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Natural tree populations consist of individuals that exhibit intraspecific adaptive variation at a range of geographic scales, as a result of the balance between gene flow and selection. The spatial distribution and magnitude of such variation will influence the capacity of populations to adapt to forthcoming changing environmental conditions. The native Scots pine populations in Scotland represent what remains of the iconic Caledonian forest. Despite being distributed within a relatively narrow geographic area these populations occur across a steep East-West environmental gradient of increasing rainfall and temperature. We hypothesised that western populations compared to those from the east may be better adapted to warmer conditions and as a consequence, may respond differently to the increased temperature predicted during climate change. We conducted an experiment lasting 22 weeks in controlled environment chambers using a nested hierarchical design based on material from different regions (west or east), populations and families (half sibs). We examined the effects of two temperature scenarios, current temperature and warmer predicted temperature on percentage germination as well as growth and morphology of above and below-ground traits. Most of the variation occurred at the family level. Nevertheless, significant regional and population differences were detected, where eastern populations invested more in roots, exhibited fewer stomatal rows per needle and produced thinner roots. In addition, warmer temperatures had strong effects on early growth that were consistent in material from both regions and resulted in earlier germination, greater growth and biomass, but these effects were not accompanied by shifts in biomass partitioning. Although the strong effect of warming suggested temperature limitation for early growth in the study areas under current conditions our results did not support the idea that low seedling recruitment resulting from poor emergence and

Genetic variation and phenotypic plasticity play a role in determining the performance of a tree provenance at a planting site. This paper explores their relative importance in determining growth, phenology and tree form in a broad geographic sample of 42 British provenances of common ash (Fraxinus excelsior L.) grown at two contrasting trial sites. We found significant genetic differences for tree height, timing of leaf flushing and leaf senescence, and stem forking among the provenances. These followed a clear latitudinal and climatic cline, where the northern provenances were shorter, their leaves flushed later and senesced earlier than the southern provenances. Provenance explained a much larger proportion of the variance for spring phenology (63 per cent) than for autumn phenology (15 per cent). The effect of the planting site was contrasting between spring and autumn: spring phenology showed very little plasticity, while autumn phenology presented higher levels of phenotypic plasticity. This could indicate that for ash spring phenology is under stronger selective pressure. We found a correlation between tree height, leaf phenology and forking, with early flushing provenances tending to be taller and more forked, which could reflect repeated frost damage. The findings underline the complexity of predicting performance in novel environments and demonstrate that small gains in tree growth may be counteracted by detrimental effects on stem form, a key contributor to timber value, due to susceptibility to the contemporary environment.

To determine the role of environmental and host genetic factors in shaping fungal endophyte communities we used culturing and metabarcoding techniques to quantify fungal taxa within healthy Scots pine (Pinus sylvestris) needles in a 7-y old provenance-progeny trial replicated at three sites. Both methods revealed a community of ascomycete and basidiomycete taxa dominated by the needle pathogen Lophodermium seditiosum. Differences in fungal endophyte taxon composition and diversity indices were highly significant among trial sites. Within two sites, fungal endophyte communities varied significantly among provenances. Furthermore, the communities differed significantly among maternal families within provenances in 11/15 and 7/15 comparisons involving culture and metabarcoding data respectively. We conclude that both environmental and host genetic variation shape the fungal endophyte community of P. sylvestris needles.

Pinus sylvestris (Scots pine) is the most widespread coniferous tree in the boreal forests of Eurasia, with major economic and ecological importance. However, its large and repetitive genome presents a challenge for conducting genome-wide analyses such as association studies, genetic mapping and genomic selection. We present a new 50K single-nucleotide polymorphism (SNP) genotyping array for Scots pine research, breeding and other applications. To select the SNP set, we first genotyped 480 Scots pine samples on a 407 540 SNP screening array and identified 47 712 high-quality SNPs for the final array (called ‘PiSy50k’). Here, we provide details of the design and testing, as well as allele frequency estimates from the discovery panel, functional annotation, tissue-specific expression patterns and expression level information for the SNPs or corresponding genes, when available. We validated the performance of the PiSy50k array using samples from Finland and Scotland. Overall, 39 678 (83.2%) SNPs showed low error rates (mean = 0.9%). Relatedness estimates based on array genotypes were consistent with the expected pedigrees, and the level of Mendelian error was negligible. In addition, array genotypes successfully discriminate between Scots pine populations of Finnish and Scottish origins. The PiSy50k SNP array will be a valuable tool for a wide variety of future genetic studies and forestry applications.

Aichi Target 13 (T13) focuses on the conservation of genetic diversity. •Major challenges in implementing T13 are that the type of genetic diversity to conserve is not clearly defined, and that key issues in genetic conservation vary across different sectors (e.g., forestry vs agriculture vs other species of socio-economic importance). •In Scotland and the UK more widely, baseline mechanisms are well established for assessing and reporting on genetic diversity in species of agricultural importance (e.g., rare livestock breeds, crop wild relatives), and a methodology has been established for ornamental plants. •A new UK Strategy for Forest Genetics Resources was launched in 2019, creating a framework for linking forest trees into T13 reporting. •However, there is no clear strategy to deal with ‘other species of socio-economic importance’ in Scotland, the UK or indeed elsewhere, and addressing this gap is the major focus of this report. •There is a lack of guidance for identifying focal species of socio-economic importance, and no clear mechanism for addressing T13 for these species once they have been identified. •To address this, we have identified a set of criteria for defining terrestrial and freshwater species of socio-economic importance in Scotland, and selected an initial list of 26 species. •The criteria applied were: -National conservation priority wild species. -Species of national cultural importance. -Species providing key ecosystem services. -Species of importance for wild harvesting (food and medicine). -Economically important game species. •We then developed a simple, readily applicable scorecard method for assessing risks to the conservation of genetic diversity in these species. •The scorecard approach is not dependent on prior genetic knowledge, and instead uses structured expert opinion assessments of whether: -Demographic declines are likely to lead to loss of genetic diversity (genetic erosion). -Hybridisation is likely to lead to undesirable rep

The dataset presented here was collected by the GenTree project (EU-Horizon 2020), which aims to improve the use of forest genetic resources across Europe by better understanding how trees adapt to their local environment. This dataset of individual tree-core characteristics including ring-width series and whole-core wood density was collected for seven ecologically and economically important European tree species: silver birch (Betula pendula), European beech (Fagus sylvatica), Norway spruce (Picea abies), European black poplar (Populus nigra), maritime pine (Pinus pinaster), Scots pine (Pinus sylvestris), and sessile oak (Quercus petraea). Tree-ring width measurements were obtained from 3600 trees in 142 populations and whole-core wood density was measured for 3098 trees in 125 populations. This dataset covers most of the geographical and climatic range occupied by the selected species. The potential use of it will be highly valuable for assessing ecological and evolutionary responses to environmental conditions as well as for model development and parameterization, to predict adaptability under climate change scenarios.

The threat from pests and pathogens to native and commercially planted forest trees is unprecedented and expected to increase under climate change. The degree to which forests respond to threats from pathogens depends on their adaptive capacity, which is determined largely by genetically controlled variation in susceptibility of the individual trees within them and the heritability and evolvability of this trait. The most significant current threat to the economically and ecologically important species Scots pine (Pinus sylvestris) is dothistroma needle blight (DNB), caused by the foliar pathogen Dothistroma septosporum. A progeny-population trial of 4-year-old Scots pine trees, comprising six populations from native Caledonian pinewoods each with three to five families in seven blocks, was artificially inoculated using a single isolate of D. septosporum. Susceptibility to D. septosporum, assessed as the percentage of non-green needles, was measured regularly over a period of 61 days following inoculation, during which plants were maintained in conditions ideal for DNB development (warm; high humidity; high leaf wetness). There were significant differences in susceptibility to D. septosporum among families indicating that variation in this trait is heritable, with high estimates of narrow-sense heritability (0.38–0.75) and evolvability (genetic coefficient of variation, 23.47). It is concluded that native Scots pine populations contain sufficient genetic diversity to evolve lower susceptibility to D. septosporum through natural selection in response to increased prevalence of this pathogen.

Editorial.

Editorial.

Forest ecosystems face a range of challenges in the coming decades, of which climate change, pests and diseases are the most serious. These challenges will be overlaid on a background of historically modified and fragmented forests managed in a wide range of ways for different objectives. As northern temperate forests are species-poor in a global context, their resilience to these challenges is fundamentally dependent on the resilience of individual species. However, dealing with each new threat as it arises is unlikely to be cost effective and in any case, probably not practically feasible. A better strategy for establishing long term resilience would be to harness evolutionary processes, to maximise the capability of individual tree species to respond to new threats by the reorganisation of populations via natural selection; in other words, to be resilient. Such processes depend on the internal variability of species, their mechanisms of dispersal and their ability to recruit new genotypes to a population. In this paper we review the theoretical concept of resilience, examine how it might be applied to tree populations and assess the state of knowledge of Britain’s forests from this perspective.

Our natural and commercially planted forests are currently facing an unprecedented threat from pests and pathogens. On the principle that ‘prevention is better than cure’, the policies and practices that influence forest management must aim to prevent epidemics rather than to fight them once they are established. Vigilance and strict security at national borders aim to prevent entry of pests and pathogens but experience shows us that this does not achieve total exclusion. Consequently, to improve the long-term resistance and resilience of tree populations to infection or herbivory, a more realistic and scientific approach may be to understand and use the resistance mechanisms that are naturally present in trees. Resistance trait variation may be genetically controlled and heritable. Populations therefore have the potential to respond to the selective pressure imposed by attack and, if the management and environmental conditions are right, adapt. This review outlines the mechanisms that trees use to defend themselves, the genetic and environmental control of these mechanisms, the subsequent phenotypic variation that we observe and how best to measure and use this to develop and maintain resilient tree populations. In order to ensure a more sustainable and stable future for commercial and native tree species there is a need to incorporate these approaches into forest management globally through collaboration between foresters and scientists and increased investment in relevant research trials.

In forests with gap disturbance regimes, pioneer tree regeneration is typically abundant following stand-replacing disturbances, whether natural or anthropogenic. Differences in pioneer tree density linked to disturbance regime can influence pollinator behaviour and impact on mating patterns and genetic diversity of pioneer populations. Such mating pattern shifts can manifest as higher selfing rates and lower pollen diversity in old growth forest populations. In secondary forest, where more closely related pollen donors occur, an increase in biparental inbreeding is a potential problem. Here, we investigate the consequences of secondary forest colonisation on the mating patterns and genetic diversity of open-pollinated progeny arrays for the long-lived, self-compatible pioneer tree, Vochysia ferruginea, at two Costa Rican sites. Five microsatellite loci were screened across adult and seed cohorts from old growth forest with lower density, secondary forest with higher density, and isolated individual trees in pasture. Progeny from both old growth and secondary forest contexts were predominantly outcrossed (tm=1.00) and experienced low levels of biparental inbreeding (tm−ts=0.00–0.04). In contrast to predictions, our results indicated that the mating patterns of V. ferruginea are relatively robust to density differences between old growth and secondary forest stands. In addition, we observed that pollen-mediated gene flow possibly maintained the genetic diversity of open-pollinated progeny arrays in stands of secondary forest adults. As part of a natural resource management strategy, we suggest that primary forest remnants should be prioritised for conservation to promote restoration of genetic diversity during forest regeneration.

There is renewed interest in the use of native tree species in ecosystem restoration for their biodiversity benefits. Growing native tree species in production systems (e.g. plantation forests and subsistence agriculture) can also ensure landscape functionality and support for human livelihoods. Achieving full benefits, however, requires consideration of genetic aspects that are often neglected, such as suitability of germplasm to the site, quality and quantity of the genetic pool used and regeneration potential. Understanding the extent and nature of gene flow across fragmented agro-ecosystems is also crucial to successful ecosystem restoration. This study, prepared within the ambit of The State of the World’s Forest Genetic Resources, reviews the role of genetic considerations in a wide range of ecosystem restoration activities involving trees. It evaluates how different approaches take, or could take, genetic aspects into account, thereby leading to the identification and selection of the most appropriate methods. The publication includes a review and syntheses of experience and results; an analysis of successes and failures in various systems; and definitions of best practices including genetic aspects. It also identifies knowledge gaps and needs for further research and development efforts. Its findings, drawn from a range of approaches, help to clarify the role of genetic diversity and will contribute to future developments.

Drylands are extensive across sub-Saharan Africa, socio-economically and ecologically important yet highly sensitive to environmental changes. Evolutionary history, as revealed by contemporary intraspecific genetic variation, can provide valuable insight into how species have responded to past environmental and population changes and guide strategies to promote resilience to future changes. The gum arabic tree (Acacia senegal) is an arid-adapted, morphologically diverse species native to the sub-Saharan drylands. We used variation in nuclear sequences (internal transcribed spacer (ITS)) and two types of chloroplast DNA (cpDNA) markers (PCR-RFLP, cpSSR) to study the phylogeography of the species with 293 individuals from 66 populations sampled across its natural range. cpDNA data showed high regional and rangewide haplotypic diversity (hT(cpSSR)=0.903–0.948) and population differentiation (GST(RFLP)=0.700–0.782) with a phylogeographic pattern that indicated extensive historical gene flow via seed dispersal. Haplotypes were not restricted to any of the four varieties, but showed significant geographic structure (GST(cpSSR)=0.392; RST=0.673; RST>RST (permuted)), with the major division separating East and Southern Africa populations from those in West and Central Africa. Phylogenetic analysis of ITS data indicated a more recent origin for the clade including West and Central African haplotypes, suggesting range expansion in this region, possibly during the Holocene humid period. In conjunction with paleobotanical evidence, our data suggest dispersal to West Africa, and across to the Arabian Peninsula and Indian subcontinent, from source populations located in the East African region during climate oscillations of the Plio-Pleistocene.

In the drylands of Africa, land degradation and soil fertility depletion are major threats to natural resource conservation and food security. A potential solution is to exploit the properties of native N2-fixing legume trees. One candidate is Acacia senegal, the main species producing the internationally traded ‘gum arabic', which also provides a multitude of ecosystem services and supports the livelihoods of many impoverished rural populations in the drylands of sub-Saharan Africa. The development of improved planting stock would help meet the demand for reliable, high quality gum and, at the same time, could enhance income generation and promote wide-scale planting giving environmental benefits for the fragile drylands ecosystem. This requires a strategic improvement programme, but traditional breeding methods require significant time. Molecular approaches are frequently touted as providing a means of increasing efficiency in breeding programmes; however it is as yet unclear whether they can deliver this efficiency, particularly in the regions in which A. senegal is an important crop. Here we review the status of genetic improvement of A. senegal, highlighting modern molecular approaches to advance the breeding efforts for gum and other important traits to enhance adaptability and sustainable management of genetic resources in the changing global climate.

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 (θsil=~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 (πtot=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 × 4Ne 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.

This article is a summary report of the international conference "Forest ecosystem genomics and adaptation" organized by the EVOLTREE Network of Excellence in San Lorenzo de El Escorial (Madrid), Spain, from 9 to 11 June 2010. Main achievements and results of the network are presented for the eight thematic sessions and a stakeholder session. The conference has shown that adaptive responses of trees to biotic or abiotic selection pressures can now be investigated at the gene level for traits of adaptive significance. Candidate genes have been catalogued for phenological and drought-related traits in important tree families (Salicaceae, Fagaceaea and Pinaceae), and their variation in natural populations is being explored. Genomics can now be integrated in ecological research to investigate evolutionary response to climate changes in a wide range of species. New avenues of research were also highlighted as the exploration of gene networks involved in adaptive responses and the combination of experimental and modelling approaches to disentangle components of evolutionary changes triggered by climate change. The main focus of the conference was the adaptation of trees to environmental changes. The conference was organized in eight thematic sessions ranging from genomic approaches aiming at identifying genes of adaptive significance to practical issues regarding mitigation options for combating climate change. A dialogue between scientists and end users took place in the form of an ad hoc stakeholder session. A panel of end users from various forest and policy-making institutions expressed their expectations, and the discussions with the scientists addressed the potential applications of research findings to the management of genetic resources in the context of climate changes. The conference was introduced by two keynote speakers Dr. Pierre Mathy from the European Commission, Directorate General of Research, and Dr. Allen Solomon, former National Program Leader for Glob

Seven polymorphic microsatellite markers isolated from Acacia brevispica and Acacia mellifera were successfully cross-amplified in Acacia senegal. The loci were surveyed for polymorphism using 30 samples. Allelic diversity ranged from 4 (Ame02, Ab06 and Ab18) to 13 (Ab26) per locus. The expected heterozygosity (HE) ranged from 0.543 (Ame02) to 0.868 (Ab26) while observed heterozygosity (HO) ranged from 0.516 (Ame05) to 0.800 (Ame03). Cross amplification of these loci represents a potential source of co-dominant marker and will be useful in the study of genetic diversity, structure, gene flow and breeding systems of this important Acacia species.

This article documents the addition of 396 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Anthocidaris crassispina, Aphis glycines, Argyrosomus regius, Astrocaryum sciophilum, Dasypus novemcinctus, Delomys sublineatus, Dermatemys mawii, Fundulus heteroclitus, Homalaspis plana, Jumellea rossii, Khaya senegalensis, Mugil cephalus, Neoceratitis cyanescens, Phalacrocorax aristotelis, Phytophthora infestans, Piper cordulatum, Pterocarpus indicus, Rana dalmatina, Rosa pulverulenta, Saxifraga oppositifolia, Scomber colias, Semecarpus kathalekanensis, Stichopus monotuberculatus, Striga hermonthica, Tarentola boettgeri and Thermophis baileyi. These loci were cross-tested on the following species: Aphis gossypii, Sooretamys angouya, Euryoryzomys russatus, Fundulus notatus, Fundulus olivaceus, Fundulus catenatus, Fundulus majalis, Jumellea fragrans, Jumellea triquetra Jumellea recta, Jumellea stenophylla, Liza richardsonii, Piper marginatum, Piper aequale, Piper darienensis, Piper dilatatum, Rana temporaria, Rana iberica, Rana pyrenaica, Semecarpus anacardium, Semecarpus auriculata, Semecarpus travancorica, Spondias acuminata, Holigarna grahamii, Holigarna beddomii, Mangifera indica, Anacardium occidentale, Tarentola delalandii, Tarentola caboverdianus and Thermophis zhaoermii.

Using databases of previously published primers, we optimised six nuclear microsatellite markers for Prunus africana for the purposes of studying spatial genetic structure and gene flow. To assess variability, these and three previously transferred loci were screened in populations from Kenya and South Africa. Across both populations most loci were polymorphic, with the exception of a single locus which failed to amplify in the South African samples, exhibiting between 2 and 22 alleles and levels of expected heterozygosity (He) ranged from 0.059 to 0.932. Departures from Hardy–Weinberg equilibrium were detected for all loci but not for all populations. The estimated null allele frequency was very low to moderate and no evidence for linkage disequilibrium was detected.

Gene dispersion processes are key mechanisms that shape the genetic structure and diversity of forest stands. Gene dispersal occurs by means of both natural migration of pollen and seed as well as via the artificial transfer of seeds and plants. These processes affect the genetic structure of forest stands and thereby influence their ability to adapt to future changes in the environment. Within the OAKFLOW project natural and artificial gene flow, including interspecific geneflow, was monitored in white oaks (mainly Q. petraea and Q.robur) in different purposely installed study plots across Europe. Three main objectives were set to the project: - To trace and quantify gene flow and hybridisation in terms of distances and rates - To evaluate genetic and ecological consequences of gene flow and hybridisation on the adaptation of oak stands - To evaluate impacts of gene flow on management rules and silvicultural regimes of oak stands