Spring phenology shows genetic variation among and within populations in seedlings of Scots pine (Pinus sylvestris L.) in the Scottish Highlands

Background: Genetic differentiation in phenotypic traits is often observed among forest tree populations, but less is known about patterns of adaptive variation within populations. Such variation is expected to enhance the survival likelihood of extant populations under climate change. Aims: Scots pine (Pinus sylvestris) occurs over a spatially and temporally heterogeneous landscape in Scotland. Our goal was to examine whether populations had differentiated genetically in timing of bud flush in response to spatial heterogeneity and whether variation was also maintained within populations. Methods: Two common-garden studies, involving maternal families of seedlings from 21 native pinewoods, were established and variation in the trait was measured at the beginning of the second growing season. Results: Populations showed genetic differences in the trait correlated with the length of growing season at their site of origin, but the majority of variation was observed within populations. Populations also differed in their levels of variation in the trait; a pattern that may be influenced by spatial variation in the extent of temporal climate variability. Conclusions: Our findings suggest that populations have adapted to their home environments and that they also have substantial ability to adapt in situ to changes in growing season length

Cryptic genetic variation and adaptation to waterlogging in Caledonian Scots pine, <i>Pinus sylvestris</i> L.

Local adaptation occurs as the result of differential selection among populations. Observations made under common environmental conditions may reveal phenotypic differences between populations with an underlying genetic basis; however, exposure to a contrasting novel environment can trigger release of otherwise unobservable (cryptic) genetic variation. We conducted a waterlogging experiment on a common garden trial of Scots pine, Pinus sylvestris (L.), saplings originating from across a steep rainfall gradient in Scotland. A flood treatment was maintained for approximately 1 year; physiological responses were gauged periodically in terms of photochemical capacity as measured via chlorophyll fluorescence. During the treatment, flooded individuals experienced a reduction in photochemical capacity, Fv/Fm, this reduction being greater for material originating from drier, eastern sites. Phenotypic variance was increased under flooding, and this increase was notably smaller in saplings originating from western sites where precipitation is substantially greater and waterlogging is more common. We conclude that local adaptation has occurred with respect to waterlogging tolerance and that, under the flooding treatment, the greater increase in variability observed in populations originating from drier sites is likely to reflect a relative absence of past selection. In view of a changing climate, we note that comparatively maladapted populations may possess considerable adaptive potential, due to cryptic genetic variation, that should not be overlooked

Genetic variation for needle traits in Scots pine (Pinus sylvestris L.)

The remnants of the Caledonian Native Pinewood are distributed across a relatively narrow geographic area in the Scottish Highlands yet inhabit a steep environmental gradient in terms of rainfall, temperature and altitude. Previous work based on common garden trials has demonstrated that native pine populations (Pinus sylvestris (L.)) exhibit differentiation in terms of growth, phenology and frost resistance. However, despite their important role in plant fitness, no such information is available on leaf traits, which have shown both plastic and adaptive genetic responses to environmental variation in other species. We analysed a subset of 11 needle characters in 192 saplings grown in a population-progeny common garden trial based on seedlots from eight native pinewoods. Narrow-sense heritability (h2) was estimated for each trait and found to be particularly high (1.30 ± 0.33) for resin canal density. The majority of the phenotypic variation found was within populations, although interpopulation differentiation was detected for needle length (ΔAICc = 2.55). Resin canal density was positively correlated with longitude (β = 0.45, ΔAICc = 4.23), whereas stomatal row density was negatively correlated (β =−0.12, ΔAICc = 2.55). These trends may reflect adaptation for differences in moisture availability and altitude between eastern and western populations in Scotland

Non-invasive genotyping and spatial mark-recapture methods to estimate European pine marten density in forested landscapes

Accurate population density estimates are important for conservation but can be difficult to obtain where species are elusive or rare. Non-invasive genotyping from hair or faeces has provided a promising solution and allowed individual identification from genotypes to inform population assessment models. We use individual genotypes derived from hair samples and Spatially Explicit Capture Recapture (SECR) models to estimate the population density of European pine marten (Martes martes) in three Scottish forests, then examine the effects of forest fragmentation on population size. Relative trends in pine marten abundance can be observed via changes in the number of scats in an area through time, but the link between this measure and population density remains unclear. We provide the first calibration of scat counts to enable population density estimation without the need for genetic analysis. Population density estimates ranged from 0.07 km-2 (95% CI 0.03 – 0.16) to 0.38 km-2 (95% CI 0.11 – 1.07), which were mid to low compared to other estimates from the Scottish population. An unequal sex ratio was found in one of the three forests. We found support for the previous finding that pine marten density in Scotland increases with forest fragmentation up to a threshold level (20 – 35% forest cover), beyond which it decreases. Our calibration suggests a non-linear relationship between scat counts and population density, although relatively small changes in population density result in marked changes in scat number. Following the recent re-introduction of pine martens to Wales, non-invasive genetic sampling for population estimation may provide an effective way of monitoring their progress

Root ectomycorrhizal status of oak trees symptomatic and asymptomatic for Acute Oak Decline in southern Britain

Acute Oak Decline (AOD) is a decline-disease that has distinctive symptoms and poses a serious threat to oak. Our understanding of the causal factors of AOD remains poor but it is likely that multiple biotic and abiotic factors contribute to a deterioration in oak condition. There is evidence that indications of above-ground tree health status are frequently reflected below-ground in roots and associated ectomycorrhizal (ECM) fungal communities. However, no study has yet explored these potential relationships specifically in AOD affected trees. In this study, we compare the composition and range of functional exploration types of ECM communities associated with AOD symptomatic oak trees and with AOD asymptomatic trees in three oak-dominated woodlands in southern England. We additionally assess the abundance of fine roots tips in surface soils beneath AOD symptomatic and asymptomatic trees and consider soil physico-chemical effects on ECM communities. The frequency of fine root tips was found to be significantly higher on asymptomatic compared with symptomatic trees in two of the three woodlands studied and long-distance ECM exploration types had a weak positive association with AOD asymptomatic trees. ECM diversity and composition were, however, unaffected by tree symptom status and were not related to the frequency of fine root tips. ECM diversity and compositional (but not exploration type) differences were evident only between the different woodlands and this was related to a small number of soil chemistry variables. This study revealed a relationship between the above-ground symptoms of AOD (i.e. stem lesions and Agrilus biguttatus exit holes) and the frequency of live root tips, providing a potential additional diagnostic tool of trees in decline and highlighting the importance of considering belowground rhizosphere microbiome communities

Adaptive introgression facilitate adaptation to high latitudes in European aspen (Populus tremula L.)

Understanding local adaptation has become a key research area given the ongoing climate challenge and the concomitant requirement to conserve genetic resources. Perennial plants, such as forest trees, are good models to study local adaptation given their wide geographic distribution, largely outcrossing mating systems and demographic histories. We evaluated signatures of local adaptation in European aspen (Populus tremula) across Europe by means of whole genome re-sequencing of a collection of 411 individual trees. We dissected admixture patterns between aspen lineages and observed a strong genomic mosaicism in Scandinavian trees, evidencing different colonization trajectories into the peninsula from Russia, Central and Western Europe. As a consequence of the secondary contacts between populations after the last glacial maximum (LGM), we detected an adaptive introgression event in a genome region of ∼500kb in chromosome 10, harboring a large-effect locus that has previously been shown to contribute to adaptation to the short growing seasons characteristic of northern Scandinavia. Demographic simulations and ancestry inference suggest an Eastern origin - probably Russian - of the adaptive Nordic allele which nowadays is present in a homozygous state at the north of Scandinavia. The strength of introgression and positive selection signatures in this region is a unique feature in the genome. Furthermore, we detected signals of balancing selection, shared across regional populations, that highlight the importance of standing variation as a primary source of alleles that facilitate local adaptation. Our results therefore emphasize the importance of migration-selection balance underlying the genetic architecture of key adaptive quantitative traits

Testing the relative sensitivity of 102 ecological variables as indicators of woodland condition in the New Forest, UK.

Forests globally are facing an increasing number of threats from modified disturbance regimes, novel stressors and changing environmental conditions. This has ultimately resulted in declines in the ecological condition of many forest and woodland ecosystems, leading to widespread tree mortality and stand dieback. Effective indicators of overall woodland ecological condition are therefore needed for environmental monitoring and to support management responses. To test the effectiveness of different variables that could potentially be used as indicators of woodland condition, 102 variables that describe woodland structure, composition, functioning, edaphic conditions and disturbance regimes were assessed along 12 replicate gradients of beech stand dieback. Results indicated that 35 variables differed significantly between at least two stages of the dieback gradient, indicating their sensitivity to stand dieback. Seven of these indicators related to woodland species composition, two to functional processes, 20 to structural features, four to edaphic conditions, and two to disturbance regimes. These results demonstrate that effective indicators can potentially be identified for each of the ecological categories. Effective composition indicators included species richness of ectomycorrhizal fungi, ground flora and epiphytic lichens; functional indicators were soil respiration rate and net nitrification rate; edaphic conditions included soil Na:Ca ratio, exchangeable sodium, total carbon, Ca:Al ratio; structural indicators included canopy openness, litter cover, sward height, and volume of deadwood, and for disturbance the indicator was Equus dung density. Other measures, such as shrub cover and species richness of carabid beetles and spiders, were not found to vary significantly along the dieback gradients, and were therefore not identified as effective indicators. These results demonstrate the value of gradient analysis for evaluating indicators of woodland condition, but also highlight the need for multi-site studies to identify indicators with widescale applicability

Patents and Industrialisation. An Historical Overview of the British Case, 1624-1907

A Report to the Strategic Advisory Board on Intellectual Property Policy (SABIP), U

Changes in symptomatology, reinfection, and transmissibility associated with the SARS-CoV-2 variant B.1.1.7: an ecological study

Background The SARS-CoV-2 variant B.1.1.7 was first identified in December, 2020, in England. We aimed to investigate whether increases in the proportion of infections with this variant are associated with differences in symptoms or disease course, reinfection rates, or transmissibility. Methods We did an ecological study to examine the association between the regional proportion of infections with the SARS-CoV-2 B.1.1.7 variant and reported symptoms, disease course, rates of reinfection, and transmissibility. Data on types and duration of symptoms were obtained from longitudinal reports from users of the COVID Symptom Study app who reported a positive test for COVID-19 between Sept 28 and Dec 27, 2020 (during which the prevalence of B.1.1.7 increased most notably in parts of the UK). From this dataset, we also estimated the frequency of possible reinfection, defined as the presence of two reported positive tests separated by more than 90 days with a period of reporting no symptoms for more than 7 days before the second positive test. The proportion of SARS-CoV-2 infections with the B.1.1.7 variant across the UK was estimated with use of genomic data from the COVID-19 Genomics UK Consortium and data from Public Health England on spike-gene target failure (a non-specific indicator of the B.1.1.7 variant) in community cases in England. We used linear regression to examine the association between reported symptoms and proportion of B.1.1.7. We assessed the Spearman correlation between the proportion of B.1.1.7 cases and number of reinfections over time, and between the number of positive tests and reinfections. We estimated incidence for B.1.1.7 and previous variants, and compared the effective reproduction number, Rt, for the two incidence estimates. Findings From Sept 28 to Dec 27, 2020, positive COVID-19 tests were reported by 36 920 COVID Symptom Study app users whose region was known and who reported as healthy on app sign-up. We found no changes in reported symptoms or disease duration associated with B.1.1.7. For the same period, possible reinfections were identified in 249 (0·7% [95% CI 0·6–0·8]) of 36 509 app users who reported a positive swab test before Oct 1, 2020, but there was no evidence that the frequency of reinfections was higher for the B.1.1.7 variant than for pre-existing variants. Reinfection occurrences were more positively correlated with the overall regional rise in cases (Spearman correlation 0·56–0·69 for South East, London, and East of England) than with the regional increase in the proportion of infections with the B.1.1.7 variant (Spearman correlation 0·38–0·56 in the same regions), suggesting B.1.1.7 does not substantially alter the risk of reinfection. We found a multiplicative increase in the Rt of B.1.1.7 by a factor of 1·35 (95% CI 1·02–1·69) relative to pre-existing variants. However, Rt fell below 1 during regional and national lockdowns, even in regions with high proportions of infections with the B.1.1.7 variant. Interpretation The lack of change in symptoms identified in this study indicates that existing testing and surveillance infrastructure do not need to change specifically for the B.1.1.7 variant. In addition, given that there was no apparent increase in the reinfection rate, vaccines are likely to remain effective against the B.1.1.7 variant. Funding Zoe Global, Department of Health (UK), Wellcome Trust, Engineering and Physical Sciences Research Council (UK), National Institute for Health Research (UK), Medical Research Council (UK), Alzheimer's Society

Hybridization between <em>Quercus robur</em> and <em>Q. petraea</em> in a mixed oak stand in Denmark

• Hybridization and mating pattern between Quercus robur and Q. petraea was studied in a 5.8 ha mixed forest stand in Jutland, Denmark which comprises in total 135 Quercus robur and 230 Q. petraea trees. Classification of the oak trees into species was performed using canonical discriminant analysis of a range of leaf morphological traits. Adult trees (365) and offspring (582) were genotyped with eight microsatellite markers. Seedlings were sampled in 2003 and acorns were collected in 2004. • Mating patterns of Q. robur and Q. petraea are expected to be different in the northern range of the distribution area and a larger hybridization rate is expected. It is further expected, that pollination from outside sources will be relatively less in small fragmented forest management systems compared to large scale oak forest. The conclusions should be verified through repeated year to year analysis of the mating pattern. • Phenological studies revealed that there was no difference in flowering time between species. Data for the adult trees revealed no significant departures from Hardy-Weinberg proportions and there was weak, but significant spatial genetic structure, which supports the idea that the stand is of natural origin. Spatial genetic structure in the first distance class is stronger for Q. petraea. The genetic composition of the offspring was remarkably consistent from year to year. Paternity analysis revealed that, on average, 85% pollination came from fathers within the stand. The direction of the pollen flow varied from year to year. Inter-specific hybridization was high and ranged from 15–17% and from 48–55% for Q. petraea and Q. robur mothers respectively. Paternity analysis revealed that the population was basically outcrossing and only 3.7% of the analysed progeny were the product of selfing. Over the two years of study, approximately 200 trees contributed to the paternity of the next generations. • The study confirms earlier studies with a greater tendency for Q. robur mothers to produce hybrid seeds than Q. petraea mothers. The rate of hybridization is higher in this Danish stand than in comparable studies elsewhere in Europe. Gene flow from outside sources are relatively low.Hybridation entre Quercus robur et Q. petraea dans un peuplement mélangé de chênes au Danemark. •  L'hybridation et le schéma de croisement entre Quercus robur et Q. petraea ont été étudiés dans une forêt mélangée de 5,8 ha dans le Jutland au Danemark. Cette forêt comprenait 135 arbres de Quercus robur et 230 de Q. petraea. Le classement des arbres dans les différentes espèces a été réalisé à partir de caractères morphologiques des feuilles grâce à une analyse canonique discriminante. Les arbres adultes (365) et leurs descendances ont été génotypés à l'aide de 8 marqueurs microsatellites. Les semis ont été échantillonnés en 2003 et les glands ont été récoltés en 2004. • Le schéma de croisement entre Q. robur et Q. petraea est suspecté différent dans la partie nord de l'aire de distribution où un plus fort taux d'hybridation est également attendu. De plus, il est probable que la pollinisation à partir de pollen étranger soit plus faible dans des forêts fragmentées que dans des forêts continues de chênes. Des observations répétées d'année en année sont nécessaires pour valider ces hypothèses. • Des études phénologiques montrent qu'il n'y a pas de différence entre les espèces pour la période de floraison. Les données sur arbres adultes ne révèlent aucun écart significatif par rapport aux proportions attendues de la loi de Hardy-Weinberg. Une structuration spatiale faible mais significative a été mise en évidence, qui suggère l'idée que le peuplement est d'origine naturelle. Cette structuration est plus forte pour Q. petraea. La composition génétique des descendances est remarquablement stable d'une année sur l'autre. Les analyses de paternité révèlent qu'en moyenne 85 % de la pollinisation provient de pères du peuplement. Le sens de pollinisation varie d'une année sur l'autre. Le taux d'hybrides interspécifiques est élevé et varie de 15–17 % et de 48–55 % respectivement pour Q. petraea et Q. robur. Les études de paternité montrent que les inter-croisements sont la règle et que seulement 3,7 % des descendants analysés sont issus d'autofécondation. Durant les deux années de l'étude, approximativement 200 arbres sont intervenus comme père pour les générations suivantes. •  Cette étude confirme des études précédentes montrant que Q. robur produit plus de semences hybrides que Q. petraea. Le taux d'hybridation est plus élevé dans ce peuplement danois que dans d'autres études similaires en Europe. Les flux de gènes à partir de sources extérieures sont faibles