Guillardin, L. | bioRxiv Science

bioRxiv2024

Low effective population size but high heterozygosity revealed by SNP analyses in adult and juvenile Thuja plicata in UK Woodlands

Thuja plicata is a conifer tree that is appreciated for its cultural, ecological and wood quality features in its natural range in western North America. It is also used in Europe and the UK for timber production. Some T. Plicata plantations in the UK are converted to Continuous Cover Forestry (CCF) management which uses natural regeneration and concerns have been raised about the genetic diversity in both the adult trees and the offspring. We studied species diversity, stand structure, and genetic diversity in four UK woodlands planted with T. plicata which contained both adults and naturally regenerated individuals. We discovered 61,104 Single Nucleotide Polymorphisms (SNPs) using Genotyping-by-Sequencing (GBS) and retained 504 SNPs for analysis. We selected 67 SNPs for PCR-based genotyping of 163 adults and 176 juveniles. We found a large number of monomorphic sites (40.3%) most of which were restricted to adults in a single woodland, indicative of a high genetic differentiation among woodlands. The effective population size (Ne) was very low across all sites (Ne < 100), varied between adults and juveniles, and was lowest in the most diverse woodland in terms of species and structure. In contrast, heterozygosity was high overall (Ho = 0.38), except in the divergent woodland (Ho = 0.26), and did not vary between adults and juveniles. Our findings and genotyping methods provide insights into the ability of CCF-managed woodlands, including instances of low genetic diversity in T. plicata, to face environmental shifts and disease threats.

genomics↗

bioRxiv2019

Adaptive Introgression Promotes Fast Adaptation In Oaks Marginal Populations

Range shifts and species range limits are two fundamental, related processes in population and evolutionary genetics that have received much attention since a large impact of climate change in species distributions was predicted. In general, there is a broad consensus on the effects of abiotic interactions on range limits, but comprehensive evidence supporting/rejecting the impact of biotic interactions is lacking. Hybridization has long been recognized as a biotic interaction favoring marginal populations establishment and range expansion through transgressive segregation or adaptive introgression, but recently new roles have been claimed for hybridization, such as the trigger of adaptive radiations, or indirect effects on population sizes that would allow persistence until new mutations arises or the environment changes. In this work, we selected two Mediterranean oak species with ecological discrimination based on soil pH, and intensively sampled three interspecific pairs of marginal populations from taxon-extreme environments under heterogeneous climate conditions. We genotyped 110 EST-SSR markers evenly distributed across their genomes and applied a variety of population and landscape genetics models to validate candidate genes for local adaptation. Then, several introgression screens on shared candidates showed that the three inter-specific population pairs contain evidences of adaptive introgression and that events occur in both directions. Other significant findings from our work are: (i) Aproximate Bayesian Computation coupled to coalescent simulations supports small hybridization rates since recent secondary contact in two population pairs affected by Quaternary climatic oscillations but continuous old interspecific gene flow in the pair less affected by climate, (ii) introgression at loci involved in local adaptations leads to strong geographic structure of marginal oak populations when sampling is large enough, and (iii) sampling efforts can be targeted to reveal different components of populations structure. Finally, we review evidences that support our conclusions and discuss some evolutionary implications of adaptive introgression on range expansion.

evolutionary biology↗