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Using gradient forest to predict climate response and adaptation in Cork Oak
Publication . Vanhove, M.; Pina-Martins, F.; Coelho, A.C.; Branquinho, C.; Costa, A.; Batista, D.; Silva, A.; Sousa, P.; Henriques, A.; Marques, I.; Belkadi, B.; Knowles, L.L.; Paulo, O.S.
Climate change is impacting locally adapted species such as the keystone tree species
cork oak (Quercus suber L.). Quantifying the importance of environmental variables in
explaining the species distribution can help build resilient populations in restoration
projects and design forest management strategies. Using landscape genomics, we
investigated the population structure and ecological adaptation of this tree species
across the Mediterranean Basin. We applied genotyping by sequencing and derived
2,583 single nucleotide polymorphism markers genotyped from 81 individuals across
17 sites in the studied region. We implemented an approach based on the nearest
neighbour haplotype ‘coancestry’ and uncovered a weak population structure
along an east–west
climatic gradient across the Mediterranean region. We identified
genomic regions potentially involved in local adaptation and predicted differences
in the genetic composition across the landscape under current and future climates.
Variants associated with temperature and precipitation variables were detected, and
we applied a nonlinear multivariate association method, gradient forest, to project
these gene–environment
relationships across space. The model allowed the identification
of geographic areas within the western Mediterranean region most sensitive
to climate change: south-western
Iberia and northern Morocco. Our findings provide
a preliminary assessment towards a potential management strategy for the conservation
of cork oak in the Mediterranean Basin
NCBI Mass Sequence Downloader–Large dataset downloading made easy
Publication . Pina Martins, Francisco; S. Paulo, Octávio
Population structure in Quercus suber L. revealed by nuclear microsatellite markers
Publication . Sousa, Filipe; Costa, Joana; Ribeiro, Carla; Varandas, Marta; Pina-Martins, Francisco; Simões, Fernanda; Matos, José; Glushkova, Maria; Miguel, Célia; Veloso, Maria Manuela; Oliveira, Margarida; Ricardo, Cândido Pinto; Batista, Dora; Paulo, Octávio S.
Quercus suber L. is a sclerophyllous tree species native to the western Mediterranean,
a region that is considered highly vulnerable to increased temperatures and severe dry
conditions due to environmental changes. Understanding the population structure
and demographics of Q. suber is essential in order to anticipate whether populations at
greater risk and the species as a whole have the genetic background and reproductive
dynamics to enable rapid adaptation. The genetic diversity of Q. suber has been subject
to different studies using both chloroplast and nuclear data, but population structure
patterns remain unclear. Here, we perform genetic analyses on Q. suber using 13
nuclear microsatellite markers, and analysed 17 distinct locations across the entire
range of the species. Structure analyses revealed that Q. suber may contain three major
genetic clusters that likely result from isolation in refugia combined with posterior
admixture and putative introgression from other Quercus species. Our results show a
more complex structure scenario than previously inferred for Q. suber using nuclear
markers and suggest that different southern populations contain high levels of genetic
variation that may contribute to the resilience of Q. suber in a context of environmental
change and adaptive pressure.
New insights into adaptation and population structure of cork oak using genotyping by sequencing
Publication . Pina-Martins, Francisco; Baptista, João; Pappas, Georgios; Paulo, Octávio S.
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.
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Fundação para a Ciência e a Tecnologia
Programa de financiamento
3599-PPCDT
Número da atribuição
SOBREIRO/0036/2009