37 research outputs found
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 (1.30â±â0.33) for resin canal density. The majority of the phenotypic variation found was within populations, although interpopulation differentiation was detected for needle length (ÎAICcâ=â2.55). Resin canal density was positively correlated with longitude (ÎČâ=â0.45, ÎAICcâ=â4.23), whereas stomatal row density was negatively correlated (ÎČâ=â0.12, ÎAICcâ=â2.55). 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 â 0.16) to 0.38 km-2 (95% CI 0.11 â 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 â 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
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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 âŒ500kb 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 36â920 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 0·6â0·8]) of 36â509 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 0·56â0·69 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 0·38â0·56 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 1·02â1·69) 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
âąâHybridization 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.
âąâMating 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.
âąâPhenological 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 15â17% and from 48â55% 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.
âąâThe 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 mĂ©langĂ© de chĂȘnes au
Danemark. âąâ
L'hybridation et le schéma de croisement entre Quercus robur et Q. petraea ont été
Ă©tudiĂ©s dans une forĂȘt mĂ©langĂ©e de 5,8 ha dans le
Jutland au Danemark. Cette forĂȘt comprenait 135 arbres de Quercus robur et 230 de Q. petraea. Le
classement des arbres dans les différentes espÚces a été
réalisé à partir de caractÚres morphologiques des feuilles
grĂące Ă 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.
âąâLe schĂ©ma de croisement entre Q. robur et Q. petraea est suspectĂ© diffĂ©rent
dans la partie nord de l'aire de distribution oĂč un plus fort taux
d'hybridation est Ă©galement attendu. De plus, il est probable que la
pollinisation Ă partir de pollen Ă©tranger soit plus faible dans des
forĂȘts fragmentĂ©es que dans des forĂȘts continues de chĂȘnes.
Des observations répétées d'année en année sont
nĂ©cessaires pour valider ces hypothĂšses. âąâDes Ă©tudes phĂ©nologiques montrent qu'il n'y a pas de diffĂ©rence
entre les espÚces pour la période de floraison. Les données sur
arbres adultes ne révÚlent 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
suggÚre 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 révÚlent qu'en moyenne 85 % de la
pollinisation provient de pĂšres du peuplement. Le sens de pollinisation
varie d'une année sur l'autre. Le taux d'hybrides interspécifiques
est Ă©levĂ© et varie de 15â17 % et de 48â55 % respectivement pour
Q. petraea et Q. robur. Les études de paternité montrent que les inter-croisements sont
la rÚgle 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 pĂšre pour les
gĂ©nĂ©rations suivantes. âąâ
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 gĂšnes Ă partir de sources
extérieures sont faibles