Standard models of speciation assume strictly dichotomous genealogies in which a species, the ancestor, is replaced by two offspring species. The reality is more complex: plant species can evolve from other species via isolation when genetic drift exceeds gene flow; lineage mixing can give rise to new species (hybrid taxa such as nothospecies and allopolyploids). The multi-copy, potentially multi-locus 5S rDNA is one of few gene regions conserving signal from dichotomous and reticulate evolutionary processes down to the level of intra-genomic recombination. Here, we provide the first high-throughput sequencing (HTS) 5S intergenic spacer (5S-IGS) data for a lineage of wind-pollinated subtropical to temperate trees, the Fagus crenata – F. sylvatica s.l. lineage, and its distant relative F. japonica. The observed 4,963 unique 5S-IGS variants reflect a long history of repeated incomplete lineage sorting and lineage mixing since the early Cenozoic of two or more paralogous-homoeologous 5S rDNA lineages. Extant species of Fagus are genetic mosaics and, at least to some part, of hybrid origin.

Little is known about the sources and age of C respired from tree roots. Previous research in tree stems has identified two functional pools of non-structural carbohydrates (NSC): an ‘active’ pool supplied directly from canopy photo-assimilates that supports metabolism and a ‘stored’ pool used when fresh C supplies are limited. We compared the C isotope composition of water soluble NSC and respired CO2 for aspen roots (Populus tremula hybrids) that were cut off fresh C supply via stem-girdling and prolonged incubation of excised roots. We used bomb radiocarbon to estimate the time elapsed since C fixation for respired CO2, water-soluble C, and structural α-cellulose. While freshly excised roots respired CO2 with mean age <1 yr, within a week the age increased to 1.6-2.9 yr. Freshly excised roots from trees girdled ~3 months previously had similar respiration rates and NSC stocks as un-girdled trees, but respired older C (~1.2 yr). We estimate the NSC in girdled roots must be replaced 5-7 times by reserves remobilized from root-external sources. Using a mixing model and observed correlations between Δ14C of water-soluble C and α-cellulose, we estimate ~30% of C is ‘active’ (~5 mg C g-1).

Measuring biological diversity is a crucial but difficult undertaking, as exemplified in oaks where complex morphological, ecological, biogeographic and genetic differentiation patterns collide with traditional taxonomy that measures biodiversity in number of species (or higher taxa). In this pilot study, we generated High-Throughput Sequencing (HTS) amplicon data of the intergenic spacer of the 5S nuclear ribosomal DNA cistron (5S-IGS) in oaks, using six mock samples that differ in geographic origin, species composition, and pool complexity. The potential of the marker for automated geno-taxonomy applications was assessed using a reference dataset of 1770 5S-IGS cloned sequences, covering the entire taxonomic breadth and distribution range of western Eurasian Quercus, and applying similarity (BLAST) and evolutionary approaches (ML trees and EPA). Both methods performed equally well, with correct identification of species in sections Ilex and Cerris in the pure and mixed samples and main genotypes shared by species of sect. Quercus. Application of different cut-off thresholds revealed that medium-high abundance sequences (>10 or 25) suffice for a net species identification of samples containing one or few individuals. Lower thresholds identify phylogenetic correspondence with all target species in highly mixed samples (analogue to environmental bulk samples) and include rare variants pointing towards reticulation, incomplete lineage sorting, pseudogenic 5S units, and in-situ (natural) contamination. Our pipeline is highly promising for future assessments of intra-specific and inter-population diversity, and of the genetic resources of natural ecosystems, which are fundamental to empower fast and solid biodiversity conservation programs worldwide.