Contrasting nuclear and cytoplasmic exchanges between phylogenetically distant oak species (Quercus suber L. and Q. ilex L.) in Southern France: inferring crosses and dynamics

Niche evolution in a northern temperate tree lineage: biogeographical legacies in cork oaks (Quercus section Cerris)

BACKGROUND AND AIMS

Cork oaks (Quercus section Cerris) comprise 15 extant species in Eurasia. Despite being a small clade, they display a range of leaf morphologies comparable to the largest sections (>100 spp.) in Quercus. Their fossil record extends back to the Eocene. Here, we explore how cork oaks achieved their modern ranges and how legacy effects might explain niche evolution in modern species of section Cerris and its sister section Ilex, the holly oaks.

METHODS

We inferred a dated phylogeny for cork and holly oaks using a reduced-representation next-generation sequencing method, restriction site-associated DNA sequencing (RAD-seq), and used D-statistics to investigate gene flow hypotheses. We estimated divergence times using a fossilized birth-death model calibrated with 47 fossils. We used Köppen profiles, selected bioclimatic parameters and forest biomes occupied by modern species to infer ancestral climatic and biotic niches.

KEY RESULTS

East Asian and Western Eurasian cork oaks diverged initially in the Eocene. Subsequently, four Western Eurasian lineages (subsections) differentiated during the Oligocene and Miocene. Evolution of leaf size, form and texture was correlated, in part, with multiple transitions from ancestral humid temperate climates to mediterranean, arid and continental climates. Distantly related but ecologically similar species converged on similar leaf traits in the process.

CONCLUSIONS

Originating in temperate (frost-free) biomes, Eocene to Oligocene ranges of the primarily deciduous cork oaks were restricted to higher latitudes (Siberia to north of Paratethys). Members of the evergreen holly oaks (section Ilex) also originated in temperate biomes but migrated southwards and south-westwards into then-(sub)tropical southern China and south-eastern Tibet during the Eocene, then westwards along existing pre-Himalayan mountain ranges. Divergent biogeographical histories and deep-time phylogenetic legacies (in cold and drought tolerance, nutrient storage and fire resistance) thus account for the modern species mosaic of Western Eurasian oak communities, which are composed of oaks belonging to four sections.

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.

The Role of Population and Half-Sib Family on Driving Suitable Functional Traits for Quercus suber L. Forest Restoration

Research Highlights: Seedlings of different Quercus suber L. populations and half-sib families differ in their response to multiple stressors, which may have consequences on the future distribution of this Mediterranean species. Background and Objectives: Global change will likely increase the frequency and severity of drought in drylands. Plant species’ distributions will largely depend on their ability to respond to the combined effect of drought and other environmental stressors. Genetic diversity in morpho-functional traits are key components of this response. Yet, information on the response to multiple stresses is scarce for many iconic species. The present study assessed the variability in the response of populations and half-sib families of a Mediterranean acidophilous tree, cork oak, to drought and changes in soil conditions. Materials and Methods: We sampled acorns of half-sib families from two cork oak populations genetically introgressed with the alkaline-tolerant species Quercus ilex L., and from a non-introgressed cork oak population located in its core habitat. We germinated the acorns and subjected seedlings to contrasted levels of water availability and additions of calcium and magnesium carbonate, and assessed their morpho-physiological response. Results: Response to drought and soil chemistry composition differed between populations and families. For some traits, introgressed populations responded similarly to drought than the non-introgressed population. Conversely, the response to soil chemistry was not clearly related to introgression. When considering half-sib families within populations, the population effect diminished, which revealed the importance of intra-population variation. However, relevant traits for water scarcity adaptations, such as specific leaf area and root:shoot ratio, remained significantly different at the population level, which highlights the relevance of these traits for management. Conclusions: Our study shows that the adaptive management and restoration of cork oak forests should consider not only geographic provenances, but also half-sib lines within populations.

Plastome Evolution in Saxifragaceae and Multiple Plastid Capture Events Involving Heuchera and Tiarella

Saxifragaceae, a family of over 600 species and approximately 30 genera of herbaceous perennials, is well-known for intergeneric hybridization. Of the main lineages in this family, the Heuchera group represents a valuable model for the analysis of plastid capture and its impact on phylogeny reconstruction. In this study, we investigated plastome evolution across the family, reconstructed the phylogeny of the Heuchera group and examined putative plastid capture between Heuchera and Tiarella. Seven species (11 individuals) representing Tiarella, as well as Mitella and Heuchera, were selected for genome skimming. We assembled the plastomes, and then compared these to six others published for Saxifragaceae; the plastomes were found to be highly similar in overall size, structure, gene order and content. Moreover, ycf15 was lost due to pseudogenization and rpl2 lost its only intron for all the analyzed plastomes. Comparative plastome analysis revealed that size variations of the plastomes are purely ascribed to the length differences of LSC, SSC, and IRs regions. Using nuclear ITS + ETS and the complete plastome, we fully resolved the species relationships of Tiarella, finding that the genus is monophyletic and the Asian species is most closely related to the western North American species. However, the position of the Heuchera species was highly incongruent between nuclear and plastid data. Comparisons of nuclear and plastid phylogenies revealed that multiple plastid capture events have occurred between Heuchera and Tiarella, through putative ancient hybridization. Moreover, we developed numerous molecular markers for Tiarella (e.g., plastid hotspot and polymorphic nuclear SSRs), which will be useful for future studies on the population genetics and phylogeography of this disjunct genus.

Exploring the History of Chloroplast Capture in Arabis Using Whole Chloroplast Genome Sequencing

Chloroplast capture occurs when the chloroplast of one plant species is introgressed into another plant species. The phylogenies of nuclear and chloroplast markers from East Asian Arabis species are incongruent, which indicates hybrid origin and shows chloroplast capture. In the present study, the complete chloroplast genomes of A. hirsuta, A. nipponica, and A. flagellosa were sequenced in order to analyze their divergence and their relationships. The chloroplast genomes of A. nipponica and A. flagellosa were similar, which indicates chloroplast replacement. If hybridization causing chloroplast capture occurred once, divergence between recipient species would be lower than between donor species. However, the chloroplast genomes of species with possible hybrid origins, A. nipponica and A. stelleri, differ at similar levels to possible maternal donor species A. flagellosa, which suggests that multiple hybridization events have occurred in their respective histories. The mitochondrial genomes exhibited similar patterns, while A. nipponica and A. flagellosa were more similar to each other than to A. hirsuta. This suggests that the two organellar genomes were co-transferred during the hybridization history of the East Asian Arabis species.

Contribution of WUSCHEL-related homeobox (WOX) genes to identify the phylogenetic relationships among Petunia species

Developmental genes are believed to contribute to major changes during plant evolution, from infrageneric to higher levels. Due to their putative high sequence conservation, developmental genes are rarely used as molecular markers, and few studies including these sequences at low taxonomic levels exist. WUSCHEL-related homeobox genes (WOX) are transcription factors exclusively present in plants and are involved in developmental processes. In this study, we characterized the infrageneric genetic variation of Petunia WOX genes. We obtained phylogenetic relationships consistent with other phylogenies based on nuclear markers, but with higher statistical support, resolution in terminals, and compatibility with flower morphological changes.

Plastome data reveal multiple geographic origins of Quercus Group Ilex

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

Plastome data reveal multiple geographic origins of Quercus Group Ilex

Nucleotide sequences from the plastome are currently the main source for assessing taxonomic and phylogenetic relationships in flowering plants and their historical biogeography at all hierarchical levels. One major exception is the large and economically important genus Quercus (oaks). Whereas differentiation patterns of the nuclear genome are in agreement with morphology and the fossil record, diversity patterns in the plastome are at odds with established taxonomic and phylogenetic relationships. However, the extent and evolutionary implications of this incongruence has yet to be fully uncovered. The DNA sequence divergence of four Euro-Mediterranean Group Ilex oak species (Quercus ilex L., Q. coccifera L., Q. aucheri Jaub. & Spach., Q. alnifolia Poech.) was explored at three chloroplast markers (rbcL, trnK/matK, trnH-psbA). Phylogenetic relationships were reconstructed including worldwide members of additional 55 species representing all Quercus subgeneric groups. Family and order sequence data were harvested from gene banks to better frame the observed divergence in larger taxonomic contexts. We found a strong geographic sorting in the focal group and the genus in general that is entirely decoupled from species boundaries. High plastid divergence in members of Quercus Group Ilex, including haplotypes shared with related, but long isolated oak lineages, point towards multiple geographic origins of this group of oaks. The results suggest that incomplete lineage sorting and repeated phases of asymmetrical introgression among ancestral lineages of Group Ilex and two other main Groups of Eurasian oaks (Cyclobalanopsis and Cerris) caused this complex pattern. Comparison with the current phylogenetic synthesis also suggests an initial high- versus mid-latitude biogeographic split within Quercus. High plastome plasticity of Group Ilex reflects geographic area disruptions, possibly linked with high tectonic activity of past and modern distribution ranges, that did not leave imprints in the nuclear genome of modern species and infrageneric lineages.

Nuclear and plastid markers reveal the persistence of genetic identity: a new perspective on the evolutionary history of Petunia exserta

Recently divergent species that can hybridize are ideal models for investigating the genetic exchanges that can occur while preserving the species boundaries. Petunia exserta is an endemic species from a very limited and specific area that grows exclusively in rocky shelters. These shaded spots are an inhospitable habitat for all other Petunia species, including the closely related and widely distributed species P. axillaris. Individuals with intermediate morphologic characteristics have been found near the rocky shelters and were believed to be putative hybrids between P. exserta and P. axillaris, suggesting a situation where Petunia exserta is losing its genetic identity. In the current study, we analyzed the plastid intergenic spacers trnS/trnG and trnH/psbA and six nuclear CAPS markers in a large sampling design of both species to understand the evolutionary process occurring in this biological system. Bayesian clustering methods, cpDNA haplotype networks, genetic diversity statistics, and coalescence-based analyses support a scenario where hybridization occurs while two genetic clusters corresponding to two species are maintained. Our results reinforce the importance of coupling differentially inherited markers with an extensive geographic sample to assess the evolutionary dynamics of recently diverged species that can hybridize.

Ancient and current gene flow between two distantly related Mediterranean oak species, Quercus suber and Q. ilex

BACKGROUND AND AIMS

Quercus suber and Q. ilex are distantly related and their distributions partially overlap. They hybridize occasionally, but the complete replacement of Q. suber chloroplast DNA (cpDNA) by that of Q. ilex was identified in two specific geographical areas. The objective of this study was to determine whether the contrasting situation reflected current or recent geographical interspecies gene flow variation or was the result of ancient introgression.

METHODS

cpDNA PCR-RFLPs (restriction fragment length polymorphisms) and variation at ten nuclear microsatellite loci were analysed in populations of each species, in 16 morphologically intermediate individuals and the progeny of several of them. Interspecies nuclear introgression was based on individual admixture rates using a Bayesian approach with no a priori species assignment, and on a maximum-likelihood (ML) method, using allele frequencies in the allopatric populations of each species as controls. Gene flow was compared specifically between populations located within and outside the specific areas.

KEY RESULTS

High interspecies nuclear genetic differentiation was observed, with twice the number of alleles in Q. ilex than in Q. suber. According to Bayesian assignment, approx. 1 % of individuals had a high probability of being F(1) hybrids, and bidirectional nuclear introgression affected approx. 4 % of individuals in each species. Hybrid and introgressed individuals were identified predominantly in mixed stands and may have a recent origin. Higher proportions including allospecific genes recovered from past hybridization were obtained using the ML method. Similar rates of hybridization and of nuclear introgression, partially independent of cpDNA interspecies transfer suggestive of gene filtering, were obtained in the populations located within and outside the areas of complete cpDNA replacement.

CONCLUSIONS

The results did not provide evidence for geographical variation in interspecies gene flow. In contrast, historical introgression is supported by palynological records and constitutes the more reliable origin of cpDNA replacement in specific regions.

One species, many terpenes: matching chemical and biological diversity

Volatile terpenes have been proposed as chemotaxonomic markers, despite the strong environmental control on their synthesis. To clarify whether chemical profiles match biological diversity, cork oak, a monoterpene-emitting species that has been bred by humans and frequently hybridizes with other oaks, is a useful case-study. Analysis of the available genetic information in cork oak provenances suggests that volatile terpenes might indeed suitably track geographical diversity even at the intraspecific level. Phylogeographical diversity does not reflect chemical diversity in other evergreen oaks that have not been intensively bred. Breeding for productive traits might therefore drive selection for terpene diversity, in turn modulating important adaptive mechanisms against biotic and abiotic stressors.