsatellites—a mean value for Australian tree species of 0.13 ± 0.01 [ 61 ]; SNPs—0.04 and 0.06 for E. marginata and E. globulus , respectively [ 62 , 63 ]). On average, these marker types are generally expected to reflect neutral variation [ 60 ], suggesting that neutral population processes are unlikely to have shaped the contemporary patterns of population differentiation of functional traits.…”

Germination temperature sensitivity differs between co‐occurring tree species and climate origins resulting in contrasting vulnerability to global warming

“…Current climate (1970–2000) temperature and precipitation layers for sampled populations were extracted from WorldClim v2 database (Fick & Hijmans, 2017 ) with a spatial resolution of approximately 1 km 2 , including annual mean temperature ( T MA ), the maximum temperature of the warmest month ( T MAX ), annual precipitation ( P MA ) and precipitation of warmest quarter ( P WQ ). Three of these represent variables ( T MAX , P MA , and P WQ ) which were shown to drive patterns of genetic adaptation in jarrah (Filipe et al, 2022 ); similarly, T MAX and P MA were also shown to be associated with genomic variation in marri (Ahrens, Byrne, et al, 2019 ). A linear model with ED 50 as the response variable was used to test each climate predictor's significance ( T MA , T MAX , P MA , and P WQ ) separately using the function lm in R. The standard error (SE) of the estimated ED 50 values was included as a weight argument for each data point in the subsequent linear regression analysis.…”

“…Current climate temperature and precipitation layers for sampled populations were extracted from WorldClim v2 database (Fick & Hijmans, 2017) with a spatial resolution of approximately 1 km 2 , including annual mean temperature (T MA ), the maximum temperature of the warmest month (T MAX ), annual precipitation (P MA ) and precipitation of warmest quarter (P WQ ). Three of these represent variables (T MAX , P MA , and P WQ ) which were shown to drive patterns of genetic adaptation in jarrah (Filipe et al, 2022); similarly, T MAX and P MA were also shown to be associated with genomic variation in marri . A linear model with ED 50 as the…”

“…Therefore, we aimed to define inter‐ and intraspecific variation in thermal thresholds for germination of both species by sampling 12 co‐occurring populations across their distribution. We tested the following hypotheses: (1) germination thermal niche will differ between species (species sensitivity), and marri will have higher thermal limits than jarrah, as jarrah has limited recruitment in the northern (warm) forests (Koch & Samsa, 2007; Norman & Koch, 2009); (2) germination responses will vary between populations (population sensitivity), where germination thermal limits will be positively correlated with maximum temperatures of origin (following genetic adaptation; Ahrens, Byrne, et al, 2019; Filipe et al, 2022); and (3) jarrah is more vulnerable to future temperature changes compared to marri, and northern (warm; Table 1) populations will be more vulnerable to future temperature conditions compared to southern (cool; Table 1) populations as a function of exposure to temperatures above the thermal limit for seed germination. By assessing the current thermal niche (sensitivity) and future windows (exposure) for germination, we quantified vulnerability to climate change at the species and population levels where the thermal safety margin of germination is exceeded.…”

“…(1) germination thermal niche will differ between species (species sensitivity), and marri will have higher thermal limits than jarrah, as jarrah has limited recruitment in the northern (warm) forests (Koch & Samsa, 2007;Norman & Koch, 2009); (2) germination responses will vary between populations (population sensitivity), where germination thermal limits will be positively correlated with maximum temperatures of origin (following genetic adaptation; Filipe et al, 2022); and (3) jarrah is more vulnerable to future temperature changes compared to marri, and northern (warm;…”