Phenotypic trait variation in a long-term multisite common garden experiment of Scots pine in Scotland

Multisite common garden experiments, exposing common pools of genetic diversity to a range of environments, allow quantification of plastic and genetic components of trait variation. For tree species, such studies must be long term as they typically only express mature traits after many years. As well as evaluating standing genetic diversity, these experiments provide an ongoing test of genetic variation against changing environmental conditions and form a vital resource for understanding how species respond to abiotic and biotic variation. Finally, quantitative assessments of phenotypic variation are essential to pair with rapidly accumulating genomic data to advance understanding of the genetic basis of trait variation, and its interaction with climatic change. We describe a multisite, population-progeny, common garden experiment of the economically and ecologically important tree species, Scots pine, collected from across its native range in Scotland and grown in three contrasting environments. Phenotypic traits, including height, stem diameter and budburst were measured over 14 growing seasons from nursery to field site. The datasets presented have a wide range of applications.

Measurement(s)	Cone length • Cone weight • Cone width • Height • Viable seed number • Viable seed weight • stem diameter • canopy width • needle length • number of buds • budburst timing • height increment • stem diameter increment • growth cessation • seed viability
Technology Type(s)	sliding caliper • balance • ruler • natural number • measuring tape • budburst scale
Factor Type(s)	field site location • tree family • tree population
Sample Characteristic - Organism	Pinus sylvestris
Sample Characteristic - Location	Scotland

Identifying and testing marker‐trait associations for growth and phenology in three pine species: implications for genomic prediction

In tree species, genomic prediction offers the potential to forecast mature trait values in early growth stages, if robust marker–trait associations can be identified. Here we apply a novel multispecies approach using genotypes from a new genotyping array, based on 20,795 single nucleotide polymorphisms (SNPs) from three closely related pine species (Pinus sylvestris, Pinus uncinata and Pinus mugo), to test for associations with growth and phenology data from a common garden study. Predictive models constructed using significantly associated SNPs were then tested and applied to an independent multisite field trial of P. sylvestris and the capability to predict trait values was evaluated. One hundred and eighteen SNPs showed significant associations with the traits in the pine species. Common SNPs (MAF > 0.05) associated with bud set were only found in genes putatively involved in growth and development, whereas those associated with growth and budburst were also located in genes putatively involved in response to environment and, to a lesser extent, reproduction. At one of the two independent sites, the model we developed produced highly significant correlations between predicted values and observed height data (YA, height 2020: r = 0.376, p < 0.001). Predicted values estimated with our budburst model were weakly but positively correlated with duration of budburst at one of the sites (GS, 2015: r = 0.204, p = 0.034; 2018: r = 0.205, p = 0.034–0.037) and negatively associated with budburst timing at the other (YA: r = −0.202, p = 0.046). Genomic prediction resulted in the selection of sets of trees whose mean height was taller than the average for each site. Our results provide tentative support for the capability of prediction models to forecast trait values in trees, while highlighting the need for caution in applying them to trees grown in different environments.

Location, but not defensive genotype, determines ectomycorrhizal community composition in Scots pine (Pinus sylvestris L.) seedlings

For successful colonization of host roots, ectomycorrhizal (EM) fungi must overcome host defense systems, and defensive phenotypes have previously been shown to affect the community composition of EM fungi associated with hosts. Secondary metabolites, such as terpenes, form a core part of these defense systems, but it is not yet understood whether variation in these constitutive defenses can result in variation in the colonization of hosts by specific fungal species.We planted seedlings from twelve maternal families of Scots pine (Pinus sylvestris) of known terpene genotype reciprocally in the field in each of six sites. After 3 months, we characterized the mycorrhizal fungal community of each seedling using a combination of morphological categorization and molecular barcoding, and assessed the terpene chemodiversity for a subset of the seedlings. We examined whether parental genotype or terpene chemodiversity affected the diversity or composition of a seedling's mycorrhizal community.While we found that terpene chemodiversity was highly heritable, we found no evidence that parental defensive genotype or a seedling's terpene chemodiversity affected associations with EM fungi. Instead, we found that the location of seedlings, both within and among sites, was the only determinant of the diversity and makeup of EM communities.These results show that while EM community composition varies within Scotland at both large and small scales, variation in constitutive defensive compounds does not determine the EM communities of closely cohabiting pine seedlings. Patchy distributions of EM fungi at small scales may render any genetic variation in associations with different species unrealizable in field conditions. The case for selection on traits mediating associations with specific fungal species may thus be overstated, at least in seedlings.

Contrasting effects of tree species and genetic diversity on the leaf-miner communities associated with silver birch

Both species and genetic diversity of plant communities can affect insect herbivores, but a few studies have compared the effects of both diversity levels within the same experimental context. We compared the effects of tree species and genetic diversity on abundance, species richness, and β-diversity of leaf-miner communities associated with silver birch using two long-term forest diversity experiments in Finland where birch trees were planted in monocultures and mixtures of birch genotypes or other trees species. Although both abundance and species richness of leaf miners differed among birch genotypes at the tree level, birch genetic diversity had no significant effect on miner abundance and species richness at the plot level. Instead, birch genetic diversity affected leaf-miner β-diversity with species turnover being higher among trees within genotypic mixtures than among trees within monoclonal plots. In contrast, tree species diversity had a significant negative effect on both leaf-miner abundance and species richness at plot level, but no effect on miner β-diversity. Significant tree species diversity effects on leaf-miner abundance and species richness were found only in plots with high tree density. We have demonstrated that plant species and genetic diversity play important but contrasting roles in structuring associated herbivore communities. Tree species diversity largely affects miner abundance and species richness, whereas tree genetic diversity affects miner β-diversity. These results have important implications for conservation and management of woodlands.

High genetic diversity at the extreme range edge: nucleotide variation at nuclear loci in Scots pine (Pinus sylvestris L.) in Scotland

Nucleotide polymorphism at 12 nuclear loci was studied in Scots pine populations across an environmental gradient in Scotland, to evaluate the impacts of demographic history and selection on genetic diversity. At eight loci, diversity patterns were compared between Scottish and continental European populations. At these loci, a similar level of diversity (θ(sil)= ~0.01) was found in Scottish vs mainland European populations, contrary to expectations for recent colonization, however, less rapid decay of linkage disequilibrium was observed in the former (ρ=0.0086±0.0009, ρ=0.0245±0.0022, respectively). Scottish populations also showed a deficit of rare nucleotide variants (multi-locus Tajima's D=0.316 vs D=-0.379) and differed significantly from mainland populations in allelic frequency and/or haplotype structure at several loci. Within Scotland, western populations showed slightly reduced nucleotide diversity (π(tot)=0.0068) compared with those from the south and east (0.0079 and 0.0083, respectively) and about three times higher recombination to diversity ratio (ρ/θ=0.71 vs 0.15 and 0.18, respectively). By comparison with results from coalescent simulations, the observed allelic frequency spectrum in the western populations was compatible with a relatively recent bottleneck (0.00175 × 4N(e) generations) that reduced the population to about 2% of the present size. However, heterogeneity in the allelic frequency distribution among geographical regions in Scotland suggests that subsequent admixture of populations with different demographic histories may also have played a role.

The role of plant secondary metabolites in mammalian herbivory: ecological perspectives

Plant secondary metabolites (PSM) have many ecological functions, but have long been considered as defences against pathogens or herbivores (vertebrate or invertebrate), reducing the likelihood and extent of attack. However, mammalian herbivores ingest many foods containing PSM and use both behavioural methods and physiological strategies to limit their negative effects. Most physiological counter-adaptations are inducible in response to ingested PSM, providing efficient protection against toxic effects. Possible positive effects of PSM include antioxidant and anthelminthic properties and complex formation between protein and condensed tannins that protects dietary protein from degradation by the symbiotic microflora of foregut fermenters, increasing its utilisation by the animal. This protein effect is probably only beneficial to animals under a narrow range of nutrient-rich conditions found mainly in agricultural systems. There are many examples of PSM causing food avoidance or reducing food intake, but there is as yet relatively little evidence for positive selection of them by herbivores. Although the feedback mechanisms relating the post-ingestive consequences of PSM to subsequent foraging behaviour are beginning to be understood, knowledge of the integration of behavioural and physiological strategies for regulating the effects of PSM is relatively poor. The opportunities for learned avoidance of PSM may be restricted in animals with complex diets that cannot associate a particular feedback signal with a given food type. A greater emphasis on the study of subclinical effects of PSM rather than acute effects, on pharmaco-kinetic studies in relation to behavioural studies and on the use of realistic experimental models is advocated.

The occurrence and abundance of helminth parasites of the mountain hare Lepus timidus (L.) and the wild rabbit Oryctolagus cuniculus (L.) in Aberdeenshire, Scotland

Mountain hares were collected each month between April 1984 and March 1985 and their intestines examined for helminths. 26 rabbits were also collected between July and December 1984 and examined for gastro-intestinal helminths. Three nematode and two cestode species were found in the hares while only two nematode and one cestode species were found in the rabbits. Trichostrongylus retortaeformis was recorded from 88% of the 193 hares and 92% of the rabbits while comparable figures for Passalurus ambiguus were 0.5% and 54% and for Mosgovoyia pectinata 14% and 81%. Seasonal fluctuations were observed in the T. retortaeformis populations in the hare; numbers tended to be low during the winter months and high throughout the summer. Paranoplocephala wimerosa was reported for the first time from the British Isles and Trichostrongylus axei was recorded for the first time in the mountain hare.