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

Abstract

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

Temperature, rainfall and wind variables underlie environmental adaptation in natural populations of Drosophila melanogaster

“…Temperature and rainfall are the most widely used variables in GEA analysis in several species including D . melanogaster (Božičević et al, 2016; Cavedon et al, 2019; Gao et al, 2017; Hopley & Byrne, 2019; Kapun et al, 2020; Leroy et al, 2020; Mayol et al, 2020; Pina‐Martins et al, 2019; Todesco et al, 2019). Our results show that the majority of genes associated with environmental variables were associated with a temperature‐related one (400/748), while the number of genes associated with rainfall was smaller (241/748) (Table ).…”

How well do revegetation plantings capture genetic diversity?

“…[52,65]). Gene flow could assist in enhancing effective population size and adaptive genetic diversity, and thus the potential fitness and adaptability of revegetation plantings aiming to maintain and restore ecosystem services [66][67][68]. Understanding changes to genetic diversity over time, including the potential influences of gene flow, will help meet the overall objective of local revegetation efforts.…”

Prospects and limitations of genomic offset in conservation management

“…Cross‐validation in machine learning methods such as gradient or random forests should be done carefully, for example based on "leave‐population‐out" instead of "leave‐individual‐out" (i.e., spatial versus random cross‐validation), because the latter can artificially inflate goodness values due to the lack of independence of the training and test datasets (Meyer et al, 2019). If possible, final genomic offset calculations should account for these values, as in Pina‐Martins et al (2019) who used weighted average (by R 2 ) to indicate average RONA values across loci.…”