A species-discriminatory single-nucleotide polymorphism set reveals maintenance of species integrity in hybridizing European white oaks (Quercus spp.) despite high levels of admixture

Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex evolutionary relationships in closely related species and to observe variations in species relationships across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution in southwest China and probably constitute a syngameon. In this study, we mapped resequencing data from different species in this group to the Quercus aquifolioides reference genome to obtain a high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. We reconstructed their phylogenetic relationships, explored the level and pattern of introgression among these species and investigated gene tree variation in the genomes of these species using sliding windows. The same or closely related plastomes were found to be shared extensively among different species within a specific geographical area. Phylogenomic analyses of genome-wide SNP data found that most oaks in the Himalayan-Hengduan subalpine clade showed genetic coherence, but several species were found to be connected by introgression. The gene trees obtained using sliding windows showed that the phylogenetic relationships in the genomes of oaks are highly heterogeneous and therefore highly obscured. Our study found that all the oaks of the Himalayan-Hengduan subalpine clade from southwest China form a syngameon. The obscured phylogenetic relationships observed empirically across the genome are best explained by interspecific gene flow in conjunction with incomplete lineage sorting.

Tracking population structure and phenology through time using ancient genomes from waterlogged white oak wood

Whole genome characterizations of crop plants based on ancient DNA have provided unique keys for a better understanding of the evolutionary origins of modern cultivars, the pace and mode of selection underlying their adaptation to new environments and the production of phenotypes of interest. Although forests are among the most biologically rich ecosystems on earth and represent a fundamental resource for human societies, no ancient genome sequences have been generated for trees. This contrasts with the generation of multiple ancient reference genomes for important crops. Here, we sequenced the first ancient tree genomes using two white oak wood remains from Germany dating to the Last Little Ice Age (15th century CE, 7.3× and 4.0×) and one from France dating to the Bronze Age (1700 BCE, 3.4×). We assessed the underlying species and identified one medieval remains as a hybrid between two common oak species (Quercus robur and Q. petraea) and the other two remains as Q. robur. We found that diversity at the global genome level had not changed over time. However, exploratory analyses suggested that a reduction of diversity took place at different time periods. Finally, we determined the timing of leaf unfolding for ancient trees for the first time. The study extends the application of ancient wood beyond the classical proxies of dendroclimatology, dendrochronology, dendroarchaeology and dendroecology, thereby enhancing resolution of inferences on the responses of forest ecosystems to past environmental changes, epidemics and silvicultural practices.

A Small Set of Nuclear Markers for Reliable Differentiation of the Two Closely Related Oak Species Quercus Robur and Q. Petraea

Quercus robur and Q. petraea are, in addition to Fagus sylvatica, the main economically used deciduous tree species in Europe. Identification of these two species is crucial because they differ in their ecological demands. Because of a changing climate, foresters must know more than ever which species will perform better under given environmental conditions. The search for differentiating molecular markers between these two species has already lasted for decades. Until now, differentiation has only been possible in approaches with a combination of several molecular markers and a subsequent statistical analysis to calculate the probability of being one or the other species. Here, we used MiSeq Illumina data from pools of Q. robur and Q. petraea specimens and identified nuclear SNPs and small InDels versus the Q. robur reference genome. Selected sequence variants with 100% allele frequency difference between the two pools were further validated in an extended set of Q. robur and Q. petraea specimens, and then the number of markers was deliberately reduced to the smallest possible set for species differentiation. A combination of six markers from four nuclear regions is enough to identify Q. robur, Q. petraea or hybrids between these two species quite well and represents a marker set that is cost-efficient and useable in every laboratory.

Genetic Variability and Admixture Zones in the Italian Populations of Turkey Oak (Quercus cerris L.)

The Turkey oak (Quercus cerris L.) is widely distributed in Italy, where it is the ecologically dominant oak on sandy and acidic soil. In this work, we analysed 23 natural populations by means of eight SSR (microsatellite) markers, to obtain the first synthetic map of genetic variability for this species and to study its dispersion during the Holocene, due to the possibility that at least one refugium during the Last Glacial Maximum was in Italy. The analyses showed a good amount of genetic variability together with fair differentiation between populations, as indicated by F_ST = 0.059. A Bayesian analysis of the amount of admixture among populations revealed the presence of four putative gene pools of origin and a rough subdivision of the populations according to their geographic location, as confirmed by the spatial analysis. No evidence for the existence of putative refugial populations was found; however, this study paves the way for the planning of conservation strategies also with regard to the relationship between Turkey oak and other oak species in Italy.

Mitochondrial Genome of Fagus sylvatica L. as a Source for Taxonomic Marker Development in the Fagales

European beech, Fagus sylvatica L., is one of the most important and widespread deciduous tree species in Central Europe and is widely managed for its hard wood. The complete DNA sequence of the mitochondrial genome of Fagus sylvatica L. was assembled and annotated based on Illumina MiSeq reads and validated using long reads from nanopore MinION sequencing. The genome assembled into a single DNA sequence of 504,715 bp in length containing 58 genes with predicted function, including 35 protein-coding, 20 tRNA and three rRNA genes. Additionally, 23 putative protein-coding genes were predicted supported by RNA-Seq data. Aiming at the development of taxon-specific mitochondrial genetic markers, the tool SNPtax was developed and applied to select genic SNPs potentially specific for different taxa within the Fagales. Further validation of a small SNP set resulted in the development of four CAPS markers specific for Fagus, Fagaceae, or Fagales, respectively, when considering over 100 individuals from a total of 69 species of deciduous trees and conifers from up to 15 families included in the marker validation. The CAPS marker set is suitable to identify the genus Fagus in DNA samples from tree tissues or wood products, including wood composite products.

Genomic and phenotypic divergence unveil microgeographic adaptation in the Amazonian hyperdominant tree Eperua falcata Aubl. (Fabaceae)

Plant populations can undergo very localized adaptation, allowing widely distributed populations to adapt to divergent habitats in spite of recurrent gene flow. Neotropical trees-whose large and undisturbed populations often span a variety of environmental conditions and local habitats-are particularly good models to study this process. Here, we explore patterns of adaptive divergence from large (i.e., regional) to small (i.e., microgeographic) spatial scales in the hyperdominant Amazonian tree Eperua falcata Aubl. (Fabaceae) under a replicated design involving two microhabitats (~300 m apart) in two study sites (~300 km apart). A three-year reciprocal transplant illustrates that, beyond strong maternal effects and phenotypic plasticity, genetically driven divergence in seedling growth and leaf traits was detected both between seedlings originating from different regions, and between seedlings from different microhabitats. In parallel, a complementary genome scan for selection was carried out through whole-genome sequencing of tree population pools. A set of 290 divergence outlier SNPs was detected at the regional scale (between study sites), while 185 SNPs located in the vicinity of 106 protein-coding genes were detected as replicated outliers between microhabitats within regions. Outlier-surrounding genomic regions are involved in a variety of physiological processes, including plant responses to stress (e.g., oxidative stress, hypoxia and metal toxicity) and biotic interactions. Together with evidence of microgeographic divergence in functional traits, the discovery of genomic candidates for microgeographic adaptive divergence represents a promising advance in our understanding of local adaptation, which probably operates across multiple spatial scales and underpins divergence and diversification in Neotropical trees.