Genome-wide evolutionary response of European oaks since the Little Ice Age

Abstract

The pace of tree microevolution during Anthropocene warming is largely unknown. We used a retrospective approach to monitor genomic changes in oak trees since the Little Ice Age (LIA). Allelic frequency changes were assessed from whole-genome pooled sequences for four age-structured cohorts of sessile oak (Quercus petraea) dating back to 1680, in each of three different oak forests in France. The genetic covariances of allelic frequency changes increased between successive time periods, highlighting genome-wide effects of linked selection. We found imprints of convergent linked selection in the three forests during the late LIA, and a shift of selection during more recent time periods. The changes in allelic covariances within and between forests mirrored the documented changes in the occurrence of extreme events (droughts and frosts) over the last three hundred years. The genomic regions with the highest covariances were enriched in genes involved in plant responses to pathogens and abiotic stresses (temperature and drought). These responses are consistent with the reported sequence of frost (or drought) and disease damage ultimately leading to the oak dieback after extreme events. Our results therefore provide evidence of selection operating on long-lived species during recent climatic changes.

Extensive genetic variation of leaf specialized metabolites in sessile oak (Quercus petraea) populations

“…We observed low genetic differentiation among the nine sessile oak populations, which is consistent with previously published observations, for the same populations, and in oaks more generally (Leroy et al 2020;Saleh et al 2022). The lack of differentiation among oak populations likely results from large population sizes, limiting genetic drift, the continuous distribution of the species and extensive long distance seed and pollen dispersal (Gerber et al…”

“…The second scenario would be analogous to the first one, but instead of varying over the landscape, selection would vary in time, favouring different phenotypes depending on the year. Investigating allele frequencies at associated markers in trees of different ages could be a way to test this scenario(Saleh et al 2022). Moreover, selective trade-off may act in combination with these two scenarios to maintain balanced frequencies of phenotypic classes and alleles(Troth, Puzey, Kim, Willis & Kelly 2018).…”

Common microgeographical selection patterns revealed in four European conifers

“…The differences among species are probably driven by the observed differences in genome-wide background diversity structure, as captured by our analysis of historical demography, as the two pines show historically smaller effective sample sizes and historical bottlenecks, unlike fir and cedar (see also Budde et al, 2017;Olsson et al, 2021). It is worth noting that the recently introduced (and therefore recently diverged) C. atlantica populations show as large estimates of selection as longer established populations, suggesting that selection operated indeed not only over short distances, but also at short timescales (Saleh et al, 2022).…”

Ancient tree genomes for old questions

“…Genomic studies of contemporary tree cohorts established during discrete time periods can elucidate what alleles were selected for by past climates (e.g. Saleh et al, 2022). Ancient genomes could complement such approaches, more directly documenting the strength and direction of selection in the past.…”