Biology subjects

KREMER, A.

Publications and source records attributed to KREMER, A..

4 recordsLinked to original sources

bioRxiv2026

Adaptive variation in drought-related traits across southern and central European white oak (Quercus sect. Quercus) populations

European white oaks grow from the Mediterranean coast to Southern Scandinavia, a huge environmental gradient that has likely fostered environmental adaptation. In the face of climate change, leveraging adaptations through assisted gene flow could help improve drought tolerance and maintain forest health, but requires an understanding of the species-specific patterns of adaptation to be successful at the target location. In this study, three common gardens were established in Switzerland, Tuerkiye, and Austria for two European white oak species (Quercus robur, and Q. pubescens) using provenances from Central and Southern Europe. Almost 900 oak seedlings were measured at key water-use efficiency and life history traits for their first two year of life and genotyped with low coverage whole-genome sequencing. Trait heritability and environmental adaptation were then explored through pedigree-free animal models, while the genomic architecture of traits was mapped using a genome wide association study ("GWAS"). Across the species, the heritability of measured traits was moderate to high, but common garden had a strong impact, signalling an environmental effect on the phenotype. Adaptation to precipitation seasonality was detected in key productivity and growth traits for both species, but had a small effect on absolute trait values. The GWAS identified a striking 150 kbp association in the Cyclic Nucleotide-Gated Ion Channel gene family with leaf d13C values. This gene family is involved in stomata opening and likely impacts the intrinsic water use efficiency under stress. Together, the strong signals of phenotypic plasticity and rather weak signals of climatic adaptation in seedlings suggest that assisted gene flow in these two white oaks is relevant only for highly drought-sensitive populations, if conducted managers should focus on seeds sources with high precipitation seasonality and smaller leaf sizes.

evolutionary biology↗

bioRxiv2026

Pervasive historical introgression across oak phylogeny shapes gene expression

Oaks were once described as the "worst-case scenario" for the biological species concept because of the presumed pervasive hybridization and introgression among species. However, we still lack a full picture of genome-wide introgression across the eight sections of the Quercus phylogeny. Furthermore, we still do not have a complete characterization of what is introgressed and how it functionally influences the recipient species. Firstly, we used 168 whole genomes from 67 Quercus species belonging to the eight sections of the Quercus phylogeny and a super pan-genome to generate a phylogeny and test for ILS and introgression. Introgression was widespread: ancient introgression occurred between ancestors of the eight sections and more recent introgression took place within sections. Secondly, using genome-wide transcriptome, methylome, and chromatin accessibility data from a subset of 19 species sampled from four sections we demonstrated that introgressed genes are more highly and uniformly expressed than non-introgressed ones. This difference in expression level between introgressed and non-introgressed genes mostly results from cis-regulation, and is most likely due to DNA methylation decay in promoter ACRs. In summary, introgression has been a major evolutionary force during the whole evolutionary history of Quercus and had a significant impact on fundamental processes such as gene regulation and expression.

evolutionary biology↗

bioRxiv2023

Whole-genome screening for near-diagnostic genetic markers for white oak species identification in Europe

ContextIdentifying species in the European white oak complex has been a long standing concern in taxonomy, evolution, forest research and management. Quercus petraea, Q. robur, Q. pubescens and Q. pyrenaica are part of this species complex in western temperate Europe and hybridize in mixed stands, challenging species identification. AimsOur aim was to identify diagnostic single nucleotide polymorphisms (SNPs) for each of the four species that are suitable for routine use and rapid diagnosis in research and applied forestry. MethodsWe first scanned existing whole-genome and target-capture data sets in a reduced number of samples (training set) to identify candidate diagnostic SNPs, ie genomic positions being characterized by a reference allele in one species and by the alternative allele in all other species. Allele frequencies of the candidates SNPs were then explored in a larger, range-wide sample of populations in each species (validation step). ResultsWe found a subset of 38 SNPs (ten for Q. petraea, seven for Q. pubescens, nine for Q. pyrenaica and twelve for Q. robur) that showed near-diagnostic features across their species distribution ranges with Q. pyrenaica and Q. pubescens exhibiting the highest and lowest diagnosticity, respectively. ConclusionsWe provide a new, efficient and reliable molecular tool for the identification of the species Q. petraea, Q. robur, Q. pubescens and Q. pyrenaica, which can be used as a routine tool in forest research and management. This study highlights the resolution offered by whole-genome sequencing data to design diagnostic marker sets for taxonomic assignment, even for species complexes with relatively low differentiation.

plant biology↗

bioRxiv2021

Genome-wide evolutionary response of European oakssince the Little Ice Age

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.

evolutionary biology↗