Common microgeographical selection patterns revealed in four European conifers

Abstract

Microgeographical adaptation occurs when the effects of directional selection persist despite gene flow. Traits and genetic loci under selection can then show adaptive divergence, against the backdrop of little differentiation at other traits or loci. How common such events are and how strong the selection is that underlies them remain open questions. Here, we discovered and analysed microgeographical patterns of genomic divergence in four European and Mediterranean conifers with widely differing life-history traits and ecological requirements (Abies alba MIll., Cedrus atlantica [Endl.] Manetti, Pinus halepensis Mill. and Pinus pinaster Aiton) by screening pairs from geographically close forest stands sampled along steep ecological gradients. We inferred patterns of genomic divergence by applying a combination of divergence outlier detection methods, demographic modelling, Approximate Bayesian Computationinferences and genomic annotation to genomic data. Surprisingly for such small geographical scales, we showed that selection is strong in all species but generally affects different loci in each. A clear signature of selection was systematically detected on a fraction of the genome, of the order of 0.1%-1% of the loci depending on the species. The novel modelling method we designed for estimating selection coefficients showed that the microgeographical selection coefficient scaled by population size (Ns) was 2-30. Our results convincingly suggest that selection maintains withinpopulation diversity at microgeographical scales in spatially heterogeneous environments. Such genetic diversity is likely to be a major reservoir of adaptive potential, helping populations to adapt under fluctuating environmental conditions.

Fire frequency, as well as stress response and developmental gene control serotiny level variation in a widespread pioneer Mediterranean conifer, Pinus halepensis

“…This could be due to a difference in fire intensity and frequency (fire regime), our study areas being less affected by fires than the ones of Budde et al ( 2017 ), for instance. At the population level, the small levels of divergence are in agreement with previous studies using similar approaches (Scotti et al, 2023 ).…”

Divergent selection in Mediterranean pine stands on local spatial scales

“…Mediterranean-type mountains). Candidate gene approaches in maritime pine also found various outlier loci related to drought response and precipitation on large spatial scales [35,39,71] and between shady and sunny stands at the microenvironmental scale [14]. Our study detected a small number of outlier loci potentially related to water availability in maritime pine on the local scale, i.e.…”

“…Several studies successfully employed the paired sampling design to detect loci under selection (e.g. [14,18,[54][55][56][57][58]). In conifers, four previous studies revealed loci significantly associated to altitudinal or other microenvironmental gradients in Abies alba [57,58], Pinus halepensis [56], and P. pinaster and Cedrus atlantica [14], but only few loci showed consistent patterns of allele frequency shifts along the replicated stand pairs.…”

“…Recent studies have started to address the factors shaping local adaptation on the microenvironmental scale in long-lived tree species [11–14]. Several tropical tree species show adaptation to microenvironmental conditions [13,14]. Eperua falcata (Fabaceae), for example, showed divergent selection between groups of individuals growing in seasonally flooded bottomlands and adjacent groups growing on dry terra firme soils [17,18].…”

“…on scales of tens of meters of distance in herbaceous species and of hundreds of meters of distance in some woody species (reviewed in [9,10]). Recent studies have started to address the factors shaping local adaptation on the microenvironmental scale in long-lived tree species [11–14]. Several tropical tree species show adaptation to microenvironmental conditions [13,14].…”