Adaptive evolution of Mediterranean pines

Intrapopulation germinability may help the Mediterranean plant species Poterium spinosum L. to cope with climate changes and landscape fragmentation

Poterium spinosum L. is a key plant species forming typical shrub communities, distributed across the Mediterranean eastern coasts. The conservation of P. spinosum is thus of the utmost importance, especially due to the ever-increasing environmental pressures like climate changes and habitat fragmentation. This study, in particular, investigated for the first time the germination variability of P. spinosum at intrapopulation level, by analysing the germination behavior of five different subpopulations growing along the coasts of Sicily. For a more exhaustive picture of the main drivers of biodiversity loss affecting the distributional area of P. spinosum, the trends of climate and land-cover changes were also studied over the periods 1931-2020 and 1958-2018, respectively. The results found significant intrapopulation variability in P. spinosum, whose germination parameters showed that fruits and seeds from distinct subpopulations respond differently to diverse temperatures. Seeds showed generally higher values of final germination percentage (FGP) compared to fruits, and at higher temperatures: the highest FGP in seeds was 70% at 20 °C, whereas in fruits was 58.2% at 15 °C. The environmental threats showed worrying trends across the study area: during 1931-2020, the average temperature increased by 1.5 °C, whereas the average rainfall declined from 710 to 650 mm. Similarly, in the period 1958-2018, the analysis of the CORINE land-cover changes showed a highly fragmented agricultural landscape, where natural areas were reduced to 2.5-5.0%. Germination variability at intrapopulation level should be considered as a fundamental adaptation strategy, which can increase the reproductive success of P. spinosum under climate and land-cover changes.

Rise, fall and hope for the Sicilian endemic plant Muscari gussonei: A story of survival in the face of narrow germination optimum, climate changes, desertification and habitat fragmentation

Muscari gussonei is an endangered endemic plant growing on fragmented Mediterranean coastal dunes. This study focused on the germination performance of M. gussonei at two fixed temperatures, 10 and 15 °C, and at an alternating one, 10/20 °C, and on the multi-temporal trends of temperature and rainfall during 1931-2020, as well as on the patterns of desertification and land-cover changes over the last 60 years. High and similar germinability was found for different populations of M. gussonei, in particular, the final germination percentage (FGP) was ≥95 % for the three treatments. The general pattern was the lower the temperature the higher and faster the germination. However, germination speed varied significantly among populations. This intraspecific variability of germination behavior may suggest a certain level of ecophysiological plasticity in M. gussonei, thus raising hopes on the capacity of M. gussonei to respond better to the ongoing severe environmental changes. In the period 1931-2020, indeed, the average temperature rose by 1.5 °C, from 16.8 to 18.3 °C, which is equivalent to the enormous increase of 0.17 °C per decade. Similarly, the average rainfall declined by 100 mm, from 600 to 500 mm. Another serious stressor was desertification, which affects >90 % of the distributional area of M. gussonei. A further factor of ecological degradation is a considerably altered landscape, where the agricultural component accounts for c. 85 %, whereas natural and seminatural areas were only c. 10 %. Increasing temperature and dryness will inevitably reduce the germinability of M. gussonei, characterized by a narrow germination optimum of 10-15 °C. The future of M. gussonei looks even more dramatic if we consider its small and scattered populations distributed in an agricultural matrix affected by high levels of desertification. Only multivariate information at different space-time scales can provide an exhaustive picture for implementing effective conservation strategies.

Research on the Differences in Phenotypic Traits and Nutritional Composition of Acer Truncatum Bunge Seeds from Various Regions

Acer truncatum Bunge (ATB) is an excellent edible woody oil tree species since it bears a huge amount of fruit and has strong adaptability to be widely cultivated. Selecting an optimal cultivation region for ATB is crucial to improving China's woody oil industrialization. Chemical analysis, correlation analysis, and affiliation function values were used in the present research to systematically analyze the phenotypic traits, organic compound content, and seed oil chemical composition of the seeds of ATB from nine regions. The average contents of oil, protein, and soluble sugar in ATB seeds were 43.30%, 17.40%, and 4.57%, respectively. Thirteen fatty acids were identified from ATB seed oil, the highest content of which was linoleic acid (37.95%) and nervonic acid content was 5-7%. The maximum content of unsaturated fatty acids in ATB seed oil was 90.09%. Alpha-tocopherol content was up to 80.75 mg/100 g. The degree of variation in seed quality traits (25.96%) was stronger than in morphological traits (14.55%). Compared to environmental factors, the phenotypic traits of seeds contribute more to organic compounds and fatty acids. Combining the values of the indicator affiliation functions, Gilgarang, Tongliao, Inner Mongolia was selected as the optimal source of ATB for fruit applications from nine regions.

Functional phenotypic plasticity mediated by water stress and [CO2] explains differences in drought tolerance of two phylogenetically close conifers

Forests are threatened globally by increased recurrence and intensity of hot droughts. Functionally close coexisting species may exhibit differences in drought vulnerability large enough to cause niche differentiation and affect forest dynamics. The effect of rising atmospheric [CO2], which could partly alleviate the negative effects of drought, may also differ between species. We analysed functional plasticity in seedlings of two taxonomically close pine species (Pinus pinaster Ait., Pinus pinea L.) under different [CO2] and water stress levels. The multidimensional functional trait variability was more influenced by water stress (preferentially xylem traits) and [CO2] (mostly leaf traits) than by differences between species. However, we observed differences between species in the strategies followed to coordinate their hydraulic and structural traits under stress. Leaf 13C discrimination decreased with water stress and increased under elevated [CO2]. Under water stress both species increased their sapwood area to leaf area ratios, tracheid density and xylem cavitation, whereas they reduced tracheid lumen area and xylem conductivity. Pinus pinea was more anisohydric than P. pinaster. Pinus pinaster produced larger conduits under well-watered conditions than P. pinea. Pinus pinea was more tolerant to water stress and more resistant to xylem cavitation under low water potentials. The higher xylem plasticity in P. pinea, particularly in tracheid lumen area, expressed a higher capacity of acclimation to water stress than P. pinaster. In contrast, P. pinaster coped with water stress comparatively more by increasing plasticity of leaf hydraulic traits. Despite the small differences observed in the functional response to water stress and drought tolerance between species, these interspecific differences agreed with ongoing substitution of P. pinaster by P. pinea in forests where both species co-occur. Increased [CO2] had little effect on the species-specific relative performance. Thus, a competitive advantage under moderate water stress of P. pinea compared with P. pinaster is expected to continue in the future.

Plant Traits and Phylogeny Predict Soil Carbon and Nutrient Cycling in Mediterranean Mixed Forests

Soil functioning is closely linked to the interactions between biological communities with the physical environment. Yet, the impact of plant community attributes on metabolic processes promoting soil nutrient cycling remains largely unknown. We hypothesized that the plant community acts as a regulating agent of nutrient mobilization in soils according to the phylogenetic and morpho-functional traits of plant species of which it is composed. Rhizosphere soils were collected in autumn and spring under 32 tree and shrub species in two Mediterranean mixed forests (four plots in each) located in southern Spain, and nine soil enzymatic activities related to C, N and P mobilization were assessed. Phylogeny and morpho-functional traits of plant species were recorded and their imprint in soil enzymatic activities across forests was determined. The results showed a plant phylogenetic signal for N mobilization in both forests, while it varied across forests for non-labile C and P mobilization. The plant phylogenetic signals were primarily driven by lineages that diversified through the Miocene, about 25 Myr ago. In addition, leaf traits and plant’s mycorrhizal type explained soil enzymatic activities independently from phylogeny. C and P mobilization increased under ectomycorrhizal plants, whilst enhanced N mobilization did occur under arbuscular mycorrhizal ones. The plant community composition led to a different carbon and nutrient mobilization degree, which in turn was mediated by distinct microbial communities mirroring differentiated resource-acquisition strategies of plants. Our results highlight the role of plant traits and mycorrhizal interactions in modulating carbon and nutrient cycling in Mediterranean mixed forest soils.

Comparative genome sequence and phylogenetic analysis of chloroplast for evolutionary relationship among Pinus species

Genus Pinus is a widely dispersed genus of conifer plants in the Northern Hemisphere. However, the inadequate accessibility of genomic knowledge limits our understanding of molecular phylogeny and evolution of Pinus species. In this study, the evolutionary features of complete plastid genome and the phylogeny of the Pinus genus were studied. A total of thirteen divergent hotspot regions (trnk-UUU, matK, trnQ-UUG, atpF, atpH, rpoC1, rpoC2, rpoB, ycf2, ycf1, trnD-GUC, trnY-GUA, and trnH-GUG) were identified that would be utilized as possible genetic markers for determination of phylogeny and population genetics analysis of Pinus species. Furthermore, seven genes (petD, psaI, psaM, matK, rps18, ycf1, and ycf2) with positive selection site in Pinus species were identified. Based on the whole genome this phylogenetic study showed that twenty-four Pinus species form a significant genealogical clade. Divergence time showed that the Pinus species originated about 100 million years ago (MYA) (95% HPD, 101.76.35–109.79 MYA), in lateral stages of Cretaceous. Moreover, two of the subgenera are consequently originated in 85.05 MYA (95% HPD, 81.04–88.02 MYA). This study provides a phylogenetic relationship and a chronological framework for the future study of the molecular evolution of the Pinus species.

Gymnosperm Resprouting—A Review

Gymnosperms are generally regarded as poor resprouters, especially when compared to angiosperms and particularly following major disturbance. However, is it this clear-cut? This review investigates two main aspects of gymnosperm resprouting: (i) various papers have provided exceptions to the above generalization—how frequent are these exceptions and are there any taxonomic trends?; and (ii) assuming gymnosperms are poor resprouters are there any anatomical or physiological reasons why this is the case? Five of six non-coniferous gymnosperm genera and 24 of 80 conifer genera had at least one species with a well-developed resprouting capability. This was a wider range than would be expected from the usual observation ‘gymnosperms are poor resprouters’. All conifer families had at least three resprouting genera, except the monospecific Sciadopityaceae. Apart from the aboveground stem, buds were also recorded arising from more specialised structures (e.g., lignotubers, tubers, burls and underground stems). In some larger genera it appeared that only a relatively small proportion of species were resprouters and often only when young. The poor resprouting performance of mature plants may stem from a high proportion of apparently ‘blank’ leaf axils. Axillary meristems have been recorded in a wide range of conifer species, but they often did not form an apical dome, leaf primordia or vascular connections. Buds or meristems that did form often abscised at an early stage. While this review has confirmed that conifers do not resprout to the same degree as angiosperms, it was found that a wide diversity of gymnosperm genera can recover vegetatively after substantial disturbance. Further structural studies are needed, especially of: (i) apparently blank leaf axils and the initial development of axillary meristems; (ii) specialised regeneration structures; and (iii) why high variability can occur in the resprouting capacity within species of a single genus and within genera of the same family.

Genetic adaptation of Tibetan poplar (Populus szechuanica var. tibetica) to high altitudes on the Qinghai-Tibetan Plateau

Plant adaptation to high altitudes has long been a substantial focus of ecological and evolutionary research. However, the genetic mechanisms underlying such adaptation remain poorly understood. Here, we address this issue by sampling, genotyping, and comparing populations of Tibetan poplar, Populus szechuanica var. tibetica, distributed from low (~2,000 m) to high altitudes (~3,000 m) of Sejila Mountain on the Qinghai-Tibet Plateau. Population structure analyses allow clear classification of two groups according to their altitudinal distributions. However, in contrast to the genetic variation within each population, differences between the two populations only explain a small portion of the total genetic variation (3.64%). We identified asymmetrical gene flow from high- to low-altitude populations. Integrating population genomic and landscape genomic analyses, we detected two hotspot regions, one containing four genes associated with altitudinal variation, and the other containing ten genes associated with response to solar radiation. These genes participate in abiotic stress resistance and regulation of reproductive processes. Our results provide insight into the genetic mechanisms underlying high-altitude adaptation in Tibetan poplar.

How Does Water Availability Affect the Allocation to Bark in a Mediterranean Conifer?

Bark thickness is a key structural feature in woody plants in the protection against fire. We used 19 provenances of Pinus halepensis, an obligate-seeder species, in a replicated common garden at two environments contrasting in water availability to assess the interacting effects of site environment and population in the relative allocation to bark, expecting lower allocation at the drier site. Secondly, given the average fire frequency, we analyzed whether trees reached the critical absolute thickness soon enough for population persistence via aerial seed bank. Our analyses indicated that trees at the moister site allocated a rather fixed quantity of resources independent of tree size, and almost all populations reached critical absolute bark thickness to eventually survive fire. In contrast, at the drier site allocation to bark reduced with tree size, and most populations did not reach the critical bark thickness. Populations from areas with higher fire frequency had thicker basal bark, while those from areas with severe droughts and short vegetative periods, had thinner bark. In conclusion, drought-stressed trees have a higher risk to die from fires before achieving reproduction and building a sufficient aerial seed bank.

Neutral and Climate-Driven Adaptive Processes Contribute to Explain Population Variation in Resin Duct Traits in a Mediterranean Pine Species

Resin ducts are important anatomical defensive traits related to biotic resistance in conifers. Previous studies have reported intraspecific genetic variation in resin duct characteristics. However, little is currently known about the micro-evolutionary patterns and adaptive value of these defensive structures. Here, we quantified inter-population genetic variation in resin duct features and their inducibility in Pinus pinaster and assessed whether such variation was associated with climate gradients. To that end, we characterized the resin duct system of 2-year-old saplings from 10 populations across the species' distribution range. We measured axial resin duct features (density, mean size, and percentage conductive area of resin ducts) and their inducibility in response to methyl jasmonate. Genotyping of single nucleotide polymorphisms allowed to account for the population genetic structure in our models in order to avoid spurious correlations between resin duct characteristics and climate. We found large inter-population variation in resin duct density and conductive area, but not in their inducibility. Our results suggest that population variation in the percentage conductive area of resin ducts likely arise from adaptation to local climate conditions. This study highlights the adaptive relevance of resin ducts and helps to shed light on the micro-evolutionary patterns of resin-based defenses in conifers.

Inducibility of Plant Secondary Metabolites in the Stem Predicts Genetic Variation in Resistance Against a Key Insect Herbivore in Maritime Pine

Resistance to herbivores and pathogens is considered a key plant trait with strong adaptive value in trees, usually involving high concentrations of a diverse array of plant secondary metabolites (PSM). Intraspecific genetic variation and plasticity of PSM are widely known. However, their ecology and evolution are unclear, and even the implication of PSM as traits that provide direct effective resistance against herbivores is currently questioned. We used control and methyl jasmonate (MJ) induced clonal copies of genotypes within families from ten populations of the main distribution range of maritime pine to exhaustively characterize the constitutive and induced profile and concentration of PSM in the stem phloem, and to measure insect herbivory damage as a proxy of resistance. Then, we explored whether genetic variation in resistance to herbivory may be predicted by the constitutive concentration of PSM, and the role of its inducibility to predict the increase in resistance once the plant is induced. We found large and structured genetic variation among populations but not between families within populations in resistance to herbivory. The MJ-induction treatment strongly increased resistance to the weevil in the species, and the genetic variation in the inducibility of resistance was significantly structured among populations, with greater inducibility in the Atlantic populations. Genetic variation in resistance was largely explained by the multivariate concentration and profile of PSM at the genotypic level, rather than by bivariate correlations with individual PSM, after accounting for genetic relatedness among genotypes. While the constitutive concentration of the PSM blend did not show a clear pattern of resistance to herbivory, specific changes in the chemical profile and the increase in concentration of the PSM blend after MJ induction were related to increased resistance. To date, this is the first example of a comprehensive and rigorous approach in which inducibility of PSM in trees and its implication in resistance was analyzed excluding spurious associations due to genetic relatedness, often overlooked in intraspecific studies. Here we provide evidences that multivariate analyses of PSM, rather than bivariate correlations, provide more realistic information about the potentially causal relationships between PSM and resistance to herbivory in pine trees.

Chemotaxonomic Considerations of the n-Alkane Composition in Pinus heldreichii, P. nigra, and P. peuce

The n-alkane composition in the leaf cuticular waxes of natural populations of Bosnian pine (Pinus heldreichii), Austrian pine (P. nigra), and Macedonian pine (P. peuce) was compared for the first time. The range of n-alkanes was wider in P. nigra (C₁₆  - C₃₃ ) than in P. heldreichii and P. peuce (C₁₈  - C₃₃ ). Species also diverged in abundance and range of dominant n-alkanes (P. heldreichii: C₂₃ , C₂₇ , and C₂₅ ; P. nigra: C₂₅ , C₂₇ , C₂₉ , and C₂₃ ; P. peuce: C₂₉ , C₂₅ , C₂₇ , and C₂₃ ). Multivariate statistical analyses (PCA, DA, and CA) generally pointed out separation of populations of P. nigra from populations of P. heldreichii and P. peuce (which were, to a greater or lesser extent, separated too). However, position of these species on the basis of n-alkane composition was in accordance neither with infrageneric classification nor with recent molecular and terpene investigations.

High rate of adaptive evolution in two widespread European pines

Comparing related organisms with differing ecological requirements and evolutionary histories can shed light on the mechanisms and drivers underlying genetic adaptation. Here, by examining a common set of hundreds of loci, we compare patterns of nucleotide diversity and molecular adaptation of two European conifers (Scots pine and maritime pine) living in contrasted environments and characterized by distinct population genetic structure (low and clinal in Scots pine, high and ecotypic in maritime pine) and demographic histories. We found higher nucleotide diversity in Scots pine than in maritime pine, whereas rates of new adaptive substitutions (ω_a ), as estimated from the distribution of fitness effects, were similar across species and among the highest found in plants. Sample size and population genetic structure did not appear to have resulted in significant bias in estimates of ω_a . Moreover, population contraction-expansion dynamics for each species did not affect differentially the rate of adaptive substitution in these two pines. Several methodological and biological factors may underlie the unusually high rate of adaptive evolution of Scots pine and maritime pine. By providing two new case studies with contrasting evolutionary histories, we contribute to disentangling the multiple factors potentially affecting adaptive evolution in natural plant populations.

Effect of Light Availability on the Interaction between Maritime Pine and the Pine Weevil: Light Drives Insect Feeding Behavior But Also the Defensive Capabilities of the Host

Light is a major environmental factor that may determine the interaction between plants and herbivores in several ways, including top-down effects through changes in herbivore behavior and bottom-up effects mediated by alterations of plant physiology. Here we explored the relative contribution of these two regulation processes to the outcome of the interaction of pine trees with a major forest pest, the pine weevil (Hylobius abietis). We studied to what extent light availability influence insect feeding behavior and/or the ability of pines to produce induced defenses in response to herbivory. For this purpose, 3-year old Pinus pinaster plants from three contrasting populations were subjected to 6 days of experimental herbivory by the pine weevil under two levels of light availability (complete darkness or natural sunlight) independently applied to the plant and to the insect in a fully factorial design. Light availability strongly affected the pine weevil feeding behavior. The pine weevil fed more and caused larger feeding scars in darkness than under natural sunlight. Besides, under the more intense levels of weevil damage (i.e., those registered with insects in darkness), light availability also affected the pine's ability to respond to insect feeding by producing induced resin defenses. These results were consistent across the three studied populations despite they differed in weevil susceptibility and inducibility of defenses. Morocco was the most damaged population and the one that induced more defensive compounds. Overall, results indicate that light availability modulates the outcome of the pine-weevil interactions through both bottom-up and top-down regulation mechanisms.

Defensive Traits in Young Pine Trees Cluster into Two Divergent Syndromes Related to Early Growth Rate

The combination of defensive traits leads to the evolution of 'plant defense syndromes' which should provide better protection against herbivores than individual traits on their own. Defense syndromes can be generally driven by plant phylogeny and/or biotic and abiotic factors. However, we lack a solid understanding of (i) the relative importance of shared evolution vs. convergence due to similar ecological conditions and (ii) the role of induced defense strategies in shaping defense syndromes. We investigate the relative roles of evolutionary and ecological factors shaping the deployment of pine defense syndromes including multiple constitutive and induced chemical defense traits. We performed a greenhouse experiment with seedlings of eighteen species of Pinaceae family, and measured plant growth rate, constitutive chemical defenses and their inducibility. Plant growth rate, but not phylogenetic relatedness, determined the deployment of two divergent syndromes. Slow-growing pine species living in harsh environments where tissue replacement is costly allocated more to constitutive defenses (energetically more costly to produce than induced). In contrast, fast-growing species living in resource-rich habitats had greater inducibility of their defenses, consistent with the theory of constitutive-induced defense trade-offs. This study contributes to a better understanding of evolutionary and ecological factors driving the deployment of defense syndromes.

Horizontal gene transfer from a flowering plant to the insular pine Pinus canariensis (Chr. Sm. Ex DC in Buch)

Horizontal gene transfer (HGT) is viewed as very common in the plant mitochondrial (mt) genome, but, to date, only one case of HGT has been found in gymnosperms. Here we report a new case of HGT, in which a mt nad5-1 fragment was transferred from an angiosperm to Pinus canariensis. Quantitative assay and sequence analyses showed that the foreign nad5-1 is located in the mt genome of P. canariensis and is nonfunctional. An extensive survey in the genus Pinus revealed that the angiosperm-derived nad5-1 is restricted to P. canariensis and present across the species' range. Molecular dating based on chloroplast DNA suggested that the HGT event occurred in the late Miocene after P. canariensis split from its closest relatives, and that the foreign copy became fixed in P. canariensis owing to drift during its colonization of the Canary Islands. The mechanism of this HGT is unclear but it was probably achieved through either direct cell-cell contact or external vectors. Our discovery provides evidence for an important role of HGT in plant mt genome evolution.

Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus

The evolution of the mitochondrial (mt) genome is far from being fully understood. Systematic investigations into the modes of inheritance, rates and patterns of recombination, nucleotide substitution, and structural changes in the mt genome are still lacking in many groups of plants. In this study, we sequenced >11kbp mtDNA segments from multiple accessions of 36 pine species to characterize the evolutionary patterns of mtDNA in the genus Pinus. We found extremely low substitution rates and complex repetitive sequences scattered across different genome regions, as well as chimeric structures that were probably generated by multiple intergenomic recombinations. The mtDNA-based phylogeny of the genus differed from that based on chloroplast and nuclear DNA in the placement of several groups of species. Such discordances suggest a series of mtDNA capture events during past range shifts of the pine species and that both vertical and horizontal inheritance are implicated in the evolution of mtDNA in Pinus. MtDNA dating revealed that most extant lineages of the genus originated during Oligocene-Miocene radiation and subgenus Strobus diversified earlier than subgenus Pinus. Our findings illustrate a reticular evolutionary pathway for the mt genome through capture and recombination in the genus Pinus, and provide new insights into the evolution of the genus.

First insights into the transcriptome and development of new genomic tools of a widespread circum-Mediterranean tree species, Pinus halepensis Mill

Aleppo pine (Pinus halepensis Mill.) is a relevant conifer species for studying adaptive responses to drought and fire regimes in the Mediterranean region. In this study, we performed Illumina next-generation sequencing of two phenotypically divergent Aleppo pine accessions with the aims of (i) characterizing the transcriptome through Illumina RNA-Seq on trees phenotypically divergent for adaptive traits linked to fire adaptation and drought, (ii) performing a functional annotation of the assembled transcriptome, (iii) identifying genes with accelerated evolutionary rates, (iv) studying the expression levels of the annotated genes and (v) developing gene-based markers for population genomic and association genetic studies. The assembled transcriptome consisted of 48,629 contigs and covered about 54.6 Mbp. The comparison of Aleppo pine transcripts to Picea sitchensis protein-coding sequences resulted in the detection of 34,014 SNPs across species, with a Ka /Ks average value of 0.216, suggesting that the majority of the assembled genes are under negative selection. Several genes were differentially expressed across the two pine accessions with contrasted phenotypes, including a glutathione-s-transferase, a cellulose synthase and a cobra-like protein. A large number of new markers (3334 amplifiable SSRs and 28,236 SNPs) have been identified which should facilitate future population genomics and association genetics in this species. A 384-SNP Oligo Pool Assay for genotyping with the Illumina VeraCode technology has been designed which showed an high overall SNP conversion rate (76.6%). Our results showed that Illumina next-generation sequencing is a valuable technology to obtain an extensive overview on whole transcriptomes of nonmodel species with large genomes.