The genomics of local adaptation in trees: are we out of the woods yet?

Lind, Brandon M.; Menon, Mitra; Bolte, Constance E.; Faske, Trevor M.; Eckert, Andrew J.

doi:10.1007/s11295-017-1224-y

Cited by 84 publications

(89 citation statements)

References 379 publications

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“…Forest scientists have traditionally used provenance trials-in situ field-based common garden 84 experiments that usually involve partial reciprocal transplants-to understand links between 85 phenotypes under divergent selection and the environments driving those differences (see 86 discussion in Lind et al 2018). Such designs have been the major source of knowledge of local 87 adaptation trees for over two centuries, where differentiation among populations is usually 88 attributed to the source environment of individuals (Langlet 1971; Morgenstern 1996).…”

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Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study

Mahony

MacLachlan

Lind

et al. 2019

Preprint

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The need for tools to cost-effectively identify adaptive variation within ecologically and 13 economically important plant species is mounting as the detrimental effects of climate change 14 become increasingly apparent. For crop and wild populations alike, mismatches between adaptive 15 variation and climatic optima will reduce health, growth, survival, reproduction, and continued 16 establishment. The ease with which land managers can quantify the relative importance of different 17climate factors or the spatial scale of local adaptation to climate will have direct implications for 18 the potential of mitigating or resolving such risks. Using seed collected from 281 provenances of 19 lodgepole pine (Pinus contorta) from across western Canada, we compare genomic data to 20 phenotypic and climatic data to assess their effectiveness in characterizing the climatic drivers and 21 spatial scale of local adaptation in this species. We find that genomic and climate data are nearly 22 equivalent for describing local adaptation in seedling traits. We also find strong agreement between 23 the climate variables associated with genomic variation and with 20-year heights from a long-term 24 provenance trial, suggesting that genomic data may be a viable option for identifying climatic 25 drivers of local adaptation where phenotypic data are unavailable. Genetic clines associated with 26 cold injury occur at broad spatial scales, suggesting that standing variation of adaptive alleles for 27 this and similar species does not require management at scales finer than are indicated by 28 phenotypic data. This study demonstrates that genomic data are most useful when paired with 29 phenotypic data, but can also fill some of the traditional roles of phenotypic data in management 30of species for which phenotypic trials are not feasible.

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confidence: 99%

Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study

Mahony

MacLachlan

Lind

et al. 2019

Preprint

Self Cite

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“…For example, maize plants growing at high elevation often accumulate flavonoids in their leaves and silks as a mechanism for coping with high levels of UV-B exposure (Zhang et al, 2003;Casati and Walbot, 2010). The recent development of highthroughput sequencing technologies has greatly accelerated the identification of key genes and genomics research, significantly promoting the research of adaptive evolution and ecology on nonmodel organisms (Stapley et al, 2010;Ekblom and Galindo, 2011), including conifers (Yeaman et al, 2016;Lind et al, 2018;De La Torre and Neale, 2019;Lu et al, 2019;Tyrmi et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Genetic Variation Related to High Elevation Adaptation Revealed by Common Garden Experiments in Pinus yunnanensis

Sun

Zhao

et al. 2020

Front. Genet.

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Local adaptation, adaptation to specialized niches and environmental clines have been extensively reported for forest trees. Investigation of the adaptive genetic variation is crucial for forest resource management and breeding, especially in the context of global climate change. Here, we utilized a Pinus yunnanensis common garden experiments established at high and low elevation sites to assess the differences in growth and survival among populations and between the two common garden sites. The studied traits showed significant variation between the two test sites and among populations, suggesting adaptive divergence. To detect genetic variation related to environment, we captured 103,608 high quality SNPs based on RNA sequencing, and used them to assess the genetic diversity and population structure. We identified 321 outlier SNPs from 131 genes showing significant divergence in allelic frequency between survival populations of two sites. Functional categories associated with adaptation to high elevation were found to be related to flavonoid biosynthesis, response to UV, DNA repair, response to reactive oxygen species, and membrane lipid metabolic process. Further investigation of the outlier genes showed overrepresentation of the flavonoid biosynthesis pathway, suggesting that this pathway may play a key role in P. yunnanensis adaptation to high elevation environments. The outlier genes identified, and their variants, provide a basic reference for advanced investigations.

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“…Genotype–environment associations (GEAs) are increasingly being used to assess genomic imprints consistent with natural selection, providing insights on adaptive responses of species to climate change (Hoban et al, 2016; Rellstab, Gugerli, Eckert, Hancock, & Holderegger, 2015; Sork et al., 2013). Many adaptive processes are expected to result in weak, multilocus signatures due to polygenic adaptation from standing variation, rather than selection on new mutations rapidly rising to fixation (Lind, Menon, Bolte, Faske, & Eckert, 2018; Savolainen, Lascoux, & Merilä, 2013). Detecting these weak signals through univariate GEAs is complicated by correcting for multiple comparisons (François, Martins, Caye, & Schoville, 2016).…”

Section: Introductionmentioning

confidence: 99%

Exploring genomic variation associated with drought stress in Picea mariana populations

Napier

Lafontaine

2020

Ecology and Evolution

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Predicted increases in drought and heat stress will likely induce shifts in species bioclimatic envelopes. Genetic variants adapted to water limitation may prove pivotal for species response under scenarios of increasing drought. In this study, we aimed to explore this hypothesis by investigating genetic variation in 16 populations of black spruce (Picea mariana) in relation to climate variables in Alaska. A total of 520 single nucleotide polymorphisms (SNPs) were genotyped for 158 trees sampled from areas of contrasting climate regimes. We used multivariate and univariate genotype‐by‐environment approaches along with available gene annotations to investigate the relationship between climate and genetic variation among sampled populations. Nine SNPs were identified as having a significant association with climate, of which five were related to drought stress response. Outlier SNPs with respect to the overall environment were significantly overrepresented for several biological functions relevant for coping with variable hydric regimes, including osmotic stress response. This genomic imprint is consistent with local adaptation of black spruce to drought stress. These results suggest that natural selection acting on standing variation prompts local adaptation in forest stands facing water limitation. Improved understanding of possible adaptive responses could inform our projections about future forest dynamics and help prioritize populations that harbor valuable genetic diversity for conservation.

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The genomics of local adaptation in trees: are we out of the woods yet?

Cited by 84 publications

References 379 publications

Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study

Evaluating genomic data for management of local adaptation in a changing climate: A lodgepole pine case study

Genetic Variation Related to High Elevation Adaptation Revealed by Common Garden Experiments in Pinus yunnanensis

Exploring genomic variation associated with drought stress in Picea mariana populations

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