Genomic basis for drought resistance in European beech forests threatened by climate change

Pfenninger, Markus; Reuss, Friederike; Kiebler, Angelika; Schönnenbeck, Philipp; Caliendo, Cosima; Gerber, Susanne; Cocchiararo, Berardino; Reuter, Sabrina; Blüthgen, Nico; Mody, Karsten; Mishra, Bagdevi; Bálint, Miklós; Thines, Marco; Feldmeyer, Barbara

doi:10.7554/elife.65532

Cited by 41 publications

(34 citation statements)

References 57 publications

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“…This is in accordance with the study by Gričar et al (2013) , who reported that anatomical characteristics and signals of hydrological changes in Quercus robur L. xylem rings showed a strong response to micro-environmental conditions. In addition, genetics might also play a role in explaining the high variability found ( Pfenninger et al, 2021 ). We cannot exclude the possibility that such a high inter-individual variability might have obscured some patterns in alder anatomical responses to waterlogging.…”

Section: Discussionmentioning

confidence: 99%

Growth and Wood Trait Relationships of Alnus glutinosa in Peatland Forest Stands With Contrasting Water Regimes

et al. 2022

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Human-driven peatland drainage has occurred in Europe for centuries, causing habitat degradation and leading to the emission of greenhouse gases. As such, in the last decades, there has been an increase in policies aiming at restoring these habitats through rewetting. Alder (Alnus glutinosa L.) is a widespread species in temperate forest peatlands with a seemingly high waterlogging tolerance. Yet, little is known about its specific response in growth and wood traits relevant for tree functioning when dealing with changing water table levels. In this study, we investigated the effects of rewetting and extreme flooding on alder growth and wood traits in a peatland forest in northern Germany. We took increment cores from several trees at a drained and a rewetted stand and analyzed changes in ring width, wood density, and xylem anatomical traits related to the hydraulic functioning, growth, and mechanical support for the period 1994–2018. This period included both the rewetting action and an extreme flooding event. We additionally used climate-growth and climate-density correlations to identify the stand-specific responses to climatic conditions. Our results showed that alder growth declined after an extreme flooding in the rewetted stand, whereas the opposite occurred in the drained stand. These changes were accompanied by changes in wood traits related to growth (i.e., number of vessels), but not in wood density and hydraulic-related traits. We found poor climate-growth and climate-density correlations, indicating that water table fluctuations have a stronger effect than climate on alder growth. Our results show detrimental effects on the growth of sudden water table changes leading to permanent waterlogging, but little implications for its wood density and hydraulic architecture. Rewetting actions should thus account for the loss of carbon allocation into wood and ensure suitable conditions for alder growth in temperate peatland forests.

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Section: Discussionmentioning

confidence: 99%

Growth and Wood Trait Relationships of Alnus glutinosa in Peatland Forest Stands With Contrasting Water Regimes

et al. 2022

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“…While environmental adaptations are commonly highly polygenic (Barghi et al, 2019;Hartke et al, 2021;Pfenninger et al, 2021;Rivas et al, 2018), there is increasing evidence of the effect of single gene content variation (Liu et al, 2021). For example, as has been recently…”

Section: Discussionmentioning

confidence: 99%

Protein kinase gene declines linearly with elevation: a shared genomic feature across species and continents in lichenized fungi suggests role in climate adaptation

Merges

Grande

Valim

et al. 2022

Preprint

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Intraspecific genomic variability affects a species' adaptive potential towards climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many species have remarkable environmental tolerances, and often form populations in different climate zones. Here we combine comparative and population genomics to assess the presence and absence of genes in high elevation and low elevation genomes of two lichenized fungi of the genus Umbilicaria. The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked which genes increase or decrease in abundance within populations along elevation. In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinases (PKs) superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents. The protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations. We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.

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“…Finally, to detect consistent changes across replicates and, therefore, to identify reliable candidates for selected SNPs, a Cochran-Mantel-Haenszel's (CMH) test was performed merging the three replicates of each experimental group. After, a BH correction for false discovery rate and a cut-off at p < 0.01 was applied (Pfenninger et al, 2021) (which was not certified by peer review) is the author/funder. All rights reserved.…”

Section: Time-series Analysis Of Dna Poolseq Datamentioning

confidence: 99%

Detecting Cd adaptation footprint in C. riparius with a multi-genomic approach

Doria

Hannapel

Pfenninger

2021

Preprint

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Evolutionary processes and acquired tolerance to toxicants are important factors governing how animals respond to chemical exposure. Evidence for increased tolerance to cadmium (Cd), a widely distributed toxic metal in aquatic environments, in Chironomus riparius is conflicting and still questioned if it happens through phenotypic plasticity or genetic adaptation. The present study considered the relevance of directional environmental changes by increasing contaminant concentration in a multigenerational selection experiment. Evaluation of measurable life-cycle traits, transcriptomic responses and quantitative genetics from an evolve and resequencing (E&R) experiment were integrated to assess the potential of C. riparius to adapt to Cd. Survival tests revealed some adaptation to Cd exposure. Genomic analyses showed a strong, genome-wide selective response in all replicates, emphasizing that even control laboratory conditions continually exert selective pressure. The integration of transcriptomic and genomic data could isolate the genes related to Cd acquired resistance. Those genes could be linked to an efflux of metals. Therefore, it is possible to conclude that C. riparius can endure long-term Cd exposure also through genetic adaptation.

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Genomic basis for drought resistance in European beech forests threatened by climate change

Cited by 41 publications

References 57 publications

Growth and Wood Trait Relationships of Alnus glutinosa in Peatland Forest Stands With Contrasting Water Regimes

Growth and Wood Trait Relationships of Alnus glutinosa in Peatland Forest Stands With Contrasting Water Regimes

Protein kinase gene declines linearly with elevation: a shared genomic feature across species and continents in lichenized fungi suggests role in climate adaptation

Detecting Cd adaptation footprint in C. riparius with a multi-genomic approach

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