Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis

Modesto, Inês; Miguel, Celia María Gonzalo; Pina‐Martins, Francisco; Glushkova, Maria; Veloso, Manuela; Paulo, Octávio S.; Batista, Dora

doi:10.1007/s11295-014-0786-1

Cited by 25 publications

(15 citation statements)

References 71 publications

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“…Our work can be expanded in several directions. First and foremost, it is mandatory to study quantum gravity beyond the tensor and momentum structures retained here, possibly including non-local invariants [66,67]. It will also be important to study extensions of functional RG flows beyond the present levels of approximation.…”

Section: Discussionmentioning

confidence: 99%

Further evidence for asymptotic safety of quantum gravity

Falls¹,

Litim²,

et al. 2016

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Article (Published Version) http://sro.sussex.ac.uk Falls, K, Litim, D, Nikolakopoulos, K and Rahmede, C (2016) Further evidence for asymptotic safety of quantum gravity. Physical Review D, 93 (10). p. 104022. ISSN 1550-7998 This version is available from Sussex Research Online: http://sro.sussex.ac.uk/63626/ This document is made available in accordance with publisher policies and may differ from the published version or from the version of record. If you wish to cite this item you are advised to consult the publisher's version. Please see the URL above for details on accessing the published version. Copyright and reuse:Sussex Research Online is a digital repository of the research output of the University.Copyright and all moral rights to the version of the paper presented here belong to the individual author(s) and/or other copyright owners. To the extent reasonable and practicable, the material made available in SRO has been checked for eligibility before being made available.Copies of full text items generally can be reproduced, displayed or performed and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way.Further evidence for asymptotic safety of quantum gravity The asymptotic safety conjecture is examined for quantum gravity in four dimensions. Using the renormalization group, we find evidence for an interacting UV fixed point for polynomial actions up to the 34th power in the Ricci scalar. The extrapolation to infinite polynomial order is given, and the selfconsistency of the fixed point is established using a bootstrap test. All details of our analysis are provided. We also clarify further aspects such as stability, convergence, the role of boundary conditions, and a partial degeneracy of eigenvalues. Within this setting we find strong support for the conjecture.

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Section: Discussionmentioning

confidence: 99%

Further evidence for asymptotic safety of quantum gravity

Falls¹,

Litim²,

et al. 2016

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“…Unlike what happen in other oak species (Rellstab et al, 2016), studies integrating genetic information and response to climatic alterations of Q. suber (e.g. (Modesto et al, 2014)) are rare and of small scale (Ramírez-Valiente, Valladares, Huertas, Granados, & Aranda, 2011). Even though this study made the important assessement that some cork oak traits can be associated with genetic variants, its local geographic scope, combined with the relatively low number if used markers, limits its utility in a distribution wide perspective.…”

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confidence: 98%

“…Both these studies also highlight the need for a genetic study regarding the adaptation potential of Q. suber. (Modesto et al, 2014)) are rare and of small scale (Ramírez-Valiente, Valladares, Huertas, Granados, & Aranda, 2011). (Modesto et al, 2014)) are rare and of small scale (Ramírez-Valiente, Valladares, Huertas, Granados, & Aranda, 2011).…”

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confidence: 99%

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Pina‐Martins

Baptista

Παππάς

et al. 2018

Global Change Biology

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Species respond to global climatic changes in a local context. Understanding this process, including its speed and intensity, is paramount due to the pace at which such changes are currently occurring. Tree species are particularly interesting to study in this regard due to their long generation times, sedentarism, and ecological and economic importance. Quercus suber L. is an evergreen forest tree species of the Fagaceae family with an essentially Western Mediterranean distribution. Despite frequent assessments of the species' evolutionary history, large-scale genetic studies have mostly relied on plastidial markers, whereas nuclear markers have been used on studies with locally focused sampling strategies. In this work, "Genotyping by sequencing" is used to derive 1,996 single nucleotide polymorphism markers to assess the species' evolutionary history from a nuclear DNA perspective, gain insights into how local adaptation is shaping the species' genetic background, and to forecast how Q. suber may respond to global climatic changes from a genetic perspective. Results reveal (a) an essentially unstructured species, where (b) a balance between gene flow and local adaptation keeps the species' gene pool somewhat homogeneous across its distribution, but still allowing (c) variation clines for the individuals to cope with local conditions. "Risk of Non-Adaptedness" (RONA) analyses suggest that for the considered variables and most sampled locations, (d) the cork oak should not require large shifts in allele frequencies to survive the predicted climatic changes. Future directions include integrating these results with ecological niche modeling perspectives, improving the RONA methodology, and expanding its use to other species. With the implementation presented in this work, the RONA can now also be easily assessed for other organisms. K E Y W O R D Sassociation study, genotyping by sequencing, local adaptation, natural selection effects, Quercus suber, risk of non-adaptedness, West Mediterranean

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“…Additionally, in cork oak seedlings exposed to high irradiance and drought under controlled environment, provenances from dry places exhibited higher tolerance to these environmental stressors, despite no relevant change in morphology (Aranda et al 2005, Rzigui et al 2017. Other studies analyzed the variability of candidate genes related to different environmental conditions, suggesting the existence of local adaptations (Modesto et al 2014, Magalhães et al 2015. Epigenetic regulation has also been reported as an important factor for adaptation of cork oak to specific environmental stresses (Correia et al 2013).…”

Section: Discussionmentioning

confidence: 99%

Delineation of seed collection zones based on environmental and genetic characteristics for Quercus suber L. in Sardinia, Italy

Dato¹,

Teani²,

Mattioni³

et al. 2018

iForest

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The assessment of seed zones or regions of provenance (RoP) to preserve local adaptation of tree species is an effective tool for the correct management of forest reproductive materials. The RoP for a species or sub-species is the area or group of areas subject to sufficiently uniform ecological conditions in which stands or seed sources show similar phenotypic or genetic characters, taking into account altitudinal boundaries where appropriate. However, the delineation of RoPs is commonly based on estimates of intrinsic environmental homogeneity, mainly climate and/or soil characteristics. The integration of genetic data into RoP maps is an important strategy to obtain a sound tool for managing forest reproductive materials. A study on Quercus suber (cork oak) in Sardinia (Italy) was carried out with the aim of determining ecological regions of provenance, investigating the genetic diversity among populations at the regional scale and identifying possible areas of interest for valorising the available germplasm. Identification of these areas was performed by Reserve Selection Analysis, which allows to identify priority areas by assessing the minimum number of sites required to include all the genetic diversity estimated by genetic analysis. Four spatial clusters were obtained based on environmental data: the northern and northern-eastern parts of the island were included in the Northern RoP; the second RoP covered the western part; and the third RoP enclosed the south-eastern region. The last group was distributed on the central part of the island (Central RoP) and includes the higher elevations. The sampled populations showed a low differentiation among populations and low diversity. According to the Reserve Selection Analysis, four conservation priority areas were identified. These indications can be useful at the local level because these sites can be proposed as stands for seed collection for future plantations.

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Identifying signatures of natural selection in cork oak (Quercus suber L.) genes through SNP analysis

Cited by 25 publications

References 71 publications

Further evidence for asymptotic safety of quantum gravity

Further evidence for asymptotic safety of quantum gravity

New insights into adaptation and population structure of cork oak using genotyping by sequencing

Delineation of seed collection zones based on environmental and genetic characteristics for Quercus suber L. in Sardinia, Italy

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