Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae)

Eckert, Andrew J.; Maloney, Patricia E.; Vogler, Detlev R.; Jensen, Camille; Mix, Annette Delfino; Neale, David B.

doi:10.1007/s11295-015-0863-0

Cited by 49 publications

(63 citation statements)

References 77 publications

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“…While bayenv2 did not identify any loci strongly associated with environment, as given from small values of Bayes factors (all

\bar{B F}

< 1.0, Table S3, Supporting information), there is a strong biological signal for adaptation to soil water availability in our data set (discussed below), evidence that other white pines within the LTB are also being structured by precipitation differences among populations (Eckert et al . ), and elevated signals of selection among focal loci associated to annual precipitation which would be unlikely to arise, given the data and methodological artefacts. Thus, it seems unlikely that the focal sets of SNPs associated to annual precipitation, and perhaps GDD‐Aug and Tmin‐Jan, are driven solely by false positives.…”

Section: Discussionmentioning

confidence: 98%

“…Variation of allele frequencies among populations accounts for less than 1% of the variance observed, which was less than that found for P. lambertiana populations within the LTB (Eckert et al . ), or among isozymes sampled from populations across the Northern P. albicaulis range (Krakowski et al . ).…”

Section: Discussionmentioning

confidence: 99%

“…Populations of forest trees, particularly conifers, have a rich history of common garden, provenance tests and genecological studies that demonstrate abundant evidence for local adaptation among populations, even over short geographic distances (e.g., Mitton et al 1989Mitton et al , 1998Budde et al 2014;Csill ery et al 2014;Vizca ıno-Palomar et al 2014;Eckert et al 2015;Holliday et al 2016;Roschanksi et al 2016) providing further support that fine spatial scales are relevant to adaptation (Richardson et al 2014). This extensive history has also revealed the highly polygenic nature of adaptive traits (Langlet 1971;Holland 2007).…”

Section: Introductionmentioning

confidence: 99%

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Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA

et al. 2017

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Patterns of local adaptation at fine spatial scales are central to understanding how evolution proceeds, and are essential to the effective management of economically and ecologically important forest tree species. Here, we employ single and multilocus analyses of genetic data (n = 116 231 SNPs) to describe signatures of fine‐scale adaptation within eight whitebark pine (Pinus albicaulis Engelm.) populations across the local extent of the environmentally heterogeneous Lake Tahoe Basin, USA. We show that despite highly shared genetic variation (FST = 0.0069), there is strong evidence for adaptation to the rain shadow experienced across the eastern Sierra Nevada. Specifically, we build upon evidence from a common garden study and find that allele frequencies of loci associated with four phenotypes (mean = 236 SNPs), 18 environmental variables (mean = 99 SNPs), and those detected through genetic differentiation (n = 110 SNPs) exhibit significantly higher signals of selection (covariance of allele frequencies) than could be expected to arise, given the data. We also provide evidence that this covariance tracks environmental measures related to soil water availability through subtle allele frequency shifts across populations. Our results replicate empirical support for theoretical expectations of local adaptation for populations exhibiting strong gene flow and high selective pressures and suggest that ongoing adaptation of many P. albicaulis populations within the Lake Tahoe Basin will not be constrained by the lack of genetic variation. Even so, some populations exhibit low levels of heritability for the traits presumed to be related to fitness. These instances could be used to prioritize management to maintain adaptive potential. Overall, we suggest that established practices regarding whitebark pine conservation be maintained, with the additional context of fine‐scale adaptation.

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“…While bayenv2 did not identify any loci strongly associated with environment, as given from small values of Bayes factors (all

\bar{B F}

Section: Discussionmentioning

confidence: 98%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA

et al. 2017

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“…Understanding how organisms adapt to their local environment is one of the key goals in molecular ecology (Bedford & Hartl, ; Chen et al., ; Dayan, Crawford, & Oleksiak, ; Fraser, ; Lenz, ; Pavey, Bernatchez, Aubin‐Horth, & Landry, ). The advent of NextGen sequencing made it possible to analyse, on a genome‐ or at least transcriptome‐wide scale, both fundamental mechanisms of surviving in an environment that changes in time and space: local adaptation (Csilléry et al., ; Dayan et al., ; Eckert et al., ; Fraser, ; Lavington et al., ; Simonson et al., ) and adaptive phenotypic plasticity (Bedford & Hartl, ; Chen, Nolte, & Schlötterer, ; Dayan et al., ; Klumpen et al., ; Rohlfs, Harrigan, & Nielsen, ; Schwerin et al., ; Yampolsky, Zeng et al., ). These two responses to environment—differentiation with respect to heritable changes and nonheritable physiological and biochemical changes—are often difficult to untangle in the field and, in case of differential mortality, even in laboratory studies.…”

Section: Introductionmentioning

confidence: 99%

Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species

et al. 2018

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Local adaptation and phenotypic plasticity are main mechanisms of organisms' resilience in changing environments. Both are affected by gene flow and are expected to be weak in zooplankton populations inhabiting large continuous water bodies and strongly affected by currents. Lake Baikal, the deepest and one of the coldest lakes on Earth, experienced epilimnion temperature increase during the last 100 years, exposing Baikal's zooplankton to novel selective pressures. We obtained a partial transcriptome of Epischura baikalensis (Copepoda: Calanoida), the dominant component of Baikal's zooplankton, and estimated SNP allele frequencies and transcript abundances in samples from regions of Baikal that differ in multiyear average surface temperatures. The strongest signal in both SNP and transcript abundance differentiation is the SW-NE gradient along the 600+ km long axis of the lake, suggesting isolation by distance. SNP differentiation is stronger for nonsynonymous than synonymous SNPs and is paralleled by differential survival during a laboratory exposure to increased temperature, indicating directional selection operating on the temperature gradient. Transcript abundance, generally collinear with the SNP differentiation, shows samples from the warmest, less deep location clustering together with the southernmost samples. Differential expression is more frequent among transcripts orthologous to candidate thermal response genes previously identified in model arthropods, including genes encoding cytoskeleton proteins, heat-shock proteins, proteases, enzymes of central energy metabolism, lipid and antioxidant pathways. We conclude that the pivotal endemic zooplankton species in Lake Baikal exists under temperature-mediated selection and possesses both genetic variation and plasticity to respond to novel temperature-related environmental pressures.

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“…This limited differentiation was unexpected given that local adaptation along environmental gradients, even at relatively fine scales, is often observed for many of the species in our study, including Douglas fir (Campbell 1979, St Clair et al 2005, ponderosa pine (Kitzmiller 2005), and sugar pine (Eckert et al 2015). This limited differentiation was unexpected given that local adaptation along environmental gradients, even at relatively fine scales, is often observed for many of the species in our study, including Douglas fir (Campbell 1979, St Clair et al 2005, ponderosa pine (Kitzmiller 2005), and sugar pine (Eckert et al 2015).…”

Section: Limited Differentiation In Performance Among Other Provenancesmentioning

confidence: 70%

Assisted gene flow in the context of large‐scale forest management in California,USA

et al. 2020

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As climate changes, locally adapted tree populations may become maladapted to the sites in which they presently occur. When natural adaptive processes are insufficient for populations to keep pace with changing climate, human-assisted relocation of genotypes (assisted gene flow) may be a useful tool for maintaining forest resilience. While existing empirical evidence provides insight into the potential outcomes and consequences of assisted gene flow, its applicability to large-scale plantings needs to be evaluated. We conducted a test of assisted gene flow in the context of operational postfire restoration plantings in three U.S. Department of Agriculture National Forests in California. Our experimental restoration plantings included seedling provenances representing both the local planting site and lower-elevation provenances that may be adapted to hotter and drier conditions. For the duration of the experiment, the planting sites experienced anomalously hot, dry conditions, offering a window into the potential outcomes of assisted gene flow in a future climate characterized by warmer temperatures and more frequent drought. In most cases, there was no significant difference in seedling growth or survival among provenances. However, in a few cases, lowerelevation provenances performed better than local provenances, suggesting a potential benefit of assisted gene flow as a management response to climate change. Our analyses accounted for spatial variation in shrub cover and detected a consistent and substantial negative association between shrub cover and seedling growth. In addition, our study revealed that the use of operational seed collections that are not geographically precise (and therefore also not climatically precise) can complicate selection of appropriate provenances and lead to unpredictable outcomes. Numerous other risks and uncertainties-including the fact that tree populations are often adapted to local site factors other than climate and that long-term outcomes may differ from short-term observations-complicate evaluations of the potential utility of assisted gene flow.

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Local adaptation at fine spatial scales: an example from sugar pine (Pinus lambertiana, Pinaceae)

Cited by 49 publications

References 77 publications

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA

Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Engelm.) across fine spatial scales of the Lake Tahoe Basin, USA

Temperature gradient affects differentiation of gene expression and SNP allele frequencies in the dominant Lake Baikal zooplankton species

Assisted gene flow in the context of large‐scale forest management in California,USA

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